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Systems Biology of Metabolism Metabolism is a complex system that encompasses all biochemical reactions and processes that occur in living organisms along with their interaction and regulation. Our incomplete knowledge of metabolism greatly limits our ability to engineer biological systems. To address this issue, our laboratory engages in fundamental studies that contribute to the creation of the knowledge base required for the effective engineering of metabolism. Our discovery that the bacterium E. colican anaerobically ferment glycerol (Appl. Environ. Microbiol. 74: 1124, 2008 ; Biotechnol. Bioeng. 94: 821, 2006 ) led us to propose a new model for the fermentative utilization of glycerol in E. coliand other bacteria (Appl. Environ. Microbiol. 75: 5871, 2009 ; Metab. Eng. 10: 234, 2008 ). The knowledge base created by these studies enabled the engineering of bacteria for the synthesis of a wide arrange of products, as described under “Metabolic Engineering & Synthetic Biology “. We have demonstrated that using a system-level approach provides an unprecedented understanding of microbial metabolism otherwise not achievable through classical biochemical and molecular genetic approaches. For example, using in silicoand in vivometabolic flux analysis we discovered the role of the pyruvate dehydrogenase complex on the fermentative metabolism of glucuronate and glucose in E. coli(J. Biol. Chem. 285: 31548, 2010 ; Microbiology-SGM 156: 1860, 2010 ). Prior to the work conducted in our laboratory, the role of PDHC in the fermentative metabolism of E. coli remained unknown and this enzyme was thought unable to support fermentative growth. In this area we have also developed new methods and tools that facilitate the system-level analysis of microbial and cellular metabolism (BMC Bioinformatics 7: 377, 2006 ; J. Theor. Biol. 263: 499, 2010 ). We have used system-level methods and tools to elucidate key aspects of microbial and cellular metabolism. For example, we conducted a quantitative analysis of the fermentative metabolism of glycerol in E. colithrough the use of kinetic modeling and Metabolic Control Analysis and elucidated the control structure of the pathways involved in glycerol utilization and ethanol synthesis (Biotechnol. Bioeng. 109: 187, 2012 ). These findings were then used to identify key targets for genetic manipulation that enhanced product synthesis. Similar approaches enabled an improved understanding of apoptosis in Chinese Hamster Ovary (CHO) cell cultures during the production of recombinant proteins (PLoS ONE 9: e93865hem, 2014 ; Chem. Eng. Sci. 66: 2431, 2011 ) and the anaerobic metabolism of E. coliduring glucose fermentation (Biotechnol. Bioprocess. Eng. 16: 419, 2011 ). More recently, we performed a comparative proteomic analysis of E. coli under octanoic acid stress and identified the underlying mechanisms of short-chain fatty acids toxicity in this bacterium (J. Proteomics 122: 86, 2015 ).

