Rice: Unconventional Wisdom
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Metabolic Engineering and Synthetic & Systems Biology Laboratory

James Clomburg

Yandi Dharmadi


B.S., Chemical Engineering, University of Texas, Austin, TX, 2006.
Ph.D., Chemical and Biomolecular Engineering, Rice University, 2012.



Project Description

My research focus is on the improved understanding of the microbial utilization of glycerol under fermentative conditions and using this knowledge base as a means for the implementation of metabolic engineering strategies for the biological production of fuels and chemical from glycerol.
The rising concerns related to the cost, sustained availability, and environmental impact of use of fossil fuels has led to the search for new technologies that generate fuels and materials from renewable carbon sources.  Although biofuels such as biodiesel and bioethanol represent a secure, renewable, and environmentally safe alternative to fossil fuels, their economic viability is a major concern.  A solution to this problem is the conversion of glycerol, a by-product generated in large amounts in the production of these biofuels, into fuels and chemicals.  Given highly reduced nature of carbon atoms in glycerol and the cost advantage of anaerobic processes, fermentative metabolism of glycerol is of special interest.  In order to utilize these advantages, however, microorganisms able to perform glycerol fermentation in the absence of electron acceptors are required.
Glycerol utilization under fermentative conditions requires cellular processes enabling functions such as the formation of glycolytic intermediates from glycerol, maintenance of an overall redox balance, and the synthesis of ATP via substrate level phosphorylation in the absence of external electron acceptors.  The ability of certain microorganisms to utilize glycerol in the absence of external electron acceptors can be grouped into specific models that encompass the genes, enzymes, and metabolic pathways required for these cellular processes enabling fermentative glycerol utilization.  The identification and understanding of these specific models for the microbial fermentation of glycerol will provide the fundamental knowledge required as a platform for the metabolic engineering of microorganisms for the use of glycerol as a feedstock for the production of reduced fuels and chemicals. 

My current work is focused on the elucidation of required pathways and mechanisms for several proposed models enabling fermentative glycerol utilization through comprehensive experimental investigation.  The investigation takes advantage of the expertise I have developed in the use of both conventional experimental approaches as well as functional genomics and systems biology tools.  At present, the knowledge gained from these investigations has been used to design and implement metabolic engineering strategies for the production of a wide range of fuels and chemicals from glycerol, including 1,2-propanediol, ethanol, lactic acid, and succinic acid.


Kim, S., Clomburg, J.M., Gonzalez, R. (2015). Synthesis of medium-chain length (C6-C10) fuels and chemicals via β-oxidation reversal in Escherichia coli. Journal of Industrial Microbiology and Biotechnology. doi:10.1007/s10295-015-1589-6.

Clomburg, J.M., Blankschien, M.D., Vick, J.E., Chou, A., Kim, S., Gonzalez, R. (2015). Integrated engineering of β-oxidation reversal and ω-oxidation pathways for the synthesis of medium chain ω-functionalized carboxylic acids. Metabolic Engineering. doi:10.1016/j.ymben.2015.01.007.

Vick, J.E., Clomburg, J.M., Blankschien, M.D., Chou, A., Kim, S., Gonzalez, R. (2015). Escherichia coli enoyl-acyl carrier protein reductase (FabI) supports efficient operation of a functional reversal of the β-oxidation cycle. Applied and Environmental Microbiology. 81(1). doi:10.1128/AEM.03521-14.

Zhao, Z., Arentz, J., Pretzer, L. A., Limpornpipat, P., Clomburg, J. M., Gonzalez, R., Schweitzer, N. M., Wu, T., Miller, J. T., Wong, M. S. (2014). Volcano-shape glycerol oxidation activity of palladium-decorated gold nanoparticles. Chemical Science. 5(10), 3715. doi:10.1039/C4SC01001A.

Cintolesi, A., Clomburg, J.M., Gonzalez, R. (2014). In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C ≥ 4) products. Metabolic Engineering. DOI: 10.1016/j.ymben.2014.02.011.

Mattam A.J, Clomburg J.M., Gonzalez R., Yazdani S.S. (2013). Fermentation of glycerol and production of valuable chemical and biofuel molecules. Biotechnology Letters. 35(6): 831-842.

Clomburg, J.M., and Gonzalez, R. (2013). Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicalsTrends in Biotechnology. 31(1): 20-28.

Mazumdar, S., Blankschien, M. D., Clomburg, J. M., and Gonzalez, R. (2013). Efficient synthesis of L-lactic acid from glycerol by metabolically engineered Escherichia coliMicrobial Cell Factories. 12(7).

Clomburg, J.M., Vick, J.E., Blankschien, M. D., Rodriguez-Moya, M., Gonzalez, R. (2012). A synthetic biology approach to engineer a functional reversal of the beta-oxidation cycleACS Synthetic Biology. 1(11): 541-554.

Cintolesi, A.*, Clomburg, J.M.*, Rigou, V., Zygourakis, K., and Gonzalez, R. (2012). Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coliBiotechnology and Bioengineering, 109 (1): 187-198. *Equal Contributions.

Clomburg, J.M., and Gonzalez, R. (2011) Metabolic Engineering of Escherichia coli for the Production of 1,2-Propanediol from Glycerol. Biotechnology and Bioengineering, 108 (4): 867-879..

Dellomonaco, C., Clomburg J.M., Miller E.N., and Gonzalez, R. (2011) Engineered reversal of the B-oxidation cycle for the synthesis of fuels and chemicals. Nature, 476:355-360.
Murarka, A., Clomburg, J. M., Moran, S., Shanks, J.V., and Gonzalez, R. (2010). Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase (PDH)-deficient derivative reveals the role of PDH in the fermentative metabolism of glucose. Journal of Biologial Chemistry, 285 (41): 31548-31558.

Mazumdar, S., Clomburg, J.M., and Gonzalez, R. (2010) Escherichia coli strains engineered for the homofermentative production of D-lactic acid from glycerol. Applied and Environmental Microbiology, 76 (13): 4327-4336.

Blankschien, M., Clomburg, J.M., and Gonzalez, R. (2010) Metabolic Engineering of Escherichia coli for the Production of Succinate from Glycerol. Metabolic Engineering, 12 (5): 409-419.

Murarka, A., Clomburg, J.M., and Gonzalez, R. (2010). Metabolic flux analysis of wild-type Escherichia coli and mutants deficient in pyruvate-dissimilating enzymes during fermentative metabolism of glucuronate. Microbiology-SGM, 156 (6): 1860 - 1872.

Clomburg, J.M., and Gonzalez, R. (2010) Biofuel production in Escherichia coli: The role of metabolic engineering and synthetic biology. Applied Microbiology and Biotechnology, 86 (2): 419-434.

Durnin, G., Clomburg, J.M., Yeates, Z., Alvarez, P.J.J., Zygourakis, K., Campbell, P., and Gonzalez, R. (2009). Understanding and Harnessing the Microaerobic Metabolism of Glycerol in Escherichia coli. Biotechnology and Bioengineering 103 (1): 148-161.

Contact Information

Abercrombie Lab, C124
Rice University
6100 Main Street MS-362
Houston, TX, 77005
Fax (713) 348-5478