Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1091883 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28467245_1.fastq.gz | Fastqsanger.gz | |||
| SRR28467245_2.fastq.gz | Fastqsanger.gz | |||
| SRR28467246_1.fastq.gz | Fastqsanger.gz | |||
| SRR28467246_2.fastq.gz | Fastqsanger.gz | |||
| SRR28467247_1.fastq.gz | Fastqsanger.gz |
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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:Dimethylsulfide is a volatile organic sulfur compound that provides the largest input of biogenic sulfur from the oceans to the atmosphere, and thence back to land, constituting an important link in the global sulfur cycle. Microorganisms degrading DMS affect fluxes of DMS in the environment, but the underlying metabolic pathways are still poorly understood. Methylophaga thiooxydans is a marine methylotrophic bacterium capable of growth on DMS as sole source of carbon and energy. Using proteomics and transcriptomics we identified genes expressed during growth on dimethylsulfide and methanol to refine our knowledge of the metabolic pathways that are involved in DMS and methanol degradation in this strain. Amongst the most highly expressed genes on DMS were the two methanethiol oxidases driving the oxidation of this reactive and toxic intermediate of DMS metabolism. Growth on DMS also increased expression of the enzymes of the tetrahydrofolate linked pathway of formaldehyde oxidation, in addition to the tetrahydromethanopterin linked pathway. Key enzymes of the inorganic sulfur oxidation pathway included flavocytochrome c sulfide dehydrogenase, sulfide quinone oxidoreductase, and persulfide dioxygenases. A sulP permease was also expressed during growth on DMS. Other enzymes of organic and inorganic sulfur metabolism previously detected in cell extracts of Methylophaga have not been characterised at the genetic level yet; their expression level and regulation could not be analysed. A pan-genome analysis of six available Methylophaga genomes suggests that only two of the six investigated bacteria have the metabolic potential to utilize methanethiol, the degradation product of DMS. These results mirror phenotypic analyses and demonstrate that DMS-utilization and subsequent C1 and sulfur oxidation are not conserved across the entire genus.
2019-11-12 | PXD011992 | Pride
Project description:Dimethyl sulfate (DMS) is a methylating reagent that has long been used to detect footprints of DNA-bound proteins in vitro as well as in vivo. Here we describe DMS-seq for in vivo genome-wide mapping of protein-DNA interactions. DMS-seq exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation, thereby simplifying the process to detect binding sites of transcription factors. Furthermore, we found that DMS preferentially attacks nucleosome centers in vivo, evidencing for DMS-seq as a first method that locates them without using genetically-modified histones and is hence applicable to any eukaryote. DMS-seq should be a simple and unique method in epigenomics.
2017-09-18 | GSE92973 | GEO
Project description:Here, we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). Our study presents an optimized DMS-MaPseq for probing in vivo RNA structure in rice.
2022-04-05 | GSE197245 | GEO
Project description:To get further insights in the dimethyl sulfide metabolism of Hyphomicrobium denitrificans, a LC-MS proteomic approach was used. The total protein of three biological replicates of H. denitrificans grown on dimethyl sulfide was compared with three biological replicates grown on dimethylamine. This approach resulted in the identification of several new proteins with a potential involvement in dimethyl sulfide degradation.
2018-06-14 | PXD009030 | Pride
Project description:Structure probing experiments were performed on in vitro transcripts and E. coli and human cell cultures under natively extracted (cell-free) and in-cell conditions to benchmark the performance of the newly introduced PAIR-MaP correlated chemical probing strategy for detecting RNA duplexes. Multiple-hit dimethyl sulfate (DMS) probing was done using new buffer conditions that facilitate DMS modification of all four nucleotides.
2019-08-01 | GSE135211 | GEO
Project description:Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features for each molecule, and allows genome-wide studies as well as focused investigations of low abundance RNAs. We apply DMS-MaPseq to Drosophila melanogaster ovaries—the first experimental analysis of RNA structure in an animal tissue—and demonstrate its utility in the discovery of a functional RNA structure involved in the non-canonical GUG translation initiation of the human FXR2 mRNA. Additionally, we use DMS-MaPseq to compare the in vivo structure of messages in their pre-mRNA and mature forms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand our ability to monitor RNA structure in vivo.
2016-09-16 | GSE84537 | GEO
Project description:Rex2013 - Genome scale metabolic model of D.shibae (iDsh827)
The aerobic anoxygenic phototroph Dinoroseobacter shibae DFL12T is a
representative of an important group of marine bacteria called the
Roseobacter clade. To gain insight into the versatile metabolism of
this clade, the authors have taken a constraint-based approach and created this
genome-scale metabolic model (iDsh827). This model is the first one to
account for the energy demand of motility, the light-driven ATP
generation and experimentally determined specific biomass composition.
This model is described in the article:
Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae.
Rex R, Bill N, Schmidt-Hohagen K, Schomburg D.
PLoS Comput Biol. 2013;9(10):e1003224.
Abstract:
The Roseobacter clade is a ubiquitous group of marine α-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae.
This model is hosted on BioModels Database
and identified
by: MODEL1308180000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2005-01-01 | MODEL1308180000 | BioModels
Project description:Trimethylated H3K4 (H3K4me3), which is often found surrounding the transcriptional start site of active genes, is strongly enriched in the promoter regions of Myc-targeted genes. Succinate, which inhibits JmjC domain-containing histone demethylases (JHDMs), can induce H3K4me3 level of the promoter regions. It's interesting to ask whether Myc can mediate H3K4me3 by regulating cellular succinate level. Here, We used ChIP-seq to study Myc modulates H3K4me3 by altering succinate levels, dimethyl succinate (DMS), a membrane-permeable succinate analog, was introduced to treat CA46 cells with high or depleted Myc expression. And we also performed RNA-seq assays in Myc expressed or depleted CA46 cells with or without DMS treatment.
2020-03-18 | GSE141227 | GEO
Project description:While various methods exist for examining and visualizing the structure of RNA molecules, dimethyl sulfate-mutational profiling and sequencing (DMS-MaPseq) stands out for its simplicity and versatility. This technique has proven effective for studying RNA structures both in vitro and in complex biological settings. We've updated the protocol for using DMS-MaPseq, and it can also be employed to identify the binding of antisense oligonucleotides (ASOs) to RNA. By applying this updated protocol, we successfully characterized the structural ensemble of the HIV1 Rev Response Element (RRE), along with its two alternative structures. The findings align with previously published research. Additionally, we resolved the structure of the long non-coding RNA PANDA, which was previously unknown. Moreover, we used PANDA as a basis for designing ASOs and confirmed their binding through a substantial decrease in DMS-reactivities at the anticipated ASO binding locations.
2024-01-09 | GSE250290 | GEO