Eubacterial genomes

Mobile DNA II

Volumn , Issue , 2022, Pages 1024-1039

  Campbell, Allan ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Eubacterial genomes; Gene transfers; Prophage; Site specific recombination

Indexed keywords

EID: 85158032422     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1128/9781555817954.ch44     Document Type: Chapter

References (43)

1. Anilionis, A., Riley M. 1980. Conservation and variation of nucleotide sequences within related bacterial genomes: Escherichia coli strains. Bacteriol J. 143:355-365.
2. Barondess, J. J., Beckwith J. 1990. A bacterial virulence determinant encoded by lysogenic coliphage lambda. Nature (London) 346:871-872.
3. Barreiro, V., Haggard-Ljungquist E. 1992. Attachment sites for bacteriophage P2 on the Escherichia coli chromosome: DNA sequences, localization on the physical map, detection of a P2-like remnant in E. coli K-12 derivatives. J. Bacte- riol. 174:4086-4093.
4. Berlyn, M. K. B. 1998. Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol. Mol. Biol. Rev. 62: 814-984.
5. Blattner, F. R., Plunkett III G., Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glassner J.D., Rode C.K., Mayhew G.F., Gregor J., David N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1468.
6. Campbell, A. 1992. Chromosomal insertion sites for phages and plasmids. Bacteriol J. 174:7495-7499.
7. Campbell, A., Kim Ha J., Limberger R.J., Schneider S.J. 1990. Bacteriophage evolution and population structure, p. 191-200. In M. Clegg and S.J. O'Brien (ed.), Molecular Evolution. Wiley-Liss, New York, N.Y.
8. Campbell, A., Schneider S.J., Song B. 1992. Lambdoid phages as elements of bacterial genomes. Genetica 86: 259-267.
9. Censini, S., Lange C., Xiang Z., Crabtree J.E., Ghiara P., Borodovsky M., Rappuoli R., Covacci A. 1996. Cag, a pathogenicity island of Helicobacter pylori, encodes I-specific and disease-associated virulence factors. Proc. Natl. Acad. Sci. USA 93:14648-14652.
10. Cheetham, B. F., Tattersoll D.B., Bloomfield G.A., Rood J.I., Katz M.E. 1995. Identification of a gene encoding a bacteriophage-related integrase in a vap region of the Dicholo- bacter nodosus genome. Gene 162:53-58.
11. Corre, J., Patte J., Louarn J.-M. 2000. Prophage \ induces terminal recombination in Escherichia coli by inhibiting chromosome dimer resolution: an orientation-dependent cis effect lending support to bipolarization of the terminus. Genetics 154:39-48.
12. Court, D., Oppenheim A. 1983. Phagelambda'saccessory genes, p. 251-278. In Hendrix R., Roberts J., Stahl F., R. Weisberg (ed.), Lambda II. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
13. Diaz, R., Kaiser K. 1981. Rac E. coli K-12 strains carry a preferential attachment site for lambda rev. Mol. Gen. Genet. 183:484-489.
14. Greener, A., Hill C.W. 1980. Identification of a novel genetic element in Escherichia coli K-12. Bacteriol J. 144: 312-321.
15. Hacker, J., Blum-Ohler G., Muhldorper L., Tschape H. 1997. Pathogenicity islands of virulent bacteria: structure, function, impact on microbial evolution. Mol. Microbiol. 236:1089-1097.
16. Haggard-Ljungquist, E., Halling C., Calender R. 1992. DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages. Bacteriol J. 174:1462-1477.
17. Hendrix, R. W., Smith M.C.M., Burns R.N., Ford M.E., Hatfull G.F. 1999. Evolutionary relationships among diverse bacteriophage and prophages: all the world's a phage. Proc. Natl. Acad. Sci. USA 96:2192-2197.
18. Hou, Y. M. 1999. Transfer RNAs and pathogenicity islands. Trends Biochem. Sci. 24:295-298.
