Methanococcus maripaludis response to hydrogen limitation
Ontology highlight
ABSTRACT:
ORGANISM(S): Methanococcus maripaludis
PROVIDER: GSE6747 | GEO | 2007/04/01
SECONDARY ACCESSION(S): PRJNA98989
REPOSITORIES: GEO
Similar Datasets
Project description:Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for phosphate or leucine were compared to determine the regulatory response to leucine limitation. Keywords: archaea, hydrogen, leucine, phosphate, nutrient limitation, growth rate, methanogen
2007-08-30 | GSE8728 | GEO
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:Methanococcus maripaludis response to hydrogen limitation
| PRJNA98989 | ENA
Project description:Catabolic and anabolic processes are finely coordinated in microbes to provide optimized fitness under varying environmental conditions. Understanding this coordination and the resulting physiological traits identifies fundamental microbial strategies of acclimation. Here, we characterized the systems-level physiology of Methanococcus maripaludis, a niche-specialized methanogenic archaeon, at different growth rates under phosphate (i.e., anabolic) limitation. We observed a decoupling of catabolism and anabolism resulting in lower biomass yield relative to catabolically limited cells. In addition, the mass abundance of several coarse-grained proteome sectors exhibited a linear relationship with growth rate, most notably ribosomes and their biogenesis. Accordingly, cellular RNA content also correlated with growth rate. Although the methanogenesis proteome sector was invariant, the metabolic capacity for methanogenesis correlated with growth rate suggesting translationally independent regulation. These observations are in stark contrast to the physiology of M. maripaludis under formate (i.e., catabolic) limitation, where cells keep an invariant proteome including ribosomal content and a high methanogenesis capacity across a wide range of growth rates. Our findings reveal that although highly niche-specialized, M. maripaludis employs fundamentally different strategies to coordinate global physiology during anabolic phosphate and catabolic formate limitation.
2021-06-14 | MSV000087621 | MassIVE
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. 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 in place of NaCl. The agitation rate was 250 revolutions per minute. The gas mixture initially supplied to the chemostat was H2/Ar/CO2/1% H2S (21/125/40/14 mLs min-1) (Proc Natl Acad Sci USA 104: 8930-8934, 2007). After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either non-limiting (described above), formate limiting (modified to contain 200 mM sodium formate and 180 mM NaCl), nitrogen limiting (2 mM NH4Cl), or phosphate limiting (0.08 mM K2HPO4). Also at this point, gas flow through the vessel was shut off, a 1 psi check valve was installed on the exhaust line to maintain positive pressure within the vessel while also allowing for exhaust of gaseous metabolic byproducts, and a 1% Na2S9H2O feed was started into the vessel at 0.83 mL/h. 48 hours later, samples were taken for physiological measurements or microarray analysis. Samples were collected for microarray analysis as follows: 1.5 mLs of chemostat culture (OD660 ~0.65) was centrifuged at 13,000 x g for 30 seconds and supernatant was discarded. The pellet was immediately placed in a dry ice/ethanol bath and stored at -80C until RNA extraction and microarrays could be performed. 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.
2013-05-03 | E-GEOD-42111 | biostudies-arrayexpress
Project description:The microbiologically influenced corrosion is one of the serious problems in petroleum tanks. It was found that the methanogenic archaea Methanococcus maripaludis OS7 isolated from the inside of petroleum tanks has the iron corrosive property. To identify the genes related to the iron corrosion, we have performed proteome analysis of iron-corrosive archaeon M. maripaludis OS7 and its corrosion-defective mutant.
2018-10-04 | PXD010311 | JPOST Repository
Project description:Steady-state samples of Methanococcus maripaludis MM901 grown on formate under hydrogen limited conditions
| PRJNA179226 | ENA
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 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