Transcriptomic analysis of the sulfate starvation response in Pseudomonas aeruginosa
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ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa
PROVIDER: GSE8408 | GEO | 2009/06/22
SECONDARY ACCESSION(S): PRJNA101467
REPOSITORIES: GEO
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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
Project description:The large-scale application of genomic and metagenomic sequencing technologies has yielded a number of insights about the metabolic potential of symbiotic human gut microbes. Bacteria that colonize the mucosal layer that overlies the gut epithelium have access to highly-sulfated polysaccharides (i.e., mucin oligosaccharides and glycosaminoglycans), which they could potentially forage as nutrient sources. To be active, sulfatases must undergo a critical post-translational modification catalyzed in anaerobic bacteria by the AdoMet enzyme anSME (anaerobic Sulfatase-Maturating Enzyme). In the present study, we have tested the role of this pathway in the prominent gut symbiont Bacteroides thetaiotaomicron, which possesses more predicted sulfatases (28) than in the human genome and a single predicted anSME. In vitro studies revealed that deletion of its anSME (BT0238) results in loss of sulfatase activity and impaired ability to use sulfated polysaccharides as carbon sources. Co-colonization of germ-free animals with both isogenic strains, or invasion experiments involving the introduction of one then the other strain, established that anSME activity and the sulfatases that are activated via this pathway, are important fitness factors for B. thetaiotaomicron, especially when mice are fed a simple sugar diet that requires this saccharolytic bacterium to adaptively forage on host glycans as nutrients. Whole genome transcriptional profiling of wild-type and the anSME mutant in vivo revealed that loss of this enzyme alters expression of genes involved in mucin utilization and that this disrupted ability to access mucosal glycans likely underlies the observed dramatic colonization defect. Comparative genomic analysis reveals that 100% of 46 fully sequenced human gut Bacteroidetes contain homologs of BT0238 and genes encoding sulfatases, suggesting that this is an important and evolutionarily conserved feature.
2011-01-01 | GSE25415 | GEO
Project description:The large-scale application of genomic and metagenomic sequencing technologies has yielded a number of insights about the metabolic potential of symbiotic human gut microbes. Bacteria that colonize the mucosal layer that overlies the gut epithelium have access to highly-sulfated polysaccharides (i.e., mucin oligosaccharides and glycosaminoglycans), which they could potentially forage as nutrient sources. To be active, sulfatases must undergo a critical post-translational modification catalyzed in anaerobic bacteria by the AdoMet enzyme anSME (anaerobic Sulfatase-Maturating Enzyme). In the present study, we have tested the role of this pathway in the prominent gut symbiont Bacteroides thetaiotaomicron, which possesses more predicted sulfatases (28) than in the human genome and a single predicted anSME. In vitro studies revealed that deletion of its anSME (BT0238) results in loss of sulfatase activity and impaired ability to use sulfated polysaccharides as carbon sources. Co-colonization of germ-free animals with both isogenic strains, or invasion experiments involving the introduction of one then the other strain, established that anSME activity and the sulfatases that are activated via this pathway, are important fitness factors for B. thetaiotaomicron, especially when mice are fed a simple sugar diet that requires this saccharolytic bacterium to adaptively forage on host glycans as nutrients. Whole genome transcriptional profiling of wild-type and the anSME mutant in vivo revealed that loss of this enzyme alters expression of genes involved in mucin utilization and that this disrupted ability to access mucosal glycans likely underlies the observed dramatic colonization defect. Comparative genomic analysis reveals that 100% of 46 fully sequenced human gut Bacteroidetes contain homologs of BT0238 and genes encoding sulfatases, suggesting that this is an important and evolutionarily conserved feature. Three replicate samples from 4 different biological treatment groups: 1. Wild-type B. thetaiotaomicron from the cecum of gnotobiotic mice fed a simple-sugar diet; 2. chuR mutant B. thetaiotaomicron from the cecum of gnotobiotic mice fed a simple-sugar diet; 3. Wild-type B. thetaiotaomicron from the cecum of gnotobiotic mice fed a plant-rich diet; 4. chuR mutant B. thetaiotaomicron from the cecum of gnotobiotic mice fed a plant-rich diet.
2011-01-01 | E-GEOD-25415 | 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. 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:We present a study combining gene expression analyses and bioinformatic assessment. 1120 sequences annotated as sulfatase encoding from eight Rhodopirellula strains were clustered into 173 groups of orthologous and paralogous genes. A selection of 709 sulfatase gene strains were aligned to 66 sulfatase genes of known function to check for their respective substrate specificity. Thereby, 22 major phylogenetic clusters were observed with just five being mixed clusters between Rhodopirellula and reference sequences. This indicates a huge diversity on the substrate recognition level, unexpected from conventional annotations in public databases. Exemplarily, Rhodopirellula baltica SH1T was grown on different sulfated polysaccharides. Subsequent gene expression analyses using whole genome microarrays revealed distinct sulfatase expression profiles based on substrates tested. Expression profiles strongly point towards a functional link between sulfated polysaccharides and sulfatases. Moreover, further potential functions can be deduced from the expression profiles. In silico assessment backed up in vivo findings and raised the question, whether related strains and species are even more adapted to utilizing sulfated polysaccharides present in marine environments. Dual channel microarrays have been used for comparing the gene expression of R. baltica SH1T under reference condition (grown on glucose) and grown on sulfated polysaccharides as substrates of interest. Substrates tested have been: Chondroitin sulfate, lambda carrageenan and fucoidan. Control: 3 Biological replicates, Substrates tested: 2-3 Biological replicates, 2-3 replicates per array
2012-03-31 | E-GEOD-35832 | 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:Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur responsive genes. Along with genes known to be involved in sulfur metabolism, the CYS-3 transcription factor also directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulating sulfur import is an important aspect of regulation by CYS-3. Additionally, CYS-3 directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism.
