The origin of DNA genomes and DNA replication proteins
Abstract
In recent years, it has became clear that most proteins involved in cellular DNA precursor synthesis or DNA replication have been 'invented' more than once, indicating that the transition from RNA to DNA genomes was more complex than previously thought. Several authors have suggested that DNA viruses, which often encode their own version of these proteins, played an important role in this process. The nature of the genome of the last universal cellular ancestor (LUCA) -- that is, RNA or DNA, prokaryotic-like or eukaryotic-like -- remains in dispute. A hyperthermophilic LUCA would have suggested a circular, double-stranded DNA genome; however, recent data favor a mesophilic or moderately thermophilic LUCA.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The last common ancestor may not have used a strictly DNA genome.
“Specifically, the last common ancestor may have had a cell membrane (Jékely 2006;Koga 2011;Lombard et al. 2012;Sojo et al. 2014;Coleman et al. 2019), RNA and phosphodiester-based energy coupling (e.g.Werner and Grohmann 2011), as well as thioester-based intermediary metabolism (Goldford et al. 2017;Weiss et al. 2018), but may not have used a strictly DNA genome (Mushegian and Koonin 1996;Leipe et”
From The Emergence of Life (2019) · cites this paper as Forterre 2002
Cites
DNA Topoisomerases: Structure, Function, and Mechanism
Champoux, J. J. (2001) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.70.1.369 · Cited by 2,748 · see citing works
Crystal structure of the ribosome at 5.5 Å resolution
Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., & Noller, H. F. (2001) · Science · doi:10.1126/science.1060089 · Cited by 1,944 · see citing works
DNA Polymerases: Structural Diversity and Common Mechanisms
Steitz, T. A. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.25.17395 · Cited by 848 · see citing works
Interpreting the universal phylogenetic tree
Woese, C. R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.15.8392 · Cited by 644 · see citing works
Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses
Iyer, L. M., Aravind, L., & Koonin, E. V. (2001) · Journal of Virology · doi:10.1128/jvi.75.23.11720-11734.2001 · Cited by 556 · see citing works
A mechanism for initiating RNA-dependent RNA polymerization
Butcher, S. J., Grimes, J. M., Makeyev, E. V., Bamford, D. H., & Stuart, D. I. (2001) · Nature · doi:10.1038/35065653 · Cited by 489 · see citing works
A Nonhyperthermophilic Common Ancestor to Extant Life Forms
Galtier, N., Tourasse, N., & Gouy, M. (1999) · Science · doi:10.1126/science.283.5399.220 · Cited by 442 · see citing works
Did DNA replication evolve twice independently?
Leipe, D. D., Aravind, L., & Koonin, E. V. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.17.3389 · Cited by 351 · see citing works
The origins and ongoing evolution of viruses
Hendrix, R. W., Lawrence, J. G., Hatfull, G. F., & Casjens, S. (2000) · Trends in Microbiology · doi:10.1016/s0966-842x(00)01863-1 · Cited by 349 · see citing works
An Alternative Flavin-Dependent Mechanism for Thymidylate Synthesis
Myllykallio, H., Lipowski, G., Leduc, D., Filée, J., Forterre, P., & Liebl, U. (2002) · Science · doi:10.1126/science.1072113 · Cited by 284 · see citing works
Self-citationArchaea and the Origin(s) of DNA Replication Proteins
Edgell, D. R., & Doolittle, W. F. (1997) · Cell · doi:10.1016/s0092-8674(00)80285-8 · Cited by 268 · see citing works
A non-hyperthermophilic ancestor for Bacteria
Brochier‐Armanet, C., & Philippe, H. (2002) · Nature · doi:10.1038/417244a · Cited by 253 · see citing works
Filée, J., Forterre, P., Sen-Lin, T., & Laurent, J. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0078-x · Cited by 247 · see citing works
Self-citationBacterial Mode of Replication with Eukaryotic-Like Machinery in a Hyperthermophilic Archaeon
Myllykallio, H., Lopez, P., López‐García, P., Heilig, R., Saurin, W., Zivanovic, Y., Philippe, H., & Forterre, P. (2000) · Science · doi:10.1126/science.288.5474.2212 · Cited by 244 · see citing works
Self-citationWhere is the root of the universal tree of life?
