The proteomic complexity and rise of the primordial ancestor of diversified life

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Kim, Kyung Mo ^a,b   Caetano Anollés, Gustavo ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ANCESTRY; ESTER; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; GENOMICS; LIPID; METABOLISM; MOLECULAR ANALYSIS; PROKARYOTE; PROTEIN; PROTEOMICS; RECONSTRUCTION;

ARCHAEA;

PROTEOME;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CHEMISTRY; EUKARYOTE; GENETICS; GENOME; MOLECULAR EVOLUTION; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE;

ARCHAEA; BACTERIA; EUKARYOTA; EVOLUTION, MOLECULAR; GENOME; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEOME;

EID: 80053304045     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-140     Document Type: Article

References (89)

1. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. CR Woese O Kandler ML Wheelis, Proc Natl Acad Sci USA 1990 87 4576 4579 10.1073/pnas.87.12.4576 2112744
2. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. CR Woese GE Fox, Proc Natl Acad Sci USA 1977 74 5088 5090 10.1073/pnas.74.11. 5088 270744 (Pubitemid 8241042)
3. How many species are there on earth? RM May, Science 1988 241 1441 1449 10.1126/science.241.4872.1441 17790039 (Pubitemid 19320384)
4. Biodiversity as a source of innovation in biotechnology. AT Bull M Goodfellow JH Slater, Annu Rev Microbiol 1992 46 219 252 10.1146/annurev.mi.46. 100192.001251 1444255
5. Prokaryotes: the unseen majority. WB Whitman DC Coleman WJ Wiebe, Proc Natl Acad Sci USA 1998 95 6578 6583 10.1073/pnas.95.12.6578 9618454 (Pubitemid 28278022)
6. The universal ancestor. CR Woese, Proc Natl Acad Sci USA 1998 95 6854 6859 10.1073/pnas.95.12.6854 9618502
7. Universal protein families and the functional content of the last universal common ancestor. N Kyrpides R Overbeek C Ouzounis, J Mol Evol 1999 49 413 423 10.1007/PL00006564 10485999 (Pubitemid 29463384)
8. The nature of the last universal common ancestor. D Penny A Poole, Curr Opin Genet Dev 1999 9 672 677 10.1016/S0959-437X(99)00020-9 10607605
9. Comparative genomics, minimal gene-sets and the last universal common ancestor. EV Koonin, Nat Rev Microbiol 2003 1 127 136 10.1038/nrmicro751 15035042
10. A minimal estimate for the gene content of the last universal common ancestor-exobiology from a terrestrial perspective. CA Ouzounis V Kunin N Darzentas L Goldovsky, Res Microbiol 2006 157 57 68 10.1016/j.resmic.2005.06.015 16431085 (Pubitemid 43202118)
11. Protein superfamily evolution and the last universal common ancestor (LUCA). JAG Ranea A Sillero JM Thornton CA Orengo, J Mol Evol 2006 63 513 525 10.1007/s00239-005-0289-7 17021929 (Pubitemid 44611738)
12. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. N Glansdorff Y Xu B Labedan, Biol Direct 2008 3 29 10.1186/1745-6150-3-29 18613974
13. A unifying scenario on the origin and evolution of cellular and viral domains. C Bandea, Nature Proceedings 2009 http://hdl.handle.net/10101/npre. 2009.3888.1
14. Giant viruses: Conflicts in revisiting the virus concept. P Forterre, Intervirology 2010 53 362 378 10.1159/000312921 20551688
15. Phylogeny of prokaryotes: does it exist and why should we care? S Gribaldo C Brochier, Res Microbiol 2009 160 513 521 10.1016/j.resmic.2009.07.006 19631737
