Amelioration of bacterial genomes: Rates of change and exchange

Journal of Molecular Evolution

Volumn 44, Issue 4, 1997, Pages 383-397

  Lawrence, Jeffrey G ^a,c   Ochman, Howard ^b  

^a UNIVERSITY OF UTAH   (United States)

^b UNIVERSITY OF ROCHESTER   (United States)

^c UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Bacterial evolution; Directed mutation pressure; Escherichia coli; GC content; Genome amelioration; Horizontal transfer; Invasion genes; Salmonella enterica

Indexed keywords

ARTICLE; BACTERIAL GENE; BIODIVERSITY; DNA BASE COMPOSITION; ENTEROBACTERIACEAE; ESCHERICHIA COLI; EVOLUTION; POINT MUTATION; SALMONELLA ENTERICA;

BACTERIA; BASE COMPOSITION; CHROMOSOMES, BACTERIAL; CODON; DNA, BACTERIAL; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENOME, BACTERIAL; SALMONELLA; TIME; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); ENTERIC BACTERIA; ENTEROBACTERIACEAE; ESCHERICHIA COLI; SALMONELLA ENTERICA;

EID: 0030994798     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006158     Document Type: Article

References (54)

1. Barinaga M (1996) A shared strategy for virulence. Science 272:1261-1263
2. Bergthorsson U, Ochman H (1995) Heterogeneity of genome size among natural isolates of Escherichia coli. J Bacteriol 177:5784-5789
3. Bernardi G (1989) The isochore organization of the human genome. Annu Rev Genet 23:637-661
4. Burland V, Plunkett III G, Daniels DL, Blattner FR (1993) DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16:551-561
5. Buvinger WE, Lampel KA, Bojanowski RJ, Riley M (1984) Location and analysis of nucleotide sequences at one end of a putative lac transposon in the Escherichia coli chromosome. J Bacteriol 159:618-623
6. 12, dimethylbenzimidazole. J Bacteriol 177:1461-1469
7. Daniels DL, Plunkett III G, Burland V, Blattner FR (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257:771-778
8. Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387-395
9. Doolittle RF, Feng DF, Tsang S, Cho G, Little E (1996) Determining the divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470-477
10. Efron B, Gong G (1983) A leisurely look at the bootstrap, the jackknife, and cross-validation. Am Stat 37:36-48
11. Felsenstein J (1985) Confidence intervals on phylogenies: an approach using the bootstrap. Evolution 39:783-791
12. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb J-F, Dougherty BA, Merrick JM et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
13. Ginocchio CC, Galàn JE (1995) Functional conservation among members of the Salmonella typhimurium InvA family of proteins. Infect Immun 63:729-732
14. Groisman EA, Ochman H (1993) Cognate genes govern invasion of host epithelial cells by Salmonella typhimurium and Shigella flexneri. EMBO J 12:3779-3787
15. Gross TJ, Schweizer HP, Datta P (1988) Molecular characterization of the tdc operon of Escherichia coli K-12. J Bacteriol 170:5352-5359
16. Guttman DS, Dykhuizen DE (1994a) Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266:1380-1383
17. Guttman DS, Dykhuizen DE (1994b) Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138:993-1003
18. Harsono KD, Caspar CW, Luchansky JB (1993) Comparison and genomic sizing of Escherichia coli O157:H7 isolates by pulsed-field gel electrophoresis. Appl Environ Microbiol 59:3141-3144
19. Jiang W, Metcalf WW, Lee KS, Wanner BL (1995) Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2. J Bacteriol 177:6411-6421
20. Kidwell M (1993) Lateral transfer in natural populations of eukaryotes. Annu Rev Genet 27:235-256
21. Klena JD, Pradel E, Schnaitman CA (1993) The rfaS gene, which is involved in production of a rough form of lipopolysaccharide core in Escherichia coli K-12, is not present in the rfa cluster of Salmonella typhimurium LT2. J Bacteriol 175:1524-1527
22. Lawrence JG, Hartl DL (1992) Inference of horizontal genetic transfer: an approach using the bootstrap. Genetics 131:753-760
23. 12) biosynthetic genes of Escherichia coli. J Bacteriol 177:6371-6380
