A transcriptional response of
ABE fermentation
Butanol shock
Clostridium beijerinckii NRRL B-598
RNA-Seq transcriptome
Journal
Biotechnology for biofuels
ISSN: 1754-6834
Titre abrégé: Biotechnol Biofuels
Pays: England
ID NLM: 101316935
Informations de publication
Date de publication:
2019
2019
Historique:
received:
10
07
2019
accepted:
04
10
2019
entrez:
23
10
2019
pubmed:
23
10
2019
medline:
23
10
2019
Statut:
epublish
Résumé
One of the main obstacles preventing solventogenic clostridia from achieving higher yields in biofuel production is the toxicity of produced solvents. Unfortunately, regulatory mechanisms responsible for the shock response are poorly described on the transcriptomic level. Although the strain In this paper, we present a transcriptional response of the strain during a butanol challenge, caused by the addition of butanol to the cultivation medium at the very end of the acidogenic phase, using RNA-Seq. We resequenced and reassembled the genome sequence of the strain and prepared novel genome and gene ontology annotation to provide the most accurate results. When compared to samples under standard cultivation conditions, samples gathered during butanol shock represented a well-distinguished group. Using reference samples gathered directly before the addition of butanol, we identified genes that were differentially expressed in butanol challenge samples. We determined clusters of 293 down-regulated and 301 up-regulated genes whose expression was affected by the cultivation conditions. Enriched term "RNA binding" among down-regulated genes corresponded to the downturn of translation and the cluster contained a group of small acid-soluble spore proteins. This explained phenotype of the culture that had not sporulated. On the other hand, up-regulated genes were characterized by the term "protein binding" which corresponded to activation of heat-shock proteins that were identified within this cluster. We provided an overall transcriptional response of the strain
Sections du résumé
BACKGROUND
BACKGROUND
One of the main obstacles preventing solventogenic clostridia from achieving higher yields in biofuel production is the toxicity of produced solvents. Unfortunately, regulatory mechanisms responsible for the shock response are poorly described on the transcriptomic level. Although the strain
RESULTS
RESULTS
In this paper, we present a transcriptional response of the strain during a butanol challenge, caused by the addition of butanol to the cultivation medium at the very end of the acidogenic phase, using RNA-Seq. We resequenced and reassembled the genome sequence of the strain and prepared novel genome and gene ontology annotation to provide the most accurate results. When compared to samples under standard cultivation conditions, samples gathered during butanol shock represented a well-distinguished group. Using reference samples gathered directly before the addition of butanol, we identified genes that were differentially expressed in butanol challenge samples. We determined clusters of 293 down-regulated and 301 up-regulated genes whose expression was affected by the cultivation conditions. Enriched term "RNA binding" among down-regulated genes corresponded to the downturn of translation and the cluster contained a group of small acid-soluble spore proteins. This explained phenotype of the culture that had not sporulated. On the other hand, up-regulated genes were characterized by the term "protein binding" which corresponded to activation of heat-shock proteins that were identified within this cluster.
CONCLUSIONS
CONCLUSIONS
We provided an overall transcriptional response of the strain
Identifiants
pubmed: 31636702
doi: 10.1186/s13068-019-1584-7
pii: 1584
pmc: PMC6790243
doi:
Types de publication
Journal Article
Langues
eng
Pagination
243Informations de copyright
© The Author(s) 2019.
Déclaration de conflit d'intérêts
Competing interestsThe authors declare that they have no competing interests.
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