Bacillus subtilis 168 cells: ccpN mutant and ccpN-yqfL double mutant analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168
SUBMITTER: Thierry Doan
PROVIDER: E-GEOD-11937 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
CcpN controls central carbon fluxes in Bacillus subtilis.
Tännler Simon S Fischer Eliane E Le Coq Dominique D Doan Thierry T Jamet Emmanuel E Sauer Uwe U Aymerich Stéphane S
Journal of bacteriology 20080627 18
The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small noncoding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and ...[more]
Similar Datasets
Project description:Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a ccpN (yqzB) non polar mutant. Abstract of associated publication (article accepted): The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes. Two-condition experiment, wt vs. ccpN mutant. 4 experiments were performed different days with 3 independent RNA preparations (from separate cultures) and 3 independent sets of macroarrays: Experiment 1 (samples wt1 and ccpN1): total RNA extract1 / membranes set A Expereince 2 (samples wt2 and ccpN2): total RNA extract 2 / membranes set A Experiment 3 (samples wt2 and ccpN2): total RNA extract 3 / membranes set B Experiment 4 (samples wt2 and ccpN2): total RNA extract 3 / membranes set C
2008-06-26 | E-GEOD-11873 | biostudies-arrayexpress
Project description:Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a (ccpN-yqfL) double mutant. Abstract of the associated publication (article accepted): The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes. Two-condition experiment: wt vs. (ccpN-yqfL) double mutant. 2 totally independent comparisons were performed different days with 2 independent RNA preparations and 2 sets of macroarrays.
2008-07-01 | E-GEOD-11876 | biostudies-arrayexpress
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2010-05-15 | E-GEOD-17435 | biostudies-arrayexpress
Project description:In this study, we tested the hypothesis that high salt concentrations might alter gene expression in H. pylori. Analysis here provides into the role that salt may play in H. pylori pathogenesis. . H. pylori strain 26695 (SC#7) was grown for 15 h in BB-FBS medium containing 0.5% sodium chloride (i.e. BB-FBS-0.5%) The bacterial cells were then grown for 10 h, in fresh brucella broth at either 0.25% or 1.5% salt, harvested by centrifugation, and frozen at -80oC. RNA isolated was reverse transcribed and used to probe H. pylori Panorama arrays
2010-06-25 | E-GEOD-7183 | biostudies-arrayexpress
Project description:In all vertebrates, the dual function of testis (production of sexual steroids and production of gametes) is mainly regulated by two gonadotropic pituitary hormones, FSH and LH. However, in fish the biological activities of the two hormones are not still clearly delineated and moreover, their molecular mechanisms are yet poorly understood. In this study we investigated the effects of FSH and LH on testicular gene expression, in the rainbow trout, at two developmental stages I-II and III (I: spermatogonia only, II: active spermatogonia proliferation, III: meiosis onset with the appearance of spermatocytes and round spermatids). Testes were collected from all-male population rainbow trout and incubated in six replicates for 96 hours, at 12°C, in the absence or presence of purified salmonid gonadotropins, FSH and LH (500 ng/mL).
2012-10-22 | E-GEOD-39465 | biostudies-arrayexpress
Project description:We recently demonstrated that Fsh modifies in vitro the testicular transcriptome of rainbow trout at early stages of spermatogenesis. Some of the regulated genes were found related to pathways highly relevant for the testicular functions i.e. spermatogenesis and steroidogenesis. Unlike in mammals, in fish both gonadotropins are able to efficiently stimulate the steroidogenesis, likely through a direct interaction with their cognate receptors present on the Leydig cells. In this context, we wondered whether the effects of Fsh on the tubular compartment were mediated through the production of steroids. To address this issue we performed in vitro incubations of testis explants in the presence of Fsh alone or in combination with an inhibitor of the steroidogenesis, the trilostane. Trilostane significantly reduced or suppressed the response to Fsh of many genes showing that important aspects of the Fsh action on fish testis is indirect and requires the production of steroids. Interestingly, most of the genes regulated in response to Fsh through the steroid mediation were similarly regulated by Lh and many were also found regulated by androgen treatment. On the other hand, for many other genes the response to Fsh was not affected in the presence of trilostane. A majority of those genes were also preferentially regulated by Fsh, as compared to Lh, suggesting that specific regulatory effects of Fsh were independent of steroid production. Finally antagonistic effects between Fsh and steroids were found, in particular for genes encoding clue factors of steroidogenesis or for genes of the Igf system that tended to be inhibited by androgens. Testes were collected from all-male population rainbow trout at early stages of spermatogenesis.Testes were chopped in small pieces, in sterile conditions and then pooled and mixed. Testis fragments were randomly distributed (60-80 mg per well) on Nunc polycarbonate membrane inserts in 24-well plates filled with 300 µL of modified L15 culture medium supplemented with 2% Ultroser SF. Incubation were performed in six replicates for 96 hours, at 12°C, in the absence or presence of purified trout Fsh alone (500 ng/mL) or in combination with 10 µg/mL trilostane, an inhibitor of 3 beta-hydroxysteroid dehydrogenase. A pre-incubation with trilostane was done for 1 hour before adding Fsh.
