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| Status |
Public on Sep 16, 2013 |
| Title |
Time series of Methanococcus maripaludis MM901:del_MMP1447, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant) |
| Organism |
Methanococcus maripaludis S2 |
| Experiment type |
Expression profiling by genome tiling array
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| Summary |
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.
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| Overall design |
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). Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. 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). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. For shifts from P-limited to P-excess conditions, phosphate was raised from 0.18 mM to the standard 0.8 mM. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat 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.
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| Contributor(s) |
Yoon S, Lie TJ, Costa KC, Pan M, Leigh JA, Baliga NS |
| Citation(s) |
24089473 |
| Submission date |
Nov 08, 2012 |
| Last update date |
Dec 02, 2013 |
| Contact name |
Sung Ho Yoon |
| Organization name |
Konkuk University
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| Department |
Department of Bioscience and Biotechnology
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| Street address |
120 Neungdong-ro, Gwangjin-gu
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| City |
Seoul |
| ZIP/Postal code |
05029 |
| Country |
South Korea |
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| Platforms (1) |
| GPL15063 |
Agilent-029364 ISB Mmp 60K 60mer tiling array |
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| Samples (20)
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| GSM1033898 |
MM901:MMP1447 H2-excess(110 mL/min) P-limiting(0.14 mM K2PO4) minus10m rep1 |
| GSM1033899 |
MM901:MMP1447 H2-excess(110 mL/min) P-limiting(0.14 mM K2PO4) minus10m rep2 |
| GSM1033900 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0000m rep1 |
| GSM1033901 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0000m rep2 |
| GSM1033902 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0010m rep1 |
| GSM1033903 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0010m rep2 |
| GSM1033904 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0020m rep1 |
| GSM1033905 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0020m rep2 |
| GSM1033906 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0030m rep1 |
| GSM1033907 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0030m rep2 |
| GSM1033908 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0045m rep1 |
| GSM1033909 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0045m rep2 |
| GSM1033910 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0060m rep1 |
| GSM1033911 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0060m rep2 |
| GSM1033912 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0090m rep1 |
| GSM1033913 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0090m rep2 |
| GSM1033914 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0120m rep1 |
| GSM1033915 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0120m rep2 |
| GSM1033916 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0180m rep1 |
| GSM1033917 |
MM901:MMP1447 H2-limiting(21 mL/min) P-excess(0.8 mM K2PO4) 0180m rep2 |
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| Relations |
| BioProject |
PRJNA181127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE42164_RAW.tar |
355.6 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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