Skip Navigation

Nucleic Acids Research 2006 34(7):1947-1958; doi:10.1093/nar/gkl138
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2382K) Freely available
Right arrow Screen PDF (589K) Freely available
Right arrow A corrigendum has been published
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (14)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Wels, M.
Right arrow Articles by Siezen, R. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wels, M.
Right arrow Articles by Siezen, R. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 13 April 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups

Michiel Wels1,2,3,*, Christof Francke1,2, Robert Kerkhoven2, Michiel Kleerebezem1,3 and Roland J. Siezen1,2,3

1 Wageningen Centre for Food Sciences PO Box 557, 6700 AN Wageningen, The Netherlands 2 Radboud University, Centre for Molecular and Biomolecular Informatics PO Box 9010, 6500 GL Nijmegen, The Netherlands 3 NIZO food research PO Box 20, 6710 BA Ede, The Netherlands

*To whom correspondence should be addressed at CMBI, Radboud University, PO Box 9010 6500 GL Nijmegen, The Netherlands. Tel: +31 024 3653398; Fax: +31 024 3652977; Email: M.Wels{at}cmbi.ru.nl

Received February 10, 2006. Revised March 1, 2006. Accepted March 15, 2006.

Cis-acting elements in Lactobacillus plantarum were predicted by comparative analysis of the upstream regions of conserved genes and predicted transcriptional units (TUs) in different bacterial genomes. TUs were predicted for two species sets, with different evolutionary distances to L.plantarum. TUs were designated ‘cluster of orthologous transcriptional units’ (COT) when >50% of the genes were orthologous in different species. Conserved DNA sequences were detected in the upstream regions of different COTs. Subsequently, conserved motifs were used to scan upstream regions of all TUs. This method revealed 18 regulatory motifs only present in lactic acid bacteria (LAB). The 18 LAB-specific candidate regulatory motifs included 13 that were not described previously. These LAB-specific different motifs were found in front of genes encoding functions varying from cold shock proteins to RNA and DNA polymerases, and many unknown functions. The best-described LAB-specific motif found was the CopR-binding site, regulating expression of copper transport ATPases. Finally, all detected motifs were used to predict co-regulated TUs (regulons) for L.plantarum, and transcriptome profiling data were analyzed to provide regulon prediction validation. It is demonstrated that phylogenetic footprinting using different species sets can identify and distinguish between general regulatory motifs and LAB-specific regulatory motifs.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 MicrobiologyHome page
F. Bringel, P. Hammann, V. Kugler, and F. Arsene-Ploetze
Lactobacillus plantarum response to inorganic carbon concentrations: PyrR2-dependent and -independent transcription regulation of genes involved in arginine and nucleotide metabolism
Microbiology, September 1, 2008; 154(9): 2629 - 2640.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Liu, X. Xu, and G. D. Stormo
The cis-regulatory map of Shewanella genomes
Nucleic Acids Res., September 1, 2008; 36(16): 5376 - 5390.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. I. Sadreyev, M. Tang, B.-H. Kim, and N. V. Grishin
COMPASS server for remote homology inference
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W653 - W658.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
J. Boekhorst, M. Wels, M. Kleerebezem, and R. J. Siezen
The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment.
Microbiology, November 1, 2006; 152(Pt 11): 3175 - 3183.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.