Transposon‐like Correia elements: structure, distribution and genetic exchange between pathogenic <i>Neisseria</i> sp

Buisine, Nicolas; Tang, Christoph M.; Chalmers, Ronald

doi:10.1016/s0014-5793(02)02882-x

Cited by 73 publications

(101 citation statements)

References 21 publications

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“…Unlike SDR elements, the previously described ERIC/IRU (De Gregario et al 2005;Wilson and Sharp 2006), RSA (Bachellier et al 1999), and BoxC (Bachellier et al 1999) elements in enteric bacteria, RUP (Oggioni and Claverys 1999) and boxAB n C (Martin et al 1992;Knutson et al 2006) elements in Streptococcus, and NEMIS (Mazzone et al 2001) and SRE/Correia (Buisine et al 2002) elements in Neisseria are all relatively long, imperfect palindromes possibly derived from transposons.…”

Section: Do Sdr Elements Function As Rna?mentioning

confidence: 96%

“…Neither convention seemed suitable for the elements described in this report, as they may be found in different genera and do not share a common structure. SRE (small repetitive elements) (Buisine et al 2002) is less restrictive, but we would like to maintain a distinction between tandem repeats and repeats well separated on the genome. We have therefore opted for a name that captures only the essential characteristics-small dispersed repeats (SDR)-and have used it as a prefix for specific families, as Tn is used for transposon names.…”

Section: Why Invent a New Name For Families Of Dispersed Repeats?mentioning

confidence: 99%

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Very small mobile repeated elements in cyanobacterial genomes

Elhai

Kato²,

Cousins³

et al. 2008

Genome Res.

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Mobile DNA elements play a major role in genome plasticity and other evolutionary processes, an insight gained primarily through the study of transposons and retrotransposons (generally ∼1000 nt or longer). These elements spawn smaller parasitic versions (generally >100 nt) that propagate through proteins encoded by the full elements. Highly repeated sequences smaller than 100 nt have been described, but they are either nonmobile or their origins are not known. We have surveyed the genome of the multicellular cyanobacterium, Nostoc punctiforme, and its relatives for small dispersed repeat (SDR) sequences and have identified eight families in the range of from 21 to 27 nucleotides. Three of the families (SDR4, SDR5, and SDR6), despite little sequence similarity, share a common predicted secondary structure, a conclusion supported by patterns of compensatory mutations. The SDR elements are found in a diverse set of contexts, often embedded within tandemly repeated heptameric sequences or within minitransposons. One element (SDR5) is found exclusively within instances of an octamer, HIP1, that is highly over-represented in the genomes of many cyanobacteria. Two elements (SDR1 and SDR4) often are found within copies of themselves, producing complex nested insertions. An analysis of SDR elements within cyanobacterial genomes indicate that they are essentially confined to a coherent subgroup. The evidence indicates that some of the SDR elements, probably working through RNA intermediates, have been mobile in recent evolutionary time, making them perhaps the smallest known mobile elements.[Supplemental material is available online at www.genome.org.] The mechanisms by which new copies of dispersed repeats are generated are well understood in some, but by no means, all cases. Transposon copies arise through DNA intermediates, catalyzed by transposases (Gueguen et al. 2005). Copies of retroposons (and degenerate retroposons, such as Alu sequences) are made through RNA intermediates, catalyzed by reverse transcriptase (Ostertag and Kazazian 2001). Minitransposons (also called MITEs), a category that may include the well-studied ERIC sequences (De Gregario et al. 2005), are thought to rely on transposases encoded outside of the mobile element (Siguier et al. 2006). The 8-nt highly iterated palindromic (HIP1) sequences observed in the genomes of many related cyanobacteria are thought not to be mobile but rather to form through mutation from pre-existing sequences (Robinson et al. 1997), The mechanisms by which small dispersed repeats are generated are otherwise unknown.The genomes of the cyanobacterium Nostoc punctiforme ATCC 29,133 and its relatives are unusual in that about 1.5% (∼7.5% of intergenic sequences) is taken up by tandem repeats at least 20 nt in length (Meeks et al. 2001; J. Elhai, T. Katayama, R. Narikawa, S. Okamoto, C. Friedland, R. Nayak, M. Ikeuchi, and M. Kanehisa, unpubl.). Repeating units of 7 nt (Mazel et al. 1990;Meeks et al. 2001) are by far the most common, with only a few of the possible families ...

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Section: Do Sdr Elements Function As Rna?mentioning

confidence: 96%

Section: Why Invent a New Name For Families Of Dispersed Repeats?mentioning

confidence: 99%

Very small mobile repeated elements in cyanobacterial genomes

Elhai

Kato²,

Cousins³

et al. 2008

Genome Res.