Forterre, P., & Philippe, H. (1999) · BioEssays · doi:10.1002/(sici)1521-1878(199910)21:10 · Cited by 244 · see citing works
Self-citationMetabolic symbiosis at the origin of eukaryotes
López‐García, P., & Moreira, D. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01342-5 · Cited by 240 · see citing works
A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein
Forterre, P. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02650-1 · Cited by 228 · see citing works
Self-citationViral Eukaryogenesis: Was the Ancestor of the Nucleus a Complex DNA Virus?
Bell, P. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010215 · Cited by 224 · see citing works
Nichols, M. D., DeAngelis, K. M., Keck, J. L., & Berger, J. M. (1999) · The EMBO Journal · doi:10.1093/emboj/18.21.6177 · Cited by 200 · see citing works
A Hypothesis for DNA Viruses as the Origin of Eukaryotic Replication Proteins
Villarreal, L. P., & DeFilippis, V. R. (2000) · Journal of Virology · doi:10.1128/jvi.74.15.7079-7084.2000 · Cited by 200 · see citing works
Archaeal Phylogeny Based on Ribosomal Proteins
Matte-Tailliez, O., Brochier‐Armanet, C., Forterre, P., & Philippe, H. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004122 · Cited by 180 · see citing works
Self-citationPoxviruses and the Origin of the Eukaryotic Nucleus
Takemura, M. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010171 · Cited by 165 · see citing works
The nature of the last universal common ancestor
Penny, D., & Poole, A. (1999) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(99)00020-9 · Cited by 162 · see citing works
Structure of the RNA Polymerase Domain of E. coli Primase
Keck, J. L., Roche, D. D., Lynch, A. S., & Berger, J. M. (2000) · Science · doi:10.1126/science.287.5462.2482 · Cited by 161 · see citing works
Ng, K. K.-S., Cherney, M. M., Vázquez, A. L., Machín, Á., Martín-Alonso, J. M., Parra, F., & James, M. N. G. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m109261200 · Cited by 155 · see citing works
Arezi, B., & Kuchta, R. D. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01680-7 · Cited by 137 · see citing works
Matsunaga, F., Forterre, P., Ishino, Y., & Myllykallio, H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191387498 · Cited by 135 · see citing works
Self-citationMacnaughton, T. B., Shi, S. T., Modahl, L. E., & Lai, M. M. C. (2002) · Journal of Virology · doi:10.1128/jvi.76.8.3920-3927.2002 · Cited by 134 · see citing works
DNA stability at temperatures typical for hyperthermophiles
Marguet, E., & Forterre, P. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.9.1681 · Cited by 127 · see citing works
Self-citationForterre, P., de la Tour, C. B., Philippe, H., & Duguet, M. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)01980-6 · Cited by 126 · see citing works
Self-citationForterre, P. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01497.x · Cited by 126 · see citing works
Self-citationThe evolutionary transition from RNA to DNA in early cells
Lazcano, A., Guerrero, R., Margulis, L., & Oró, J. (1988) · Journal of Molecular Evolution · doi:10.1007/bf02101189 · Cited by 119 · see citing works
About the last common ancestor, the universal life‐tree and lateral gene transfer: a reappraisal
Glansdorff, N. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.02126.x · Cited by 115 · see citing works
Bacterial-type DNA Holliday junction resolvases in eukaryotic viruses
García, A. D., Aravind, L., Koonin, E. V., & Moss, B. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.150238697 · Cited by 108 · see citing works
Freeland, S. J., Knight, R. D., & Landweber, L. F. (1999) · Science · doi:10.1126/science.286.5440.690 · Cited by 98 · see citing works
Ribonucleotide reductases: the link between an RNA and a DNA world?
