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7. An Update on Eukaryotic Viruses Revived from Ancient Permafrost

Author

Alempic, Jean-Marie, primary, Lartigue, Audrey, additional, Goncharov, Artemiy E., additional, Grosse, Guido, additional, Strauss, Jens, additional, Tikhonov, Alexey N., additional, Fedorov, Alexander N., additional, Poirot, Olivier, additional, Legendre, Matthieu, additional, Santini, Sébastien, additional, Abergel, Chantal, additional, and Claverie, Jean-Michel, additional

Published
2023
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9. An Update on Eukaryotic Viruses Revived from Ancient Permafrost

Author

Alempic, Jean-Marie, Lartigue, Audrey, Goncharov, Artemiy E, Grosse, Guido, Strauss, Jens, Tikhonov, Alexey N, Fedorov, Alexander N, Poirot, Olivier, Legendre, Matthieu, Santini, Sébastien, Abergel, Chantal, Claverie, Jean-Michel, Alempic, Jean-Marie, Lartigue, Audrey, Goncharov, Artemiy E, Grosse, Guido, Strauss, Jens, Tikhonov, Alexey N, Fedorov, Alexander N, Poirot, Olivier, Legendre, Matthieu, Santini, Sébastien, Abergel, Chantal, and Claverie, Jean-Michel

Abstract

One quarter of the Northern hemisphere is underlain by permanently frozen ground, referred to as permafrost. Due to climate warming, irreversibly thawing permafrost is releasing organic matter frozen for up to a million years, most of which decomposes into carbon dioxide and methane, further enhancing the greenhouse effect. Part of this organic matter also consists of revived cellular microbes (prokaryotes, unicellular eukaryotes) as well as viruses that have remained dormant since prehistorical times. While the literature abounds on descriptions of the rich and diverse prokaryotic microbiomes found in permafrost, no additional report about “live” viruses have been published since the two original studies describing pithovirus (in 2014) and mollivirus (in 2015). This wrongly suggests that such occurrences are rare and that “zombie viruses” are not a public health threat. To restore an appreciation closer to reality, we report the preliminary characterizations of 13 new viruses isolated from seven different ancient Siberian permafrost samples, one from the Lena river and one from Kamchatka cryosol. As expected from the host specificity imposed by our protocol, these viruses belong to five different clades infecting Acanthamoeba spp. but not previously revived from permafrost: Pandoravirus, Cedratvirus, Megavirus, and Pacmanvirus, in addition to a new Pithovirus strain.

Published
2023

10. An update on eukaryotic viruses revived from ancient permafrost

Author

Alempic, Jean-Marie, primary, Lartigue, Audrey, additional, Goncharov, Artemiy E, additional, Grosse, Guido, additional, Strauss, Jens, additional, Tikhonov, Alexey N., additional, Fedorov, Alexander N., additional, Poirot, Olivier, additional, Legendre, Matthieu, additional, Santini, Sébastien, additional, Abergel, Chantal, additional, and Claverie, Jean-Michel, additional

Published
2022
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12. Evolution of giant pandoravirus from small icosahedral viruses revealed by CRISPR/Cas9

Author

Bisio, Hugo, Legendre, Matthieu, Giry, Claire, Philippe, Nadège, Alempic, Jean-Marie, Jeudy, Sandra, Abergel, Chantal, Information génomique et structurale (IGS), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of “Virus” and the existence of a fourth domain of life1-3. While increasing knowledge of genome diversity has accumulated4, functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and its host Acanthamoeba castellanii using CRISPR/Cas9, allowing us to uncover the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the evolutionary intermediate mollivirus highlights a stepwise transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. Genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and demonstrate that viral gigantism can arise as an emerging trait.

