Evolution of phage with chemically ambiguous proteomes

BMC Evolutionary Biology

Volumn 3, Issue , 2003, Pages

  Bacher, Jamie M ^a,b   Bull, James J ^a   Ellington, Andrew D ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE QBETA;

PROTEOME; TRYPTOPHAN; VIRUS PROTEIN;

ALLOLEVIVIRUS; AMINO ACID SUBSTITUTION; ANALOGS AND DERIVATIVES; BACTERIOPHAGE; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; GENETICS; MOLECULAR GENETICS; MUTATION; PROCEDURES; VIRUS GENOME;

ALLOLEVIVIRUS; AMINO ACID SUBSTITUTION; BACTERIOPHAGES; DIRECTED MOLECULAR EVOLUTION; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; MUTATION; PROTEOME; TRYPTOPHAN; VIRAL PROTEINS;

EID: 2942615280     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-3-24     Document Type: Article

References (52)

1. Fox TD: Natural variation in the genetic code. Annu Rev Genet 1987, 21:67-91.
2. Jakubowski H, Goldman E: Editing of errors in selection of amino acids for protein synthesis. Microbiol Rev 1992, 56:412-429.
3. Rodnina MV, Wintermeyer W: Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu Rev Biochem 2001, 70:415-435.
4. Radman M, Matic I, Taddei F: Evolution of evolvability. Ann N Y Acad Sci 1999, 870:146-155.
5. Xu ZJ, Love ML, Ma LY, Blum M, Bronskill PM, Bernstein J, Grey AA, Hofmann T, Camerman N, Wong JT: Tryptophanyl-tRNA synthetase from Bacillus subtilis. Characterization and role of hydrophobicity in substrate recognition. J Biol Chem 1989, 264:4304-4311.
6. Bacher JM, Ellington AD: Selection and Characterization of Escherichia coli Variants Capable of Growth on an Otherwise Toxic Tryptophan Analogue. J Bacteriol 2001, 183:5414-5425.
7. Browne DR, Kenyon GL, Hegeman GD: Incorporation of monoflurotryptophans into protein during the growth of Escherichia coli. Biochem Biophys Res Commun 1970, 39:13-19.
8. Zhang QS, Shen L, Wang ED, Wang YL: Biosynthesis and characterization of 4-fluorotryptophan-labeled Escherichia coli arginyl-tRNA synthetase. J Protein Chem 1999, 18:187-192.
9. Pratt EA, Ho C: Incorporation of fluorotryptophans into proteins of escherichia coli. Biochemistry 1975, 14:3035-3040.
10. Parsons JF, Xiao G, Gilliland GL, Armstrong RN: Enzymes harboring unnatural amino acids: mechanistic and structural analysis of the enhanced catalytic activity of a glutathione transferase containing 5-fluorotryptophan. Biochemistry 1998, 37:6286-6294.
11. Randhawa ZI, Witkowska HE, Cone J, Wilkins JA, Hughes P, Yamanishi K, Yasuda S, Masui Y, Arthur P, Kletke C, Bitsch F, Shackleton CHL: Incorporation of norleucine at methionine positions in recombinant human macrophage colony stimulating factor (M-CSF, 4-153) expressed in Escherichia coli: structural analysis. Biochemistry 1994, 33:4352-4362.
12. Tsai LB, Lu HS, Kenney WC, Curless CC, Klein ML, Lai PH, Fenton DM, Altrock BW, Mann MB: Control of misincorporation of de novo synthesized norleucine into recombinant interleukin-2 in E. coli. Biochem Biophys Res Commun 1988, 156:733-739.
13. Döring V, Mootz HD, Nangle LA, Hendrickson TL, de Crécy-Lagard V, Schimmel P, Marlière P: Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway. Science 2001, 292:501-504.
14. Perreau VM, Keith G, Holmes WM, Przykorska A, Santos MA, Tuite MF: The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure. J Mol Biol 1999, 293:1039-1053.
15. Santos MA, Ueda T, Watanabe K, Tuite MF: The non-standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation? Mol Microbiol 1997, 26:423-431.
16. Santos MA, Cheesman C, Costa V, Moradas-Ferreira P, Tuite MF: Selective advantages created by codon ambiguity allowed for the evolution of an alternative genetic code in Candida spp. Mol Microbiol 1999, 31:937-947.
17. Mehl RA, Anderson JC, Santoro SW, Wang L, Martin AB, King DS, Horn DM, Schultz PG: Generation of a bacterium with a 21 amino Acid genetic code. J Am Chem Soc 2003, 125:935-939.
18. Wang L, Brock A, Herberich B, Schultz PG: Expanding the genetic code of Escherichia coli. Science 2001, 292:498-500.
19. Wong JT: Membership mutation of the genetic code: loss of fitness by tryptophan. Proc Natl Acad Sci U S A 1983, 80:6303-6306.
20. Iglesias-Ussel MD, Casado C, Yuste E, Olivares I, Lopez-Galindez C: In vitro analysis of human immunodeficiency virus type 1 resistance to nevirapine and fitness determination of resistant variants. J Gen Virol 2002, 83:93-101.
21. Wichman HA, Badgett MR, Scott LA, Boulianne CM, Bull JJ: Different trajectories of parallel evolution during viral adaptation. Science 1999, 285:422-424.
