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2018 |
Ferreira, Flávia Viana; Aguiar, Eric Roberto Guimarães Rocha; Olmo, Roenick Proveti; de Oliveira, Karla Pollyanna Vieira; Silva, Emanuele Guimarães; Sant'Anna, Maurício Roberto Viana; de Gontijo, Nelder Figueiredo; Kroon, Erna Geessien; Imler, Jean-Luc; Marques, João Trindade The small non-coding RNA response to virus infection in the Leishmania vector Lutzomyia longipalpis Article de journal PLoS Negl Trop Dis, 12 (6), p. e0006569, 2018, ISSN: 1935-2735. Résumé | Liens | BibTeX | Étiquettes: Animals, Host-Pathogen Interactions, imler, Insect Vectors, Leishmania, M3i, ncRNA, Psychodidae, RNA, RNA Interference, Small Interfering, Untranslated, Vesicular stomatitis Indiana virus, Viral @article{ferreira_small_2018, title = {The small non-coding RNA response to virus infection in the Leishmania vector Lutzomyia longipalpis}, author = {Flávia Viana Ferreira and Eric Roberto Guimarães Rocha Aguiar and Roenick Proveti Olmo and Karla Pollyanna Vieira de Oliveira and Emanuele Guimarães Silva and Maurício Roberto Viana Sant'Anna and Nelder Figueiredo de Gontijo and Erna Geessien Kroon and Jean-Luc Imler and João Trindade Marques}, doi = {10.1371/journal.pntd.0006569}, issn = {1935-2735}, year = {2018}, date = {2018-01-01}, journal = {PLoS Negl Trop Dis}, volume = {12}, number = {6}, pages = {e0006569}, abstract = {Sandflies are well known vectors for Leishmania but also transmit a number of arthropod-borne viruses (arboviruses). Few studies have addressed the interaction between sandflies and arboviruses. RNA interference (RNAi) mechanisms utilize small non-coding RNAs to regulate different aspects of host-pathogen interactions. The small interfering RNA (siRNA) pathway is a broad antiviral mechanism in insects. In addition, at least in mosquitoes, another RNAi mechanism mediated by PIWI interacting RNAs (piRNAs) is activated by viral infection. Finally, endogenous microRNAs (miRNA) may also regulate host immune responses. Here, we analyzed the small non-coding RNA response to Vesicular stomatitis virus (VSV) infection in the sandfly Lutzoymia longipalpis. We detected abundant production of virus-derived siRNAs after VSV infection in adult sandflies. However, there was no production of virus-derived piRNAs and only mild changes in the expression of vector miRNAs in response to infection. We also observed abundant production of virus-derived siRNAs against two other viruses in Lutzomyia Lulo cells. Together, our results suggest that the siRNA but not the piRNA pathway mediates an antiviral response in sandflies. In agreement with this hypothesis, pre-treatment of cells with dsRNA against VSV was able to inhibit viral replication while knock-down of the central siRNA component, Argonaute-2, led to increased virus levels. Our work begins to elucidate the role of RNAi mechanisms in the interaction between L. longipalpis and viruses and should also open the way for studies with other sandfly-borne pathogens.}, keywords = {Animals, Host-Pathogen Interactions, imler, Insect Vectors, Leishmania, M3i, ncRNA, Psychodidae, RNA, RNA Interference, Small Interfering, Untranslated, Vesicular stomatitis Indiana virus, Viral}, pubstate = {published}, tppubtype = {article} } Sandflies are well known vectors for Leishmania but also transmit a number of arthropod-borne viruses (arboviruses). Few studies have addressed the interaction between sandflies and arboviruses. RNA interference (RNAi) mechanisms utilize small non-coding RNAs to regulate different aspects of host-pathogen interactions. The small interfering RNA (siRNA) pathway is a broad antiviral mechanism in insects. In addition, at least in mosquitoes, another RNAi mechanism mediated by PIWI interacting RNAs (piRNAs) is activated by viral infection. Finally, endogenous microRNAs (miRNA) may also regulate host immune responses. Here, we analyzed the small non-coding RNA response to Vesicular stomatitis virus (VSV) infection in the sandfly Lutzoymia longipalpis. We detected abundant production of virus-derived siRNAs after VSV infection in adult sandflies. However, there was no production of virus-derived piRNAs and only mild changes in the expression of vector miRNAs in response to infection. We also observed abundant production of virus-derived siRNAs against two other viruses in Lutzomyia Lulo cells. Together, our results suggest that the siRNA but not the piRNA pathway mediates an antiviral response in sandflies. In agreement with this hypothesis, pre-treatment of cells with dsRNA against VSV was able to inhibit viral replication while knock-down of the central siRNA component, Argonaute-2, led to increased virus levels. Our work begins to elucidate the role of RNAi mechanisms in the interaction between L. longipalpis and viruses and should also open the way for studies with other sandfly-borne pathogens. |
2015 |
Aguiar, Eric Roberto Guimarães Rocha; Olmo, Roenick Proveti; Paro, Simona; Ferreira, Flavia Viana; da de Faria, Isaque João Silva; Todjro, Yaovi Mathias Honore; Lobo, Francisco Pereira; Kroon, Erna Geessien; Meignin, Carine; Gatherer, Derek; Imler, Jean-Luc; Marques, João Trindade Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host Article de journal Nucleic Acids Research, 43 (13), p. 6191–6206, 2015, ISSN: 1362-4962. Résumé | Liens | BibTeX | Étiquettes: Animals, Contig Mapping, Female, imler, insects, M3i, meignin, Ovary, Plants, RNA, Sequence Analysis, Small Untranslated, Vertebrates, Viral, Viral Tropism, viruses @article{aguiar_sequence-independent_2015, title = {Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host}, author = {Eric Roberto Guimarães Rocha Aguiar and Roenick Proveti Olmo and Simona Paro and Flavia Viana Ferreira and Isaque João Silva da de Faria and Yaovi Mathias Honore Todjro and Francisco Pereira Lobo and Erna Geessien Kroon and Carine Meignin and Derek Gatherer and Jean-Luc Imler and João Trindade Marques}, url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv587}, doi = {10.1093/nar/gkv587}, issn = {1362-4962}, year = {2015}, date = {2015-07-01}, journal = {Nucleic Acids Research}, volume = {43}, number = {13}, pages = {6191--6206}, abstract = {Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.}, keywords = {Animals, Contig Mapping, Female, imler, insects, M3i, meignin, Ovary, Plants, RNA, Sequence Analysis, Small Untranslated, Vertebrates, Viral, Viral Tropism, viruses}, pubstate = {published}, tppubtype = {article} } Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects. |
Paro, Simona; Imler, Jean-Luc; Meignin, Carine Sensing viral RNAs by Dicer/RIG-I like ATPases across species Article de journal Current Opinion in Immunology, 32 , p. 106–113, 2015, ISSN: 1879-0372. Résumé | Liens | BibTeX | Étiquettes: Adenosine Triphosphatases, Animals, DEAD-box RNA Helicases, Humans, imler, M3i, meignin, Protein Binding, Protein Interaction Domains and Motifs, Ribonuclease III, RNA, Viral, Virus Diseases, viruses @article{paro_sensing_2015, title = {Sensing viral RNAs by Dicer/RIG-I like ATPases across species}, author = {Simona Paro and Jean-Luc Imler and Carine Meignin}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0952791515000102}, doi = {10.1016/j.coi.2015.01.009}, issn = {1879-0372}, year = {2015}, date = {2015-02-01}, journal = {Current Opinion in Immunology}, volume = {32}, pages = {106--113}, abstract = {Induction of antiviral immunity in vertebrates and invertebrates relies on members of the RIG-I-like receptor and Dicer families, respectively. Although these proteins have different size and domain composition, members of both families share a conserved DECH-box helicase domain. This helicase, also known as a duplex RNA activated ATPase, or DRA domain, plays an important role in viral RNA sensing. Crystallographic and electron microscopy studies of the RIG-I and Dicer DRA domains indicate a common structure and that similar conformational changes are induced by dsRNA binding. Genetic and biochemical studies on the function and regulation of DRAs reveal similarities, but also some differences, between viral RNA sensing mechanisms in nematodes, flies and mammals.}, keywords = {Adenosine Triphosphatases, Animals, DEAD-box RNA Helicases, Humans, imler, M3i, meignin, Protein Binding, Protein Interaction Domains and Motifs, Ribonuclease III, RNA, Viral, Virus Diseases, viruses}, pubstate = {published}, tppubtype = {article} } Induction of antiviral immunity in vertebrates and invertebrates relies on members of the RIG-I-like receptor and Dicer families, respectively. Although these proteins have different size and domain composition, members of both families share a conserved DECH-box helicase domain. This helicase, also known as a duplex RNA activated ATPase, or DRA domain, plays an important role in viral RNA sensing. Crystallographic and electron microscopy studies of the RIG-I and Dicer DRA domains indicate a common structure and that similar conformational changes are induced by dsRNA binding. Genetic and biochemical studies on the function and regulation of DRAs reveal similarities, but also some differences, between viral RNA sensing mechanisms in nematodes, flies and mammals. |
2013 |
Petrillo, Jessica E; Venter, Arno P; Short, James R; Gopal, Radhika; Deddouche, Safia; Lamiable, Olivier; Imler, Jean-Luc; Schneemann, Anette Cytoplasmic granule formation and translational inhibition of nodaviral RNAs in the absence of the double-stranded RNA binding protein B2 Article de journal Journal of Virology, 87 (24), p. 13409–13421, 2013, ISSN: 1098-5514. Résumé | Liens | BibTeX | Étiquettes: Animals, Capsid Proteins, Cell Line, Cricetinae, Cytoplasmic Granules, Double-Stranded, imler, M3i, Nodaviridae, Protein Biosynthesis, RNA, RNA Virus Infections, RNA-Binding Proteins, Viral, Viral Proteins @article{petrillo_cytoplasmic_2013, title = {Cytoplasmic granule formation and translational inhibition of nodaviral RNAs in the absence of the double-stranded RNA binding protein B2}, author = {Jessica E Petrillo and Arno P Venter and James R Short and Radhika Gopal and Safia Deddouche and Olivier Lamiable and Jean-Luc Imler and Anette Schneemann}, doi = {10.1128/JVI.02362-13}, issn = {1098-5514}, year = {2013}, date = {2013-12-01}, journal = {Journal of Virology}, volume = {87}, number = {24}, pages = {13409--13421}, abstract = {Flock House virus (FHV) is a positive-sense RNA insect virus with a bipartite genome. RNA1 encodes the RNA-dependent RNA polymerase, and RNA2 encodes the capsid protein. A third protein, B2, is translated from a subgenomic RNA3 derived from the 3' end of RNA1. B2 is a double-stranded RNA (dsRNA) binding protein that inhibits RNA silencing, a major antiviral defense pathway in insects. FHV is conveniently propagated in Drosophila melanogaster cells but can also be grown in mammalian cells. It was previously reported that B2 is dispensable for FHV RNA replication in BHK21 cells; therefore, we chose this cell line to generate a viral mutant that lacked the ability to produce B2. Consistent with published results, we found that RNA replication was indeed vigorous but the yield of progeny virus was negligible. Closer inspection revealed that infected cells contained very small amounts of coat protein despite an abundance of RNA2. B2 mutants that had reduced affinity for dsRNA produced analogous results, suggesting that the dsRNA binding capacity of B2 somehow played a role in coat protein synthesis. Using fluorescence in situ hybridization of FHV RNAs, we discovered that RNA2 is recruited into large cytoplasmic granules in the absence of B2, whereas the distribution of RNA1 remains largely unaffected. We conclude that B2, by binding to double-stranded regions in progeny RNA2, prevents recruitment of RNA2 into cellular structures, where it is translationally silenced. This represents a novel function of B2 that further contributes to successful completion of the nodaviral life cycle.}, keywords = {Animals, Capsid Proteins, Cell Line, Cricetinae, Cytoplasmic Granules, Double-Stranded, imler, M3i, Nodaviridae, Protein Biosynthesis, RNA, RNA Virus Infections, RNA-Binding Proteins, Viral, Viral Proteins}, pubstate = {published}, tppubtype = {article} } Flock House virus (FHV) is a positive-sense RNA insect virus with a bipartite genome. RNA1 encodes the RNA-dependent RNA polymerase, and RNA2 encodes the capsid protein. A third protein, B2, is translated from a subgenomic RNA3 derived from the 3' end of RNA1. B2 is a double-stranded RNA (dsRNA) binding protein that inhibits RNA silencing, a major antiviral defense pathway in insects. FHV is conveniently propagated in Drosophila melanogaster cells but can also be grown in mammalian cells. It was previously reported that B2 is dispensable for FHV RNA replication in BHK21 cells; therefore, we chose this cell line to generate a viral mutant that lacked the ability to produce B2. Consistent with published results, we found that RNA replication was indeed vigorous but the yield of progeny virus was negligible. Closer inspection revealed that infected cells contained very small amounts of coat protein despite an abundance of RNA2. B2 mutants that had reduced affinity for dsRNA produced analogous results, suggesting that the dsRNA binding capacity of B2 somehow played a role in coat protein synthesis. Using fluorescence in situ hybridization of FHV RNAs, we discovered that RNA2 is recruited into large cytoplasmic granules in the absence of B2, whereas the distribution of RNA1 remains largely unaffected. We conclude that B2, by binding to double-stranded regions in progeny RNA2, prevents recruitment of RNA2 into cellular structures, where it is translationally silenced. This represents a novel function of B2 that further contributes to successful completion of the nodaviral life cycle. |
2012 |
Deleury, Emeline; Dubreuil, Géraldine; Elangovan, Namasivayam; Wajnberg, Eric; Reichhart, Jean-Marc; Gourbal, Benjamin; Duval, David; Baron, Olga Lucia; Gouzy, Jérôme; Coustau, Christine Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study Article de journal PLoS ONE, 7 (3), p. e32512, 2012, ISSN: 1932-6203. Résumé | Liens | BibTeX | Étiquettes: Animals, Biomphalaria, Calmodulin, Cluster Analysis, Complementary, DNA, Expressed Sequence Tags, Ferritins, Gene Expression Profiling, Gene Expression Regulation, High-Throughput Nucleotide Sequencing, Immunity, Innate, M3i, messenger, Pattern Recognition, Phylogeny, Receptors, reichhart, RNA, Signal Transduction, Zinc Fingers @article{deleury_specific_2012, title = {Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study}, author = {Emeline Deleury and Géraldine Dubreuil and Namasivayam Elangovan and Eric Wajnberg and Jean-Marc Reichhart and Benjamin Gourbal and David Duval and Olga Lucia Baron and Jérôme Gouzy and Christine Coustau}, doi = {10.1371/journal.pone.0032512}, issn = {1932-6203}, year = {2012}, date = {2012-01-01}, journal = {PLoS ONE}, volume = {7}, number = {3}, pages = {e32512}, abstract = {Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5'-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs) of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences) belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance of gene duplication and acquisition of paralog functional diversity in the evolution of specific invertebrate immune responses.}, keywords = {Animals, Biomphalaria, Calmodulin, Cluster Analysis, Complementary, DNA, Expressed Sequence Tags, Ferritins, Gene Expression Profiling, Gene Expression Regulation, High-Throughput Nucleotide Sequencing, Immunity, Innate, M3i, messenger, Pattern Recognition, Phylogeny, Receptors, reichhart, RNA, Signal Transduction, Zinc Fingers}, pubstate = {published}, tppubtype = {article} } Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5'-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs) of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences) belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance of gene duplication and acquisition of paralog functional diversity in the evolution of specific invertebrate immune responses. |
2010 |
Garcia, Alvaro Baeza; Pierce, Raymond J; Gourbal, Benjamin; Werkmeister, Elisabeth; Colinet, Dominique; Reichhart, Jean-Marc; Dissous, Colette; Coustau, Christine Involvement of the cytokine MIF in the snail host immune response to the parasite Schistosoma mansoni Article de journal PLoS Pathog., 6 (9), p. e1001115, 2010, ISSN: 1553-7374. Résumé | Liens | BibTeX | Étiquettes: Amino Acid, Animals, Apoptosis, Biomphalaria, Blotting, Cell Proliferation, Cells, Cricetinae, Cultured, Hemocytes, Host-Parasite Interactions, Humans, Liver, M3i, Macrophage Migration-Inhibitory Factors, messenger, Oocysts, Recombinant Proteins, reichhart, Reverse Transcriptase Polymerase Chain Reaction, RNA, Schistosoma mansoni, Schistosomiasis mansoni, Sequence Homology, Small Interfering, Western @article{baeza_garcia_involvement_2010, title = {Involvement of the cytokine MIF in the snail host immune response to the parasite Schistosoma mansoni}, author = {Alvaro Baeza Garcia and Raymond J Pierce and Benjamin Gourbal and Elisabeth Werkmeister and Dominique Colinet and Jean-Marc Reichhart and Colette Dissous and Christine Coustau}, doi = {10.1371/journal.ppat.1001115}, issn = {1553-7374}, year = {2010}, date = {2010-01-01}, journal = {PLoS Pathog.}, volume = {6}, number = {9}, pages = {e1001115}, abstract = {We have identified and characterized a Macrophage Migration Inhibitory Factor (MIF) family member in the Lophotrochozoan invertebrate, Biomphalaria glabrata, the snail intermediate host of the human blood fluke Schistosoma mansoni. In mammals, MIF is a widely expressed pleiotropic cytokine with potent pro-inflammatory properties that controls cell functions such as gene expression, proliferation or apoptosis. Here we show that the MIF protein from B. glabrata (BgMIF) is expressed in circulating immune defense cells (hemocytes) of the snail as well as in the B. glabrata embryonic (Bge) cell line that has hemocyte-like features. Recombinant BgMIF (rBgMIF) induced cell proliferation and inhibited NO-dependent p53-mediated apoptosis in Bge cells. Moreover, knock-down of BgMIF expression in Bge cells interfered with the in vitro encapsulation of S. mansoni sporocysts. Furthermore, the in vivo knock-down of BgMIF prevented the changes in circulating hemocyte populations that occur in response to an infection by S. mansoni miracidia and led to a significant increase in the parasite burden of the snails. These results provide the first functional evidence that a MIF ortholog is involved in an invertebrate immune response towards a parasitic infection and highlight the importance of cytokines in invertebrate-parasite interactions.}, keywords = {Amino Acid, Animals, Apoptosis, Biomphalaria, Blotting, Cell Proliferation, Cells, Cricetinae, Cultured, Hemocytes, Host-Parasite Interactions, Humans, Liver, M3i, Macrophage Migration-Inhibitory Factors, messenger, Oocysts, Recombinant Proteins, reichhart, Reverse Transcriptase Polymerase Chain Reaction, RNA, Schistosoma mansoni, Schistosomiasis mansoni, Sequence Homology, Small Interfering, Western}, pubstate = {published}, tppubtype = {article} } We have identified and characterized a Macrophage Migration Inhibitory Factor (MIF) family member in the Lophotrochozoan invertebrate, Biomphalaria glabrata, the snail intermediate host of the human blood fluke Schistosoma mansoni. In mammals, MIF is a widely expressed pleiotropic cytokine with potent pro-inflammatory properties that controls cell functions such as gene expression, proliferation or apoptosis. Here we show that the MIF protein from B. glabrata (BgMIF) is expressed in circulating immune defense cells (hemocytes) of the snail as well as in the B. glabrata embryonic (Bge) cell line that has hemocyte-like features. Recombinant BgMIF (rBgMIF) induced cell proliferation and inhibited NO-dependent p53-mediated apoptosis in Bge cells. Moreover, knock-down of BgMIF expression in Bge cells interfered with the in vitro encapsulation of S. mansoni sporocysts. Furthermore, the in vivo knock-down of BgMIF prevented the changes in circulating hemocyte populations that occur in response to an infection by S. mansoni miracidia and led to a significant increase in the parasite burden of the snails. These results provide the first functional evidence that a MIF ortholog is involved in an invertebrate immune response towards a parasitic infection and highlight the importance of cytokines in invertebrate-parasite interactions. |
