Functional and evolutionary roles of long repeats in prokaryotes

Rocha, Eduardo P. C.; Danchin, Antoine; Viari, Alain

doi:10.1016/s0923-2508(99)00120-5

Cited by 50 publications

(34 citation statements)

References 49 publications

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“…Repeats of this length are highly unlikely to exist in bacteria (17), and that this repeat should be so highly conserved when not encoding a functional gene product indicates that the composition is important. The juxtaposition of this repeat next to the pseudogenes for two gene families that undergo an extremely high rate of recombination is surely important.…”

Section: Resultsmentioning

confidence: 99%

Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens

Brayton

Knowles

McGuire

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

128

154

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Ehrlichiae are responsible for important tick-transmitted diseases, including anaplasmosis, the most prevalent tick-borne infection of livestock worldwide, and the emerging human diseases monocytic and granulocytic ehrlichiosis. Antigenic variation of major surface proteins is a key feature of these pathogens that allows persistence in the mammalian host, a requisite for subsequent tick transmission. In Anaplasma marginale pseudogenes for two antigenically variable gene families, msp 2 and msp 3, appear in concert. These pseudogenes can be recombined into the functional expression site to generate new antigenic variants. Coordinated control of the recombination of these genes would allow these two gene families to act synergistically to evade the host immune response.

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Section: Resultsmentioning

confidence: 99%

Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens

Brayton

Knowles

McGuire

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

128

154

View full text Add to dashboard Cite

show abstract

“…5, compositional strand bias varies significantly from genome to genome. This may be related to the different stability of the genomes, as chromosome shuffling will tend to level off the bias (Achaz et al, 2003;Mackiewicz et al, 2001b;Rocha et al, 1999b;Tillier & Collins, 2000b). The different length of the Okazaki fragments may also contribute to modulating the bias, since a smaller exposure in the ssDNA state would lead to less cytosine deamination (Mrázek & Karlin, 1998).…”

Section: Compositional Strand Biasmentioning

confidence: 99%

“…Mycoplasmas, which are less stable, show lower compositional strand bias. Repeats induce frequent chromosomal rearrangements, and may thus reduce strand biases (Rocha et al, 1999b). Genomes depleted of repeats would then be more stable and thus accumulate larger compositional strand bias (Achaz et al, 2003;Frank et al, 2002).…”

Section: Understanding Replication From the Organization It Inducesmentioning

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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“…A genetic mechanism mediating such phenotype variation involves repetitive DNA sequences that are known to promote genetic variability through homologous and illegitimate recombination processes (Achaz et al, 2002;Bichara et al, 2006). Homologous recombination occurs between large repetitive DNA sequences and may involve conversion or reciprocal strand exchange, duplication or deletion, thereby introducing changes in the genome (Rocha et al, 1999). Illegitimate recombination occurs between short closely spaced repetitive DNA sequences with few or no identical nucleotides (Bichara et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage

2010

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Members of the Burkholderia cepacia complex (Bcc) are respiratory pathogens in patients with cystic fibrosis (CF). Close repetitive DNA sequences often associate with surface antigens to promote genetic variability in pathogenic bacteria. The genome of Burkholderia cenocepacia J2315, a CF isolate belonging to the epidemic lineage Edinburgh-Toronto (ET-12), was analysed for the presence of close repetitive DNA sequences. Among the 422 DNA close repeats, 45 genes potentially involved in virulence were identified and grouped into 12 classes; of these, 13 genes were included in the antigens class. Two trimeric autotransporter adhesins (TAA) among the 13 putative antigens are absent from the other Burkholderia genomes and are clustered downstream of the cci island that is a marker for transmissible B. cenocepacia strains. This cluster contains four adhesins, one outer-membrane protein, one sensor histidine kinase and two transcriptional regulators. By using PCR, we analysed three genes among 47 Bcc isolates to determine whether the cluster was conserved. These three genes were present in the isolates of the ET-12 lineage but absent in all the other members. Furthermore, the BCAM0224 gene was exclusively detected in this epidemic lineage and may serve as a valuable new addition to the field of Bcc diagnostics. The BCAM0224 gene encodes a putative TAA that demonstrates adhesive properties to the extracellular matrix protein collagen type I. Quantitative real-time PCR analysis indicated that BCAM0224 gene expression occurred preferentially for cells grown under high osmolarity, oxygen-limited conditions and oxidative stress. Inactivation of BCAM0224 in B. cenocepacia attenuates the ability of the mutant to promote cell adherence in vitro and impairs the overall bacterial virulence against Galleria mellonella as a model of infection. Together, our data show that BCAM0224 from B. cenocepacia J2315 represents a new collagen-binding TAA with no bacterial orthologues which has an important role in cellular adhesion and virulence.

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Functional and evolutionary roles of long repeats in prokaryotes

Cited by 50 publications

References 49 publications

Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens

Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens

The replication-related organization of bacterial genomes

Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage

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