The argRB of Escherichia coli is rare in isolates obtained from natural sources

Gene

Volumn 376 376, Issue 2, 2006, Pages 240-247

  Merlo, Lauren M F ^a   Sadowsky, Michael J ^a   Ferguson, John A ^a   Dean, Antony M ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Arginine repressor; Haploid polymorphism; Regulatory polymorphism

Indexed keywords

ARGININE; ESCHERICHIA COLI PROTEIN; REPRESSOR PROTEIN;

ALLELE; ANIMAL; ARTICLE; BACTERIAL GENE; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; DOMESTIC ANIMAL; ESCHERICHIA COLI; FECES; GENE FREQUENCY; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; STOP CODON; WILD ANIMAL;

ALLELES; ANIMALS; ANIMALS, DOMESTIC; ANIMALS, WILD; ARGININE; BASE SEQUENCE; CODON, TERMINATOR; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FECES; GENE FREQUENCY; GENES, BACTERIAL; HAPLOTYPES; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SEQUENCE ANALYSIS, PROTEIN; VARIATION (GENETICS);

EID: 33748118904     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2006.04.002     Document Type: Article

References (66)

1. Baumberg, S., 1970. Acetylhistidine as a substrate for acetylornithinase: a new system for the selection of arginine regulation mutants in Escherichia coli. Mol. Gen. Genet. 106, 162-173.
2. Blattner, F.R., et al., 1997. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1469.
3. Boyd, E.F., Nelson, K., Wang, F.-S., Whittam, T.S., Selander, R.K., 1994. Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. Proc. Natl. Acad. Sci. U. S. A. 91, 1280-1284.
4. Bulmer, M., 1988. J. Theor. Biol. 133, 67-71.
5. Chang, D.E., et al., 2004. Carbon nutrition of Escherichia coli in the mouse intestine. Proc. Natl. Acad. Sci. U. S. A. 101, 7427-7432.
6. Colosimo, P.F., et al., 2005. Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science 307, 1928-1933.
7. Cooper, V.S., Schneider, D., Blot, M., Lenski, R.E., 2001. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J. Bacteriol. 183, 2834-2841.
8. Cooper, T.F., Rozen, D.E., Lenski, R.E., 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc.Natl.Acad. Sci. U. S. A. 100, 1072-1077.
9. Cunin, R., Glansdorff, N., Pierard, A., Stalon, V., 1986. Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 50, 314-352.
10. Cunningham, C.W., et al., 1997. Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7. Mol. Biol. Evol. 14, 113-116.
11. Delbruck, M., Luria, S.E., 1942. Interference between bacterial viruses. I. Interference between two bacterial viruses acting upon the same host, and the mechanism of virus growth. Arch. Biochem. 1, 111-143.
12. Dennis, C.A., Glykos, N.M., Parsonsa, M.R., Phillipsa, S.E.V., 2002. The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Crystallogr., D Biol. Crystallogr. 58, 421-430.
13. Dombek, P.E., Johnson, L.K., Zimmerley, S.T., Sadowsky, M.J., 2000. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl. Environ. Microbiol. 147, 2572-2577.
14. Drake, J.W., Charlesworth, B., Charlesworth, D., Crow, J.F., 1998. Rates of spontaneous mutation. Genetics 148, 1667-1686.
15. Dufour, A.P., Strickland, E.R., Cabelli, V.J., 1981. Membrane filter method for enumerating Escherichia coli. Appl. Environ. Microbiol. 41, 1152-1158.
16. Dykhuizen, D.E., Dean, A.M., 2004. Evolution of specialists in an experimental microcosm. Genetics 167, 2015-2026.
17. Eyre-Walker, A., Bulmer, M., 1993. Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res. 21, 4599-4603.
18. Freter, R., 1983. In: Hentges, D.J. (Ed.), Human Intestinal Microflora in Health and Disease. Academic, New York, pp. 33-54.
