- Bacterial microcompartments, biofuels and renewable chemicals and vitamin B12 metabolism
2152 Molecular Biology Building
Dept. of Biochemistry, Biophysics & Molecular Biology
Iowa State University
Ames, IA 50011
Phone: (515) 294-8247
B.S., Microbiology, Indiana Univ. Bloomington, IN, 1979
M.S., Microbiology, Univ. of IL, Urbana, 1986
Ph.D., Microbiology, Univ. of IL, Urbana, 1990
Post Doctoral Fellow, Univ. of Utah, Salt Lake City, 1990-95
Our specific areas of research are bacterial microcompartments, vitamin B12 metabolism and the genetic engineering of E. coli for the production of renewable chemicals and biofuels. Our general area of expertise is bacterial metabolism which has broad application to the production of chemicals and pharmaceuticals, the prevention and treatment of human disease, and the cycling of matter that is essential to a healthy environment. Our investigative approach is highly interdisciplinary involving genetics, biochemistry, biophysics and structural biology.
- Bacterial microcompartments. A major focus of the lab is bacterial microcompartments (MCPs). MCPs are sophisticated subcellular organelles used to optimize metabolic processes that have toxic or volatile chemical intermediates. They consist of metabolic enzymes encapsulated within a complex multi-protein shell (Fig. 1). About 20-25% of bacteria produce MCPs and they have important roles in global carbon fixation and bacterial pathogenesis. In addition, MCPs have potential applications in biotechnology as nanoscale intracellular reactors and as drug delivery vehicles. However, many of the principles that underlie the assembly and operation of bacterial MCPs are unknown and this knowledge is needed for technology applications. Hence, our lab is working to discover the key operational and design principles of bacterial MCPs. In addition to facilitating technology development, we think that this search will reveal new paradigms by which protein sheets (the MCP shell, viral capids and the rotein layers that surround a wide variety of cells) are used to regulate and organize biological processes.
Figure 1. Bacterial MCPs consist of metabolic enzyme encapsulated within a protein shell. This arrangement optimizes metabolic throughput while protecting cells from toxic metabolic intermediates. The cutout in the figure which is used to reveal the encapsulated enzymes in not present in native MCPs.
- Engineering E. coli to produce renewable chemicals. A second major goal of the lab is to use synthetic biology approaches to engineer E. coli for the production of a variety of renewable chemicals that are currently derived from petroleum. This project is part of the NSF CBiRC engineering research center. The goal of CBiRC is to transform the chemical industry by achieving the sustainable production of renewable industrial chemicals. ISU is the lead institution of CBiRC which includes over 20 faculty from around the country as well as 15 industrial partners. Regular meeting allow students and other members to actively participate in diverse center activities and obtain a broad view of the renewable chemicals industry. http://cbirc.blogspot.com/
- Metabolism of vitamin B12. Our lab is also interested the enzymatic systems needed to support vitamin B12-dependent chemistry. Currently work focuses on how Salmonella bacteria supply vitamin B12 to the diol dehydratase enzyme that is encapsulated within a bacterial MCP. Hence, these studies overlap with our work on bacterial MCPs.
1: Bobik, TA, Lehman BP and Yeates, TO. (2015) Bacterial microcompartments: widespreadprokaryotic organelles for isolation and optimization of metabolic pathways. Mol. Microbiol. epub ahead of print.
2: Liu Y, Jorda J, Yeates TO, Bobik TA. (2015) The PduL phosphotransacylase is used to recycle coenzyme A within the Pdu microcompartment. J. Bacteriol. 197, 2392-2399
3: Sturms R, Streauslin NA, Cheng S, Bobik TA. (2015). In Salmonella enterica, ethanolamine utilization is repressed by 1,2-Propanediol to prevent detrimental mixing of components of two different bacterial microcompartments. J. Bacteriol. 197, 2412-2421
4: Chowdhury C, Chun S, Pang A, Sawaya MR, Sinha S, Yeates TO, Bobik TA. (2015) Selective molecular transport through the protein shell of a bacterial microcompartment organelle. PNAS 112, 2990-2995
5: Jorda J, Liu Y, Bobik TA, Yeates TO. (2015) Exploring bacterial organelle interactomes: a model of the protein-protein interaction network in the pdu microcompartment. PLoS Comput Biol. 3,11(2):e1004067
6: Thompson M. C., Crowley C. S., Kopstein, J. S., Bobik T. A., Yeates T. O. (2014) Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor.” Acta Cryst. F Struct Biol Commun. 70, 1584-1590
7: Bobik T. A., Morales E. J., Shin A, Cascio D, Sawaya M. R., Arbing M, Yeates T. O., Rasche M. E. (2014). Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii. Acta. Crystallogr. F Struct. Biol. Commun. 70, 1472-9.
8: Sinha, S., Cheng, S., Sung, Y., McNamara, D. E., Sawaya, M. R., Yeates, T. O., and Bobik, T. A. (2014) Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment. J. Mol. Biol. 78, 2328-2345
9: Chowdhury, C., Sinha, S., Chun, S., Yeates, T. O. and Bobik, T. A. (2014) Diverse bacterial microcompartment organelles. Microbiol. Mol. Biol. Rev. 426, 438-468
10: Volker AR, Gogerty DS, Bartholomay C, Hennen-Bierwagen T, Zhu H, Bobik TA. (2014) Fermentative production of short-chain fatty acids in Escherichia coli. Microbiology. 160, 1513-1522
11: McNamara, D. E., Cascio, D., Jorda, J., Bustos, C., Wang, T. C., Rasche, M. E., Yeates, T. O. and Bobik, T. A. (2014). Structure of dihydromethanopterin reductase: a cubic protein cage for redox transfer. J Biol Chem. 289, 8852-8864