Parallel evolution of transcriptome structure during genome reorganization
Ontology highlight
ABSTRACT:
ORGANISM(S): Methanococcus maripaludis S2 Saccharolobus solfataricus P2 Pyrococcus furiosus DSM 3638
PROVIDER: GSE26782 | GEO | 2011/06/27
SECONDARY ACCESSION(S): PRJNA136281
REPOSITORIES: GEO
Similar Datasets
Project description:Genome reorganization by large scale indels, gene displacements, and horizontal gene transfers allow an organism to re-organize genes into operons (“operonization”) and explore novel strategies for adapting to its changing environment. We have characterized the process of operonization by mapping and comparing transcriptome structures (TSs) of four phylogenetically diverse exptremophilic archaea: a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an anaerobic thermophile (Pyrococcus furiosis DSM 3638), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and a photoheterotrophic halophile (Halobacterium salinarum NRC-1). We demonstrate how the evolution of new transcriptional elements (promoters and terminators) is utilized as a mechanism to incorporate translocated, inverted, and newly acquired genes into existing gene regulatory programs. This SuperSeries is composed of the following subset Series: GSE26777: Methanococcus maripaludis S2 growth curve, tiling arrays GSE26778: Pyrococcus furiosus DSM 3638 growth curve, tiling arrays GSE26779: Sulfolobus solfataricus P2 growth curve, tiling arrays Refer to individual Series
2011-06-27 | E-GEOD-26782 | biostudies-arrayexpress
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
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and identified by:
MODEL1607200000.
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2016-12-08 | MODEL1607200000 | BioModels
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: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 | GSE42162 | 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.
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.
2013-09-16 | GSE42159 | 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.
2013-09-16 | GSE42143 | 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.
2013-09-16 | GSE42130 | 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.
2013-09-16 | GSE42126 | 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.
2013-09-16 | GSE42167 | GEO