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For: Cavalier-Smith T. Rooting the tree of life by transition analyses. Biol Direct 2006;1:19. [PMID: 16834776 PMCID: PMC1586193 DOI: 10.1186/1745-6150-1-19] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 07/11/2006] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
101
Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010;5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022]  Open
102
Cavalier-Smith T. Deep phylogeny, ancestral groups and the four ages of life. Philos Trans R Soc Lond B Biol Sci 2010;365:111-32. [PMID: 20008390 PMCID: PMC2842702 DOI: 10.1098/rstb.2009.0161] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
103
A modular BAM complex in the outer membrane of the alpha-proteobacterium Caulobacter crescentus. PLoS One 2010;5:e8619. [PMID: 20062535 PMCID: PMC2797634 DOI: 10.1371/journal.pone.0008619] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 12/11/2009] [Indexed: 11/19/2022]  Open
104
Bodył A, Mackiewicz P, Stiller JW. Early steps in plastid evolution: current ideas and controversies. Bioessays 2009;31:1219-32. [DOI: 10.1002/bies.200900073] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
105
Avonce N, Wuyts J, Verschooten K, Vandesteene L, Van Dijck P. The Cytophaga hutchinsonii ChTPSP: First Characterized Bifunctional TPS–TPP Protein as Putative Ancestor of All Eukaryotic Trehalose Biosynthesis Proteins. Mol Biol Evol 2009;27:359-69. [DOI: 10.1093/molbev/msp241] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
106
Foster PG, Cox CJ, Embley TM. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philos Trans R Soc Lond B Biol Sci 2009;364:2197-207. [PMID: 19571240 DOI: 10.1098/rstb.2009.0034] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
107
Lake JA, Skophammer RG, Herbold CW, Servin JA. Genome beginnings: rooting the tree of life. Philos Trans R Soc Lond B Biol Sci 2009;364:2177-85. [PMID: 19571238 DOI: 10.1098/rstb.2009.0035] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
108
Bradley RK, Holmes I. Evolutionary triplet models of structured RNA. PLoS Comput Biol 2009;5:e1000483. [PMID: 19714212 PMCID: PMC2725318 DOI: 10.1371/journal.pcbi.1000483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 07/23/2009] [Indexed: 12/31/2022]  Open
109
Valas RE, Bourne PE. Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct 2009;4:30. [PMID: 19706177 PMCID: PMC3224940 DOI: 10.1186/1745-6150-4-30] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 08/25/2009] [Indexed: 11/18/2022]  Open
110
Mulkidjanian AY, Galperin MY. On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biol Direct 2009;4:27. [PMID: 19703275 PMCID: PMC2749021 DOI: 10.1186/1745-6150-4-27] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 08/24/2009] [Indexed: 11/28/2022]  Open
111
Thomas H, Huang L, Young M, Ougham H. Evolution of plant senescence. BMC Evol Biol 2009;9:163. [PMID: 19602260 PMCID: PMC2716323 DOI: 10.1186/1471-2148-9-163] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 07/14/2009] [Indexed: 01/07/2023]  Open
112
Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A. Initial implementation of a comparative data analysis ontology. Evol Bioinform Online 2009;5:47-66. [PMID: 19812726 PMCID: PMC2747124 DOI: 10.4137/ebo.s2320] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
113
Phylogenetic ubiquity and shuffling of the bacterial RecBCD and AddAB recombination complexes. J Bacteriol 2009;191:5076-84. [PMID: 19542287 DOI: 10.1128/jb.00254-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
114
Hochstrasser M. Origin and function of ubiquitin-like proteins. Nature 2009;458:422-9. [PMID: 19325621 DOI: 10.1038/nature07958] [Citation(s) in RCA: 605] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
115
Valas RE, Yang S, Bourne PE. Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol 2009;19:329-34. [PMID: 19394812 DOI: 10.1016/j.sbi.2009.03.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/19/2009] [Accepted: 03/16/2009] [Indexed: 12/27/2022]
116
Mulkidjanian AY, Galperin MY, Koonin EV. Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci 2009;34:206-15. [PMID: 19303305 DOI: 10.1016/j.tibs.2009.01.005] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 01/20/2009] [Accepted: 01/21/2009] [Indexed: 01/14/2023]
117
Forterre P, Gadelle D. Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res 2009;37:679-92. [PMID: 19208647 PMCID: PMC2647321 DOI: 10.1093/nar/gkp032] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
118
The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U S A 2008;105:20356-61. [PMID: 19073919 DOI: 10.1073/pnas.0810647105] [Citation(s) in RCA: 267] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
119
Galperin MY. Sorting out the mix in microbial genomics. Environ Microbiol 2008;10:3187-92. [PMID: 19025554 PMCID: PMC2702502 DOI: 10.1111/j.1462-2920.2008.01811.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
120
Lake JA, Servin JA, Herbold CW, Skophammer RG. Evidence for a New Root of the Tree of Life. Syst Biol 2008;57:835-43. [DOI: 10.1080/10635150802555933] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
121
Gatsos X, Perry AJ, Anwari K, Dolezal P, Wolynec PP, Likić VA, Purcell AW, Buchanan SK, Lithgow T. Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev 2008;32:995-1009. [PMID: 18759741 PMCID: PMC2635482 DOI: 10.1111/j.1574-6976.2008.00130.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/23/2008] [Accepted: 07/18/2008] [Indexed: 11/17/2022]  Open
122
