Ontology highlight
ABSTRACT:
PROVIDER: PRJNA599954 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10852219_1.fastq.gz | Fastqsanger.gz | |||
| SRR10852219_2.fastq.gz | Fastqsanger.gz | |||
| SRR10851022_1.fastq.gz | Fastqsanger.gz | |||
| SRR10851022_2.fastq.gz | Fastqsanger.gz | |||
| SRR10852343_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Our goal is to convert methane efficiently into liquid fuels that may be more readily transported. Since aerobic oxidation of methane is less efficient, we focused on anaerobic processes to capture methane, which are accomplished by anaerobic methanotrophic archaea (ANME) in consortia. However, no pure culture capable of oxidizing and growing on methane anaerobically has been isolated. In this study, Methanosarcina acetivorans, an archaeal methanogen, was metabolically engineered to take up methane, rather than to generate it. To capture methane, we cloned the DNA coding for the enzyme methyl-coenzyme M reductase (Mcr) from an unculturable archaeal organism from a Black Sea mat into M. acetivorans to effectively run methanogenesis in reverse. The engineered strain produces primarily acetate, and our results demonstrate that pure cultures can grow anaerobically on methane.
2015-12-20 | GSE66445 | GEO
Project description:Our goal is to convert methane efficiently into liquid fuels that may be more readily transported. Since aerobic oxidation of methane is less efficient, we focused on anaerobic processes to capture methane, which are accomplished by anaerobic methanotrophic archaea (ANME) in consortia. However, no pure culture capable of oxidizing and growing on methane anaerobically has been isolated. In this study, Methanosarcina acetivorans, an archaeal methanogen, was metabolically engineered to take up methane, rather than to generate it. To capture methane, we cloned the DNA coding for the enzyme methyl-coenzyme M reductase (Mcr) from an unculturable archaeal organism from a Black Sea mat into M. acetivorans to effectively run methanogenesis in reverse. The engineered strain produces primarily acetate, and our results demonstrate that pure cultures can grow anaerobically on methane. Differential gene analysis of two growth conditions (three biological replicates each) was performed: (i) M. acetivorans/pES1-MATmcr3 grown on methane and (ii) M. acetivorans/pES1-MATmcr3 grown on methanol. All starter cultures (200 mL) were grown on methanol for 5 days, and harvested by centrifugation. Cell pellets were washed three times with HS medium, and resuspended using 5 mL HS medium, 2 µg/mL puromycin, and 0.1 mM FeCl3. For condition (i), methane was filled into the headspace of the cultures. For condition (ii), 150 mM methanol was added. All cultures were incubated at 37C for 5 days, followed by rapid centrifugation in the presence of 50 µL RNAlater solution (Ambion, Austin, TX) per mL of culture. Total RNA was isolated using RNeasy Mini kit (Qiagen, Valencia, CA) were then digested with terminator 5â-phosphate-dependent exonuclease (Epicentre, Madison, WI) to partially remove ribosomal RNA. Digested RNA were cleaned up using AgenCourt RNAClean XP beads (AgenCourt Bioscience, Beverly, MA) and used for cDNA library construction using the TruSeq Stranded mRNA Library kit (Illumina). Pooled and barcoded cDNA library was then sequenced on a HiSeq sequencing platform (Illumina). Obtained reads were mapped to the reference genome of M. acetivorans (Genbank accession NC_003552.1) using STAR. The mapped reads were assembled using Cufflink v2.2.1 to identify potential novel transcripts. Assembled, unannotated novel transcripts for all the strains were combined with the list of known genes. Differential expression of genes and potential novel transcripts were determined using Cuffdiff at a significance cutoff at q < 0.07 with a false discovery rate of 0.05. Expression levels of gene transcripts are expressed as fragments per kilobase of transcript per million mapped fragments (FPKM), and expression changes are determined by the ratio of FPKM of culture replicates grown on methane to FPKM of culture replicates grown on methanol.
