Functional Validation of SAM Riboswitch Element A from Listeria monocytogenes
Ontology highlight
ABSTRACT:
ORGANISM(S): Listeria monocytogenes
PROVIDER: GSE266872 | GEO | 2025/05/05
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:Candidatus Pelagibacter ubique is the most abundant marine microorganism, but is unable to utilize inorganic sulfur compounds that are plentiful in the ocean. To investigate how these cells adapt to organic sulfur limitation, batch cultures were grown in defined media containing either limiting or non-limiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured during exponential growth, immediately prior to stationary phase, and in late stationary phase. Two distinct responses were observed: one as DMSP approached exhaustion, and another after the DMSP supply was depleted. The first response was characterized by increased transcription and translation of all Ca. P. ubique genes downstream of previously confirmed S-adenosyl methionine (SAM) riboswitches: bhmT, mmuM, and metY. These genes were up to 33 times more abundant during low DMSP conditions and shunt all available sulfur to methionine. The osmotically inducible organic hydroperoxidase OsmC was the most up-regulated protein as DMSP (an osmolyte) became scarce. The second response, during sulfur-depleted stationary phase, saw increased transcription of the heme c shuttle ccmC and two small genes of unknown function (SAR11_1163 and SAR11_1164) which were 6-10 times higher in sulfur-starved cultures. No known membrane transporters were up-regulated in response to sulfur limitation, suggesting that this bacterium's strategy for coping with sulfur stress focuses on intracellularly redistributing, rather than importing, organic sulfur compounds. This supports the conclusion that the few organosulfur molecules that Ca. P. ubique is able to metabolize are rarely limiting in the marine environment.
2016-06-26 | GSE31630 | GEO
Project description:Candidatus Pelagibacter ubique is the most abundant marine microorganism, but is unable to utilize inorganic sulfur compounds that are plentiful in the ocean. To investigate how these cells adapt to organic sulfur limitation, batch cultures were grown in defined media containing either limiting or non-limiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured during exponential growth, immediately prior to stationary phase, and in late stationary phase. Two distinct responses were observed: one as DMSP approached exhaustion, and another after the DMSP supply was depleted. The first response was characterized by increased transcription and translation of all Ca. P. ubique genes downstream of previously confirmed S-adenosyl methionine (SAM) riboswitches: bhmT, mmuM, and metY. These genes were up to 33 times more abundant during low DMSP conditions and shunt all available sulfur to methionine. The osmotically inducible organic hydroperoxidase OsmC was the most up-regulated protein as DMSP (an osmolyte) became scarce. The second response, during sulfur-depleted stationary phase, saw increased transcription of the heme c shuttle ccmC and two small genes of unknown function (SAR11_1163 and SAR11_1164) which were 6-10 times higher in sulfur-starved cultures. No known membrane transporters were up-regulated in response to sulfur limitation, suggesting that this bacterium's strategy for coping with sulfur stress focuses on intracellularly redistributing, rather than importing, organic sulfur compounds. This supports the conclusion that the few organosulfur molecules that Ca. P. ubique is able to metabolize are rarely limiting in the marine environment. Batch cultures of P. ubique were grown in a defined arificial seawater media. Five cultures were amended with a limiting concentration of DMSP as the sole sulfur source and another four control cultures were amended with a non-limiting DMSP concentration. Cultures were harvested for microarray analyses at multiple timepoints for the purpose of observing differences in gene expression related to sulfur limitation. Proteomic analyses were conducted in parallel and are available at https://www.ebi.ac.uk/pride/archive/projects/PXD003672 .
