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Gonzalez Reseach Group. Metabolic Engineering & Biomanufacturing. Engineering metabolismfor energy, chemical and pharmaceutical production. Heading 3 Welcome to the laboratory for Metabolic Engineering & Biomanufacturing Engineering metabolism for energy, chemical, and pharmaceutical production Dr. Ramon Gonzalez Principal Investigator The laboratory for Metabolic Engineering and Biomanufacturing focusses on engineering microbial systems that have the potential to revolutionize energy, chemical & pharmaceutical production, environmental remediation, and agricultural systems. Current projects include the bioconversion of C1 feedstocks, synthesis of polyketides and isoprenoids, nitrogen fixation and ammonia production, and bio-upcycling of plastic waste. Projects Our group News Social Media Sponsors

Patents and Patent Applications Full Publication and Citation Details RESEARCH PUBLICATIONS 2024 Gao, Z., Guo, S., Chen, Y., Chen, H., Fu, R., Song, Q., Li, S., Lou, W., Fan, D., Li, Y., Yang, S., Gonzalez, R., & Fei, Q. (2024). A novel nutritional induction strategy flexibly switching the biosynthesis of food-like products from methane by a methanotrophic bacterium . In Green Chemistry. Royal Society of Chemistry (RSC). https://doi.org/10.1039/d3gc04674e Kim, Y., Lee, S.H., Gade, P. et al. Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family . Commun Chem 7, 160 (2024). https://doi.org/10.1038/s42004-024-01242-y Joachimiak, A., Youngchang, K., Lee, S.H. et al. Revealing reaction intermediates in one-carbon elongation ThDP/CoA dependent enzyme family . Lee, S.H., Hu, Y., Chou, A., Chen, J., Gonzalez, R., Metabolic flux optimization of iterative pathways through orthogonal gene expression control: Application to the β- oxidation reversal , Metabolic Engineering (2024), doi: https://doi.org/10.1016/j.ymben.2024.02.007. Li, J., Mu, X., Dong, W. et al. A non-carboxylative route for the efficient synthesis of central metabolite malonyl-CoA and its derived products. Nat Catal 7, 361–374 (2024). https://doi.org/10.1038/s41929-023-01103-2 2023 Lee, S.H., Chou, A., Nattermann, M., Zhu, F., Clomburg, J.M., Paczia, N., Erb, T.J., Gonzalez, R. (2023). Identification of 2-hydroxyacyl-CoA synthases with high acyloin condensation activity for orthogonal one-carbon bioconversion . ACS Catalysis. Chen, J., and Gonzalez, R. (2023). Engineering Escherichia coli for selective 1-decanol production using the reverse β-oxidation (rBOX) pathway . Metab. Eng. 79: 173-181. Nattermann, M., Wenk, S., Pfister, P., He, H., Lee, S. H., Szymanski, W., Guntermann, N., Zhu, F., Nickel, L., Wallner, C., Zarzycki, J., Paczia, N., Gaißert, N., Franciò, G., Leitner, W., Gonzalez, R., and Erb, T.J. (2023). Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo . Nat Commun 14, 2682 (2023). . Tan, Z., Li, J. and Gonzalez, R. (2023). Designing artificial pathways for improving chemical production . Biotechnology Advances 59, 108119. 2 022 Clomburg, J., Cintolesi, A. & Gonzalez, R. (2022) In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli. Micro Biotech. 15(1), 289-304. Hu, L., Guo, S., Wang, B., Fu, R., Fan, D., Jiang, M., Fei, Q. & Gonzalez, R. (2022) Bio-valorization of C1 gaseous substrates into bioalcohols: Potentials and challenges in reducing carbon emissions. Biotechnology Advances. https://doi.org/10.1016/j.biotechadv.2022.107954 Tarasava, K., Lee, S.H., Chen, J., Köpke, M., Jewett, M.C., & Gonzalez, R. (2020) Reverse β-oxidation pathways for efficient chemical production, Journal of Industrial Microbiology and Biotechnology. Journal of Industrial Microbiology and Biotechnology. https://doi.org/10.1093/jimb/kuac003 Vögeli, B., Schulz, L., Garg, S., Tarasava, K., Clomburg, J., Hwan Lee, S., Gonnot, A., Moully, E.H., Kimmel, B.R., Tran, L., Zeleznik, H., Brown, S.D., Simpson, S.D., Mrksich, M., Karim A.S., Gonzalez, R., Köpke, M. & Jewett, M.C. (2022) Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria. Nat Commun. 13, 3058. Wang, Y., Nguyen, N., Lee, S., Wang, Q., May, J.A., Gonzalez, R. & Cirino, P.C. (2022) Engineering Escherichia coli for anaerobic alkane activation: Biosynthesis of (1-methylalkyl)succinates. Biotechnol Bioeng. Biotechnol Bioeng. 119(1), 315-320. 2021 Chou, A., Lee, S.H., Zhu, F., Clomburg, J. & Gonzalez, R. (2021) An orthogonal metabolic framework for one-carbon utilization . Nat Metab 3, 1385–1399. Nattermann, M., Burgener, S., Pfister, P., Chou, A., Schulz, L., Lee, S. H., Paczia, N., Zarzycki, J., Gonzalez, R., & Erb, T. (2021) Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism. ACS Catalysis, 5396–5404 Shen, B., Tang, Y., Baltz, R. H., & Gonzalez, R. (2021). Introduction to the special issue: “Natural Product Discovery and Development in the Genomic Era: 2021.” J Ind Microbiol Biotechnol. 