As a member of the UCLA-DOE Institute for Genomics and Proteomics, we are applying LC-MS-based proteomics to elucidate biological pathways relevant to biofuel production.

Cell surface proteins are key to understanding how organisms interact with their environment and with other organisms. We have characterized the surface-layer (S-layer) glycoprotein of Methanosarcina mazei (MM1976) and other surface proteins, to understand the mechanism of methane biosynthesis for Methanosarcina. Very little information is known about archaea glycans, and our work could provide some insight in this area.

With Dr. Sabeeha Merchant (UCLA), we have compared the metal-responsive proteomes in Chlamydomonas reinhardtii. Micronutrients such as Cu, Fe, Zn, and Mn play important roles in several biochemical processes including respiration and photosynthesis. Utilizing large-scale quantitative proteomics MS techniques, we found statistically significant changes in over 200 proteins in each metal deficient growth condition relative to cells grown in nutrient replete media. We also examined the correlation between protein abundance and transcript abundance and found moderate correlations at steady state conditions but strong correlations in gene/protein pairs where significant changes were found at the transcript level, i.e., changes at the RNA level can serve as reliable predictors of changes at the protein level but do not reveal all changes to protein levels.

In our projects examining the importance of protein post-translational modifications (PTMs) to metabolic regulation within microbial consortia, the major goals for our work with Professors Robert Gunsalus (UCLA) and Michael McInerney (Univ. Oklahoma) are to discover acylated proteins in syntrophic bacterial systems, to examine the impact of lysine acylation on metabolic enzymes and metabolic processes, and to reveal quantitative variations in acylation sites and acylating groups. We have discovered novel lysine acylations present on important syntrophic bacterial proteins. Characterizing these modifications informs us about abundant metabolites, thus presenting a novel approach to pathway elucidation.