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Highly efficient methane biocatalysis revealed in a methanotrophic bacterium

ABSTRACT: RNA-Seq profiling of Methylomicrobium alcaliphilum strain 20Z grown in batch on methane. The RNA-Seq work is one part of a systems approach to characterizing metabolism of 20Z during growth on methane. We demonstrate that methane assimilation is coupled with a highly efficient pyrophosphate-mediated glycolytic pathway, which under O2 limitation participates in a novel form of fermentation-based methanotrophy. This surprising discovery suggests a novel mode of methane utilization in oxygen-limited environments, and opens new opportunities for a modular approach towards producing a variety of excreted chemical products using methane as a feedstock. Four replicates of batch growth

ORGANISM(S): Methylomicrobium alcaliphilum 20Z

SUBMITTER: David Beck

PROVIDER: E-GEOD-51145 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Highly efficient methane biocatalysis revealed in a methanotrophic bacterium

Project description:RNA-Seq profiling of Methylomicrobium alcaliphilum strain 20Z grown in batch on methane. The RNA-Seq work is one part of a systems approach to characterizing metabolism of 20Z during growth on methane. We demonstrate that methane assimilation is coupled with a highly efficient pyrophosphate-mediated glycolytic pathway, which under O2 limitation participates in a novel form of fermentation-based methanotrophy. This surprising discovery suggests a novel mode of methane utilization in oxygen-limited environments, and opens new opportunities for a modular approach towards producing a variety of excreted chemical products using methane as a feedstock.

2013-09-25 | GSE51145 | GEO

Genomic and Transcriptomic Analyses of the Facultative Methanotroph, Methylocystis Strain SB2

Project description:Here we present the assembled genome of the facultative methanotroph, Methylocystis strain SB2, along with assessment of its transcriptome when grown on methane vs. ethanol. As expected, transcriptomic analyses indicate methane is converted to carbon dioxide via the canonical methane oxidation pathway for energy generation, and that carbon is assimilated at the level of formaldehyde via the serine cycle. When grown on ethanol, it appears this strain converts ethanol to acetyl-CoA and then utilizes the TCA cycle for energy generation and the ethylmalonyl CoA pathway for the production of biomass. All cultures were grown in triplicates for subsequent DNA and RNA extraction as well as for subsequent sequencing using Illumina. Transcriptomic analysis results presented in this Series.

2014-03-20 | E-GEOD-51345 | biostudies-arrayexpress

OXYGEN-LIMITED METABOLISM IN THE METHANOTROPH METHYLOMICROBIUM BURYATENSE 5GB1C

Project description:The bacteria that grow on methane aerobically (methanotrophs) support populations of non-methanotrophs in the natural environment by excreting methane-derived carbon. One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O2-starvation. We examined this O2-starvation condition in the methanotroph Methylomicrobium buryatense 5GB1C . Under prolonged O2-starvation in a closed vial, this methanotroph increases the amount of acetate excreted about 10-fold, but the formate, lactate, and succinate excreted do not respond to this culture condition. In bioreactor cultures, the amount of each excreted product is similar across a range of growth rates and limiting substrates, including O2-limitation. A set of mutants were generated in genes predicted to be involved in generating or regulating excretion of these compounds and tested for growth defects, and changes in excretion products. The phenotypes and associated metabolic flux modeling suggested that in M. buryatense 5GB1C, formate and acetate are excreted in response to redox imbalance, and the resulting metabolic state represents a combination of fermentation and respiration metabolism.

2017-08-24 | GSE101981 | GEO

Heterotrophic growth on formate is dependent on the maintenance of intracellular pH for the thermoacidophilic methanotroph Methylacidiphilum sp RTK17.1.

Project description:In this work, we investigated intracellular pH homeostasis within the thermoacidophilc methanotroph Methylacidiphilum sp. RTK17.1. Our findings show the proton motive force for this species is primarily generated by a pH gradient across the cellular membrane. In batch experiments, the addition of formate resulted in no observable cell growth and, correspondingly, acidification of the cytosol, decreased formate dehydrogenase activity and (presumably) cell-death. Nevertheless, we were able to demonstrable growth on formate as the sole source of metabolizable energy was possible in steady-state (continuous) cultures following the transition from methanol to formate. Under these conditions, biomass productivity yields on formate were 63% less than for growth on methanol. Transcriptome analysis revealed key genes associated with pH homeostasis, methane, methanol and formate metabolism were significantly regulated in response to growth on formate. Collectively, these results suggest environmental formate represents a utilisable source of energy/carbon to the acidophilic methanotrophs during periods of methane starvations and highlights potential short-comings of traditional batch-culture physiological characterisation studies in acidophilic species.

