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Chapter 13 : “Stable” Genomes

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Abstract:

This chapter evaluates the present knowledge about the degree of stability of the genome of enteric bacteria. It discusses about the forces which have contributed to maintaining stability, and considers the types of rearrangements which can and do occur even in those genomes generally considered to be stable. With the use of methods of physical analysis of DNA, and especially the introduction of the use of pulsed-field gel electrophoresis (PFGE), used first in by Smith and colleagues, the genomes of many strains were determined and conservation of gene order was shown to be the rule. It talks about two modifications of PFGE methods, which allow the determination of genome structure in many strains, have been used in representative enteric bacteria. It focuses on the forces which would be expected to act in a conservative way to maintain gene order. It is possible that transspecies recombination due to conjugation or transduction followed by homologous recombination, though very rare, is so important that colinearity is an important advantage. The author concludes that the overall conservation of gene order within the enteric bacteria which was reported many years ago in comparisons of and has been confirmed by the analysis of the physical maps of many strains of and other enteric bacteria determined by PFGE and by the comparison of nucleotide sequences.

Citation: Sanderson K, McClelland M, Liu S. 1999. “Stable” Genomes, p 217-233. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch13

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Image of FIGURE 1
FIGURE 1

Comparison of the genomic maps for the endonuclease and positions of selected genes determined by analysis of the locations of insertions of Tn in LT2 ( ) and Ty2 ( ). The arrows beside the operons indicate the direction of transcription. There are three types of rearrangements in with respect to . (i) The arc with arrowheads at both ends indicates a segment of the Ty2 genome within the I- I-A fragment which is inverted relative to LT2. (ii) The open arrows indicate three regions in which the intervals between homologous genes are much longer in than in these are postulated to be insertions of DNA (pathogenicity islands), (iii) The I- I fragments, which are in the order ABCDEFG in (and most others enteric bacteria studied), are in the order AGCEFDB in , presumably due to homologous recombination among the operons.

Citation: Sanderson K, McClelland M, Liu S. 1999. “Stable” Genomes, p 217-233. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch13
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Image of FIGURE 2
FIGURE 2

Separation by PFGE of fragments from I- I digestion of DNA from independent wild-type strains of from the SARA set of strains ( ), taken from Fig. 1 of reference . The lanes marked LT2 represent DNA from strain LT2 (which is SARA2); other lanes show the number of the strain from the SARA set. The normal I- I fragments and their sizes in kilobases are shown as single letters on the right. Unusual bands for a few of the strains are indicated on the left, along with their sizes. Some of the partial digestion products, such as D+E and E + F, are shown on the right; these show that the fragment order is DEF.

Citation: Sanderson K, McClelland M, Liu S. 1999. “Stable” Genomes, p 217-233. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch13
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Image of FIGURE 3
FIGURE 3

Inversions covering the region (adapted from Fig. 6 of reference ). The open vertical bar and genes on the left (S.tm) show the order of genes in LT2, with the positions of these genes shown in kilobases ( ). The shorter bars to the right indicate segments of the chromosomes of (S.en) ( ), (S.ty) ( ), and K-12 (E.co) ( ), which are inverted. The hatched horizonal lines join homologous genes. (equivalent to ) and (equivalent to ) indicate the locations of replication termination in K-12 ( ).

Citation: Sanderson K, McClelland M, Liu S. 1999. “Stable” Genomes, p 217-233. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch13
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Image of FIGURE 4
FIGURE 4

(A) Partial digestion of DNA of independent strains of S. with the endonuclease I-, separation by PFGE, and staining with ethidium bromide (from Fig. 2 of reference ). Lanes: 1, strain 26T4; 2, strain 26T9; 3, strain 26T12; 4, strain 26T19; 5, strain 26T38; 6, strain 26T48, 7, strain 26T49. (B) The fragments shown in panel A are indicated by bars, and their sizes and the fragments they are inferred to include are labelled on the left.

Citation: Sanderson K, McClelland M, Liu S. 1999. “Stable” Genomes, p 217-233. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch13
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Image of FIGURE 5
FIGURE 5

The order of I I fragments in 127 strains of 5. and in other enteric bacteria, showing 26 different genome types (adapted from Fig. 2 of reference ). The order of I- I fragments B to G was determined from data of the type shown in Fig. 2 . The order of I I fragments from strain Ty2 (genomic type 9) had been previously determined by analysis with Tn insertions ( ). The same order was confirmed by partial I I digestion (as shown in Fig. 3 ). The I I fragment joins the left ends of the fragments shown to the right end, forming circles, but their orientations are not known. The orientations of fragments B, D, E, F, and G can be inferred from the polarities of the operons. The solid dots in the I- I fragments indicate the location of . The number of strains of each genome type is shown; some of the theoretical genome types were not detected. The order and sizes of the fragments between operons were previously determined for K-12 ( ), ( ), S. ? ( ), and LT2 ( ). These are illustrated at the bottom, drawn to scale, and all have the same order of fragments as genome type 1 of .

Citation: Sanderson K, McClelland M, Liu S. 1999. “Stable” Genomes, p 217-233. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch13
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