A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

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Title
A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen
Author(s)
Sung Ho Yoon; S Turkarslan; D J Reiss; M Pan; J A Burn; K C Costa; T J Lie; J Slagel; R L Moritz; M Hackett; J A Leigh; N S Baliga
Bibliographic Citation
Genome Research, vol. 23, no. 11, pp. 1839-1851
Publication Year
2013
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.
ISSN
1088-9051
Publisher
Cold Spring Harbor Lab Press, Publications Dept
DOI
http://dx.doi.org/10.1101/gr.153916.112
Type
Article
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1. Journal Articles > Journal Articles
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