Published
2022

15. Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Zhang, Hua-Hao, Zhou, Qiu-Zhong, Wang, Ping-Lan, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Drezen, Jean-Michel, Béliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas E., Cheng, Peng-Fei, Han, Min-Jin, Zhang, Ze, Zhang, Xiao-Gu, and Dai, Fang-Yin

Published
2018
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23. L’épigénome des virus géants: Stratégies d’attaque et d’autodéfense

Author

Legendre, Matthieu, Sciences, EDP, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience; No abstract available

Published
2020

27. Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world

Author

Jeudy, Sandra, primary, Bertaux, Lionel, additional, Alempic, Jean-Marie, additional, Lartigue, Audrey, additional, Legendre, Matthieu, additional, Belmudes, Lucid, additional, Santini, Sébastien, additional, Philippe, Nadège, additional, Beucher, Laure, additional, Biondi, Emanuele G., additional, Juul, Sissel, additional, Turner, Daniel J., additional, Couté, Yohann, additional, Claverie, Jean-Michel, additional, and Abergel, Chantal, additional

Published
2019
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29. Diversity and evolution of the emerging $Pandoraviridae$ family

Author

Legendre, Matthieu, Fabre, Elisabeth, Poirot, Olivier, Jeudy, Sandra, Lartigue, Audrey, Alempic, Jean-Marie, Beucher, Laure, Philippe, Nadège, Bertaux, Lionel, Christo-Foroux, Eugène, Labadie, Karine, Couté, Yohann, Abergel, Chantal, Claverie, Jean-Michel, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), This work was partially supported by the French National Research Agency (ANR-14-CE14-0023-01), France Genomique (ANR-10-INSB-01-01), Institut Français de Bioinformatique (ANR–11–INSB–0013), the Fondation Bettencourt-Schueller (OTP51251), by a DGA-MRIS scholarship, and by the Provence-Alpes-Côte-d’Azur région (2010 12125)., ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Service de génétique et embryologie médicales [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Trousseau [APHP], Etude de la dynamique des protéomes (EDyP), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), ANR-10-INBS-08-01/10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), ANR-10-LABX-49-01,Labex GRAL, Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Équipe Services et Architectures pour Réseaux Avancés (LAAS-SARA), Laboratoire d'analyse et d'architecture des systèmes [Toulouse] (LAAS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées, Poirot, Olivier, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, and Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID

Subjects
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Proteomics, Gene Transfer, Horizontal, Science, [SDV]Life Sciences [q-bio], DNA Viruses, Virion, Genetic Variation, Acanthamoeba, Molecular Sequence Annotation, Genome, Viral, Sequence Analysis, DNA, Virus Replication, Article, Evolution, Molecular, Gene Duplication, DNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Environmental Microbiology, lcsh:Q, lcsh:Science, human activities, Phylogeny, ComputingMilieux_MISCELLANEOUS
Abstract

With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes. Here we show that the pandoraviruses exhibit an open pan-genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain-specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggest that de novo gene creation could contribute to the evolution of the giant pandoravirus genomes., Giant viruses are visible by light microscopy and have unusually long genomes. Here, the authors report three new members of the Pandoraviridae family and investigate their evolution and diversity.

Published
2018

32. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis

Author

Legendre, Matthieu, Lartigue, Audrey, Bertaux, Lionel, Jeudy, Sandra, Bartoli, Julia, Lescot, Magali, Alempic, Jean-Marie, Ramus, Claire, Bruley, Christophe, Labadie, Karine, Shmakova, Lyubov, Rivkina, Elizaveta, Coute, Yohann, Abergel, Chantal, Claverie, Jean-Michel, Institut d'oncologie/développement Albert Bonniot de Grenoble (INSERM U823), Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de génétique et embryologie médicales [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Trousseau [APHP], Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Équipe Services et Architectures pour Réseaux Avancés (LAAS-SARA), Laboratoire d'analyse et d'architecture des systèmes [Toulouse] (LAAS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées, Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Physicochemical and Biological Problems in Soil Science, RAS, CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Etude de la dynamique des protéomes (EDyP ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])

Subjects
sporulation, Saccharomyces cerevisiae Proteins, [SDV]Life Sciences [q-bio], genetic processes, Saccharomyces cerevisiae, histone, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Histone H4, Histones, 03 medical and health sciences, 0302 clinical medicine, Meiosis, DNA Breaks, Double-Stranded, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Recombination, Genetic, meiotic recombination, 0303 health sciences, fungi, Acetylation, Spores, Fungal, biology.organism_classification, Chromatin, Cell biology, Histone, lcsh:Biology (General), biology.protein, Homologous recombination, 030217 neurology & neurosurgery, Recombination
Abstract