2009 |
Kemp, Cordula; Imler, Jean-Luc Antiviral immunity in drosophila Article de journal Current Opinion in Immunology, 21 (1), p. 3–9, 2009, ISSN: 1879-0372. Résumé | Liens | BibTeX | Étiquettes: Animals, Argonaute Proteins, Caspases, DEAD-box RNA Helicases, Evolution, Gene Expression Regulation, Host-Pathogen Interactions, imler, M3i, Membrane Proteins, Molecular, Nuclear Proteins, Ribonuclease III, RNA, RNA Helicases, RNA Interference, RNA Virus Infections, RNA Viruses, RNA-Induced Silencing Complex, Viral, Virulence @article{kemp_antiviral_2009, title = {Antiviral immunity in drosophila}, author = {Cordula Kemp and Jean-Luc Imler}, doi = {10.1016/j.coi.2009.01.007}, issn = {1879-0372}, year = {2009}, date = {2009-02-01}, journal = {Current Opinion in Immunology}, volume = {21}, number = {1}, pages = {3--9}, abstract = {Genetic analysis of the drosophila antiviral response indicates that RNA interference plays a major role. This contrasts with the situation in mammals, where interferon-induced responses mediate innate antiviral host-defense. An inducible response also contributes to antiviral immunity in drosophila, and similarities in the sensing and signaling of viral infection are becoming apparent between drosophila and mammals. In particular, DExD/H box helicases appear to play a crucial role in the cytosolic detection of viral RNAs in flies and mammals.}, keywords = {Animals, Argonaute Proteins, Caspases, DEAD-box RNA Helicases, Evolution, Gene Expression Regulation, Host-Pathogen Interactions, imler, M3i, Membrane Proteins, Molecular, Nuclear Proteins, Ribonuclease III, RNA, RNA Helicases, RNA Interference, RNA Virus Infections, RNA Viruses, RNA-Induced Silencing Complex, Viral, Virulence}, pubstate = {published}, tppubtype = {article} } Genetic analysis of the drosophila antiviral response indicates that RNA interference plays a major role. This contrasts with the situation in mammals, where interferon-induced responses mediate innate antiviral host-defense. An inducible response also contributes to antiviral immunity in drosophila, and similarities in the sensing and signaling of viral infection are becoming apparent between drosophila and mammals. In particular, DExD/H box helicases appear to play a crucial role in the cytosolic detection of viral RNAs in flies and mammals. |
Kondo, J [Exploring the "motion" = "function" of the ribosomal A-site molecular switch] Article de journal Tanpakushitsu Kakusan Koso, 54 (11), p. 1356-62, 2009, (0039-9450 (Print) 0039-9450 (Linking) Journal Article Review). BibTeX | Étiquettes: *Binding, *RNA/genetics, Agents/adverse, Anti-Bacterial, Bacteria/drug, Biosynthesis/genetics, Crystallography, Disorders/genetics, effects, effects/pharmacology, Hearing, Humans, Mutation, Protein, Ribosomes/chemistry/*genetics/*physiology, RNA, Sites, Transfer, Untranslated, WESTHOF, X-Ray @article{, title = {[Exploring the "motion" = "function" of the ribosomal A-site molecular switch]}, author = { J. Kondo}, year = {2009}, date = {2009-01-01}, journal = {Tanpakushitsu Kakusan Koso}, volume = {54}, number = {11}, pages = {1356-62}, note = {0039-9450 (Print) 0039-9450 (Linking) Journal Article Review}, keywords = {*Binding, *RNA/genetics, Agents/adverse, Anti-Bacterial, Bacteria/drug, Biosynthesis/genetics, Crystallography, Disorders/genetics, effects, effects/pharmacology, Hearing, Humans, Mutation, Protein, Ribosomes/chemistry/*genetics/*physiology, RNA, Sites, Transfer, Untranslated, WESTHOF, X-Ray}, pubstate = {published}, tppubtype = {article} } |
Berry, Bassam; Deddouche, Safia; Kirschner, Doris; Imler, Jean-Luc; Antoniewski, Christophe Viral suppressors of RNA silencing hinder exogenous and endogenous small RNA pathways in Drosophila Article de journal PloS One, 4 (6), p. e5866, 2009, ISSN: 1932-6203. Résumé | Liens | BibTeX | Étiquettes: Animals, Antiviral Agents, Crosses, Double-Stranded, Gene Silencing, Genetic, Genetically Modified, Heterozygote, imler, Invertebrate, M3i, Photoreceptor Cells, Reverse Transcriptase Polymerase Chain Reaction, RNA, RNA Interference, Transgenes @article{berry_viral_2009, title = {Viral suppressors of RNA silencing hinder exogenous and endogenous small RNA pathways in Drosophila}, author = {Bassam Berry and Safia Deddouche and Doris Kirschner and Jean-Luc Imler and Christophe Antoniewski}, doi = {10.1371/journal.pone.0005866}, issn = {1932-6203}, year = {2009}, date = {2009-01-01}, journal = {PloS One}, volume = {4}, number = {6}, pages = {e5866}, abstract = {BACKGROUND: In plants and insects, RNA interference (RNAi) is the main responder against viruses and shapes the basis of antiviral immunity. Viruses counter this defense by expressing viral suppressors of RNAi (VSRs). While VSRs in Drosophila melanogaster were shown to inhibit RNAi through different modes of action, whether they act on other silencing pathways remained unexplored. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that expression of various plant and insect VSRs in transgenic flies does not perturb the Drosophila microRNA (miRNA) pathway; but in contrast, inhibits antiviral RNAi and the RNA silencing response triggered by inverted repeat transcripts, and injection of dsRNA or siRNA. Strikingly, these VSRs also suppressed transposon silencing by endogenous siRNAs (endo-siRNAs). CONCLUSIONS/SIGNIFICANCE: Our findings identify VSRs as tools to unravel small RNA pathways in insects and suggest a cosuppression of antiviral RNAi and endo-siRNA silencing by viruses during fly infections.}, keywords = {Animals, Antiviral Agents, Crosses, Double-Stranded, Gene Silencing, Genetic, Genetically Modified, Heterozygote, imler, Invertebrate, M3i, Photoreceptor Cells, Reverse Transcriptase Polymerase Chain Reaction, RNA, RNA Interference, Transgenes}, pubstate = {published}, tppubtype = {article} } BACKGROUND: In plants and insects, RNA interference (RNAi) is the main responder against viruses and shapes the basis of antiviral immunity. Viruses counter this defense by expressing viral suppressors of RNAi (VSRs). While VSRs in Drosophila melanogaster were shown to inhibit RNAi through different modes of action, whether they act on other silencing pathways remained unexplored. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that expression of various plant and insect VSRs in transgenic flies does not perturb the Drosophila microRNA (miRNA) pathway; but in contrast, inhibits antiviral RNAi and the RNA silencing response triggered by inverted repeat transcripts, and injection of dsRNA or siRNA. Strikingly, these VSRs also suppressed transposon silencing by endogenous siRNAs (endo-siRNAs). CONCLUSIONS/SIGNIFICANCE: Our findings identify VSRs as tools to unravel small RNA pathways in insects and suggest a cosuppression of antiviral RNAi and endo-siRNA silencing by viruses during fly infections. |
Stombaugh, J; Zirbel, C L; Westhof, E; Leontis, N B Frequency and isostericity of RNA base pairs Article de journal Nucleic Acids Res, 37 (7), p. 2294-2312, 2009, ISBN: 19240142, (1362-4962 (Electronic) Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.). Résumé | Liens | BibTeX | Étiquettes: Bacterial/chemistry RNA, Molecular Nucleic Acid Conformation RNA/*chemistry RNA, Ribosomal/chemistry Sequence Alignment Sequence Analysis, RNA, Unité ARN, WESTHOF Base Pairing Base Sequence Models @article{, title = {Frequency and isostericity of RNA base pairs}, author = {J Stombaugh and C L Zirbel and E Westhof and N B Leontis}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19240142}, isbn = {19240142}, year = {2009}, date = {2009-01-01}, journal = {Nucleic Acids Res}, volume = {37}, number = {7}, pages = {2294-2312}, abstract = {Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson-Crick base pairs play a central role. Non-Watson-Crick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation without disrupting the 3D structure. Here, we introduce a quantitative measure of base pair isostericity, the IsoDiscrepancy Index (IDI), to more accurately determine which base pair substitutions can potentially occur in conserved motifs. We extract and classify base pairs from a reduced-redundancy set of RNA 3D structures from the Protein Data Bank (PDB) and calculate centroids (exemplars) for each base combination and geometric base pair type (family). We use the exemplars and IDI values to update our online Basepair Catalog and the Isostericity Matrices (IM) for each base pair family. From the database of base pairs observed in 3D structures we derive base pair occurrence frequencies for each of the 12 geometric base pair families. In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments.}, note = {1362-4962 (Electronic) Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.}, keywords = {Bacterial/chemistry RNA, Molecular Nucleic Acid Conformation RNA/*chemistry RNA, Ribosomal/chemistry Sequence Alignment Sequence Analysis, RNA, Unité ARN, WESTHOF Base Pairing Base Sequence Models}, pubstate = {published}, tppubtype = {article} } Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson-Crick base pairs play a central role. Non-Watson-Crick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation without disrupting the 3D structure. Here, we introduce a quantitative measure of base pair isostericity, the IsoDiscrepancy Index (IDI), to more accurately determine which base pair substitutions can potentially occur in conserved motifs. We extract and classify base pairs from a reduced-redundancy set of RNA 3D structures from the Protein Data Bank (PDB) and calculate centroids (exemplars) for each base combination and geometric base pair type (family). We use the exemplars and IDI values to update our online Basepair Catalog and the Isostericity Matrices (IM) for each base pair family. From the database of base pairs observed in 3D structures we derive base pair occurrence frequencies for each of the 12 geometric base pair families. In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments. |
2008 |
Geary, C; Baudrey, S; Jaeger, L Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors Article de journal Nucleic Acids Res, 36 (4), p. 1138-52, 2008, (1362-4962 (Electronic) Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.). Résumé | BibTeX | Étiquettes: Acid, Adenine/chemistry, Analysis, Base, Conformation, Data, dimerization, directed, Evolution, KROL, Models, Molecular, Nucleic, RNA, RNA/*chemistry/classification, Sequence, Thermodynamics @article{, title = {Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors}, author = { C. Geary and S. Baudrey and L. Jaeger}, year = {2008}, date = {2008-01-01}, journal = {Nucleic Acids Res}, volume = {36}, number = {4}, pages = {1138-52}, abstract = {Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. However, in contrast to GYRA and GAAA tetraloops, very few GNRA/receptor interactions have yet been identified to involve GGAA tetraloops in nature. A novel in vitro selection scheme based on a rigid self-assembling tectoRNA scaffold designed for isolation of intermolecular interactions with A-minor motifs has yielded new GGAA tetraloop-binding receptors with affinity in the nanomolar range. One of the selected receptors is a novel 12 nt RNA motif, (CCUGUG. AUCUGG), that recognizes GGAA tetraloop hairpin with a remarkable specificity and affinity. Its physical and chemical characteristics are comparable to those of the well-studied '11nt' GAAA tetraloop receptor motif. A second less specific motif (CCCAGCCC. GAUAGGG) binds GGRA tetraloops and appears to be related to group IC3 tetraloop receptors. Mutational, thermodynamic and comparative structural analysis suggests that natural and in vitro selected GNRA receptors can essentially be grouped in two major classes of GNRA binders. New insights about the evolution, recognition and structural modularity of GNRA and A-minor RNA-RNA interactions are proposed.}, note = {1362-4962 (Electronic) Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.}, keywords = {Acid, Adenine/chemistry, Analysis, Base, Conformation, Data, dimerization, directed, Evolution, KROL, Models, Molecular, Nucleic, RNA, RNA/*chemistry/classification, Sequence, Thermodynamics}, pubstate = {published}, tppubtype = {article} } Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. However, in contrast to GYRA and GAAA tetraloops, very few GNRA/receptor interactions have yet been identified to involve GGAA tetraloops in nature. A novel in vitro selection scheme based on a rigid self-assembling tectoRNA scaffold designed for isolation of intermolecular interactions with A-minor motifs has yielded new GGAA tetraloop-binding receptors with affinity in the nanomolar range. One of the selected receptors is a novel 12 nt RNA motif, (CCUGUG. AUCUGG), that recognizes GGAA tetraloop hairpin with a remarkable specificity and affinity. Its physical and chemical characteristics are comparable to those of the well-studied '11nt' GAAA tetraloop receptor motif. A second less specific motif (CCCAGCCC. GAUAGGG) binds GGRA tetraloops and appears to be related to group IC3 tetraloop receptors. Mutational, thermodynamic and comparative structural analysis suggests that natural and in vitro selected GNRA receptors can essentially be grouped in two major classes of GNRA binders. New insights about the evolution, recognition and structural modularity of GNRA and A-minor RNA-RNA interactions are proposed. |
2007 |
Mandin, P; Repoila, F; Vergassola, M; Geissmann, T; Cossart, P Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets Article de journal Nucleic Acids Res, 35 (3), p. 962-74, 2007, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't). Résumé | BibTeX | Étiquettes: 5', Assay, Bacterial, Base, Biology, Computational, Data, DNA, Electrophoretic, Flanking, Genes, Genomics, Intergenic/chemistry, Listeria, Messenger/chemistry/*metabolism, Mobility, Molecular, monocytogenes/*genetics/metabolism, Region, RNA, ROMBY, Sequence, Shift, Untranslated/analysis/*genetics/metabolism @article{, title = {Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets}, author = { P. Mandin and F. Repoila and M. Vergassola and T. Geissmann and P. Cossart}, year = {2007}, date = {2007-01-01}, journal = {Nucleic Acids Res}, volume = {35}, number = {3}, pages = {962-74}, abstract = {To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA-mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs.}, note = {1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't}, keywords = {5', Assay, Bacterial, Base, Biology, Computational, Data, DNA, Electrophoretic, Flanking, Genes, Genomics, Intergenic/chemistry, Listeria, Messenger/chemistry/*metabolism, Mobility, Molecular, monocytogenes/*genetics/metabolism, Region, RNA, ROMBY, Sequence, Shift, Untranslated/analysis/*genetics/metabolism}, pubstate = {published}, tppubtype = {article} } To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA-mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs. |
2006 |
Shiao, Shin-Hong; Whitten, Miranda M A; Zachary, Daniel; Hoffmann, Jules A; Levashina, Elena A Fz2 and cdc42 mediate melanization and actin polymerization but are dispensable for Plasmodium killing in the mosquito midgut Article de journal PLoS Pathog., 2 (12), p. e133, 2006, ISSN: 1553-7374. Résumé | Liens | BibTeX | Étiquettes: Actins, Animals, Anopheles, Carrier Proteins, cdc42 GTP-Binding Protein, Double-Stranded, Electron, Frizzled Receptors, Gastrointestinal Tract, hoffmann, Host-Parasite Interactions, Immunity, Innate, Insect Vectors, Intestinal Mucosa, M3i, Melanins, Microarray Analysis, Microscopy, Plasmodium berghei, Polymers, Protozoan, RNA, scanning, telomerase @article{shiao_fz2_2006, title = {Fz2 and cdc42 mediate melanization and actin polymerization but are dispensable for Plasmodium killing in the mosquito midgut}, author = {Shin-Hong Shiao and Miranda M A Whitten and Daniel Zachary and Jules A Hoffmann and Elena A Levashina}, doi = {10.1371/journal.ppat.0020133}, issn = {1553-7374}, year = {2006}, date = {2006-12-01}, journal = {PLoS Pathog.}, volume = {2}, number = {12}, pages = {e133}, abstract = {The midgut epithelium of the mosquito malaria vector Anopheles is a hostile environment for Plasmodium, with most parasites succumbing to host defenses. This study addresses morphological and ultrastructural features associated with Plasmodium berghei ookinete invasion in Anopheles gambiae midguts to define the sites and possible mechanisms of parasite killing. We show by transmission electron microscopy and immunofluorescence that the majority of ookinetes are killed in the extracellular space. Dead or dying ookinetes are surrounded by a polymerized actin zone formed within the basal cytoplasm of adjacent host epithelial cells. In refractory strain mosquitoes, we found that formation of this zone is strongly linked to prophenoloxidase activation leading to melanization. Furthermore, we identify two factors controlling both phenomena: the transmembrane receptor frizzled-2 and the guanosine triphosphate-binding protein cell division cycle 42. However, the disruption of actin polymerization and melanization by double-stranded RNA inhibition did not affect ookinete survival. Our results separate the mechanisms of parasite killing from subsequent reactions manifested by actin polymerization and prophenoloxidase activation in the A. gambiae-P. berghei model. These latter processes are reminiscent of wound healing in other organisms, and we propose that they represent a form of wound-healing response directed towards a moribund ookinete, which is perceived as damaged tissue.}, keywords = {Actins, Animals, Anopheles, Carrier Proteins, cdc42 GTP-Binding Protein, Double-Stranded, Electron, Frizzled Receptors, Gastrointestinal Tract, hoffmann, Host-Parasite Interactions, Immunity, Innate, Insect Vectors, Intestinal Mucosa, M3i, Melanins, Microarray Analysis, Microscopy, Plasmodium berghei, Polymers, Protozoan, RNA, scanning, telomerase}, pubstate = {published}, tppubtype = {article} } The midgut epithelium of the mosquito malaria vector Anopheles is a hostile environment for Plasmodium, with most parasites succumbing to host defenses. This study addresses morphological and ultrastructural features associated with Plasmodium berghei ookinete invasion in Anopheles gambiae midguts to define the sites and possible mechanisms of parasite killing. We show by transmission electron microscopy and immunofluorescence that the majority of ookinetes are killed in the extracellular space. Dead or dying ookinetes are surrounded by a polymerized actin zone formed within the basal cytoplasm of adjacent host epithelial cells. In refractory strain mosquitoes, we found that formation of this zone is strongly linked to prophenoloxidase activation leading to melanization. Furthermore, we identify two factors controlling both phenomena: the transmembrane receptor frizzled-2 and the guanosine triphosphate-binding protein cell division cycle 42. However, the disruption of actin polymerization and melanization by double-stranded RNA inhibition did not affect ookinete survival. Our results separate the mechanisms of parasite killing from subsequent reactions manifested by actin polymerization and prophenoloxidase activation in the A. gambiae-P. berghei model. These latter processes are reminiscent of wound healing in other organisms, and we propose that they represent a form of wound-healing response directed towards a moribund ookinete, which is perceived as damaged tissue. |
