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.

Representative publications

1. Francoleon DR, Boontheung P, Yang Y, Kim U, Ytterberg AJ, Denny PA, Denny PC, Loo JA, Gunsalus RP, and Ogorzalek Loo RR. “S-layer, Surface-Accessible, and Concanavalin A Binding Proteins of Methanosarcina acetivorans and Methanosarcina mazei.” J Proteome Res 2009; 8: 1972-1982.

2. Rohlin L, Leon DR, Kim U, Loo JA, Ogorzaleck Loo RR, and Gunsalus RP. “Identification of the major expressed S-layer and cell surface layer related proteins in the model methanogenic archaea, Methanosarcina barkeri Fusaro and Methanosarcina acetivroans C2A.” Archaea 2012, Article ID 873589, 10 pp.

3. Hsieh SI, Castruita M, Malasarn D, Urzica E, Erde J, Page MD, Yamasaki H, Casero D, Pellegrini M, Merchant SS, and Loo JA. “The Proteome of Copper, Iron, Zinc, and Manganese Micronutrient Deficiency in Chlamydomonas reinhardtii.” Mol Cell Proteomics 2013; 12: 65-86.

4. Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, and Merchant SS. “Sub-cellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas.” Nature Chem Biol 2014; 10: 1034–1042.

5. Leon DR, Ytterberg AJ, Boontheung P, Kim U, Loo JA, Gunsalus RP, and Ogorzalek Loo RR. “Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1.” Frontiers Microbiol 2015; 6 (March): 149 (16 pp).