Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code

Genome Biology and Evolution

Volumn 6, Issue 3, 2014, Pages 629-641

  Yu, Allen Chi Shing ^a   Yim, Aldrin Kay Yuen ^a   Mat, Wai Kin ^b   Tong, Amy Hin Yan ^c   Lok, Si ^c   Xue, Hong ^b   Tsui, Stephen Kwok Wing ^a   Wong, J Tze Fei ^b   Chan, Ting Fung ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^b HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

^c Prince of Wales Hospital   (Hong Kong)

Author keywords

Amino acid analogs; Bacillus subtilis; Fluorotryptophan; Genetic code evolution; Unnatural amino acids

Indexed keywords

4 FLUOROTRYPTOPHAN; 4-FLUOROTRYPTOPHAN; AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; DRUG DERIVATIVE; FLUOROTRYPTOPHAN; SIGMA FACTOR; TRANSFER RNA; TRYPTOPHAN;

AMINO ACID ANALOGS; AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; CHEMISTRY; DNA SEQUENCE; GENETIC CODE; GENETIC CODE EVOLUTION; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUTATION; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; UNNATURAL AMINO ACIDS;

AMINO ACID ANALOGS; BACILLUS SUBTILIS; FLUOROTRYPTOPHAN; GENETIC CODE EVOLUTION; UNNATURAL AMINO ACIDS;

AMINO ACID SEQUENCE; AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; BACILLUS SUBTILIS; EVOLUTION, MOLECULAR; GENETIC CODE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; RNA, TRANSFER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SIGMA FACTOR; TRYPTOPHAN;

EID: 84902962353     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu044     Document Type: Article

References (53)