24. 12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. Genetics 142:11-24
25. Lawrence JG, Roth JR (1996b) Selfish operons-horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860
26. Li J, Ochman H, Groisman EA, Boyd EF, Nelson K, Solomon F, Selander RK (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
27. Maurelli AT (1994) Virulence protein export systems in Salmonella and Shigella: a new family or lost relatives. Trends Cell Biol 4:240-242
28. Médigue C, Rouxel T, Vigier P, Hénaut A, Danchin A (1991) Evidence of horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222:851-856
29. Metcalf WW, Wanner BL (1993) Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli. Gene 129:27-32
30. Milkman R, Bridges MM (1990) Molecular evolution of the E. coli chromosome. III. Clonal frames. Genetics 126:505-517
31. Milkman R, Bridges MM (1993) Molecular evolution of the E. coli chromosome. IV. Sequence comparisons. Genetics 133:455-468
32. Muto A, Osawa S (1987) The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci USA 84:166-169
33. Ochman H, Groisman EA (1995) The evolution of invasion in enteric bacteria. Can J Microbiol 41:555-561
34. Ochman H, Lawrence JG (1996) Phylogenetics and the amelioration of bacterial genomes. In: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology. 2nd ed. American Society for Microbiology, Washington, DC, pp 2627-2637
35. Ochman H, Wilson AC (1987) Evolutionary history of enteric bacteria. In: Neidhardt FC, Ingraham JL, Low KB, Magasanik B, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, DC, pp 1649-1654
36. Ochman H, Wilson AC (1988) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26:74-86
37. Ochman H, Whittam TS, Caugant DA, Selander RK (1983) Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella. J Gen Microbiol 129:2715-2726
38. Ochman H, Soncini FC, Solomon F, Groisman EA (1996) Identification of a pathogenicity island required for Salmonella survival in host cells. Proc Natl Acad Sci USA 93:7800-7804
39. Plunkett G, Burland V, Daniels D, Blattner F (1993) Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res 21:3391-3398
40. Rolfe R, Meselson M (1959) The relative homogeneity of microbial DNA. Proc Natl Acad Sci USA 45:1039-1042
41. 12) biosynthetic genes of Salmonella typhimurium. J Bacteriol 175:3303-3316
42. Schildkraut CL, Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol 4:430-443
43. Sharp PM (1991) Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium. J Mol Evol 33:23-33
44. Sharp PM, Li W-H (1987) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281-1295
45. Sofia HJ, Burland V, Daniels DL, Plunkett G, Blattner FR (1994) Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res 22:2576-2586
46. Sueoka N (1961) Variation and heterogeneity of base composition of deoxy-ribonucleic acids: a compilation of old and new data. J Mol Biol 3:31-40
47. Sueoka N (1962) On the genetic basis of variation and heterogeneity in base composition. Proc Natl Acad Sci USA 48:582-592
48. Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85:2653-2657
49. Sueoka N (1992) Directional mutation pressure, selective constraints, and genetic equilibria. J Mol Evol 34:95-114
50. Sueoka N (1993) Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J Mol Evol 37:137-153
51. Sueoka N, Marmur J, Doty P (1959) Heterogeneity in deoxyribonucleic acids. II. Dependence of the density of deoxyribonucleic acids on guanine-cytosine. Nature 183:1429-1431
52. Syvanen M (1994) Horizontal gene flow: evidence and possible consequences. Annu Rev Genet 28:237-261
53. Wanner BL, Metcalf WW (1992) Molecular genetic studies of a 10.9kb operon in Escherichia coli for phosphonate uptake and biodegradation. FEMS Microbiol Lett 79:133-139
54. Whittam TS, Ake S (1992) Genetic polymorphisms and recombination in natural populations of Escherichia coli. In: Takahata N, Clark AG (eds) Mechanisms of molecular evolution. Japan Scientific Society Press, Tokyo, pp 223-246