Stubbe, J. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00153-6 · Cited by 94 · see citing works
Pyrococcus genome comparison evidences chromosome shuffling-driven evolution
Zivanovic, Y. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.9.1902 · Cited by 85 · see citing works
Evolved RNA Secondary Structure and the Rooting of the Universal Tree of Life
Caetano‐Anollés, G. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0048-3 · Cited by 81 · see citing works
Host RNA Polymerase Requirements for Transcription of the Human Hepatitis Delta Virus Genome
Moraleda, G., & Taylor, J. M. (2001) · Journal of Virology · doi:10.1128/jvi.75.21.10161-10169.2001 · Cited by 71 · see citing works
DNA Topoisomerase VI Generates ATP-dependent Double-strand Breaks with Two-nucleotide Overhangs
Buhler, C., Lebbink, J. H. G., Bocs, C., Ladenstein, R., & Forterre, P. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101823200 · Cited by 70 · see citing works
Self-citationConfounded cytosine! Tinkering and the evolution of DNA
Poole, A. M., Penny, D., & Sjöberg, B. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35052091 · Cited by 67 · see citing works
DNA replication: Partners in the Okazaki two-step
MacNeill, S. A. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00500-0 · Cited by 64 · see citing works
Balter, M. (2000) · Science · doi:10.1126/science.289.5486.1866 · Cited by 59 · see citing works
RNA Folding Argues Against a Hot-Start Origin of Life
Moulton, V., Gardner, P. P., Pointon, R. F., Creamer, L. K., Jameson, G. B., & Penny, D. (2000) · Journal of Molecular Evolution · doi:10.1007/s002390010104 · Cited by 56 · see citing works
Methyl-RNA: an evolutionary bridge between RNA and DNA?
Poole, A. M., Penny, D., & Sjöberg, B. (2000) · Chemistry & Biology · doi:10.1016/s1074-5521(00)00042-9 · Cited by 55 · see citing works
Moreira, D. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01692.x · Cited by 51 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Evolutionary history and higher order classification of AAA+ ATPases
Iyer, L. M., Leipe, D. D., Koonin, E. V., & Aravind, L. (2003) · Journal of Structural Biology · doi:10.1016/j.jsb.2003.10.010 · Cited by 782 · see citing works
Comparative genomics, minimal gene-sets and the last universal common ancestor
Koonin, E. V. (2003) · Nature Reviews Microbiology · doi:10.1038/nrmicro751 · Cited by 661 · see citing works
Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense
Vasu, K., & Nagaraja, V. (2013) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00044-12 · Cited by 606 · see citing works
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses
Iyer, L. M., Balaji, S., Koonin, E. V., & Aravind, L. (2006) · Virus Research · doi:10.1016/j.virusres.2006.01.009 · Cited by 585 · see citing works
On the origin of genomes and cells within inorganic compartments
Koonin, E. V., & Martin, W. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.09.006 · Cited by 406 · see citing works
The origin of viruses and their possible roles in major evolutionary transitions
Forterre, P. (2006) · Virus Research · doi:10.1016/j.virusres.2006.01.010 · Cited by 377 · see citing works
Self-citationIyer, L. M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki702 · Cited by 274 · see citing works
Glansdorff, N., Xu, Y., & Labedan, B. (2008) · Biology Direct · doi:10.1186/1745-6150-3-29 · Cited by 264 · see citing works
The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells
Forterre, P. (2005) · Biochimie · doi:10.1016/j.biochi.2005.03.015 · Cited by 256 · see citing works
Self-citationParallel adaptations to high temperatures in the Archaean eon
Boussau, B., Blanquart, S., Necsulea, A., Lartillot, N., & Gouy, M. (2008) · Nature · doi:10.1038/nature07393 · Cited by 242 · see citing works
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements
Koonin, E. V., & Dolja, V. V. (2014) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00049-13 · Cited by 242 · see citing works
Forterre, P. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510333103 · Cited by 242 · see citing works
Self-citationViruses take center stage in cellular evolution.
Claverie, J. (2006) · Genome biology · doi:10.1186/gb-2006-7-6-110 · Cited by 237 · see citing works
Wolf, Y. I., & Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-14 · Cited by 235 · see citing works
“Thus, plausible, even if conflicting, accounts of the emergence of these systems have been derived from comparative-genomic data and evolutionary reasoning [70,140-144].”
