The origin of a derived superkingdom: How a gram-positive bacterium crossed the desert to become an archaeon

Biology Direct

Volumn 6, Issue , 2011, Pages

  Valas, Ruben E ^a   Bourne, Philip E ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOBACTERIA; ARCHAEA; BACILLI (CLASS); BACTERIA (MICROORGANISMS); POSIBACTERIA; PROKARYOTA;

ARCHAEBACTERIUM; ARTICLE; CLASSIFICATION; EVOLUTION; GENETICS; GRAM POSITIVE BACTERIUM; PHYLOGENY;

ARCHAEA; BIOLOGICAL EVOLUTION; GRAM-POSITIVE BACTERIA; PHYLOGENY;

EID: 79952059449     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-6-16     Document Type: Article

References (131)

1. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977, 74:5088-5090. 10.1073/pnas.74.11.5088, 432104, 270744.
2. Lecompte O, Ripp R, Thierry JC, Moras D, Poch O. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 2002, 30:5382-5390. 10.1093/nar/gkf693, 140077, 12490706.
3. De Rosa M, Gambacorta A, Gliozzi A. Structure, biosynthesis, and physicochemical properties of archaebacterial lipids. Microbiol Rev 1986, 50:70-80. 373054, 3083222.
4. Leipe DD, Aravind L, Koonin EV. Did DNA replication evolve twice independently?. Nucleic Acids Res 1999, 27:3389-3401. 10.1093/nar/27.17.3389, 148579, 10446225.
5. Woese CR. The Archaeal Concept and the World it Lives in: A Retrospective. Photosynth Res 2004, 80:361-372. 10.1023/B:PRES.0000030445.04503.e6, 16328833.
6. Koonin EV, Martin W. On the origin of genomes and cells within inorganic compartments. Trends Genet 2005, 21:647-654. 10.1016/j.tig.2005.09.006, 16223546.
7. Battistuzzi FU, Hedges SB. A major clade of prokaryotes with ancient adaptations to life on land. Mol Biol Evol 2009, 26:335-343. 10.1093/molbev/msn247, 18988685.
8. Cavalier-Smith T. Rooting the tree of life by transition analyses. Biol Direct 2006, 1:19. 10.1186/1745-6150-1-19, 1586193, 16834776.
9. Gupta RS. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 1998, 62:1435-1491. 98952, 9841678.
10. Lake JA, Servin JA, Herbold CW, Skophammer RG. Evidence for a new root of the tree of life. Syst Biol 2008, 57:835-843. 10.1080/10635150802555933, 19085327.
11. 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. 10.1186/1745-6150-4-30, 19706177.
12. Skophammer RG, Servin JA, Herbold CW, Lake JA. Evidence for a gram-positive, eubacterial root of the tree of life. Mol Biol Evol 2007, 24:1761-1768. 10.1093/molbev/msm096, 17513883.
13. Lake JA, Henderson E, Oakes M, Clark MW. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc Natl Acad Sci USA 1984, 81:3786-3790. 10.1073/pnas.81.12.3786, 345305, 6587394.
14. Rivera MC, Lake JA. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 1992, 257:74-76. 10.1126/science.1621096, 1621096.
15. Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 2002, 52:297-354.
16. Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 2002, 52:7-76.
17. Forterre P. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc Natl Acad Sci USA 2006, 103:3669-3674. 10.1073/pnas.0510333103, 1450140, 16505372.
18. Forterre P. The origin of viruses and their possible roles in major evolutionary transitions. Virus Res 2006, 117:5-16. 10.1016/j.virusres.2006.01.010, 16476498.
19. Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol Direct 2006, 1:29. 10.1186/1745-6150-1-29, 1594570, 16984643.
20. McGeoch AT, Bell SD. Extra-chromosomal elements and the evolution of cellular DNA replication machineries. Nat Rev Mol Cell Biol 2008, 9:569-574. 10.1038/nrm2426, 18523437.
21. Boucher Y, Kamekura M, Doolittle WF. Origins and evolution of isoprenoid lipid biosynthesis in archaea. Mol Microbiol 2004, 52:515-527. 10.1111/j.1365-2958.2004.03992.x, 15066037.
