RNA-Seq of MeOH-R2: Methanosarcina barkeri - SRA

SRX24386661: RNA-Seq of MeOH-R2: Methanosarcina barkeri
1 ILLUMINA (Illumina HiSeq 4000) run: 16.5M spots, 4.9G bases, 592.6Mb downloads

Design: Cells representing the mid-exponential phase were collected from all treatments for total RNA extraction, which was performed using a RNAprep pure Cell/Bacteria Kit (Cat. No. DP430; TIANGEN, Beijing, China). RNA purity and concentrations in the samples were determined by gel electrophoresis and a NanoDrop2000 spectrophotometer (Thermo Scientific, Waltham, MA). Ribosomal RNA was removed from total RNA using the RiboMinus TM kit (Lot. No.1539791, Invitrogen, Waltham, MA). Samples were then submitted to GENEWIZ (Suzhou, China) for library construction and sequencing on an Illumina HiSeq 4000 system (Illumina, San Diego, CA). The sequencing reads were mapped to the M. barkeri DSM800 genome using Bowtie 2. HTSeq 2.0 was used to determine the read numbers mapped to each gene, after which the FPKM (fragments per kilobase per million reads) for each gene could be calculated. Differential transcription analysis for the substrate conditions (acetate vs. CO2/H2, acetate vs. methanol, and methanol vs. CO2/H2) was performed using the DESeq2 (1.42.0) R package. Genes with an adjusted p-value < 0.01 from the DESeq2 package and a FPKM value >100 in the groups sample were classified as demonstrating differential transcription.

Submitted by: Biogas Science Research Institute, Ministry of Agriculture and Rural Areas

Study: The novel regulator HdrR controls the transcription of the heterodisulfide reductase operon hdrBCA in Methanosarcina barkeri

PRJNA1105475 • SRP504445 • All experiments • All runs

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Methanogenic archaea play a key role in the global carbon cycle since these microorganisms remineralize organic compounds in various anaerobic environments. The microorganism Methanosarcina barkeri is a metabolically versatile methanogen which can utilize acetate, methanol, and H2/CO2 to synthesize methane. However, the regulatory mechanisms underlying methanogenesis for different substrates remain unknown. In this study, RNA-seq analysis was used to investigate M. barkeri growth and gene transcription under different substrate regimes. According to the results, M. barkeri showed the best growth under methanol, followed by H2/CO2 and acetate, and these findings corresponded well with the observed variations in genes transcription abundance for different substrates. In addition, we identified a novel regulator, MSBRM_RS03855 (designated as HdrR), which specifically activates the transcription of the heterodisulfide reductase hdrBCA operon in M. barkeri. HdrR was able to bind to the hdrBCA operon promoter to regulate transcription. Furthermore, the structural model analyses revealed a helix-turn-helix domain, which is likely involved in DNA binding. Taken together, HdrR serves as a model to reveal how certain regulatory factors control the expression of key enzymes in the methanogenic pathway.

Sample:

SAMN41103235 • SRS21142736 • All experiments • All runs

Organism: Methanosarcina barkeri

Library:

Name: MeOH-R2

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PCR

Layout: SINGLE

Runs: 1 run, 16.5M spots, 4.9G bases, 592.6Mb

Run	# of Spots	# of Bases	Size	Published
SRR28823719	16,493,573	4.9G	592.6Mb	2024-04-30

ID:: 32701533

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