Summary Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) occurring on the nucleosomal lateral surface. We show that H4K44 is acetylated at pre-meiosis and meiosis and displays genome-wide enrichment at recombination hotspots in meiosis. Acetylation at H4K44 is required for normal meiotic recombination, normal levels of double-strand breaks (DSBs) during meiosis, and optimal sporulation. Non-modifiable H4K44R results in increased nucleosomal occupancy around DSB hotspots. Our results indicate that H4K44ac functions to facilitate chromatin accessibility favorable for normal DSB formation and meiotic recombination.

Published
2015
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33. Additional file 9: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Subjects
fungi
Abstract

Figure S5. Multiple alignments of seven MITEs involved in HTs between viruses and its cellular hosts or species related to their hosts. (PDF 5206Â kb)

Published
2018
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34. Additional file 1: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Abstract

Table S1. Characteristics of ten MITEs and its autonomous elements identified in this study. (DOC 144Â kb)

Published
2018
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35. Additional file 4: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Abstract

Figure S2. Gene synteny and collinearity of three Pandoraviruses and distribution of six MITEs on its genomes. A Circle plot showing patterns of synteny and collinearity of three Pandoraviruses. MITEs on the genomes of three Pandoraviruses are shown using different colored lines. B One example of the present of one copy of MITEs in orthologous genomic site of P. salinus and P. dulcis but absent in that of P. inopinatum. C One example of the absence of one copy of MITEs orthologous genomic site of P. inopinatum and P. dulcis but present in that of P. salinus. (PDF 431Â kb)

Published
2018
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36. Additional file 3: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Subjects
integumentary system, immune system diseases, parasitic diseases, respiratory tract diseases
Abstract

Figure S1. Characteristics of ten MITEs from the viral genomes. A Multiple alignments of full-length copies as well as the flanking sequences of each MITE. TSD is shown in red and the boundary is indicated using black shading. B One empty paralogous site of CMC-NA_1_GfIV. C Secondary structure of ten MITEs. D Length distribution of MITEs with more than 14 copies in one viral genome. E Nucleotide genetic distances between each MITE copy and the corresponding consensus sequences. Only MITEs with reliable consensus sequences in one virus were included in this analysis. Because more than 50% copies of hAT-NA5_PD were shorter than 50% length of the consensus sequence, and it was also excluded in this analysis. Species abbreviations of viruses were listed in Additional file 1: Table S1. (PDF 3703Â kb)

Published
2018
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37. Additional file 6: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Subjects
bacteria
Abstract

Table S3. Target site duplications of hATm transposons. (DOC 59Â kb)

Published
2018
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38. Additional file 5: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, Béliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Abstract

Figure S3. Phylogeny of three known families (Buster, Ac and Tip) of the hAT transposons with the hATm family and characteristics of TSD of two members of the hATm family. A Phylogenetic analysis of hAT transposases, performed through Maximum Likelihood method. Numbers at nodes represent bootstrap support after 500 replicates. Four members (hAT5-AC, hAT5_AP, hAT5_APo and hAT5_AQ) of the Ac family were found in this study. The detail information of the hATm transposons is listed in Additional file 1: Table S2. B TSD of hATm-1_CuQ and hATm-1_BeT. The results of sequence logos and empty paralogous site analysis indicated that hATm-1_CuQ and hATm-1_BeT created a 9-bp TSD upon insertion. C Multiple alignments of the 5′ and 3′ terminal sequences of 28 hATm transposons identified in this study. Because hATm transposons are generally flanked by long TIRs (e.g. TIRs of hATm-6_RP are 417 bp), and only 40 bp of both termini of these transposons were shown arrows. (PDF 1651 kb)

Published
2018
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39. Additional file 7: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Subjects
endocrine system, integumentary system, fungi
Abstract

Figure S4. Determination of the boundary and TSD of seven MITEs identified in viral hosts or species related to their hosts. A Multiple alignments of full-length copies as well as the flanking sequences of each MITE. TSD is shown using red color and the boundary is indicated usingi black shading. B Empty paralogous sites of five MITEs identified in viral cellular hosts. (PDF 2219Â kb)