22. Wong JT, 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. 10.1016/j.gene.2007.07.032, 17884304.
23. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Mol Biosyst 2009, 5:1636-1660. 10.1039/b917682a, 20023723.
24. Valas RE, Bourne PE. Rethinking proteasome evolution: two novel bacterial proteasomes. J Mol Evol 2008, 66:494-504. 10.1007/s00239-008-9075-7, 18389302.
25. Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA. Evidence that the root of the tree of life is not within the Archaea. Mol Biol Evol 2006, 23:1648-1651. 10.1093/molbev/msl046, 16801395.
26. Klein DJ, Moore PB, Steitz TA. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J Mol Biol 2004, 340:141-177. 10.1016/j.jmb.2004.03.076, 15184028.
27. Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 2001, 107:679-688. 10.1016/S0092-8674(01)00546-3, 11733066.
28. O'Brien TW. Properties of human mitochondrial ribosomes. IUBMB Life 2003, 55:505-513.
29. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311:1283-1287. 10.1126/science.1123061, 16513982.
30. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci USA 2008, 105:20356-20361. 10.1073/pnas.0810647105, 2629343, 19073919.
31. Zhang R, Ou HY, Zhang CT. DEG: a database of essential genes. Nucleic Acids Res 2004, 32:D271-272. 10.1093/nar/gkh024, 308758, 14681410.
32. Fang G, Rocha E, Danchin A. How essential are nonessential genes?. Mol Biol Evol 2005, 22:2147-2156. 10.1093/molbev/msi211, 16014871.
33. Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008, 134:341-352. 10.1016/j.cell.2008.05.042, 2696314, 18662548.
34. Sutter M, Striebel F, Damberger FF, Allain FH, Weber-Ban E. A distinct structural region of the prokaryotic ubiquitin-like protein (Pup) is recognized by the N-terminal domain of the proteasomal ATPase Mpa. FEBS Lett 2009, 583:3151-3157. 10.1016/j.febslet.2009.09.020, 19761766.
35. Makarova KS, Ponomarev VA, Koonin EV. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol 2001, 2:RESEARCH 0033. 56895, 11574053.
36. Dupont CL, Yang S, Palenik B, Bourne PE. Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci USA 2006, 103:17822-17827. 10.1073/pnas.0605798103, 1635651, 17098870.
37. Dupont CL, Butcher A, Valas RE, Bourne PE, Caetano-Anolles G. History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci USA 2010, 107:10567-10572. 10.1073/pnas.0912491107, 2890839, 20498051.
38. Filee J, Forterre P, Sen-Lin T, Laurent J. Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol 2002, 54:763-773. 10.1007/s00239-001-0078-x, 12029358.
39. Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV. Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol Direct 2009, 4:11. 10.1186/1745-6150-4-11, 2669801, 19296856.
40. Koonin EV, Wolf YI, Kondrashov AS, Aravind L. Bacterial homologs of the small subunit of eukaryotic DNA primase. J Mol Microbiol Biotechnol 2000, 2:509-512.
41. Della M, Palmbos PL, Tseng HM, Tonkin LM, Daley JM, Topper LM, Pitcher RS, Tomkinson AE, Wilson TE, Doherty AJ. Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science 2004, 306:683-685. 10.1126/science.1099824, 15499016.
42. Yutin N, Koonin EV. Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity. Biol Direct 2009, 4:51. 10.1186/1745-6150-4-51, 2806865, 20021668.
43. Samuels M, Gulati G, Shin JH, Opara R, McSweeney E, Sekedat M, Long S, Kelman Z, Jeruzalmi D. A biochemically active MCM-like helicase in Bacillus cereus. Nucleic Acids Res 2009, 37:4441-4452. 10.1093/nar/gkp376, 2715239, 19474351.
44. Ammelburg M, Frickey T, Lupas AN. Classification of AAA+ proteins. J Struct Biol 2006, 156:2-11.
45. Chen YJ, Yu X, Egelman EH. The hexameric ring structure of the Escherichia coli RuvB branch migration protein. J Mol Biol 2002, 319:587-591. 10.1016/S0022-2836(02)00353-4, 12054856.
46. Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y. A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. Proc Natl Acad Sci USA 1999, 96:8873-8878. 10.1073/pnas.96.16.8873, 17700, 10430863.
47. Forterre P, Gribaldo S, Gadelle D, Serre MC. Origin and evolution of DNA topoisomerases. Biochimie 2007, 89:427-446. 10.1016/j.biochi.2006.12.009, 17293019.
48. Forterre P, Gadelle D. Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res 2009, 37:679-692. 10.1093/nar/gkp032, 2647321, 19208647.
49. Becerra A, Delaye L, Islas S, Lazcano A. The Very Early Stages of Biological Evolution and the Nature of the Last Common Ancestor of the Three Major Cell Domains. Annual Review of Ecology, Evolution, and Systematics 2007, 38:361-379.
50. Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV. The deep archaeal roots of eukaryotes. Mol Biol Evol 2008, 25:1619-1630. 10.1093/molbev/msn108, 2464739, 18463089.
51. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 2008, 6:245-252. 10.1038/nrmicro1852, 18274537.
52. Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci USA 2008, 105:8102-8107. 10.1073/pnas.0801980105, 2430366, 18535141.
53. Martin W, Muller M. The hydrogen hypothesis for the first eukaryote. Nature 1998, 392:37-41. 10.1038/32096, 9510246.
54. Ettema TJ, Bernander R. Cell division and the ESCRT complex: A surprise from the archaea. Commun Integr Biol 2009, 2:86-88. 2686351, 19704896.
55. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
56. Schmitt E, Panvert M, Blanquet S, Mechulam Y. Structural basis for tRNA-dependent amidotransferase function. Structure 2005, 13:1421-1433. 10.1016/j.str.2005.06.016, 16216574.
57. Schwartz JH, Reeves JY, Broome JD. Two L-asparaginases from E. coli and their action against tumors. Proc Natl Acad Sci USA 1966, 56:1516-1519. 10.1073/pnas.56.5.1516, 220017, 5339624.
58. Poole AM, Penny D. Evaluating hypotheses for the origin of eukaryotes. Bioessays 2007, 29:74-84. 10.1002/bies.20516, 17187354.
59. Hou S, Makarova KS, Saw JH, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, et al. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 2008, 3:26. 10.1186/1745-6150-3-26, 2474590, 18593465.
60. De Mot R. Actinomycete-like proteasomes in a Gram-negative bacterium. Trends Microbiol 2007, 15:335-338. 10.1016/j.tim.2007.06.002, 17587582.
61. Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, et al. The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res 2009, 37:D216-223. 10.1093/nar/gkn734, 2686591, 18940865.
62. Wilson D, Madera M, Vogel C, Chothia C, Gough J. The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res 2007, 35:D308-313. 10.1093/nar/gkl910, 1669749, 17098927.
63. Nes WR, Nes WD. Lipids in evolution 1980, New York: Plenum Press.
64. Lamb DC, Kelly DE, Manning NJ, Kelly SL. A sterol biosynthetic pathway in Mycobacterium. FEBS Lett 1998, 437:142-144. 10.1016/S0014-5793(98)01218-6, 9804188.
65. Desmond E, Gribaldo S. Phylogenomics of Sterol Synthesis: Insights into the Origin, Evolution, and Diversity of a Key Eukaryotic Feature. Genome Biol Evol 2009, 2009:364-381.
66. Smucker RA. Biochemistry of the Streptomyces spore sheath. Biological, biochemical, and biomedical aspects of actinomycetes 1984, xv:643. Orlando: Academic Press, Ortiz-Ortiz L, Bojalil LF, Yakoleff V.
67. Wehenkel A, Bellinzoni M, Grana M, Duran R, Villarino A, Fernandez P, Andre-Leroux G, England P, Takiff H, Cervenansky C, et al. Mycobacterial Ser/Thr protein kinases and phosphatases: physiological roles and therapeutic potential. Biochim Biophys Acta 2008, 1784:193-202.
