Sulfate assimilation in Clostridium thermocellum
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ABSTRACT:
ORGANISM(S): Acetivibrio thermocellus DSM 1313
PROVIDER: GSE100047 | GEO | 2020/11/01
REPOSITORIES: GEO
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Project description:In this study, we combined metabolic reconstruction, growth assays, metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway and of thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, of at least one gene of the transsulfuration pathway (aecD) and of genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC9175 during sulfur starvation and in the presence of sulfate, cystine or methionine plus cystine. In sulfur starvation, 690 genes including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in presence of cysteine, while the expression of metX, metY, metE1, metE2 and BL613 encoding a probable cystathionine-γ-synthase decreased in the presence of methionine. We identified three ABC transporters: two stronger transcribed during cysteine limitation and one during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase, BL929, and a methionine transporter (metPS) was induced in the presence of methionine, in conjunction with a significant increase of volatile sulfur compounds production. Refer to individual Series. This SuperSeries is composed of the following subset Series: GSE25418: BA-Methionine plus Cystine vs Cystine GSE25419: BA-Sulfate vs Cystine GSE25420: BA-Methionine plus Cystine vs Sulfate GSE25421: BA-Sulfate vs Sulfate starvation
2010-11-25 | E-GEOD-25422 | biostudies-arrayexpress
Project description:Four C. thermocellum DSM-1313 derived strains were assessed using metabolite and DNA microarray tools in order to better understand carbon and electron flow within this organism. C. thermocellum is able to ferment cellulose into its fermentation end products L-lactate, acetate, formate, hydrogen gas, and ethanol, with the latter being the desired end product to be used as biorenewable fuel. In addition to the parent strain (genotype: hpt spo0A), strains with either or both of the genes encoding lactate dehydrogenase (ldh) and phosphate acetyltransferase (pta) deleted were studied. The strains used are a parent strain (M1726: genotype: hpt spo0A), and strains with either the gene encoding lactate dehydrogenase (M1629: hpt spo0A ldh) or phosphate acetyltransferase (M1630: hpt spo0A pta) deleted, or with both genes deleted (M1725: hpt spo0A ldh pta). Controlled batch fermentations using cellobiose as sole carbon source were grown for each strain, and samples in mid-exponential phase and at the time of carbon depletion were examined by DNA microarray.
2012-03-01 | GSE27046 | GEO
Project description:The batch fermentation of Clostridium acetobutylicum is characterized by an acetogenic growth phase during exponential growth when mainly acetate and butyrate are fermentation products. Then, at the end of exponential growth and during stationary phase, the organism switches to solventogenic growth and large amounts of acetone, ethanol and butanol are produced. These growth phases can be studied independent from each other in a phosphate-limited continuous culture. In transcription analysis of continuous cultures using DNA microarrays it became evident that, among others, operons involved in sulfur assimilation are strongly up-regulated during solventogenesis. Using the ClosTron technique we constructed two knock-out mutants in the genes CAC0105 and CAC0930 annotated as involved in sulfate reduction and cysteine biosynthesis. Complementation experiments were carried out with sulfite and cysteine to prove the predicted function. The fermentation experiments of wild type and mutants using phosphate-limited and sulfur-limited continuous culture demonstrated that less sulfur source was consumed in solventogenic phase and the efficiency of cysteine uptake became lower. DNA microarrays were performed to study the difference of transcriptional expression when the wild type was challenged with insufficient sulfur source and the mccB (CAC0930) mutant was inactivated in the continuous culture. The result provided insights into understanding the sulfur metabolism regulatory.
2015-04-15 | E-MTAB-2745 | biostudies-arrayexpress
Project description:ABSTRACT: Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development, and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations, and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis thaliana accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme adenosine 5-phosphosulfate reductase 2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction and its reduced activity in the loss-of-function allele apr2-1 and the two A. thaliana accessions Hodon¨ªn (Hod) and Shahdara (Sha), leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Sha accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by four orders of magnitude across the A. thaliana species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored. genomic hybridization bulked segregant analysis Hybridizations from a set of Bulk Segregant analysis. We measured the elemental profile of 328 F2 plants from a cross between the high sulfur and selenium Arabidopsis thaliana accession Hod and the Col-0 accession, data available at www.ionomicshub.org <http://www.ionomicshub.org>). Leaves from the 57 highest and 61 lowest sulfur and selenium accumulating plants (calculated as a percentage of the Col-0 accumulation in the same growth tray) were pooled and the genomic DNA was extracted using Qiagen kits.
