Phylogenetic and Phyletic Studies of Informational Genes in Genomes Highlight Existence of a 4th Domain of Life Including Giant Viruses
The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life (Eukarya, Bacteria and Archaea) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we use...
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| Published in | PloS one Vol. 5; no. 12; p. e15530 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
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Public Library of Science
02.12.2010
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| Online Access | Get full text |
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| Abstract | The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life (Eukarya, Bacteria and Archaea) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we used sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing. Compared to the three ribosomal defined domains, we report a single common origin for Nucleocytoplasmic Large DNA Viruses (NCLDV), DNA processing genes rooted between Archaea and Eukarya, with a topology congruent with that of the ribosomal tree. As for translation, we found in our new viruses, together with Mimivirus, five proteins rooted deeply in the eukaryotic clade. In addition, comparison of informational genes repertoire based on phyletic pattern analysis supports existence of a clade containing NCLDVs clearly distinct from that of Eukarya, Bacteria and Archaea. We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life. |
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| AbstractList | The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life ( Eukarya , Bacteria and Archaea ) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we used sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing. Compared to the three ribosomal defined domains, we report a single common origin for Nucleocytoplasmic Large DNA Viruses (NCLDV), DNA processing genes rooted between Archaea and Eukarya , with a topology congruent with that of the ribosomal tree. As for translation, we found in our new viruses, together with Mimivirus, five proteins rooted deeply in the eukaryotic clade. In addition, comparison of informational genes repertoire based on phyletic pattern analysis supports existence of a clade containing NCLDVs clearly distinct from that of Eukarya , Bacteria and Archaea . We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life. The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life ( Eukarya , Bacteria and Archaea ) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we used sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing. Compared to the three ribosomal defined domains, we report a single common origin for Nucleocytoplasmic Large DNA Viruses (NCLDV), DNA processing genes rooted between Archaea and Eukarya , with a topology congruent with that of the ribosomal tree. As for translation, we found in our new viruses, together with Mimivirus, five proteins rooted deeply in the eukaryotic clade. In addition, comparison of informational genes repertoire based on phyletic pattern analysis supports existence of a clade containing NCLDVs clearly distinct from that of Eukarya , Bacteria and Archaea . We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life. |
| Author | Gimenez, Gregory Madoui, Mohammed-Amine Raoult, Didier La Scola, Bernard Boyer, Mickaël |
| AuthorAffiliation | URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France Institute of Infectious Disease and Molecular Medicine, South Africa |
| AuthorAffiliation_xml | – name: URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France – name: Institute of Infectious Disease and Molecular Medicine, South Africa |
| Author_xml | – sequence: 1 givenname: Mickaël surname: Boyer fullname: Boyer, Mickaël – sequence: 2 givenname: Mohammed-Amine surname: Madoui fullname: Madoui, Mohammed-Amine – sequence: 3 givenname: Gregory surname: Gimenez fullname: Gimenez, Gregory – sequence: 4 givenname: Bernard surname: La Scola fullname: La Scola, Bernard – sequence: 5 givenname: Didier surname: Raoult fullname: Raoult, Didier |
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| Cites_doi | 10.1017/CBO9780511661686.007 10.1128/JVI.79.23.14967-14970.2005 10.1038/nrmicro2033 10.1111/j.1749-6632.1987.tb40596.x 10.1006/jmbi.2000.4042 10.1016/S0168-9525(02)02744-0 10.1128/MCB.20.17.6195-6200.2000 10.1038/nature07745 10.1093/molbev/msm092 10.1093/nar/29.1.22 10.1128/MMBR.64.1.202-236.2000 10.1038/nrmicro1527 10.1186/1471-2148-8-12 10.1038/nrmicro1858 10.1111/j.1469-0691.2008.02216.x 10.1016/j.jtbi.2009.10.014 10.1016/S1369-5274(02)00360-0 10.1007/s00239-002-2311-7 10.1126/science.1101485 10.1038/nrmicro2030 10.1093/nar/gkh340 10.1126/science.278.5338.631 10.1016/j.virusres.2006.01.010 10.1159/000312919 10.1016/S0140-6736(09)61958-9 10.1038/nrmicro2108-c6 10.1073/pnas.0404505101 10.1016/j.virusres.2006.01.009 10.1006/viro.2000.0776 10.1093/nar/25.17.3389 10.1146/annurev.biochem.67.1.71 10.1093/bioinformatics/btg180 10.1007/s002390010215 10.1080/10635150701472164 10.1159/000312921 10.1186/1471-2148-8-320 10.1371/journal.pone.0009490 10.1038/nrmicro2108 10.1007/s00705-006-0849-1 10.1186/1743-422X-6-223 10.1006/viro.2001.1190 |