48, 3-4. Baltz, R., Vandamme E., Bennett, J., Agathos, S., Sánchez, S., Osada, H., Deng, Z. & Gonzalez, R. (2021) Introduction and Commentaries for the Special Issue: “Arnold L. Demain - a Life Lived”. Journal of Industrial Microbiology and Biotechnology. https://doi.org/10.1093/jimb/kuab082. 2020 Tan, Z., Clomburg, J. M., Cheong, S., Qian, S., & Gonzalez, R. (2020) A polyketoacyl-CoA thiolase-dependent pathway for the synthesis of polyketide backbones. Nat Catal 3:593–603 Fei, Q., Liang, B., Tao, L., Tan, E. C. D., Gonzalez, R., Henard, C., & Guarnieri, M. (2020) Biological valorization of natural gas for the production of lactic acid: techno-economic analysis and life cycle assessment. Biochem Eng J 107500 Baltz, R. H., Kao, K., Link, A. J., Marsili, E., Reguera, G., Shao, Z., Vandamme, E. J., Jeffries T. W., & Gonzalez, R. (2020) Introduction to Special Issue on “Frontiers in Industrial Microbiology and Biotechnology 2020.” J Ind Microbiol Biotechnol 47:621–622. Baltz, R. H., Greasham, R., Schwartz, R., Rau, T., Davies, T., & Gonzalez, R. (2020) Introduction to the Special Issue on “Recent Advances in Fermentation Technology 2020.” J Ind Microbiol Biotechnol 47:909–91. ___ 2019 Chou, A., Clomburg, J. M., Qian, S., & Gonzalez, R. (2019) 2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion. Nat Chem Biol 15:900–906 Clomburg, J. M., Qian, S., Tan, Z., Cheong, S., & Gonzalez, R. (2019) The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis. Proc Natl Acad Sci 116:12810–1281 Qian, S., Clomburg, J. M., & Gonzalez, R. (2019) Engineering Escherichia coli as a platform for the in vivo synthesis of prenylated aromatics. Biotechnol Bioeng 116:1116–1127 Baltz, R. H., & Gonzalez, R. (2019) Introduction to Special Issue on “Frontiers in Industrial Microbiology and Biotechnology 2019.” J Ind Microbiol Biotechnol 46:1237. __ 2018 Cheong, S., Clomburg, J. M., & Gonzalez, R. (2018) A synthetic pathway for the production of 2-hydroxyisovaleric acid in Escherichia coli. J Ind Microbiol Biotechnol 45:579–588. Clomburg, J. M., Contreras, S. C., Chou, A., Siegel, J. B., & Gonzalez, R. (2018) Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal. Metab Eng 45:11–19 Crumbley, A. M., & Gonzalez, R. (2018) Cracking “Economies of Scale”: Biomanufacturing on Methane-Rich Feedstock. In: Methane Biocatalysis: Paving the Way to Sustainability. Springer, pp 271–292 Garg, S., Clomburg, J. M., & Gonzalez, R. (2018) A modular approach for high-flux lactic acid production from methane in an industrial medium using engineered Methylomicrobium buryatense 5GB1. J Ind Microbiol Biotechnol 45:379–391. Katz, L., Chen, Y. Y., Gonzalez, R., Peterson, T. C., Zhao, H., & Baltz, R. H. (2018) Synthetic biology advances and applications in the biotechnology industry: a perspective. J Ind Microbiol Biotechnol 45:449–461. Kim, S., & Gonzalez, R. (2018) Selective production of decanoic acid from iterative reversal of β‐oxidation pathway. Biotechnol Bioeng 115:1311–1320 Tan, Z., Clomburg, J. M., & Gonzalez, R. (2018) Synthetic pathway for the production of olivetolic acid in Escherichia coli. ACS Synth Biol 7:1886–1896 __ 2017 Baltz, R. H., Vandamme, E., Zhang, L., & Gonzalez, R. (2017) Introduction to the Special Issue:“Arnold Demain—Industrial Microbiologist Extraordinaire.” J Ind Microbiol Biotechnol 44:503. Clomburg, J. M., Crumbley, A. M., & Gonzalez, R. (2017) Industrial biomanufacturing: the future of chemical production. Science (80- ) 355: __ 2016 Cheong, S., Clomburg, J. M., & Gonzalez, R. (2016) Energy-and carbon-efficient synthesis of functionalized small molecules in bacteria using non-decarboxylative Claisen condensation reactions. Nat Biotechnol 34:556 Gonzalez, R. (2016) From the New Editor-in-Chief. J Ind Microbiol Biotechnol 43:1–2. Kim, S., Cheong, S., Chou, A., & Gonzalez, R. (2016) Engineered fatty acid catabolism for fuel and chemical production. Curr Opin Biotechnol 42:206–215 Kim, S., Cheong, S., & Gonzalez, R. (2016) Engineering Escherichia coli for the synthesis of short-and medium-chain α, β-unsaturated carboxylic acids. Metab Eng 36:90–98 Wittmann, C., & Gonzalez, R. (2016) Editorial overview: Chemical biotechnology . Curr Opin Biotechnol 42:iv–v. __ 2015 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. Metab Eng 28:202–212 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. J Ind Microbiol Biotechnol 42:465–475. Nielsen, J., & Gonzalez, R. (2015) Editorial – Special Issue: Metabolic Engineering. J Ind Microbiol Biotechnol 