68. Macek B, Mijakovic I, Olsen JV, Gnad F, Kumar C, Jensen PR, Mann M. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics 2007, 6:697-707. 10.1074/mcp.M600464-MCP200, 17218307.
69. Sandoval-Calderon M, Geiger O, Guan Z, Barona-Gomez F, Sohlenkamp C. A eukaryote-like cardiolipin synthase is present in Streptomyces coelicolor and in most actinobacteria. J Biol Chem 2009, 284:17383-17390. 10.1074/jbc.M109.006072, 2719378, 19439403.
70. Da Lage JL, Feller G, Janecek S. Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the alpha-amylase model. Cell Mol Life Sci 2004, 61:97-109. 10.1007/s00018-003-3334-y, 14704857.
71. Leibundgut M, Maier T, Jenni S, Ban N. The multienzyme architecture of eukaryotic fatty acid synthases. Curr Opin Struct Biol 2008, 18:714-725. 10.1016/j.sbi.2008.09.008, 18948193.
72. Cavalier-Smith T. The origin of eukaryotic and archaebacterial cells. Ann N Y Acad Sci 1987, 503:17-54. 10.1111/j.1749-6632.1987.tb40596.x, 3113314.
73. Bell PJ. Sex and the eukaryotic cell cycle is consistent with a viral ancestry for the eukaryotic nucleus. J Theor Biol 2006, 243:54-63. 10.1016/j.jtbi.2006.05.015, 16846615.
74. Aravind L, Koonin EV. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res 2001, 11:1365-1374. 10.1101/gr.181001, 311082, 11483577.
75. Grangeasse C, Cozzone AJ, Deutscher J, Mijakovic I. Tyrosine phosphorylation: an emerging regulatory device of bacterial physiology. Trends Biochem Sci 2007, 32:86-94. 10.1016/j.tibs.2006.12.004, 17208443.
76. Kanehisa M. The KEGG database. Novartis Found Symp 2002, 247:91-101. discussion 101-103, 119-128, 244-152., full_text, 12539951.
77. Payandeh J, Pai EF. Enzyme-driven speciation: crystallizing Archaea via lipid capture. J Mol Evol 2007, 64:364-374. 10.1007/s00239-006-0141-8, 17253090.
78. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. The Pfam protein families database. Nucleic Acids Res 2008, 36:D281-288. 10.1093/nar/gkm960, 2238907, 18039703.
79. Sojka L, Fucik V, Krasny L, Barvik I, Jonak J. YbxF, a protein associated with exponential-phase ribosomes in Bacillus subtilis. J Bacteriol 2007, 189:4809-4814. 10.1128/JB.01786-06, 1913448, 17468242.
80. Stechmann A, Cavalier-Smith T. Evolutionary origins of Hsp90 chaperones and a deep paralogy in their bacterial ancestors. J Eukaryot Microbiol 2004, 51:364-373. 10.1111/j.1550-7408.2004.tb00580.x, 15218707.
81. Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010, 5:7. 10.1186/1745-6150-5-7, 2837639, 20132544.
82. van den Bosch H, Schutgens RB, Wanders RJ, Tager JM. Biochemistry of peroxisomes. Annu Rev Biochem 1992, 61:157-197. 10.1146/annurev.bi.61.070192.001105, 1353950.
83. De Duve C. Blueprint for a cell: the nature and origin of life 1991, Burlington, N.C.: N. Patterson.
84. Cavalier-Smith T. Symbiotic origin of peroxisomes. Endocytobiology IV; Paris 1990, 515-521. Institut national de la recherche agronomique, Nardon P, Gianinazzi-Pearson V, Grenier AM, Margulis L, Smith DC.
85. Gabaldon T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA. Origin and evolution of the peroxisomal proteome. Biol Direct 2006, 1:8. 10.1186/1745-6150-1-8, 1472686, 16556314.
86. Schluter A, Fourcade S, Ripp R, Mandel JL, Poch O, Pujol A. The evolutionary origin of peroxisomes: an ER-peroxisome connection. Mol Biol Evol 2006, 23:838-845. 10.1093/molbev/msj103, 16452116.
