Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
Ontology highlight
ABSTRACT:
ORGANISM(S): Methanosarcina acetivorans Methanosarcina acetivorans C2A
PROVIDER: GSE263381 | GEO | 2024/10/18
REPOSITORIES: GEO
Similar Datasets
Project description:Biogenic methane formation, methanogenesis, a key process in the global carbon cycle is the only energy metabolism known to sustain growth of the microorganisms employing it, the methanogenic archaea. All known methanogenic pathways converge at the methane-liberating step where also the terminal electron acceptor of methanogenic respiration, the heterodisulfide of coenzyme M and coenzyme B is formed. Carbon monoxide (CO) utilization of Methanosarcina acetivorans is unique in that the organism can shift from methanogenesis towards acetogenesis. Here, we show that M. acetivorans can dispense of methanogenesis for energy conservation completely. By disrupting the methanogenic pathway through targeted mutagenesis, followed by adaptive evolution, a strain capable of sustained growth by CO-dependent acetogenesis was created. Still, a minute flux through the methane-liberating reaction remained essential, which was attributed to the involvement of the heterodisulfide in at least one essential anabolic reaction. Genomic and proteomic analysis showed that substantial metabolic rewiring had occurred in the strain. Most notably, heterodisulfide reductase, the terminal respiratory oxidoreductase was eliminated to funnel the heterodisulfide towards anabolism. These results suggest that the metabolic flexibility of “methanogenic” archaea is much greater than anticipated and open avenues for probing the mechanism of energetic coupling and the crosstalk between catabolism and anabolism.
2021-10-05 | PXD022016 | Pride
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
Project description:Richards2016 - Genome-scale metabolic
reconstruction of Methanococcus maripaludis (iMR539)
This model is described in the article:
Exploring Hydrogenotrophic
Methanogenesis: a Genome Scale Metabolic Reconstruction of
Methanococcus maripaludis.
Richards MA, Lie TJ, Zhang J,
Ragsdale SW, Leigh JA, Price ND.
J. Bacteriol. 2016 Dec; 198(24):
3379-3390
Abstract:
Hydrogenotrophic methanogenesis occurs in multiple
environments, ranging from the intestinal tracts of animals to
anaerobic sediments and hot springs. Energy conservation in
hydrogenotrophic methanogens was long a mystery; only within
the last decade was it reported that net energy conservation
for growth depends on electron bifurcation. In this work, we
focus on Methanococcus maripaludis, a well-studied
hydrogenotrophic marine methanogen. To better understand
hydrogenotrophic methanogenesis and compare it with
methylotrophic methanogenesis that utilizes oxidative
phosphorylation rather than electron bifurcation, we have built
iMR539, a genome scale metabolic reconstruction that accounts
for 539 of the 1,722 protein-coding genes of M. maripaludis
strain S2. Our reconstructed metabolic network uses recent
literature to not only represent the central electron
bifurcation reaction but also incorporate vital biosynthesis
and assimilation pathways, including unique cofactor and
coenzyme syntheses. We show that our model accurately predicts
experimental growth and gene knockout data, with 93% accuracy
and a Matthews correlation coefficient of 0.78. Furthermore, we
use our metabolic network reconstruction to probe the
implications of electron bifurcation by showing its
essentiality, as well as investigating the infeasibility of
aceticlastic methanogenesis in the network. Additionally, we
demonstrate a method of applying thermodynamic constraints to a
metabolic model to quickly estimate overall free-energy changes
between what comes in and out of the cell. Finally, we describe
a novel reconstruction-specific computational toolbox we
created to improve usability. Together, our results provide a
computational network for exploring hydrogenotrophic
methanogenesis and confirm the importance of electron
bifurcation in this process.Understanding and applying
hydrogenotrophic methanogenesis is a promising avenue for
developing new bioenergy technologies around methane gas.
