E-GEOD-42115 - Steady-state samples of Methanococcus maripaludis MM901 grown on formate-excess medium

Status
Released on 16 September 2013, last updated on 2 June 2014
Organism
Methanococcus maripaludis S2
Samples (8)
Array (1)
Protocols (6)
Description
Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 100 different steady-state and time course experiments that were performed in chemostats, or batch cultures, under a spectrum of environmental perturbations that modulated methanogenesis. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to inter-coordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel TFs in the regulation of phosphate-dependent repression of formate dehydorgenase -- a key enzyme in the methanogenesis pathway. The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The medium contained 380 mM sodium formate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). Hydrogen limited condition was 21 mL/min H2. Culture samples (1.5 mL) were rapidly removed from the vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C. Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.
Experiment type
transcription profiling by tiling array 
Contacts
Sung Ho Yoon <geo@ncbi.nlm.nih.gov>, John A Leigh, June Burn, Min Pan, Nitin S Baliga, Sung-Ho Yoon
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-42115.idf.txt
Sample and data relationshipE-GEOD-42115.sdrf.txt
Raw data (1)E-GEOD-42115.raw.1.zip
Processed data (1)E-GEOD-42115.processed.1.zip
Array designA-GEOD-15063.adf.txt
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