GEO DataSets

(Submitter supplied) 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. more...

Organism:

Methanosarcina acetivorans C2A; Methanosarcina acetivorans

Type:

Expression profiling by array

Platform:

GPL34364

16 Samples

Download data: CALLS, PAIR, TXT

(Submitter supplied) We used ribosome profiling (Ribo-seq) to generate a translatome map for the archaeon M. mazei under two growth conditions. The analysis of the datasets allowed to generate a high confidence inventory of small proteins in the model archaeon M. mazei and their regulation under nitrogen limiting conditions.

Organism:

Methanosarcina mazei Go1

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL33665

8 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Methanosarcina acetivorans C2A

Type:

Other

Platform:

GPL33336

12 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Methanosarcina barkeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29851

12 Samples

Download data: TXT

(Submitter supplied) CRISPR loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the cas genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 of Methanosarcina mazei Gö1 associated to the type I-B CRISPR-locus providing evidence for its relevance in regulating this system. more...

Organism:

Methanosarcina mazei Go1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28591

4 Samples

Download data: TSV, WIG

(Submitter supplied) Trans-encoded sRNA154 is exclusively expressed under nitrogen (N)-deficiency in Methanosarcina mazei strain Gö1. The respective deletion strain showed a significant growth defect under N-limitation, pointing towards a regulatory role of sRNA154 in the N-metabolism. Aiming to elucidate this regulatory function we characterized sRNA154 by biochemical and genetic approaches. 24 homologs of sRNA154 were identified in recently reported draft genomes of Methanosarcina strains, demonstrating high conservation in sequence and predicted secondary structure with two highly conserved single stranded loop regions. more...

Organism:

Methanosarcina mazei Go1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22308

4 Samples

Download data: WIG

(Submitter supplied) Hydrogenases are a critical component of H2-dependent energy-conservation pathways in Methanosarcina barkeri. To allow phenotypic analysis of the hydrogenases, we constructed mutants lacking the frhADGB, freAEGB, vhtGACD, vhxGAC and echABCDEF operons, individually and in all possible combinations. In addition to measuring the effect of each deletion on growth, methane production, and hydrogenase activity, the effect on gene expression was measured by RNA sequencing to detect potential transcriptional regulation by the hydrogenases.

Organism:

Methanosarcina barkeri str. Fusaro

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20638

27 Samples

Download data: XLSX

(Submitter supplied) 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.

Organism:

Methanosarcina acetivorans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19842

61 Samples

Download data: XLS, XLSX

(Submitter supplied) 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. more...

Organism:

Methanosarcina acetivorans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19842

6 Samples

Download data: XLSX

(Submitter supplied) The goal of this work was to elucidate the mechanism by which pyruvate is utilized as a substrate in a mutant strain of Methanosarcina barkeri Fusaro. In this study, using RNAseq we gained insight into how the mutant strain modulate its transcriptional profile in order to use pyruvate as a substrate. In addition, we obtained information on how methanogens respond to pyruvate at the transcriptional level.

Organism:

Methanosarcina barkeri str. Fusaro

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20638

54 Samples

Download data: XLSX

(Submitter supplied) 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.

Organism:

Methanosarcina acetivorans C2A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19569

15 Samples

Download data: XLSX

(Submitter supplied) cat# A7240-00-01 Expr 4x72K arr Del-Microarrays for Expression Submitter states that the NDF file for this array was lost. Protocol: see website

Organism:

Methanosarcina acetivorans C2A

1 Series

16 Samples

Download data: TXT