RNA-seq analysis of virR and revR mutants of Clostridium perfringens. (December 2016)

• Record Type: Journal Article
• Authors: Low, Lee-Yean; Harrison, Paul; Lin, Ya-Hsun; Boyce, John; Rood, Julian; Cheung, Jackie
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 14
• Publication Date: 2016-12
• Subjects: RNA-seq -- Gene transcription -- Reciprocal gene expression -- C. perfringens; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2706-2
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Clostridium perfringens causes toxin-mediated diseases, including gas gangrene (clostridial myonecrosis) and food poisoning in humans. The production of the toxins implicated in gas gangrene, α-toxin and perfringolysin O, is regulated by the VirSR two-component regulatory system. In addition, RevR, an orphan response regulator, has been shown to affect virulence in the mouse myonecrosis model. RevR positively regulates the expression of genes that encode hydrolytic enzymes, including hyaluronidases and sialidases. Results To further characterize the VirSR and RevR regulatory networks, comparative transcriptomic analysis was carried out with strand-specific RNA-seq onC. perfringens strain JIR325 and its isogenicvirR andrevR regulatory mutants. Using the edgeR analysis package, 206 genes in thevirR mutant and 67 genes in therevR mutant were found to be differentially expressed. Comparative analysis revealed that VirR acts as a global negative regulator, whilst RevR acts as a global positive regulator. Therefore, about 95 % of the differentially expressed genes were up-regulated in thevirR mutant, whereas 81 % of the differentially expressed genes were down-regulated in therevR mutant. Importantly, we identified 23 genes that were regulated by both VirR and RevR, 18 of these genes, which included the sporulation-specificspoIVA, sigG andsigF genes, were regulated positively and negatively by RevR and VirR, respectively. Furthermore, analysis of the mapped RNA-seq reads visualized as depth of coverage plots showed that there were 93 previously unannotated transcripts in intergenic regions. These transcripts potentially encode small RNA molecules. Conclusion In conclusion, using strand-specific RNA-seq analysis, this study has identified differentially expressed chromosomal and pCP13 native plasmid-encoded genes, antisense transcripts, and transcripts within intergenic regions that are controlled by the VirSR or RevR regulatory systems.