1. Arthur TM, Anthony LC, Burgess RR. 2000. Mutational analysis of beta '260-309, a sigma 70 binding site located on Escherichia coli core RNA polymerase. J Biol Chem. 275(30): 23113-23119.
2. Bacher JM, Bull JJ, Ellington AD. 2003. Evolution of phage with chemically ambiguous proteomes. BMC Evol Biol. 3: 24.
3. Bacher JM, Ellington AD. 2001. Selection and characterization of Escherichia coli variants capable of growth on an otherwise toxic tryptophan analogue. J Bacteriol. 183(18): 5414-5425.
4. Bacher JM, Hughes RA, Tze-FeiWong J, Ellington AD. 2004. Evolving new genetic codes. Trends Ecol Evol. 19(2): 69-75.
5. Barbe V, et al. 2009. From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155(Pt 6): 1758-1775.
6. Belda E, et al. 2013. An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology 159(Pt 4): 757-770.
7. Berry MJ, et al. 1991. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 30 untranslated region. Nature 353(6341): 273-276.
8. Browne DT, Kenyon GL, Hegeman GD. 1970. Incorporation ofmonofluorotryptophans into protein during the growth of Escherichia coli. Biochem Biophys Res Commun. 39(1): 13-19.
9. Caspi R, et al. 2008. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 36(Database issue):D623-D631. (Pubitemid 351149796)
10. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. 2012. Predicting the functional effect of amino acid substitutions and indels. PLoS One 7(10):e46688.
11. Chomczynski P, Mackey K, Drews R, Wilfinger W. 1997. DNAzol: a reagent for the rapid isolation of genomic DNA. BioTechniques 22(3): 550-553.
12. Chow KC, Wong JT. 1996. Isolation and characterization of the Bacillus subtilis tryptophanyl-tRNA synthetase gene (trpS) conferring 5-fluorotryptophan resistance and temperature sensitivity. Biochim Biophys Acta. 1309(1-2): 42-46.
13. Cramer P. 2002. Multisubunit RNA polymerases. Curr Opin Struct Biol. 12(1): 89-97.
14. David M, Dzamba M, Lister D, Ilie L, Brudno M. 2011. SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics 27(7): 1011-1012.
15. Du H, Tarpey R, Babitzke P. 1997. The trp RNA-binding attenuation protein regulates TrpG synthesis by binding to the trpG ribosome binding site of Bacillus subtilis. J Bacteriol. 179(8): 2582-2586.
16. Gollnick P, Ishino S, Kuroda MI, Henner DJ, Yanofsky C. 1990. The mtr locus is a two-gene operon required for transcription attenuation in the trp operon of Bacillus subtilis. Proc Natl Acad Sci U S A. 87(22): 8726-8730.
17. Haldenwang WG. 1995. The sigma factors of Bacillus subtilis. Microbiol Rev. 59(1): 1-30.
18. Jakubowski H. 2012. Quality control in tRNA charging. Wiley Interdiscip Rev RNA. 3(3): 295-310.
19. Karp PD, et al. 2010. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 11(1): 40-79.
20. Karst JC, et al. 2009. The ATPase activity of an "essential" Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization. Microbiology 155(Pt 3): 944-956.
21. Knight RD, Landweber LF, Yarus M. 2001. Howmitochondria redefine the code. J Mol Evol. 53(4-5): 299-313.
22. Krzycki JA. 2004. Function of genetically encoded pyrrolysine in corrinoiddependent methylamine methyltransferases. Curr Opin Chem Biol. 8(5): 484-491.
23. Lane WJ, Darst SA. 2010a. Molecular evolution of multisubunit RNA polymerases: sequence analysis. J Mol Biol. 395(4): 671-685.
24. Lane WJ, Darst SA. 2010b. Molecular evolution of multisubunit RNA polymerases: structural analysis. J Mol Biol. 395(4): 686-704.
25. Lauhon CT. 2012. Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl- AMP. Biochemistry 51(44): 8950-8963.
26. Lemeignan B, Sonigo P, Marliere P. 1993. Phenotypic suppression by incorporation of an alien amino acid. J Mol Biol. 231(2): 161-166.
27. Li H, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16): 2078-2079.
28. Mat WK, Xue H, Wong JT. 2010. Genetic code mutations: the breaking of a three billion year invariance. PLoS One 5(8):e12206.
29. Murakami KS, Masuda S, Darst SA. 2002. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science 296(5571): 1280-1284.
30. Nakano MM, Zuber P, Glaser P, Danchin A, Hulett FM. 1996. Two-component regulatory proteins ResD-ResE are required for transcriptional activation of fnr upon oxygen limitation in Bacillus subtilis. J Bacteriol. 178(13): 3796-3802.
31. Opalka N, et al. 2010. Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol. 8(9):e1000483.
32. Parkhomchuk D, et al. 2009. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37(18):e123.
33. Polycarpo C, et al. 2004. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc Natl Acad Sci U S A. 101(34): 12450-12454.
34. Pratt EA, Ho C. 1975. Incorporation of fluorotryptophans into proteins of Escherichia coli. Biochemistry 14(13): 3035-3040.
35. Punta M, et al. 2012. The Pfam protein families database. Nucleic Acids Res. 40(Database issue):D290-D301.
36. Richards FJ. 1959. A flexible growth function for empirical use. J Exp Bot. 10(2): 290-301.
37. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. 2011. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 12(3):R22.
38. Santoro SW, Anderson JC, Lakshman V, Schultz PG. 2003. An archaebacteria- derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. Nucleic Acids Res. 31(23): 6700-6709.
39. Sarsero JP, Merino E, Yanofsky C. 2000. A Bacillus subtilis gene of previously unknown function, yhaG, is translationally regulated by tryptophan- activated TRAP and appears to be involved in tryptophan transport. J Bacteriol. 182(8): 2329-2331.
40. Sierro N, Makita Y, de Hoon M, Nakai K. 2008. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 36(Database issue): D93-D96. (Pubitemid 351149702)
41. Silva RM, et al. 2007. Critical roles for a genetic code alteration in the evolution of the genus Candida. EMBO J. 26(21): 4555-4565.
42. Tatusov RL, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
43. Trapnell C, et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28(5): 511-515.
44. Vassylyev DG, et al. 2002. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417(6890): 712-719.
45. Wang L, Brock A, Herberich B, Schultz PG. 2001. Expanding the genetic code of Escherichia coli. Science 292(5516): 498-500.
46. Wong JT. 1983. Membership mutation of the genetic code: loss of fitness by tryptophan. Proc Natl Acad Sci U S A. 80(20): 6303-6306.
47. Wong JT, Xue H. 2011. Synthetic genetic codes as the basis of synthetic life. Chemical synthetic biology. Chichester (United Kingdom): John Wiley & Sons, Ltd. p. 175-199.
48. Xie J, Schultz PG. 2006. A chemical toolkit for proteins-an expanded genetic code. Nat Rev Mol Cell Biol. 7(10): 775-782.
49. Xu ZJ, et al. 1989. Tryptophanyl-tRNA synthetase from Bacillus subtilis. Characterization and role of hydrophobicity in substrate recognition. J Biol Chem. 264(8): 4304-4311.
50. Yakhnin H, Yakhnin AV, Babitzke P. 2006. The trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis regulates translation initiation of ycbK, a gene encoding a putative efflux protein, by blocking ribosome binding. Mol Microbiol. 61(5): 1252-1266.
51. Yakhnin H, Zhang H, Yakhnin AV, Babitzke P. 2004. The trp RNA-binding attenuation protein of Bacillus subtilis regulates translation of the tryptophan transport gene trpP (yhaG) by blocking ribosome binding. J Bacteriol. 186(2): 278-286.
52. Yanofsky C. 2007. RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria. RNA 13(8): 1141-1154.
53. Yu CS, Yim KY, Tsui SK, Chan TF. 2012. Complete genome sequence of Bacillus subtilis strain QB928, a strain widely used in B. subtilis genetic studies. J Bacteriol. 194(22): 6308-6309.