42:315–316. Rodriguez-Moya, M., & Gonzalez, R. (2015) Proteomic analysis of the response of Escherichia coli to short-chain fatty acids. J Proteomics 122:86–99 Vergara, M., Berrios, J., Martínez, I., Díaz-Barrera, A., Acevedo, C., Reyes, J. G., … Altamirano, C. (2015) Endoplasmic reticulum-Associated rht-PA Processing in CHO Cells: Influence of mild hypothermia and specific growth rates in batch and chemostat cultures. PLoS One 10:e0144224 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. Appl Environ Microbiol 81:1406–1416 __ 2014 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. Metab Eng 23:100–115 Conrado, R. J., & Gonzalez, R. (2014) Envisioning the bioconversion of methane to liquid fuels. Science (80- ) 343:621–623 Haynes, C. A., & Gonzalez, R (2014) Rethinking biological activation of methane and conversion to liquid fuels. Nat Chem Biol 10:331 Vergara, M., Becerra, S., Berrios, J., Osses, N., Reyes, J., Rodriguez-Moya, M., Gonzalez, R., & Altamirano, C. (2014) Differential effect of culture temperature and specific growth rate on CHO cell behavior in chemostat culture. PLoS One 9:e93865 Zhao, Z., Arentz, J., Pretzer, L. A., Limpornpipat, P., Clomburg, J. M., Gonzalez, R., Schweitzer, N. M. , Wu, T. , Miller J. M., & Wong, M. S. (2014) Volcano-shape glycerol oxidation activity of palladium-decorated gold nanoparticles. Chem Sci 5:3715–3728 __ 2013 Blankschien, M. D., Pretzer, L. A., Huschka, R., Halas, N. J., Gonzalez, R., & Wong, M. S (2013) Light-triggered biocatalysis using thermophilic enzyme–gold nanoparticle complexes. ACS Nano 7:654–663 Cintolesi, Angela, Rodríguez‐Moyá, M., & Gonzalez, R. (2013) Fatty acid oxidation: Systems analysis and applications. Wiley Interdiscip Rev Syst Biol Med 5:575–585 Clomburg, J. M., & Gonzalez, R. (2013) Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals. Trends Biotechnol 31:20–28 González, R. (2013) Metabolic engineering: Use of system-level approaches and application to fuel production in Escherichia coli. Electron J Biotechnol 16:17 Mattam, A. J., Clomburg, J. M., Gonzalez, R., & Yazdani, S. S. (2013) Fermentation of glycerol and production of valuable chemical and biofuel molecules. Biotechnol Lett 35:831–842 Mazumdar, S., Blankschien, M. D., Clomburg, J. M., & Gonzalez, R. (2013) Efficient synthesis of L-lactic acid from glycerol by metabolically engineered Escherichia coli. Microb Cell Fact 12:7 Vergara, M., Becerra, S., Berrios, J., Reyes, J., Acevedo, C., Gonzalez, R., Osses, N., & Altamirano, C. (2013) Protein folding and glycosylation process are influenced by mild hypothermia in batch culture and by specific growth rate in continuous cultures of CHO cells producing rht-PA. In: BMC Proceedings. Springer, p P108 Rastogi, G., Gurram, R., Bhalla, A., Gonzalez, R., Bischoff, K., Hughes, S., Kumar, S., & Sani, R. K (2013) Presence of glucose, xylose, and glycerol fermenting bacteria in the deep biosphere of the former Homestake gold mine, South Dakota. Front Microbiol 4:18 __ 2012 Cintolesi, Angela, Clomburg, J. M., Rigou, V., Zygourakis, K., & Gonzalez, R. (2012) Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 109:187–198 Clomburg, J. M., Vick, J. E., Blankschien, M. D., Rodríguez-Moyá, M., & Gonzalez, R. (2012) A synthetic biology approach to engineer a functional reversal of the β-oxidation cycle. ACS Synth Biol 1:541–554 Park, J., Rodríguez-Moyá, M., Li, M., Pichersky, E., San, K.-Y., & Gonzalez, R. (2012) Synthesis of methyl ketones by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol 39:1703–1712. Posada, J. A., Cardona, C. A., & Gonzalez, R. (2012) Analysis of the production process of optically pure D-lactic acid from raw glycerol using engineered Escherichia coli strains. Appl Biochem Biotechnol 166:680–699 __ 2011 Becerra, S., Vergara, M., González, R., Osses, N., & Altamirano, C. (2011) Condition of mild hypothermia does not promote an increase in specific productivity of recombinant protein at high specific growth rate. Curr Opin Biotechnol S35–S36 Berrios, J., Altamirano, C., Osses, N., & Gonzalez, R. (2011) Continuous CHO cell cultures with improved recombinant protein productivity by using mannose as carbon source: Metabolic analysis and scale-up simulation. Chem Eng Sci 66:2431–2439 Clomburg, J. M., & Gonzalez, R. (2011) Metabolic engineering of Escherichia coli for the production of 1, 2‐propanediol from glycerol. Biotechnol Bioeng 108:867–879 Choudhary, M. K., Yoon, J. M., Gonzalez, R., & Shanks, J. V. (2011) Re-examination of metabolic fluxes in Escherichia coli during anaerobic fermentation of glucose using 13 C labeling experiments and 2-dimensional nuclear magnetic resonance (NMR) spectroscopy. Biotechnol