2014-10-01 | E-GEOD-61922 | biostudies-arrayexpress
Project description:In this study, we combined metabolic reconstruction, growth assays, metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway and of thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, of at least one gene of the transsulfuration pathway (aecD) and of genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC9175 during sulfur starvation and in the presence of sulfate, cystine or methionine plus cystine. In sulfur starvation, 690 genes including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in presence of cysteine, while the expression of metX, metY, metE1, metE2 and BL613 encoding a probable cystathionine-γ-synthase decreased in the presence of methionine. We identified three ABC transporters: two stronger transcribed during cysteine limitation and one during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase, BL929, and a methionine transporter (metPS) was induced in the presence of methionine, in conjunction with a significant increase of volatile sulfur compounds production. This SuperSeries is composed of the SubSeries listed below.
2010-11-25 | GSE25422 | GEO
Project description:ABSTRACT: Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development, and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations, and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis thaliana accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme adenosine 5-phosphosulfate reductase 2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction and its reduced activity in the loss-of-function allele apr2-1 and the two A. thaliana accessions Hodon¨ªn (Hod) and Shahdara (Sha), leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Sha accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by four orders of magnitude across the A. thaliana species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.
2014-10-01 | GSE61922 | GEO
Project description:All yeast strains used in this study (Table 1) are in the W303 background (ade2-1 can1-100, his3-1,15 leu2-3,112 trp1-1 ura3). For sulfur limitation microarray studies, WT, met4 delete, met31 delete met32 delete, cbf1 delete, and met28 delete strains were grown in minimal B-media [see Cherest, H., and Surdin-Kerjan, Y. (1992). Genetic analysis of a new mutation conferring cysteine auxotrophy in Saccharomyces cerevisiae: updating of the sulfur metabolism pathway. Genetics 130, p51-58 for B-media composition] supplemented with 0.5mM methionine as the sole sulfur source. An aliquot of cells was harvested for a t=0 time point while the remainder were filtered through a .22um Stericup filter (Millipore), then washed and resuspended in pre-warmed (30 C) B-media lacking any source of sulfur. Cells were harvested after 20, 40, and 80 minutes.
2009-11-30 | E-MEXP-2429 | biostudies-arrayexpress
Project description:A comparison between high and low sulfur source supplies, i.e., sulfate, methionine or cystine, was carried out in order to identify key steps in the biosynthetic and catabolic pathways of the sulfur amino acids.
2012-12-01 | GSE39834 | GEO
Project description:A comparison between high and low sulfur source supplies, i.e., sulfate, methionine or cystine, was carried out in order to identify key steps in the biosynthetic and catabolic pathways of the sulfur amino acids. Two conditions experiment, high versus low sulfur conditions (sulfate, cystine or methionine with a ratio of 1 to 1000). Three biological experiments with a dye swap for each for cystine and sulfate. Two biological experiments with a dye swap for each for methionine.
2012-12-01 | E-GEOD-39834 | biostudies-arrayexpress
Project description:Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome, and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as sulfur source led to a sulfate starvation response, but also to induction of genes involved with type III secretion systems. Experiment Overall Design: Gene expression in exponential-phase cells was analysed using Affymetrix arrays. Sulfur was supplied either as sulfate, or as the non-sulfate S sources cyclamate (sodium cyclohexylsulfamate) and mucin (human colon cell line mucin LS174T). Control experiments were also done with combinations of these sulfur sources. Studies with mucin as sulfur source were carried out with P. aeruginosa E601 (a CF isolate with mucin sulfatase activity) and comparative studies were performed with P. aeruginosa PAO1. Experiments with strain E601 were done in 3-4 fold replication, experiments with strain PAO1 with 2-3 fold replication.
2008-06-16 | E-GEOD-8408 | biostudies-arrayexpress