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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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 Samples for biofilm cells and planktonic cells were withdrawn at four diffierent fermentation phases.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.

ORGANISM(S): Clostridium acetobutylicum

SUBMITTER: Dong Liu

PROVIDER: E-GEOD-68900 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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 Samples for biofilm cells and planktonic cells were withdrawn at four diffierent fermentation phases.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 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

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

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-05-15 | E-GEOD-68901 | biostudies-arrayexpress

A large-scale overexpression screen uncovers two paralogous genes ZCF15 and ZCF26 modulating Candida albicans biofilm gene circuitry (RNA-seq data)

Project description:To identify novel genes modulating Candida albicans biofilm formation, a screen of 2451 overexpression strains allowed us to identify 16 genes whose overexpression significantly reduced biofilm formation. Genome-wide expression and binding analyses were conducted upon overexpression of ZCF15 and ZCF26 and wild type planktonic and biofilm cells were performed. This study has identified new sets of biofilm regulators, including ZCF15 and ZCF26 whose specific role in metabolic remodelling during C. Albicans biofilm development. Triplicates data of RNAseq data are provided here with 6 conditions including the ZCF15 and ZCF16 cases mentioned here above

2022-06-01 | E-MTAB-11383 | biostudies-arrayexpress

Nitric oxide modulates Saccharomyces cerevisiae biofilm formation though regulating the transmembrane protein CTR1 by activating its transcriptional factor MAC1.

Project description:Biofilms with immobilized cells in industrial fermentation are beneficial. Encased in extracellular polymeric substance, cells forming biofilms are regulated by various factors. Nitric oxide (NO), as a signaling molecule, recognized as quorum sensing molecule regulating microbe biofilm formation. Regulation mechanisms of NO on bacteria biofilm have been studied extensively and deeply, while on fungus are rarely studied. In this study, we observed that low concentration of NO enhanced S. cerevisiae biofilm formation. Transcriptional and proteomic analysis revealed that transcription factor MAC1 was activated in biofilm cells under NO treatment. Overexpressed MAC1 increased yeast biofilm formation bypassing regulating the expression level of FLO11. Increased copper and iron contents in NO treated and MAC1 overexpressed cells were not responsible for increased biofilm formation. Among six downstream genes of MAC1, overexpressed CTR1 contributed yeast biofilm formation. Moreover, MAC1 and CTR1 contributed to biofilm cells ethanol resistance resulting from enhanced biofilm. The role of CTR1 protein in yeast biofilm formation may result from its hydrophobic residues in N-terminal extracellular domain. These findings suggested a NO-mediated biofilm formation mechanism that NO regulated expression levels of CTR1 through activating its transcription factor MAC1, leading enhanced biofilm formation.

2019-11-12 | PXD010751 | Pride

Phenotype and RNA-Seq-Based Transcriptome Profiling of Staphylococcus aureus biofilms in response to Tea tree oil

Project description:RNA sequencing (RNA-Seq) was used in our study to elucidate the mechanism of Tea tree oil (TTO) as a potential antibacterial agent to evaluate differentially expressed genes and functional network analysis in S. aureus ATCC 29213 biofilms. Staphylococcus aureus biofilm cells were exposed for 60 minutes to TTO at concentration of 1/2ÃMBIC (1 mg/ml).2 samples including 2 control samples are analyzed.

2016-08-19 | E-GEOD-85787 | biostudies-arrayexpress

Transcriptional Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress exemplified by 1-butanol exposure

Project description:To study the cellular global response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius upon solvent exposure we performed transcriptome comparing the response of planktonic and biofilm cells in absence and presence 1-butanol. S. acidocaldarius was grown in Petri dishes (static incubation) in the absence and presence of 0.5% and 1% (v/v) 1-butanol at 76°C for four days. Planktonic and biofilm cells were harvested and the transcriptional response towards 1-butanol was analysed via RNA-seq. In detail:Biofilm and planktonic cell samples (supernatant after static incubation) were generated in Petri dishes (92 x 16 mm, Polystyrene, without cams, Sarstedt) as described before. Cells grown under six different conditions, including Biofilm-Control (BF0), Biofilm-0.5% (v/v) 1-Butanol (BF05), Biofilm-1% (v/v) 1-Butanol (BF1), Planktonic-Control (PL0), Planktonic-0.5% (v/v) 1-Butanol (PL05), Planktonic-1% (v/v) 1-Butanol (PL1), were seperated, harvested by centrifugation (10 min, 5,000 x g, 4 °C) and immediately frozen at -70 °C. Isolation of cells was performed in triplicates with ten technical replicas each. Samples were pooled to obtain sufficient cell mass for further processing. RNA was isolated using Trizol (Thermo Fisher Scientific). In accordance, sequencing libraries were prepared via Illumina TruSeq stranded mRNA using Ribozero for RNA depletion. Sequencing was performed on a MiSeq instrument (Illumina, San Diego, California, USA) using v3 chemistry with a read length of 2x76 nt.