19. Jacob, F., Wollman E.L. 1961. Sexuality and the Genetics of Bacteria. Academic Press, New York, N.Y.
20. Juhala, R. J., Ford M.E., Duda R.L., Youlton A., Hatfull G.F., Hendrix R.W. 2000. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. Mol J. Biol. 299:27-52.
21. Karlin, S., Campbell A.M., Mrazek J. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32: 185-226.
22. Karlin, S., Mrazek J. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. Bacteriol J. 182: 5238-5250.
23. Karlin, S., Mrazek J., Campbell A.M. 1998. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29:1341-1345.
24. Kuhn, J., Campbell A. 2001. The bacteriophage K attachment site in wild strains of Escherichia coli. Mol J. Evol. 53:607-614.
25. Lawrence, J.G., Ochman H. 1997. Ameliorationofbacte- rial genomes: rates of change and exchange. Mol J. Evol. 44: 383-397.
26. Lawrence, J.G., Ochman H., D.Hartl L. 1992. Theevolu- tion of marker sequences within enteric bacteria. Genetics 131: 9-20.
27. Lawrence J.G., Roth J.R. 1996. Selfish operons: horizontal transfer may drive the evolution of gene cluster. Genetics 143:1843-1860.
28. Lederberg, E. M. 1951. Lysogenicity in E. coli K-12. Genetics 36:560.
29. Lindsey, D. R., Mullin D.A., Walker J.P. 1989. Characterization of the cryptic lambdoid prophage DLP12 of Escherichia coli and overlap of the DLP12 integrase gene with the tRNA gene argBacteriol U.J. 171:6197-6205.
30. Mahillon, J., Chandler M. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62:725-774.
31. Mrnzek, J., Karlin S. 1998. Strand compositional symmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95:3720-3725.
32. Noas, T., Blot M., Fitch W.M., Arber W. 1994. Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 136:721-730.
33. Ochman, H., Selander R.K. 1984. Evidence for clonal population structure in Escherichia coli. Proc. Natl. Acad. Sci. USA 81:198-201.
34. Pierson, L. S., Kahn M.L. 1987. Integration of satellite bacteriophage P4 in Escherichia coli DNA sequence of the phage and host regions involved in site-specific recombination. Mol J. Btol. 196:487-496.
35. Rappleye, C. A., Roth J.R. 1997. Transposition without a transposase: a spontaneous mutation in bacteria. Bacteriol J. 179:2047-2052.
36. Reuter, W.-D., Palm P., Yeats S. 1989. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17: 1907-1914.
37. Retallack, D. M., Johnson L.L., Friedman D.I. 1994. Role of 10Sa RNA in the growth of X.-P22 hybrid phage. Bacteriol J. 176:2082-2089.
38. Sawyer, S. A., Dykhuizen D.E., DuBose R.F., Green L., Mutagandura-Mhlanga T., Wolczyk D.F., Hartl D.L. 1987. Distribution and abundance of insertion sequences among natural isolates of Escherichia coli. Genetics 115:51-63.
39. Shimada, K., Weisberg R.A., Gottesman M.E. 1972. Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogens. Mol J. Biol. 63:483-503.
40. Stoltzfus, A. B. 1991. A survey of natural variation in the trp- tonB region of the E. coli chromosome. Thesis. University of Iowa, Ames.
41. Trempy, J.E., Kirby J.E., Gottesman S. 1994. Alpsuppres- sion of lon: dependence on the slpA gene. Bacteriol J. 176: 2061-2067.
42. Wang, H., Yang C.-H., Lee G., Chang F., Wilson H., A. del Campillo-Campbell, Campbell A. 1997. Integration specificities of two lambdoid phages (21 and el4) that insert at the same attB site. Bacteriol J. 179:5705-5711.
43. Wang, F. S., Whittam T.S., Selander R.K. 1997. Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica. Bacteriol J. 179: 6551-6559.