Hydrogen Regulation and Global Responses to Electron, Carbon and Nitrogen Sources of Methanococcus Maripaludis

Leigh, John A.

关键词: methanogenesis;    hydrogenotrophic methanogen;    gene regulatory influence network;    Methanococcus maripaludis;   

DOI  :  10.2172/1079840
RP-ID  :  DOE/ER64685
PID  :  OSTI ID: 1079840

学科分类：生物科学（综合）

美国|英语

来源: SciTech Connect

【 摘 要 】

Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter. This project has generated 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 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 non-coding RNA. 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 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. In addition, we have published an analysis of transcriptome architecture in M. maripaludis and an analysis of the effects of H2 and formate on growth yield and regulation of methanogenesis in M. maripaludis.