87. Gabaldon T, Huynen MA. Reconstruction of the proto-mitochondrial metabolism. Science 2003, 301:609. 10.1126/science.1085463, 12893934.
88. Duhita N, Le HA, Satoshi S, Kazuo H, Daisuke M, Takao S. The origin of peroxisomes: The possibility of an actinobacterial symbiosis. Gene 2009, 450:18-24.
89. Race HL, Herrmann RG, Martin W. Why have organelles retained genomes?. Trends Genet 1999, 15:364-370. 10.1016/S0168-9525(99)01766-7, 10461205.
90. Allen JF. Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 1993, 165:609-631. 10.1006/jtbi.1993.1210, 8114509.
91. Koonin EV. Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol Direct 2006, 1:39. 10.1186/1745-6150-1-39, 1766352, 17176463.
92. Rothschild LJ, Mancinelli RL. Life in extreme environments. Nature 2001, 409:1092-1101. 10.1038/35059215, 11234023.
93. Valentine DL. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat Rev Microbiol 2007, 5:316-323. 10.1038/nrmicro1619, 17334387.
94. Fogg MJ, Pearl LH, Connolly BA. Structural basis for uracil recognition by archaeal family B DNA polymerases. Nat Struct Biol 2002, 9:922-927. 10.1038/nsb867, 12415291.
95. Isambert H, Stein RR. On the need for widespread horizontal gene transfers under genome size constraint. Biol Direct 2009, 4:28. 10.1186/1745-6150-4-28, 2740843, 19703318.
96. Heddle JA, Bielas JH. Unifying concept of DNA repair: the polymerase scanning hypothesis. Environ Mol Mutagen 2005, 45:143-149. 10.1002/em.20112, 15672383.
97. Bielas JH. Non-transcribed strand repair revealed in quiescent cells. Mutagenesis 2006, 21:49-53. 10.1093/mutage/gei073, 16394029.
98. Bell PJ. The viral eukaryogenesis hypothesis: a key role for viruses in the emergence of eukaryotes from a prokaryotic world environment. Ann N Y Acad Sci 2009, 1178:91-105. 10.1111/j.1749-6632.2009.04994.x, 19845630.
99. Bell PJ. Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus?. J Mol Evol 2001, 53:251-256. 10.1007/s002390010215, 11523012.
100. Vermeij GJ. Evolution and escalation an ecological history of life 1987, Princeton, N.J.: Princeton University Press.
101. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008, 36:D901-906. 10.1093/nar/gkm958, 2238889, 18048412.
102. Beiko RG, Harlow TJ, Ragan MA. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 2005, 102:14332-14337. 10.1073/pnas.0504068102, 1242295, 16176988.
103. Sioud M, Possot O, Elie C, Sibold L, Forterre P. Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme. J Bacteriol 1988, 170:946-953. 210746, 2828337.
104. Jolly L, Newell J, Porcelli I, Vincent SJ, Stingele F. Lactobacillus helveticus glycosyltransferases: from genes to carbohydrate synthesis. Glycobiology 2002, 12:319-327. 10.1093/glycob/12.5.319, 12070074.
105. Hansen JL, Moore PB, Steitz TA. Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J Mol Biol 2003, 330:1061-1075. 10.1016/S0022-2836(03)00668-5, 12860128.
106. Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol Cell 2002, 10:117-128. 10.1016/S1097-2765(02)00570-1, 12150912.
107. Pfister P, Corti N, Hobbie S, Bruell C, Zarivach R, Yonath A, Bottger EC. 23S rRNA base pair 2057-2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A-->G. Proc Natl Acad Sci USA 2005, 102:5180-5185. 10.1073/pnas.0501598102, 555689, 15795375.
108. Vester B, Douthwaite S. Macrolide resistance conferred by base substitutions in 23S rRNA. Antimicrob Agents Chemother 2001, 45:1-12. 10.1128/AAC.45.1.1-12.2001, 90232, 11120937.
109. Tu D, Blaha G, Moore PB, Steitz TA. Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 2005, 121:257-270. 10.1016/j.cell.2005.02.005, 15851032.
