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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12520%2F18%3A43897366" target="_blank" >RIV/60076658:12520/18:43897366 - isvavai.cz</a>

Alternative codes found

RIV/60461373:22330/18:43916901 RIV/00216305:26220/18:PU128058

Result on the web

<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4805-8" target="_blank" >https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4805-8</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12864-018-4805-8" target="_blank" >10.1186/s12864-018-4805-8</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/GA17-00551S" target="_blank" >GA17-00551S: Relationship between butanol efflux and butanol tolerance of Clostridia</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2018

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

BMC Genomics

ISSN

1471-2164

e-ISSN

—

Volume of the periodical

19

Issue of the periodical within the volume

05/2018

Country of publishing house

GB - UNITED KINGDOM

Number of pages

13

Pages from-to

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UT code for WoS article

000433580600001

EID of the result in the Scopus database

2-s2.0-85047797874