16. A format test of the theory of universal common ancestry. DL Theobald, Nature 2010 465 219 222 10.1038/nature09014 20463738
17. Where is the root of the universal tree of life? P Forterre H Philippe, BioEssays 1999 21 871 879 10.1002/(SICI)1521-1878(199910)21:10<871::AID- BIES103.0.CO;2-Q 10497338 (Pubitemid 29475496)
18. Ribosomal history reveals origins of modern protein synthesis. A Harish G Caetano-Anollés, 2011
19. Proteome evolution and the metabolic origins of translation and cellular life. D Caetano-Anollés KM Kim JM Mittenthal G Caetano-Anollés, J Mol Evol 2011 72 14 32 10.1007/s00239-010-9400-9 21082171
20. A universal molecular clock of folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. M Wang Y-Y Jiang KM Kim G Qu HF- Ji JE Mittenthal HY- Zhang G Caetano-Anollés, Mol Biol Evol 2011 28 567 582 10.1093/molbev/msq232 20805191
21. On the origin of prokaryotes. DC Reanney, Theor Biol 1974 48 243 251 10.1016/0022-5193(74)90194-5
22. Evolutionary patterns in the sequence and structure of transfer RNA: early origins of Archaea and viruses. F-J Sun G Caetano-Anollés, PLoS Comput Biol 2008 4 1000018 10.1371/journal.pcbi.1000018 18369418
23. Archaea and the origin(s) of DNA replication proteins. DR Edgell WF Doolittle, Cell 1997 89 995 998 10.1016/S0092-8674(00)80285-8 9215620 (Pubitemid 127678731)
24. Lessons from an archaeal genome: What are we learning from Methanococcus jannaschii? GJ Olsen CR Woese, Trends Genet 1996 12 377 379 10.1016/0168- 9525(96)30092-9 8909123 (Pubitemid 26336469)
25. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. CJ Bult O White GJ Olsen L Zhou RD Fleischmann GG Sutton JA Blake LM FitzGerald RA Clayton JD Gocayne,, et al. Science 1996 273 1058 1073 10.1126/science.273.5278.1058 8688087 (Pubitemid 26278157)
26. The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. WM Fitch K Upper, Cold Spring Harb Symp Quant Biol 1987 52 759 767 3454288 (Pubitemid 18262388)
27. The origin, evolution and structure of the protein world. G Caetano-Anollés M Wang D Caetano-Anollés JE Mittenthal, Biochemical J 2009 417 621 637 10.1042/BJ20082063
28. An approach of orthology detection from homologous sequences under minimum evolution. KM Kim S Sung G Caetano-Anollés JY Han H Kim, Nucleic Acids Res 2008 36 110 10.1093/nar/gkn485 18676448
29. Why would phylogenetics ignore computerized sequence alignment? DA Morrison, Syst Biol 2009 58 150 158 10.1093/sysbio/syp009 20525575
30. SCOP: a structural classification of proteins for the investigation of sequences and structures. A Murzin SE Brenner T Hubbard C Chothia, J Mol Biol 1995 247 536 540 7723011
31. The genome on line database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. K Liolios K Mavrommatis N Tavernarakis NC Kyrpides, Nucleic Acids Res 2007 36 475 D479 10.1093/nar/gkm884 17981842
32. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Gough K Karplus R Hughey C Chothia, J Mol Biol 2001 313 903 919 10.1006/jmbi.2001.5080 11697912 (Pubitemid 33063435)
33. Structure is three to ten times more conserved than sequence - a study of structural response in protein cores. K Illergård DH Ardell A Elofsson, Proteins 2009 77 499 508 10.1002/prot.22458 19507241
34. Phylogeny determined based on protein domain content. S Yang RF Doolittle PE Bourne, Proc Natl Acad Sci USA 2005 102 373 378 10.1073/pnas.0408810102 15630082 (Pubitemid 40116774)
