Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis
| العنوان: | Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis |
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| المؤلفون: | Disa Bäckström, Mart Krupovic, Eugene V. Koonin, Natalya Yutin, Thijs J. G. Ettema |
| المساهمون: | National Center for Biotechnology Information (NCBI), Uppsala University, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institutes of Health [Bethesda] (NIH), NY and EVK are supported by intramural funds of the US Department of Health and Human Services (to the National Library of Medicine). TJGE is supported by grants of the European Research Council (ERC Starting Grant 310039-PUZZLE_CELL), the Swedish Foundation for Strategic Research (SSF-FFL5) and the Swedish Research Council (VR grant 2015–04959). MK is supported by l’Agence Nationale de la Recherche (France) project ENVIRA., We acknowledge the help from chief scientist R. B. Pedersen, the scientific party and the entire crew on board the Norwegian research vessel G.O. Sars for providing marine sediment samples from the Loki’s Castle hydrothermal vent area during the summer 2010 expedition., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 310039,EC:FP7:ERC,ERC-2012-StG_20111109,PUZZLE_CELL(2012), Institut Pasteur [Paris] |
| المصدر: | Virology Journal Virology Journal, 2018, 15 (1), pp.67. ⟨10.1186/s12985-018-0974-y⟩ Virology journal 15 (2018) 1 Virology Journal, Vol 15, Iss 1, Pp 1-17 (2018) Virology Journal, BioMed Central, 2018, 15 (1), pp.67. ⟨10.1186/s12985-018-0974-y⟩ Virology journal, 15(1) |
| بيانات النشر: | HAL CCSD, 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | 0301 basic medicine, Archaeal Viruses, [SDV]Life Sciences [q-bio], Genome, MESH: Archaeal Viruses, Databases, Genetic, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, MESH: Capsid Proteins, MESH: Databases, Genetic, Genetics, MESH: Genomics, Genomics, Infectious Diseases, MESH: Archaea, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Genome, Viral, MESH: Metagenomics, Tectiviridae, Sequence analysis, Bioinformatik och systembiologi, Genome, Viral, Biology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Phylogenetics, Virology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Life Science, Human virome, lcsh:RC109-216, Gene, MESH: Tectiviridae, Bioinformatics and Systems Biology, Bacteria, Research, Genetic Variation, Archaea, Mikrobiologi, MESH: Bacteria, 030104 developmental biology, Metagenomics, Capsid Proteins |
| الوصف: | Background Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome. Results We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double Jelly-Roll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of virus-like elements that are similar in size to tectiviruses (10–15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by archaea and others by bacteria, suggesting that collectively, the DJR MCP-encoding elements have a broad host range among prokaryotes. Conclusions The findings reported here greatly expand the known host range of (putative) viruses of bacteria and archaea that encode a DJR MCP. They also demonstrate the extreme diversity of genome architectures in these viruses that encode no universal proteins other than the capsid protein that was used as the marker for their identification. From a supposedly minor group of bacterial and archaeal viruses, these viruses are emerging as a substantial component of the prokaryotic virome. Electronic supplementary material The online version of this article (10.1186/s12985-018-0974-y) contains supplementary material, which is available to authorized users. |
| وصف الملف: | text/html; application/pdf; application/octet-stream |
| اللغة: | English |
| تدمد: | 1743-422X |
| DOI: | 10.1186/s12985-018-0974-y⟩ |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f1cc9105a9a9b4eee919a5374aac9268 https://hal-pasteur.archives-ouvertes.fr/pasteur-01977335 |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....f1cc9105a9a9b4eee919a5374aac9268 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 1743422X |
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| DOI: | 10.1186/s12985-018-0974-y⟩ |