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Title 

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

Authors 

Sung Ho YoonS TurkarslanD J ReissM PanJ A BurnK C CostaT J LieJ SlagelR L MoritzM HackettJ A LeighN S Baliga

Publisher 

Cold Spring Harbor Laboratory Press

Issue Date 

2013

Citation 

Genome Research, vol. 23, no. 11, pp. 1839-1851

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

Link 

http://dx.doi.org/10.1101/gr.153916.112

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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