Galiana-Arnoux, Delphine; Dostert, Catherine; Schneemann, Anette; Hoffmann, Jules A; Imler, Jean-Luc Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Article de journal Nature Immunology, 7 (6), p. 590–597, 2006, ISSN: 1529-2908. Résumé | Liens | BibTeX | Étiquettes: Animals, Genetically Modified, hoffmann, imler, M3i, Mutation, Nodaviridae, Ribonuclease III, RNA, RNA Helicases, RNA Interference, RNA Viruses, Viral, Viral Proteins, Virus Replication @article{galiana-arnoux_essential_2006, title = {Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila}, author = {Delphine Galiana-Arnoux and Catherine Dostert and Anette Schneemann and Jules A Hoffmann and Jean-Luc Imler}, doi = {10.1038/ni1335}, issn = {1529-2908}, year = {2006}, date = {2006-06-01}, journal = {Nature Immunology}, volume = {7}, number = {6}, pages = {590--597}, abstract = {The fruit fly Drosophila melanogaster is a model system for studying innate immunity, including antiviral host defense. Infection with drosophila C virus triggers a transcriptional response that is dependent in part on the Jak kinase Hopscotch. Here we show that successful infection and killing of drosophila with the insect nodavirus flock house virus was strictly dependent on expression of the viral protein B2, a potent inhibitor of processing of double-stranded RNA mediated by the essential RNA interference factor Dicer. Conversely, flies with a loss-of-function mutation in the gene encoding Dicer-2 (Dcr-2) showed enhanced susceptibility to infection by flock house virus, drosophila C virus and Sindbis virus, members of three different families of RNA viruses. These data demonstrate the importance of RNA interference for controlling virus replication in vivo and establish Dcr-2 as a host susceptibility locus for virus infections.}, keywords = {Animals, Genetically Modified, hoffmann, imler, M3i, Mutation, Nodaviridae, Ribonuclease III, RNA, RNA Helicases, RNA Interference, RNA Viruses, Viral, Viral Proteins, Virus Replication}, pubstate = {published}, tppubtype = {article} } The fruit fly Drosophila melanogaster is a model system for studying innate immunity, including antiviral host defense. Infection with drosophila C virus triggers a transcriptional response that is dependent in part on the Jak kinase Hopscotch. Here we show that successful infection and killing of drosophila with the insect nodavirus flock house virus was strictly dependent on expression of the viral protein B2, a potent inhibitor of processing of double-stranded RNA mediated by the essential RNA interference factor Dicer. Conversely, flies with a loss-of-function mutation in the gene encoding Dicer-2 (Dcr-2) showed enhanced susceptibility to infection by flock house virus, drosophila C virus and Sindbis virus, members of three different families of RNA viruses. These data demonstrate the importance of RNA interference for controlling virus replication in vivo and establish Dcr-2 as a host susceptibility locus for virus infections. |
2005 |
Kocks, Christine; Cho, Ju Hyun; Nehme, Nadine; Ulvila, Johanna; Pearson, Alan M; Meister, Marie; Strom, Charles; Conto, Stephanie L; Hetru, Charles; Stuart, Lynda M; Stehle, Thilo; Hoffmann, Jules A; Reichhart, Jean-Marc; Ferrandon, Dominique; Rämet, Mika; Ezekowitz, Alan R B Eater, a transmembrane protein mediating phagocytosis of bacterial pathogens in Drosophila Article de journal Cell, 123 (2), p. 335–346, 2005, ISSN: 0092-8674. Résumé | Liens | BibTeX | Étiquettes: Amino Acid, Amino Acid Motifs, Animals, Bacterial Infections, Cell Surface, Embryo, Escherichia coli, ferrandon, Flow Cytometry, Frameshift Mutation, Genes, Histidine, hoffmann, In Situ Hybridization, Insect, Insect Proteins, M3i, Macrophages, Membrane Proteins, messenger, Nonmammalian, Open Reading Frames, Phagocytosis, Receptors, reichhart, RNA, RNA Interference, Sequence Homology, Serratia marcescens @article{kocks_eater_2005, title = {Eater, a transmembrane protein mediating phagocytosis of bacterial pathogens in Drosophila}, author = {Christine Kocks and Ju Hyun Cho and Nadine Nehme and Johanna Ulvila and Alan M Pearson and Marie Meister and Charles Strom and Stephanie L Conto and Charles Hetru and Lynda M Stuart and Thilo Stehle and Jules A Hoffmann and Jean-Marc Reichhart and Dominique Ferrandon and Mika Rämet and Alan R B Ezekowitz}, doi = {10.1016/j.cell.2005.08.034}, issn = {0092-8674}, year = {2005}, date = {2005-10-01}, journal = {Cell}, volume = {123}, number = {2}, pages = {335--346}, abstract = {Phagocytosis is a complex, evolutionarily conserved process that plays a central role in host defense against infection. We have identified a predicted transmembrane protein, Eater, which is involved in phagocytosis in Drosophila. Transcriptional silencing of the eater gene in a macrophage cell line led to a significant reduction in the binding and internalization of bacteria. Moreover, the N terminus of the Eater protein mediated direct microbial binding which could be inhibited with scavenger receptor ligands, acetylated, and oxidized low-density lipoprotein. In vivo, eater expression was restricted to blood cells. Flies lacking the eater gene displayed normal responses in NF-kappaB-like Toll and IMD signaling pathways but showed impaired phagocytosis and decreased survival after bacterial infection. Our results suggest that Eater is a major phagocytic receptor for a broad range of bacterial pathogens in Drosophila and provide a powerful model to address the role of phagocytosis in vivo.}, keywords = {Amino Acid, Amino Acid Motifs, Animals, Bacterial Infections, Cell Surface, Embryo, Escherichia coli, ferrandon, Flow Cytometry, Frameshift Mutation, Genes, Histidine, hoffmann, In Situ Hybridization, Insect, Insect Proteins, M3i, Macrophages, Membrane Proteins, messenger, Nonmammalian, Open Reading Frames, Phagocytosis, Receptors, reichhart, RNA, RNA Interference, Sequence Homology, Serratia marcescens}, pubstate = {published}, tppubtype = {article} } Phagocytosis is a complex, evolutionarily conserved process that plays a central role in host defense against infection. We have identified a predicted transmembrane protein, Eater, which is involved in phagocytosis in Drosophila. Transcriptional silencing of the eater gene in a macrophage cell line led to a significant reduction in the binding and internalization of bacteria. Moreover, the N terminus of the Eater protein mediated direct microbial binding which could be inhibited with scavenger receptor ligands, acetylated, and oxidized low-density lipoprotein. In vivo, eater expression was restricted to blood cells. Flies lacking the eater gene displayed normal responses in NF-kappaB-like Toll and IMD signaling pathways but showed impaired phagocytosis and decreased survival after bacterial infection. Our results suggest that Eater is a major phagocytic receptor for a broad range of bacterial pathogens in Drosophila and provide a powerful model to address the role of phagocytosis in vivo. |
2004 |
Costa, A; de Barros, Pais J P; Keith, G; Baranowski, W; Desgres, J Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal liver cells Article de journal J Chromatogr B Analyt Technol Biomed Life Sci, 801 (2), p. 237-47, 2004, (1570-0232 Journal Article). Résumé | BibTeX | Étiquettes: *Chromatography, &, Acyl/chemistry, Amino, Animals, Asn/chemistry, Cells, Chickens, Cultured, derivatives/*analysis, Experimental, Gov't, Hepatocytes/chemistry, high, KEITH, liquid, Liver, Liver/*chemistry, Neoplasms, Non-U.S., Nucleoside, Pressure, purification, Q/*analogs, Rats, RNA, Support, Transfer, Transfer/*chemistry/isolation, tumor @article{, title = {Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal liver cells}, author = { A. Costa and J. P. Pais de Barros and G. Keith and W. Baranowski and J. Desgres}, year = {2004}, date = {2004-01-01}, journal = {J Chromatogr B Analyt Technol Biomed Life Sci}, volume = {801}, number = {2}, pages = {237-47}, abstract = {Three queuosine derivatives (Q-derivatives) have been found at position 34 of four mammalian so-called Q-tRNAs: queuosine (Q) in tRNA(Asn) and tRNA(His), mannosyl-queuosine (manQ) in tRNA(Asp), and galactosyl-queuosine (galQ) in tRNA(Tyr). An analytical procedure based on the combined means of purified tRNA isolation from liver cells and ribonucleoside analysis by reverse-phase high performance liquid chromatography coupled with real-time UV-spectrometry (RPLC-UV) was developed for the quantitative analysis of the three Q-derivatives present in total tRNA from liver tissues and liver cell cultures. Using this analytical procedure, the rates of Q-tRNA modification were studied in total tRNAs from various mammalian hepatic cells. Our results show that the four Q-tRNAs are fully modified in liver tissues from adult mammals, regardless of the mammal species. However, a lack in the Q-modification level was observed in Q-tRNAs from newborn rat liver, as well in Q-tRNAs from normal rat liver cell cultures growing in a low queuine content medium, and from a rat hepatoma cell line. It is noteworthy that in all cases of Q-tRNA hypomodification, our analytical procedure showed that tRNA(Asp) is always the least affected by the hypomodification. The biological significance of this phenomenon is discussed.}, note = {1570-0232 Journal Article}, keywords = {*Chromatography, &, Acyl/chemistry, Amino, Animals, Asn/chemistry, Cells, Chickens, Cultured, derivatives/*analysis, Experimental, Gov't, Hepatocytes/chemistry, high, KEITH, liquid, Liver, Liver/*chemistry, Neoplasms, Non-U.S., Nucleoside, Pressure, purification, Q/*analogs, Rats, RNA, Support, Transfer, Transfer/*chemistry/isolation, tumor}, pubstate = {published}, tppubtype = {article} } Three queuosine derivatives (Q-derivatives) have been found at position 34 of four mammalian so-called Q-tRNAs: queuosine (Q) in tRNA(Asn) and tRNA(His), mannosyl-queuosine (manQ) in tRNA(Asp), and galactosyl-queuosine (galQ) in tRNA(Tyr). An analytical procedure based on the combined means of purified tRNA isolation from liver cells and ribonucleoside analysis by reverse-phase high performance liquid chromatography coupled with real-time UV-spectrometry (RPLC-UV) was developed for the quantitative analysis of the three Q-derivatives present in total tRNA from liver tissues and liver cell cultures. Using this analytical procedure, the rates of Q-tRNA modification were studied in total tRNAs from various mammalian hepatic cells. Our results show that the four Q-tRNAs are fully modified in liver tissues from adult mammals, regardless of the mammal species. However, a lack in the Q-modification level was observed in Q-tRNAs from newborn rat liver, as well in Q-tRNAs from normal rat liver cell cultures growing in a low queuine content medium, and from a rat hepatoma cell line. It is noteworthy that in all cases of Q-tRNA hypomodification, our analytical procedure showed that tRNA(Asp) is always the least affected by the hypomodification. The biological significance of this phenomenon is discussed. |
Martineau, Y; Bec, Le C; Monbrun, L; Allo, V; Chiu, I M; Danos, O; Moine, H; Prats, H; Prats, A C Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs Article de journal Mol Cell Biol, 24 (17), p. 7622-35, 2004, (0270-7306 Journal Article). Résumé | BibTeX | Étiquettes: (Genetics), *5', *Alternative, *Nucleic, *Promoter, 1/*genetics, Acid, Alignment, Animals, Base, Cell, Conformation, Data, EHRESMANN, Factor, Fibroblast, Gene, Genes, Genetic, Gov't, Growth, Human, Line, Messenger/chemistry/*genetics/metabolism, Mice, Molecular, Muscle, Mutagenesis, Non-U.S., Regions, Ribosomes/*metabolism, RNA, Sequence, Site-Directed, Skeletal/cytology/physiology, Splicing, Structural/genetics, Support, Techniques, Transfer, Untranslated, Vectors @article{, title = {Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs}, author = { Y. Martineau and C. Le Bec and L. Monbrun and V. Allo and I. M. Chiu and O. Danos and H. Moine and H. Prats and A. C. Prats}, year = {2004}, date = {2004-01-01}, journal = {Mol Cell Biol}, volume = {24}, number = {17}, pages = {7622-35}, abstract = {Fibroblast growth factor 1 (FGF-1) is a powerful angiogenic factor whose gene structure contains four promoters, giving rise to a process of alternative splicing resulting in four mRNAs with alternative 5' untranslated regions (5' UTRs). Here we have identified, by using double luciferase bicistronic vectors, the presence of internal ribosome entry sites (IRESs) in the human FGF-1 5' UTRs, particularly in leaders A and C, with distinct activities in mammalian cells. DNA electrotransfer in mouse muscle revealed that the IRES present in the FGF-1 leader A has a high activity in vivo. We have developed a new regulatable TET OFF bicistronic system, which allowed us to rule out the possibility of any cryptic promoter in the FGF-1 leaders. FGF-1 IRESs A and C, which were mapped in fragments of 118 and 103 nucleotides, respectively, are flexible in regard to the position of the initiation codon, making them interesting from a biotechnological point of view. Furthermore, we show that FGF-1 IRESs A of murine and human origins show similar IRES activity profiles. Enzymatic and chemical probing of the FGF-1 IRES A RNA revealed a structural domain conserved among mammals at both the nucleotide sequence and RNA structure levels. The functional role of this structural motif has been demonstrated by point mutagenesis, including compensatory mutations. These data favor an important role of IRESs in the control of FGF-1 expression and provide a new IRES structural motif that could help IRES prediction in 5' UTR databases.}, note = {0270-7306 Journal Article}, keywords = {(Genetics), *5', *Alternative, *Nucleic, *Promoter, 1/*genetics, Acid, Alignment, Animals, Base, Cell, Conformation, Data, EHRESMANN, Factor, Fibroblast, Gene, Genes, Genetic, Gov't, Growth, Human, Line, Messenger/chemistry/*genetics/metabolism, Mice, Molecular, Muscle, Mutagenesis, Non-U.S., Regions, Ribosomes/*metabolism, RNA, Sequence, Site-Directed, Skeletal/cytology/physiology, Splicing, Structural/genetics, Support, Techniques, Transfer, Untranslated, Vectors}, pubstate = {published}, tppubtype = {article} } Fibroblast growth factor 1 (FGF-1) is a powerful angiogenic factor whose gene structure contains four promoters, giving rise to a process of alternative splicing resulting in four mRNAs with alternative 5' untranslated regions (5' UTRs). Here we have identified, by using double luciferase bicistronic vectors, the presence of internal ribosome entry sites (IRESs) in the human FGF-1 5' UTRs, particularly in leaders A and C, with distinct activities in mammalian cells. DNA electrotransfer in mouse muscle revealed that the IRES present in the FGF-1 leader A has a high activity in vivo. We have developed a new regulatable TET OFF bicistronic system, which allowed us to rule out the possibility of any cryptic promoter in the FGF-1 leaders. FGF-1 IRESs A and C, which were mapped in fragments of 118 and 103 nucleotides, respectively, are flexible in regard to the position of the initiation codon, making them interesting from a biotechnological point of view. Furthermore, we show that FGF-1 IRESs A of murine and human origins show similar IRES activity profiles. Enzymatic and chemical probing of the FGF-1 IRES A RNA revealed a structural domain conserved among mammals at both the nucleotide sequence and RNA structure levels. The functional role of this structural motif has been demonstrated by point mutagenesis, including compensatory mutations. These data favor an important role of IRESs in the control of FGF-1 expression and provide a new IRES structural motif that could help IRES prediction in 5' UTR databases. |
Mohr, S; Bottin, M C; Lannes, B; Neuville, A; Bellocq, J P; Keith, G; Rihn, B H Microdissection, mRNA amplification and microarray: a study of pleural mesothelial and malignant mesothelioma cells Article de journal Biochimie, 86 (1), p. 13-9, 2004, (0300-9084 Journal Article). Résumé | BibTeX | Étiquettes: Analysis, Array, Chain, Epithelium/*metabolism, Expression, Female, Gene, Genetic, Human, KEITH, Lasers, Male, Markers, Mesothelioma/*genetics/metabolism, messenger, Microdissection, Neoplasms/*genetics/metabolism, Neoplastic/*genetics, Oligonucleotide, Pleura/*cytology/*metabolism, Pleural, Polymerase, Profiling, Reaction, Regulation, Reverse, RNA, Sequence, Transcriptase @article{, title = {Microdissection, mRNA amplification and microarray: a study of pleural mesothelial and malignant mesothelioma cells}, author = { S. Mohr and M.C. Bottin and B. Lannes and A. Neuville and J.P. Bellocq and G. Keith and B.H. Rihn}, year = {2004}, date = {2004-01-01}, journal = {Biochimie}, volume = {86}, number = {1}, pages = {13-9}, abstract = {The studies of molecular alterations in tumor cells with microarrays are often hampered by inherent tissue heterogeneity. The emergence of Laser Capture Microdissection (LCM) allowed us to overcome this challenge since it gives selective access to cancer cells that are isolated from their native tissue environment. In this report, we microdissected mesothelial cells and malignant mesothelioma cells of ex vivo resected specimens using LCM. Amplified RNA from mesothelial and mesothelioma microdissected cells allowed us to measure global gene expression with 10 K-microarrays in four independent experiments. We screened 9850 annotated human genes, 1275 of which have satisfied our data analysis requirements. They included 302 overexpressed genes and 160 downregulated genes in mesothelioma microdissected cells as compared to mesothelial microdissected cells. Among them, the expression levels of eight genes, namely BF, FTL, IGFBP7, RARRES1, RARRES2, RBP1, SAT, and TXN according to HUGO nomenclature, were increased, whereas six: ALOX5AP, CLNS1A, EIF4A2, ELK3, REQ and SYPL, were found to be underexpressed in mesothelioma microdissected cells. The ferritin light polypeptide (FTL) gene overexpression was confirmed by real time quantitative PCR. Our approach allowed a comprehensive in situ examination of mesothelioma and provided an accurate way to find new marker genes that may be useful for diagnosis and treatment of malignant pleural mesothelioma.}, note = {0300-9084 Journal Article}, keywords = {Analysis, Array, Chain, Epithelium/*metabolism, Expression, Female, Gene, Genetic, Human, KEITH, Lasers, Male, Markers, Mesothelioma/*genetics/metabolism, messenger, Microdissection, Neoplasms/*genetics/metabolism, Neoplastic/*genetics, Oligonucleotide, Pleura/*cytology/*metabolism, Pleural, Polymerase, Profiling, Reaction, Regulation, Reverse, RNA, Sequence, Transcriptase}, pubstate = {published}, tppubtype = {article} } The studies of molecular alterations in tumor cells with microarrays are often hampered by inherent tissue heterogeneity. The emergence of Laser Capture Microdissection (LCM) allowed us to overcome this challenge since it gives selective access to cancer cells that are isolated from their native tissue environment. In this report, we microdissected mesothelial cells and malignant mesothelioma cells of ex vivo resected specimens using LCM. Amplified RNA from mesothelial and mesothelioma microdissected cells allowed us to measure global gene expression with 10 K-microarrays in four independent experiments. We screened 9850 annotated human genes, 1275 of which have satisfied our data analysis requirements. They included 302 overexpressed genes and 160 downregulated genes in mesothelioma microdissected cells as compared to mesothelial microdissected cells. Among them, the expression levels of eight genes, namely BF, FTL, IGFBP7, RARRES1, RARRES2, RBP1, SAT, and TXN according to HUGO nomenclature, were increased, whereas six: ALOX5AP, CLNS1A, EIF4A2, ELK3, REQ and SYPL, were found to be underexpressed in mesothelioma microdissected cells. The ferritin light polypeptide (FTL) gene overexpression was confirmed by real time quantitative PCR. Our approach allowed a comprehensive in situ examination of mesothelioma and provided an accurate way to find new marker genes that may be useful for diagnosis and treatment of malignant pleural mesothelioma. |
