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Diversity in coding tandem repeats in related Neisseria spp.

Jordan P, Snyder LA, Saunders NJ - BMC Microbiol. (2003)

Bottom Line: Coding tandem repeats are those which do not alter the reading frame with copy number, and the changes in copy number of these repeats may then potentially alter the function or antigenicity of the protein encoded.Three complete neisserial genomes were analyzed and compared to identify coding tandem repeats where the number of copies of the repeat will have some structural consequence for the protein.Eighteen genes were identified which have variation in repeat copy number between strains of the same species, twelve of which show greater diversity in repeat copy number than is present in the sequenced genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bacterial Pathogenesis and Functional Genomics Group, The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK. philip.jordan@pathology.oxford.ac.uk

ABSTRACT

Background: Tandem repeats contained within coding regions can mediate phase variation when the repeated units change the reading frame of the coding sequence in a copy number dependent manner. Coding tandem repeats are those which do not alter the reading frame with copy number, and the changes in copy number of these repeats may then potentially alter the function or antigenicity of the protein encoded. Three complete neisserial genomes were analyzed and compared to identify coding tandem repeats where the number of copies of the repeat will have some structural consequence for the protein. This is the first study to address coding tandem repeats that may affect protein structures using comparative genomics, combined with a population survey to investigate which show interstrain variability.

Results: A total of 28 genes were identified. Of these, 22 contain coding tandem repeats that vary in copy number between the three sequenced strains, three strain specific genes were included for investigation on the basis of having >90% identity between repeated units, and three genes with repeated elements of >250 bp were included although no length variations were seen in the genomes. Amplification, and sequencing of repeats showing altered copy number, of these 28 coding tandem repeat containing regions, from a set of largely unrelated strains, revealed further repeat length variation in several cases.

Conclusion: Eighteen genes were identified which have variation in repeat copy number between strains of the same species, twelve of which show greater diversity in repeat copy number than is present in the sequenced genomes. In some cases, this may reflect a mechanism for the generation of antigenic variation, as previously described in other species. However, some of the genes identified encode proteins with cytoplasmic functions, including sugar metabolism, DNA repair, and protein production, in which repeat length variation may have other functions. Coding tandem repeats appear to represent a largely unexplored mechanism of generating diversity in the Neisseria spp.

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Two consecutive tandem repeat elements exist in pilQ (TR5). The first repeated unit is 66 bp. The first 24 bp of this 66 bp repeat is homologous to the second repeated unit of 24 bp. Both repeats in this compound coding tandem repeat are present in different lengths in the strains.
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Figure 1: Two consecutive tandem repeat elements exist in pilQ (TR5). The first repeated unit is 66 bp. The first 24 bp of this 66 bp repeat is homologous to the second repeated unit of 24 bp. Both repeats in this compound coding tandem repeat are present in different lengths in the strains.

Mentions: Primers were designed flanking the tandem repeats such that PCR product size could be used to determine the number of copies of the coding tandem repeated unit. In the case of TR19 (tonB), the gene contains 2 tandem repeats, which were addressed separately (TR19a and TR19b). In the case of TR5 (pilQ) a compound tandem repeat is present, such that the 5' 24 bp of the 66 bp tandem repeat is then repeated itself as a 24 bp tandem repeat immediately following the 66 bp repeat (Figure 1). Therefore, TR5 was evaluated by sequencing in all strains. Additional sequencing was done for all of the products where the size of the PCR product suggested that the length of the tandemly repeated region might differ from the sequenced strains. In all, over 200 sequencing reactions were conducted to ascertain the sequence of the coding tandem repeat containing region(s) of the 28 coding sequences.


Diversity in coding tandem repeats in related Neisseria spp.

Jordan P, Snyder LA, Saunders NJ - BMC Microbiol. (2003)

Two consecutive tandem repeat elements exist in pilQ (TR5). The first repeated unit is 66 bp. The first 24 bp of this 66 bp repeat is homologous to the second repeated unit of 24 bp. Both repeats in this compound coding tandem repeat are present in different lengths in the strains.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC305346&req=5

Figure 1: Two consecutive tandem repeat elements exist in pilQ (TR5). The first repeated unit is 66 bp. The first 24 bp of this 66 bp repeat is homologous to the second repeated unit of 24 bp. Both repeats in this compound coding tandem repeat are present in different lengths in the strains.
Mentions: Primers were designed flanking the tandem repeats such that PCR product size could be used to determine the number of copies of the coding tandem repeated unit. In the case of TR19 (tonB), the gene contains 2 tandem repeats, which were addressed separately (TR19a and TR19b). In the case of TR5 (pilQ) a compound tandem repeat is present, such that the 5' 24 bp of the 66 bp tandem repeat is then repeated itself as a 24 bp tandem repeat immediately following the 66 bp repeat (Figure 1). Therefore, TR5 was evaluated by sequencing in all strains. Additional sequencing was done for all of the products where the size of the PCR product suggested that the length of the tandemly repeated region might differ from the sequenced strains. In all, over 200 sequencing reactions were conducted to ascertain the sequence of the coding tandem repeat containing region(s) of the 28 coding sequences.

Bottom Line: Coding tandem repeats are those which do not alter the reading frame with copy number, and the changes in copy number of these repeats may then potentially alter the function or antigenicity of the protein encoded.Three complete neisserial genomes were analyzed and compared to identify coding tandem repeats where the number of copies of the repeat will have some structural consequence for the protein.Eighteen genes were identified which have variation in repeat copy number between strains of the same species, twelve of which show greater diversity in repeat copy number than is present in the sequenced genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bacterial Pathogenesis and Functional Genomics Group, The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK. philip.jordan@pathology.oxford.ac.uk

ABSTRACT

Background: Tandem repeats contained within coding regions can mediate phase variation when the repeated units change the reading frame of the coding sequence in a copy number dependent manner. Coding tandem repeats are those which do not alter the reading frame with copy number, and the changes in copy number of these repeats may then potentially alter the function or antigenicity of the protein encoded. Three complete neisserial genomes were analyzed and compared to identify coding tandem repeats where the number of copies of the repeat will have some structural consequence for the protein. This is the first study to address coding tandem repeats that may affect protein structures using comparative genomics, combined with a population survey to investigate which show interstrain variability.

Results: A total of 28 genes were identified. Of these, 22 contain coding tandem repeats that vary in copy number between the three sequenced strains, three strain specific genes were included for investigation on the basis of having >90% identity between repeated units, and three genes with repeated elements of >250 bp were included although no length variations were seen in the genomes. Amplification, and sequencing of repeats showing altered copy number, of these 28 coding tandem repeat containing regions, from a set of largely unrelated strains, revealed further repeat length variation in several cases.

Conclusion: Eighteen genes were identified which have variation in repeat copy number between strains of the same species, twelve of which show greater diversity in repeat copy number than is present in the sequenced genomes. In some cases, this may reflect a mechanism for the generation of antigenic variation, as previously described in other species. However, some of the genes identified encode proteins with cytoplasmic functions, including sugar metabolism, DNA repair, and protein production, in which repeat length variation may have other functions. Coding tandem repeats appear to represent a largely unexplored mechanism of generating diversity in the Neisseria spp.

Show MeSH
Related in: MedlinePlus