High-throughput RNA sequencing of methanosarcina grown on methylated sulfur compounds
Ontology highlight
ABSTRACT:
ORGANISM(S): Methanosarcina acetivorans C2A
PROVIDER: GSE64349 | GEO | 2015/02/18
SECONDARY ACCESSION(S): PRJNA270832
REPOSITORIES: GEO
Similar Datasets
Project description:Methylated sulfur compounds, including dimethylsulfide (DMS), methylmercaptopropionic acid (MMPA) and methylsulfide (MeSH), are well-documented to play roles in global sulfur cycle and climate homeostasis, yet the molecular mechanisms of how they are metabolized by methanogens remain largely uncharacterized. Here, using high-throughtput sequencing of RNA (RNA-seq), we gained insight into how methanogens respond to methylated sulfur compounds at the transcriptional level. The mRNA from wild-type of Methanosarcina acetivorans C2A grown on methylated sulfur compounds were harvested, sequenced and mapped to the genome. Then, we compared RNA-seq profiles to that grown on MeOH in search of unque genes.
2015-02-18 | E-GEOD-64349 | biostudies-arrayexpress
Project description:High-throughput RNA sequencing of methanosarcina grown on methylated sulfur compounds
| PRJNA270832 | ENA
Project description:Natural and anthropogenic wetlands are main sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic microorganisms and by processes at the oxic-anoxic interface, such as sulfur cycling, that reduce the activity of methanogens. In this study, we obtained a pure culture (strain HY1) of a versatile wetland methanotroph that oxidizes various organic and inorganic compounds. This strain represents (i) the first isolate that can aerobically oxidize both methane and reduced sulfur compounds and (ii) a new alphapoteobacterial species, named Candidatus Methylovirgula thiovorans. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are the only enzymes for methane and methanol oxidation, respectively. Unexpectedly, strain HY1 harbors various pathways for respiratory sulfur oxidation and oxidized reduced sulfur compounds to sulfate using the Sox-rDsr pathway (without SoxCD) and the S4I system. It employed the Calvin-Benson-Bassham cycle for CO2 fixation during chemolithoautotrophic growth on the reduced sulfur compounds. Methane and thiosulfate were independently and simultaneously oxidized by strain HY1 for growth. Proteomic and microrespiratory analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of their substrates. The discovery of this versatile methanotroph demonstrates that methanotrophy and thiotrophy is compatible in a single bacterium and adds a new aspect to interactions of methane and sulfur cycles in oxic-anoxic interface environments.
2022-07-11 | PXD025979 | Pride
Project description:The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd.
2010-08-05 | GSE21325 | GEO
Project description:Marine phytoplankton produce ~109 tons of dimethylsulfoniopropionate (DMSP) per year, an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide (DMS). SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemoorganotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell’s unusual requirement for reduced sulfur. Here we report that Pelagibacter HTCC1062 produces the gas methanethiol (MeSH) and that simultaneously a second DMSP catabolic pathway, mediated by a DMSP lyase, shunts as much as 59% of DMSP uptake to DMS production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release DMS when the supply of DMSP exceeds cellular sulfur demands for biosynthesis. These findings suggest that DMSP supply and demand relationships can significantly control rates of oceanic DMS production.
2017-12-08 | PXD001717 | Pride
Project description:The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd. DMSP-related gene expression in the Roseobacter group was investigated using an environmental microarray. Coastal seawater from the Gulf of Mexico was collected and dispensed into 20-L microcosms. Two replicate cubitainers were amended with nutrients (N and P) to stimulate phytoplankton bloom, while two untreated cubitainers served as controls. The microcosms were incubated at 27ºC in a temperature-controlled incubator on a 12 h light/dark cycle for total of 7 days. Ten RNA samples (Day 0: 2 conditions with 1 biological replicate each; Days 2 and 4: 2 conditions with 2 biological replicates each) were prepared for microarray hybridization. After total RNA extraction, rRNAs were removed and mRNA transcripts were amplified and labeled with Alexa Fluor 647. Two technical replicates were hybridized from each RNA sample. The microarray was designed based on selected Ruegeria pomeroyi DSS-3 genes and their orthologs in 12 other sequenced Roseobacter genomes. Probes were designed from the orthologs using the Hierarchical Probe Design (HPD) algorithm.
2010-08-05 | E-GEOD-21325 | biostudies-arrayexpress
Project description:Spaceflight induces hepatic damage, partially owing to oxidative stress caused by the space environment such as microgravity and space radiation. We examined the roles of anti-oxidative sulfur-containing compounds on hepatic damage after spaceflight. We analyzed the livers of mice on board the International Space Station for 30 days. During spaceflight, half of the mice were exposed to artificial earth gravity (1 g) using centrifugation cages. Sulfur-metabolomics of the livers of mice after spaceflight revealed a decrease in sulfur antioxidants (ergothioneine, glutathione, cysteine, taurine, thiamine, etc.) and their intermediates (cysteine sulfonic acid, hercynine, N-acethylserine, serine, etc.) compared to the controls on the ground. Furthermore, RNA-sequencing showed upregulation of gene sets related to oxidative stress and sulfur metabolism, and downregulation of gene sets related to glutathione reducibility in the livers of mice after spaceflight, compared to controls on the ground. These changes were partially mitigated by exposure to 1 g centrifugation. For the first time, we observed a decrease in sulfur antioxidants based on a comprehensive analysis of the livers of mice after spaceflight. Our data suggest that a decrease in sulfur-containing compounds owing to both microgravity and other spaceflight environments (radiation and stressors) contributes to liver damage after spaceflight.
2023-08-14 | GSE240751 | 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.
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:We used comparative transcriptomics to explore cellular responses to growth on pyrite (FeS2) or aqueous iron (Fe(II)) and sulfur (cysteine or sulfide). Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study. Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study.
2022-03-13 | GSE168895 | GEO