Principal Investigator DR. RAMON GONZALEZ Publications Dr. Ramon Gonzalez is the Chief Scientific Officer of MojiaBio (a global biomanufacturing company) and the President of the Society for Industrial Microbiology & Biotechnology (SIMB, founded in 1949). He is an elected Fellow of the American Association for the Advancement of Science (AAAS) and the American Institute for Medical and Biological Engineering (AIMBE). Dr. Gonzalez’s career has spanned the academic, private, and public sectors. Most of his academic work was conducted at Rice University, where he led the laboratory for Metabolic Engineering and Biomanufacturing and rose through the ranks from Assistant Professor to Full Professor. While at Rice, he was the founding director of the Advanced Biomanufacturing Initiative and served as Director of the Energy and Environment Initiative. More recently, Dr. Gonzalez was a Professor and Florida World Class Scholar in the Department of Chemical, Biological and Materials Engineering at the University of South Florida. In addition to his role as Editor-in-Chief of the Journal of Industrial Microbiology & Biotechnology (JIMB) from 2015 to 2023, he has served on the Editorial Boards of Science, Biotechnology Journal, Applied and Environmental Microbiology, Applied Biochemistry and Biotechnology, Food Biotechnology . Dr. Gonzalez also served as Program Director with the Advanced Research Projects Agency-Energy (ARPA-E) of the U.S. Department of Energy and with the U.S. National Science Foundation, as well as on the Board of Directors of SIMB. Dr. Gonzalez has published over 100 papers in prestigious scientific journals, including Nature and its portfolio Journals (Nature Biotechnology , Nature Catalysis , Nature Metabolism , Nature Chemical Biology , Nature Communications ), PNAS , and Science . He is the lead inventor in 25 patents/patent applications and founded/co-founded Glycos Biotechnologies, Creo Ingredients, RBN Bio, and C1Plus Bio. He has advised major industrial bio and Fortune 500 companies and is currently a member of the scientific advisory boards of several companies and research institutions. Dr. Gonzalez has received numerous recognitions, including, Discovery Series Lecture (BioDesign Institute, Arizona State University), Tiangong Forum Lecture (TIB-CAS, China), ‘Inspiring Wisdom’ Distinguished Lecture (SKMML, SJTU, China), AIChE Division 15c Plenary Lecture, ASM Distinguished Lecturer, SDA/NBB Glycerine Innovation Research Award, and NSF CAREER Award. Dr. Gonzalez obtained a Ph.D. in Chemical Engineering from the University of Chile, an M.S. in Biochemical Engineering from the Pontifical Catholic University of Valparaíso (Chile), and a B.S. in Chemical Engineering from the Central University “Marta Abreu” of Las Villas (Cuba). ALUMNI Dr. Yang Hu , currently at Mojia Inc, Tampa, FL Mohammardreza Nezamirad Dr. Jing Chen , currently at Mojia Inc, Tampa, FL Dr. Seung Hwan (Allen) Lee , currently at University of Minnesota, Minneapolis, MN Dr. Fayin Zhu , currently at Mojia Inc, Tampa, FL Dr. Pablo Fuentealba G , currently CSO & CTO at EatNova Hyperfoods Benard Nyawanga , currently at Intel Dr. James Clombur g , 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 LanzaTech , Skokie, 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

Metabolic Engineering and Synthetic Biology Metabolic engineering and synthetic biology are emerging disciplines that enable the design and engineering of biological systems for a wide range of applications. In this area, our laboratory has pioneered the engineering of glycerol fermentation and metabolism of waste fatty acids for the synthesis of fuels and chemicals and the development of a functional reversal of the β-oxidation cycle as an efficient platform for the synthesis of longer-chain (C ≥ 4) products. The knowledge base created by fundamental studies of glycerol metabolism in our laboratory (see “Systems biology of metabolism “) has laid the foundation to establish glycerol fermentation as a new metabolic engineering platform for fuel and chemical production. We pioneered the engineering of bacteria to efficiently convert glycerol to fuels and chemicals such as succinate, ethanol, hydrogen, formate, D- and L-lactate, and 1,2-propanediol (Trends Biotechnol. 31: 20, 2013 ; Microb. Cell Fact. 12: 7, 2013 ; Appl. Bioch. Biotechnol. 166: 680, 2012 ; Biotechnol. Bioeng. 108: 86, 2011 ; Metab. Eng. 12: 409, 2010 ; Appl. Environ. Microbiol. 76: 4327, 2010 ; Biotechnol. Lett. 32: 405, 2010 ; Biotechnol. Bioeng. 103: 148, 2009 ; Metab. Eng. 10: 340, 2008 ; Curr. Opin. Biotechnol. 18: 213, 2007 ). We have also established a novel platform for the production of fuels and chemicals from fatty acid-rich feedstocks by engineering a respiro-fermentative metabolic mode that enables the efficient production of target products in combination with adequate catabolism of FAs. We engineered efficient synthesis of ethanol, butanol, acetate, acetone, isopropanol, succinate, and propionate from fatty acids in bacteria (Rev.-Syst. Biol. 5: 575, 2013 ; Appl. Environ. Microbiol. 76: 5067, 2010 ). Advanced, higher-chain (C ≥ 4) fuels and chemicals are generated from short-chain, 2- or 3-C metabolic intermediates through pathways that require carbon-chain elongation. While our laboratory and others around the world have engineered native carbon-chain elongation pathways, such as the fatty acid biosynthesis pathway, to produce higher-chain molecules like methylketones (J. Industrial Microbiol. Biotechnol. 39: 1703, 2012 ), this pathway suffers from major energy constraints. Motivated in part by these limitations, we recently engineered a functional reversal of the β-oxidation cycle that can be used as a general platform for the synthesis of short-, medium- and long-chain products with structural and functional diversity (Metab. Eng. 28: 202, 2015 ; Appl. Environ. Microbiol. 81: 1406, 2015 ; J. Industrial Microbiol. Biotechnol. 42:465, 2015 ; ACS Synth. Biol. 1: 541, 2012 ; Nature 476: 355, 2011 ). Through a systems-level, quantitative assessment of the metabolic capabilities of the engineered reversal of the β-oxidation cycle, we demonstrated that product synthesis can be coupled to cell growth and achieved at high fluxes, titers and yields (Metab. Eng. 23: 100, 2014 ). The superior capabilities of the β-oxidation reversal, when compared to other pathways used for carbon-chain elongation, originate from its higher energetic efficiency, which is enabled by the use of acetyl-CoA as an extender unit. This engineered β-oxidation reversal is currently being exploited in our laboratory for the production of alcohols, alkanes, and omega-functionalized products.

