Methanosarcina acetivorans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA311346 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3158230.fastq.gz | Fastqsanger.gz | |||
| SRR3158240.fastq.gz | Fastqsanger.gz | |||
| SRR3158250.fastq.gz | Fastqsanger.gz | |||
| SRR3158260.fastq.gz | Fastqsanger.gz | |||
| SRR3158270.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans. Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.
2023-06-27 | GSE229536 | GEO
Project description:The genomic expression patterns of Methansarcina mazei growing with trimethylamine or methanol were measured.
2009-08-05 | E-MEXP-2108 | biostudies-arrayexpress
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:Gene expression of M. acetivorans producing ANME-1 Mcr during growth on methane vs. growth on methanol
| PRJNA276978 | ENA
Project description:Methanosarcina acetivorans Raw sequence reads
| PRJNA681769 | ENA
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:Kumar2011 - Genome-scale metabolic network of Methanosarcina acetivorans (iVS941)
This model is described in the article:
Metabolic reconstruction of
the archaeon methanogen Methanosarcina Acetivorans.
Satish Kumar V, Ferry JG, Maranas
CD.
BMC Syst Biol 2011; 5: 28
Abstract:
BACKGROUND: Methanogens are ancient organisms that are key
players in the carbon cycle accounting for about one billion
tones of biological methane produced annually. Methanosarcina
acetivorans, with a genome size of ~5.7 mb, is the largest
sequenced archaeon methanogen and unique amongst the
methanogens in its biochemical characteristics. By following a
systematic workflow we reconstruct a genome-scale metabolic
model for M. acetivorans. This process relies on previously
developed computational tools developed in our group to correct
growth prediction inconsistencies with in vivo data sets and
rectify topological inconsistencies in the model. RESULTS: The
generated model iVS941 accounts for 941 genes, 705 reactions
and 708 metabolites. The model achieves 93.3% prediction
agreement with in vivo growth data across different substrates
and multiple gene deletions. The model also correctly
recapitulates metabolic pathway usage patterns of M.
acetivorans such as the indispensability of flux through
methanogenesis for growth on acetate and methanol and the
unique biochemical characteristics under growth on carbon
monoxide. CONCLUSIONS: Based on the size of the genome-scale
metabolic reconstruction and extent of validated predictions
this model represents the most comprehensive up-to-date effort
to catalogue methanogenic metabolism. The reconstructed model
is available in spreadsheet and SBML formats to enable
dissemination.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180035.
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To the extent possible under law, all copyright and related or
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2015-07-30 | MODEL1507180035 | BioModels
Project description:Methanosarcina acetivorans Genome sequencing and assembly
| PRJNA477340 | ENA
Project description:Methanosarcina acetivorans Genome sequencing and assembly
| PRJNA859536 | ENA
Project description:Methanosarcina acetivorans UV mutant raw sequence reads
| PRJNA335646 | ENA