Bioprocess Eng 16:419–437 Dellomonaco, C., Clomburg, J. M., Miller, E. N., & Gonzalez, R. (2011) Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 476:355–359 Zhu, H., Gonzalez, R., & Bobik, T. A. (2011) Coproduction of acetaldehyde and hydrogen during glucose fermentation by Escherichia coli. Appl Environ Microbiol 77:6441–6450 __ 2010 Blankschien, M. D., Clomburg, J. M., & Gonzalez, R. (2010) Metabolic engineering of Escherichia coli for the production of succinate from glycerol. Metab Eng 12:409–419 Clomburg, J. M., & Gonzalez, R. (2010) Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 86:419–434 Dellomonaco, C., Fava, F., & Gonzalez, R. (2010) The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 9:1–15 Dellomonaco, C., Rivera, C., Campbell, P., & Gonzalez, R. (2010) Engineered respiro-fermentative metabolism for the production of biofuels and biochemicals from fatty acid-rich feedstocks. Appl Environ Microbiol 76:5067–5078 Dharmadi, Y., & Gonzalez, R. (2010) Elementary network reconstruction: A framework for the analysis of regulatory networks in biological systems. J Theor Biol 263:499–509 Gonzalez, R., Campbell, P., & Wong, M. (2010) Production of ethanol from thin stillage by metabolically engineered Escherichia coli. Biotechnol Lett 32:405–411 Murarka, A., Clomburg, J. M., & Gonzalez, R. (2010) Metabolic flux analysis of wild-type Escherichia coli and mutants deficient in pyruvate-dissimilating enzymes during the fermentative metabolism of glucuronate. Microbiology 156:1860–1872 Murarka, A., Clomburg, J. M., Moran, S., Shanks, J. V, & Gonzalez, R. (2010) Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase complex (PDHC)-deficient derivative reveals the role of PDHC in the fermentative metabolism of glucose. J Biol Chem 285:31548–31558 Mazumdar, S., Clomburg, J. M., & Gonzalez, R. (2010) Escherichia coli strains engineered for homofermentative production of D-lactic acid from glycerol. Appl Environ Microbiol 76:4327–4336 Rodríguez-Moyá, M., & Gonzalez, R. (2010) Systems biology approaches for the microbial production of biofuels. Biofuels 1:291–310 Yazdani, S. S., Mattam, A. J., & Gonzalez, R. (2010) Fuel and chemical production from glycerol, a biodiesel waste product. In "Biofuels from Agric wastes Byprod" Blaschek H, Ezeji T, and Scheffran J (Eds) Blackwell Publishing. 97–116 __ 2009 Dharmadi, Y., & Gonzalez, R. (2009) Metabolic Engineering for alternative fuels. The Metabolic Pathway Engineering Handbook. Smolke CD (Ed) Cameron D and Brazeau B (Eds) CRC Press. Boca Raton. FL Durnin, G., Clomburg, J., Yeates, Z., Alvarez, P. J. J., Zygourakis, K., Campbell, P., & Gonzalez, R. (2009) Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 103:148–161 Gupta, A., Murarka, A., Campbell, P., & Gonzalez, R. (2009) Anaerobic fermentation of glycerol in Paenibacillus macerans: metabolic pathways and environmental determinants. Appl Environ Microbiol 75:5871–5883 __ 2008 Gonzalez, Ramon, Murarka, A., Dharmadi, Y., & Yazdani, S. S. (2008) A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli. Metab Eng 10:234–245 Murarka, A., Dharmadi, Y., Yazdani, S. S., & Gonzalez, R. (2008) Fermentative utilization of glycerol by Escherichia coli and its implications for the production of fuels and chemicals. Appl Environ Microbiol 74:1124–1135 Yazdani, S. S., & Gonzalez, R. (2008) Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metab Eng 10:340–351 __ 2007 Gonzalez, R. (2007) Metabolic engineering of bacteria for food ingredients. In: Functional Foods and Biotechnology. pp. 501-520. Shetty K, Paliyath G, Pometto A and Levin RE (Eds) CRC Press. Boca Raton, FL Murarka, A., & Gonzalez, R. (2007) Metabolic Engineering of Bacteria. Encyclopedia of Agricultural, Food, and Biological Engineering. Heldman DR (Ed) Taylor & Francis Group LLC. New York, NY Yazdani, S. S., & Gonzalez, R. (2007) Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Curr Opin Biotechnol 18:213–219 __ 2006 Dharmadi, Y., Murarka, A., & Gonzalez, R. (2006) Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering. Biotechnol Bioeng 94:821–829 Glatz, C. E., Gonzalez, R., Huba, M. E., Mallapragada, S. K., Narasimhan, B., Reilly, P. J., Saunders, K., & Shanks, J. V. (2006) Problem‐Based Learning Biotechnology Courses in Chemical Engineering. Biotechnol Prog 22:173–178 Rollins, D. K., Zhai, D., Joe, A. L., Guidarelli, J. W., Murarka, A., & Gonzalez, R. (2006) A novel data mining method to identify assay-specific signatures in functional genomic studies. BMC Bioinformatics 7:377 __ 2005 Gonzalez, R. (2005) Metabolic Engineering of Bacteria for Food Ingredients. Food Biotechnology: Second Edition. Shetty K, Pometto A and Paliyath G (Eds) CRC Press. Boca Raton, FL Dharmadi, Y., & Gonzalez, R. (2005) A better global resolution function and a novel iterative stochastic search method for optimization of high-performance liquid chromatographic separation. J Chromatogr A 1070:89–101 __ 2004 Dharmadi, Y., & Gonzalez, R. (2004) DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol Prog 20:1309–1324 Gonzalez, Ramon, Gentina, J. C., & Acevedo, F. (2004) Biooxidation of a gold concentrate in a continuous stirred tank reactor: mathematical model and optimal configuration. Biochem Eng J 19:33–42 __ 2003 Gonzalez, Ramon, Andrews, B. A., Molitor, J., & Asenjo, J. A. (2003) Metabolic analysis of the synthesis of high levels of intracellular human SOD in Saccharomyces cerevisiae rhSOD 2060 411 SGA122. Biotechnol Bioeng 82:152–169 González, Ramón, Gentina, J. C., & Acevedo, F. (2003) Optimisation of the solids suspension conditions in a continuous stirred tank reactor for the biooxidation of refractory gold concentrates. Electron J Biotechnol 6:233–243 Gonzalez, Ramon, Tao, H., Purvis, J. E., York, S. W., Shanmugam, K. T., & Ingram, L. O. (2003) Gene array‐based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (parent) to LY01 (resistant mutant). Biotechnol Prog 19:612–623 __ 2002 Gonzalez, Ramon, Andrews, B. A., & Asenjo, J. A. (2002) Kinetic model of BiP-and PDI-mediated protein folding and assembly. J Theor Biol 214:529–537 Gonzalez, Ramon, Tao, H., Shanmugam, K. T., York, S. W., & Ingram, L. O. (2002) Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol Prog 18:6–20 __ 2001 Gonzalez, Ramon, Asenjo, J. A., & Andrews, B. A. (2001) Metabolic control analysis of monoclonal antibody synthesis. Biotechnol Prog 17:217–226 Tao, H., Gonzalez, R., Martinez, A., Rodriguez, M., Ingram, L. O., Preston, J. F., & Shanmugam, K. T. (2001) Engineering a homo-ethanol pathway inEscherichia coli: Increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. J Bacteriol 183:2979–2988 __ 1999 Gonzalez, R, Gentina, J. C., & Acevedo, F. (1999) Attachment behaviour of Thiobacillus ferrooxidans cells to refractory gold concentrate particles. Biotechnol Lett 21:715–718 González, R, Gentina, J. C., & Acevedo, F. (1999) Continuous biooxidation of a refractory gold concentrate. In: Process Metallurgy. Elsevier, pp 309–317 PATENTS AND PATENT APPLICATIONS Gonzalez, R., Chou, A. Bioconversion of 1-carbon feedstocks to fuels and chemicals . Pub. No. WO2017210381. Gonzalez, R., Clomburg, J.M., Chou, A. Conversion of 1-carbon compounds to products . Pub. No. WO2017190056. Gonzalez, R., Cheong, S., Clomburg, J.M. Microbial synthesis of isoprenoid precursors, isoprenoids and derivatives including prenylated aromatics . Pub. No. WO2017161041. Gonzalez, R., Cheong, S., Clomburg, J.M. Biosynthesis of polyketides . Pub. No. WO2017020043. Gonzalez, R., Chou, A., Clomburg, J.M. Synthetic pathway for biosynthesis from 1-carbon compounds . Pub. No. WO2016069929. Gonzalez, R., Clomburg, J.M. Bioconversion of short-chain hydrocarbons to fuels and chemicals . Pub. No. WO2016161043. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-phenyl products and derivatives thereof . Pub. No. WO2016176339. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-1 functionalized products and derivatives thereof . Pub. No. WO2016176347. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega functionalized methyketones, 2-alcohols, 2-amines, and derivatives thereof . Pub. No. WO2016168708. Gonzalez, R., Clomburg, J.M., Cheong, S. Iterative platform for the synthesis of alpha functionalized products . Pub. No. WO2016168681. Gonzalez, R., Clomburg, J.M. Modified fatty acid biosynthesis with ACP-dependent thiolases . Pub. No. WO2016168247. Gonzalez, R., Clomburg, J.M. Omega-carboxylated carboxylic acids and derivatives . Pub. No. WO2015191972. Gonzalez, R., Clomburg, J.M. Omega-aminated carboxylic acids . Pub. No. WO2016007258. Gonzalez, R., Clomburg, J.M. Omega-hydroxylated carboxylic acids . Pub. No. WO2015191422. Gonzalez, R., Clomburg, J.M. Functionalized carboxylic acids and alcohols by reverse fatty acid oxidation. Patent No. US 9,994,881. Gonzalez, R., Clomburg, J.M., Vick, J. Type II fatty acid synthesis enzymes in reverse β-oxidation . Pub. No. WO2015112988. Gonzalez, R., Clomburg, J.M., Dellomonaco, C., Miller, E.N. Reverse beta oxidation pathway. Patent No. US 9,416,364 . Campbell, P., and Gonzalez, R. Microbial conversion of oils and fatty acids to high-value chemicals. Pub. No. WO2009078973. Gonzalez, R., and Campbell, P. Microaerobic cultures for converting glycerol to chemicals. Patent No. US 8,691,552. Gonzalez, R. Anaerobic fermentation of glycerol . Patent No. US 8,129,157.

