Evidence for genetic drift in endosymbionts (Buchnera): Analyses of protein-coding genes

Molecular Biology and Evolution

Volumn 16, Issue 1, 1999, Pages 83-97

  Wernegreen, Jennifer J ^a   Moran, N A ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b NONE

Author keywords

Buchnera; Codon bias; Drift; Endosymbionts; Population size

Indexed keywords

ARTICLE; CODON; EMBRYO DEVELOPMENT; GENE LOCATION; GENE MUTATION; GENETIC ANALYSIS; GENETIC DRIFT; GENETIC RECOMBINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN ANALYSIS; SYMBIOSIS;

APHIDIDAE; BACTERIA (MICROORGANISMS); ENTERIC BACTERIA; ESCHERICHIA COLI;

EID: 0032948901     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026040     Document Type: Article

References (62)

1. AKASHI, H., and S. W. SCHAEFFER. 1997. Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophilia. Genetics 146:295-307.
2. AKSOY, S. 1995. Molecular analysis of the endosymbionts of tsetse flies: 16S rDNA locus and over-expression of a chaperonin. Insect Mol. Biol. 4:23-29.
3. ANDERSSON, S. G. E., and P. M. SHARP. 1996. Codon usage and base composition in Rickettsia prowazekii. J. Mol. Evol. 42:525-536.
4. BAUMANN, P., L. BAUMANN, and M. CLARK. 1996. Levels of Buchnera aphidicola chaperonin groEL during growth of the aphid Schizaphis graminum. Curr. Microbiol. 32:279-285.
5. BAUMANN, P., L. BAUMANN, M. A. CLARK, and M. L. THAO. 1998a. Buchnera aphidicola: the endosymbiont of aphids. ASM News 64:203-209.
6. BAUMANN, P., L. BAUMANN, C. LAI, D. ROUHBAKHSH, N. MORAN, and M. CLARK. 1995. Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. Ann. Rev. Microbiol. 49:55-94.
7. BAUMANN, L., P. BAUMANN, N. A. MORAN, J. SANDSTROM, and M. L. THAO. 1998b. Genetic characterization of plasmids containing genes encoding enzymes of leucine biosynthesis in endosymbionts (Buchnera) of aphids. J. Mol. Evol., in press.
8. BAUMANN, L., M. A. CLARK, D. ROUHBAKHSH, P. BAUMANN, N. A. MORAN, and D. J. VOEGTLIN. 1997. Endosymbionts (Buchnera) of the aphid Uroleucon sonchi contain plasmids with trpEG and remnants of trpE pseudogenes. Curr. Microbiol. 35:18-21.
9. BERG, O. G. 1995. Kinetics of synonymous codon change for an amino acid of arbitrary degeneracy. J. Mol. Evol. 41: 345-352.
10. BOCHDAREVA, E. S., N. M. LISSEN, and A. S. GIRSHOVICH. 1988. Transient association of newly synthesized unfolded proteins with the heat-shock GroEL protein. Nature 336: 254-257.
11. BRACHO, A. M., D. MARTINEZ-TORRES, A. MOYA, and A. LATORRE. 1995. Discovery and molecular characterization of a plasmid localized in Buchnera sp. bacterial endosymbiont of the aphid Rhopalosiphum padi. J. Mol. Evol. 41:67-73.
12. BRYNNEL, E. U., C. G. KURLAND, N. A. MORAN, and S. G. E. ANDERSSON. 1998. Evolutionary rates for tuf genes in endosymbionts of aphids. Mol. Biol. Evol. 15:574-582.
13. BUCHNER, P. 1965. Endosymbiosis of animals with plant microorganisms. Wiley and Sons, New York.
14. BULMER, M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907.
15. CLARK, M. A., L. BAUMANN, and P. BAUMANN. 1992. Sequence analysis of an aphid endosymbiont DNA fragment containing rpoB (S-subunit of RNA polymerase) and portions of rplL and rpoC. Curr. Microbiol. 25:283-290.
16. _. 1998. Sequence analysis of a 34.7-kb DNA segment from the genome of Buchnera aphidicola (endosymbiont of aphids) containing groEL, dnaA, the atp operon, gidA, and rho. Curr. Microbiol. 36:158-163.
