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

K. Sedlar, P. Koscova, M. Vasylkivska, B. Branska, J. Kolek, K. Kupkova, P. Patakova, I. Provaznik,

. 2018 ; 19 (1) : 415. [pub] 20180530

Jazyk angličtina Země Anglie, Velká Británie

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc19000692

BACKGROUND: 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.

Citace poskytuje Crossref.org

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$a Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq / $c K. Sedlar, P. Koscova, M. Vasylkivska, B. Branska, J. Kolek, K. Kupkova, P. Patakova, I. Provaznik,
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$a BACKGROUND: 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.
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$a Vasylkivska, Maryna $u Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czechia.
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$a Branska, Barbora $u Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czechia.
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$a Kolek, Jan $u Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czechia. Institute of Aquaculture and Protection of Waters, University of South Bohemia in České Budějovice, Na Sádkách 1780, 370 05, České Budějovice, Czechia.
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$a Kupkova, Kristyna $u Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00, Brno, Czechia. Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
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$a Patakova, Petra $u Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czechia.
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$a Provaznik, Ivo $u Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00, Brno, Czechia.
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