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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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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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