Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003
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BACKGROUND: Bifidobacterium 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. RESULTS: The 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. CONCLUSION: The 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.
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As a qualitative validation step, the matching procedure was applied to B. breve strain UCC2003, confirming that the pipeline correctly identified the expected RPB sequences in the upstream regions of this strain, consistent with previously reported transcriptional data.
“As a qualitative validation step, the matching procedure was applied to the well-characterized B. breve strain UCC2003 [52] , confirming that the pipeline correctly identified the expected RPB sequences in the upstream regions of this strain, consistent with previously reported transcriptional data.”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [52]
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- Authors
- Bottacini, F., Zomer, A., Milani, C., Ferrario, C., Lugli, G. A., Egan, M., Ventura, M., & van Sinderen, D.
- Affiliations
- University College Cork (IE)
- Utrecht University (NL)
- University of Parma (IT)
- ORCID
- Venue
- BMC Genomics
- Published
- 2017-12
- Volume
- 18
- Issue
- 1
- Pages
- 991-991
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC5746004
- OpenAlex
- W2778305687
- Cited by
- 37
- References
- 38
- Citations by year
- 2026: 6 · 2025: 2 · 2024: 2 · 2023: 1 · 2022: 5 · 2021: 7 · 2020: 5 · 2019: 7 · 2018: 2
- FWCI
- 2.53
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Genomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Arrow@dit (Dublin Institute of Technology) (acceptedVersion)
- Cork Open Research Archive (University College Cork, Ireland) (acceptedVersion, cc-by)
- Cork Open Research Archive (University College Cork, Ireland) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Science Foundation Ireland (07/CE/B1368, SFI/12/RC/2273, 08/SRC/B1393)
- Federation of European Microbiological Societies (GB) (FEMS-RG-2016-0103)
- EU Joint Programming Initiative (JPI HDHL)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- promoter mapping, transcriptional landscape, transcriptional regulation, operon transcription, rho-independent termination, logarithmic growth, infant gut microbiota, gut commensals, Bifidobacterium
- MeSH terms
- Bifidobacterium breve, Promoter Regions, Genetic, Sequence Analysis, RNA, Genes, Essential, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, RNA, Small Untranslated, Riboswitch, Transcriptome, Transcription Initiation, Genetic, Transcription Termination, Genetic
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