35. Global phylogeny determined by the combination of protein domains in proteomes. M Wang G Caetano-Anollés, Mol Biol Evol 2006 23 2444 2454 10.1093/molbev/msl117 16971695 (Pubitemid 44737138)
36. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. G Caetano-Anollés HS Kim JE Mittenthal, Proc Natl Acad Sci USA 2007 104 9358 9363 10.1073/pnas.0701214104 17517598 (Pubitemid 47185784)
37. Convergent evolution of domain architectures (is rare). J Gough, Bioinformatics 2005 21 1464 1471 10.1093/bioinformatics/bti204 15585523 (Pubitemid 40552751)
38. Domain tree-based analysis of protein architecture evolution. K Forslund A Henricson V Hollich ELL Sonnhammer, Mol Biol Evol 2007 25 254 264 18025066
39. The evolutionary history of proteins domains viewed by species phylogeny. S Yang PE Bourne, PLoS One 2009 4 8378 10.1371/journal.pone.0008378 20041107
40. Ancient horizontal gene transfer. JR Brown, Nat Rev Genet 2003 4 121 132 12560809 (Pubitemid 36150684)
41. Protein family expansions and biological complexity. C Vogel C Chothia, PLoS Comput Biol 2006 2 48 10.1371/journal.pcbi.0020048 16733546
42. Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. M Wang LS Yafremava D Caetano-Anollés JE Mittenthal G Caetano-Anollés, Genome Res 2007 17 1572 1585 10.1101/gr.6454307 17908824 (Pubitemid 350074853)
43. Signal, noise, and reliability in molecular phylogenetic analyses. DM Hillis JP Huelsenbeck, J Hered 1992 83 189 195 1624764 (Pubitemid 23097535)
44. Phylogenetic analysis using parsimony and other program (PAUP*), ver. 4.0b10. DL Swofford, Sinauer, Sunderland, MA 2002
45. Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. KM Kim G Caetano-Anollés, Mol Biol Evol 2010 27 1710 1733 10.1093/molbev/msq106 20418223
46. The last common ancestor: What's in a name? L Delaye A Becerra A Lazcano, Orig Life Evol Biosph 2005 35 537 554 10.1007/s11084-005-5760-3 16254691 (Pubitemid 41563535)
47. An evolutionarily structured universe of protein architecture. G Caetano-Anollés D Caetano-Anollés, Genome Res 2003 13 1563 1571 10.1101/gr.1161903 12840035 (Pubitemid 36874472)
48. Universal sharing patterns in proteomes and evolution of protein fold architecture and life. G Caetano-Anollés D Caetano-Anollés, J Mol Evol 2005 60 484 498 10.1007/s00239-004-0221-6 15883883 (Pubitemid 40754789)
49. GeneTRACE - reconstruction of gene content of ancestral species. V Kunin CA Ouzounis, Bioinformatics 2003 19 1412 1416 10.1093/bioinformatics/btg174 12874054 (Pubitemid 36939820)
50. Wagner networks and ancestors. JG Lundberg, Syst Zool 1972 18 1 32
51. Origins and evolution of modern biochemistry: insights from genomes and molecular structure. G Caetano-Anollés FJ Sun M Wang LS Yafremava A Harish HS Kim V Knudsen D Caetano-Anollés JE Mittenthal, Front Biosci 2008 13 5212 5240 18508583
52. The origin and evolution of tRNA infrerred from phylogenetic analysis of structure. F-J Sun G Caetano-Anollés, J Mol Evol 2008 66 21 35 10.1007/s00239-007-9050-8 18058157
53. The evolutionary history of the structure of 5S ribosomal RNA. F-J Sun G Caetano-Anollés, J Mol Evol 2009 69 430 443 10.1007/s00239-009-9264-z 19639237
54. The ancient history of the structure of ribonuclease P and the early origins of Archaea. F-J Sun G Caetano-Anollés, BMC Bioinformatics 2010 11 153 10.1186/1471-2105-11-153 20334683
55. Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life. H Xue K-L Tong C Marck H Grosjean JT-F Wong, Gene 2003 310 59 66 12801633 (Pubitemid 36703300)
56. Congruence of evidence for a Methanopyrus-proximal root of life based on transfer RNA and aminoacyl-tRNA synthetase genes. H Xue S-K Ng K-L Tong JT-F Wong, Gene 2005 360 120 130 10.1016/j.gene.2005.06.027 16153784 (Pubitemid 41446886)
57. Polyphasic evidence delineating the root of life and roots of biological domains. JT-F Wong J Chen W-K Mat S-K Ng H Xue, Gene 2007 403 39 52 10.1016/j.gene.2007.07.032 17884304 (Pubitemid 47488703)
58. The tree of life might be rooted in the branch leading to Nanoarchaeota. M Di Giulio, Gene 2007 401 108 113 10.1016/j.gene.2007.07.004 17689206 (Pubitemid 47379518)
59. A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture. M Wang SM Boca R Kalelkar JE Mittenthal G Caetano-Anollés, Complexity 2006 12 27 40 10.1002/cplx.20141 (Pubitemid 44720446)
60. The evolutionary mechanics of domain organization in proteomes and the rise ofmodularity in the protein world. M Wang G Caetano-Anollés, Structure 2009 17 66 78 10.1016/j.str.2008.11.008 19141283
61. The origins of modern proteomes. CG Kurland B Canbäck OG Berg, Biochimie 2007 89 1454 1463 10.1016/j.biochi.2007.09.004 17949885 (Pubitemid 350122859)
62. Genomics and the irreducible nature of eukaryotic cells. CG Kurland LJ Collins D Penny, Science 2006 312 1011 1016 10.1126/science.1121674 16709776
63. Horizontal gene transfer among genomes: The complexity hypothesis. R Jain MC Rivera JA Lake, Proc Natl Acad Sci USA 1999 96 3801 3806 10.1073/pnas.96.7.3801 10097118 (Pubitemid 29168991)
64. Global extent of horizontal gene transfer. I-G Choi SH Kim, Proc Natl Acad Sci USA 2007 104 4489 4494 10.1073/pnas.0611557104 17360551 (Pubitemid 47186252)
65. The extant core bacterial proteome is an archive of the origin of life. A Danchin G Fang S Noria, Proteomics 2007 7 875 889 10.1002/pmic.200600442 17370266 (Pubitemid 46506735)
66. Structure of ribonucleotide reductase protein R1. U Uhlin H Eklund, Nature 1994 370 533 539 10.1038/370533a0 8052308 (Pubitemid 24264919)
67. Ribonucleotide reductases: the link between an RNA and a DNA world? J Stubbe, Curr Op Struct Biol 2000 10 731 736 10.1016/S0959-440X(00)00153-6 (Pubitemid 32061489)
68. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. MV Rodnina A Savelsbergh VI Katunin W Wintermeyer, Nature 1997 385 37 41 10.1038/385037a0 8985244 (Pubitemid 27024544)
69. Stimulation of the GTPase activity of translation elongation factor G by ribosomal protein L7/12. A Savelsbergh D Mohr B Wilden W Wintermeyer MV Rodnina, J Biol Chem 2000 275 890 894 10.1074/jbc.275.2.890 10625623 (Pubitemid 30051131)
70. The continuing puzzle of the great oxidation event. AL Sessions DM Doughty PV Welander RE Summons DK Newman, Curr Biol 2009 19 567 R574 10.1016/j.cub.2009.05.054 19640495
71. The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives. A Tomitani AH Knoll CM Cavanaugh T Ohno, Proc Natl Acad Sci USA 2006 103 5442 5447 10.1073/pnas.0600999103 16569695
72. Groundworks for an evolutionary biochemistry: the iron-sulphur world. G Wächtershäuser, Prog Biophys Mol Biol 1992 58 85 201 10.1016/0079-6107(92)90022-X 1509092