2016-06-26 | E-GEOD-31630 | 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:We performed Illumina sequencing to acquire the differentially expressed genes induced by arsenate and sulfur treatments. We found that sulfur (S) application reduced As concentration of rice grains harvested at 20 days after anthesis (DAA). By contrast with the control, the expression of 1001 genes were found to be significantly changed, 46 genes up-regulated and 954 genes down-regulated in the 20As grains. 1169 genes expressed significantly differently between the samples of control and 20As+120S, with 16 genes up-regulated and 1153 genes down-regulated. Among the differentially expressed genes (DEGs) regulated by As and S treatment, there were 10 DEGs encoding phosphate transporter, and 24 DEGs encoding aquaporin transporter. Some genes involved in As detoxification, such as ABC transporter, glutathione S-transferase and phytochelatin synthase were up-regulated by sulfur treatment. The results provide an insight into the molecular basis of how sulfur application regulates As accumulation in rice grains. Arsenic (As) was artificially added to soil with 20 mg/kg As (Na2AsO4.12H2O, 20As), another treatment was 20As+120S, sulfur (S) were supplied artificially with 120 mg/kg (Na2S2O3•5H2O) to the As-added soil (20As+120S).
2015-07-01 | E-GEOD-48799 | biostudies-arrayexpress
Project description:Reyes-Palomares2012 - a combined model hepatic polyamine and sulfur aminoacid metabolism - version2
Mammalian polyamine metabolism consists of a bi-cycle with two required entrances, omithine and S-adenosyl methionine (SAM), and several alternative exists. The relevant regulatory roles of the short half-life enzymes ornithine decarboxylase (ODC), S-adenosyl methione decarboxylase (SAMDC) and spermindine/spermine acetyl transferase (SSAT) in polyamine metabolism are well studied, and has been modelled here.
This model is described in the article:
A combined model of hepatic polyamine and sulfur amino acid metabolism to analyze S-adenosyl methionine availability.
Reyes-Palomares A, Montañez R, Sánchez-Jiménez F, Medina MA
Amino Acids, February 2012, Volume 42, Issue 2-3, pp 597-610
Abstract:
Many molecular details remain to be uncovered concerning the regulation of polyamine metabolism. A previous model of mammalian polyamine metabolism showed that S-adenosyl methionine availability could play a key role in polyamine homeostasis. To get a deeper insight in this prediction, we have built a combined model by integration of the previously published polyamine model and one-carbon and glutathione metabolism model, published by different research groups. The combined model is robust and it is able to achieve physiological steady-state values, as well as to reproduce the predictions of the individual models. Furthermore, a transition between two versions of our model with new regulatory factors added properly simulates the switch in methionine adenosyl transferase isozymes occurring when the liver enters in proliferative conditions. The combined model is useful to support the previous prediction on the role of S-adenosyl methionine availability in polyamine homeostasis. Furthermore, it could be easily adapted to get deeper insights on the connections of polyamines with energy metabolism.
Notes by the author:
This model combines BIOMD0000000190 and BIOMD0000000268 from BioModels Database, both models include corrections respect to their originals publications.
To simulate a MATI/MATIII switch to MATII in proliferating liver:
We set to 0 the Vmax parameters of MATI and MATIII
We included MATII reaction equation.
We add a regulation factor dependent of SAM levels in ODC and SAMDCe rates of synthesis (66.5/[SAM]).
H2O2 was increased in a 50 % according to an initial state ofproliferating and regenerating liver.
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2024-09-02 | BIOMD0000000450 | BioModels
Project description:The SIN3 histone modifying complex regulates the expression of multiple methionine catabolic genes including SAM synthetase (Sam-S) as well as the level of S-adenosyl-methionine (SAM). To further investigate the relationship between methionine catabolism and epigenetic regulation by SIN3, we identified genes controlled by SIN3 and SAM-S. As a global transcriptional regulator, SIN3 impacted a wide range of genes. Independently, SAM-S affected a narrow range of genes. Additional genes, however, were influenced in dual knockdown cells. At some genes, SIN3 and SAM-S act independently, for others, redundantly and for a third set, in opposition. Together, the results obtained in the study of SIN3, a cofactor associated with histone modification, and SAM-S, a metabolic enzyme, uncover a complex relationship on regulating transcription.
2019-11-26 | GSE129145 | 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