Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003
| Autor: | Bottacini, Francesca, Zomer, Aldert, Milani, Christian, Ferrario, Chiara, Lugli, Gabriele Andrea, Egan, Muireann, Ventura, Marco, van Sinderen, Douwe, dI&I I&I-4 |
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| Přispěvatelé: | dI&I I&I-4 |
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
lcsh:QH426-470 Operon lcsh:Biotechnology 030106 microbiology ved/biology.organism_classification_rank.species Biology Bifidobacterium breve Transcriptome 03 medical and health sciences Bifidobacteria Transcription (biology) lcsh:TP248.13-248.65 Genetics Promoter Regions Genetic Gene Transcription Initiation Genetic Oligonucleotide Array Sequence Analysis Tiling array Genes Essential ved/biology Sequence Analysis RNA Gene Expression Profiling Probiotics Promoter lcsh:Genetics 030104 developmental biology Riboswitch Transcription Termination Genetic RNA Small Untranslated Gene expression DNA microarray Transcription Biotechnology Research Article |
| Zdroj: | BMC Genomics BMC Genomics, 18(1). BioMed Central BMC Genomics, Vol 18, Iss 1, Pp 1-14 (2017) |
| ISSN: | 1471-2164 |
| Popis: | 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. Electronic supplementary material The online version of this article (10.1186/s12864-017-4387-x) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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