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“…Transposons are important in the spread of antibiotic resistance and as natural genomic engineers: most pathogenic bacteria, for example, have many transposons which function in phase variation and mobilization of pathogenicity islands [e.g. (2)]. During the course of evolution, transposons have diversi®ed to provide functions ranging from HIV integrase to the bene®cial V(D)J recombination machinery (3,4).…”

Section: Introductionmentioning

confidence: 99%

The positive and negative regulation of Tn10 transposition by IHF is mediated by structurally asymmetric transposon arms

Sewitz

Crellin

Chalmers

2003

Nucleic Acids Research

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The Tn10 transpososome has symmetrical components on either side: there are two transposon ends each of which has binding sites for a monomer of transposase and an IHF heterodimer. The DNA bending activity of IHF stimulates assembly of an intermediate with tightly folded transposon ends in which transposase has additional`subterminal' DNA contacts, located distal to the IHF site. These subterminal contacts are required to activate later steps in the reaction. Quantitative hydroxyl radical footprinting and gel retardation unfolding experiments show that the transpososome is fundamentally asymmetric, despite having identical components on either side. Major differences between the transposon ends de®ne a and b sides of the complex. IHF can dissociate from the transposon arm on the b side of the complex in the absence of metal ion. However, IHF is locked onto the a side of the complex, probably by the subterminal transposase contacts, until released by a metal iondependent conformational change. Later in the reaction, IHF inhibits target interactions. Using a very short transposon arm, target interactions are demonstrated at a saturating IHF concentration. This suggests that inhibition of target interactions is due to steric hindrance of the target binding site by a single IHF-folded transposon arm.

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“…1). CREEs have been divided into four families (a, a9, b and b9), distinguished by a 50 bp internal deletion and five point mutations (Buisine et al, 2002). In N. meningitidis strain MC58, the downstream region of nmb0088 contains a Meningococcal antigen characterization 155 bp a-family CREE with 26 bp terminal inverted repeats.…”

Section: Results Nmb0088 and Deduced Protein Featuresmentioning

confidence: 99%

“…It was suggested that these repetitive arrays may encourage sequence variation in neighbouring genes by increasing the frequency of recombination with exogenous DNA (Bentley et al, 2007). Among the most abundant repeat types are the CREEs, which are often located upstream of genes (Liu et al, 2002;De Gregorio et al, 2003a), have been shown to affect gene expression (De Gregorio et al, 2003b), and may be transposable or mobilizable (Buisine et al, 2002). The downstream CREE reported in the present study could also be involved in the expression of NMB0088 since a family of long CREEs has been considered to be a transcriptional terminator in the dcw cluster of N. gonorrhoeae CH811 (Francis et al, 2000).…”

Section: Meningococcal Antigen Characterizationmentioning

confidence: 99%

Neisseria meningitidis antigen NMB0088: sequence variability, protein topology and vaccine potential

Sardiñas

Yero

Climent

et al. 2009

Journal of Medical Microbiology

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The significance of Neisseria meningitidis serogroup B membrane proteins as vaccine candidates is continually growing. Here, we studied different aspects of antigen NMB0088, a protein that is abundant in outer-membrane vesicle preparations and is thought to be a surface protein. The gene encoding protein NMB0088 was sequenced in a panel of 34 different meningococcal strains with clinical and epidemiological relevance. After this analysis, four variants of NMB0088 were identified; the variability was confined to three specific segments, designated VR1, VR2 and VR3. Secondary structure predictions, refined with alignment analysis and homology modelling using FadL of Escherichia coli, revealed that almost all the variable regions were located in extracellular loop domains. In addition, the NMB0088 antigen was expressed in E. coli and a procedure for obtaining purified recombinant NMB0088 is described. The humoral immune response elicited in BALB/c mice was measured by ELISA and Western blotting, while the functional activity of these antibodies was determined in a serum bactericidal assay and an animal protection model. After immunization in mice, the recombinant protein was capable of inducing a protective response when it was administered inserted into liposomes. According to our results, the recombinant NMB0088 protein may represent a novel antigen for a vaccine against meningococcal disease. However, results from the variability study should be considered for designing a cross-protective formulation in future studies.

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Transposon‐like Correia elements: structure, distribution and genetic exchange between pathogenic Neisseria sp

Cited by 73 publications

References 21 publications

Very small mobile repeated elements in cyanobacterial genomes

Very small mobile repeated elements in cyanobacterial genomes

The positive and negative regulation of Tn10 transposition by IHF is mediated by structurally asymmetric transposon arms

Neisseria meningitidis antigen NMB0088: sequence variability, protein topology and vaccine potential

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