Published
2018
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40. Additional file 8: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Abstract

Table S4. Pairwise comparison of nucleotide sequence identity of seven MITEs involved in HTs between viruses and their cellular hosts or species closely related to their hosts. (DOC 68Â kb)

Published
2018
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41. Commensalism in theMimiviridaegiant virus family

Author

Jeudy, Sandra, primary, Bertaux, Lionel, additional, Alempic, Jean-Marie, additional, Lartigue, Audrey, additional, Legendre, Matthieu, additional, Belmudes, Lucid, additional, Santini, Sébastien, additional, Philippe, Nadège, additional, Beucher, Laure, additional, Biondi, Emanuele G., additional, Juul, Sissel, additional, Turner, Daniel J., additional, Couté, Yohann, additional, Claverie, Jean-Michel, additional, and Abergel, Chantal, additional

Published
2019
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43. Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing

Author

Claverie Jean-Michel, Abergel Chantal, Rico Alain, Santini Sébastien, and Legendre Matthieu

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Mimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic large DNA viruses (NCLDVs). Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely mapped many transcript boundaries and identified 75 new genes. Findings We now report a much deeper analysis using the SOLiD™ technology combining RNA-Seq of the Mimivirus transcriptome during the infectious cycle (202.4 Million reads), and a complete genome re-sequencing (45.3 Million reads). This study corrected the genome sequence and identified several single nucleotide polymorphisms. Our results also provided clear evidence of previously overlooked transcription units, including an important RNA polymerase subunit distantly related to Euryarchea homologues. The total Mimivirus gene count is now 1018, 11% greater than the original annotation. Conclusions This study highlights the huge progress brought about by ultra-deep sequencing for the comprehensive annotation of virus genomes, opening the door to a complete one-nucleotide resolution level description of their transcriptional activity, and to the realistic modeling of the viral genome expression at the ultimate molecular level. This work also illustrates the need to go beyond bioinformatics-only approaches for the annotation of short protein and non-coding genes in viral genomes.

Published
2011
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46. Computing expectation values for RNA motifs using discrete convolutions

Author

Fontaine Jean-Fred, Legendre Matthieu, Lambert André, and Gautheret Daniel

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Computational biologists use Expectation values (E-values) to estimate the number of solutions that can be expected by chance during a database scan. Here we focus on computing Expectation values for RNA motifs defined by single-strand and helix lod-score profiles with variable helix spans. Such E-values cannot be computed assuming a normal score distribution and their estimation previously required lengthy simulations. Results We introduce discrete convolutions as an accurate and fast mean to estimate score distributions of lod-score profiles. This method provides excellent score estimations for all single-strand or helical elements tested and also applies to the combination of elements into larger, complex, motifs. Further, the estimated distributions remain accurate even when pseudocounts are introduced into the lod-score profiles. Estimated score distributions are then easily converted into E-values. Conclusion A good agreement was observed between computed E-values and simulations for a number of complete RNA motifs. This method is now implemented into the ERPIN software, but it can be applied as well to any search procedure based on ungapped profiles with statistically independent columns.

Published
2005
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47. Noumeavirus replication relies on a transient remote control of the host nucleus

Author

Fabre, Elisabeth, Jeudy, Sandra, Santini, Sébastien, Legendre, Matthieu, Trauchessec, Mathieu, Couté, Yohann, Claverie, Jean-Michel, Abergel, Chantal, Technische Universität Dresden = Dresden University of Technology (TU Dresden), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hereditary Metabolic Diseases Department, East Medical Group, Hospices Civils de Lyon (HCL), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), DGA-MRIS scholarshipRégion Provence-Alpes-Côte-d’Azur (2010 12125), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), ANR-14-CE14-0023,Pandoravirus,Caractérisation fonctionnelle et moléculaire des Pandoravirus(2014), Service de génétique et embryologie médicales [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Trousseau [APHP], Etude de la dynamique des protéomes (EDyP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])

