Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli

Genetics

Volumn 147, Issue 4, 1997, Pages 1509-1520

  Nelson, Kimberlyn ^a,d   Wang, Fu Sheng ^c   Boyd, E Fidelma ^b   Seiander, Robert K ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b Institute of Molecular Evolutionary Genetics   (United States)

^c UNIVERSITY OF WESTERN ONTARIO   (Canada)

^d HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOCITRATE DEHYDROGENASE; PHOSPHATASE; PHOSPHOTRANSFERASE;

ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; DNA FLANKING REGION; DNA SEQUENCE; ESCHERICHIA COLI; EVOLUTION; GENE LOCUS; GENE SEQUENCE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SALMONELLA ENTERICA;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; MANNOSYLTRANSFERASES; MOLECULAR SEQUENCE DATA; PHOSPHOPROTEIN PHOSPHATASE; POLYMORPHISM, GENETIC; PROTEIN-SERINE-THREONINE KINASES; REPRESSOR PROTEINS; SALMONELLA ENTERICA; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SALMONELLA ENTERICA;

EID: 0030834799     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (43)

1. ACHTMAN, M., 1994 Clonal spread of serogroup A meningococci: a paradigm for the analysis of microevolution in bacteria. Mol. Microbiol. 11: 15-22.
2. BELTRAN, P.,J. M. MUSSER, R. HELMUTH.J.J. FARMER III, W. M. FRERiciis et al., 1988 To^vard a population genetic analysis of Salmonella: genetic diversity and relationships among strains of serotypes S. choleraesuis, S. derby, S. dublin, S. enleritidis, S. Heidelberg, S. infanta, S. neii'port, and S. typhimurium. Proc. Natl. Acad. Sci. USA 85: 7753-7757.
3. BF.RGTHORSSON, U., and H. OCHMAN, 1995 Heterogeneity of genome size among natural isolates of Escherichia coli.]. Bacteriol. 177: 5784-5789.
4. BISERCIC, M., J.Y. FEUTRIER and P. R. REEVES, 1991 Nucleotide sequence 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.
5. BOYD, E. F., K. NEI.SON, F.-S. WANG, T. S. WIIITTAM and R. K. SEI, ANDER, 1994 Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural population^ of Escherichia coli and Salmonella enterica. Proc. Natl. Acad. Sci. USA 91: 1280-1284.
6. BOYD, E. F., F.-S. WANG, T. S. WIIITTAM and R. K. SEIANDER, 1996 Molecular genetic relationships of the salmonellae. Appl. Environ. Microbiol. 62: 804-808.
7. BOYD, E. F., J. Li, H. OCHMAN and R. K. SEIENDER, 1997 Comparative genetics of the inn-spa invasion gene complex of Salmonella enterica.]. Bacteriol. 179: 1985-1991.
8. BRUNIIAM, R. C., F. A. PLUMMER and R. S. STEPHENS, 1993 Bacterial antigenic variation, host immune response, and pathogen-host coevolution. Infect. Immunol. 61: 2273-2276.
9. CABOT, E. L., and A. T. BECKENBACH, 1989 Simultaneous editing of multiple nucleic acid and protein sequences with ESEE. Comput. Appl. Biosci. 5: 233-234.
10. CORTAY, J.-C., F. BLEICHER, C. RIEUL, H. C. REEVES and A.J. COZZONE, 1988 Nucleotide sequence and expression of the aceK gene coding for isocitrate dehydrogenase kinase/phosphatase in Escherichia coli.]. Bacteriol. 170: 89-97.
11. DVKHUIZEN, D. E., and L. GREEN, 1991 Recombination in Escherichia coli and the definition of the biological species. J. Bacteriol. 173: 7257-7268.
12. FRANKEL, G., S. M. C. NEWTON-, G. K. SCIIOOI.NIK and B. A. D. STOCKER, 1989 Intragenic recombination in a flagellin gene: characterization of the IIl.j gene of Salmonella typhi. E.MBOJ. 8: 3149-3152.
13. GALINIER, L., F. BLEICHER, D. NèGRE, G. PERRIèRE, B. Duci.os et al., 1991 Primär)' structure of the intergenic region between aceK and iclR'm the Escherichia coli chromosome. Gène 97: 149-150.
14. HALL, B. G., and P. M. SILVRT, 1992 Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, or, and giilli loci of natural isolates. Mol. Biol. Evol. 9: 654-665.
15. HERZER,P.J.,S.lNOUYE,M.lNOUYEandT. S.WIIITTAM, 1990 Phylogenetic distribution of branched RNA-linked multicopy singlestranded DN'A among natural isolates of Escherichia coli. J. Bacteriol. 172: 6175-6181.
16. KI.UMPP, D. J., D. W. PIANK, L. J. BOWDIX, C. S. STUEIAND, T. CIIUNC. et al., 1988 Nucleotide sequence of aceK, the gene encoding isocitrate dehydrogenase kinase/phosphatase. J. Bacteriol. 170: 2763-2769.
17. KUMAR, S., K. TAMURA and M. NF.I, 1993 MEGA: molecular evolutionär)' genetics analysis, version 1. The Pennsylvania State University, University Park, PA 16802.