Mohr, S; Keith, G; Galateau-Salle, F; Icard, P; Rihn, B H Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray Article de journal Biochim Biophys Acta-Mol Basis Dis, 1688 (1), p. 43-60, 2004, (0006-3002 Journal Article). Résumé | BibTeX | Étiquettes: Analysis, Array, Biological/genetics, Cell, Expression, Family, Gene, Human, KEITH, Line, Markers, Mesothelioma/etiology/genetics/*pathology, Messenger/analysis, Multigene, Neoplasms/etiology/genetics/*pathology, Neoplastic, Pleural, Profiling, Protein, Regulation, RNA, tumor @article{, title = {Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray}, author = { S. Mohr and G. Keith and F. Galateau-Salle and P. Icard and B. H. Rihn}, year = {2004}, date = {2004-01-01}, journal = {Biochim Biophys Acta-Mol Basis Dis}, volume = {1688}, number = {1}, pages = {43-60}, abstract = {Malignant pleural mesothelioma (MPM) is an aggressive serosal tumor, strongly associated with former exposure to asbestos fibers and for which there is currently no effective treatment available. In human, MPM is characterized by a high local invasiveness, poor prognosis and therapeutic outcomes. In order to assess molecular changes that specify this phenotype, we performed a global gene expression profiling of human MPM. Using a 10,000-element microarray, we analyzed mRNA relative gene expression levels by comparing a mesothelioma cell line to either a pleural cell line or tumor specimens. To analyze these gene expression data, we used various bioinformatics softwares. Hierarchical clustering methods were used to group genes and samples with similar expression in an unsupervised mode. Genes of known function were further sorted by enzyme, function and pathway clusters using a supervised software (IncyteGenomics). Taken together, these data defined a molecular fingerprint of human MPM with more than 700 up- or down-regulated genes related to several traits of the malignant phenotype, specially associated with MPM invasiveness, protection and resistance to anticancer defenses. This portrait is meaningful in disease classification and management, and relevant in finding new specific markers of MPM. These molecular markers should improve the accuracy of mesothelioma diagnosis, prognosis and therapy.}, note = {0006-3002 Journal Article}, keywords = {Analysis, Array, Biological/genetics, Cell, Expression, Family, Gene, Human, KEITH, Line, Markers, Mesothelioma/etiology/genetics/*pathology, Messenger/analysis, Multigene, Neoplasms/etiology/genetics/*pathology, Neoplastic, Pleural, Profiling, Protein, Regulation, RNA, tumor}, pubstate = {published}, tppubtype = {article} } Malignant pleural mesothelioma (MPM) is an aggressive serosal tumor, strongly associated with former exposure to asbestos fibers and for which there is currently no effective treatment available. In human, MPM is characterized by a high local invasiveness, poor prognosis and therapeutic outcomes. In order to assess molecular changes that specify this phenotype, we performed a global gene expression profiling of human MPM. Using a 10,000-element microarray, we analyzed mRNA relative gene expression levels by comparing a mesothelioma cell line to either a pleural cell line or tumor specimens. To analyze these gene expression data, we used various bioinformatics softwares. Hierarchical clustering methods were used to group genes and samples with similar expression in an unsupervised mode. Genes of known function were further sorted by enzyme, function and pathway clusters using a supervised software (IncyteGenomics). Taken together, these data defined a molecular fingerprint of human MPM with more than 700 up- or down-regulated genes related to several traits of the malignant phenotype, specially associated with MPM invasiveness, protection and resistance to anticancer defenses. This portrait is meaningful in disease classification and management, and relevant in finding new specific markers of MPM. These molecular markers should improve the accuracy of mesothelioma diagnosis, prognosis and therapy. |
Blandin, Stephanie A; Shiao, Shin-Hong; Moita, Luis F; Janse, Chris J; Waters, Andrew P; Kafatos, Fotis C; Levashina, Elena A Complement-like protein TEP1 is a determinant of vectorial capacity in the malaria vector Anopheles gambiae Article de journal Cell, 116 (5), p. 661–670, 2004, ISSN: 0092-8674. Résumé | BibTeX | Étiquettes: Animals, Anopheles, blandin, Female, Genetic, Humans, Insect Proteins, Insect Vectors, M3i, Malaria, Models, Molecular, Plasmodium berghei, Polymorphism, Protein Structure, RNA, Sequence Alignment, Tertiary @article{blandin_complement-like_2004, title = {Complement-like protein TEP1 is a determinant of vectorial capacity in the malaria vector Anopheles gambiae}, author = {Stephanie A Blandin and Shin-Hong Shiao and Luis F Moita and Chris J Janse and Andrew P Waters and Fotis C Kafatos and Elena A Levashina}, issn = {0092-8674}, year = {2004}, date = {2004-01-01}, journal = {Cell}, volume = {116}, number = {5}, pages = {661--670}, abstract = {Anopheles mosquitoes are major vectors of human malaria in Africa. Large variation exists in the ability of mosquitoes to serve as vectors and to transmit malaria parasites, but the molecular mechanisms that determine vectorial capacity remain poorly understood. We report that the hemocyte-specific complement-like protein TEP1 from the mosquito Anopheles gambiae binds to and mediates killing of midgut stages of the rodent malaria parasite Plasmodium berghei. The dsRNA knockdown of TEP1 in adults completely abolishes melanotic refractoriness in a genetically selected refractory strain. Moreover, in susceptible mosquitoes this knockdown increases the number of developing parasites. Our results suggest that the TEP1-dependent parasite killing is followed by a TEP1-independent clearance of dead parasites by lysis and/or melanization. Further elucidation of the molecular mechanisms of TEP1-mediated parasite killing will be of great importance for our understanding of the principles of vectorial capacity in insects.}, keywords = {Animals, Anopheles, blandin, Female, Genetic, Humans, Insect Proteins, Insect Vectors, M3i, Malaria, Models, Molecular, Plasmodium berghei, Polymorphism, Protein Structure, RNA, Sequence Alignment, Tertiary}, pubstate = {published}, tppubtype = {article} } Anopheles mosquitoes are major vectors of human malaria in Africa. Large variation exists in the ability of mosquitoes to serve as vectors and to transmit malaria parasites, but the molecular mechanisms that determine vectorial capacity remain poorly understood. We report that the hemocyte-specific complement-like protein TEP1 from the mosquito Anopheles gambiae binds to and mediates killing of midgut stages of the rodent malaria parasite Plasmodium berghei. The dsRNA knockdown of TEP1 in adults completely abolishes melanotic refractoriness in a genetically selected refractory strain. Moreover, in susceptible mosquitoes this knockdown increases the number of developing parasites. Our results suggest that the TEP1-dependent parasite killing is followed by a TEP1-independent clearance of dead parasites by lysis and/or melanization. Further elucidation of the molecular mechanisms of TEP1-mediated parasite killing will be of great importance for our understanding of the principles of vectorial capacity in insects. |
2003 |
Goto, Akira; Blandin, Stéphanie A; Royet, Julien; Reichhart, Jean-Marc; Levashina, Elena A Silencing of Toll pathway components by direct injection of double-stranded RNA into Drosophila adult flies Article de journal Nucleic Acids Res., 31 (22), p. 6619–6623, 2003, ISSN: 1362-4962. Résumé | BibTeX | Étiquettes: Animals, blandin, Cell Surface, Double-Stranded, Epistasis, Female, Genetic, Green Fluorescent Proteins, Homeodomain Proteins, Luminescent Proteins, M3i, Phenotype, Receptors, reichhart, RNA, RNA Interference, Serpins, Signal Transduction, Time Factors, Toll-Like Receptors, Transcription Factors @article{goto_silencing_2003, title = {Silencing of Toll pathway components by direct injection of double-stranded RNA into Drosophila adult flies}, author = {Akira Goto and Stéphanie A Blandin and Julien Royet and Jean-Marc Reichhart and Elena A Levashina}, issn = {1362-4962}, year = {2003}, date = {2003-11-01}, journal = {Nucleic Acids Res.}, volume = {31}, number = {22}, pages = {6619--6623}, abstract = {Double-stranded RNA (dsRNA) gene interference is an efficient method to silence gene expression in a sequence-specific manner. Here we show that the direct injection of dsRNA can be used in adult Drosophila flies to disrupt function of endogenous genes in vivo. As a proof of principle, we have used this method to silence components of a major signaling cascade, the Toll pathway, which controls fruit fly resistance to fungal and Gram-positive bacterial infections. We demonstrate that the knockout is efficient only if dsRNA is injected in 4- or more day-old flies and that it lasts for at least 1 week. Furthermore, we report dsRNA-based epistatic gene analysis via injection of a mixture of two dsRNAs and propose that injection of dsRNA represents a powerful method for rapid functional analysis of genes in Drosophila melanogaster adults, particularly of those whose mutations are lethal during development.}, keywords = {Animals, blandin, Cell Surface, Double-Stranded, Epistasis, Female, Genetic, Green Fluorescent Proteins, Homeodomain Proteins, Luminescent Proteins, M3i, Phenotype, Receptors, reichhart, RNA, RNA Interference, Serpins, Signal Transduction, Time Factors, Toll-Like Receptors, Transcription Factors}, pubstate = {published}, tppubtype = {article} } Double-stranded RNA (dsRNA) gene interference is an efficient method to silence gene expression in a sequence-specific manner. Here we show that the direct injection of dsRNA can be used in adult Drosophila flies to disrupt function of endogenous genes in vivo. As a proof of principle, we have used this method to silence components of a major signaling cascade, the Toll pathway, which controls fruit fly resistance to fungal and Gram-positive bacterial infections. We demonstrate that the knockout is efficient only if dsRNA is injected in 4- or more day-old flies and that it lasts for at least 1 week. Furthermore, we report dsRNA-based epistatic gene analysis via injection of a mixture of two dsRNAs and propose that injection of dsRNA represents a powerful method for rapid functional analysis of genes in Drosophila melanogaster adults, particularly of those whose mutations are lethal during development. |
Luna, C; Hoa, N T; Zhang, J; Kanzok, S M; Brown, S E; Imler, Jean-Luc; Knudson, D L; Zheng, L Characterization of three Toll-like genes from mosquito Aedes aegypti Article de journal Insect Molecular Biology, 12 (1), p. 67–74, 2003, ISSN: 0962-1075. Résumé | BibTeX | Étiquettes: Aedes, Animals, Base Sequence, Cell Surface, Chimera, Cloning, Developmental, Female, Gene Expression Regulation, Genetic, imler, Insect Proteins, M3i, Male, messenger, Models, Molecular, Mutagenesis, Promoter Regions, Receptors, Reverse Transcriptase Polymerase Chain Reaction, RNA, Sequence Alignment, Signal Transduction, Site-Directed, Transfection @article{luna_characterization_2003, title = {Characterization of three Toll-like genes from mosquito Aedes aegypti}, author = {C Luna and N T Hoa and J Zhang and S M Kanzok and S E Brown and Jean-Luc Imler and D L Knudson and L Zheng}, issn = {0962-1075}, year = {2003}, date = {2003-02-01}, journal = {Insect Molecular Biology}, volume = {12}, number = {1}, pages = {67--74}, abstract = {Three Toll-related genes (AeToll1A, AeToll1B and AeToll5) were cloned and characterized from the yellow fever vector mosquito, Aedes aegypti. All three genes exhibited high levels of amino acid sequence similarity with Drosophila melanogaster (Dm)Toll1 and DmTehao (Toll5). AeToll1A and AeToll1B are 1124 and 1076 amino acid residues long, respectively. Both contain a carboxyl extension downstream of the Toll/interleukin-1 receptor (TIR) domain. AeToll5 is 1007 residues long and, like DmTehao, lacks the carboxyl terminal extension. Expression of these three genes was examined throughout development and after immune challenge. Both AeToll1A and AeToll5, like their Drosophila counterparts, activate transcription of drosomycin promoter in both Aedes and Drosophila cell lines. Deletion of the carboxyl extension of AeToll1A did not result in a further elevated level of the antifungal response. The intracellular signalling process appears to be species specific based on two observations. (1) DmToll is completely inactive in an Aedes cell line, suggesting a higher specificity requirement for DmToll in the intracellular signalling process. (2) Only one of three amino acid residues essential for DmToll function is required for AeToll1A function.}, keywords = {Aedes, Animals, Base Sequence, Cell Surface, Chimera, Cloning, Developmental, Female, Gene Expression Regulation, Genetic, imler, Insect Proteins, M3i, Male, messenger, Models, Molecular, Mutagenesis, Promoter Regions, Receptors, Reverse Transcriptase Polymerase Chain Reaction, RNA, Sequence Alignment, Signal Transduction, Site-Directed, Transfection}, pubstate = {published}, tppubtype = {article} } Three Toll-related genes (AeToll1A, AeToll1B and AeToll5) were cloned and characterized from the yellow fever vector mosquito, Aedes aegypti. All three genes exhibited high levels of amino acid sequence similarity with Drosophila melanogaster (Dm)Toll1 and DmTehao (Toll5). AeToll1A and AeToll1B are 1124 and 1076 amino acid residues long, respectively. Both contain a carboxyl extension downstream of the Toll/interleukin-1 receptor (TIR) domain. AeToll5 is 1007 residues long and, like DmTehao, lacks the carboxyl terminal extension. Expression of these three genes was examined throughout development and after immune challenge. Both AeToll1A and AeToll5, like their Drosophila counterparts, activate transcription of drosomycin promoter in both Aedes and Drosophila cell lines. Deletion of the carboxyl extension of AeToll1A did not result in a further elevated level of the antifungal response. The intracellular signalling process appears to be species specific based on two observations. (1) DmToll is completely inactive in an Aedes cell line, suggesting a higher specificity requirement for DmToll in the intracellular signalling process. (2) Only one of three amino acid residues essential for DmToll function is required for AeToll1A function. |
Bonnal, S; Schaeffer, C; Creancier, L; Clamens, S; Moine, H; Prats, A C; Vagner, S A single internal ribosome entry site containing a G quartet RNA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons Article de journal J Biol Chem, 278 (41), p. 39330-6, 2003, (0021-9258 Journal Article). Résumé | BibTeX | Étiquettes: 2/*genetics, Acid, Alternative, Base, Cell, Chain, Codon, Complementary/genetics, Conformation, Data, Deletion, DNA, Expression, Factor, Fibroblast, Gene, Gov't, Growth, Human, initiation, Initiator/genetics, Line, Messenger/*chemistry/*genetics, Molecular, Non-U.S., Nucleic, Peptide, Ribosomes/*metabolism, RNA, Sequence, Splicing, Support, Transfection @article{, title = {A single internal ribosome entry site containing a G quartet RNA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons}, author = { S. Bonnal and C. Schaeffer and L. Creancier and S. Clamens and H. Moine and A. C. Prats and S. Vagner}, year = {2003}, date = {2003-01-01}, journal = {J Biol Chem}, volume = {278}, number = {41}, pages = {39330-6}, abstract = {The 484-nucleotide (nt) alternatively translated region (ATR) of the human fibroblast growth factor 2 (FGF-2) mRNA contains four CUG and one AUG translation initiation codons. Although the 5'-end proximal CUG codon is initiated by a cap-dependent translation process, the other four initiation codons are initiated by a mechanism of internal entry of ribosomes. We undertook here a detailed analysis of the cis-acting elements defining the FGF-2 internal ribosome entry site (IRES). A thorough deletion analysis study within the 5'-ATR led us to define a 176-nt region as being necessary and sufficient for IRES function at four codons present in a downstream 308-nt RNA segment. Unexpectedly, a single IRES module is therefore responsible for translation initiation at four distantly localized codons. The determination of the FGF-2 5'-ATR RNA secondary structure by enzymatic and chemical probing experiments showed that the FGF-2 IRES contained two stem-loop regions and a G quartet motif that constitute novel structural determinants of IRES function.}, note = {0021-9258 Journal Article}, keywords = {2/*genetics, Acid, Alternative, Base, Cell, Chain, Codon, Complementary/genetics, Conformation, Data, Deletion, DNA, Expression, Factor, Fibroblast, Gene, Gov't, Growth, Human, initiation, Initiator/genetics, Line, Messenger/*chemistry/*genetics, Molecular, Non-U.S., Nucleic, Peptide, Ribosomes/*metabolism, RNA, Sequence, Splicing, Support, Transfection}, pubstate = {published}, tppubtype = {article} } The 484-nucleotide (nt) alternatively translated region (ATR) of the human fibroblast growth factor 2 (FGF-2) mRNA contains four CUG and one AUG translation initiation codons. Although the 5'-end proximal CUG codon is initiated by a cap-dependent translation process, the other four initiation codons are initiated by a mechanism of internal entry of ribosomes. We undertook here a detailed analysis of the cis-acting elements defining the FGF-2 internal ribosome entry site (IRES). A thorough deletion analysis study within the 5'-ATR led us to define a 176-nt region as being necessary and sufficient for IRES function at four codons present in a downstream 308-nt RNA segment. Unexpectedly, a single IRES module is therefore responsible for translation initiation at four distantly localized codons. The determination of the FGF-2 5'-ATR RNA secondary structure by enzymatic and chemical probing experiments showed that the FGF-2 IRES contained two stem-loop regions and a G quartet motif that constitute novel structural determinants of IRES function. |
Wilhelm, F X; Wilhelm, M; Gabriel, A Extension and cleavage of the polypurine tract plus-strand primer by Ty1 reverse transcriptase Article de journal J Biol Chem, 278 (48), p. 47678-84, 2003, (0021-9258 Journal Article). Résumé | BibTeX | Étiquettes: Base, Calf, Data, DNA, DNA/chemistry, Genetic, Gov't, H, Messenger/metabolism, Models, Molecular, Non-U.S., P.H.S., Polymerase/*chemistry, Primers, Proteins/chemistry, Purines/*chemistry, Recombinant, Replication, Retroelements/*genetics, Ribonuclease, RNA, RNA-Directed, RNA/chemistry, Sequence, Support, Templates, Thymus/chemistry, U.S., Viral @article{, title = {Extension and cleavage of the polypurine tract plus-strand primer by Ty1 reverse transcriptase}, author = { F. X. Wilhelm and M. Wilhelm and A. Gabriel}, year = {2003}, date = {2003-01-01}, journal = {J Biol Chem}, volume = {278}, number = {48}, pages = {47678-84}, abstract = {Using hybrid RNA/DNA substrates containing the polypurine tract (PPT) plus-strand primer, we have examined the interaction between the Ty1 reverse transcriptase (RT) and the plus-strand initiation complex. We show here that, although the PPT sequence is relatively resistant to RNase H cleavage, it can be cleaved internally by the polymerase-independent RNase H activity of Ty1 RT. Alternatively, this PPT can be used to initiate plus-strand DNA synthesis. We demonstrate that cleavage at the PPT/DNA junction occurs only after at least 9 nucleotides are extended. Cleavage leaves a nick between the RNA primer and the nascent plus-strand DNA. We show that Ty1 RT has a strand displacement activity beyond a gap but that the PPT is not efficiently re-utilized in vitro for another round of DNA synthesis after a first plus-strand DNA has been synthesized and cleaved at the PPT/U3 junction.}, note = {0021-9258 Journal Article}, keywords = {Base, Calf, Data, DNA, DNA/chemistry, Genetic, Gov't, H, Messenger/metabolism, Models, Molecular, Non-U.S., P.H.S., Polymerase/*chemistry, Primers, Proteins/chemistry, Purines/*chemistry, Recombinant, Replication, Retroelements/*genetics, Ribonuclease, RNA, RNA-Directed, RNA/chemistry, Sequence, Support, Templates, Thymus/chemistry, U.S., Viral}, pubstate = {published}, tppubtype = {article} } Using hybrid RNA/DNA substrates containing the polypurine tract (PPT) plus-strand primer, we have examined the interaction between the Ty1 reverse transcriptase (RT) and the plus-strand initiation complex. We show here that, although the PPT sequence is relatively resistant to RNase H cleavage, it can be cleaved internally by the polymerase-independent RNase H activity of Ty1 RT. Alternatively, this PPT can be used to initiate plus-strand DNA synthesis. We demonstrate that cleavage at the PPT/DNA junction occurs only after at least 9 nucleotides are extended. Cleavage leaves a nick between the RNA primer and the nascent plus-strand DNA. We show that Ty1 RT has a strand displacement activity beyond a gap but that the PPT is not efficiently re-utilized in vitro for another round of DNA synthesis after a first plus-strand DNA has been synthesized and cleaved at the PPT/U3 junction. |
