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Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching
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Snyder, Lori A. S., Loman, Nicholas J., Linton, James D., Langdon, Rebecca R., Weinstock, George M., Wren, Brendan and Pallen, Mark J. (2010) Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching. BMC Genomics, Volume 11 (Number 1). Article number 67. doi:10.1186/1471-2164-11-67
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WRAP_Biomed_1471-2164-11-67.pdf - Published Version Available under License Creative Commons Attribution 2.0.. Download (310Kb) | Preview |
Official URL: http://dx.doi.org/10.1186/1471-2164-11-67
Abstract
Background: Helicobacter canadensis is an emerging human pathogen and zoonotic agent. The genome of H.
canadensis was sequenced previously and determined to contain 29 annotated coding regions associated with
homopolymeric tracts.
Results: Twenty-one of the repeat-associated coding regions were determined to be potentially transcriptionally or
translationally phase variable. In each case the homopolymeric tract was within the predicted promoter region or
at the 5’ end of the coding region, respectively. However, eight coding sequences were identified with simple
sequence repeats toward the 3’ end of the open reading frame. In these cases, the repeat tract would be too far
into the coding region to be mediating translational phase variation. All of the 29 coding region-associated
homopolymeric tracts display variability in tract length in the sequencing read data.
Conclusions: Twenty-nine coding regions have been identified in the genome sequence of Helicobacter
canadensis strain NCTC13241 that show variations in homopolymeric tract length in the bacterial population,
indicative of phase variation. Five of these are potentially associated with promoter regions, which would lead to
transcriptional phase variation. Translational phase variation usually switches expression of a gene ON and OFF due
to the repeat region being located sufficiently close to the initiation codon for the resulting frame-shift to lead to a
premature termination codon and stop the translation of the protein. Sixteen of the 29 coding regions have
homopolymeric tracts characteristic of translational phase variation. For eight coding sequences with repeats
located later in the reading frame, changes in the repeat tract length would alter the protein sequence at the Cterminus
but not stop the expression of the protein. This mechanism of C-terminal phase variation has implications
for stochastic switching of protein sequence in bacterial species that already undergo transcriptional and
translational phase variation.
| Item Type: | Journal Article | ||||
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| Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics |
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| Divisions: | Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Medicine > Warwick Medical School |
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| Library of Congress Subject Headings (LCSH): | Helicobacter, Helicobacter infections, Bacterial genetics, Bacterial genomes | ||||
| Journal or Publication Title: | BMC Genomics | ||||
| Publisher: | BioMed Central Ltd. | ||||
| ISSN: | 1471-2164 | ||||
| Official Date: | 2010 | ||||
| Dates: |
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| Volume: | Volume 11 | ||||
| Number: | Number 1 | ||||
| Page Range: | Article number 67 | ||||
| DOI: | 10.1186/1471-2164-11-67 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Open Access | ||||
| Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC) | ||||
| Grant number: | BBE111791 (BBSRC) | ||||
| Open Access Version: |
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