Low synonymous site variation at the lacY locus in Escherichia coli suggests the action of positive selection

Journal of Molecular Evolution

Volumn 42, Issue 2, 1996, Pages 79-84

  Wagner, Robert R ^a   Riley, Margaret A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

E. coli; Evolution; Lactose permease; lacY; Positive selection; Reduced synonymous polymorphism

Indexed keywords

ALLELE; ARTICLE; BACTERIAL GENE; ESCHERICHIA COLI; EVOLUTION; GENETIC POLYMORPHISM; NONHUMAN; NUCLEOTIDE SEQUENCE;

ALLELES; BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENES, BACTERIAL; HETEROZYGOTE; MEMBRANE TRANSPORT PROTEINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MONOSACCHARIDE TRANSPORT PROTEINS; POLYMORPHISM, GENETIC; SELECTION (GENETICS); SYMPORTERS; VARIATION (GENETICS);

EID: 0029878248     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02198831     Document Type: Article

References (30)

1. Bachmann BJ (1990) Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev 54(2):130-197
2. Bisercic M, Feutrier JY, Reeves PR (1991) Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus. J Bacteriol 173:3894-3900
3. Buchel DE, Gronenborn B, Muller-Hill B (1980) Sequence of the lactose permease gene. Nature 283:541-545
4. Dean AM (1989) Selection and neutrality in lactose operons of Escherichia coli. Genetics 123:441-454
5. Dykhuizen DE, Dean AM, Hartl DL (1987) Metabolic flux and fitness. Genetics 115:25-31
6. Dubose R, Dykhuizen DE, Hartl D (1988) Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. Proc Natl Acad Sci USA 85:7036-7040
7. Franco PJ, Brooker RJ (1994) Functional roles of Glu-269 and Glu-325 within the lactose permease of Escherichia coli. J Biol Chem 269: 7379-7386
8. Gillespie JH (1991) The causes of molecular evolution. Oxford University Press, New York, pp 1-40
9. Guttman DS, Dykhuizen D (1994) Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138:993-1003
10. Hall BG, Sharp PM (1992) 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
11. Innis MA, Gelfand DH, Sninsky JJ, White TJ (1990) PCR Protocols: a guide to methods and applications. Academic Press, San Diego, pp 3-20
12. Jung K, Jung H, Wu J, Prive GG, Kaback HR (1993) Use of site directed fluorescence labeling to study proximity relationships in the lactose permease of Escherichia coli. Biochemistry 32:12273-12278
13. Kaback HR, Jung K, Jung H, Wu J, Prive G, Zen K (1993) What's new with lactose permease. J Bioenerget Biomembr 25(6):627-636
14. Kascer H, Burns JA (1973) The control of flux. Symp Soc Exp Biol 27:65-104
15. Kascer H, Burns JA (1981) The molecular basis of dominance. Genetics 97:639-666
16. Koehn RK, Zera AJ, Hall JG (1983) Enzyme polymorphism and natural selection. In: Nei M, Koehn RC (eds) Evolution of genes and proteins. Sinauer Associates, Sunderland, pp 115-136
17. Li WH, Wu CI, Luo CC (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150-174
18. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 1.38
19. Milkman R, Crawford IP (1983) Clustered third base substitutions among wild strains of Escherichia coli. Science 221:378-379
20. Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, p 21
21. Ochman H, Selander RK (1984) Standard reference strains of Escherichia coli from natural populations. J Bacteriol 157:690-691
22. Ohta T (1992) A statistical examination of hypervariability in complementarity-determining regions of immunoglobulins. Mol Phylogenet Evol 1(4):305-311
23. Sahin-Toth MJ, Kaback HR (1993) Properties of interacting aspartic acid and lysine residues in the lactose permease of Escherichia coli. Biochemistry 32(38):10027-10035
24. Selander RK, Caugant DM, Whittam TS (1987) Genetic structure and variation in natural populations of Escherichia coli. In: Neidhardt FC (ed in chief) Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, DC
25. Sharp PM (1991) Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol 33:23-33
26. Sharp PM, Li W (1986) An evolutionary perspective on synonomous codon usage in unicellular organisms. J Mol Evol 24:28-38
27. Sharp PM, Li W (1987) The codon adaptation index - a measure of directional synonomous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281-1295
28. Sharp PM, Shields DC, Wolfe KH, Li W (1989) Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 246:808-810
29. Sokal RR, Rohlf FJ (1981) Biometry, 2nd ed. WH Freeman and Company, New York, p 783
30. Tanaka T, Nei M (1989) Positive Darwinian selection observed at the variable-region genes of immunoglobulins. Mol Biol Evol 6:447-459