Kambris, Zakaria; Bilak, Hana; D'Alessandro, Rosalba; Belvin, Marcia; Imler, Jean-Luc; Capovilla, Maria DmMyD88 controls dorsoventral patterning of the Drosophila embryo Article de journal EMBO reports, 4 (1), p. 64–69, 2003, ISSN: 1469-221X. Résumé | Liens | BibTeX | Étiquettes: Adaptor Proteins, Alleles, Animals, Antigens, Base Sequence, Cell Surface, Complementary, Developmental, Differentiation, DNA, DNA Transposable Elements, Egg Proteins, Embryo, Exons, Female, Gene Expression Regulation, Genetically Modified, Genotype, imler, Immunity, Immunologic, Innate, Insertional, M3i, Male, messenger, Morphogenesis, Mutagenesis, Myeloid Differentiation Factor 88, Nonmammalian, Oocytes, Protein Biosynthesis, Protein Structure, Receptors, Reverse Transcriptase Polymerase Chain Reaction, RNA, Signal Transducing, Tertiary, Toll-Like Receptors, Zygote @article{kambris_dmmyd88_2003, title = {DmMyD88 controls dorsoventral patterning of the Drosophila embryo}, author = {Zakaria Kambris and Hana Bilak and Rosalba D'Alessandro and Marcia Belvin and Jean-Luc Imler and Maria Capovilla}, doi = {10.1038/sj.embor.embor714}, issn = {1469-221X}, year = {2003}, date = {2003-01-01}, journal = {EMBO reports}, volume = {4}, number = {1}, pages = {64--69}, abstract = {MyD88 is an adapter protein in the signal transduction pathway mediated by interleukin-1 (IL-1) and Toll-like receptors. A Drosophila homologue of MyD88 (DmMyD88) was recently shown to be required for the Toll-mediated immune response. In Drosophila, the Toll pathway was originally characterized for its role in the dorsoventral patterning of the embryo. We found that, like Toll, DmMyD88 messenger RNA is maternally supplied to the embryo. Here we report the identification of a new mutant allele of DmMyD88, which generates a protein lacking the carboxy-terminal extension, normally located downstream of the Toll/IL-1 receptor domain. Homozygous mutant female flies lay dorsalized embryos that are rescued by expression of a transgenic DmMyD88 complementary DNA. The DmMyD88 mutation blocks the ventralizing activity of a gain-of-function Toll mutation. These results show that DmMyD88 encodes an essential component of the Toll pathway in dorsoventral pattern formation.}, keywords = {Adaptor Proteins, Alleles, Animals, Antigens, Base Sequence, Cell Surface, Complementary, Developmental, Differentiation, DNA, DNA Transposable Elements, Egg Proteins, Embryo, Exons, Female, Gene Expression Regulation, Genetically Modified, Genotype, imler, Immunity, Immunologic, Innate, Insertional, M3i, Male, messenger, Morphogenesis, Mutagenesis, Myeloid Differentiation Factor 88, Nonmammalian, Oocytes, Protein Biosynthesis, Protein Structure, Receptors, Reverse Transcriptase Polymerase Chain Reaction, RNA, Signal Transducing, Tertiary, Toll-Like Receptors, Zygote}, pubstate = {published}, tppubtype = {article} } MyD88 is an adapter protein in the signal transduction pathway mediated by interleukin-1 (IL-1) and Toll-like receptors. A Drosophila homologue of MyD88 (DmMyD88) was recently shown to be required for the Toll-mediated immune response. In Drosophila, the Toll pathway was originally characterized for its role in the dorsoventral patterning of the embryo. We found that, like Toll, DmMyD88 messenger RNA is maternally supplied to the embryo. Here we report the identification of a new mutant allele of DmMyD88, which generates a protein lacking the carboxy-terminal extension, normally located downstream of the Toll/IL-1 receptor domain. Homozygous mutant female flies lay dorsalized embryos that are rescued by expression of a transgenic DmMyD88 complementary DNA. The DmMyD88 mutation blocks the ventralizing activity of a gain-of-function Toll mutation. These results show that DmMyD88 encodes an essential component of the Toll pathway in dorsoventral pattern formation. |
2002 |
Gottar, Marie; Gobert, Vanessa; Michel, Tatiana; Belvin, Marcia; Duyk, Geoffrey; Hoffmann, Jules A; Ferrandon, Dominique; Royet, Julien The Drosophila immune response against Gram-negative bacteria is mediated by a peptidoglycan recognition protein Article de journal Nature, 416 , p. 640–644, 2002, ISBN: 0028-0836. Résumé | Liens | BibTeX | Étiquettes: Animal, Anti-Infective Agents/metabolism, Carrier Proteins/biosynthesis/genetics/*immunology, Drosophila melanogaster/genetics/*immunology/*microbiology, Drosophila Proteins/genetics/metabolism, Epistasis, Female, ferrandon, Genes, Genetic, Genetic Predisposition to Disease, Gram-Negative Bacteria/*immunology/physiology, hoffmann, Human, Insect/genetics, M3i, Messenger/genetics/metabolism, Mutation, Non-U.S. Gov't, P.H.S., Phenotype, RNA, Signal Transduction, Support, Survival Rate, Transgenes/genetics, U.S. Gov't @article{gottar_drosophila_2002b, title = {The Drosophila immune response against Gram-negative bacteria is mediated by a peptidoglycan recognition protein}, author = {Marie Gottar and Vanessa Gobert and Tatiana Michel and Marcia Belvin and Geoffrey Duyk and Jules A Hoffmann and Dominique Ferrandon and Julien Royet}, doi = {10.1038/nature734}, isbn = {0028-0836}, year = {2002}, date = {2002-03-01}, journal = {Nature}, volume = {416}, pages = {640--644}, abstract = {The antimicrobial defence of Drosophila relies largely on the challenge-induced synthesis of an array of potent antimicrobial peptides by the fat body. The defence against Gram-positive bacteria and natural fungal infections is mediated by the Toll signalling pathway, whereas defence against Gram-negative bacteria is dependent on the Immune deficiency (IMD) pathway. Loss-of-function mutations in either pathway reduce the resistance to corresponding infections. The link between microbial infections and activation of these two pathways has remained elusive. The Toll pathway is activated by Gram-positive bacteria through a circulating Peptidoglycan recognition protein (PGRP-SA). PGRPs appear to be highly conserved from insects to mammals, and the Drosophila genome contains 13 members. Here we report a mutation in a gene coding for a putative transmembrane protein, PGRP-LC, which reduces survival to Gram-negative sepsis but has no effect on the response to Gram-positive bacteria or natural fungal infections. By genetic epistasis, we demonstrate that PGRP-LC acts upstream of the imd gene. The data on PGRP-SA with respect to the response to Gram-positive infections, together with the present report, indicate that the PGRP family has a principal role in sensing microbial infections in Drosophila.}, keywords = {Animal, Anti-Infective Agents/metabolism, Carrier Proteins/biosynthesis/genetics/*immunology, Drosophila melanogaster/genetics/*immunology/*microbiology, Drosophila Proteins/genetics/metabolism, Epistasis, Female, ferrandon, Genes, Genetic, Genetic Predisposition to Disease, Gram-Negative Bacteria/*immunology/physiology, hoffmann, Human, Insect/genetics, M3i, Messenger/genetics/metabolism, Mutation, Non-U.S. Gov't, P.H.S., Phenotype, RNA, Signal Transduction, Support, Survival Rate, Transgenes/genetics, U.S. Gov't}, pubstate = {published}, tppubtype = {article} } The antimicrobial defence of Drosophila relies largely on the challenge-induced synthesis of an array of potent antimicrobial peptides by the fat body. The defence against Gram-positive bacteria and natural fungal infections is mediated by the Toll signalling pathway, whereas defence against Gram-negative bacteria is dependent on the Immune deficiency (IMD) pathway. Loss-of-function mutations in either pathway reduce the resistance to corresponding infections. The link between microbial infections and activation of these two pathways has remained elusive. The Toll pathway is activated by Gram-positive bacteria through a circulating Peptidoglycan recognition protein (PGRP-SA). PGRPs appear to be highly conserved from insects to mammals, and the Drosophila genome contains 13 members. Here we report a mutation in a gene coding for a putative transmembrane protein, PGRP-LC, which reduces survival to Gram-negative sepsis but has no effect on the response to Gram-positive bacteria or natural fungal infections. By genetic epistasis, we demonstrate that PGRP-LC acts upstream of the imd gene. The data on PGRP-SA with respect to the response to Gram-positive infections, together with the present report, indicate that the PGRP family has a principal role in sensing microbial infections in Drosophila. |
Cristofari, G; Bampi, C; Wilhelm, M; Wilhelm, F X; Darlix, J L A 5'-3' long-range interaction in Ty1 RNA controls its reverse transcription and retrotransposition Article de journal EMBO J, 21 (16), p. 4368-79, 2002, (0261-4189 Journal Article). Résumé | BibTeX | Étiquettes: *Gene, *Transcription, Acid, cerevisiae/*genetics, Complementary/biosynthesis, Conformation, DNA, Expression, Fungal, Fungal/chemistry/*metabolism, Genetic, Gov't, in, Messenger/chemistry/*metabolism, Non-U.S., Nucleic, Phylogeny, Regulation, Retroelements/*genetics, RNA, Saccharomyces, Support, vitro @article{, title = {A 5'-3' long-range interaction in Ty1 RNA controls its reverse transcription and retrotransposition}, author = { G. Cristofari and C. Bampi and M. Wilhelm and F. X. Wilhelm and J. L. Darlix}, year = {2002}, date = {2002-01-01}, journal = {EMBO J}, volume = {21}, number = {16}, pages = {4368-79}, abstract = {LTR-retrotransposons are abundant components of all eukaryotic genomes and appear to be key players in their evolution. They share with retroviruses a reverse transcription step during their replication cycle. To better understand the replication of retrotransposons as well as their similarities to and differences from retroviruses, we set up an in vitro model system to examine minus-strand cDNA synthesis of the yeast Ty1 LTR-retrotransposon. Results show that the 5' and 3' ends of Ty1 genomic RNA interact through 14 nucleotide 5'-3' complementary sequences (CYC sequences). This 5'-3' base pairing results in an efficient initiation of reverse transcription in vitro. Transposition of a marked Ty1 element and Ty1 cDNA synthesis in yeast rely on the ability of the CYC sequences to base pair. This 5'-3' interaction is also supported by phylogenic analysis of all full-length Ty1 and Ty2 elements present in the Saccharomyces cerevisiae genome. These novel findings lead us to propose that circularization of the Ty1 genomic RNA controls initiation of reverse transcription and may limit reverse transcription of defective retroelements.}, note = {0261-4189 Journal Article}, keywords = {*Gene, *Transcription, Acid, cerevisiae/*genetics, Complementary/biosynthesis, Conformation, DNA, Expression, Fungal, Fungal/chemistry/*metabolism, Genetic, Gov't, in, Messenger/chemistry/*metabolism, Non-U.S., Nucleic, Phylogeny, Regulation, Retroelements/*genetics, RNA, Saccharomyces, Support, vitro}, pubstate = {published}, tppubtype = {article} } LTR-retrotransposons are abundant components of all eukaryotic genomes and appear to be key players in their evolution. They share with retroviruses a reverse transcription step during their replication cycle. To better understand the replication of retrotransposons as well as their similarities to and differences from retroviruses, we set up an in vitro model system to examine minus-strand cDNA synthesis of the yeast Ty1 LTR-retrotransposon. Results show that the 5' and 3' ends of Ty1 genomic RNA interact through 14 nucleotide 5'-3' complementary sequences (CYC sequences). This 5'-3' base pairing results in an efficient initiation of reverse transcription in vitro. Transposition of a marked Ty1 element and Ty1 cDNA synthesis in yeast rely on the ability of the CYC sequences to base pair. This 5'-3' interaction is also supported by phylogenic analysis of all full-length Ty1 and Ty2 elements present in the Saccharomyces cerevisiae genome. These novel findings lead us to propose that circularization of the Ty1 genomic RNA controls initiation of reverse transcription and may limit reverse transcription of defective retroelements. |
Perederina, A; Nevskaya, N; Nikonov, O; Nikulin, A; Dumas, P; Yao, M; Tanaka, I; Garber, M; Gongadze, G; Nikonov, S Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex Article de journal RNA, 8 (12), p. 1548-57, 2002, (1355-8382 Journal Article). Résumé | BibTeX | Étiquettes: 5S/*chemistry/*metabolism, Acid, Amino, Bacterial, Base, Binding, Bonding, coli/genetics, Conformation, Data, Escherichia, Fragments/chemistry/metabolism, Gov't, Hydrogen, Models, Molecular, Non-U.S., Nucleic, Peptide, Protein, Proteins/*chemistry/*metabolism, Proteins/chemistry/metabolism, Ribosomal, RNA, Sequence, Sites, Support @article{, title = {Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex}, author = { A. Perederina and N. Nevskaya and O. Nikonov and A. Nikulin and P. Dumas and M. Yao and I. Tanaka and M. Garber and G. Gongadze and S. Nikonov}, year = {2002}, date = {2002-01-01}, journal = {RNA}, volume = {8}, number = {12}, pages = {1548-57}, abstract = {The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.}, note = {1355-8382 Journal Article}, keywords = {5S/*chemistry/*metabolism, Acid, Amino, Bacterial, Base, Binding, Bonding, coli/genetics, Conformation, Data, Escherichia, Fragments/chemistry/metabolism, Gov't, Hydrogen, Models, Molecular, Non-U.S., Nucleic, Peptide, Protein, Proteins/*chemistry/*metabolism, Proteins/chemistry/metabolism, Ribosomal, RNA, Sequence, Sites, Support}, pubstate = {published}, tppubtype = {article} } The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit. |
2001 |
Vizioli, J; Bulet, Philippe; Hoffmann, Jules A; Kafatos, Fotis C; Müller, H M; Dimopoulos, G Gambicin: a novel immune responsive antimicrobial peptide from the malaria vector Anopheles gambiae Article de journal Proc. Natl. Acad. Sci. U.S.A., 98 (22), p. 12630–12635, 2001, ISSN: 0027-8424. Résumé | Liens | BibTeX | Étiquettes: Animals, Anopheles, Anti-Bacterial Agents, Anti-Infective Agents, Base Sequence, Chromosome Mapping, hoffmann, Insect Proteins, Insect Vectors, M3i, Malaria, messenger, RNA @article{vizioli_gambicin:_2001, title = {Gambicin: a novel immune responsive antimicrobial peptide from the malaria vector Anopheles gambiae}, author = {J Vizioli and Philippe Bulet and Jules A Hoffmann and Fotis C Kafatos and H M Müller and G Dimopoulos}, doi = {10.1073/pnas.221466798}, issn = {0027-8424}, year = {2001}, date = {2001-10-01}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, volume = {98}, number = {22}, pages = {12630--12635}, abstract = {A novel mosquito antimicrobial peptide, gambicin, and the corresponding gene were isolated in parallel through differential display-PCR, an expressed sequence tag (EST) project, and characterization of an antimicrobial activity in a mosquito cell line by reverse-phase chromatography. The 616-bp gambicin ORF encodes an 81-residue protein that is processed and secreted as a 61-aa mature peptide containing eight cysteines engaged in four disulfide bridges. Gambicin lacks sequence homology with other known proteins. Like other Anopheles gambiae antimicrobial peptide genes, gambicin is induced by natural or experimental infection in the midgut, fatbody, and hemocyte-like cell lines. Within the midgut, gambicin is predominantly expressed in the anterior part. Both local and systemic gambicin expression is induced during early and late stages of natural malaria infection. In vitro experiments showed that the 6.8-kDa mature peptide can kill both Gram-positive and Gram-negative bacteria, has a morphogenic effect on a filamentous fungus, and is marginally lethal to Plasmodium berghei ookinetes. An oxidized form of gambicin isolated from the cell line medium was more active against bacteria than the nonoxidized form from the same medium.}, keywords = {Animals, Anopheles, Anti-Bacterial Agents, Anti-Infective Agents, Base Sequence, Chromosome Mapping, hoffmann, Insect Proteins, Insect Vectors, M3i, Malaria, messenger, RNA}, pubstate = {published}, tppubtype = {article} } A novel mosquito antimicrobial peptide, gambicin, and the corresponding gene were isolated in parallel through differential display-PCR, an expressed sequence tag (EST) project, and characterization of an antimicrobial activity in a mosquito cell line by reverse-phase chromatography. The 616-bp gambicin ORF encodes an 81-residue protein that is processed and secreted as a 61-aa mature peptide containing eight cysteines engaged in four disulfide bridges. Gambicin lacks sequence homology with other known proteins. Like other Anopheles gambiae antimicrobial peptide genes, gambicin is induced by natural or experimental infection in the midgut, fatbody, and hemocyte-like cell lines. Within the midgut, gambicin is predominantly expressed in the anterior part. Both local and systemic gambicin expression is induced during early and late stages of natural malaria infection. In vitro experiments showed that the 6.8-kDa mature peptide can kill both Gram-positive and Gram-negative bacteria, has a morphogenic effect on a filamentous fungus, and is marginally lethal to Plasmodium berghei ookinetes. An oxidized form of gambicin isolated from the cell line medium was more active against bacteria than the nonoxidized form from the same medium. |
Boutabout, M; Wilhelm, M; Wilhelm, F X DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1 Article de journal Nucleic Acids Res, 29 (11), p. 2217-22, 2001, (1362-4962 Journal Article). Résumé | BibTeX | Étiquettes: cerevisiae/*genetics/metabolism, DNA, Fungal/genetics, Fungal/genetics/*metabolism, Genetic, Gov't, Kinetics, Non-U.S., Nucleotides/genetics/metabolism, Polymerase/*metabolism, Retroelements/*genetics, RNA, RNA-Directed, Saccharomyces, Support, Templates @article{, title = {DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1}, author = { M. Boutabout and M. Wilhelm and F. X. Wilhelm}, year = {2001}, date = {2001-01-01}, journal = {Nucleic Acids Res}, volume = {29}, number = {11}, pages = {2217-22}, abstract = {The fidelity of the yeast retrotransposon Ty1 reverse transcriptase (RT) was determined by an assay based on gel electrophoresis. Steady-state kinetics analyses of deoxyribonucleotide (dNTP) incorporation at a defined primer-template site indicate that Ty1 RT misincorporates dNTP at a frequency of 0.45 x 10(-5) for the A(t):A mispair in which dATP is misincorporated opposite a template A to 6.27 x 10(-5) for the C(t):A mispair. The G(t):G and T(t):T mispairs are formed with very low efficiency. The fidelity parameters of Ty1 RT do not depend on whether RNA or DNA are copied. Relative to lentiviral RTs (HIV-1, HIV-2 or EIAV) Ty1 RT is approximately 10-fold less error prone. Our data also show that the Ty1 RT is able to recapitulate two error-generating mechanisms: extension of mismatches and non-templated addition of nucleotides at the end of a blunt-end primer-template.}, note = {1362-4962 Journal Article}, keywords = {cerevisiae/*genetics/metabolism, DNA, Fungal/genetics, Fungal/genetics/*metabolism, Genetic, Gov't, Kinetics, Non-U.S., Nucleotides/genetics/metabolism, Polymerase/*metabolism, Retroelements/*genetics, RNA, RNA-Directed, Saccharomyces, Support, Templates}, pubstate = {published}, tppubtype = {article} } The fidelity of the yeast retrotransposon Ty1 reverse transcriptase (RT) was determined by an assay based on gel electrophoresis. Steady-state kinetics analyses of deoxyribonucleotide (dNTP) incorporation at a defined primer-template site indicate that Ty1 RT misincorporates dNTP at a frequency of 0.45 x 10(-5) for the A(t):A mispair in which dATP is misincorporated opposite a template A to 6.27 x 10(-5) for the C(t):A mispair. The G(t):G and T(t):T mispairs are formed with very low efficiency. The fidelity parameters of Ty1 RT do not depend on whether RNA or DNA are copied. Relative to lentiviral RTs (HIV-1, HIV-2 or EIAV) Ty1 RT is approximately 10-fold less error prone. Our data also show that the Ty1 RT is able to recapitulate two error-generating mechanisms: extension of mismatches and non-templated addition of nucleotides at the end of a blunt-end primer-template. |