Principal Investigator Professor, Department of Chemical, Biological and Materials Engineering Editor-in-Chief, Journal of Industrial Microbiology and Biotechnology RAMON GONZALEZ Publications Research Scientist Postdoctoral JING CHEN Graduate Students SEUNG HWAN (ALLEN) LEE BENARD NYAWANGA JAMES M. CLOMBURG PABLO FUENTEALBA G YANG HU COLLABORATORS Qiang Fei , School of Chemical Engineering and Technology, Xi'an Jiaotong University, China Tobias Erb , Max Planck Institute for Terrestrial Microbiology, Germany George N. Bennett - Rice University Patrick C. Cirino - University of Houston Michael C. Jewett - Northwestern University George N. Phillips - Rice University Ka-Yiu San - Rice University Jacqueline V. Shanks - Iowa State University Justin Siegel - University of California, Davis Lee H. Spangler - Montana State University ALUMNI Dr. James Clomburg , currently at LanzaTech , Skokie, IL. Dr. Katia Tarasava , currently at Inscripta Inc , Tampa, FL Dr. Anna M. Crumbley, currently at U.S. Army DEVCOM Chemical Biological Center , Edgewood, MR Dr. Alex Chou , currently at ADM , Decatur, IL Dr. Zaigao Tan, currently at School of Life Sciences and Biotechnology SJTU , Shangai, China Dr. Shuai Qian , currently at Solugen , Houston, TX Dr. Seohyoung Kim , currently at CJ - CheilJedang , South Korea Dr. Shivani Garg , currently at LanzaTech , Skokie, IL Dr. Seokjung Cheong , currently works at Keasling Lab, South Korea Dr. John M. Leavitt , currently at Texas Department of State Health , Austin, TX Dr. Maria Rodriguez-Moya , currently at Shell , Houston, TX Dr. Jacob Vick , currently at Conagen Inc. , Bedford, MA Dr. Matthew Blankschien , currently at Absci , Tarrytown, NY Dr. Angela Cintolesi , currently at Genomatica , San Diego, CA Satyakam Dash , currently at Zymergen, Inc. , Emeryville, CA Dr. Elliot Miller , currently at Corteva Agriscience , Wilmington, DL Dr. Clementina Dellomonaco , currently at International Flavors & Fragrances , Leiden, Netherlands John Park , currently at Google , Mountain View, CA Dr. John Posada , currently at TU Delft , Delft, Netherlands Dr. Mauricio Vergara , currently at CREAS , Valparaíso, Chile Ruiqiang Sun, currently at WuXi Biologics , Shanghai, China Suman Mazumdar , currently at Ministry of Science and Technology. Govt. of India , India Dr. Ashutosh Gupta , currently at Takeda , Boston, MA Yandi Dharmadi, currently at Amyris Biotechnologies , Emeryville, CA Guyton Durnin , currently at HDR , Omaha, NEB Seth Hoffman , currently at DuPont , Cedar Rapids, IA. Dr. Abhishek Murarka , currently at Amyris Biotechnologies , Emeryville, CA Michael Prachar, currently at Elly Lilly , Indianapolis, IN. Dr. Tristan Pritchard-Meaker , currently at NECSTGEN , Leiden, Netherland Jonathan Rixen, J.D. , currently at Lemaire Patent Law Firm , Burnsville, MN Dr. Venetia Rigou , currently at PM Group , Ireland Dr. Syed Shams Yazdani , currently at ICGEB , New Delhi, India Dr. Kevin Smith , currently at Moderna Therapeutics , Cambridge, MA Dr. Matt Tobelmann, currently at Verily Life Sciences , South San Francisco, CA MOHAMMADREZA NEZAMIRAD FAYIN ZHU

RESEARCH Engineering metabolism for fuel, chemical, and pharmaceutical production Advancements in our knowledge and understanding of biology, coupled with the emergence of fields such as synthetic biology and metabolic engineering have led to an unprecedented ability to harness cellular metabolism. However, the full potential of biological systems remains unrealized due to critical limitations in our ability to engineer and control them. The Metabolic Engineering and Biomanufacturing Laboratory seeks to overcome these limitations by designing and implementing transformational metabolic engineering and synthetic biology approaches to engineer biological systems. Combined with advancement of our fundamental knowledge of cellular metabolism, these approaches exploit the power and diversity of biology for the development of novel technologies across a range of applications. With a focus on the biomanufacturing of small molecules, this has enabled us to engineer cellular metabolism for the production of fuel, chemical, and pharmaceutical compounds from cost-effective and sustainable feedstocks .