2021-07-12 | GSE173890 | GEO
Project description:Responses of photosynthetic organisms to sulfur starvation include (i) increasing the capacity of the cell for transporting and/or assimilating exogenous sulfate, (ii) restructuring cellular features to conserve sulfur resources, and (iii) modulating metabolic processes and rates of cell growth and division. We used microarray analyses to obtain a genome-level view of changes in mRNA abundances in the green alga Chlamydomonas reinhardtii during sulfur starvation. The work confirms and extends upon previous findings showing that sulfur deprivation elicits changes in levels of transcripts for proteins that help scavenge sulfate and economize on the use of sulfur resources. Changes in levels of transcripts encoding members of the light-harvesting polypeptide family, such as LhcSR2, suggest restructuring of the photosynthetic apparatus during sulfur deprivation. There are also significant changes in levels of transcripts encoding enzymes involved in metabolic processes (e.g., carbon metabolism), intracellular proteolysis, and the amelioration of oxidative damage; a marked and sustained increase in mRNAs for a putative vanadium chloroperoxidase and a peroxiredoxin may help prolong survival of C. reinhardtii during sulfur deprivation. Furthermore, many of the sulfur stress-regulated transcripts (encoding polypeptides associated with sulfate uptake and assimilation, oxidative stress, and photosynthetic function) are not properly regulated in the sac1 mutant of C. reinhardtii, a strain that dies much more rapidly than parental cells during sulfur deprivation. Interestingly, sulfur stress elicits dramatic changes in levels of transcripts encoding putative chloroplast-localized chaperones in the sac1 mutant but not in the parental strain. These results suggest various strategies used by photosynthetic organisms during acclimation to nutrient-limited growth.
2005-07-22 | E-SMDB-2992 | biostudies-arrayexpress
Project description:Cell-surface signaling is a sophisticated regulatory mechanism used by gram-negative bacteria to sense signals from outside the cell and transmit them into the cytoplasm. This regulatory system consists of an outer membrane-localized TonB-dependent receptor (TonB-dependent transducer), a cytoplasmic membrane-localized anti-sigma factor and an extracytoplasmic function (ECF) sigma factor. By microarray analysis we have identified the regulons of four novel P. aeruginosa signaling systems. For that, the ECF sigmas PA0149, PA2050, PA2093 and PA4896 have been overexpressed in P. aeruginosa and their target gene candidates have been identified using DNA microarray. Keywords: Overexpression of ECF sigma factors
2007-11-24 | GSE9657 | GEO
Project description:Responses of photosynthetic organisms to sulfur starvation include (i) increasing the capacity of the cell for transporting and/or assimilating exogenous sulfate, (ii) restructuring cellular features to conserve sulfur resources, and (iii) modulating metabolic processes and rates of cell growth and division. We used microarray analyses to obtain a genome-level view of changes in mRNA abundances in the green alga Chlamydomonas reinhardtii during sulfur starvation. The work confirms and extends upon previous findings showing that sulfur deprivation elicits changes in levels of transcripts for proteins that help scavenge sulfate and economize on the use of sulfur resources. Changes in levels of transcripts encoding members of the light-harvesting polypeptide family, such as LhcSR2, suggest restructuring of the photosynthetic apparatus during sulfur deprivation. There are also significant changes in levels of transcripts encoding enzymes involved in metabolic processes (e.g., carbon metabolism), intracellular proteolysis, and the amelioration of oxidative damage; a marked and sustained increase in mRNAs for a putative vanadium chloroperoxidase and a peroxiredoxin may help prolong survival of C. reinhardtii during sulfur deprivation. Furthermore, many of the sulfur stress-regulated transcripts (encoding polypeptides associated with sulfate uptake and assimilation, oxidative stress, and photosynthetic function) are not properly regulated in the sac1 mutant of C. reinhardtii, a strain that dies much more rapidly than parental cells during sulfur deprivation. Interestingly, sulfur stress elicits dramatic changes in levels of transcripts encoding putative chloroplast-localized chaperones in the sac1 mutant but not in the parental strain. These results suggest various strategies used by photosynthetic organisms during acclimation to nutrient-limited growth. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Computed
2005-07-28 | E-GEOD-3015 | biostudies-arrayexpress