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Chapter 44 : Eubacterial Genomes

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Abstract:

In this chapter, eubacterial genomes are discussed first with respect to the presence of prophages and transposable elements, as well as their obvious derivatives, and finally with respect to horizontal gene transfer. The mechanism of conservative site-specific recombination generally entails DNA-DNA recognition of the two partners (phage and host), as well as protein recognition of the flanking sequences. Most prophages in natural strains have experienced at least one debilitating change and are therefore unable to undergo a complete lytic cycle following induction of phage development. The prophages detected in strains other than K-12 are all of the 21 variety, with integrase genes that are more than 99% identical to those of 21 and are located next to the site. Most of these are probably defective; in a PCR screen, the right end of the prophage was present in only two of five strains. The evolution of natural strains differs from the test tube evolution in the agar stab experiment in that gene transfers from diverse, sometimes unknown, sources happen in the natural population. Most ECOR strains also harbor at least one plasmid, which may have played a role in determining their distribution. A molecular evolutionist comparing the sequences of strains with and without the pathogenicity island places the boundary of the island at the first nucleotide where the two strains diverge, which is of course the 3' end of the repeat.

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44
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Figures

Image of Figure 1.
Figure 1.

Insertion of phage 21 into the gene of . The phage DNA includes a 165-bp homolog of the 3′ end of .

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44
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Image of Figure 2.
Figure 2.

Individual gene homologies from phages of taxonomically distant hosts. Reprinted from ( ) with permission from the publisher.

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44
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Image of Figure 3.
Figure 3.

Location of major groups of IS elements in K-12. Tickmarks are either above or below the line, depending on orientation. Also shown are the locations of phage-like elements and restriction sites. Reprinted from ( ) with permission of the publisher

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44
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Image of Figure 4.
Figure 4.

50-kb sliding window analysis of the genome for G+C content (top), dinucleotide relative abundance (middle), and codon bias (bottom). Reprinted from the ( ) with permission of the publisher.

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44
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Image of Figure 5.
Figure 5.

Genes of with codon bias relative to the average gene >0.520 and with S3 (= G+C content in third position) < 45% are shown as arrows pointing inwards; genes with S3 > 68% are shown as arrows pointing outwards. Marks without arrows indicate genes with S3 between 45% and 68%. The genes transcribed clockwise are in the outer circle; those transcribed inward are in the middle circle. Genes with arrows are considered alien. Those without arrows are predominantly highly expressed genes. Reprinted from ( ) with permission of the publisher.

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44
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References

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

Tables

Generic image for table
Table 1.

Types of temperate phages that insert into the chromosome

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44
Generic image for table
Table 2.

Phage-related elements of the K-12 chromosome

Citation: Campbell A. 2002. Eubacterial Genomes, p 1024-1039. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch44

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