73. Did archaeal and bacterial cells arise independently from noncelullar precursors? A hypothesis stating that the advent of membrane phospholipids with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent. Y Koga T Kyuragi M Nishihara N Sone, J Mol Evol 1998 46 54 63 10.1007/PL00006283 9419225 (Pubitemid 28047239)
74. Ancestral lipid biosynthesis and early membrane evolution. J Peretá P Lápez-Garcia D Moreira, Trends Biochem Sci 2004 29 469 477 10.1016/j.tibs.2004.07.002 15337120 (Pubitemid 39158870)
75. From pre-cells to eukarya: a tale of two lipids. G Wächtershä user, Mol Microbiol 2003 47 13 22 12492850 (Pubitemid 36051320)
76. Enzyme-driven speciation: crystallizing Archaea via lipid capture. J Payandeh EF Pai, J Mol Evol 2007 64 364 374 10.1007/s00239-006-0141-8 17253090 (Pubitemid 46364874)
77. CTP: 2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. H Morii M Nishimara Y Koga, J Biol Chem 2000 275 36568 36574 10.1074/jbc.M005925200 10960477 (Pubitemid 32002055)
78. (S)-geranylgeranylglyceryl phosphate synthase. Purification and characterization of the first pathway-specific enzyme in archaebacterial membrane lipid biosynthesis. A Chen D Zhang CD Poulter, J Biol Chem 1993 268 21701 217055 8408023
79. Analysis of membrane stereochemistry with homology modeling of sn-glycerol-1-phosphate dehydrogenase. H Daiyasu T Hiroike Y Koga H Toh, Prot Eng 2002 15 987 995 10.1093/protein/15.12.987 (Pubitemid 36331370)
80. Molecular evidence of Late Archean archaea and the presence of a subsurface hydrothermal biosphere. GT Ventura F Kenig CM Reddy J Schieber GS Frysinger RK Nelson E Dinel RB Gaines P Schaeffer, Proc Natl Acad Sci USA 2007 104 14260 14265 10.1073/pnas.0610903104 17726114 (Pubitemid 350003250)
81. Life before the rise of oxygen. WW Fischer, Nature 2008 455 1051 1052 10.1038/4551051a 18948942
82. SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny. D Wilson R Pethica Y Zhou C Talbot C Vogel M Madera C Chothia J Gough, Nucleic Acids Res 2009 37 380 D386 10.1093/nar/gkn762 19036790
83. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments, and genome assignments. J Gough C Chothia, Nucleic Acids Res 2002 30 268 272 10.1093/nar/30.1.268 11752312 (Pubitemid 34679561)
84. The SUPERFAMILY database in 2007: families and functions. D Wilson M Madera C Vogel C Chothia J Gough, Nucleic Acids Res 2007 35 308 D313 10.1093/nar/gkl910 17098927
85. The evolutionary history of carbamoyltransferases: a complex set of paralogous genes was already present in the last universal common ancestor. B Labedan A Boyen M Baetens D Charlier P Chen R Cunin V Durbeco N Glansdorff G Herve C Legrain,, et al. J Mol Evol 1999 49 461 473 10.1007/PL00006569 10486004 (Pubitemid 29463389)
86. The holy grail of the perfect character: The cladistic treatment of morphometric data. K Thiele, Cladistics 1993 9 275 304 10.1111/j.1096-0031.1993. tb00226.x
87. SumTrees: summarization of split support on phylogenetic trees. version 10.0.2. J Sukumaran MT Holder, 2008 (part of the DendroPy phylogenetic computation library version 2.1.3);
88. The parsimony ratchet, a new method for rapid parsimony analysis. KC Nixon, Cladistics 1999 15 407 414 10.1111/j.1096-0031.1999.tb00277.x (Pubitemid 30203167)
89. Data growth and its impact on the SCOP database: new developments. A Andreeva D Howorth J-M Chandonia SE Brenner TJP Hubbard C Chothia AG Murzin, Nucleic Acids Res 2008 36 419 D425 18000004