An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes

BMC Genomics

Research Article

Renato Hohl Orsi¹  Martin Wiedmann¹  Yichang Liu¹  Kathryn Jean Boor¹  Veronica Guariglia-Oropeza¹ 

[1] Department of Food Science, Cornell University, 14853, Ithaca, NY, USA;

关键词: RNA-seq;    Listeria monocytogenes;    Sigma H;    Competence;   

DOI  :  10.1186/s12864-016-2432-9

 received in 2015-09-11, accepted in 2016-02-03,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundAlternative σ factors are important transcriptional regulators in bacteria. While σB has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σH has not yet been well defined in Listeria, even though σH controls a large regulon in the closely related non-pathogenic Bacillus subtilis.ResultsUsing RNA-seq characterization of a L. monocytogenes strain with deletions of all 4 genes encoding alternative σ factors (ΔBCHL), which was further modified to overexpress sigH (ΔBCHL::Prha-sigH), we identified 6 transcription units (TUs) that are transcribed from σH-dependent promoters. Five of these TUs had not been previously identified. Identification of these promoters was facilitated by use of a bio-informatics approach that compared normalized RNA-seq coverage (NRC), between ΔBCHL::Prha-sigH and a ΔBCHL control, using sliding windows of 51 nt along the whole genome rather than comparing NRC calculated only for whole genes. Interestingly, we found that three operons that encode competence genes (comGABCDEFG, comEABC, coiA) are transcribed from σH-dependent promoters. While these promoters were highly conserved in L. monocytogenes, none of them were found in all Listeria spp. and coiA and its σH-dependent promoter were only found in L. monocytogenes.ConclusionsOur data indicate that a number of L. monocytogenes competence genes are regulated by σH. This σH-dependent regulation of competence related genes is conserved in the pathogen L. monocytogenes, but not in other non-pathogenic Listeria strains. Combined with prior data that indicated a role of σH in virulence in a mouse model, this suggests a possible novel role of σH-dependent competence genes in L. monocytogenes virulence. Development and implementation of a sliding window approach to identify differential transcription using RNA-seq data, not only allowed for identification of σH-dependent promoters, but also provides a general approach for sensitive identification of differentially transcribed promoters and genes, particularly for genes that are transcribed from multiple promoter elements only some of which show differential transcription.

【 授权许可】

CC BY   
© Liu et al. 2016