Cavalier-Smith T. Predation and eukaryote cell origins: a coevolutionary perspective. Int J Biochem Cell Biol 2008;41:307-22. [PMID: 18935970 DOI: 10.1016/j.biocel.2008.10.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 10/06/2008] [Accepted: 10/08/2008] [Indexed: 12/23/2022]
123
Macroamphiphilic components of thermophilic actinomycetes: identification of lipoteichoic acid in Thermobifida fusca. J Bacteriol 2008;191:152-60. [PMID: 18931132 DOI: 10.1128/jb.01105-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
124
Boussau B, Guéguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol 2008;8:272. [PMID: 18834516 PMCID: PMC2584045 DOI: 10.1186/1471-2148-8-272] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 10/03/2008] [Indexed: 01/09/2023]  Open
125
Glansdorff N, Xu Y, Labedan B. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct 2008;3:29. [PMID: 18613974 PMCID: PMC2478661 DOI: 10.1186/1745-6150-3-29] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 07/09/2008] [Indexed: 11/10/2022]  Open
126
Tuon FF, Neto VA, Amato VS. Leishmania: origin, evolution and future since the Precambrian. ACTA ACUST UNITED AC 2008;54:158-66. [PMID: 18631183 DOI: 10.1111/j.1574-695x.2008.00455.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
127
Valas RE, Bourne PE. Rethinking proteasome evolution: two novel bacterial proteasomes. J Mol Evol 2008;66:494-504. [PMID: 18389302 PMCID: PMC3235984 DOI: 10.1007/s00239-008-9075-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 01/23/2008] [Accepted: 01/25/2008] [Indexed: 12/22/2022]
128
Vesteg M, Krajcovic J. Origin of eukaryotic cells as a symbiosis of parasitic alpha-proteobacteria in the periplasm of two-membrane-bounded sexual pre-karyotes. Commun Integr Biol 2008;1:104-13. [PMID: 19513207 PMCID: PMC2633810 DOI: 10.4161/cib.1.1.6349] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 05/29/2008] [Indexed: 11/19/2022]  Open
129
Poole AM, Willerslev E. Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars? ASTROBIOLOGY 2007;7:801-814. [PMID: 17963478 DOI: 10.1089/ast.2006.0094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
130
Wong JTF, Chen J, Mat WK, Ng SK, Xue H. Polyphasic evidence delineating the root of life and roots of biological domains. Gene 2007;403:39-52. [PMID: 17884304 DOI: 10.1016/j.gene.2007.07.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2007] [Revised: 07/22/2007] [Accepted: 07/23/2007] [Indexed: 12/29/2022]
131
Fondi M, Brilli M, Emiliani G, Paffetti D, Fani R. The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. BMC Evol Biol 2007;7 Suppl 2:S3. [PMID: 17767731 PMCID: PMC1963480 DOI: 10.1186/1471-2148-7-s2-s3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
132
Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME JOURNAL 2007;1:419-35. [DOI: 10.1038/ismej.2007.63] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
133
Davidov Y, Jurkevitch E. Comments of Poole and Penny's essay "Evaluating hypotheses for the origin of eukaryotes", BioEssays 29:74-84. Bioessays 2007;29:615-6. [PMID: 17508407 DOI: 10.1002/bies.20587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
134
Lee J, Michael AJ, Martynowski D, Goldsmith EJ, Phillips MA. Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases. J Biol Chem 2007;282:27115-27125. [PMID: 17626020 DOI: 10.1074/jbc.m704066200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
135
De Mot R. Actinomycete-like proteasomes in a Gram-negative bacterium. Trends Microbiol 2007;15:335-8. [PMID: 17587582 DOI: 10.1016/j.tim.2007.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 05/22/2007] [Accepted: 06/11/2007] [Indexed: 12/23/2022]
136
Zhou Y, Landweber LF. BLASTO: a tool for searching orthologous groups. Nucleic Acids Res 2007;35:W678-82. [PMID: 17483516 PMCID: PMC1933156 DOI: 10.1093/nar/gkm278] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
137
Sghaier H, Narumi I, Satoh K, Ohba H, Mitomo H. Problems with the current deinococcal hypothesis: an alternative theory. Theory Biosci 2007;126:43-5. [DOI: 10.1007/s12064-007-0004-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 03/06/2007] [Indexed: 01/08/2023]
138
Doolittle WF, Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci U S A 2007;104:2043-9. [PMID: 17261804 PMCID: PMC1892968 DOI: 10.1073/pnas.0610699104] [Citation(s) in RCA: 366] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2006] [Indexed: 11/18/2022]  Open
139
Jékely G. Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms. Biol Direct 2007;2:3. [PMID: 17239231 PMCID: PMC1794243 DOI: 10.1186/1745-6150-2-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 01/19/2007] [Indexed: 12/28/2022]  Open
140
Forterre P, Gribaldo S, Gadelle D, Serre MC. Origin and evolution of DNA topoisomerases. Biochimie 2007;89:427-46. [PMID: 17293019 DOI: 10.1016/j.biochi.2006.12.009] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 12/12/2006] [Indexed: 12/28/2022]
141
Jékely G. Did the last common ancestor have a biological membrane? Biol Direct 2006;1:35. [PMID: 17129384 PMCID: PMC1675992 DOI: 10.1186/1745-6150-1-35] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Accepted: 11/27/2006] [Indexed: 12/24/2022]  Open
142
Bredemeier R, Schlegel T, Ertel F, Vojta A, Borissenko L, Bohnsack MT, Groll M, von Haeseler A, Schleiff E. Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family. J Biol Chem 2006;282:1882-90. [PMID: 17088246 DOI: 10.1074/jbc.m609598200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
143
Cavalier-Smith T. Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 2006;361:969-1006. [PMID: 16754610 PMCID: PMC1578732 DOI: 10.1098/rstb.2006.1842] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
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