Although a significant portion of biological methane is
generated through this environmentally ubiquitous pathway,
existing methanogen models portray the more traditional energy
conservation mechanisms that are found in other methanogens. We
have constructed a genome scale metabolic network of
Methanococcus maripaludis that explicitly accounts for all
major reactions involved in hydrogenotrophic methanogenesis.
Our reconstruction demonstrates the importance of electron
bifurcation in central metabolism, providing both a window into
hydrogenotrophic methanogenesis and a hypothesis-generating
platform to fuel metabolic engineering efforts.
This model is hosted on
BioModels Database
and identified by:
MODEL1607200000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-10-15 | MODEL1607200000 | BioModels
Project description:Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during shifts in electron acceptor availability. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs), ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate > 80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Finally, based on the data we propose a feedforward with feedback trim regulatory scheme by showing extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r2 (p < 1e-6) correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. We also are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network. Biological replicates were performed in triplicate for M-NM-^Tfnr, M-NM-^TarcA, and wild type Escherichia coli K12 MG1655 strains under both fully fermentative and nitrate respiratory conditions. An 18 chip study with three different strains under two different culture conditions.
2014-02-27 | E-GEOD-55365 | biostudies-arrayexpress
Project description:Spatial Heterogeneity in Electron Acceptor Availability Stimulates Clonal Diversification in Biofilms
| PRJEB6010 | ENA
Project description:Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during shifts in electron acceptor availability. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs), ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate > 80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Finally, based on the data we propose a feedforward with feedback trim regulatory scheme by showing extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r2 (p < 1e-6) correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. We also are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network.
2014-02-27 | GSE55366 | GEO
Project description:Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during shifts in electron acceptor availability. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs), ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate > 80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Finally, based on the data we propose a feedforward with feedback trim regulatory scheme by showing extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r2 (p < 1e-6) correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. We also are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network.
2014-02-27 | GSE55365 | GEO
Project description:Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during shifts in electron acceptor availability. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs), ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate > 80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Finally, based on the data we propose a feedforward with feedback trim regulatory scheme by showing extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r2 (p < 1e-6) correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. We also are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network. We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the ArcA and Fnr regulons experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 harboring ArcA-8myc or Fnr-8myc under various conditions. The E. coli strains harboring Fnr-8myc and ArcA-8myc were generated as described previously [PMID 16454042]. A 12 chip study with two different strains under two different culture conditions.
2014-02-27 | E-GEOD-55366 | biostudies-arrayexpress
Project description:The Geobacter species evolved respiratory versatility to utilize a wide range of terminal electron acceptors. To explore this adaptive mechanism, Fe(III) citrate, hydrous ferric oxide, and fumarate were selected as electron acceptors, and the methylome and metabolome of Geobacter sulfurreducens PCA grown on each electron acceptor were investigated via third-generation, single-molecule real-time DNA sequencing.Results showed that the patterns of 4-methylcytosine (m4C) and 6-methyladenine (m6A) modification were all varied in different electron acceptor cultures. Moreover, genes (e.g., GSU0466 and GSU1467) with low expression levels generally had high methylation levels. These findings suggest that m4C and m6A modifications play a role in the adaption of G. sulfurreducens to diverse electron acceptors, and DNA methylation may be involved in the adaption mainly via gene expression regulation.
2021-08-31 | GSE157224 | GEO
Project description:Methane-generating Archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth’s diverse anaerobic ecosystems. Although such Archaea were presumed to be restricted to life on simple compounds like H2, acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds as component of lignin and coal are present in most subsurface sediments. Despite the significance and novelty of this outstanding archaeon its metabolism has not yet been explored. In this study, transcriptomics and proteomics reveal that M. shengliensis uses a demethoxylation system that is more related to that from acetogenic bacteria than to the methyl transferase system used for methylotrophic methanogenesis. It activates methoxy-groups using tetrahydromethanopterin as the carrier, a mechanism distinct from conventional methanogenic methyl-transfer systems dependent on Coenzyme M.
2021-06-20 | PXD018934 | Pride