Sung Ho Yoon1,4, Serdar Turkarslan1, David J. Reiss1, Min Pan1, June A. Burn2, Kyle C. Costa2, Thomas J. Lie2, Joseph Slagel1, Robert L. Moritz1, Murray Hackett3, John A. Leigh2,5 and Nitin S. Baliga1,5
1Institute for Systems Biology, Seattle, Washington 98109, USA;
2Department of Microbiology, University of Washington, Seattle, Washington 98195, USA;
3Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA;
4Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
5 Corresponding authors
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.