Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

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dc.contributor.authorSedlář, Karelcs
dc.contributor.authorCicková, Pavlínacs
dc.contributor.authorVasylkivska, Marynacs
dc.contributor.authorBranská, Barboracs
dc.contributor.authorKolek, Jancs
dc.contributor.authorKupková, Kristýnacs
dc.contributor.authorPatáková, Petracs
dc.contributor.authorProvazník, Valentýnacs
dc.coverage.issue415cs
dc.coverage.volume19cs
dc.date.issued2018-05-30cs
dc.description.abstractBackground Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. Results In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation. Conclusions We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering.en
dc.formattextcs
dc.format.extent1-1cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationBMC GENOMICS. 2018, vol. 19, issue 415, p. 1-1.en
dc.identifier.doi10.1186/s12864-018-4805-8cs
dc.identifier.issn1471-2164cs
dc.identifier.orcid0000-0002-8269-4020cs
dc.identifier.orcid0000-0003-1341-7975cs
dc.identifier.orcid0000-0002-6774-2709cs
dc.identifier.orcid0000-0002-3422-7938cs
dc.identifier.other147805cs
dc.identifier.researcheridK-1120-2014cs
dc.identifier.researcheridP-1695-2016cs
dc.identifier.researcheridF-4121-2012cs
dc.identifier.scopus56309904900cs
dc.identifier.scopus57190019500cs
dc.identifier.scopus6701729526cs
dc.identifier.urihttp://hdl.handle.net/11012/82994
dc.language.isoencs
dc.publisherBioMed Centralcs
dc.relation.ispartofBMC GENOMICScs
dc.relation.urihttp://link.springer.com/article/10.1186/s12864-018-4805-8cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1471-2164/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectClostridium beijerinckii NRRL B-598en
dc.subjectRNA-Seq transcriptomeen
dc.subjectABE fermentationen
dc.titleTranscription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seqen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-147805en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:40:06en
sync.item.modts2025.01.17 15:18:58en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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