Highly plastic chromosomal organization in Salmonella typhi.

Liu, Shulin; Sanderson, Kenneth E.

doi:10.1073/pnas.93.19.10303

Cited by 159 publications

(128 citation statements)

References 33 publications

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“…The presence of multi-copy sequence elements interspersed in the genome opens up the possibility of homologous recombination within the genome (Krawiec & Riley, 1990;Liu & Sanderson, 1996;Hughes, 2000). For two elements present in the same orientation, such an intragenomic recombination may result in the deletion of the intervening region, including loss of one copy of the element, and if the circular deleted segment inserts into the chromosome by homologous recombination with a different copy of the element, the result is a transposition.…”

Section: Discussionmentioning

confidence: 99%

Intragenomic recombination in the highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans

2005

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The highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans is strongly associated with aggressive periodontitis in adolescents of African descent. DNA fingerprinting using the frequently cutting restriction enzyme MspI and multilocus sequence typing (MLST) showed that five strains of this clone were genetically virtually identical, although ribotyping of the six rrn genes and EcoRI RFLP analysis of the seven IS150-like elements revealed differences. PCR analyses demonstrated that these multi-copy sequences are subject to intragenomic homologous recombination, resulting in translocations or large inversions. The genome rearrangements were reflected in differences among 25 strains representing the JP2 clone in DNA fingerprinting using the rare-cutting restriction enzyme XhoI and resolved by PFGE. XhoI DNA fingerprinting provides a tool for studying local epidemiology, including transmission of this particularly pathogenic clone of A. actinomycetemcomitans.

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Section: Discussionmentioning

confidence: 99%

Intragenomic recombination in the highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans

2005

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“…6). Although gene dosage effects have rarely been tested experimentally, they have been frequently invoked to explain the deleterious effect of chromosomal rearrangements (Liu & Sanderson, 1996;Roth et al, 1996). Experimentally induced inversions in the E. coli chromosome altering the distance of genes to the origin of replication can lead to halving growth rates (Louarn et al, 1985).…”

Section: Gene Distributionmentioning

confidence: 99%

The replication-related organization of bacterial genomes

2004

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The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division. Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes. Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions. These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome. When asymmetries or gradients increase in some genomes, e.g. due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases. As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation. Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division. Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.

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“…We tuned the parameters used in the different steps based on comparisons between the bacteria Shigella flexneri 2457t serotype 2a (S. flexneri 2457t) [62] and S. typhi ty2, which are among the most difficult and the least stable genomes in the enterobacteria family, since they contain more ISs, prophages, and rearrangements than other Escherichia or Salmonella [63]. A summary of the parameters and their default values is given in Table 1.…”

Section: Mapping Phase: Clustering Into Rf Segmentsmentioning

confidence: 99%

An Integrative Method for Accurate Comparative Genome Mapping

Swidan¹,

Rocha²,

Shmoish³

et al. 2005

PLoS Comp Biol

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We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying ''maximal similar segments,'' and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their most recent common ancestor. We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes. We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics computed for each type of these large-scale mutations. MAGIC enabled us to conduct a comprehensive analysis of the different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use these results to investigate the breakpoint distribution in several prokaryotic genomes.

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Highly plastic chromosomal organization in Salmonella typhi.

Cited by 159 publications

References 33 publications

Intragenomic recombination in the highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans

Intragenomic recombination in the highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans

The replication-related organization of bacterial genomes

An Integrative Method for Accurate Comparative Genome Mapping

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