19. Fu, Y.-X., Li, W.-H., 1993. Statistical tests of neutrality of mutations. Genetics 133, 693-709.
20. Gordon, D.M., Bauer, S., Johnson, J.R., 2002. The genetic structure of Escherichia coli populations in primary and secondary habitats. Microbiology 148, 1513-1522.
21. Hall, B.G., 1984. The evolved β-galactosidase system of Escherichia coli. In: Mortlock, R.P. (Ed.), Microorganisms as Model Systems for Studying Evolution. Plenum, New York, pp. 165-185.
22. Harris, H., Hopkinson, D.A., 1972. Average heterozygosity per locus in man: an estimate based on the incidence of enzyme polymorphisms. Ann. Hum. Genet. Lond. 36, 9-20.
23. Hirano, H.-Y., Eiguchi, M., Sano, Y., 1998. A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Mol. Biol. Evol. 15, 978-987.
24. Horiuchi, T., Horiuchi, S., Novick, A., 1963. The genetic basis of hyper-synthesis of β-galactosidase. Genetics 48, 157-169.
25. Johnson, L.K., Brown, M.B., Carruthers, E.A., Ferguson, J.A., Dombek, P.E., Sadowsky, M.J., 2004. Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl. Environ. Microbiol. 70, 4478-4485.
26. Jolley, K.A., Feil, E.J., Chan, M.S., Maiden, M.C., 2001. Sequence type analysis and recombination tests (START). Bioinformatics 17, 1230-1231.
27. Kadner, R.J., Maas, W.K., 1971. Regulatory gene mutations affecting arginine biosynthesis in Escherichia coli. Mol. Gen. Genet. 111, 1-14.
28. Kosakovsky Pond, S.L., Frost, S.D.W., Muse, S.V., 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21, 676-679.
29. Lim, D., Oppenheim, J.D., Eckhardt, T.,Maas,W.K., 1987. Nucleotide sequence of the argR gene of Escherichia coli K-12 and isolation of its product, the arginine repressor. Proc. Natl. Acad. Sci. U. S. A. 84, 6697-6701.
30. Lim, D., Oppenheim, J.D., Eckhardt, T., Maas, W.K., 1988. The unitary hypothesis for the repression mechanism of arginine biosynthesis in E. coli B and E. coli K12-revisited after 18 years. In: Bissel, M., Deho, G., Sironi, G., Torriani, A. (Eds.), Gene Expression and Regulation: the Legacy of Luigi Gorinini. Excerpta Medica, New York, pp. 55-63.
31. Maas,W.K., 1961. Repression of arginine formation. Cold Spring Harbor Symp. Quant. Biol. 26, 183-190.
32. McDonald, J.H., Kreitman, M., 1991. Adaptive protein evolution and the Adh locus in Drosophila. Nature 351, 652-654.
33. Miller, J.H., 1992. A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory Press, pp. 437-440.
34. Monod, J., 1942. Recherches sur la croissance des cultures bactériennes. Herman et Cie, Paris.
35. Nakatsu, C.H., Korona, R., Lenski, R.E., de Brujin, F.J., Marsh, T.L., Forney, L.J., 1998. Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp. J. Bacteriol. 180, 4325-4331.
36. Notley-McRobb, L., Ferenci, T., 2000. Experimental analysis of molecular events during mutational periodic selections in bacterial evolution. Genetics 156, 1493-1501.
37. Ochman, H., Selander, R.K., 1984. Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157, 690-693.
38. Posada, D., Crandall, K., Holmes, E.C., 2002. Recombination in evolutionary genomics. Annu. Rev. Genet. 36, 75-97.
39. Poulsen, L.K., Licht, T.R., Rang, C., Krogfelt, K.A., Molin, S., 1995. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycin-treated mice. J. Bacteriol. 177, 5840-5845.
40. Prokunina, L., et al., 2002. A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. Nat. Genet. 32, 666.
41. Pupo, G.M., Lan, R., Reeves, P.R., Baverstock, P.R., 2000. Population genetics of Escherichia coli in a natural population of native Australian rats. Environ. Microbiol. 2, 594-610.
42. Purugganan, M.D., 2000. The molecular population genetics of regulatory genes. Mol. Ecol. 9, 1451-1461.
