Constraints in chromosomal inversions in <i>Escherichia coli</i> are not explained by replication pausing at inverted terminator‐like sequences

Vincent, François; Patte, Josette; Rebollo, J. E.; Louarn, Jean-Michel

doi:10.1111/j.1365-2958.1990.tb00621.x

Cited by 16 publications

(8 citation statements)

References 16 publications

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“…Interestingly, and despite containing noninvertible segments [20][21][22][23], both S. typhimurium and E. coli mg1655 passed the uniformity test. The fit of uniformity in four pairwise comparisons is surprising for two additional reasons.…”

Section: Breakpoint Distributionmentioning

confidence: 99%

“…Furthermore, we utilized MAGIC's results to analyze the breakpoint distribution in bacteria. Previous studies, on Salmonella typhimurium [20,21] and on Escherichia coli [22,23], have shown that they contain noninvertible (or nonpermissive) segments. For some of these segments, forcing an inversion by mechanisms different from those found in the cell resulted in organisms that are viable and that grow normally [24].…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Breakpoint Distributionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An Integrative Method for Accurate Comparative Genome Mapping

Swidan¹,

Rocha²,

Shmoish³

et al. 2005

PLoS Comp Biol

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“…Moreover, some inversions of E. coli chromosomal regions are deleterious and induce an abnormal nucleoid structure [36,37] . The solenoidal model dictates that site position must be respected for full functionality.…”

Section: Explanatory Powermentioning

confidence: 99%

Transcription-Based Solenoidal Model of Chromosomes

Képès

Vaillant²

2003

ComPlexUs

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The organization of transcription within the eukaryotic nucleus or the prokaryotic nucleoid may be expected to both depend on and determine the structure of the chromosomes. In yeast and bacteria, genes that are controlled by the same sequence-specific transcription factor tend to be either clustered or regularly spaced along the chromosomes. The same spacing is found for most transcription factors within a chromosome. Furthermore, in bacteria, the gene encoding the transcription factor tends to locate at identical regular intervals from its targets. This periodicity is consistent with a solenoidal epi-organization of the chromosome, which would dynamically gather the interacting partners into foci. Binding at genuine regulatory sites on DNA would thus be optimized by locally increasing the concentration of transcription factors and their binding sites. As many transcription factors are simultaneously active and some share targets, the resulting collection of foci provides a potent self-organizational principle for the chromosome, and consequently for the functional nuclear architecture.

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“…Extensive analysis in E. coli K12, selecting for inversions between homologous regions (such as Tn10s) inserted into the chromosome, has shown that many inversions in regions flanking TER are deleterious or not detected; these are called nondivisible zones (15). The region close to TER, including pyrC (b1062) to pyrF (b1281) (see Fig.…”

Section: Discussionmentioning

confidence: 99%

Inversions over the Terminus Region in Salmonella and Escherichia coli : IS 200 s as the Sites of Homologous Recombination Inverting the Chromosome of Salmonella enterica Serovar Typhi

Alokam¹,

Liu

Said³

et al. 2002

J Bacteriol

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Genomic rearrangements (duplications and inversions) in enteric bacteria such as Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12 are frequent (10 ؊3 to 10 ؊5 ) in culture, but in wild-type strains these genomic rearrangements seldom survive. However, inversions commonly survive in the terminus of replication (TER) region, where bidirectional DNA replication terminates; nucleotide sequences from S. enterica serovar Typhimurium LT2, S. enterica serovar Typhi CT18, E. coli K12, and E. coli O157:H7 revealed genomic inversions spanning the TER region. Assuming that S. enterica serovar Typhimurium LT2 represents the ancestral genome structure, we found an inversion of 556 kb in serovar Typhi CT18 between two of the 25 IS200 elements and an inversion of about 700 kb in E. coli K12 and E. coli O157:H7. In addition, there is another inversion of 500 kb in E. coli O157:H7 compared with E. coli K12. PCR analysis confirmed that all S. enterica serovar Typhi strains tested, but not strains of other Salmonella serovars, have an inversion at the exact site of the IS200 insertions. We conclude that inversions of the TER region survive because they do not significantly change replication balance or because they are part of the compensating mechanisms to regain chromosome balance after it is disrupted by insertions, deletions, or other inversions.The order of orthologous genes on the chromosomes of enteric bacteria such as Escherichia coli K12 and Salmonella enterica serovar Typhimurium LT2 was shown by classical genetic exchange methods to be strongly conserved (24, 37), and this has now been confirmed by nucleotide sequence data (6, 30). This conservation was retained even after the genera diverged over 100 million years ago (32) and in spite of base pair divergence of orthologues, which averages about 15%. In addition, lateral genetic transfer has inserted nonorthologous genes that comprise about 30% of the total genetic structure, resulting in mosaic chromosomes. This conservation is surprising, because during growth in culture, chromosome rearrangements such as duplications occur at high frequencies (10 Ϫ3 to 10 Ϫ5 ) (3, 19) and some inversions and translocations, especially those with end points in the rrn operons, are common (36). These rearrangement types must have been selected against in evolution, because they are rarely detected in wildtype strains from nature. In contrast to this conservation within the enteric bacteria, gene order in most bacteria is not conserved during evolution (10, 21, 31), though species of Chlamydia also show striking conservation (35).However, even in the enteric bacteria, two types of genomic rearrangements are often observed. Firstly, inversions and translocations due to homologous recombination between the seven rrn operons are common in species such as Salmonella enterica serovar Typhi; among 127 wild-type strains there were 21 different genome types, based on differences in order of the fragments between the rrn operons (28). Rearrangements were also found in some ot...

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Constraints in chromosomal inversions in Escherichia coli are not explained by replication pausing at inverted terminator‐like sequences

Cited by 16 publications

References 16 publications

An Integrative Method for Accurate Comparative Genome Mapping

An Integrative Method for Accurate Comparative Genome Mapping

Transcription-Based Solenoidal Model of Chromosomes

Inversions over the Terminus Region in Salmonella and Escherichia coli : IS 200 s as the Sites of Homologous Recombination Inverting the Chromosome of Salmonella enterica Serovar Typhi

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