Carnicelli, D; Brigotti, M; Rizzi, S; Keith, G; Montanaro, L; Sperti, S Nucleotides U28-A42 and A37 in unmodified yeast tRNA(Trp) as negative identity elements for bovine tryptophanyl-tRNA synthetase Article de journal FEBS Lett, 492 (3), p. 238-41, 2001, (0014-5793 Journal Article). Résumé | BibTeX | Étiquettes: Acid, Adenine/chemistry, Animals, Base, Cattle, cerevisiae/genetics, Conformation, Data, Fungal/genetics/metabolism, Gov't, Kinetics, Ligase/*metabolism, Molecular, Non-U.S., Nucleic, RNA, Saccharomyces, Sequence, Species, Specificity, Substrate, Support, Transfer, Trp/chemistry/*metabolism, Tryptophan-tRNA, Uridine/chemistry @article{, title = {Nucleotides U28-A42 and A37 in unmodified yeast tRNA(Trp) as negative identity elements for bovine tryptophanyl-tRNA synthetase}, author = { D. Carnicelli and M. Brigotti and S. Rizzi and G. Keith and L. Montanaro and S. Sperti}, year = {2001}, date = {2001-01-01}, journal = {FEBS Lett}, volume = {492}, number = {3}, pages = {238-41}, abstract = {Wild-type bovine and yeast tRNA(Trp) are efficiently aminoacylated by tryptophanyl-tRNA synthetase both from beef and from yeast. Upon loss of modified bases in the synthetic transcripts, mammalian tRNA(Trp) retains the double recognition by the two synthetases, while yeast tRNA(Trp) loses its substrate properties for the bovine enzyme and is recognised only by the cognate synthetase. By testing chimeric bovine-yeast transcripts with tryptophanyl-tRNA synthetase purified from beef pancreas, the nucleotides responsible for the loss of charging of the synthetic yeast transcript have been localised in the anticodon arm. A complete loss of charging akin to that observed with the yeast transcript requires substitution in the bovine backbone of G37 in the anticodon loop with yeast A37 and of C28-G42 in the anticodon stem with yeast U28-A42. Since A37 does not prevent aminoacylation of the wild-type yeast tRNA(Trp) by the beef enzyme, a negative combination apparently emerges in the synthetic transcript after unmasking of U28 by loss of pseudourydilation.}, note = {0014-5793 Journal Article}, keywords = {Acid, Adenine/chemistry, Animals, Base, Cattle, cerevisiae/genetics, Conformation, Data, Fungal/genetics/metabolism, Gov't, Kinetics, Ligase/*metabolism, Molecular, Non-U.S., Nucleic, RNA, Saccharomyces, Sequence, Species, Specificity, Substrate, Support, Transfer, Trp/chemistry/*metabolism, Tryptophan-tRNA, Uridine/chemistry}, pubstate = {published}, tppubtype = {article} } Wild-type bovine and yeast tRNA(Trp) are efficiently aminoacylated by tryptophanyl-tRNA synthetase both from beef and from yeast. Upon loss of modified bases in the synthetic transcripts, mammalian tRNA(Trp) retains the double recognition by the two synthetases, while yeast tRNA(Trp) loses its substrate properties for the bovine enzyme and is recognised only by the cognate synthetase. By testing chimeric bovine-yeast transcripts with tryptophanyl-tRNA synthetase purified from beef pancreas, the nucleotides responsible for the loss of charging of the synthetic yeast transcript have been localised in the anticodon arm. A complete loss of charging akin to that observed with the yeast transcript requires substitution in the bovine backbone of G37 in the anticodon loop with yeast A37 and of C28-G42 in the anticodon stem with yeast U28-A42. Since A37 does not prevent aminoacylation of the wild-type yeast tRNA(Trp) by the beef enzyme, a negative combination apparently emerges in the synthetic transcript after unmasking of U28 by loss of pseudourydilation. |
Moine, H; Mandel, J L Biomedicine. Do G quartets orchestrate fragile X pathology? Article de journal Science, 294 (5551), p. 2487-8, 2001, (0036-8075 Journal Article). BibTeX | Étiquettes: Acid, Analysis, Animals, Array, Binding, Brain/metabolism, Conformation, Crystallography, Expression, Fragile, Gene, Genetic, Human, Messenger/*chemistry/genetics/*metabolism, Mice, Nerve, Nucleic, Oligonucleotide, Protein, Proteins/chemistry/genetics/*metabolism, Regions, Regulation, RNA, Sequence, Sites, structure, Synapses/physiology, Syndrome/genetics/*metabolism, Tertiary, Tissue, Translation, Untranslated, X, X-Ray @article{, title = {Biomedicine. Do G quartets orchestrate fragile X pathology?}, author = { H. Moine and J. L. Mandel}, year = {2001}, date = {2001-01-01}, journal = {Science}, volume = {294}, number = {5551}, pages = {2487-8}, note = {0036-8075 Journal Article}, keywords = {Acid, Analysis, Animals, Array, Binding, Brain/metabolism, Conformation, Crystallography, Expression, Fragile, Gene, Genetic, Human, Messenger/*chemistry/genetics/*metabolism, Mice, Nerve, Nucleic, Oligonucleotide, Protein, Proteins/chemistry/genetics/*metabolism, Regions, Regulation, RNA, Sequence, Sites, structure, Synapses/physiology, Syndrome/genetics/*metabolism, Tertiary, Tissue, Translation, Untranslated, X, X-Ray}, pubstate = {published}, tppubtype = {article} } |
Levashina, Elena A; Moita, L F; Blandin, Stéphanie A; Vriend, G; Lagueux, Marie; Kafatos, F C Conserved role of a complement-like protein in phagocytosis revealed by dsRNA knockout in cultured cells of the mosquito, Anopheles gambiae Article de journal Cell, 104 (5), p. 709–718, 2001, ISSN: 0092-8674. Résumé | BibTeX | Étiquettes: alpha-Macroglobulins, Animals, Anopheles, blandin, Cells, Cloning, Complement C3, Cultured, DNA Fragmentation, Double-Stranded, Female, Genetic, Gram-Negative Bacteria, Hemocytes, Insect Proteins, M3i, Molecular, Nucleic Acid Denaturation, Phagocytosis, Protein Structure, RNA, Tertiary, Transcription @article{levashina_conserved_2001, title = {Conserved role of a complement-like protein in phagocytosis revealed by dsRNA knockout in cultured cells of the mosquito, Anopheles gambiae}, author = {Elena A Levashina and L F Moita and Stéphanie A Blandin and G Vriend and Marie Lagueux and F C Kafatos}, issn = {0092-8674}, year = {2001}, date = {2001-01-01}, journal = {Cell}, volume = {104}, number = {5}, pages = {709--718}, abstract = {We characterize a novel hemocyte-specific acute phase glycoprotein from the malaria vector, Anopheles gambiae. It shows substantial structural and functional similarities, including the highly conserved thioester motif, to both a central component of mammalian complement system, factor C3, and to a pan-protease inhibitor, alpha2-macroglobulin. Most importantly, this protein serves as a complement-like opsonin and promotes phagocytosis of some Gram-negative bacteria in a mosquito hemocyte-like cell line. Chemical inactivation by methylamine and depletion by double-stranded RNA knockout demonstrate that this function is dependent on the internal thioester bond. This evidence of a complement-like function in a protostome animal adds substantially to the accumulating evidence of a common ancestry of immune defenses in insects and vertebrates.}, keywords = {alpha-Macroglobulins, Animals, Anopheles, blandin, Cells, Cloning, Complement C3, Cultured, DNA Fragmentation, Double-Stranded, Female, Genetic, Gram-Negative Bacteria, Hemocytes, Insect Proteins, M3i, Molecular, Nucleic Acid Denaturation, Phagocytosis, Protein Structure, RNA, Tertiary, Transcription}, pubstate = {published}, tppubtype = {article} } We characterize a novel hemocyte-specific acute phase glycoprotein from the malaria vector, Anopheles gambiae. It shows substantial structural and functional similarities, including the highly conserved thioester motif, to both a central component of mammalian complement system, factor C3, and to a pan-protease inhibitor, alpha2-macroglobulin. Most importantly, this protein serves as a complement-like opsonin and promotes phagocytosis of some Gram-negative bacteria in a mosquito hemocyte-like cell line. Chemical inactivation by methylamine and depletion by double-stranded RNA knockout demonstrate that this function is dependent on the internal thioester bond. This evidence of a complement-like function in a protostome animal adds substantially to the accumulating evidence of a common ancestry of immune defenses in insects and vertebrates. |
2000 |
Delagoutte, B; Keith, G; Moras, D; Cavarelli, J Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes Article de journal Acta Crystallogr D Biol Crystallogr, 56 (Pt 4), p. 492-4, 2000, (0907-4449 Journal Article). Résumé | BibTeX | Étiquettes: &, Arg/*chemistry/isolation, Arginine-tRNA, cerevisiae/enzymology/genetics, Crystallization, Crystallography, Fungal/chemistry/isolation, Gov't, Ligase/*chemistry/isolation, Non-U.S., purification/*metabolism, purification/metabolism, RNA, Saccharomyces, Support, Transfer, X-Ray @article{, title = {Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes}, author = { B. Delagoutte and G. Keith and D. Moras and J. Cavarelli}, year = {2000}, date = {2000-01-01}, journal = {Acta Crystallogr D Biol Crystallogr}, volume = {56}, number = {Pt 4}, pages = {492-4}, abstract = {Three different crystal forms of complexes between arginyl-tRNA synthetase from the yeast Saccharomyces cerevisae (yArgRS) and the yeast second major tRNA(Arg) (tRNA(Arg)(ICG)) isoacceptor have been crystallized by the hanging-drop vapour-diffusion method in the presence of ammonium sulfate. Crystal form II, which diffracts beyond 2.2 A resolution at the European Synchrotron Radiation Facility ID14-4 beamline, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 129.64}, note = {0907-4449 Journal Article}, keywords = {&, Arg/*chemistry/isolation, Arginine-tRNA, cerevisiae/enzymology/genetics, Crystallization, Crystallography, Fungal/chemistry/isolation, Gov't, Ligase/*chemistry/isolation, Non-U.S., purification/*metabolism, purification/metabolism, RNA, Saccharomyces, Support, Transfer, X-Ray}, pubstate = {published}, tppubtype = {article} } Three different crystal forms of complexes between arginyl-tRNA synthetase from the yeast Saccharomyces cerevisae (yArgRS) and the yeast second major tRNA(Arg) (tRNA(Arg)(ICG)) isoacceptor have been crystallized by the hanging-drop vapour-diffusion method in the presence of ammonium sulfate. Crystal form II, which diffracts beyond 2.2 A resolution at the European Synchrotron Radiation Facility ID14-4 beamline, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 129.64 |
Jaeger, L; Leontis, N B Tecto-RNA: One-Dimensional Self-Assembly through Tertiary Interactions Article de journal Angew Chem Int Ed Engl, 39 (14), p. 2521-2524, 2000. Résumé | BibTeX | Étiquettes: Chemistry, RNA, self-organisation, supramolecular @article{, title = {Tecto-RNA: One-Dimensional Self-Assembly through Tertiary Interactions}, author = { L. Jaeger and N. B. Leontis}, year = {2000}, date = {2000-01-01}, journal = {Angew Chem Int Ed Engl}, volume = {39}, number = {14}, pages = {2521-2524}, abstract = {The modularity of natural RNA is the basis for the design of tecto-RNA, modular RNA units capable of directed self-assembly. One such modular association through specific RNA loopreceptor tertiary interactions, which leads to one-dimensional oligomer arrays, is demonstrated (see picture).}, keywords = {Chemistry, RNA, self-organisation, supramolecular}, pubstate = {published}, tppubtype = {article} } The modularity of natural RNA is the basis for the design of tecto-RNA, modular RNA units capable of directed self-assembly. One such modular association through specific RNA loopreceptor tertiary interactions, which leads to one-dimensional oligomer arrays, is demonstrated (see picture). |
1999 |
Auxilien, S; Keith, G; Grice, Le S F; Darlix, J L Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription Article de journal J Biol Chem, 274 (7), p. 4412-20, 1999, (0021-9258 Journal Article). Résumé | BibTeX | Étiquettes: *RNA, *Transcription, Acid, Base, Calf, Conformation, Data, DNA, Genetic, Gov't, H, HIV-1, HIV-1/*physiology, Lys/*metabolism, Molecular, Non-U.S., Nucleic, post-transcriptional, Processing, Reverse, Ribonuclease, RNA, Sequence, Support, Templates, Thymus/metabolism, Transcriptase/metabolism, Transfer, Viral/*metabolism, Viral/metabolism @article{, title = {Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription}, author = { S. Auxilien and G. Keith and S. F. Le Grice and J. L. Darlix}, year = {1999}, date = {1999-01-01}, journal = {J Biol Chem}, volume = {274}, number = {7}, pages = {4412-20}, abstract = {During HIV reverse transcription, (+) strand DNA synthesis is primed by an RNase H-resistant sequence, the polypurine tract, and continues as far as a 18-nt double-stranded RNA region corresponding to the 3' end of tRNALys,3 hybridized to the viral primer binding site (PBS). Before (+) strand DNA transfer, reverse transcriptase (RT) needs to unwind the double-stranded tRNA-PBS RNA in order to reverse-transcribe the 3' end of primer tRNALys,3. Since the detailed mechanism of (+) strand DNA transfer remains incompletely understood, we developed an in vitro system to closely examine this mechanism, composed of HIV 5' RNA, natural modified tRNALys,3, synthetic unmodified tRNALys,3 or oligonucleotides (RNA or DNA) complementary to the PBS, as well as the viral proteins RT and nucleocapsid protein (NCp7). Prior to (+) strand DNA transfer, RT stalls at the double-stranded tRNA-PBS RNA complex and is able to reverse-transcribe modified nucleosides of natural tRNALys,3. Modified nucleoside m1A-58 of natural tRNALys,3 is only partially effective as a stop signal, as RT can transcribe as far as the hyper-modified adenosine (ms2t6A-37) in the anticodon loop. m1A-58 is almost always transcribed into A, whereas other modified nucleosides are transcribed correctly, except for m7G-46, which is sometimes transcribed into T. In contrast, synthetic tRNALys,3, an RNA PBS primer, and a DNA PBS primer are completely reverse-transcribed. In the presence of an acceptor template, (+) strand DNA transfer is efficient only with templates containing natural tRNALys,3 or the RNA PBS primer. Sequence analysis of transfer products revealed frequent errors at the transfer site with synthetic tRNALys,3, not observed with natural tRNALys,3. Thus, modified nucleoside m1A-58, present in all retroviral tRNA primers, appears to be important for both efficacy and fidelity of (+) strand DNA transfer. We show that other factors such as the nature of the (-) PBS of the acceptor template and the RNase H activity of RT also influence the efficacy of (+) strand DNA transfer.}, note = {0021-9258 Journal Article}, keywords = {*RNA, *Transcription, Acid, Base, Calf, Conformation, Data, DNA, Genetic, Gov't, H, HIV-1, HIV-1/*physiology, Lys/*metabolism, Molecular, Non-U.S., Nucleic, post-transcriptional, Processing, Reverse, Ribonuclease, RNA, Sequence, Support, Templates, Thymus/metabolism, Transcriptase/metabolism, Transfer, Viral/*metabolism, Viral/metabolism}, pubstate = {published}, tppubtype = {article} } During HIV reverse transcription, (+) strand DNA synthesis is primed by an RNase H-resistant sequence, the polypurine tract, and continues as far as a 18-nt double-stranded RNA region corresponding to the 3' end of tRNALys,3 hybridized to the viral primer binding site (PBS). Before (+) strand DNA transfer, reverse transcriptase (RT) needs to unwind the double-stranded tRNA-PBS RNA in order to reverse-transcribe the 3' end of primer tRNALys,3. Since the detailed mechanism of (+) strand DNA transfer remains incompletely understood, we developed an in vitro system to closely examine this mechanism, composed of HIV 5' RNA, natural modified tRNALys,3, synthetic unmodified tRNALys,3 or oligonucleotides (RNA or DNA) complementary to the PBS, as well as the viral proteins RT and nucleocapsid protein (NCp7). Prior to (+) strand DNA transfer, RT stalls at the double-stranded tRNA-PBS RNA complex and is able to reverse-transcribe modified nucleosides of natural tRNALys,3. Modified nucleoside m1A-58 of natural tRNALys,3 is only partially effective as a stop signal, as RT can transcribe as far as the hyper-modified adenosine (ms2t6A-37) in the anticodon loop. m1A-58 is almost always transcribed into A, whereas other modified nucleosides are transcribed correctly, except for m7G-46, which is sometimes transcribed into T. In contrast, synthetic tRNALys,3, an RNA PBS primer, and a DNA PBS primer are completely reverse-transcribed. In the presence of an acceptor template, (+) strand DNA transfer is efficient only with templates containing natural tRNALys,3 or the RNA PBS primer. Sequence analysis of transfer products revealed frequent errors at the transfer site with synthetic tRNALys,3, not observed with natural tRNALys,3. Thus, modified nucleoside m1A-58, present in all retroviral tRNA primers, appears to be important for both efficacy and fidelity of (+) strand DNA transfer. We show that other factors such as the nature of the (-) PBS of the acceptor template and the RNase H activity of RT also influence the efficacy of (+) strand DNA transfer. |
Perreau, V M; Keith, G; Holmes, W M; Przykorska, A; Santos, M A; Tuite, M F The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure Article de journal J Mol Biol, 293 (5), p. 1039-53, 1999, (0022-2836 Journal Article). Résumé | BibTeX | Étiquettes: *Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S. @article{, title = {The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure}, author = { V. M. Perreau and G. Keith and W. M. Holmes and A. Przykorska and M. A. Santos and M. F. Tuite}, year = {1999}, date = {1999-01-01}, journal = {J Mol Biol}, volume = {293}, number = {5}, pages = {1039-53}, abstract = {In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.}, note = {0022-2836 Journal Article}, keywords = {*Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S.}, pubstate = {published}, tppubtype = {article} } In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it. |
Lowenberger, C A; Kamal, S; Chiles, J; Paskewitz, S; Bulet, Philippe; Hoffmann, Jules A; Christensen, B M Mosquito-Plasmodium interactions in response to immune activation of the vector Article de journal Exp. Parasitol., 91 (1), p. 59–69, 1999, ISSN: 0014-4894. Résumé | Liens | BibTeX | Étiquettes: Aedes, Animals, Anopheles, Culicidae, Defensins, Digestive System, Escherichia coli, Female, Genetic, Hemolymph, hoffmann, Insect Vectors, M3i, messenger, Micrococcus luteus, Plasmodium, Plasmodium berghei, Plasmodium gallinaceum, Proteins, Reverse Transcriptase Polymerase Chain Reaction, RNA, Transcription @article{lowenberger_mosquito-plasmodium_1999, title = {Mosquito-Plasmodium interactions in response to immune activation of the vector}, author = {C A Lowenberger and S Kamal and J Chiles and S Paskewitz and Philippe Bulet and Jules A Hoffmann and B M Christensen}, doi = {10.1006/expr.1999.4350}, issn = {0014-4894}, year = {1999}, date = {1999-01-01}, journal = {Exp. Parasitol.}, volume = {91}, number = {1}, pages = {59--69}, abstract = {During the development of Plasmodium sp. within the mosquito midgut, the parasite undergoes a series of developmental changes. The elongated ookinete migrates through the layers of the midgut where it forms the oocyst under the basal lamina. We demonstrate here that if Aedes aegypti or Anopheles gambiae, normally susceptible to Plasmodium gallinaceum and P. berghei, respectively, are immune activated by the injection of bacteria into the hemocoel, and subsequently are fed on an infectious bloodmeal, there is a significant reduction in the prevalence and mean intensity of infection of oocysts on the midgut. Only those mosquitoes immune activated prior to, or immediately after, parasite ingestion exhibit this reduction in parasite development. Mosquitoes immune activated 2-5 days after bloodfeeding show no differences in parasite burdens compared with naive controls. Northern analyses reveal that transcriptional activity for mosquito defensins is not detected in the whole bodies of Ae. aegypti from 4 h to 10 days after ingesting P. gallinaceum, suggesting that parasite ingestion, passage from the food bolus through the midgut, oocyst formation, and subsequent release of sporozoites into the hemolymph do not induce the production of defensin. However, reverse transcriptase-PCR of RNA isolated solely from the midguts of Ae. aegypti indicates that transcription of mosquito defensins occurs in the midguts of naive mosquitoes and those ingesting an infectious or noninfectious bloodmeal. Bacteria-challenged Ae. aegypti showed high levels of mature defensin in the hemolymph that correlate with a lower prevalence and mean intensity of infection with oocysts. Because few oocysts were found on the midgut of immune-activated mosquitoes, the data suggest that some factor, induced by bacterial challenge, kills the parasite at a preoocyst stage.}, keywords = {Aedes, Animals, Anopheles, Culicidae, Defensins, Digestive System, Escherichia coli, Female, Genetic, Hemolymph, hoffmann, Insect Vectors, M3i, messenger, Micrococcus luteus, Plasmodium, Plasmodium berghei, Plasmodium gallinaceum, Proteins, Reverse Transcriptase Polymerase Chain Reaction, RNA, Transcription}, pubstate = {published}, tppubtype = {article} } During the development of Plasmodium sp. within the mosquito midgut, the parasite undergoes a series of developmental changes. The elongated ookinete migrates through the layers of the midgut where it forms the oocyst under the basal lamina. We demonstrate here that if Aedes aegypti or Anopheles gambiae, normally susceptible to Plasmodium gallinaceum and P. berghei, respectively, are immune activated by the injection of bacteria into the hemocoel, and subsequently are fed on an infectious bloodmeal, there is a significant reduction in the prevalence and mean intensity of infection of oocysts on the midgut. Only those mosquitoes immune activated prior to, or immediately after, parasite ingestion exhibit this reduction in parasite development. Mosquitoes immune activated 2-5 days after bloodfeeding show no differences in parasite burdens compared with naive controls. Northern analyses reveal that transcriptional activity for mosquito defensins is not detected in the whole bodies of Ae. aegypti from 4 h to 10 days after ingesting P. gallinaceum, suggesting that parasite ingestion, passage from the food bolus through the midgut, oocyst formation, and subsequent release of sporozoites into the hemolymph do not induce the production of defensin. However, reverse transcriptase-PCR of RNA isolated solely from the midguts of Ae. aegypti indicates that transcription of mosquito defensins occurs in the midguts of naive mosquitoes and those ingesting an infectious or noninfectious bloodmeal. Bacteria-challenged Ae. aegypti showed high levels of mature defensin in the hemolymph that correlate with a lower prevalence and mean intensity of infection with oocysts. Because few oocysts were found on the midgut of immune-activated mosquitoes, the data suggest that some factor, induced by bacterial challenge, kills the parasite at a preoocyst stage. |