43. Rainey, P.B., Travisano, M., 1998. Adaptive radiation in a heterogeneous environment. Nature 394, 69-72.
44. Reid, S.D., Herbelin, C.J., Bumbaugh, A.C., Selander, R.K., Whittam, T.S., 2000. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406, 64-67.
45. Riehle, M.M., Bennett, A.F., Long, A.D., 2001. Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 98, 525-530.
46. Rosenzweig, R.F., Sharp, R.R., Treves, D.S., Adams, J., 1994. Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Genetics 137, 903-917.
47. Rozas, J., Sanchez-DelBarrio, J.C., Messeguer, X., Rozas, R., 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497.
48. Savageau, M.A., 1983. Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122, 732-744.
49. Sawyer, S., 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6, 526-538.
50. Sawyer, S.A., Dykhuizen, D.E., Hartl, D.L., 1987. Confidence interval for the number of selectively neutral amino acid polymorphisms. Proc. Natl. Acad. Sci. U. S. A. 84, 6225-6228.
51. Schaechter, M., et al., 1996. The view from here. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella.ASMPress,Washington DC, p. 8. chapter 155.
52. Schulte, P.M., Glemet, H.C., Fiebig, A.A., Powers, D.A., 2000. Adaptive variation in lactate dehydrogenase-B gene expression: role of a stress-responsive regulatory element. Proc. Natl. Acad. Sci. U. S. A. 97, 6597-6602.
53. Suiter, A.M., Dean, A.M., 2005. Selection in a cyclical environment: possible impact of phenotypic lag on Darwinian fitness. J. Mol. Evol. 61, 153-170.
54. Suiter,A.M., Banziger,O.,Dean,A.M., 2003. Fitness consequences of a regulatory polymorphism in a seasonal environment. Proc. Natl. Acad. Sci. U. S. A. 100, 12782-12786.
55. Sunnerhagen, M., Nilges, M., Otting, G., Carey, J., 1997. Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA. Nat. Struct. Biol. 4, 819-826.
56. Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
57. Tian, G., Maas, W.K., 1994. Mutational analysis of the arginine repressor of Escherichia coli. Mol. Microbiol. 13, 599-608.
58. Tian, G., Lim, D., Oppenheim, J.D., Maas, W.K., 1994. Explanation for different types of regulation of arginine biosynthesis in Escherichia coli B and Escherichia coli K12 caused by a difference between their arginine repressors. J. Mol. Biol. 235, 221-230.
59. Treves, D.S., Manning, S., Adams, J., 1998. Repeated evolution of an acetatecrossfeeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15, 789-797.
60. Van Duyne, G.D., Ghosh, G., Maas, W.K., Sigler, P.B., 1996. Structure of the oligomerization and arginine binding domain of the arginine repressor of Escherichia coli. J. Mol. Biol. 256, 377-391.
61. Wang, R.-L., Stec, A., Hey, J., Lukens, L., Doebley, J., 1999. The limits of selection during maize domestication. Nature 398, 236-239.
62. Waterworth, D.M., et al., 1997. Linkage and association of insulin gene VNTR regulatory polymorphism with polycystic ovary syndrome. Lancet 349, 986-990.
63. Wichman, H.A., Scott, L.A., Yarber, C.D., Bull, J.J., 2000. Experimental evolution recapitulates natural evolution. Philos. Trans. R. Soc. Lond., B 355, 1677-1684.
64. Winfield, M.D., Groisman, E.A., 2003. Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli. Appl. Environ. Microbiol. 69, 3687-3694.
65. Zambrano, M.M., Siegele, D.A., Almiron, M., Tormo, A., Kolter, R., 1993. Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 259, 1757-1760.
66. Zhong, S., Khodursky, A., Dykhuizen, D.E., Dean, A.M., 2004. Evolutionary genomics of ecological specialization. Proc. Natl. Acad. Sci. U. S. A. 101, 11719-11724.