17. DOUGLAS, A. 1998. Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera. Annu. Rev. Entomol. 43:17-37.
18. DYKHUIZEN, D. E., and L. GREEN. 1993. Recombination in E. coli and the definition of biological species. J. Bacteriol. 173:7257-7268.
19. GARDUNO, R. A., G. FAULKNER, M. A. TREVORS, N. VATS, and P. S. HOFFMAN. 1998. Immunolocalization of Hsp60 in Legionella pneumonphila. J. Bacteriol. 180:505-513.
20. GOLOUBINOFF, P., J. T. CHRISTELLER, A. A. GATENBY, and G. H. LORIMER. 1989. Reconstitution of active dimeric ribulose bisphosphate carboxylase from an unfolded state depends on two chaperonin proteins and Mg-ATP. Nature 342:884-889.
21. GOLOUBINOFF, P., A. A. GATENBY, and G. H. LORIMER. 1989. GroE heat-shock proteins promote assembly of foreign prokaryotic ribulose bisphosphate carboxylase oligomers in Escherichia coli. Nature 337:44-47.
22. GOUY, M., and C. GAUTIER. 1982. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10: 7055-7074.
23. HARA, E., T. FUKATSU, K. KAKEDA, M. KENGAKU, C. OHTAKA, and H. ISHIKAWA. 1990. The predominant protein in an aphid endosymbiont is homologous to an E. coli heat shock protein. Symbiosis 8:271-283.
24. HINDE, R. 1971. The control of the mycetocyte symbiotes of the aphids Brevicoryne brassicae, Myzus persicae and Macrosiphum rosae. J. Insect Physiol. 17:1791-1800.
25. IKEMURA, T. 1981. Correlation between the abundance of E. coli transfer RNA's and the occurrence of respective codons in its protein genes. J. Mol. Biol. 146:1-21.
26. _. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:13-34.
27. INA, Y. 1995. New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40:190-226.
28. ISHIKAWA, H. 1984. Characterization of the protein species synthesized in vivo and in vitro by an aphid endosymbiont. Insect Biochem. 14:417-425.
29. _. 1987. Nucleotide composition and kinetic complexity of the genomic DNA of an intracellular symbiont in the pea aphid Acyrthosiphon pisum. J. Mol. Evol. 24:205-211.
30. LAI, C. Y., L. BAUMANN, and P. BAUMANN. 1994. Amplification of trpEG: adaptation of Buchnera aphidicola to an endosymbiotic association with aphids. Proc. Natl. Acad. Sci. USA 91(38): 19-23.
31. LAMBERT, J. D., and N. A. MORAN. 1998. Deleterious mutations destabilize ribosomal RNA in endosymbiotic bacteria. Proc. Natl. Acad. Sci. USA 95:4458-4462.
32. Li, W. H. 1987. Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J. Mol. Evol. 24:337-345.
33. _. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
34. MADDISON, W. P., and D. R. MADDISON. 1992. MacClade: analysis of phylogeny and character evolution. Version 3.0. Sinauer Associates, Sunderland, Mass.
35. MAYNARD SMITH, J., C. B. DOWSON, and B. G. SPRATT. 1991. Localized sex in bacteria. Nature 349:29-31.
36. MAYNARD SMITH, J., N. SMITH, M. O'ROURKE, and B. SPRATT. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-4388.
37. MORAN, N. 1996. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl. Acad. Sci. USA 93: 2873-2878.
38. MORAN, N., and P. BAUMANN. 1994. Phylogenetics of cytoplasmically inherited microorganisms or arthropods. Trends Ecol. Evol. 9:15-20.
39. MORAN, N. A., C. D. VON DOHLEN, and P. BAUMANN. 1995. Faster evolutionary rates in endosymbiotic bacteria than in cospeciating insect hosts. J. Mol. Evol. 41:727-731.
40. MORTON, B. R. 1998. Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal line-ages. J. Mol. Evol. 46:449-459.