BackgroundLong non-coding RNA: its evolutionary relics and biological implications in mammals: a review
Dhanoa, J. K., Sethi, R. S., Verma, R., Arora, J. S., & Mukhopadhyay, C. S. (2018) · Journal of Animal Science and Technology · doi:10.1186/s40781-018-0183-7 · Cited by 222 · see citing works
A phylogenomic data-driven exploration of viral origins and evolution
Nasir, A., & Caetano‐Anollés, G. (2015) · Science Advances · doi:10.1126/sciadv.1500527 · Cited by 212 · see citing works
Viruses are essential agents within the roots and stem of the tree of life
Villarreal, L. P., & Witzany, G. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.10.014 · Cited by 211 · see citing works
Defining Life: The Virus Viewpoint
Forterre, P. (2010) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-010-9194-1 · Cited by 199 · see citing works
Self-citationForterre, P., & Gadelle, D. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp032 · Cited by 190 · see citing works
Self-citationThe universal tree of life: an update
Forterre, P. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00717 · Cited by 186 · see citing works
Self-citationBoyer, M., Madoui, M., Gimenez, G., Scola, B. L., & Raoult, D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015530 · Cited by 178 · see citing works
Forterre, P., & Prangishvili, D. A. (2009) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2009.04993.x · Cited by 172 · see citing works
Self-citationMedusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water
Yoshikawa, G., Blanc‐Mathieu, R., Song, C., Kayama, Y., Mochizuki, T., Murata, K., Ogata, H., & Takemura, M. (2019) · Journal of Virology · doi:10.1128/jvi.02130-18 · Cited by 166 · see citing works
The evolution of large DNA viruses: combining genomic information of viruses and their hosts
Shackelton, L. A., & Holmes, E. C. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.08.005 · Cited by 149 · see citing works
The hybrid nature of the Eukaryota and a consilient view of life on Earth
McInerney, J. O., O’Connell, M. J., & Pisani, D. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3271 · Cited by 138 · see citing works
Nitschke, W., & Russell, M. J. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9289-3 · Cited by 132 · see citing works
Phylogenomics of type II DNA topoisomerases
Gadelle, D., Filée, J., Buhler, C., & Forterre, P. (2003) · BioEssays · doi:10.1002/bies.10245 · Cited by 126 · see citing works
Self-citationForterre, P., & Prangishvili, D. A. (2009) · Research in Microbiology · doi:10.1016/j.resmic.2009.07.008 · Cited by 124 · see citing works
Self-citationOn the Origin of Cells and Viruses
Koonin, E. V. (2009) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2009.04992.x · Cited by 122 · see citing works
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
Forterre, P. (2013) · Archaea · doi:10.1155/2013/372396 · Cited by 112 · see citing works
Self-citationManipulation of cellular syntheses and the nature of viruses: The virocell concept
Forterre, P. (2010) · Comptes Rendus Chimie · doi:10.1016/j.crci.2010.06.007 · Cited by 111 · see citing works
Self-citationThe Universal Ancestor and the Ancestor of Bacteria Were Hyperthermophiles
Giulio, M. D. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2522-6 · Cited by 110 · see citing works
Structure of a bifunctional DNA primase-polymerase
Lipps, G., Weinzierl, A. O., von Scheven, G., Buchen, C., & Cramer, P. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb723 · Cited by 109 · see citing works
The major role of viruses in cellular evolution: facts and hypotheses
Forterre, P., & Prangishvili, D. A. (2013) · Current Opinion in Virology · doi:10.1016/j.coviro.2013.06.013 · Cited by 101 · see citing works
Self-citationForterre, P. (2016) · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences · doi:10.1016/j.shpsc.2016.02.013 · Cited by 99 · see citing works
Self-citationKoonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-15 · Cited by 97 · see citing works
Comparative genomics of Archaea: how much have we learned in six years, and what's next?
Makarova, K. S., & Koonin, E. V. (2003) · Genome biology · doi:10.1186/gb-2003-4-8-115 · Cited by 94 · see citing works
The not so universal tree of life or the place of viruses in the living world
Brüssow, H. (2009) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0036 · Cited by 90 · see citing works
Evolutionary analyses of non-genealogical bonds produced by introgressive descent
Bapteste, E. P., Lopez, P., Bouchard, F., Baquero, F., McInerney, J. O., & Burian, R. M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1206541109 · Cited by 87 · see citing works
Archaeology of Eukaryotic DNA Replication
Makarova, K. S., & Koonin, E. V. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012963 · Cited by 87 · see citing works
Moreira, D., & López‐García, P. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0327 · Cited by 86 · see citing works
Diversity and evolution of B-family DNA polymerases
Kazlauskas, D., Krupovìč, M., Guglielmini, J., Forterre, P., & Venclovas, Č. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa760 · Cited by 85 · see citing works
Self-citationCamprubí, E., de Leeuw, J. W., House, C. H., Raulin, F., Russell, M. J., Spang, A., Tirumalai, M. R., & Westall, F. (2019) · Space Science Reviews · doi:10.1007/s11214-019-0624-8 · Cited by 84 · see citing works
The Last Common Ancestor: What's in a name?
