Comparative genomics of VirR regulons in Clostridium perfringens strains

BMC Microbiology

Research Article

Antonio Frandi¹  Alessio Mengoni¹  Matteo Brilli² 

[1] Department of Evolutionary Biology, via Romana 17-19, I-50125, Firenze, Italy;Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS; INRIA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France;

关键词: Regulon;    Draft Genome;    Toxin Gene;    Clostridium Perfringens;    Genome Scanning;   

DOI  :  10.1186/1471-2180-10-65

 received in 2009-08-18, accepted in 2010-02-25,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundClostridium perfringens is a Gram-positive anaerobic bacterium causing severe diseases such as gas gangrene and pseudomembranosus colitis, that are generally due to the secretion of powerful extracellular toxins. The expression of toxin genes is mainly regulated by VirR, the response regulator of a two-component system. Up to now few targets only are known for this regulator and mainly in one strain (Strain 13). Due to the high genomic and phenotypic variability in toxin production by different strains, the development of effective strategies to counteract C. perfringens infections requires methodologies to reconstruct the VirR regulon from genome sequences.ResultsWe implemented a two step computational strategy allowing to consider available information concerning VirR binding sites in a few species to scan all genomes of the same species, assuming the VirR targets are at least partially conserved across these strains. Results obtained are in agreement with previous works where experimental validation of the promoters have been performed and showed the presence of a core and an accessory regulon of VirR in C. perfringens strains with three target genes also located on plasmids. Moreover, the type E strain JGS1987 has the largest predicted regulon with as many as 10 VirR targets not found in the other genomes.ConclusionsIn this work we exploited available experimental information concerning the targets of the VirR toxin regulator in one C. perfringens strain to obtain plausible predictions concerning target genes in genomes and plasmids of nearby strains. Our predictions are available for wet-lab researchers working on less characterized C. perfringens strains that can thus design focused experiments reducing the search space of their experiments and increasing the probability of characterizing positive targets with less efforts. Main result was that the VirR regulon is variable in different C. perfringens strains with 4 genes controlled in all but one strains and most genes controlled in one or two strains only.

【 授权许可】

Unknown   
© Frandi et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.