1998 |
Uttenweiler-Joseph, S; Moniatte, M; Lagueux, Marie; Dorsselaer, Van A; Hoffmann, Jules A; Bulet, Philippe Differential display of peptides induced during the immune response of Drosophila: a matrix-assisted laser desorption ionization time-of-flight mass spectrometry study Article de journal Proc. Natl. Acad. Sci. U.S.A., 95 (19), p. 11342–11347, 1998, ISSN: 0027-8424. Résumé | BibTeX | Étiquettes: Animals, bacteria, Chromatography, Cloning, Hemolymph, High Pressure Liquid, hoffmann, Immunity, Insect Proteins, M3i, Mass, Matrix-Assisted Laser Desorption-Ionization, messenger, Molecular, Peptides, Protein Precursors, RNA, Sequence Analysis, Spectrometry, Time Factors @article{uttenweiler-joseph_differential_1998, title = {Differential display of peptides induced during the immune response of Drosophila: a matrix-assisted laser desorption ionization time-of-flight mass spectrometry study}, author = {S Uttenweiler-Joseph and M Moniatte and Marie Lagueux and Van A Dorsselaer and Jules A Hoffmann and Philippe Bulet}, issn = {0027-8424}, year = {1998}, date = {1998-09-01}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, volume = {95}, number = {19}, pages = {11342--11347}, abstract = {We have developed an approach based on a differential mass spectrometric analysis to detect molecules induced during the immune response of Drosophila, regardless of their biological activities. For this, we have applied directly matrix-assisted laser desorption/ionization MS to hemolymph samples from individual flies before and after an immune challenge. This method provided precise information on the molecular masses of immune-induced molecules and allowed the detection, in the molecular range of 1.5-11 kDa, of 24 Drosophila immune-induced molecules (DIMs). These molecules are all peptides, and four correspond to already characterized antimicrobial peptides. We have further analyzed the induction of the various peptides by immune challenge in wild-type flies and in mutants with a compromised antimicrobial response. We also describe a methodology combining matrix-assisted laser desorption ionization time-of-flight MS, HPLC, and Edman degradation, which yielded the peptide sequence of three of the DIMs. Finally, molecular cloning and Northern blot analyses revealed that one of the DIMs is produced as a prepropeptide and is inducible on a bacterial challenge.}, keywords = {Animals, bacteria, Chromatography, Cloning, Hemolymph, High Pressure Liquid, hoffmann, Immunity, Insect Proteins, M3i, Mass, Matrix-Assisted Laser Desorption-Ionization, messenger, Molecular, Peptides, Protein Precursors, RNA, Sequence Analysis, Spectrometry, Time Factors}, pubstate = {published}, tppubtype = {article} } We have developed an approach based on a differential mass spectrometric analysis to detect molecules induced during the immune response of Drosophila, regardless of their biological activities. For this, we have applied directly matrix-assisted laser desorption/ionization MS to hemolymph samples from individual flies before and after an immune challenge. This method provided precise information on the molecular masses of immune-induced molecules and allowed the detection, in the molecular range of 1.5-11 kDa, of 24 Drosophila immune-induced molecules (DIMs). These molecules are all peptides, and four correspond to already characterized antimicrobial peptides. We have further analyzed the induction of the various peptides by immune challenge in wild-type flies and in mutants with a compromised antimicrobial response. We also describe a methodology combining matrix-assisted laser desorption ionization time-of-flight MS, HPLC, and Edman degradation, which yielded the peptide sequence of three of the DIMs. Finally, molecular cloning and Northern blot analyses revealed that one of the DIMs is produced as a prepropeptide and is inducible on a bacterial challenge. |
Brigotti, M; Keith, G; Pallanca, A; Carnicelli, D; Alvergna, P; Dirheimer, G; Montanaro, L; Sperti, S Identification of the tRNAs which up-regulate agrostin, barley RIP and PAP-S, three ribosome-inactivating proteins of plant origin Article de journal FEBS Lett, 431 (2), p. 259-62, 1998, (0014-5793 Journal Article). Résumé | BibTeX | Étiquettes: &, Acid, Adenosine, Base, Conformation, Data, effects/*metabolism, Gov't, Hordeum/metabolism, Hydrolases/*metabolism, Molecular, N-Glycosyl, Non-U.S., Nucleic, Plant, Plant/chemistry/isolation, Proteins/drug, purification/*metabolism, RNA, Sequence, Support, Transfer/chemistry/isolation, Triphosphate/pharmacology, Up-Regulation @article{, title = {Identification of the tRNAs which up-regulate agrostin, barley RIP and PAP-S, three ribosome-inactivating proteins of plant origin}, author = { M. Brigotti and G. Keith and A. Pallanca and D. Carnicelli and P. Alvergna and G. Dirheimer and L. Montanaro and S. Sperti}, year = {1998}, date = {1998-01-01}, journal = {FEBS Lett}, volume = {431}, number = {2}, pages = {259-62}, abstract = {Ribosome-inactivating proteins (RIP) are RNA-N-glycosidases widely diffused in plants which depurinate ribosomal RNA at a specific universally conserved position, A4324 in rat ribosomes. A small group of RIPs (cofactor-dependent RIPs) require ATP and tRNA to reach maximal activity on isolated ribosomes. The tRNA which stimulates gelonin was identified as tRNA(Trp). The present paper reports the identification of three other tRNAs which stimulate agrostin (tRNA(Ala)), barley RIP (tRNA(Ala), tRNA(Val)) and PAP-S (tRNA(Gly)), while for tritin-S no particular stimulating tRNA emerged. The sequences of tRNA(Val) and tRNA(Gly) correspond to the already known ones (rabbit and man, respectively). The tRNA(Ala) (anticodon IGC) identifies a new isoacceptor. Only the stimulating activity of the tRNA(Ala) for agrostin approaches the specificity previously observed for the couple gelonin-tRNA(Trp).}, note = {0014-5793 Journal Article}, keywords = {&, Acid, Adenosine, Base, Conformation, Data, effects/*metabolism, Gov't, Hordeum/metabolism, Hydrolases/*metabolism, Molecular, N-Glycosyl, Non-U.S., Nucleic, Plant, Plant/chemistry/isolation, Proteins/drug, purification/*metabolism, RNA, Sequence, Support, Transfer/chemistry/isolation, Triphosphate/pharmacology, Up-Regulation}, pubstate = {published}, tppubtype = {article} } Ribosome-inactivating proteins (RIP) are RNA-N-glycosidases widely diffused in plants which depurinate ribosomal RNA at a specific universally conserved position, A4324 in rat ribosomes. A small group of RIPs (cofactor-dependent RIPs) require ATP and tRNA to reach maximal activity on isolated ribosomes. The tRNA which stimulates gelonin was identified as tRNA(Trp). The present paper reports the identification of three other tRNAs which stimulate agrostin (tRNA(Ala)), barley RIP (tRNA(Ala), tRNA(Val)) and PAP-S (tRNA(Gly)), while for tritin-S no particular stimulating tRNA emerged. The sequences of tRNA(Val) and tRNA(Gly) correspond to the already known ones (rabbit and man, respectively). The tRNA(Ala) (anticodon IGC) identifies a new isoacceptor. Only the stimulating activity of the tRNA(Ala) for agrostin approaches the specificity previously observed for the couple gelonin-tRNA(Trp). |
Friant, S; Heyman, T; Bystrom, A S; Wilhelm, M; Wilhelm, F X Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo Article de journal Mol Cell Biol, 18 (2), p. 799-806, 1998, (0270-7306 Journal Article). Résumé | BibTeX | Étiquettes: *Retroelements, *Transcription, Acid, Base, Binding, cerevisiae, Conformation, Data, DNA, Fungal/*metabolism, Fungal/biosynthesis, Genetic, Gov't, Met/*metabolism, Molecular, Mutagenesis, Non-U.S., Nucleic, Primers, Replication, RNA, Saccharomyces, Sequence, Sites, Support, Transfer @article{, title = {Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo}, author = { S. Friant and T. Heyman and A. S. Bystrom and M. Wilhelm and F. X. Wilhelm}, year = {1998}, date = {1998-01-01}, journal = {Mol Cell Biol}, volume = {18}, number = {2}, pages = {799-806}, abstract = {Reverse transcription of the Saccharomyces cerevisiae Ty1 retrotransposon is primed by tRNA(iMet) base paired to the primer binding site (PBS) near the 5' end of Ty1 genomic RNA. The 10-nucleotide PBS is complementary to the last 10 nucleotides of the acceptor stem of tRNA(iMet). A structural probing study of the interactions between the Ty1 RNA template and the tRNA(iMet) primer showed that besides interactions between the PBS and the 3' end of tRNA(iMet), three short regions of Ty1 RNA, named boxes 0, 1, and 2.1, interact with the T and D stems and loops of tRNA(iMet). To determine if these sequences are important for the reverse transcription pathway of the Ty1 retrotransposon, mutant Ty1 elements and tRNA(iMet) were tested for the ability to support transposition. We show that the Ty1 boxes and the complementary sequences in the T and D stems and loops of tRNA(iMet) contain bases that are critical for Ty1 retrotransposition. Disruption of 1 or 2 bp between tRNA(iMet) and box 0, 1, or 2.1 dramatically decreases the level of transposition. Compensatory mutations which restore base pairing between the primer and the template restore transposition. Analysis of the reverse transcription intermediates generated inside Ty1 virus-like particles indicates that initiation of minus-strand strong-stop DNA synthesis is affected by mutations disrupting complementarity between Ty1 RNA and primer tRNA(iMet).}, note = {0270-7306 Journal Article}, keywords = {*Retroelements, *Transcription, Acid, Base, Binding, cerevisiae, Conformation, Data, DNA, Fungal/*metabolism, Fungal/biosynthesis, Genetic, Gov't, Met/*metabolism, Molecular, Mutagenesis, Non-U.S., Nucleic, Primers, Replication, RNA, Saccharomyces, Sequence, Sites, Support, Transfer}, pubstate = {published}, tppubtype = {article} } Reverse transcription of the Saccharomyces cerevisiae Ty1 retrotransposon is primed by tRNA(iMet) base paired to the primer binding site (PBS) near the 5' end of Ty1 genomic RNA. The 10-nucleotide PBS is complementary to the last 10 nucleotides of the acceptor stem of tRNA(iMet). A structural probing study of the interactions between the Ty1 RNA template and the tRNA(iMet) primer showed that besides interactions between the PBS and the 3' end of tRNA(iMet), three short regions of Ty1 RNA, named boxes 0, 1, and 2.1, interact with the T and D stems and loops of tRNA(iMet). To determine if these sequences are important for the reverse transcription pathway of the Ty1 retrotransposon, mutant Ty1 elements and tRNA(iMet) were tested for the ability to support transposition. We show that the Ty1 boxes and the complementary sequences in the T and D stems and loops of tRNA(iMet) contain bases that are critical for Ty1 retrotransposition. Disruption of 1 or 2 bp between tRNA(iMet) and box 0, 1, or 2.1 dramatically decreases the level of transposition. Compensatory mutations which restore base pairing between the primer and the template restore transposition. Analysis of the reverse transcription intermediates generated inside Ty1 virus-like particles indicates that initiation of minus-strand strong-stop DNA synthesis is affected by mutations disrupting complementarity between Ty1 RNA and primer tRNA(iMet). |
Gabus, C; Ficheux, D; Rau, M; Keith, G; Sandmeyer, S; Darlix, J L The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7 Article de journal EMBO J, 17 (16), p. 4873-80, 1998, (0261-4189 Journal Article). Résumé | BibTeX | Étiquettes: *Capsid, *Retroelements, Acid, Base, Binding, Capsid/*genetics, cerevisiae/*genetics, dimerization, gag/*genetics, Gene, Gov't, Homology, Met/genetics/*metabolism, Non-U.S., Nucleic, P.H.S., Products, Proteins, RNA, Saccharomyces, Sequence, Sites, Support, Transfer, U.S. @article{, title = {The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7}, author = { C. Gabus and D. Ficheux and M. Rau and G. Keith and S. Sandmeyer and J. L. Darlix}, year = {1998}, date = {1998-01-01}, journal = {EMBO J}, volume = {17}, number = {16}, pages = {4873-80}, abstract = {Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3' PBS for primer tRNAiMet annealing to the genomic RNA, and the 5' PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNAiMet bound to the PBS was found to direct dimerization of Ty3 RNA-tRNAiMet. Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs.}, note = {0261-4189 Journal Article}, keywords = {*Capsid, *Retroelements, Acid, Base, Binding, Capsid/*genetics, cerevisiae/*genetics, dimerization, gag/*genetics, Gene, Gov't, Homology, Met/genetics/*metabolism, Non-U.S., Nucleic, P.H.S., Products, Proteins, RNA, Saccharomyces, Sequence, Sites, Support, Transfer, U.S.}, pubstate = {published}, tppubtype = {article} } Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3' PBS for primer tRNAiMet annealing to the genomic RNA, and the 5' PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNAiMet bound to the PBS was found to direct dimerization of Ty3 RNA-tRNAiMet. Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs. |
Motorin, Y; Keith, G; Simon, C; Foiret, D; Simos, G; Hurt, E; Grosjean, H The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity Article de journal RNA, 4 (7), p. 856-69, 1998, (1355-8382 Journal Article). Résumé | BibTeX | Étiquettes: *RNA, cerevisiae, Cloning, Fractions/metabolism, Fungal, Fungal/metabolism, Gov't, Hydro-Lyases/biosynthesis/genetics/*metabolism, Molecular, Mutation, Non-U.S., Plant/metabolism, post-transcriptional, Precursors/*metabolism, Processing, Proteins/biosynthesis, Proteins/biosynthesis/genetics/metabolism, Pseudouridine/*biosynthesis, Recombinant, RNA, Saccharomyces, Specificity, Subcellular, Substrate, Support, Transfer/*metabolism @article{, title = {The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity}, author = { Y. Motorin and G. Keith and C. Simon and D. Foiret and G. Simos and E. Hurt and H. Grosjean}, year = {1998}, date = {1998-01-01}, journal = {RNA}, volume = {4}, number = {7}, pages = {856-69}, abstract = {We have previously shown that the yeast gene PUS1 codes for a tRNA:pseudouridine synthase and that recombinant Pus1p catalyzes, in an intron-dependent way, the formation of psi34 and psi36 in the anticodon loop of the yeast minor tRNA(Ile) in vitro (Simos G et al., 1996, EMBO J 15:2270-2284). Using a set of T7 transcripts of different tRNA genes, we now demonstrate that yeast pseudouridine synthase 1 catalyzes in vitro pseudouridine formation at positions 27 and/or 28 in several yeast cytoplasmic tRNAs and at position 35 in the intron-containing tRNA(Tyr) (anticodon GUA). Thus, Pus1p not only displays a broad specificity toward the RNA substrates, but is also capable of catalyzing the pseudouridine (psi) formation at distinct noncontiguous sites within the same tRNA molecule. The cell-free extract prepared from the yeast strain bearing disrupted gene PUS1 is unable to catalyze the formation of psi27, psi28, psi34, and psi36 in vitro, however, psi35 formation in the intron-containing tRNA(Tyr)(GUA) remains unaffected. Thus, in yeast, only one gene product accounts for tRNA pseudouridylation at positions 27, 28, 34, and 36, whereas for position 35 in tRNA(Tyr), another site-specific tRNA:pseudouridine synthase with overlapping specificity exists. Mapping of pseudouridine residues present in various tRNAs extracted from the PUS1-disrupted strain confirms the in vitro data obtained with the recombinant Pus1p. In addition, they suggest that Pus1p is implicated in modification at positions U26, U65, and U67 in vivo.}, note = {1355-8382 Journal Article}, keywords = {*RNA, cerevisiae, Cloning, Fractions/metabolism, Fungal, Fungal/metabolism, Gov't, Hydro-Lyases/biosynthesis/genetics/*metabolism, Molecular, Mutation, Non-U.S., Plant/metabolism, post-transcriptional, Precursors/*metabolism, Processing, Proteins/biosynthesis, Proteins/biosynthesis/genetics/metabolism, Pseudouridine/*biosynthesis, Recombinant, RNA, Saccharomyces, Specificity, Subcellular, Substrate, Support, Transfer/*metabolism}, pubstate = {published}, tppubtype = {article} } We have previously shown that the yeast gene PUS1 codes for a tRNA:pseudouridine synthase and that recombinant Pus1p catalyzes, in an intron-dependent way, the formation of psi34 and psi36 in the anticodon loop of the yeast minor tRNA(Ile) in vitro (Simos G et al., 1996, EMBO J 15:2270-2284). Using a set of T7 transcripts of different tRNA genes, we now demonstrate that yeast pseudouridine synthase 1 catalyzes in vitro pseudouridine formation at positions 27 and/or 28 in several yeast cytoplasmic tRNAs and at position 35 in the intron-containing tRNA(Tyr) (anticodon GUA). Thus, Pus1p not only displays a broad specificity toward the RNA substrates, but is also capable of catalyzing the pseudouridine (psi) formation at distinct noncontiguous sites within the same tRNA molecule. The cell-free extract prepared from the yeast strain bearing disrupted gene PUS1 is unable to catalyze the formation of psi27, psi28, psi34, and psi36 in vitro, however, psi35 formation in the intron-containing tRNA(Tyr)(GUA) remains unaffected. Thus, in yeast, only one gene product accounts for tRNA pseudouridylation at positions 27, 28, 34, and 36, whereas for position 35 in tRNA(Tyr), another site-specific tRNA:pseudouridine synthase with overlapping specificity exists. Mapping of pseudouridine residues present in various tRNAs extracted from the PUS1-disrupted strain confirms the in vitro data obtained with the recombinant Pus1p. In addition, they suggest that Pus1p is implicated in modification at positions U26, U65, and U67 in vivo. |
1997 |
Friant, S; Heyman, T; Poch, O; Wilhelm, M; Wilhelm, F X Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex Article de journal Yeast, 13 (7), p. 639-45, 1997, (0749-503x Journal Article). Résumé | BibTeX | Étiquettes: *Sequence, Acid, Alignment, Amino, Analysis, Base, Data, DNA, Elements/*genetics, Fungal/genetics, Gov't, Met/*chemistry/*genetics, Molecular, Non-U.S., RNA, Sequence, structure, Support, Transfer, Transposable, Yeasts/*genetics @article{, title = {Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex}, author = { S. Friant and T. Heyman and O. Poch and M. Wilhelm and F. X. Wilhelm}, year = {1997}, date = {1997-01-01}, journal = {Yeast}, volume = {13}, number = {7}, pages = {639-45}, abstract = {In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex.}, note = {0749-503x Journal Article}, keywords = {*Sequence, Acid, Alignment, Amino, Analysis, Base, Data, DNA, Elements/*genetics, Fungal/genetics, Gov't, Met/*chemistry/*genetics, Molecular, Non-U.S., RNA, Sequence, structure, Support, Transfer, Transposable, Yeasts/*genetics}, pubstate = {published}, tppubtype = {article} } In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex. |