110. Gregory ST, Cate JH, Dahlberg AE. Spontaneous erythromycin resistance mutation in a 23S rRNA gene, rrlA, of the extreme thermophile Thermus thermophilus IB-21. J Bacteriol 2001, 183:4382-4385. 10.1128/JB.183.14.4382-4385.2001, 95329, 11418580.
111. Cavalier-Smith T. Predation and eukaryote cell origins: a coevolutionary perspective. Int J Biochem Cell Biol 2009, 41:307-322. 10.1016/j.biocel.2008.10.002, 18935970.
112. Martin W, Koonin EV. Introns and the origin of nucleus-cytosol compartmentalization. Nature 2006, 440:41-45. 10.1038/nature04531, 16511485.
113. Lopez-Garcia P, Moreira D. Selective forces for the origin of the eukaryotic nucleus. Bioessays 2006, 28:525-533. 10.1002/bies.20413, 16615090.
114. Jekely G. Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell. Biol Direct 2008, 3:31. 10.1186/1745-6150-3-31, 2503971, 18652645.
115. Csuros M, Miklos I. Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol 2009, 26:2087-2095. 10.1093/molbev/msp123, 2726834, 19570746.
116. Krokan H, Wist E, Krokan RH. Aphidicolin inhibits DNA synthesis by DNA polymerase alpha and isolated nuclei by a similar mechanism. Nucleic Acids Res 1981, 9:4709-4719. 10.1093/nar/9.18.4709, 327469, 6795595.
117. Forterre P, Elie C, Kohiyama M. Aphidicolin inhibits growth and DNA synthesis in halophilic arachaebacteria. J Bacteriol 1984, 159:800-802. 215722, 6204969.
118. Anbar AD, Knoll AH. Proterozoic ocean chemistry and evolution: a bioinorganic bridge?. Science 2002, 297:1137-1142. 10.1126/science.1069651, 12183619.
119. Cavalier-Smith T. Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 2006, 361:969-1006. 10.1098/rstb.2006.1842, 1578732, 16754610.
120. Aravind L, Iyer LM, Koonin EV. Comparative genomics and structural biology of the molecular innovations of eukaryotes. Curr Opin Struct Biol 2006, 16:409-419. 10.1016/j.sbi.2006.04.006, 16679012.
121. Cavalier-Smith T. Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J Mol Evol 2001, 53:555-595. 10.1007/s002390010245, 11675615.
122. Blobel G. Intracellular protein topogenesis. Proc Natl Acad Sci USA 1980, 77:1496-1500. 10.1073/pnas.77.3.1496, 348522, 6929499.
123. Griffiths G. Cell evolution and the problem of membrane topology. Nat Rev Mol Cell Biol 2007, 8:1018-1024. 10.1038/nrm2287, 17971839.
124. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998, 11:739-747. 10.1093/protein/11.9.739, 9796821.
125. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
126. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25:1189-1191. 10.1093/bioinformatics/btp033, 2672624, 19151095.
127. Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 2009, 537:113-137. full_text, 19378142.
128. Puigbo P, Wolf YI, Koonin EV. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 2009, 8:59. 10.1186/jbiol159, 2737373, 19594957.
129. Kelman Z, White MF. Archaeal DNA replication and repair. Curr Opin Microbiol 2005, 8:669-676. 10.1016/j.mib.2005.10.001, 16242991.
130. Sarubbi E, Monti F, Corti E, Miele A, Selva E. Mode of action of the microbial metabolite GE23077, a novel potent and selective inhibitor of bacterial RNA polymerase. Eur J Biochem 2004, 271:3146-3154. 10.1111/j.1432-1033.2004.04244.x, 15265034.
131. Masullo M, Cantiello P, De Paola B, Fiengo A, Vitagliano L, Zagari A, Arcari P. Valine 114 replacements in archaeal elongation factor 1 alpha enhanced its ability to interact with aminoacyl-tRNA and kirromycin. Biochemistry 2002, 41:14482-14488. 10.1021/bi026428n, 12463746.