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 ISSN 1471-2164.

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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
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
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:	Date Event 2010 Published
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 (Creative Commons)
Date of first compliant deposit:	26 December 2015
Date of first compliant Open Access:	26 December 2015
Funder:	Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC)
Grant number:	BBE111791 (BBSRC)
Open Access Version:	PubMed Central

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