ArticleBMC genomics2018
Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Augusta: From RNA-Seq to gene regulatory networks and Boolean models.Computational and structural biotechnology journal · 2024Article
- Genome-Wide Transcriptomic Analysis ofJournal of microbiology and biotechnology · 2021Article
- Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia.Biotechnology for biofuels · 2021Article
- Sporulation in solventogenic and acetogenic clostridia.Applied microbiology and biotechnology · 2021Review
- Deeper below the surface-transcriptional changes in selected genes of Clostridium beijerinckii in response to butanol shock.MicrobiologyOpen · 2021Article
- Changes in efflux pump activity of Clostridium beijerinckii throughout ABE fermentation.Applied microbiology and biotechnology · 2021Article
- Identification and Validation of Reference Genes inFrontiers in microbiology · 2021Article
- Phenotypic and Genomic Analysis ofFrontiers in bioengineering and biotechnology · 2020Article
- Synthetic Biology Tools for Genome and Transcriptome Engineering of SolventogenicFrontiers in bioengineering and biotechnology · 2020Review
- Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level.Scientific reports · 2019Article
- Article
- A transcriptional response ofBiotechnology for biofuels · 2019Article
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Authors and funding
8 authors.
Funding
Abstract
backgroundThinning 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.
resultsIn 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.
conclusionsWe 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.
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