Delaye, L., Becerra, A., & Lazcano, A. (2005) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-005-5760-3 · Cited by 83 · see citing works
Poole, A. M., & Logan, D. T. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi132 · Cited by 82 · see citing works
The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism
Goldman, A. D., Beatty, J. T., & Landweber, L. F. (2016) · Journal of Molecular Evolution · doi:10.1007/s00239-015-9722-8 · Cited by 81 · see citing works
Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Kottur, J., & Nair, D. T. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky402 · Cited by 78 · see citing works
Biocommunication and natural genome editing
Witzany, G. (2010) · World Journal of Biological Chemistry · doi:10.4331/wjbc.v1.i11.348 · Cited by 75 · see citing works
Viruses and cells intertwined since the dawn of evolution
Durzyńska, J., & Goździcka‐Józefiak, A. (2015) · Virology Journal · doi:10.1186/s12985-015-0400-7 · Cited by 75 · see citing works
Mekuchi, M., Asakura, T., Sakata, K., Yamaguchi, T., Teruya, K., & Kikuchi, J. (2018) · PLoS ONE · doi:10.1371/journal.pone.0197256 · Cited by 73 · see citing works
Giraldo, R., & Fernández-Tresguerres, M. E. (2004) · Plasmid · doi:10.1016/j.plasmid.2004.06.002 · Cited by 72 · see citing works
Evolution of Tertiary Structure of Viral RNA Dependent Polymerases
Černý, J., Bolfíková, B. Č., Valdés, J. J., Grubhoffer, L., & Růžek, D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096070 · Cited by 71 · see citing works
Cellular domains and viral lineages
Forterre, P., Krupovìč, M., & Prangishvili, D. A. (2014) · Trends in Microbiology · doi:10.1016/j.tim.2014.07.004 · Cited by 70 · see citing works
Self-citationLee, J., Park, S., Hahm, K., & Park, Y. (2013) · Biomaterials · doi:10.1016/j.biomaterials.2013.10.035 · Cited by 70 · see citing works
RNA oligomerization in laboratory analogues of alkaline hydrothermal vent systems
Burcar, B. T., Barge, L. M., Trail, D., Watson, E. B., Russell, M. J., & McGown, L. B. (2015) · Astrobiology · doi:10.1089/ast.2014.1280 · Cited by 68 · see citing works
The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor
Catchpole, R. J., & Forterre, P. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz180 · Cited by 66 · see citing works
Self-citationPlasmids, viruses and virus-like membrane vesicles from Thermococcales
Soler, N., Gaudin, M., Marguet, E., & Forterre, P. (2011) · Biochemical Society Transactions · doi:10.1042/bst0390036 · Cited by 63 · see citing works
Self-citationArchaea Carotenoids: Natural Pigments with Unexplored Innovative Potential
Grivard, A., Goubet, I., Filho, L. A. M. D. S. D., Thiéry, V., Chevalier, S., Júnior, R. G. D. O., Aouad, N. E., Almeida, J. R. G. D. S., Sitarek, P., Quintans‐Júnior, L. J., et al. (2022) · Marine Drugs · doi:10.3390/md20080524 · Cited by 61 · see citing works
Gregory, T. R. (2005) · Elsevier eBooks · doi:10.1016/b978-012301463-4/50013-9 · Cited by 60 · see citing works
Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-39 · Cited by 59 · see citing works
LUCApedia: a database for the study of ancient life
Goldman, A. D., Bernhard, T. M., Dolzhenko, E., & Landweber, L. F. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1217 · Cited by 58 · see citing works
The distribution and impact of viral lineages in domains of life
Nasir, A., Forterre, P., Kim, K. M., & Caetano-Anollés, G. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00194 · Cited by 58 · see citing works
Self-citationSoler, N., Marguet, E., Cortez, D., Desnoues, N., Keller, J., TILBEURGH, H. V., Sezonov, G., & Forterre, P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq236 · Cited by 57 · see citing works
Self-citationAutomated Structural Comparisons Clarify the Phylogeny of the Right-Hand-Shaped Polymerases
Mönttinen, H. A. M., Ravantti, J., Stuart, D. I., & Poranen, M. M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu219 · Cited by 55 · see citing works