41. MUNSON, M. A., P. BAUMANN, M. A. CLARK, L. BAUMANN, N. A. MORAN, D. J. VOEGTLIN, and B. C. CAMPBELL. 1991. Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families. J. Bacteriol. 173:6321-6324.
42. MUSE, S. V., and B. S. WEIR. 1992. Testing for equality of evolutionary rates. Genetics 132:269-275.
43. MUTO, A., and S. OSAWA. 1987. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84:166-169.
44. OHTA, T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96-98.
45. OHTAKA, C., and H. ISHIKAWA. 1993. Accumulation of adenine and thymine in a groE-homologous operon of an intracellular symbiont. J. Mol. Evol. 36:121-126.
46. OHTAKA, C., H. NAKAMURA, and J. ISHIKAWA. 1992. Structures of chaperonins from an intracellular symbiont and their functional expression in E. coli groE mutants. J. Bacteriol. 174:1869-74.
47. ROUHBAKHSH, D., M. A. CLARK, L. BAUMANN, N. A. MORAN, and P. BAUMANN. 1997. Evolution of the tryptophan biosynthetic pathway in Buchnera (aphid endosymbionts): studies of plasmid-associated trpEG within the genus Uroleucon. Mol. Phylogenet. Evol. 8:167-176.
48. ROUHBAKHSH, D., C. Y. LAI, C. D. VON DOHLEN, M. A. CLARK, L. BAUMANN, P. BAUMANN, N. A. MORAN, and D. J. VOEGTLIN. 1996. The tryptophan biosynthetic pathway of aphid endosymbionts (Buchnera): genetics and evolution of plasmid-associated anthranilate synthase (trpEG) within the aphididae. J. Mol. Evol. 42:414-421.
49. SELANDER, R. K., D. A. CAUGANT, and T. S. WHITTAM. 1987. Genetic structure and variation in natural populations of Escherichia coli. Pp. 1625-1648 in F. NEIDHARDT, ed. Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society of Microbiology, Washington, D.C.
50. SHARP, P., E. COWE, D. G. HIGGINS, D. C. SHIELDS, K. H. WOLFE, and F. WRIGHT. 1988. Codon usage patterns in E. coli, B. subtilis, S. cerevisiae, S. pombe, D. melanogaster and H. sapiens: a review of the considerable within-species diversity. Nucleic Acids Res. 16:8207-8211.
51. SHARP, P. M., and K. M. DEVINE. 1989. Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons. Nucleic Acids Res. 17:5029-39.
52. SHARP, P. M., and W. H. LI. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15: 1281-1295.
53. SHARP, P., T. M. F. TUOHY, and K. R. MOSURSKI. 1986. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14:5125-5143.
54. SHIELDS, D. C. 1990. Switches in species-specific codon preferences: the influence of mutation biases. J. Mol. Evol. 31: 71-80.
55. SHIELDS, D. C., and P. M. SHARP. 1987. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res. 16:8023-8040.
56. SHIELDS, D. C., P. M. SHARP, D. G. HIGGINS, and F. WRIGHT. 1988. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5:704-716.
57. SOKAL, R. R., and F. J. ROHLF. 1981. Biometry. W.H. Freeman and Co., New York.
58. SUOEKA, N. 1961. Correlation between base composition of DNA and amino acid composition of protein. Proc. Natl. Acad. Sci. USA 47:1141-1149.
59. SWOFFORD, D. L. 1993. PAUP: phylogenetic analysis using parsimony. Version 3.1.1. Illinois Natural History Survey, Champaign.
60. VAN HAM, R., A. MOYA, and A. LATORRE. 1997. Putative evolutionary origin of plasmids carrying the genes involved in leucine biosynthesis in Buchnera aphidicola. J. Bacteriol. 179:4768-4777.
61. WRIGHT, F., and M. J. BIBB. 1992. Codon usage in the G+C-rich Streptomyces genome. Gene 113:55-65.
62. WRIGHT, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.