Small cofactors may assist protein emergence from RNA world: Clues from RNA-protein complexes

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Shen, Liang ^a   Ji, Hong Fang ^a  

^a SHANDONG UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; NUCLEOTIDE; PROTEIN; RNA; RNA BINDING PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; CONTROLLED STUDY; EUKARYOTE; EUKARYOTE EVOLUTION; LIGAND BINDING; PROKARYOTE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN RNA BINDING; RNA ANALYSIS; SIGNAL TRANSDUCTION; BIOGENESIS; DATA BASE; METABOLISM; MOLECULAR EVOLUTION; PROTEIN BINDING;

BIOGENESIS; DATABASES AS TOPIC; EVOLUTION, MOLECULAR; NUCLEOTIDES; PROTEIN BINDING; PROTEINS; RNA; RNA-BINDING PROTEINS;

EID: 79960580102     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022494     Document Type: Article

References (53)

1. Crick FHC, (1968) The origin of the genetic code. J Mol Biol 38: 367-379.
2. Gilbert W, (1986) The RNA world. Nature 319: 618.
3. Cech TR, (1986) The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell 44: 207-210.
4. Joyce GF, (2002) The antiquity of RNA-based evolution. Nature 418: 214-221.
5. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S, (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35: 849-857.
6. Orgel LE, (1986) RNA catalysis and the origin of life. J theor Biol 123: 127-149.
7. Orgel LE, (1968) Evolution of the genetic apparatus. J Mol Biol 38: 381-393.
8. Smith CA, Calabro V, Frankel AD, (2000) An RNA-binding chameleon. Mol Cell 6: 1067-1076.
9. Spirin S, Titov M, Karyagina A, Alexeevski A, (2007) NPIDB: a database of nucleic acids-protein interactions. Bioinformatics 23: 3247-3248.
10. Alexeevski A, Spirin S, Alexeevski D, Klychnikov O, Ershova A, et al. (2004) CluD, a program for the determination of hydrophobic clusters in 3D structures of protein and protein-nucleic acids complexes. Biofizika 48 (Suppl 1): 146-156.
11. Karyagina A, Ershova A, Titov M, Olovnikov I, Aksianov E, et al. (2006) Analysis of conserved hydrophobic cores in proteins and supramolecular complexes. J Bioinform Comput Biol 4: 357-372.
12. Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
13. Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJP, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36: D419-D425.
14. Rose GD, (1979) Hierarchic organization of domains in globular proteins. J Mol Biol 134: 447-470.
15. Koonin EV, Wolf YI, Karev GP, (2002) The structure of the protein universe and genome evolution. Nature 420: 218-223.
16. Ma BG, Chen L, Ji HF, Chen ZH, Yang FR, et al. (2008) Characters of very ancient proteins. Biochem Biophys Res Commun 366: 607-611.
17. Ji HF, Kong DX, Shen L, Chen LL, Ma BG, et al. (2007) Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biol 8: R176.
18. Ji HF, Chen L, Zhang HY, (2008) Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins. Bio Essays 30: 766-771.
19. Bairoch A, Apweiler R, (1999) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res 27: 49-54.
20. Hall DO, Cammack R, Rao KK, (1971) Role for ferredoxins in the origin of life and biological evolution. Nature 233: 136-138.
21. Wächtershäuser G, (1992) Groundworks for an evolutionary biochemistry: the iron-sulfur world. Prog Biophys Mol Biol 58: 85-202.
22. Caetano-Anollés G, Caetano-Anollés D, (2003) An evolutionarily structured universe of protein architecture. Genome Res 13: 1563-1571.
23. Caetano-Anolles G, Caetano-Anolles D, (2005) Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol 60: 484-498.
24. Wang M, Boca SM, Kalelkar R, Mittenthal JE, Caetano-Anolles G, (2006) A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture. Complexity 12: 27-40.
