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

Francesca Bottacini,Gabriele Andrea Lugli,Muireann Egan,Christian Milani,Douwe Van Sinderen,Aldert Zomer,Chiara Ferrario,Marco Ventura

doi:10.1186/s12864-017-4387-x

Francesca Bottacini, Gabriele Andrea Lugli + Show 6 more

Open Access

https://doi.org/10.1186/s12864-017-4387-x

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Abstract

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.

Highlights

Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being
Extensive studies performed in E. coli have employed Ribonucleic acid (RNA) sequencing (RNA-Seq) to identify and assess promoters recognized by the vegetative sigma70 or RpoD sigma factor, which is responsible for transcription of housekeeping genes active during the exponential growth phase [3]
Tiling arrays and RNA-Seq alignment The transcriptome of exponentially growing B. breve UCC2003 cells, when cultivated under standard laboratory conditions, was determined in this study using two different technologies involving a hybridization-based approach availing of whole-genome tiling arrays integrated with data obtained by (Illumina) high throughput RNA sequencing (Additional file 1: Table S1) (Additional file 2: Figure S1 panel a)

Summary

Introduction

Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. Transcription levels in bacteria may vary considerably from gene to gene, and may vary in response to (changes in) environmental conditions. Extensive studies performed in E. coli have employed RNA sequencing (RNA-Seq) to identify and assess promoters recognized by the vegetative sigma or RpoD sigma factor, which is responsible for transcription of housekeeping genes active during the exponential growth phase [3]. Transcription of such housekeeping genes is directed by constitutive promoters, which do not normally depend on particular transcription factors (TFs), and which consist of sequences that exhibit a high level of conservation [6]

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