2013-09-23 | E-GEOD-46458 | biostudies-arrayexpress
Project description:Transcriptome analysis was used to investigate the global stress response of the Gram-positive bacterium Bacillus subtilis caused by overproduction of the well-secreted AmyQ α-amylase from Bacillus amyloliquefaciens. Analyses of the control and overproducing strains were carried out at the end of exponential growth and in stationary phase, when protein secretion from B. subtilis is optimal. Among the genes that showed increased expression were htrA and htrB, which are part of the CssRS regulon that responds to high-level protein secretion and heat stress. The analysis of the transcriptome profiles of a cssS mutant compared to the wild-type, under identical secretion stress conditions, revealed several genes with altered transcription in a CssRS-dependent manner, for example citM, ylxF, yloA, ykoJ and several genes of the flgB operon. However, a high affinity CssR-binding was only observed for htrA and htrB, and possibly for citM. In addition, the DNA macroarray approach reveal that several genes of the sporulation pathway are downregulated by AmyQ overexpression, and a group of motility-specific (σD-dependent) transcripts were clearly upregulated. Subsequent flow cytometric analyses demonstrate that upon overproduction of AmyQ as well as a non-secretable variant of the α-amylase, the process of sporulation is severely inhibited. The same experiments were implemented to investigate the expression levels of the hag promoter, a well-established reporter for σD-dependent gene expression. This approach confirmed the observations based on our DNA macroarray analyses and led us to conclude that expression levels of several genes involved in motility are maintained at high levels under all conditions of α-amylase overproduction. Secretion stress was applied by overproducing the well-secreted AmyQ α-amylase (pKTH10 vector) from B. amyloliquefaciens. Besides examining secretion stress in wild-type cells, we compared transcriptome profiles of a cssS mutant strain under conditions of high-level AmyQ production. Samples for transcriptome analyses were collected at the late exponential growth stage (one hour before the transition point) and 3 hours upon entry in the stationary growth phase. Three independent cultures of each strain were used and cells were sampled for macroarray experiments. Duplicate spots were averaged in Array-Pro software (Media Cybernetics, Inc.) and the signal was normalized after background subtraction by calculation of the percentage of total signal per gene using Microsoft Excel.
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2010-11-11 | E-GEOD-25279 | biostudies-arrayexpress
Project description:Sexual steroids play an important role in gonad maturation in all vertebrates. However, the molecular mechanisms regulating of spermatogenesis in seasonal breeding species are yet poorly understood. In this study we investigated the effects of testosterone and 11-ketotestosterone (11KT) - a teleost fish specific androgen - on testicular gene expression at the onset of puberty in the rainbow trout, Oncorhynchus mykiss. Rainbow trout 13 months old were used. Immature males (spermatogonia only, stage I-II) were submitted to androgen supplementation by hormone implants for 7 or 14 days. This included : - untreated animal controls (N=14) - animals subjected to testosterone supplementation (0.1mg) for 7 days (N=5) - animals subjected to testosterone supplementation (0.2mg) for 7 days (N=4) - animals subjected to testosterone supplementation (0.2mg) for 14 days (N=5) - animals subjected to 11-ketotestosterone supplementation (0.25mg) for 7 days (N=7). Individual testes were recovered for microarray experiments and histological analyses. Circulating levels of corresponding androgens were also determined.
2009-09-01 | E-GEOD-16030 | biostudies-arrayexpress
Project description:Trout spermatogenesis proceeds seasonally in a way that all morphological and cellular events tend to be synchronized. We thus used gonads at key stages of the male reproductive cycle together with isolated germ cell populations to study the changes in gene expression underlying testis development. Statistical analysis followed by clustering of expression profiles allowed the discrimination of sequential events of gene activation or repression during testis development and/or throughout the germline. 38 samples covering 6 developmental stages (as defined in Gomez et al. 1998 Biol. Reprod. 58, 483-491) and 3 isolated germ cell populations were analysed. This included: - Testes at early stages containing slowly-dividing type A spermatogonia (Stage_I, n=5) or growing numbers of actively-dividing type B spermatogonia (Stages_IIa, n= 4; Stage_IIb, n= 4) - Maturing testes containing in addition large numbers of meiotic spermatocytes (Stage_IIIb, n=3) and post-meiotic spermatids (Stage_V, n=4) - Spawning testes containing essentially mature spermatozoa (Stage_VIII, n=3) - Fractions of isolated germ cells enriched in spermatogonia (Spermatogonia, N=6), spermatocytes (Spermatocyte, N=6) and spermatids (Spermatid, N=3).
2010-05-06 | E-GEOD-16029 | biostudies-arrayexpress