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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.
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“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
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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 2,804
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
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
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
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
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 496
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
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
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
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
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
A non-hyperthermophilic ancestor for Bacteria
Brochier‐Armanet, C., & Philippe, H. (2002) · Nature · doi:10.1038/417244a · Cited by 254
Filée, J., Forterre, P., Sen-Lin, T., & Laurent, J. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0078-x · Cited by 247
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
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 244
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
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
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
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
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
Self-citationPoxviruses and the Origin of the Eukaryotic Nucleus
Takemura, M. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010171 · Cited by 165
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
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
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
Arezi, B., & Kuchta, R. D. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01680-7 · Cited by 137
Matsunaga, F., Forterre, P., Ishino, Y., & Myllykallio, H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191387498 · Cited by 135
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
DNA stability at temperatures typical for hyperthermophiles
Marguet, E., & Forterre, P. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.9.1681 · Cited by 129
Self-citationForterre, P. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01497.x · Cited by 128
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
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
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 116
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
Freeland, S. J., Knight, R. D., & Landweber, L. F. (1999) · Science · doi:10.1126/science.286.5440.690 · Cited by 99
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
Pyrococcus genome comparison evidences chromosome shuffling-driven evolution
Zivanovic, Y. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.9.1902 · Cited by 85
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 82
Chromosomal elements conferring epigenetic inheritance
Lyko, F., & Paro, R. (1999) · BioEssays · doi:10.1002/(sici)1521-1878(199910)21:10 · Cited by 79
Self-citationHost 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
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
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 68
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
Balter, M. (2000) · Science · doi:10.1126/science.289.5486.1866 · Cited by 59
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
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
Moreira, D. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01692.x · Cited by 51
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Metadata
- 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
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