PROJECTS In the Gonzalez Lab, we are engineering native and synthetic pathways for the cost-effective bioconversion of sustainable feedstocks to fuels, chemicals, and natural products ENGINEERED METABOLISM FOR CHEMICAL PRODUCTION FROM ONE-CARBON SUBSTRATES One-carbon (C1) compounds, including carbon dioxide, carbon monoxide, formate, methanol, and methane, are attractive feedstocks for fuel and chemical production due to their availability and sustainability. However, the efficient and economical utilization of these feedstocks can be challenging for traditional chemical processes due, in part, to their diffuse nature. As a result, biological processes are gaining increased attention as alternatives due to safer, milder processing conditions and potential for scale-down, which may allow for decentralized, distributed chemical manufacturing that can make better use of these resources. READ MORE ENGINEERED METABOLIC PATHWAYS FOR THE SYNTHESIS OF PLANT NATURAL PRODUCTS The structural and chemical diversity of plant natural products (PNPs) offers an enormous chemical space from which molecules with beneficial characteristics can be discovered and produced. To date, thousands of PNPs have been exploited for human benefit with applications ranging from drugs and nutraceuticals to industrial chemicals. However, agricultural and geographic variations and extraction of the desired compound(s) poses a significant challenge for cost-effective production due to the high cost associated with downstream processing and purification. READ MORE Β-OXIDATION REVERSAL AS A PLATFORM FOR SMALL MOLECULE BIOSYNTHESIS Economical industrialization of bio-based chemical production that have no petrochemical counterparts, such as alkylpolyglucoside and PLA polymers, highlights the importance of bio-based approaches to developing newly functionalized chemicals. The r-BOX platform is expected to play a crucial role in helping bio-based chemicals tackle competition from much cheaper counterparts derived from conventional fossil-based routes. READ MORE FUEL AND CHEMICAL PRODUCTION FROM GLYCEROL FERMENTATION In order to ensure the long-term viability of biorefineries, it is essential to go beyond the carbohydrate-based platform and develop complementing technologies capable of producing fuels and chemicals from a wide array of available materials. Glycerol, a readily available and inexpensive compound, is generated during biodiesel, oleochemical, and bioethanol production processes, making its conversion into value-added products of great interest. READ MORE

The Team Who We Are Dr. Ramon Gonzalez Principal Investigator Professor Department of Chemical, Biological and Materials Engineering Editor-i n-Chief Journal of Industrial Microbiology and Biotechnology ramongonzale@usf.edu Yang Hu Graduate Research Assistant Ph.D. Student in Biomedical Engineering yanghu1@usf.edu Mohhamadreza Nezamirad Graduate Research Assistant Ph.D. Student in Chemical Engineering mnezamirad@usf.edu

Alumni JAMES M. CLOMBURG PABLO FUENTEALBA G JING CHEN SEUNG HWAN (ALLEN) LEE BENARD NYAWANGA FAYIN ZHU

LAB CAPACITY General equipment Cell Culture and Fermentation

JAMES M. CLOMBURG Dr. James Clomburg is a Research Scientist in the Department of Chemical, Biological, and Materials Engineering at the University of South Florida and a Principal Investigator in the laboratory for Metabolic Engineering and Biomanufacturing. His research focuses on understanding and engineering of metabolic pathways for the utilization of abundant and sustainable feedstocks as well as the development and optimization of biological platforms for the production of organic molecules with applications in fuel, chemical, and pharmaceutical production. He has lead various research projects in these areas combining broad-based knowledge of metabolic pathways, biochemical reactions, and microbial metabolism to design and optimize biological platforms for the conversion of various carbon sources to novel compounds through the implementation of metabolic engineering and synthetic biology approaches. Dr. Clomburg has co-authored nineteen articles in leading scientific journals, including Nature, Nature Biotechnology, Metabolic Engineering, and ACS Synthetic Biology and is an inventor in over fifteen patents or patent applications. He received his Ph.D. in Chemical and Biomolecular Engineering from Rice University and B.S. in Chemical Engineering from the University of Texas at Austin. Publications Professional Experience 2018 to present – Research Scientist, Chemical & Biomedical Engineering, University of South Florida 2014 to 2018 – Research Scientist, Chemical and Biomolecular Engineering, Rice University 2012 to 2014 – Post-Doctoral Research Associate, Chemical and Biomolecular Engineering, Rice University Education 2012 – Rice University, PhD in Chemical and Biomolecular Engineering 2006 – University of Texas, BS in Chemical Engineering CONTACT INFORMATION James Clomburg Research Scientist Department of Chemical, Biological, and Materials Engineering University of South Florida ENB 376 | 4202 E Fowler Ave | Tampa, FL 33620 jmclomburg@usf.edu (813)-974-4563

PATENTS AND PATENT APPLICATIONS Gonzalez, R., Chou, A. Bioconversion of 1-carbon feedstocks to fuels and chemicals . Pub. No. WO2017210381. Gonzalez, R., Clomburg, J.M., Chou, A. Conversion of 1-carbon compounds to products . Pub. No. WO2017190056. Gonzalez, R., Cheong, S., Clomburg, J.M. Microbial synthesis of isoprenoid precursors, isoprenoids and derivatives including prenylated aromatics . Pub. No. WO2017161041. Gonzalez, R., Cheong, S., Clomburg, J.M. Biosynthesis of polyketides . Pub. No. WO2017020043. Gonzalez, R., Chou, A., Clomburg, J.M. Synthetic pathway for biosynthesis from 1-carbon compounds . Pub. No. WO2016069929. Gonzalez, R., Clomburg, J.M. Bioconversion of short-chain hydrocarbons to fuels and chemicals . Pub. No. WO2016161043. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-phenyl products and derivatives thereof . Pub. No. WO2016176339. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-1 functionalized products and derivatives thereof . Pub. No. WO2016176347. