Influence of 3HP and PDO on cell metabolism at the transcriptional level in Halomonas bluephagenesis
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ABSTRACT:
ORGANISM(S): Halomonas bluephagenesis
PROVIDER: GSE159233 | GEO | 2021/01/01
REPOSITORIES: GEO
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Project description:Hydroxyproline in decaying organic matter and root exudates and is a source of carbon and nitrogen to soil-dwelling microorganisms. A bacterial pathway for hydroxyproline catabolism was elucidated over 30 years ago however genes and gene function relationships were not established. In that pathway, trans-4-hydroxy-L-proline (4-L-Hyp) is epimerized to cis-4-hydroxy-D-proline (4-D-Hyp), and then, in three enzymatic reactions, the D-diastereomer is converted via 1-pyrroline-4-hydroxy-2-carboxylate and alpha-ketoglutaric semialdehyde to alpha-ketoglutaric acid. Here we report on the regulation and functions of several genes from a hydroxyproline catabolism locus on the pSymB megaplasmid of the legume endosymbiont Sinorhizobium meliloti. The hydroxyproline catabolism genes (hyp) are negatively regulated by hypR and are organized as four single transcripts (hypR, hypD, hypS and hypH) and a 9 gene transcript (hypMNPQ(RE)XYZ). Transcription of these genes was induced in the presence of either 4-L-Hyp and 4-D-Hyp, and was not subject to nitrogen source regulation. The hypRE gene is shown to encode 4-hydroxyproline 2-epimerase (HypRE) responsible for the reversible isomerization of 4-L-Hyp and 4-D-Hyp, whereas a hypRE mutant grew with 4-D-Hyp but not of 4-L-Hyp as carbon source. hypO, hypD and hypH are predicted to encode the 4-D-Hyp oxidase, the 1-pyrroline-4-hydroxy-2-carboxylate deaminase and alpha-ketoglutaric semialdehyde dehydrogenase respectively. No epimerase activity was detected for the HypY (Smb20270), a predicted racemase, and activities from four other genes (designated hypS, hypX and hypZ) remain to be determined. In summary, the 4-hydroxyproline (4-Hyp) catabolic pathway for S. meliloti is similar to that previously elucidated for Pseudomonas however the presence of additional genes at the hyp locus suggests that additional metabolic steps still remain to be elucidated.
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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:It is now possible to discover the physiological function of LysR-family transcription factors (LLTF) in E. coli using ChIP-Exo (in vivo DNA-binding), growth phenotype, conserved gene clustering, and transcriptional analysis (RNA-seq deletion mutants). The LysR-family regulator phenotype microarray has been detected for YbdO, YbeF, YcaN, YiaU, and YgfI deletion mutants and for the isogenic E. coli BW25113 strain in minimal medium at carbon/nitrogen starvation or L-threonine supplement conditions. The LLTF YbdO and YgfI regulation is important for bacterial growth adaptation to low pH with citrate supplementation or glycerol as the carbon source, respectively. A systems analysis approach allows for the identification of the YneJ (putrescine utilization), YgfI, and YbdO transcription factor regulated genes in Escherichia coli. YgfI regulates DhaKLM, the phosphotransferase system involved in glycerol and dihydroxyacetone utilization. YbdO is a repressor for ybdMN and is likely involved in citrate lyase regulation. YneJ, re-named PtrR, directly controls the expression of the succinate-semialdehyde dehydrogenase Sad (YneI) and is important for bacterial growth in the presence of L-glutamate as a nitrogen source. The sad promoter is repressed by PtrR. PtrR is also a repressor of the fnrS gene, encoding a small regulatory RNA involved in the regulation of the sodB gene, as shown by RNA-seq data. A 15-bp palindromic PtrR-binding site was identified in the upstream regions of the sad / ptrR and fnrS genes and confirmed by ChIP-Exo and fluorescent polarization assays. The PtrR-dependent regulation of fnrS likely leads to a regulatory cascade induced by this small RNA.
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Project description:Glucose is a widely used carbon source in laboratory practice to culture Aspergillus fumigatus, however, glucose availability is often low in its “natural habitats” including the human body. We used a physiological–transcriptomical approach to reveal differences between A. fumigatus Af293 cultures incubated on glucose, glucose and peptone, peptone (carbon limitation), or without any carbon source (carbon starvation). Autolytic cell wall degradation was upregulated by both carbon starvation and limitation. The importance of autolytic cell wall degradation in adaptation to carbon stress was also highlighted by approximately 12.4% of the A. fumigatus genomes harbor duplication of genes involved in N-acetyl glucosamine utilization. Glucose withdrawal increased redox imbalance, altered both the transcription of antioxidative enzyme genes and oxidative stress tolerance, downregulated iron acquisition, but upregulated heme protein genes. Transcriptional activity of the Gliotoxin cluster was low in all experiments, while the Fumagillin cluster showed substantial activity both on glucose and under carbon starvation, and the Hexadehydro-astechrome cluster only on glucose. We concluded that glucose withdrawal substantially modified the physiology of A. fumigatus including processes that contribute to virulence. This may explain the challenge of predicting the in vivo behavior of A. fumigatus based on data from glucose rich cultures.
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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. Four strains were grown each as three independent biological replicates (fresh batch of media was made before each run). Per fermentation, two samples were taken for DNA microarray analysis as was determined by the optical density: mid-exponential was defined as O.D. 0.4 (measured by Dasgip probe); point of carbon depletion was defined by both the maximum O.D. reached and observation that no base was added to the fermentation to control pH. In total, 4 strains x 3 fermentation x 2 time points per fermentor = 24 arrays. Parent strain was used as reference strain.
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Project description:The enteric bacterium Proteus mirabilis is a common cause of complicated urinary tract infections. In the study, microrarrays were used to analyze P. mirabilis gene expression in vivo from experimentally infected mice. Urine was collected at 1, 3, and 7d postinfection, and RNA was isolated from bacteria in the urine for transcriptional analysis. Across 9 microarrays, 471 genes were upregulated and 82 were downregulated in vivo compared to in vitro broth culture. Genes upregulated in vivo encoded MR/P fimbriae, urease, iron uptake systems, amino acid and peptide transporters, pyruvate metabolism, and portions of the TCA cycle. Flagella were downregulated. Ammonia assimilation gene glnA (glutamine synthetase) was repressed in vivo while gdhA (glutamate dehydrogenase) was upregulated in vivo. Contrary to our expectations, ammonia availability due to urease activity in P. mirabilis did not drive this gene expression. A gdhA mutant was growth-deficient in minimal medium with citrate as the sole carbon source, and loss of gdhA resulted in a significant fitness defect in the mouse model of urinary tract infection. Unlike Escherichia coli, which represses gdhA and upregulates glnA in vivo and cannot utilize citrate, the data suggest that P. mirabilis uses glutamate dehydrogenase to monitor carbon-nitrogen balance, and this ability contributes to the pathogenic potential of P. mirabilis in the urinary tract.
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Project description:Purpose: We explore gene expression changes when Neurospora crassa wild type responds to different carbon sources in Vogel's medium. Method: We obtained mRNA samples of Neurospora crassa WT in Vogel's minimal medium (VMM) with different carbon source and used RNA-seq technique to measure the trancriptome changes. Results: We identified many genes of transcription factors and enzymes that were up regulated or down regulated in response to the different carbon stimulation. Conclusion: Our data represents a systematic transcriptome profiling of filamentous fungi on different carbon source and identify COL-26 as a critical regulator in degradation of starch components.
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