Steady-state samples of Methanococcus maripaludis MM901 grown on N14 or N15
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ABSTRACT:
ORGANISM(S): Methanococcus maripaludis S2
PROVIDER: GSE42124 | GEO | 2013/09/16
SECONDARY ACCESSION(S): PRJNA179322
REPOSITORIES: GEO
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Project description:Effects of mtd (MMP0372) on physiology and regulation of methanogenesis in Methanococcus maripaludis
2013-09-16 | GSE42123 | GEO
Project description:Effects of frcA (MMP0820) on physiology and regulation of methanogenesis in Methanococcus maripaludis
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Project description:Effects of fruA (MMP1382) and frcA (MMP0820) on physiology and regulation of methanogenesis in Methanococcus maripaludis
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Project 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.
2013-09-16 | GSE42115 | GEO
Project 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 37M-BM-0C (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 -80M-BM-0C. 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.
2013-09-16 | E-GEOD-42115 | biostudies-arrayexpress
Project description:Effects of hydrogen on physiology and regulation of methanogenesis in Methanococcus maripaludis The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37M-BM-0C (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 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. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or nitrogen limiting (3 mM NH4Cl). 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 -80M-BM-0C. 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.
2013-09-16 | E-GEOD-42124 | biostudies-arrayexpress
Project description:Hydrogenotrophic methanogenic Archaea are defined by a H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. Hydrogenotrophs respond to H2 starvation both phenotypically and at the level of gene expression; however, the responses during growth on formate have not been characterized. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess, suggesting that energy spilling occurs. Using microarray analysis, we show that the expression of genes encoding F420-dependent steps of methanogenesis, including one of two formate dehydrogenases, increased with H2 starvation, but with formate occurred at high levels regardless of limitation or excess. One gene, encoding H2-dependent methylene-tetrahydromethanopterin dehydrogenase, decreased in expression with either H2 limitation or formate limitation. Expression of genes for the second formate dehydrogenase, molybdenum-dependent formylmethanofuran dehydrogenase, and molybdenum transport increased specifically with formate limitation. Of the two formate dehydrogenases, only the first could support growth on formate in batch culture where formate was in excess.
2013-05-03 | GSE42111 | GEO
Project description:Effects of mtd (MMP0372) on physiology and regulation of methanogenesis in Methanococcus maripaludis The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37M-BM-0C (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 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 20 mL/min H2. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or phosphate excess (0.8 mM K2HPO4). 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 -80M-BM-0C. 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.
2013-09-16 | E-GEOD-42123 | biostudies-arrayexpress
Project description:Effects of frcA (MMP0820) on physiology and regulation of methanogenesis in Methanococcus maripaludis The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37M-BM-0C (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 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. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or phosphate excess (0.8 mM K2HPO4). Different nitrogen sources of NH4Cl and alanine was used (10mM). 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 -80M-BM-0C. 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.
2013-09-16 | E-GEOD-42121 | biostudies-arrayexpress
Project description:Effects of fruA (MMP1382) and frcA (MMP0820) on physiology and regulation of methanogenesis in Methanococcus maripaludis The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37M-BM-0C (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 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 22 mL/min H2. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or phosphate excess (0.8 mM K2HPO4). 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 -80M-BM-0C. 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.
2013-09-16 | E-GEOD-42122 | biostudies-arrayexpress