18. LAPORTE, D. C., 1993 The isocitrate dehydrogenase phosphorylation cycle: regulation and enzymology. J. Cell. Biochem. 51: 1418.
19. LI, J., K. NELSON, A. C. MCWIIORTER, T. S. WIHTTAM and R. K. SELANDER, 1994 Recombinational basis of serovar diversity in Salmonella enterica. Proc. Natl. Acad. Sci. USA 91: 2552-2556.
20. LI,J., H. OCIIMAN, E. A. GROISMAN, E. F. BOYD, F. SOLOMON et al., 1995 Relationship between evolutionary rate and cellular location among the Inv/Spa invasion proteins of Salmonella enterica. Proc. Natl. Acad. Sci. USA 92: 7252-7256.
21. LIU, S.-L., and K. E. SANDERSON, 1995a I-CcwI reveals conservation of the genome of independent strains of Salmonella lyphimurium. J. Bacteriol. 177: 3355-3357.
22. LIU, S.-L., and K. E. SAXDERSON, 1995b Rearrangement in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. USA 92: 1018-1022.
23. LIU, S.-L., and K. E. SANDERSON, 1995c The chromosome of Salmonella jiaratyphi A is inverted by recombination between rnhH and rnG. J. Bacteriol. 177: 6585-6592.
24. MATSUOKA, M., and B. A. MCFADDEN, 1988 Isolation, hyperexpression, and sequencing of the aceA gene encoding isocitrate lyase in Escherichia coli.]. Bacteriol. 170: 4528-4536.
25. MILKMAN, R., and M. M. BRIDGES, 1993 Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons. Genetics 133: 455-468.
26. MOXON, E. R., P. B. RAINEY, M. A. NOWAK and R. E. LENSKI, 1994 Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4: 24-33.
27. NELSON, K., and R. K. SEIANDER, 1992 Evolutionary genetics of the proline permease gene (pntlr) and the control region of the proline utilization operon in populations of SalmoneHa and Escherichia coli.]. Bacteriol. 174: 6886-6895.
28. NELSON, K., and R. K. SEIANDER, 1994a Analysis of genetic variation by polymerase chain reaction-based nucleotide sequencing. Methods Enzymol. 235: 174-183.
29. NEI.SON, K., and R. K. SEIENDER, 1994b Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria. Proc. Natl. Acad. Sci. USA 91: 1022710231.
30. NELSON, K., T. S. WIIITTAM and R. K. SEIENDER, 1991 Nucleotide polymorphism and evolution in the glyccraldehycle-3-pliosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl. Acad. Sci. USA 88: 6667-6671.
31. OCHMAN, H., and R. K. SEIANDER, 1984 Standard reference strains of Escherichia coli from natural populations.J. Bacteriol. 157:690693.
32. REEVES, M.W., G. M. EVINS, A.A. HF.IRA, B.D. PIJKAYTIS and J.J. FARMER III, 1989 Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov.J. Clin. Microbiol. 27: 311-320.
33. REEVES, P. R., 1992 Variation in O-antigens, niche-specific selection and bacterial populations. FEMS Microbiol. Lett. 100: 509-516.
34. RIEUL, C., F. BLEICHER, B. Duci.os, J.-C. CORTAV and A.J. COZXONE, 1988 Nucleotide sequence of the aceA gene coding for isocitrate lyase in Escherichia coli. Nucleic Acids Res. 16: 5689.
35. SAIKI, R. K., D. H. GELFAND, S. STOFFEL, S.J. SCHARF, R. HIGUCHI et al., 1988 Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
36. SAITOU, N., and M. NEI, 1987 The neighborjoining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
37. SELANDER, R. K., and B. R. LEVIN, 1980 Genetic diversity and structure in Escherichia coli populations. Science 210: 545-547.
38. SEIANDER, R. K., J. Li, E. F. BOYD, F.-S. WANG and K. NEI.SOX, 1994 DNA sequence analysis of the genetic structure of populations of Salmonella enlerica and Escherichia coli, pp. 17-49 in Bacterial Diversity and Systematics, edited by F. G. PRIEST, A. RVMOS-CORMEXZAXA and B. J. TINDALL. Plenum Press, New York.
39. SMITH, N. H., P. BELTRAN and R. K. SELANDER, 1990 Recombination of Salmonella phase 1 flagellin genes generates new serovars. J. Bacteriol. 172: 2209-2216.
40. STEPHENS, J. C., 1985 Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2: 539-556.
41. THAMPAPAPILLAI, G., R. LAN and P. R. REEVES, 1994 Molecular evolution in the gnd locus of Salmonella enterica. Mol. Biol. Evol. 11: 813-828.
42. WANG, F.-S., T. S. WHITTAM and R. K. SEIANDER, 1997 Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia for and Salmonella enterica.]. Bacteriol. (in press).
43. WILSON, D. R., and T.J. BEVERIDGE, 1993 Bacterial flagellar filaments and their component flagellins. Can. J. Microbiol. 39: 451-472.