| ContentType | Journal Article |
| Copyright | 2010 Boyer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Boyer et al. 2010 |
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| References | M Krupovic (ref3) 2008; 6 D Moreira (ref5) 2008; 8 RL Tatusov (ref40) 1997; 278 D Raoult (ref4) 2004; 306 F Ronquist (ref38) 2003; 19 B La Scola (ref14) 2009; 53 P Forterre (ref9) 2006; 117 YI Wolf (ref20) 2002; 18 ML Baker (ref2) 2005; 79 D Raoult (ref7) 2009; 7 X Peng (ref29) 2001; 291 K Tamura (ref39) 2007; 24 J Filee (ref12) 2008; 8 N Yutin (ref13) 2009; 6 D Prangishvili (ref26) 2006; 4 LP Villarreal (ref22) 2010; 262 A Jordan (ref11) 1998; 67 C Moliner (ref15) 2009; 15 DJ McGeoch (ref24) 1995 H Blum (ref28) 2001; 281 C Notredame (ref34) 2000; 302 RL Tatusov (ref41) 2001; 29 P Forterre (ref8) 2002; 5 SF Altschul (ref33) 1997; 25 P Forterre (ref16) 2010; 53 RC Edgar (ref35) 2004; 32 PJ Keeling (ref18) 2004; 101 A Dias (ref30) 2009; 458 T Cavalier-Smith (ref21) 1987; 503 D Raoult (ref6) 2008; 6 EV Koonin (ref31) 2008; 6 MN Price (ref37) 2010; 5 HW Ackermann (ref27) 2007; 152 E Torrents (ref10) 2002; 55 G Talavera (ref36) 2007; 56 LM Iyer (ref23) 2006; 117 D Raoult (ref32) 2010; 375 PJ Bell (ref25) 2001; 53 D Moreira (ref1) 2009; 7 S Senju (ref19) 2000; 20 CR Woese (ref17) 2000; 64 |
| References_xml | – year: 1995 ident: ref24 article-title: Origins of DNA viruses. doi: 10.1017/CBO9780511661686.007 – volume: 79 start-page: 14967 year: 2005 ident: ref2 article-title: Common ancestry of herpesviruses and tailed DNA bacteriophages. publication-title: J Virol doi: 10.1128/JVI.79.23.14967-14970.2005 – volume: 6 start-page: 941 year: 2008 ident: ref3 article-title: Virus evolution: how far does the double beta-barrel viral lineage extend? publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2033 – volume: 503 start-page: 17 year: 1987 ident: ref21 article-title: The origin of eukaryotic and archaebacterial cells. publication-title: Ann N Y Acad Sci doi: 10.1111/j.1749-6632.1987.tb40596.x – volume: 302 start-page: 205 year: 2000 ident: ref34 article-title: T-Coffee: A novel method for fast and accurate multiple sequence alignment. publication-title: J Mol Biol doi: 10.1006/jmbi.2000.4042 – volume: 18 start-page: 472 year: 2002 ident: ref20 article-title: Genome trees and the tree of life. publication-title: Trends Genet doi: 10.1016/S0168-9525(02)02744-0 – volume: 20 start-page: 6195 year: 2000 ident: ref19 article-title: Immunocytochemical analyses and targeted gene disruption of GTPBP1. publication-title: Mol Cell Biol doi: 10.1128/MCB.20.17.6195-6200.2000 – volume: 458 start-page: 914 year: 2009 ident: ref30 article-title: The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. publication-title: Nature doi: 10.1038/nature07745 – volume: 24 start-page: 1596 year: 2007 ident: ref39 article-title: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. publication-title: Mol Biol Evol doi: 10.1093/molbev/msm092 – volume: 29 start-page: 22 year: 2001 ident: ref41 article-title: The COG database: new developments in phylogenetic classification of proteins from complete genomes. publication-title: Nucleic Acids Res doi: 10.1093/nar/29.1.22 – volume: 64 start-page: 202 year: 2000 ident: ref17 article-title: Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. publication-title: Microbiol Mol Biol Rev doi: 10.1128/MMBR.64.1.202-236.2000 – volume: 4 start-page: 837 year: 2006 ident: ref26 article-title: Viruses of the Archaea: a unifying view. publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro1527 – volume: 8 start-page: 12 year: 2008 ident: ref5 article-title: Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes. publication-title: BMC Evol Biol doi: 10.1186/1471-2148-8-12 – volume: 6 start-page: 315 year: 2008 ident: ref6 article-title: Redefining viruses: lessons from Mimivirus. publication-title: Nature Rev Microbiol doi: 10.1038/nrmicro1858 – volume: 15 start-page: 178 year: 2009 ident: ref15 article-title: Evidence of horizontal gene transfer between amoeba and bacteria. publication-title: Clin Microbiol Infect doi: 10.1111/j.1469-0691.2008.02216.x – volume: 262 start-page: 698 year: 2010 ident: ref22 article-title: Viruses are essential agents within the roots and stem of the tree of life. publication-title: J Theor Biol doi: 10.1016/j.jtbi.2009.10.014 – volume: 5 start-page: 525 year: 2002 ident: ref8 article-title: The origin of DNA genomes and DNA replication proteins. publication-title: Curr Opin Microbiol doi: 10.1016/S1369-5274(02)00360-0 – volume: 55 start-page: 138 year: 2002 ident: ref10 article-title: Ribonucleotide reductases: divergent evolution of an ancient enzyme. publication-title: J Mol Evol doi: 10.1007/s00239-002-2311-7 – volume: 306 