22. Hanczyc MM, Dorit RL: Replicability and recurrence in the experimental evolution of a group I ribozyme. Mol Biol Evol 2000, 17:1050-1060.
23. Mekler P: Determination of nucleotide sequence of the bacteriophage QB genome: organization and evolution of an RNA virus. University of Zurich; 1981.
24. Domingo E, Sabo D, Taniguchi T, Weissmann C: Nucleotide sequence heterogeneity of an RNA phage population. Cell 1978, 13:735-744.
25. Crill WD, Wichman HA, Bull JJ: Evolutionary reversals during viral adaptation to alternating hosts. Genetics 2000, 154:27-37.
26. Drake JW: Rates of spontaneous mutation among RNA viruses. Proc Natl Acad Sci U S A 1993, 90:4171-4175.
27. Drake JW, Charlesworth B, Charlesworth D, Crow JF: Rates of spontaneous mutation. Genetics 1998, 148:1667-1686.
28. Palasingam K, Shaklee PN: Reversion of Q beta RNA phage mutants by homologous RNA recombination. J Virol 1992, 66:2435-2442.
29. Mills DR, Priano C, DiMauro P, Binderow BD: Q beta replicase: mapping the functional domains of an RNA-dependent RNA polymerase. J Mol Biol 1989, 205:751-764.
30. van Duin Jan: The single-stranded RNA bacteriophages. The Viruses: The Bacteriophages Edited by: Calendar Richard. New York, Plenum Press; 1988:2 v..
31. Schuppli D, Miranda G, Tsui HC, Winkler ME, Sogo JM, Weber H: Altered 3′-terminal RNA structure in phage Qbeta adapted to host factor-less Escherichia coli. Proc Natl Acad Sci U S A 1997, 94:10239-10242.
32. Schumacher MA, Pearson RF, Møller T, Valentin-Hansen P, Brennan RG: Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. Embo J 2002, 21:3546-3556.
33. Møller T, Franch T, Højrup P, Keene DR, Bächinger HP, Brennan RG, Valentin-Hansen P: Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 2002, 9:23-30.
34. Bernhardt TG, Wang IN, Struck DK, Young R: A protein antibiotic in the phage Qbeta virion: diversity in lysis targets. Science 2001, 292:2326-2329.
35. Kozlovska TM, Cielens I, Dreilinna D, Dislers A, Baumanis V, Ose V, Pumpens P: Recombinant RNA phage Q beta capsid particles synthesized and self-assembled in Escherichia coli. Gene 1993, 137:133-137.
36. Arora R, Priano C, Jacobson AB, Mills DR: cis-acting elements within an RNA coliphage genome: fold as you please, but fold you must!! J Mol Biol 1996, 258:433-446.
37. Olsthoorn RC, Licis N, van Duin J: Leeway and constraints in the forced evolution of a regulatory RNA helix. Embo J 1994, 13:2660-2668.
38. Skripkin EA, Jacobson AB: A two-dimensional model at the nucleotide level for the central hairpin of coliphage Q beta RNA. J Mol Biol 1993, 233:245-260.
39. Schuppli D, Georgijevic J, Weber H: Synergism of mutations in bacteriophage Qbeta RNA affecting host factor dependence of Qbeta replicase. J Mol Biol 2000, 295:149-154.
40. Travisano M, Mongold JA, Bennett AF, Lenski RE: Experimental tests of the roles of adaptation, chance, and history in evolution. Science 1995, 267:87-90.
41. Travisano M: Long-term experimental evolution in Escherichia coli. VI. Environmental constraints on adaptation and divergence. Genetics 1997, 146:471-479.
42. Cooper VS, Bennett AF, Lenski RE: Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment. Evolution Int J Org Evolution 2001, 55:889-896.
43. Knight RD, Freeland SJ, Landweber LF: Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2001, 2:49-58.
44. Osawa S, Jukes TH: Codon reassignment (codon capture) in evolution. J Mol Evol 1989, 28:271-278.
45. Osawa S, Jukes TH: Evolution of the genetic code as affected by anticodon content. Trends Genet 1988, 4:191-198.
46. Jukes TH, Osawa S: Evolutionary changes in the genetic code. Comp Biochem Physiol B 1993, 106:489-494.
47. Andersson SG, Kurland CG: Genomic evolution drives the evolution of the translation system. Biochem Cell Biol 1995, 73:775-787.
48. Yarus M, Schultz DW: Further comments on codon reassignment. Response. J Mol Evol 1997, 45:3-6.
49. Schultz DW, Yarus M: On malleability in the genetic code. J Mol Evol 1996, 42:597-601.
50. Schultz DW, Yarus M: Transfer RNA mutation and the malleability of the genetic code. J Mol Biol 1994, 235:1377-1380.
51. Beekwilder MJ, Nieuwenhuizen R, van Duin J: Secondary structure model for the last two domains of single-stranded RNA phage Q beta. J Mol Biol 1995, 247:903-917.
52. Crameri A, Whitehorn EA, Tate E, Stemmer WP: Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol 1996, 14:315-319.