Wilhelm, M; Heyman, T; Friant, S; Wilhelm, F X Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts Article de journal Nucleic Acids Res, 25 (11), p. 2161-6, 1997, (0305-1048 Journal Article). Résumé | BibTeX | Étiquettes: *Nucleic, *Transcription, Acid, Calf, Chain, Conformation, DNA, Fungal/*chemistry/metabolism, Genetic, Gov't, H, Hybridization, Non-U.S., Nucleic, Plasmids/chemistry/genetics/metabolism, Polymerase, Reaction, Replication, Retroelements/*genetics, Ribonuclease, RNA, Support, Thymus/metabolism, Transfer/chemistry @article{, title = {Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts}, author = { M. Wilhelm and T. Heyman and S. Friant and F. X. Wilhelm}, year = {1997}, date = {1997-01-01}, journal = {Nucleic Acids Res}, volume = {25}, number = {11}, pages = {2161-6}, abstract = {A specific terminal structure of preintegrative DNA is required for transposition of retroviruses and LTR-retrotransposons. We have used an anchored PCR technique to map the 3'ends of DNA intermediates synthesized inside yeast Ty1 and Ty3 retrotransposon virus-like particles. We find that, unlike retroviruses, Ty1 replicated DNA does not have two extra base pairs at its 3'ends. In contrast some Ty3 preintegrative DNA molecules have two extra nucleotides at the 3'end of upstream and downstream long terminal repeats. Moreover we find that some molecules of replicated Ty3 DNA have more than two extra nucleotides at the 3'end of the upstream LTR. This observation could be accounted for by imprecise RNAse H cutting of the PPT sequence. The site of Ty1 and Ty3 plus-strand strong-stop DNA termination was also examined. Our results confirm that the prominent Ty1 and Ty3 plus-strand strong-stop molecules harbor 12 tRNA templated bases but also show that some Ty1 and Ty3 plus-strand strong-stop DNA molecules harbor less tRNA templated bases. We propose that these less than full length plus-strand molecules could be active intermediates in Ty retrotransposon replication.}, note = {0305-1048 Journal Article}, keywords = {*Nucleic, *Transcription, Acid, Calf, Chain, Conformation, DNA, Fungal/*chemistry/metabolism, Genetic, Gov't, H, Hybridization, Non-U.S., Nucleic, Plasmids/chemistry/genetics/metabolism, Polymerase, Reaction, Replication, Retroelements/*genetics, Ribonuclease, RNA, Support, Thymus/metabolism, Transfer/chemistry}, pubstate = {published}, tppubtype = {article} } A specific terminal structure of preintegrative DNA is required for transposition of retroviruses and LTR-retrotransposons. We have used an anchored PCR technique to map the 3'ends of DNA intermediates synthesized inside yeast Ty1 and Ty3 retrotransposon virus-like particles. We find that, unlike retroviruses, Ty1 replicated DNA does not have two extra base pairs at its 3'ends. In contrast some Ty3 preintegrative DNA molecules have two extra nucleotides at the 3'end of upstream and downstream long terminal repeats. Moreover we find that some molecules of replicated Ty3 DNA have more than two extra nucleotides at the 3'end of the upstream LTR. This observation could be accounted for by imprecise RNAse H cutting of the PPT sequence. The site of Ty1 and Ty3 plus-strand strong-stop DNA termination was also examined. Our results confirm that the prominent Ty1 and Ty3 plus-strand strong-stop molecules harbor 12 tRNA templated bases but also show that some Ty1 and Ty3 plus-strand strong-stop DNA molecules harbor less tRNA templated bases. We propose that these less than full length plus-strand molecules could be active intermediates in Ty retrotransposon replication. |
1996 |
Lowenberger, C A; Ferdig, M T; Bulet, Philippe; Khalili, S; Hoffmann, Jules A; Christensen, B M Aedes aegypti: induced antibacterial proteins reduce the establishment and development of Brugia malayi Article de journal Exp. Parasitol., 83 (2), p. 191–201, 1996, ISSN: 0014-4894. Résumé | Liens | BibTeX | Étiquettes: Aedes, Analysis of Variance, Animals, Anti-Bacterial Agents, Base Sequence, Blood Proteins, Blotting, Brugia malayi, Culicidae, Defensins, DNA, Escherichia coli, Fat Body, Genetic, Gerbillinae, hoffmann, M3i, Micrococcus luteus, Microfilaria, Northern, RNA, Transcription @article{lowenberger_aedes_1996, title = {Aedes aegypti: induced antibacterial proteins reduce the establishment and development of Brugia malayi}, author = {C A Lowenberger and M T Ferdig and Philippe Bulet and S Khalili and Jules A Hoffmann and B M Christensen}, doi = {10.1006/expr.1996.0066}, issn = {0014-4894}, year = {1996}, date = {1996-07-01}, journal = {Exp. Parasitol.}, volume = {83}, number = {2}, pages = {191--201}, abstract = {The effect of host immune activation on the development of Brugia malayi in one susceptible and four refractory strains of Aedes aegypti and in Armigeres subalbatus was assessed. A. aegypti that were immune activated by the injection of saline or bacteria 24 hr before feeding on a B. malayi-infected gerbil had significantly reduced prevalences and mean intensities of infection from those of naive controls when exposed to bloodmeals with low (105 mf/20 microliters) and medium (160 mf/20 microliters) microfilaremias. At a higher microfilaremia (237 mf/20 microliters) there were no significant differences in mean intensities, suggesting that the number of parasites ingested may affect the host's ability to mount an effective defense response. Because the major immune proteins in A. aegypti are defensins, we did Northern analyses of fat body RNA 8 hr after immune activation or bloodfeeding. All mosquitoes demonstrated rapid transcriptional activity for defensins following immune activation by intrathoracic inoculation with either saline or bacteria. However, no strain of A. aegypti, susceptible or refractory to B. malayi, nor Ar. subalbatus produced defensin transcripts after bloodfeeding on an uninfected or a B. malayi-infected gerbil. These data suggest that inducible immune proteins of mosquitoes can reduce the prevalence and mean intensity of infections with ingested parasites, but these proteins are not expressed routinely after parasite ingestion and midgut penetration and probably do not contribute to existing refractory mechanisms. Immune proteins such as defensins, however, represent potential candidates to genetically engineer mosquitoes for resistance to filarial worms.}, keywords = {Aedes, Analysis of Variance, Animals, Anti-Bacterial Agents, Base Sequence, Blood Proteins, Blotting, Brugia malayi, Culicidae, Defensins, DNA, Escherichia coli, Fat Body, Genetic, Gerbillinae, hoffmann, M3i, Micrococcus luteus, Microfilaria, Northern, RNA, Transcription}, pubstate = {published}, tppubtype = {article} } The effect of host immune activation on the development of Brugia malayi in one susceptible and four refractory strains of Aedes aegypti and in Armigeres subalbatus was assessed. A. aegypti that were immune activated by the injection of saline or bacteria 24 hr before feeding on a B. malayi-infected gerbil had significantly reduced prevalences and mean intensities of infection from those of naive controls when exposed to bloodmeals with low (105 mf/20 microliters) and medium (160 mf/20 microliters) microfilaremias. At a higher microfilaremia (237 mf/20 microliters) there were no significant differences in mean intensities, suggesting that the number of parasites ingested may affect the host's ability to mount an effective defense response. Because the major immune proteins in A. aegypti are defensins, we did Northern analyses of fat body RNA 8 hr after immune activation or bloodfeeding. All mosquitoes demonstrated rapid transcriptional activity for defensins following immune activation by intrathoracic inoculation with either saline or bacteria. However, no strain of A. aegypti, susceptible or refractory to B. malayi, nor Ar. subalbatus produced defensin transcripts after bloodfeeding on an uninfected or a B. malayi-infected gerbil. These data suggest that inducible immune proteins of mosquitoes can reduce the prevalence and mean intensity of infections with ingested parasites, but these proteins are not expressed routinely after parasite ingestion and midgut penetration and probably do not contribute to existing refractory mechanisms. Immune proteins such as defensins, however, represent potential candidates to genetically engineer mosquitoes for resistance to filarial worms. |
Friant, S; Heyman, T; Wilhelm, F X; Wilhelm, M Role of RNA primers in initiation of minus-strand and plus-strand DNA synthesis of the yeast retrotransposon Ty1 Article de journal Biochimie, 78 (7), p. 674-80, 1996, (0300-9084 Journal Article). Résumé | BibTeX | Étiquettes: *DNA, Acid, Bacterial/*metabolism, Complementary/metabolism, Conformation, Data, DNA, Elements, Gov't, Molecular, Mutagenesis, Non-U.S., Nucleic, Replication, RNA, RNA/*metabolism, Sequence, Support, Transposable @article{, title = {Role of RNA primers in initiation of minus-strand and plus-strand DNA synthesis of the yeast retrotransposon Ty1}, author = { S. Friant and T. Heyman and F. X. Wilhelm and M. Wilhelm}, year = {1996}, date = {1996-01-01}, journal = {Biochimie}, volume = {78}, number = {7}, pages = {674-80}, abstract = {The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae is a long terminal repeat mobile genetic element that transposes through an RNA intermediate. Initiation of minus-strand and plus-strand DNA synthesis are two critical steps during reverse transcription of the retrotransposon genome. Initiation of minus-strand DNA synthesis of the Ty1 element is primed by the cytoplasmic initiator methionine tRNA base paired to the primer binding site near the 5' end of the genomic RNA. A structural probing study of the primer tRNA-Ty1 RNA binary complex reveals that besides interactions between the primer binding site and the last 10 nucleotides at the 3' end of the primer tRNA, three short regions of Ty1 RNA named box 0, box 1 and box 2.1 interact with the T and D stems and loops of the primer tRNA. Some in vivo results underline the functional importance of the nucleotide sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primer tRNA play a role in the reverse transcription pathway. Plus-strand DNA synthesis is initiated from an RNase H resistant oligoribonucleotide spanning a purine-rich sequence, the polypurine tract (PPT). Two sites of initiation located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the TyB (pol) gene in the integrase coding sequence (PPT2) have been identified in the genome of Ty1. The two PPTs have an identical sequence, TGGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand DNA synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.}, note = {0300-9084 Journal Article}, keywords = {*DNA, Acid, Bacterial/*metabolism, Complementary/metabolism, Conformation, Data, DNA, Elements, Gov't, Molecular, Mutagenesis, Non-U.S., Nucleic, Replication, RNA, RNA/*metabolism, Sequence, Support, Transposable}, pubstate = {published}, tppubtype = {article} } The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae is a long terminal repeat mobile genetic element that transposes through an RNA intermediate. Initiation of minus-strand and plus-strand DNA synthesis are two critical steps during reverse transcription of the retrotransposon genome. Initiation of minus-strand DNA synthesis of the Ty1 element is primed by the cytoplasmic initiator methionine tRNA base paired to the primer binding site near the 5' end of the genomic RNA. A structural probing study of the primer tRNA-Ty1 RNA binary complex reveals that besides interactions between the primer binding site and the last 10 nucleotides at the 3' end of the primer tRNA, three short regions of Ty1 RNA named box 0, box 1 and box 2.1 interact with the T and D stems and loops of the primer tRNA. Some in vivo results underline the functional importance of the nucleotide sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primer tRNA play a role in the reverse transcription pathway. Plus-strand DNA synthesis is initiated from an RNase H resistant oligoribonucleotide spanning a purine-rich sequence, the polypurine tract (PPT). Two sites of initiation located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the TyB (pol) gene in the integrase coding sequence (PPT2) have been identified in the genome of Ty1. The two PPTs have an identical sequence, TGGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand DNA synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition. |
Friant, S; Heyman, T; Wilhelm, M L; Wilhelm, F X Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon Article de journal Nucleic Acids Res, 24 (3), p. 441-9, 1996, (0305-1048 Journal Article). Résumé | BibTeX | Étiquettes: Acid, Base, cerevisiae, Conformation, Data, Gov't, Met/genetics/*metabolism, Molecular, Mutation, Non-U.S., Nucleic, Retroelements/*genetics, RNA, RNA/genetics/*metabolism, Saccharomyces, Sequence, structure, Support, Transfer @article{, title = {Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon}, author = { S. Friant and T. Heyman and M. L. Wilhelm and F. X. Wilhelm}, year = {1996}, date = {1996-01-01}, journal = {Nucleic Acids Res}, volume = {24}, number = {3}, pages = {441-9}, abstract = {Reverse transcription of the yeast Ty1 retrotransposon is primed by tRNAi(Met) base paired to the primer binding site near the 5'-end of Ty1 genomic RNA. To understand the molecular basis of the tRNAi(Met)-Ty1 RNA interaction the secondary structure of the binary complex was analysed. Enzymatic probes were used to test the conformation of tRNAi(Met) and of Ty1 RNA in the free form and in the complex. A secondary structure model of the tRNAi(Met) Ty1 RNA complex consistent with the probing data was constructed with the help of a computer program. The model shows that besides interactions between the primer binding site and the last 10 nt at the 3'-end of tRNAi(Met), three short regions of Ty1 RNA named boxes 0, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Mutations were made in the boxes or in the complementary sequences of tRNAi(Met) to study the contribution of these sequences to formation of the complex. We find that interaction with at least one of the two boxes 0 or 1 is absolutely required for efficient annealing of the two RNAs. Sequence comparison showing that the primary sequence of the boxes is strictly conserved in Ty1 and Ty2 elements and previously published in vivo results underline the functional importance of the primary sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primary tRNAi(Met) play a role in the reverse transcription pathway.}, note = {0305-1048 Journal Article}, keywords = {Acid, Base, cerevisiae, Conformation, Data, Gov't, Met/genetics/*metabolism, Molecular, Mutation, Non-U.S., Nucleic, Retroelements/*genetics, RNA, RNA/genetics/*metabolism, Saccharomyces, Sequence, structure, Support, Transfer}, pubstate = {published}, tppubtype = {article} } Reverse transcription of the yeast Ty1 retrotransposon is primed by tRNAi(Met) base paired to the primer binding site near the 5'-end of Ty1 genomic RNA. To understand the molecular basis of the tRNAi(Met)-Ty1 RNA interaction the secondary structure of the binary complex was analysed. Enzymatic probes were used to test the conformation of tRNAi(Met) and of Ty1 RNA in the free form and in the complex. A secondary structure model of the tRNAi(Met) Ty1 RNA complex consistent with the probing data was constructed with the help of a computer program. The model shows that besides interactions between the primer binding site and the last 10 nt at the 3'-end of tRNAi(Met), three short regions of Ty1 RNA named boxes 0, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Mutations were made in the boxes or in the complementary sequences of tRNAi(Met) to study the contribution of these sequences to formation of the complex. We find that interaction with at least one of the two boxes 0 or 1 is absolutely required for efficient annealing of the two RNAs. Sequence comparison showing that the primary sequence of the boxes is strictly conserved in Ty1 and Ty2 elements and previously published in vivo results underline the functional importance of the primary sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primary tRNAi(Met) play a role in the reverse transcription pathway. |
de Barros, Pais J P; Keith, G; Adlouni, El C; Glasser, A L; Mack, G; Dirheimer, G; Desgres, J 2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver Article de journal Nucleic Acids Res, 24 (8), p. 1489-96, 1996, (0305-1048 Journal Article). Résumé | BibTeX | Étiquettes: &, Acid, Acyl/*chemistry/isolation, Amino, Animals, Base, Borohydrides/chemistry, Cattle, Cells, Conformation, Cytidine/*analogs, Cytoplasm, Data, derivatives/chemistry/isolation, Fragmentography, Gov't, Hela, Human, Liver/*chemistry, Mass, Molecular, Non-U.S., Nucleic, purification, RNA, Sequence, structure, Support, Transfer @article{, title = {2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver}, author = { J. P. Pais de Barros and G. Keith and C. El Adlouni and A. L. Glasser and G. Mack and G. Dirheimer and J. Desgres}, year = {1996}, date = {1996-01-01}, journal = {Nucleic Acids Res}, volume = {24}, number = {8}, pages = {1489-96}, abstract = {The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals.}, note = {0305-1048 Journal Article}, keywords = {&, Acid, Acyl/*chemistry/isolation, Amino, Animals, Base, Borohydrides/chemistry, Cattle, Cells, Conformation, Cytidine/*analogs, Cytoplasm, Data, derivatives/chemistry/isolation, Fragmentography, Gov't, Hela, Human, Liver/*chemistry, Mass, Molecular, Non-U.S., Nucleic, purification, RNA, Sequence, structure, Support, Transfer}, pubstate = {published}, tppubtype = {article} } The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals. |
1995 |
Dirheimer, G; Baranowski, W; Keith, G Variations in tRNA modifications, particularly of their queuine content in higher eukaryotes. Its relation to malignancy grading Article de journal Biochimie, 77 (1-2), p. 99-103, 1995, (0300-9084 Journal Article Review Review, Tutorial). Résumé | BibTeX | Étiquettes: &, Animals, Cell, derivatives/analysis, Female, Gov't, Guanine/*analogs, Human, Neoplasms/*genetics/pathology, Neoplastic/genetics, Non-U.S., Ovarian, post-transcriptional, Processing, Purines/analysis, Pyrimidines/analysis, RNA, Support, Transfer/*chemistry/metabolism, Transformation @article{, title = {Variations in tRNA modifications, particularly of their queuine content in higher eukaryotes. Its relation to malignancy grading}, author = { G. Dirheimer and W. Baranowski and G. Keith}, year = {1995}, date = {1995-01-01}, journal = {Biochimie}, volume = {77}, number = {1-2}, pages = {99-103}, abstract = {Literature references dealing with the variations in the modification level of nucleosides in total eukaryotic tRNAs as a function of different physiological status and after drug administration as well as in sequenced cytoplasmic tRNAs between normal and tumor cells and in SV40-transformed cells are reviewed. In addition, special attention is given to guanine replacement of queuine in the first position of the anticodon of tRNAs. A correlation between the level of this undermodification in cancer tissues and the malignancy grading could be found in human ovarian tumors, confirming the results reported in several laboratories for lymphomas and lung cancer tissues. Indeed tRNAs from primary and metastatic human ovarian malignant tumors are Q deficient as compared to tRNAs from normal tissues or benign tumors: thus queuine deficiency increases with malignancy and grading of differentiation.}, note = {0300-9084 Journal Article Review Review, Tutorial}, keywords = {&, Animals, Cell, derivatives/analysis, Female, Gov't, Guanine/*analogs, Human, Neoplasms/*genetics/pathology, Neoplastic/genetics, Non-U.S., Ovarian, post-transcriptional, Processing, Purines/analysis, Pyrimidines/analysis, RNA, Support, Transfer/*chemistry/metabolism, Transformation}, pubstate = {published}, tppubtype = {article} } Literature references dealing with the variations in the modification level of nucleosides in total eukaryotic tRNAs as a function of different physiological status and after drug administration as well as in sequenced cytoplasmic tRNAs between normal and tumor cells and in SV40-transformed cells are reviewed. In addition, special attention is given to guanine replacement of queuine in the first position of the anticodon of tRNAs. A correlation between the level of this undermodification in cancer tissues and the malignancy grading could be found in human ovarian tumors, confirming the results reported in several laboratories for lymphomas and lung cancer tissues. Indeed tRNAs from primary and metastatic human ovarian malignant tumors are Q deficient as compared to tRNAs from normal tissues or benign tumors: thus queuine deficiency increases with malignancy and grading of differentiation. |