The enzymatic and metabolic capabilities of early life

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Goldman, Aaron David ^a   Baross, John A ^b,c   Samudrala, Ram ^c  

^a PRINCETON UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COENZYME A; HYDROLASE; LIGASE; LYASE; OXIDOREDUCTASE; STARCH; SUGAR; TRANSFERASE; ENZYME; METAL; NUCLEOTIDE;

AMINO ACID SYNTHESIS; ARTICLE; BIOINFORMATICS; CONSENSUS SEQUENCE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME METABOLISM; ENZYME SYNTHESIS; METABOLISM; METACONSENSUS; PHOSPHOLIPID METABOLISM; BIOGENESIS; BIOLOGY; CHEMISTRY; PROTEIN SECONDARY STRUCTURE;

BIOGENESIS; COMPUTATIONAL BIOLOGY; ENZYMES; METABOLIC NETWORKS AND PATHWAYS; METALS; NUCLEOTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 84877149265     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039912     Document Type: Article

References (54)

1. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32:D115-D119.
2. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res (Epub ahead of print)
3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242.
4. Andreeva A, Howorth D, Chandonia J, Brenner SE, Hubbard TJP, et al. (2007) Data growth and its impact on the SCOP database: New developments. Nucleic Acids Res 36:D419-D425.
5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25-29.
6. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354-D357.
7. McDermott J, Samudrala R (2003) Bioverse: Functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res 31:3736-3737.
8. Becerra A, Delaye L, Islas S, Lazcano A (2007) The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains. Annu Rev Ecol Evol Syst 38:361-379
9. Harris JK, Kelley ST, Spiegelman GB, Pace NR (2003) The genetic core of the universal ancestor. Genome Res 13:407-412.
10. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22-28.
11. Caetano-Anollés G, Caetano-Anolles D (2005) Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol 60:484-498.
12. Wang M, Caetano-Anollés G (2006) Global phylogeny determined by the combination of protein domains in proteomes. Mol Biol Evol 23:2444-2453.
13. Wang M, Boca SM, Kalelkas R, Mittenthal JE, Caetano-Anollés G (2006) A phylogenomics reconstruction of the protein world based on a genomic census of protein fold architecture. Complexity 12:27-40
14. Caetano-Anollés G, Wang M, Caetano-Anollés D, Mittenthal JE (2009) The origin, evolution and structure of the protein world. Biochem J 417:621-637.
15. Goldman AD, Horst JA, Hung L-H, Samudrala R (2012) Evolution of the Protein Repertoire. Systems Biology (R Meyers, Ed.) 207-237. Wiley-VCH, Wienheim, Germany
16. Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Ceatano-Anollés G (2007) Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res 17:1572-1585.
17. Wang M, Caetano-Anollés G (2009) The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 17:66-78.
18. Jeffery CJ (1999) Moonlighting proteins. Trends Biochem Sci 24:8-11.
19. Petrey D, Fischer M, Honig B (2009) Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci 106:17377-17382.
20. Sadowski M, Taylor WR (2010) On the evolutionary origins of "Fold Space Continuity": A study of topological convergence and divergence in mixed alphabeta domains. J Struct Biol: in press
21. Srinivasan V, Morowitz HJ (2009) The canonical network of autotrophic intermediary metabolism: Minimal metabolome of a reductive chemoautotroph. Biol Bull 216:126-130.
22. Koonin EV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1:127-136.
23. Theobald D (2010) A formal test of the theory of universal common ancestry. Nature 465:219-222
24. Woese C (1998) The universal ancestor. Proc Natl Acad Sci U S A 95:6854-6859
25. Doolittle FW (1999) Phylogenetic classification of the universal tree. Science 284:2124-2128
26. Kim HS, Mittenthal JE, Caetano-Anollés G (2006) MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics 7:351
27. White H (1976) Coenzymes as fossils of an earlier metabolic state. J Mol Evol 7:101-104
28. Lazcano A, Miller SL (1999) On the origin of metabolic pathways. J Mol Evol 49:424-431.
29. Cody GD (2004) Transition metal sulfides and the origin of metabolism. Ann Rev Earth Planet Sci 32:569-599.
30. van der Gulik P, Serge Masser, Dimitri Gilis, Harry Buhrman, Marianne Rooman (2009) The first peptides: The evolutionary transition between prebiotic amino acids and early proteins. Journal of Theoretical Biology 261:531-539.
31. Dupont CL, Butcher A, Valas RE, Bourne PE, Gustavo Caetano-Anollése G (2010) History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci U S A 107:10567-10572
32. Jadhav VR, Yarus M (2002) Acyl-CoAs from coenzyme ribozymes. Biochemistry 41:723-729
33. Huber C, Wächtershäuser G (1997) Activated acetic acid by carbon fixation on (Fe, Ni) S under primordial conditions. Science 276:245-247.
34. Huber C, Wächtershäuser G (1998) Peptides by activation of amino acids with CO on (Ni, Fe) S surfaces: implications for the origin of life. Science 281:670-672.
35. Mulkidjanian AY (2009) On the origin of life in the zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth. Biol Direct 4:26.
36. Mulkidjanian AY, Galperin MY (2009) 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 4:27.
37. Caetano-Anolles G, Caetano-Anolles D (2003). "An evolutionarily structured universe of protein architecture". Genome Res 13(7):1563-71
38. Goldman AD, Samudrala R, Baross JA (2010) The evolution and functional repertoire of translation proteins following the origin of life. Biol Direct 5:15.
39. Freeland SJ, Knight RD, Landweber LF (1999) Do proteins predate DNA?. Science 286:690-692.
40. Wierenga RK (2001) The TIM-barrel fold: a versatile framework for efficient enzymes. FEBS Letters 492:193-198.
41. Dickson RC, Lester RL (2002) Sphingolipid functions in Saccharomyces cerevisiae. Biochim Biophys Acta 1583:13-25.
42. Rao RP, Acharya JK (2008) Sphingolipids and membrane biology as determined from genetic models. Prostaglandins Other Lipid Mediat 85:1-16.
43. de Duve C (1995) Vital Dust: The Origin And Evolution Of Life On Earth, BasicBooks, New York
44. Martin W, Russell MJ (2007) On the origin of biochemistry at an alkaline hydrothermal vent. Philos Trans R Soc Lond B Biol Sci 362:1887-1925.
45. Shimizu M, Yamagishi A, Kinoshita K, Shida Y, Oshima T (2008) Prebiotic origin of glycolytic metabolism: histidine and cysteine can produce acetyl CoA from glucose via reactions homologous to non-phosphorylated Entner-Doudoroff pathway. J Biochem 144:383-388.
46. Say RF and Fuchs G (2010) Fructose 1, 6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature 464:1077-1081.
47. Filée J, Forterre P, Sen-Lin T, Laurent J (2002) Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol 54, 763-77
48. Goldman AD, Landweber LF (2012) Oxytricha as a modern analog of ancient genome evolution. DOI: 10.1016/j.tig.2012.03.010
49. Poole A, Logan DT (2005) Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 22:1444-1455
50. Delaye et al (2005) Prebiological evolution and the physics of the origin of life. Origins Life Evol Biosph 35:47-64
51. Jensen RA (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30:409-25
52. Yamada T, Bork P (2009) Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 10:791-803
53. Caetano-Anolles G, Kim HS, Mittenthal JE (2007) The origins of modern metabolic networks inferred from phylogenomic analysis of protein structure. Proc Natl Acad Sci U S A 104:9358-9363.
54. Breitkreutz B, Stark C, Tyers M (2003) Osprey: a network visualization system. Genome Biol 4:R22.