ArticleGenome research2013
A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 34 citations in OpenAlex.
- Microbiota in cancer: current understandings and future perspectives.Signal transduction and targeted therapy · 2026Review
- Metabolic adaptation of a methanogen to a ferruginous environment associated with intracellular Fe- and S-rich nanoparticles.Frontiers in microbiology · 2026Article
- Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression.Nature communications · 2025Article
- Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms.Scientific reports · 2020Article
- The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.Nucleic acids research · 2020Article
- Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis.Journal of bacteriology · 2020Article
- Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.Journal of molecular biology · 2019Review
- It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.Briefings in bioinformatics · 2019Review
- Conserved principles of transcriptional networks controlling metabolic flexibility in archaea.Emerging topics in life sciences · 2018Article
- Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638.Life (Basel, Switzerland) · 2018Article
- Detecting differential growth of microbial populations with Gaussian process regression.Genome research · 2017Article
- Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis.Journal of bacteriology · 2016Article
- Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans.BMC genomics · 2016Article
- cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.Nucleic acids research · 2015Article
- A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.PLoS genetics · 2015Article
- Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.Biotechnology for biofuels · 2015Article
- Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities.Frontiers in microbiology · 2015Article
- The putative tRNA 2-thiouridine synthetase Ncs6 is an essential sulfur carrier in Methanococcus maripaludis.FEBS letters · 2014Article
- Network portal: a database for storage, analysis and visualization of biological networks.Nucleic acids research · 2014Article
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
Abstract
Methanogens catalyze the critical methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter. 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 noncoding) 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 58 different steady-state and time-course experiments that were performed in chemostats or batch cultures under a spectrum of environmental perturbations that modulated methanogenesis. Analyses of the EGRIN model have revealed novel components of methanogenesis that included at least three additional protein-coding genes of previously unknown function as well as one noncoding RNA. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to intercoordinate 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 transcription factors in the regulation of phosphate-dependent repression of formate dehydrogenase-a key enzyme in the methanogenesis pathway. The EGRIN model demonstrates regulatory affiliations within methanogenesis as well as between methanogenesis and other cellular functions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.