The close proximity of Escherichia coli genes: Consequences for stop codon and synonymous codon use

Journal of Molecular Evolution

Volumn 42, Issue 2, 1996, Pages 73-78

  Eyre Walker, Adam ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Escherichia coli; Shine Dalgarno; Stop codons; Synonymous codons

Indexed keywords

MESSENGER RNA;

ARTICLE; BACTERIAL GENE; CODON; ESCHERICHIA COLI; EVOLUTION; NONHUMAN; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS;

BASE SEQUENCE; BINDING SITES; CODON, TERMINATOR; DNA, BACTERIAL; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; RIBOSOMES; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

EID: 0029878715     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02198830     Document Type: Article

References (25)

1. Ser/Phe. Nucleic Acids Res 21:2891-2897
2. Brown CM, Stockwell PA, Trotman CNA, Tate WP (1990) The signal for the termination of protein synthesis in procaryotes. Nucleic Acids Res 18:2079-2086
3. Bulmer M (1988) Are codon usage patterns in unicellular organisms determined by a mutation-selection balance? J Evol Biol 1:15-26
4. Bulmer M (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907
5. de Smit MH, van Druin J (1990) Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc Natl Acad Sci USA 87:7668-7672
6. Eyre-Walker A, Bulmer M (1993) Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res 21: 4599-4603
7. Eyre-Walker A (1995) The distance between Encherichia coli genes is related to gene expression levels. J Bacteriol 177:5368-5369
8. Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 83:9373-9377
9. Guttman DS, Dykhuizen DE (1994) Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138:993-1003
10. Gold L (1988) Posttranscriptional regulatory mechanisms in Excherichia coli. Ann Rev Biochem 57:199-233
11. Grosjean H, Fiers W (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anti-codon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18:199-209
12. Hall BG, Sharp PM (1991) Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, crr, and gutB loci of natural isolates. Mol Biol Evol 9:654-665
13. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13-34
14. Jaeger JA, Turner DH, Zuker M (1989) Improved prediction of secondary structures for RNA. Proc Natl Acad Sci USA 86:7706-7710
15. Konigsberg WJN, Godson GN (1983) Evidence for the use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc Natl Acad Sci USA 80:687-691
16. Kurland CG (1991) Codon bias and gene expression. FEBS Lett 285: 165-169
17. Lawrence JG, Hartl DL (1991) Unusual codon bias occurring within insertion sequences in Escherichia coli. Genetica 84:23-29
18. Rudd KE (1992) Alignment of E. coli DNA sequences to a revised integrated genomic restriction map. In: Miller J (ed) A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Press, Cold Spring Harbor
19. Schurr T, Nadir E, Margalit H (1993) Identification and characterization of E. coli ribosomal binding sites by tree energy computation. Nucleic Acids Res 21:4019-4023
20. Sharp PM (1989) Evolution at silent-sites in DNA. In: Hill WG, McKay TFC (eds) Evolution and animal breeding: reviews of molecular and quantitative approaches in honour of Alan Robertson. CAB International, Wallingford, p 23
21. Sharp PM, Li W-H (1987) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acid Res 15:1281-1295
22. Sharp PM, Bulmer M (1988) Selective differences among translation termination codons. Gene 63:141-145
23. Shields DC (1990) Switches in species-specific codon preferences: the influence of mutation biases. J Mol Evol 31:71-80
24. Shine J, Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71:1342-1346
25. Vallanoweth RL, Rabinowitz JC (1992) The influence of ribosome-binding-site elements on the translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Mol Microbiol 6:1105-1114