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega functionalized methyketones, 2-alcohols, 2-amines, and derivatives thereof . Pub. No. WO2016168708. Gonzalez, R., Clomburg, J.M., Cheong, S. Iterative platform for the synthesis of alpha functionalized products . Pub. No. WO2016168681. Gonzalez, R., Clomburg, J.M. Modified fatty acid biosynthesis with ACP-dependent thiolases . Pub. No. WO2016168247. Gonzalez, R., Clomburg, J.M. Omega-carboxylated carboxylic acids and derivatives . Pub. No. WO2015191972. Gonzalez, R., Clomburg, J.M. Omega-aminated carboxylic acids . Pub. No. WO2016007258. Gonzalez, R., Clomburg, J.M. Omega-hydroxylated carboxylic acids . Pub. No. WO2015191422. Gonzalez, R., Clomburg, J.M. Functionalized carboxylic acids and alcohols by reverse fatty acid oxidation. Patent No. US 9,994,881. Gonzalez, R., Clomburg, J.M., Vick, J. Type II fatty acid synthesis enzymes in reverse β-oxidation . Pub. No. WO2015112988. Gonzalez, R., Clomburg, J.M., Dellomonaco, C., Miller, E.N. Reverse beta oxidation pathway. Patent No. US 9,416,364 . Campbell, P., and Gonzalez, R. Microbial conversion of oils and fatty acids to high-value chemicals. Pub. No. WO2009078973. Gonzalez, R., and Campbell, P. Microaerobic cultures for converting glycerol to chemicals. Patent No. US 8,691,552. Gonzalez, R. Anaerobic fermentation of glycerol . Patent No. US 8,129,157. Gonzalez, R., Chou, A. Bioconversion of 1-carbon feedstocks to fuels and chemicals . Pub. No. WO2017210381. Gonzalez, R., Clomburg, J.M., Chou, A. Conversion of 1-carbon compounds to products . Pub. No. WO2017190056. Gonzalez, R., Cheong, S., Clomburg, J.M. Microbial synthesis of isoprenoid precursors, isoprenoids and derivatives including prenylated aromatics . Pub. No. WO2017161041. Gonzalez, R., Cheong, S., Clomburg, J.M. Biosynthesis of polyketides . Pub. No. WO2017020043. Gonzalez, R., Chou, A., Clomburg, J.M. Synthetic pathway for biosynthesis from 1-carbon compounds . Pub. No. WO2016069929. Gonzalez, R., Clomburg, J.M. Bioconversion of short-chain hydrocarbons to fuels and chemicals . Pub. No. WO2016161043. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-phenyl products and derivatives thereof . Pub. No. WO2016176339. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-1 functionalized products and derivatives thereof . Pub. No. WO2016176347. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega functionalized methyketones, 2-alcohols, 2-amines, and derivatives thereof . Pub. No. WO2016168708. Gonzalez, R., Clomburg, J.M., Cheong, S. Iterative platform for the synthesis of alpha functionalized products . Pub. No. WO2016168681. Gonzalez, R., Clomburg, J.M. Modified fatty acid biosynthesis with ACP-dependent thiolases . Pub. No. WO2016168247. Gonzalez, R., Clomburg, J.M. Omega-carboxylated carboxylic acids and derivatives . Pub. No. WO2015191972. Gonzalez, R., Clomburg, J.M. Omega-aminated carboxylic acids . Pub. No. WO2016007258. Gonzalez, R., Clomburg, J.M. Omega-hydroxylated carboxylic acids . Pub. No. WO2015191422. Gonzalez, R., Clomburg, J.M. Functionalized carboxylic acids and alcohols by reverse fatty acid oxidation. Patent No. US 9,994,881. Gonzalez, R., Clomburg, J.M., Vick, J. Type II fatty acid synthesis enzymes in reverse β-oxidation . Pub. No. WO2015112988. Gonzalez, R., Clomburg, J.M., Dellomonaco, C., Miller, E.N. Reverse beta oxidation pathway. Patent No. US 9,416,364 . Campbell, P., and Gonzalez, R. Microbial conversion of oils and fatty acids to high-value chemicals. Pub. No. WO2009078973. Gonzalez, R., and Campbell, P. Microaerobic cultures for converting glycerol to chemicals. Patent No. US 8,691,552. Gonzalez, R. Anaerobic fermentation of glycerol . Patent No. US 8,129,157.

Alumni Dr. James Clomburg Director of New Systems at LanzaTech Specialties: Metabolic Engineering, Biochemical Engineering, Fermentation Technology, Chemical Engineering Dr. Fayin Zhu Postdoctoral Researcher at USF Strong research professional skills in Metabolic Engineering, Molecular Biology, Biochemistry, Microbiology. Special interests in value-added chemicals production using microbial systems and scale-up of the microbial cell factories for industrial applications. Dr. Pablo Omar Fuentealba González Chief Technology Officer - Founder - EatNova Hyperfoods Specialty in formulation and development innovation projects with high scientific component in the areas of molecular biology, microbiology and bioprocesses, whose approach seeks to develop technologies that impact the productive sector. Dr. Jing Chen Postdoctoral Researcher at USF Her research focuses on investigating bio-based chemical production using the r-BOX platform as well as the biosynthesis of natural products in E. coli. Dr. Seung Hwan (Allen) Lee Postdoctoral associate at MIT In the journey to find enzymes, metabolic pathways, microbial hosts and fermentation processes to accomplish sustainable biomanufacturing. Benard Nyawanga Benard Nyawanga Dr. Katia Tarasava Science Writer | Biotech Consultant | SynBio Explainer Science writer and biotechnology geek 🤓 Dr. Anna M. Crumbley Research Chemical Engineer at U.S. Army DEVCOM Chemical Biological Center Google Scholar profile: https://scholar.google.com/citations?user=Fos7tvIAAAAJ&hl=en Alex Chou Lead Scientist at LanzaTech Experienced lead scientist with a strong background in both chemical and biological engineering. Expert in metabolic engineering, microbial genetic engineering, biochemistry, and bioprocesses. Alex Chou Lead Scientist at LanzaTech Experienced lead scientist with a strong background in both chemical and biological engineering. Expert in metabolic engineering, microbial genetic engineering, biochemistry, and bioprocesses. Alex Chou Lead Scientist at LanzaTech Experienced lead scientist with a strong background in both chemical and biological engineering. Expert in metabolic engineering, microbial genetic engineering, biochemistry, and bioprocesses. Alex Chou Lead Scientist at LanzaTech Experienced lead scientist with a strong background in both chemical and biological engineering. Expert in metabolic engineering, microbial genetic engineering, biochemistry, and bioprocesses. Apply Today This is a Paragraph. Click on "Edit Text" or double click on the text box to start editing the content. info@mysite.com 123-456-7890