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Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes

Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named ‘TRUC’ (for “Things Resisting Uncompleted Classifications”) alongside Bacteria, Archaea, and Eukarya. Their origin and ancestral...

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Autores principales: Colson, Philippe, Levasseur, Anthony, La Scola, Bernard, Sharma, Vikas, Nasir, Arshan, Pontarotti, Pierre, Caetano-Anollés, Gustavo, Raoult, Didier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277510/
https://www.ncbi.nlm.nih.gov/pubmed/30538677
http://dx.doi.org/10.3389/fmicb.2018.02668
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author Colson, Philippe
Levasseur, Anthony
La Scola, Bernard
Sharma, Vikas
Nasir, Arshan
Pontarotti, Pierre
Caetano-Anollés, Gustavo
Raoult, Didier
author_facet Colson, Philippe
Levasseur, Anthony
La Scola, Bernard
Sharma, Vikas
Nasir, Arshan
Pontarotti, Pierre
Caetano-Anollés, Gustavo
Raoult, Didier
author_sort Colson, Philippe
collection PubMed
description Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named ‘TRUC’ (for “Things Resisting Uncompleted Classifications”) alongside Bacteria, Archaea, and Eukarya. Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs). Hierarchical clustering analysis was performed based on a binary presence/absence matrix constructed using 727 informational COGs from cellular organisms. The presence/absence of ‘universal’ FSF domains was used to generate an unrooted maximum parsimony phylogenomic tree. Comparison of the gene content of a giant virus with those of a bacterium, an archaeon, and a eukaryote with small genomes was also performed. Overall, both cladistic analyses based on gene sequences of very central and ancient proteins and on highly conserved protein fold structures as well as phenetic analyses were congruent regarding the delineation of a fourth branch of microbes comprised by giant viruses. Giant viruses appeared as a basal group in the tree of all proteomes. A pangenome and core genome determined for Rickettsia bellii (bacteria), Methanomassiliicoccus luminyensis (archaeon), Encephalitozoon intestinalis (eukaryote), and Tupanvirus (giant virus) showed a substantial proportion of Tupanvirus genes that overlap with those of the cellular microbes. In addition, a substantial genome mosaicism was observed, with 51, 11, 8, and 0.2% of Tupanvirus genes best matching with viruses, eukaryota, bacteria, and archaea, respectively. Finally, we found that genes themselves may be subject to lateral sequence transfers. In summary, our data highlight the quantum leap between classical and giant viruses. Phylogenetic and phyletic analyses and the study of protein fold superfamilies confirm previous evidence of the existence of a fourth TRUC of life that includes giant viruses, and highlight its ancestrality and mosaicism. They also point out that best evolutionary representations for giant viruses and cellular microorganisms are rhizomes, and that sequence transfers rather than gene transfers have to be considered.
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spelling pubmed-62775102018-12-11 Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes Colson, Philippe Levasseur, Anthony La Scola, Bernard Sharma, Vikas Nasir, Arshan Pontarotti, Pierre Caetano-Anollés, Gustavo Raoult, Didier Front Microbiol Microbiology Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named ‘TRUC’ (for “Things Resisting Uncompleted Classifications”) alongside Bacteria, Archaea, and Eukarya. Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs). Hierarchical clustering analysis was performed based on a binary presence/absence matrix constructed using 727 informational COGs from cellular organisms. The presence/absence of ‘universal’ FSF domains was used to generate an unrooted maximum parsimony phylogenomic tree. Comparison of the gene content of a giant virus with those of a bacterium, an archaeon, and a eukaryote with small genomes was also performed. Overall, both cladistic analyses based on gene sequences of very central and ancient proteins and on highly conserved protein fold structures as well as phenetic analyses were congruent regarding the delineation of a fourth branch of microbes comprised by giant viruses. Giant viruses appeared as a basal group in the tree of all proteomes. A pangenome and core genome determined for Rickettsia bellii (bacteria), Methanomassiliicoccus luminyensis (archaeon), Encephalitozoon intestinalis (eukaryote), and Tupanvirus (giant virus) showed a substantial proportion of Tupanvirus genes that overlap with those of the cellular microbes. In addition, a substantial genome mosaicism was observed, with 51, 11, 8, and 0.2% of Tupanvirus genes best matching with viruses, eukaryota, bacteria, and archaea, respectively. Finally, we found that genes themselves may be subject to lateral sequence transfers. In summary, our data highlight the quantum leap between classical and giant viruses. Phylogenetic and phyletic analyses and the study of protein fold superfamilies confirm previous evidence of the existence of a fourth TRUC of life that includes giant viruses, and highlight its ancestrality and mosaicism. They also point out that best evolutionary representations for giant viruses and cellular microorganisms are rhizomes, and that sequence transfers rather than gene transfers have to be considered. Frontiers Media S.A. 2018-11-27 /pmc/articles/PMC6277510/ /pubmed/30538677 http://dx.doi.org/10.3389/fmicb.2018.02668 Text en Copyright © 2018 Colson, Levasseur, La Scola, Sharma, Nasir, Pontarotti, Caetano-Anollés and Raoult. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Colson, Philippe
Levasseur, Anthony
La Scola, Bernard
Sharma, Vikas
Nasir, Arshan
Pontarotti, Pierre
Caetano-Anollés, Gustavo
Raoult, Didier
Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
title Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
title_full Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
title_fullStr Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
title_full_unstemmed Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
title_short Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
title_sort ancestrality and mosaicism of giant viruses supporting the definition of the fourth truc of microbes
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277510/
https://www.ncbi.nlm.nih.gov/pubmed/30538677
http://dx.doi.org/10.3389/fmicb.2018.02668
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