The origin of modern terrestrial life
Forterre, P., & Gribaldo, S. (2007) · HFSP journal · doi:10.2976/1.2759103 · Cited by 54 · see citing works
Self-citationInnovation in gene regulation: The case of chromatin computation
Prohaska, S. J., Stadler, P. F., & Krakauer, D. C. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.03.011 · Cited by 54 · see citing works
Evidence for a Xer/dif System for Chromosome Resolution in Archaea
Cortez, D., Quevillon‐Chéruel, S., Gribaldo, S., Desnoues, N., Sezonov, G., Forterre, P., & Serre, M.-C. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001166 · Cited by 53 · see citing works
Self-citationThe ancestor of the Bacteria domain was a hyperthermophile
Giulio, M. D. (2003) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(03)00164-4 · Cited by 52 · see citing works
A consensus view of the proteome of the last universal common ancestor
Crapitto, A. J., Campbell, A. E., Harris, A., & Goldman, A. D. (2022) · Ecology and Evolution · doi:10.1002/ece3.8930 · Cited by 50 · see citing works
Sun, F.-J., & Caetano‐Anollés, G. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000018 · Cited by 50 · see citing works
Montalvão, M. F., Sampaio, L. L. G., Gomes, H. H. F., & Malafaia, G. (2018) · Environmental Science and Pollution Research · doi:10.1007/s11356-018-3731-2 · Cited by 48 · see citing works
Origin and Evolution of DNA and DNA Replication Machineries
Forterre, P., Filée, J., & Myllykallio, H. (2007) · Springer eBooks · doi:10.1007/0-387-26887-1_10 · Cited by 47 · see citing works
Self-citationHydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage
Liu, Z.-X., Zhang, S., Zhu, H.-Z., Chen, Z.-H., Yang, Y., Li, L.-Q., Lei, Y., Liu, Y., Li, D., Sun, A., et al. (2024) · Science · doi:10.1126/science.adh4859 · Cited by 46 · see citing works
Why Are There So Many Diverse Replication Machineries?
Forterre, P. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.09.032 · Cited by 46 · see citing works
Self-citationLuca : À la recherche du plus proche ancêtre commun universel
Forterre, P., Gribaldo, S., & Brochier‐Armanet, C. (2005) · médecine/sciences · doi:10.1051/medsci/20052110860 · Cited by 46 · see citing works
Self-citationAstrovirology: Viruses at Large in the Universe
Berliner, A. J., Mochizuki, T., & Stedman, K. M. (2018) · Astrobiology · doi:10.1089/ast.2017.1649 · Cited by 45 · see citing works
Noncoding RNAs: Persistent Viral Agents as Modular Tools for Cellular Needs
Witzany, G. (2009) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2009.04989.x · Cited by 45 · see citing works
Merhej, V., & Raoult, D. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00113 · Cited by 42 · see citing works
Gadelle, D., Krupovìč, M., Raymann, K., Mayer, C., & Forterre, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku568 · Cited by 40 · see citing works
Self-citationNatural Genome-Editing Competences of Viruses
Witzany, G. (2006) · Acta Biotheoretica · doi:10.1007/s10441-006-9000-7 · Cited by 39 · see citing works
The Origin of Virions and Virocells: The Escape Hypothesis Revisited
Forterre, P., & Krupovìč, M. (2012) · Springer eBooks · doi:10.1007/978-94-007-4899-6_3 · Cited by 38 · see citing works
Self-citationEgel, R., & Penny, D. (2007) · Genome dynamics and stability · doi:10.1007/7050_2007_036 · Cited by 38 · see citing works
Witzany, G. (2008) · Biosemiotics · doi:10.1007/s12304-008-9018-0 · Cited by 38 · see citing works
Steps Towards the Formation of A Protocell: The Possible Role of Short Peptides
Fishkis, M. (2007) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-007-9111-4 · Cited by 38 · see citing works
Untangling the origin of viruses and their impact on cellular evolution
Nasir, A., Sun, F., Kim, K. M., & Caetano‐Anollés, G. (2015) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12735 · Cited by 37 · see citing works
DNA polymerase IV - DNA ternary complex 14