2021-02-20 | E-MTAB-10093 | biostudies-arrayexpress

E coli MG1655 biofilm and planktonic gene expression

Project description:Bacteria growing as surface-adherent biofilms are better able to withstand chemical and physical stresses than their unattached, planktonic counterparts. Using transcriptional profiling and quantitative PCR, we observed a previously uncharacterized gene, yjfO, to be upregulated during Escherichia coli MG1655 biofilm growth in a chemostat on serine-limited defined medium. A yjfO mutant, developed through targeted insertion mutagenesis, and a yjfO-complemented strain, were obtained for further characterization. While bacterial surface colonization levels (CFU/cm2) were similar in all three strains, the mutant strain exhibited reduced microcolony formation when observed in flow cells, and greatly enhanced flagellar motility on soft (0.3%) agar. Complementation of yjfO restored microcolony formation and flagellar motility to wild type levels. Cell surface hydrophobicity and twitching motility were unaffected by the presence or absence of yjfO. In contrast to the parent strain, biofilms from the mutant strain were less able to resist acid and peroxide stresses. yjfO had no significant effect on E. coli biofilm susceptibility to alkali or heat stress. Planktonic cultures from all three strains showed similar responses to these stresses. Regardless of the presence of yjfO, planktonic E. coli withstood alkali stress better than biofilm populations. Complementation of yjfO restored viability following exposure to peroxide stress, but did not restore acid resistance. Based on its influence on biofilm formation, stress response, and effects on motility, we propose renaming the uncharacterized gene, yjfO, as bsmA (biofilm stress and motility). Transcriptional profiling of duplicate biofilm and planktonic cultures of E. coli MG1655 grown in serine-limited MOPS minimal media.

2010-06-21 | E-GEOD-18362 | biostudies-arrayexpress

Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli

Project description:Most bacteria can form biofilms, which typically have a life cycle from cells initially attaching to a surface before aggregation and growth produces biomass and an extracellular matrix before finally cells disperse. To maximise fitness at each stage of this life cycle, and given the different events taking place within a biofilm, temporal regulation of gene expression is essential. We recently described the genes required for optimal fitness over time during biofilm formation in Escherichia coli using a massively parallel transposon mutagenesis approach called TraDIS-Xpress. We have now repeated this study in Salmonella enterica serovar Typhimurium to determine the similarities and differences in biofilm formation through time between these species. This work deepens understanding of the core requirements for biofilm formation in the Enterobacteriaceae whilst also identifying some genes with specialised roles in biofilm formation in each species.

2022-05-27 | E-MTAB-11765 | biostudies-arrayexpress

Increased mutability of staphylococci in biofilms as a consequence of oxidative stress

Project description:In this work we have demonstrated increased mutability of Staphylococcus aureus and S. epidermidis in biofilms and have explored the mechanisms underlying the enhanced mutability. A novel static biofilm model, utilising cellulose filter disks, was developed to support the formation of mature biofilms with sufficiently high cell densities to permit determination of mutation frequencies. The mutability of biofilm cultures increased up to 60 fold and 4 fold for S. aureus and S. epidermidis, respectively, compared with planktonic cultures. Incorporation of antioxidants into S. aureus biofilms reduced mutation frequencies, indicating that increased oxidative stress underlies increased mutability in the biofilm. Transcriptional profiling revealed upregulation of the superoxide dismutase gene, sodA, in early biofilm cultures, also suggesting enhanced oxidative stress in these cultures. However, loss of the genes encoding superoxide dismutases or peroxidases did not specifically exacerabate biofilm mutability. In S. aureus SH1000, hydrogen peroxide was found to contribute to biofilm mutability. Three growth conditions (18 hr planktonic growth, 48 hr biofilm growth and 144 biofilm growth) of which there are three biological replicates of each

2012-03-01 | E-GEOD-35837 | biostudies-arrayexpress

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