2015-12-20 | E-GEOD-66445 | biostudies-arrayexpress
Project description:Biogenic methane formation, methanogenesis, a key process in the global carbon cycle is the only energy metabolism known to sustain growth of the microorganisms employing it, the methanogenic archaea. All known methanogenic pathways converge at the methane-liberating step where also the terminal electron acceptor of methanogenic respiration, the heterodisulfide of coenzyme M and coenzyme B is formed. Carbon monoxide (CO) utilization of Methanosarcina acetivorans is unique in that the organism can shift from methanogenesis towards acetogenesis. Here, we show that M. acetivorans can dispense of methanogenesis for energy conservation completely. By disrupting the methanogenic pathway through targeted mutagenesis, followed by adaptive evolution, a strain capable of sustained growth by CO-dependent acetogenesis was created. Still, a minute flux through the methane-liberating reaction remained essential, which was attributed to the involvement of the heterodisulfide in at least one essential anabolic reaction. Genomic and proteomic analysis showed that substantial metabolic rewiring had occurred in the strain. Most notably, heterodisulfide reductase, the terminal respiratory oxidoreductase was eliminated to funnel the heterodisulfide towards anabolism. These results suggest that the metabolic flexibility of “methanogenic” archaea is much greater than anticipated and open avenues for probing the mechanism of energetic coupling and the crosstalk between catabolism and anabolism.
2021-10-05 | PXD022016 | Pride
Project description:Benedict2011 - Genome-scale metoblic network
of Methanosarcina acetivorans (iMB745)
This model is described in the article:
Genome-scale metabolic
reconstruction and hypothesis testing in the methanogenic
archaeon Methanosarcina acetivorans C2A.
Benedict MN, Gonnerman MC, Metcalf
WW, Price ND.
J. Bacteriol. 2012 Feb; 194(4):
855-865
Abstract:
Methanosarcina acetivorans strain C2A is a marine
methanogenic archaeon notable for its substrate utilization,
genetic tractability, and novel energy conservation mechanisms.
To help probe the phenotypic implications of this organism's
unique metabolism, we have constructed and manually curated a
genome-scale metabolic model of M. acetivorans, iMB745, which
accounts for 745 of the 4,540 predicted protein-coding genes
(16%) in the M. acetivorans genome. The reconstruction effort
has identified key knowledge gaps and differences in peripheral
and central metabolism between methanogenic species. Using flux
balance analysis, the model quantitatively predicts wild-type
phenotypes and is 96% accurate in knockout lethality
predictions compared to currently available experimental data.
The model was used to probe the mechanisms and energetics of
by-product formation and growth on carbon monoxide, as well as
the nature of the reaction catalyzed by the soluble
heterodisulfide reductase HdrABC in M. acetivorans. The
genome-scale model provides quantitative and qualitative
hypotheses that can be used to help iteratively guide
additional experiments to further the state of knowledge about
methanogenesis.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180040.
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.
2024-10-15 | MODEL1507180040 | BioModels
Project description:Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans. In order to gain insight into how the cells sense and respond to availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that depletion of HdrED in vivo results in higher abundance of transcripts for methyltransferases (mtaC2, mtaB3, mtaC3), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability.
2024-10-18 | GSE263381 | GEO
Project description:Peptide mass fingerprinting of Methanosarcina acetivorans wt and mu3 differentially regulated bands obtained by submitting whole cell lysates to SDS-PAGE
2011-07-13 | PRD000398 | Pride
Project description:The goal of this work was to measure the half-lives of RNA transcripts and identify which genes in Methanosarcina acetivorans C2A were differentially expressed between methylotrophic and acetitrophic growth substrates. We used this data to predict metabolic phenotype under different growth condition and hypothesize whether key metabolic genes were transcriptionally or degradationally regulated.
2016-10-10 | GSE77738 | GEO
Project description:Methanosarcina acetivorans C2A transcriptome
| PRJNA263068 | ENA
Project description:Methanosarcina acetivorans C2A - LK82
| PRJNA410622 | ENA
Project description:Methanosarcina acetivorans C2A - LK75
| PRJNA410616 | ENA