start-page: 1344 year: 2004 ident: ref4 article-title: The 1.2-megabase genome sequence of Mimivirus. publication-title: Science doi: 10.1126/science.1101485 – volume: 6 start-page: 925 year: 2008 ident: ref31 article-title: The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2030 – volume: 32 start-page: 1792 year: 2004 ident: ref35 article-title: MUSCLE: multiple sequence alignment with high accuracy and high throughput. publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh340 – volume: 278 start-page: 631 year: 1997 ident: ref40 article-title: A genomic perspective on protein families. publication-title: Science doi: 10.1126/science.278.5338.631 – volume: 117 start-page: 5 year: 2006 ident: ref9 article-title: The origin of viruses and their possible roles in major evolutionary transitions. publication-title: Virus Res doi: 10.1016/j.virusres.2006.01.010 – volume: 53 start-page: 344 year: 2009 ident: ref14 article-title: A burden of new giant viruses from environment and their tentative characterization by MALDI-TOF mass-spectrometry. publication-title: Intervirology doi: 10.1159/000312919 – volume: 375 start-page: 104 year: 2010 ident: ref32 article-title: The post-Darwinist rhizome of life. publication-title: Lancet doi: 10.1016/S0140-6736(09)61958-9 – volume: 7 start-page: 615; year: 2009 ident: ref7 article-title: There is no such thing as a tree of life (and of course viruses are out!). publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2108-c6 – volume: 101 start-page: 15380 year: 2004 ident: ref18 article-title: A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha. publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0404505101 – volume: 117 start-page: 156 year: 2006 ident: ref23 article-title: Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. publication-title: Virus Res doi: 10.1016/j.virusres.2006.01.009 – volume: 281 start-page: 6 year: 2001 ident: ref28 article-title: The genome of the archaeal virus SIRV1 has features in common with genomes of eukaryal viruses. publication-title: Virology doi: 10.1006/viro.2000.0776 – volume: 25 start-page: 3389 year: 1997 ident: ref33 article-title: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. publication-title: Nucleic Acids Res doi: 10.1093/nar/25.17.3389 – volume: 67 start-page: 71 year: 1998 ident: ref11 article-title: Ribonucleotide reductases. publication-title: Annu Rev Biochem doi: 10.1146/annurev.biochem.67.1.71 – volume: 19 start-page: 1572 year: 2003 ident: ref38 article-title: MrBayes 3: Bayesian phylogenetic inference under mixed models. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btg180 – volume: 53 start-page: 251 year: 2001 ident: ref25 article-title: Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? publication-title: J Mol Evol doi: 10.1007/s002390010215 – volume: 56 start-page: 564 year: 2007 ident: ref36 article-title: Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. publication-title: Syst Biol doi: 10.1080/10635150701472164 – volume: 53 start-page: 362 year: 2010 ident: ref16 article-title: Giant viruses: conflicts in revisiting the virus concept. publication-title: Intervirology doi: 10.1159/000312921 – volume: 8 start-page: 320 year: 2008 ident: ref12 article-title: Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses. publication-title: BMC Evol Biol doi: 10.1186/1471-2148-8-320 – volume: 5 start-page: e9490 year: 2010 ident: ref37 article-title: FastTree 2–approximately maximum-likelihood trees for large alignments. publication-title: PLoS One doi: 10.1371/journal.pone.0009490 – volume: 7 start-page: 306 year: 2009 ident: ref1 article-title: Ten reasons to exclude viruses from the tree of life. publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2108 – volume: 152 start-page: 227 year: 2007 ident: ref27 article-title: 5500 Phages examined in the electron microscope. publication-title: Arch Virol doi: 10.1007/s00705-006-0849-1 – volume: 6 start-page: 223 year: 2009 ident: ref13 article-title: Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution. publication-title: Virol J doi: 10.1186/1743-422X-6-223 – volume: 291 start-page: 226 year: 2001 ident: ref29 article-title: Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. publication-title: Virology doi: 10.1006/viro.2001.1190 |
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| Snippet | The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life (Eukarya, Bacteria and... The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life ( Eukarya , Bacteria and... The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life ( Eukarya , Bacteria and... |
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| SubjectTerms | Archaea Bacteria Biology Biosynthesis Deoxyribonucleic acid DNA DNA viruses Enzymes Eukarya Eukaryotes Gene sequencing Genes Genomes Influenza Pattern analysis Phylogenetics Phylogeny Proteins Ribonucleotide reductase Topology Transcription factors Trees Viruses |
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