2020-10-31 | GSE145277 | GEO

Small RNA sequencing of control and Su(var)3-7 mutant Drosophila ovary

Project description:Comparison of small RNA fractions derived from piRNA clusters and transposon sequences in control and Su(var)3-7 null mutant. Small RNA profile of 3-day old control and Su(var)3-7 mutant ovaries were generated by high-throughput sequencing on Illumina HiSeq 2000

2014-05-12 | E-GEOD-53015 | biostudies-arrayexpress

Background Proteins in Human Chorionic Gonadotrophin Pharmaceutical Formulations of Different Origin

Project description:Gonadotrophins, including Human chorionic gonadotrophin (hCG), have been used since and for several decades to treat infertility by ovarian stimulation. The hCG is being extracted from urine of pregnant women and it does inevitably contains other proteins secreted into urine. The presence of other proteins varies from batch to batch and it can be significantly high. Current study investigated the presence of proteins other than hCG in different batches of commercial formulations produced by extraction from urine and by using the recombinant approach. The total protein content varied from batch to batch and a large number of contaminant urinary proteins were identified in all analyzed samples except for the recombinant product

2019-03-21 | PXD010471 | Pride

Genome wide RNA-seq analysis of E14.5 Smchd1 wild type and mutant placenta

Project description:We report the deregulation of expression in Fi (C57Bl6/J x FVB/n) E14.5 male mouse placenta are that homozygous for a mutant allele of the Smchd1 gene (ie Smchd1MommeD1/MommeD1). RNA-seq analysis of Smchd1+/+ vs Smchd1MommeD1/MommeD1

2013-07-03 | E-GEOD-44668 | biostudies-arrayexpress

MmoD regulates soluble methane monooxygenase and methanobactin production in Methylosinus trichosporium OB3b

Project description:Methane oxidation by aerobic methanotrophs is well-known to be strongly regulated by the availability of copper, i.e., the “copper-switch”. That is, there are two forms of the methane monooxygenase: a cytoplasmic or soluble methane monooxygenase (sMMO) and a membrane-bound or particulate methane monooxygenase (pMMO). sMMO is only expressed and active in the absence of copper, while pMMO requires copper. Previous work has also shown that one gene in the operon of the soluble methane monooxygenase – mmoD – also plays a critical role, but its function is still vague. Herein we show that MmoD is not needed for expression of genes in the sMMO gene cluster but is critical for formation of sMMO polypeptides and sMMO activity in Methylosinus trichosporium OB3b, indicating that MmoD plays a key post-transcriptional role in maturation of sMMO. Further, data also show that MmoD controls expression of methanobactin, a unique copper-binding compound used by some methanotrophs for copper collection. Collectively these results provide greater insights into the components of the “copper-switch” and thus provide new strategies to manipulate methanotrophic activity.

2023-09-29 | PXD045741 | Pride

Gene expression of M. acetivorans producing ANME-1 Mcr during growth on methane vs. growth on methanol

Project description:Our goal is to convert methane efficiently into liquid fuels that may be more readily transported. Since aerobic oxidation of methane is less efficient, we focused on anaerobic processes to capture methane, which are accomplished by anaerobic methanotrophic archaea (ANME) in consortia. However, no pure culture capable of oxidizing and growing on methane anaerobically has been isolated. In this study, Methanosarcina acetivorans, an archaeal methanogen, was metabolically engineered to take up methane, rather than to generate it. To capture methane, we cloned the DNA coding for the enzyme methyl-coenzyme M reductase (Mcr) from an unculturable archaeal organism from a Black Sea mat into M. acetivorans to effectively run methanogenesis in reverse. The engineered strain produces primarily acetate, and our results demonstrate that pure cultures can grow anaerobically on methane.

2015-12-20 | GSE66445 | GEO

Metabolic regulation of ‘Ca. Methylacidiphilum fumariolicum’ SolV cells grown under different nitrogen and oxygen limitations

Project description:Aerobic methanotrophic bacteria can use methane as their sole energy source. The discovery of ‘Ca. Methylacidiphilum fumariolicum’ strain SolV and other verrucomicrobial methanotrophs has revealed that the ability of bacteria to oxidize CH4 is much more diverse than has previously been assumed in terms of ecology, phylogeny and physiology. A remarkable characteristic of the methane-oxidizing Verrucomicrobia is their extremely acidophilic phenotype, growing even below pH 1. In this study we used RNA-Seq to analyze the metabolic regulation of ‘Ca. M. fumariolicum’ SolV cells growing at μmax in batch culture or under nitrogen fixing or oxygen limited conditions in chemostats, all at pH 2. The analysis showed that two of the three pmoCAB operons each encoding particulate methane monoxygenases were differentially expressed, probably regulated by the available oxygen. The hydrogen produced during N2 fixation is apparently recycled as demonstrated by the upregulation of the genes encoding a Ni/Fe-dependent hydrogenase. These hydrogenase genes were also upregulated under low oxygen conditions. Handling of nitrosative stress was shown by the expression of the nitric oxide reductase encoding genes norB and norC under all conditions tested, the upregulation of nitrite reductase nirK under oxygen limitation and of hydroxylamine oxidoreductase hao in the presence of ammonium. Unraveling the gene regulation of carbon and nitrogen metabolism helps to understand the underlying physiological adaptations of strain SolV in view of the harsh conditions of its natural ecosystem.

2012-09-01 | GSE40528 | GEO

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