Chapter 3 : Genome Rearrangements in

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A small number of serovars are host specific, only causing infection in one host species or a few closely related species. The diseases caused by broad-host-range and host-restricted serovars also differ. Rearrangements can occur via recombination between short repeat sequences, but most large chromosomal rearrangements in bacteria occur by recombination between repeated sequences with several kbp of homology. IS200 is the most common IS element in , it transposes infrequently. Thus, in contrast to many bacteria that have a high background of transposition-mediated rearrangements, most genome rearrangements in are due to recombination. In contrast to the broad-host-range serovars, isolates of host-specific serovars have large-scale chromosomal rearrangements resulting from recombination between the operons. Inversions and translocations change the order of the chromosomal regions between the operons from the conserved arrangement type found in the broad-host-range serovars to one of over fifty arrangement types identified so far in host-specific serovars. Comparative genomics has revealed that many host-specific pathogens show greater genome plasticity than closely related bacteria that live in a wider variety of environmental conditions. Although the genome rearrangements in other bacteria are often mediated by active transposons, it seems likely that the observed differences in genome plasticity are simply determined by the selective constraints of their distinct ecological niches. Genome rearrangements also have practical implications for foodborne pathogens, as they can complicate the identification and tracking of outbreak strains.

Citation: Matthews T, Maloy S. 2011. Genome Rearrangements in , p 41-48. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch3

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Genetic Elements
Chromosome Structure
Chromosome Types
Pulsed-Field Gel Electrophoresis
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Figure 1

Genetic map of serovar Typhimurium and chromosomes showing that except for an inversion in the terminus region, the order of shared genes is highly conserved.

Citation: Matthews T, Maloy S. 2011. Genome Rearrangements in , p 41-48. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch3
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Figure 2

Chromosomal rearrangements through homologous recombination between direct and indirect repeats. (A) Unequal exchange between direct repeats on sister chromosomes results in one sister chromosome containing a duplication and the other containing a deletion (not shown). (B) Recombination between direct repeats on the same chromosome results in a levitation of the intervening region (B1). A translocation occurs when recombination with a homologous repeat somewhere else on the chromosome integrates the levitating region back into the chromosome (B2). (C) Recombination between inverted repeats results in an inversion of the intervening region.

Citation: Matthews T, Maloy S. 2011. Genome Rearrangements in , p 41-48. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch3
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Figure 3

Conserved physical map of broad-host-range serovars. The location and orientation of the seven operons are indicated by arrows. Numbers represent the regions between each of the operons. The order of the regions shown here is the conserved arrangement type 1234567. The origin of chromosome replication is indicated by a circle, and the location of the terminus region (approximately 180° from the origin) is indicated.

Citation: Matthews T, Maloy S. 2011. Genome Rearrangements in , p 41-48. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch3
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Figure 4

Recombination events that change the arrangement type from the conserved arrangement type (1234567) to the most common arrangement type observed in strains belonging to the Typhi serovar (1′ 235647). Recombination between the and operons inverts Region 1 (including the terminus) region to 1′. Levitation of region 4 leaves behind the hybrid operon, and translocation of region 4 into the operon yields the hybrid and operons.

Citation: Matthews T, Maloy S. 2011. Genome Rearrangements in , p 41-48. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch3
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Table 1

Chromosome arrangement types observed in serovars

Citation: Matthews T, Maloy S. 2011. Genome Rearrangements in , p 41-48. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch3

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