25. Wright PE, Dyson HJ, (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293: 321-331.
26. Dyson HJ, Wright PE, (2002) Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12: 54-60.
27. Fink AL, (2005) Natively unfolded proteins. Curr Opin Struct Biol 15: 35-41.
28. Dyson HJ, Wright PE, (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6: 197-208.
29. Grandori R, Schwarzinger S, Müller N, (2000) Cloning, overexpression and characterization of micro-myoglobin: a minimal heme-binding fragment. Eur J Biochem 267: 1168-1172.
30. Reanney DC, (1977) Aminoacyl thiol esters and the origins of genetic specificity. J Theor Biol 65: 555-569.
31. Rucker RB, Wold F, (1988) Cofactors in and as posttranslational protein modifications. FASEB J 2: 2252-2261.
32. Wong JT, (1991) Origin of genetically encoded protein synthesis: a model based on selection for RNA peptidation. Orig Life Evol Biosph 21: 165-176.
33. Szathmary E, (1993) Coding coenzyme handles: A hypothesis for the origin of the genetic code. Proc Natl Acad Sci USA 90: 9916-9920.
34. Szathmary E, (1999) The origin of the genetic code: amino acids as cofactors in an RNA world. Trends Genet 15: 223-229.
35. Rodin AS, Szathmary E, Rodin SN, (2009) One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation. Biol Direct 4: 4.
36. Rodin AS, Szathmary E, Rodin SN, (2011) On the origin of the genetic code and tRNA before translation. Biol Direct 6: 14.
37. Di Giulio M, (1997) On the RNA world: evidence in favor of an early ribonucleopeptide world. J Mol Evol 45: 571-578.
38. Blackmond DG, (2004) Asymmetric autocatalysis and its implications for the origin of homochirality. Proc Natl Acad Sci USA 101: 5732-5736.
39. Fujii N, Saito T, (2004) Homochirality and life. Chem Rec 4: 267-278.
40. Keszthelyi L, (1995) Origin of the homochirality of biomolecules. Q Rev Biophys 28: 473-507.
41. Klabunovskii EI, (2001) Can enantiomorphic crystals like quartz play role in the origin of homochirality on Earth. Astrobiology 1: 127-131.
42. Podlech J, (2001) Origin of organic molecules and biomolecular homochirality. Cell Mol Life Sci 58: 44-60.
43. Ji HF, Zhang HY, (2005) Low-lying free energy levels of amino acids and their implications for the origin of life. J Mol Struct (Theochem) 756: 109-112.
44. Milton RC, Milton SCF, Kent SBH, (1992) Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity. Science 256: 1445-1448.
45. Bolik S, Rubhausen M, Binder S, Schulz B, Perbandt M, et al. (2007) First experimental evidence for the preferential stabilization of the natural D- over the nonnatural L-configuration in nucleic acids. RNA 13: 1877-1880.
46. Yamagata Y, (1966) A hypothesis for the asymmetric appearance of biomolecules on Earth. J Theor Biol 11: 495-498.
47. Hazen R, Filley T, Goodfriend G, (2001) Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality. Proc Natl Acad Sci USA 98: 5487-5490.
48. Faglioni F, Passalacqua A, Lazzeretti P, (2005) Parity violation energy of biomolecules I: Polypeptides. Orig Life Evol Biosph 35: 461-475.
49. Stoks PG, Schwartz AW, (1981) Nitrogen-heterocyclic compounds in meteorites: Significance and mechanisms of formation. Geochim Cosmochim Acta 45: 563-569.
50. Stoks PG, Schwartz AW, (1979) Uracil in carbonaceous chondrites. Nature 282: 709-710.
51. Taylor WR, (2005) Modelling molecular stability in the RNA world. Comput Biol Chem 29: 259-272.
52. McGiness KE, Joyce GF, (2003) In search of an RNA replicase ribozyme. Chem Biol 10: 5-14.
53. Marx PA, Pridgen C, Kingsbury DW, (1975) Location and abundance of Poly(A) sequences in Sendai virus messenger RNAs. J Gen Virol 27: 247-250.