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Transcriptomic analysis of Clostridium acetobutylicum biofilm cells in repeated-batch fermentation

ABSTRACT: Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes.

ORGANISM(S): Clostridium acetobutylicum Arthrobacter sp. Clostridium acetobutylicum DSM 1731

PROVIDER: GSE72765 | GEO | 2015/09/09

SECONDARY ACCESSION(S): PRJNA295017

REPOSITORIES: GEO

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Transcriptomic analysis of Clostridium acetobutylicum biofilm cells in repeated-batch fermentation

Project description:Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes. Repeated-batch fermentation was carried out in 2-L stainless steel columns packed with 40 g of cotton towel ?cut into pieces?approximately 3 cm × 5 cm) containing 1.5 L of P2 medium. Medium circulation rate was maintained at 35 mL/min via a peristaltic pump and the temperature was controlled at 37°C. Fermentation broth was replaced with fresh P2 medium every 12 h. Samples were withdrawn at 6 h after the medium replacement at predetermined interval, except for the last 3 samples. The last 3 samples were withdrawn at 12 h, 15 h, and 17 h after the medium replacement, respectively, to study the transcriptomic response to the adverse condition at the end of fermentation. A total of 8 samples were withdrawn over a period of 7 days, and time course gene expression profiles were studied.

2015-09-09 | E-GEOD-72765 | biostudies-arrayexpress

Clostridium acetobutylicum

Project description:Transcriptomic analysis of Clostridium acetobutylicum biofilm cells in repeated-batch fermentation

| PRJNA295017 | ENA

Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [I]

Project description:Immobilization of Clostridium acetobutylicum B3 onto fibrous matrix by surface-adsorption was developed and applied to biobutanol production. The immobilized C. acetobutylicum B3 cells formed biofilm and showed dramatically improved butanol tolerance and production rate. DNA array-based transcriptional analysis of C.acetobutylicum B3 biofilm cells was conducted to elucidate the gene expression profile of the biofilm cells. Results showed that about 16% of the whole genome was differentially expressed. The most apparently differentially expressed genes were involved in amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, and coenzyme transport and metabolism. Samples for biofilm cells and planktonic cells were withdrawn at four diffierent fermentation phases. The gene expression pattern of biofilm cells were investigated relative to that of planktonic cells from the same phase. The experiment was carried out twice independently. Cotton fibrous matrix (60 g/L) was used as biofilm carrier.

2015-05-15 | E-GEOD-68899 | biostudies-arrayexpress

Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [II]

2015-05-15 | E-GEOD-68900 | biostudies-arrayexpress

Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [II]

2015-05-15 | GSE68900 | GEO

Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [I]

2015-05-15 | GSE68899 | GEO

Clostridium acetobutylicum

Project description:Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [I]

| PRJNA283992 | ENA

Clostridium acetobutylicum

Project description:Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [II]

| PRJNA283991 | ENA

Identification of a sensor histidine kinase (BfcK) controlling biofilm formation in Clostridium acetobutylicum

Project description:Clostridium acetobutylicum has been extensively exploited to produce biofuels and solvents and its biofilm could dramatically improve its productivities. However, genetic control of C. acetobutylicum biofilm has not been dissected so far. Here, a total of 24 disruptants were finally obtained over several years of attempts. Biofilm formation and physiological phenotypes were characterized for these disruptants and most of them showed robust biofilm formation still, or showed both impaired biofilm formation and cell growth. Only a mutant with a disputed histidine kinase gene (CA_C2730, designated bfcK in this study) abolished biofilm formation without impaired cell growth or solvent production. Phosphoproteomic analysis revealed that bfcK could control C. acetobutylicum flagellar motility at both translational and post-translational (protein phosphorylation) levels. The bfcK also showed apparent regulation of a serine/threonine protein kinase (encoded by CA_C0404) which was involved in protein secretion. Based on these findings, possible bfcK-based mechanisms for biofilm formation in C. acetobutylicum were proposed.

2021-07-30 | PXD021161 | Pride

Metabolite stress response to butanol in Clostridium acetobutylicum ATCC 824

Project description:Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyrate posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butanol.

2013-08-20 | GSE48031 | GEO

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