Subjects
Cell Nucleus, Gene Expression Regulation, Viral, Cytoplasm, Transcription, Genetic, viruses, Science, [SDV]Life Sciences [q-bio], DNA Viruses, Virion, Acanthamoeba, DNA, Genome, Viral, Virus Replication, Article, DNA, Viral, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ComputingMilieux_MISCELLANEOUS, Phylogeny
Abstract

Acanthamoeba are infected by a remarkable diversity of large dsDNA viruses, the infectious cycles of which have been characterized using genomics, transcriptomics and electron microscopy. Given their gene content and the persistence of the host nucleus throughout their infectious cycle, the Marseilleviridae were initially assumed to fully replicate in the cytoplasm. Unexpectedly, we find that their virions do not incorporate the virus-encoded transcription machinery, making their replication nucleus-dependent. However, instead of delivering their DNA to the nucleus, the Marseilleviridae initiate their replication by transiently recruiting the nuclear transcription machinery to their cytoplasmic viral factory. The nucleus recovers its integrity after becoming leaky at an early stage. This work highlights the importance of virion proteomic analyses to complement genome sequencing in the elucidation of the replication scheme and evolution of large dsDNA viruses., Large dsDNA viruses either replicate in or disrupt the nucleus to gain access to host RNA polymerases, or they rely on virus-encoded, packaged RNA polymerases. Here, the authors show that Noumeavirus replicates in the cytoplasm and relies on a transient recruitment of nuclear proteins to initiate replication.

Published
2017

48. Sequence determinants in human polyadenylation site selection

Author

Gautheret Daniel and Legendre Matthieu

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Differential polyadenylation is a widespread mechanism in higher eukaryotes producing mRNAs with different 3' ends in different contexts. This involves several alternative polyadenylation sites in the 3' UTR, each with its specific strength. Here, we analyze the vicinity of human polyadenylation signals in search of patterns that would help discriminate strong and weak polyadenylation sites, or true sites from randomly occurring signals. Results We used human genomic sequences to retrieve the region downstream of polyadenylation signals, usually absent from cDNA or mRNA databases. Analyzing 4956 EST-validated polyadenylation sites and their -300/+300 nt flanking regions, we clearly visualized the upstream (USE) and downstream (DSE) sequence elements, both characterized by U-rich (not GU-rich) segments. The presence of a USE and a DSE is the main feature distinguishing true polyadenylation sites from randomly occurring A(A/U)UAAA hexamers. While USEs are indifferently associated with strong and weak poly(A) sites, DSEs are more conspicuous near strong poly(A) sites. We then used the region encompassing the hexamer and DSE as a training set for poly(A) site identification by the ERPIN program and achieved a prediction specificity of 69 to 85% for a sensitivity of 56%. Conclusion The availability of complete genomes and large EST sequence databases now permit large-scale observation of polyadenylation sites. Both U-rich sequences flanking both sides of poly(A) signals contribute to the definition of "true" sites. However, the downstream U-rich sequences may also play an enhancing role. Based on this information, poly(A) site prediction accuracy was moderately but consistently improved compared to the best previously available algorithm.

Published
2003
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49. Diversity and evolution of the emerging Pandoraviridae family

Author

Legendre, Matthieu, primary, Fabre, Elisabeth, additional, Poirot, Olivier, additional, Jeudy, Sandra, additional, Lartigue, Audrey, additional, Alempic, Jean-Marie, additional, Beucher, Laure, additional, Philippe, Nadège, additional, Bertaux, Lionel, additional, Christo-Foroux, Eugène, additional, Labadie, Karine, additional, Couté, Yohann, additional, Abergel, Chantal, additional, and Claverie, Jean-Michel, additional

Published
2018
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50. Diversity and evolution of the emerging Pandoraviridae family

Author

Legendre, Matthieu, primary, Fabre, Elisabeth, additional, Poirot, Olivier, additional, Jeudy, Sandra, additional, Lartigue, Audrey, additional, Alempic, Jean-Marie, additional, Beucher, Laure, additional, Philippe, Nadège, additional, Bertaux, Lionel, additional, Labadie, Karine, additional, Couté, Yohann, additional, Abergel, Chantal, additional, and Claverie, Jean-Michel, additional

Published
2017
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