PROJECTS We have engineered 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

Engineering Metabolism for Chemical production from One-Carbon substrates. 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 (Clomburg, Crumbley, Gonzalez. Science 355, 38, 2017: doi: 10.1126/science.aag0804 ). In order for this potential to be realized, however, significant advances in the performance of C1-metabolizing enzymes, pathways and microorganisms must be achieved. Our current efforts focus on engineering and implementing biological C1 conversion pathways for chemical production. In one approach, we have leveraged the existing C1-utilization pathways of native methanotroph Methylomicrobium buryatense5GB1 for the production of industrially relevant products such as lactate (JIMB 45:379, 2018 ). In an alternative approach, we engineered a synthetic metabolic pathway for C1 conversion to multi-carbon products that is distinctive from and orthogonal to any known metabolic network (Nature Chemical Biology 15 , 900–906, 2019 ). We have prototyped the pathway using a cell-free system with different C1 substrates and showed operation by synthesis of glycolaldehyde, glycolate, ethylene glycol, acetaldehyde, and lactate. We also demonstrated in vivofeasibility through the synthesis of glycolic acid and ethylene glycol by E. coliusing formaldehyde as the sole carbon source. Our work establishes the potential of this synthetic pathway for both bioconversion of C1 feedstocks as well as synthetic methylotrophy and autotrophy.

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 products due to the high cost associated with downstream processing and purification. Furthermore, native metabolic pathways for product synthesis often limit the attainable product titers, rates, and yields due to intrinsic inefficiencies and negative cross-talk between product-forming and growth-sustaining reactions. To address these limitations, we are working on engineering microbial-based platforms for the efficient synthesis of PNPs. This includes a synthetic pathway for the production of isoprenoids (PNAS June 25, 2019 116 (26) 12810-12815) and a PKS-independent platform for the synthesis of polyketide backbones (Manuscript in Review).(PNAS June 25, 2019 116 (26) 12810-12815 ). Our current efforts focus on developing microbial platforms for the synthesis of isoprenoid and polyketide products as well as their derivatives, including compounds like prenylated aromatics (PAs) that are currently sourced from plants. We have used plant enzymes for product synthesis in Escherichia coli, such as the functional expression of a polyketide synthase and olivetolic acid cyclase from Cannabis sativa, which when combined with engineering pathways for precursor generation enabled olivetolic acid production (ACS Synthetic Biology 7: 1886, 2018 ). However, in many cases, such as the integral membrane aromatic prenyltransferases (aPTases) involved in the production of PAs, functional heterologous expression of the plant enzymes in microbial systems can prove a major challenge. We have demonstrated how the use of soluble, bacterial-derived enzymes catalyzing the condensation reaction between a prenyl chain and an aromatic ring can be used in place of plant aPTases to enable the synthesis of PAs in bacteria. Key to our approach was the engineering of soluble aPTases through protein modeling and rational design, resulting in significant improvement to their catalytic efficiency. Expression of engineered aPTases coupled with exogenous addition of aromatic substrates and pyrophosphate supply through an engineered mevalonate pathway enabled the synthesis of an array of PA compounds, including medicinally important cannabigerovarinic, cannabigerolic, and grifolic acids (Biotechnol. Bioeng. doi:10.1002/bit.26932, 2019 ). Finally, we have also engineered non-natural routes for the generation of the prenyl and polyketide moieties used in the synthesis of PAs. This includes a synthetic pathway for the production of isoprenoids and a PKS-independent platform for the synthesis of polyketide backbones (PNAS June 25, 2019 116 (26) 12810-12815 ). These new systems enable the efficient synthesis of isoprenoids, polyketides, and their derivatives, including PAs, in microorganisms.

