Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

BMC Genomics

Research Article

Muireann Egan¹  Douwe van Sinderen¹  Francesca Bottacini¹  Aldert Zomer²  Christian Milani³  Chiara Ferrario³  Marco Ventura³  Gabriele Andrea Lugli³ 

[1] APC Microbiome Institute and School of Microbiology, University College Cork, Cork, Ireland;Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands;Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy;

关键词: Gene expression;    Bifidobacteria;    Probiotics;    Transcription;   

DOI  :  10.1186/s12864-017-4387-x

 received in 2017-09-06, accepted in 2017-12-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundBifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and activities of this gut commensal in the host environment.ResultsThe assessment of vegetative promoters in the bifidobacterial prototype Bifidobacterium breve UCC2003 was performed employing a combination of RNA tiling array analysis and cDNA sequencing. Canonical −10 (TATAAT) and −35 (TTGACA) sequences were identified upstream of transcribed genes or operons, where deviations from this consensus correspond to transcription level variations. A Random Forest analysis assigned the −10 region of B. breve promoters as the element most impacting on the level of transcription, followed by the spacer length and the 5’-UTR length of transcripts. Furthermore, our transcriptome study also identified rho-independent termination as the most common and effective termination signal of highly and moderately transcribed operons in B. breve.ConclusionThe present study allowed us to identify genes and operons that are actively transcribed in this organism during logarithmic growth, and link promoter elements with levels of transcription of essential genes in this organism. As homologs of many of our identified genes are present across the whole genus Bifidobacterium, our dataset constitutes a transcriptomic reference to be used for future investigations of gene expression in members of this genus.

【 授权许可】

CC BY   
© The Author(s). 2017