Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology > Tom Bobik

Tom Bobik

Professor
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
Email: bobik@iastate.edu

Education
B.S., Microbiology, Indiana Univ. Bloomington, IN, 1979
M.S., Microbiology, Univ. of IL, Urbana, 1986
PhD, Microbiology, Univ. of IL, Urbana, 1990
Post Doctoral Fellow, Univ. of Utah, Salt Lake City, 1990-95.

Research Interests.

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.

Selected Publications

1: Fan C, Cheng S, Sinha S, Bobik TA. Interactions between the termini of lumen
enzymes and shell proteins mediate enzyme encapsulation into bacterial
microcompartments. Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):14995-5000. doi:
10.1073/pnas.1207516109. Epub 2012 Aug 27. PubMed PMID: 22927404; PubMed Central
PMCID: PMC3443165.

2: Sinha S, Cheng S, Fan C, Bobik TA. The PduM protein is a structural component
of the microcompartments involved in coenzyme B(12)-dependent 1,2-propanediol
degradation by Salmonella enterica. J Bacteriol. 2012 Apr;194(8):1912-8. doi:
10.1128/JB.06529-11. Epub 2012 Feb 17. PubMed PMID: 22343294; PubMed Central
PMCID: PMC3318458.

3: Fan C, Bobik TA. The N-terminal region of the medium subunit (PduD) packages
adenosylcobalamin-dependent diol dehydratase (PduCDE) into the Pdu
microcompartment. J Bacteriol. 2011 Oct;193(20):5623-8. doi: 10.1128/JB.05661-11.
Epub 2011 Aug 5. PubMed PMID: 21821773; PubMed Central PMCID: PMC3187188.

4: Zhu H, Gonzalez R, Bobik TA. Coproduction of acetaldehyde and hydrogen during
glucose fermentation by Escherichia coli. Appl Environ Microbiol. 2011
Sep;77(18):6441-50. doi: 10.1128/AEM.05358-11. Epub 2011 Jul 29. PubMed PMID:
21803884; PubMed Central PMCID: PMC3187147.

5: Cheng S, Sinha S, Fan C, Liu Y, Bobik TA. Genetic analysis of the protein
shell of the microcompartments involved in coenzyme B12-dependent 1,2-propanediol
degradation by Salmonella. J Bacteriol. 2011 Mar;193(6):1385-92. doi:
10.1128/JB.01473-10. Epub 2011 Jan 14. PubMed PMID: 21239588; PubMed Central
PMCID: PMC3067621.

6: Gogerty DS, Bobik TA. Formation of isobutene from 3-hydroxy-3-methylbutyrate
by diphosphomevalonate decarboxylase. Appl Environ Microbiol. 2010
Dec;76(24):8004-10. doi: 10.1128/AEM.01917-10. Epub 2010 Oct 22. PubMed PMID:
20971863; PubMed Central PMCID: PMC3008229.

7: Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO. Structural
insight into the mechanisms of transport across the Salmonella enterica Pdu
microcompartment shell. J Biol Chem. 2010 Nov 26;285(48):37838-46. doi:
10.1074/jbc.M110.160580. Epub 2010 Sep 24. PubMed PMID: 20870711; PubMed Central
PMCID: PMC2988387.

8: Cheng S, Bobik TA. Characterization of the PduS cobalamin reductase of
Salmonella enterica and its role in the Pdu microcompartment. J Bacteriol. 2010
Oct;192(19):5071-80. doi: 10.1128/JB.00575-10. Epub 2010 Jul 23. PubMed PMID:
20656910; PubMed Central PMCID: PMC2944522.

9: Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, Yeates TO, Bobik
TA. Short N-terminal sequences package proteins into bacterial microcompartments.
Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7509-14. doi:
10.1073/pnas.0913199107. Epub 2010 Mar 22. PubMed PMID: 20308536; PubMed Central
PMCID: PMC2867708.

10: Fan C, Fromm HJ, Bobik TA. Kinetic and functional analysis of L-threonine
kinase, the PduX enzyme of Salmonella enterica. J Biol Chem. 2009 Jul
24;284(30):20240-8. doi: 10.1074/jbc.M109.027425. Epub 2009 Jun 9. PubMed PMID:
19509296; PubMed Central PMCID: PMC2740450.

11: Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA. Bacterial microcompartments:
their properties and paradoxes. Bioessays. 2008 Nov;30(11-12):1084-95. doi:
10.1002/bies.20830. Review. PubMed PMID: 18937343; PubMed Central PMCID:
PMC3272490.

12: Fan C, Bobik TA. The PduX enzyme of Salmonella enterica is an L-threonine
kinase used for coenzyme B12 synthesis. J Biol Chem. 2008 Apr 25;283(17):11322-9.
doi: 10.1074/jbc.M800287200. Epub 2008 Feb 28. PubMed PMID: 18308727.

13: Sampson EM, Bobik TA. Microcompartments for B12-dependent 1,2-propanediol
degradation provide protection from DNA and cellular damage by a reactive
metabolic intermediate. J Bacteriol. 2008 Apr;190(8):2966-71. doi:
10.1128/JB.01925-07. Epub 2008 Feb 22. PubMed PMID: 18296526; PubMed Central
PMCID: PMC2293232.

14: Fan C, Bobik TA. Functional characterization and mutation analysis of human
ATP:Cob(I)alamin adenosyltransferase. Biochemistry. 2008 Mar 4;47(9):2806-13.
doi: 10.1021/bi800084a. Epub 2008 Feb 6. PubMed PMID: 18251506.

15: Liu Y, Leal NA, Sampson EM, Johnson CL, Havemann GD, Bobik TA. PduL is an
evolutionarily distinct phosphotransacylase involved in B12-dependent
1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2. J
Bacteriol. 2007 Mar;189(5):1589-96. Epub 2006 Dec 8. PubMed PMID: 17158662;
PubMed Central PMCID: PMC1855771.

16: Do YS, Smeenk J, Broer KM, Kisting CJ, Brown R, Heindel TJ, Bobik TA,
DiSpirito AA. Growth of Rhodospirillum rubrum on synthesis gas: conversion of CO
to H2 and poly-beta-hydroxyalkanoate. Biotechnol Bioeng. 2007 Jun 1;97(2):279-86.
PubMed PMID: 17054121.

17: Bobik TA. Polyhedral organelles compartmenting bacterial metabolic processes.
Appl Microbiol Biotechnol. 2006 May;70(5):517-25. Epub 2006 Mar 9. Review. PubMed
PMID: 16525780.