Kottur, J., & Nair, D. T. (2017) · Worldwide Protein Data Bank · doi:10.2210/pdb5yv2/pdb · Cited by 35 · see citing works
Gull, M., Tian, G., Wang, Y., He, C., Shi, Z., Yuan, H., & Feng, S. (2010) · Heteroatom Chemistry · doi:10.1002/hc.20591 · Cited by 34 · see citing works
Darwin's goldmine is still open: variation and selection run the world
Forterre, P. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00106 · Cited by 33 · see citing works
Self-citationForterre, P., Krupovìč, M., Raymann, K., & Soler, N. (2014) · Microbiology Spectrum · doi:10.1128/microbiolspec.plas-0027-2014 · Cited by 30 · see citing works
Self-citationDeep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers
Zhu, B., Wang, L., Mitsunobu, H., Lu, X., Hernandez, A. J., Yoshida‐Takashima, Y., Nunoura, T., Tabor, S., & Richardson, C. C. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700280114 · Cited by 30 · see citing works
An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes
Stern, A., Mayrose, I., Penn, O., Shaul, S., Gophna, U., & Pupko, T. (2010) · Systematic Biology · doi:10.1093/sysbio/syp104 · Cited by 30 · see citing works
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life
Valas, R. E., & Bourne, P. E. (2009) · Biology Direct · doi:10.1186/1745-6150-4-30 · Cited by 28 · see citing works
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA
Forterre, P. (2024) · Journal of Molecular Evolution · doi:10.1007/s00239-024-10186-9 · Cited by 26 · see citing works
Self-citationViral origin of eukaryotic type IIA DNA topoisomerases
Guglielmini, J., Gaïa, M., Cunha, V. D., Criscuolo, A., Krupovìč, M., & Forterre, P. (2022) · Virus Evolution · doi:10.1093/ve/veac097 · Cited by 26 · see citing works
Self-citationThe Case for an Early Biological Origin of DNA
Poole, A. M., Horinouchi, N., Catchpole, R. J., Si, D., Hibi, M., Tanaka, K., & Ogawa, J. (2014) · Journal of Molecular Evolution · doi:10.1007/s00239-014-9656-6 · Cited by 26 · see citing works
Restriction–Modification Systems as a Barrier for Genetic Manipulation of Staphylococcus aureus
Sadykov, M. R. (2014) · Methods in molecular biology · doi:10.1007/7651_2014_180 · Cited by 26 · see citing works
In Situ Imidazole Activation of Ribonucleotides for Abiotic RNA Oligomerization Reactions
Burcar, B. T., Jawed, M., Shah, H., & McGown, L. B. (2015) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-015-9412-y · Cited by 26 · see citing works
Glacial Periods on Early Earth and Implications for the Evolution of Life
Vincent, W. F., Mueller, D., Van Hove, P., & Howard-Williams, C. (2004) · Cellular Origin, Life in Extreme Habitats and Astrobiology · doi:10.1007/1-4020-2522-x_29 · Cited by 25 · see citing works
How Viruses Shape the Tree of Life
Villarreal, L. P. (2006) · Future Virology · doi:10.2217/17460794.1.5.587 · Cited by 25 · see citing works
Mechanisms for RNA Capture by ssDNA Viruses: Grand Theft RNA
Stedman, K. M. (2013) · Journal of Molecular Evolution · doi:10.1007/s00239-013-9569-9 · Cited by 24 · see citing works
- Authors
- Forterre, P.
- Affiliations
- Université Paris-Sud (FR)
- Corresponding author
- Forterre, P
- ORCID
- Forterre, P
- Venue
- Current Opinion in Microbiology
- Publisher
- Elsevier BV
- Published
- 2002-10-01
- Volume
- 5
- Issue
- 5
- Pages
- 525-532
- ISSN
- 1369-5274 (ISSN-L)
- OpenAlex
- W1998172162
- Cited by
- 190
- References
- 46
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 4 · 2023: 6 · 2022: 5 · 2021: 5 · 2020: 6 · 2019: 4 · 2018: 9 · 2017: 4 · 2016: 5 · 2015: 10 · 2014: 13 · 2013: 11 · 2012: 11
- FWCI
- 5.07
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Current Opinion in Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- DNA replication proteins, RNA to DNA transition, DNA viruses, last universal common ancestor
- MeSH terms
- DNA, DNA Replication, Biological Evolution, Models, Genetic, Proteins, RNA, Selection, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review