Methanosarcina Genomics

This project will exploit the recently completed genomic sequence of Methanosarcina acetivorans to identify novel genes/proteins for two key physiological processes. A functional genomics approach will be taken to further the understanding of (i) the fermentation of acetate to methane (the pathway by which two-thirds of the global output of methane is produced) by M. acetivorans, and (ii) the response to environmental stress by M. acetivorans and the Archaea in general. A large percentage of the open reading frames of sequenced microbial genomes have no significant deduced identity to any known proteins; thus it is expected that novel proteins and enzymes will be discovered and that their characterization will uncover new biochemical principles.

Whole genome DNA microarray and two-dimensional gel electrophoresis methods will be employed to identify genes that are differentially expressed during growth on acetate versus methanol or methylamines, and in media containing high and low salt. The results are expected to (i) identify genes specific for methane formation from acetate and (ii) uncover general principles of Archaeal adaptation to changing environmental conditions. The differentially expressed genes will be characterized by transcriptional mapping and the gene sequences will be analyzed for information regarding their potential function. Gene knockout experiments will be performed to validate their role in the acetate fermentation pathway or osmotic stress, and also to aid in the determination of their specific function. Selected genes will be over-expressed and the gene products characterized to determine their biochemical properties and specific physiological function

By elucidating physiological processes in greater detail, the project is expected to increase the understanding of biocomplexity by revealing how M. acetivorans reacts to changing environmental conditions and how it interacts with other members in microbial consortia that comprise the anaerobic link in the global carbon cycle. In addition, students from each academic institution will be exposed to a wide variety of experimental approaches and methods from each of the collaborating academic institutions . The fundamental interactive nature of the research will provide participating students with broad exposure to genetics, genomics, fermentation, microbial physiology, and enzyme characterization. This type of broad training is designed to provide personnel for future research that will be based on the plethora of genomic information expected in the next decade and beyond