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.

Full Publication and Citation Details 2025 Zhang, X.; Li, A.; Huang, X.; Guo, S.; Zhang, C.; Gonzalez, R.*; Fei, Q*. Metabolic Engineering of Methanotrophic Bacteria for De Novo Production of Taxadiene from Methane . ACS Synth. Biol. 2025. https://doi.org/10.1021/acssynbio.5c00109 . Liu, H.; Chen, Y.; Li, J.; Zhu, C.; Peng, J.; Gonzalez, R.; Bai, Y.; Tan, Z. Scavenging Intracellular Reactive Oxygen Species to Boost Methanol Assimilation . Chemical Engineering Journal 2025, 516, 164002. https://doi.org/10.1016/j.cej.2025.164002 . Zhu, C.; Chen, Y.; Sun, W.; Li, J.; Liu, H.; Peng, J.; Bai, Y.; Gonzalez, R.; Tan, Z. Repair of DNA and Protein Damages Caused by Formaldehyde Improves Methanol Assimilation . Fundamental Research 2025. https://doi.org/10.1016/j.fmre.2025.05.007. Lee, S. H.; Cirino, P. C.; Gonzalez, R*. Metabolic Engineering of Escherichia Coli for the Utilization of Methylsuccinate, the Product of Methane Activation via Fumarate Addition . Bioresource Technology 2025, 416, 131700. https://doi.org/10.1016/j.biortech.2024.131700. 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 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 (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. 2022 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 RESEARCH PUBLICATIONS

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. The high degree of reduction of carbon atoms in glycerol confers the ability to produce fuels and reduced chemicals at higher yields when compared to the use of carbohydrates. However, this highly reduced nature also results in unique challenges for microorganisms in order to utilize glycerol under fermentative conditions (i.e., absence of external electron acceptors), a metabolic mode essential to fully exploit the high degree of reduction (Clomburg and Gonzalez, 2013 ). Building off our discovery that Escherichia coli, an organism previously thought to require external electron acceptors for glycerol utilization, is able utilize glycerol under fermentative conditions (Dharmadi et al., 2006 ), we have elucidated key pathways and mechanisms critical for the ability of this biotechnology workhorse to ferment glycerol (Gonzalez et al., 2008 ; Murarka et al., 2008 ). Central to this glycerol fermentation ability are: (i) the production of 1,2-propanediol (1,2-PDO) providing a means to consume reducing equivalents generated in the synthesis of cell mass, thus facilitating redox balance, and (ii) the conversion of glycerol to ethanol, through a redox-balanced pathway, fulfilling energy requirements by generating ATP via substrate-level phosphorylation. Furthermore, glycerol dissimilation into glycolytic intermediates under fermentative conditions was determined to be mediated by a type II glycerol dehydrogenase (glyDH-II) and a dihydroxyacetone kinase (DHAK), the former of previously unknown physiological role. The activity of the formate hydrogen-lyase and F0F1-ATPase systems were also found to facilitate the fermentative metabolism of glycerol. Additional key insights into the fermentative metabolism of glycerol by E. coliwere elucidated through a quantitative analysis employing kinetic modeling and metabolic control analysis (MCA). This analysis indicated that glycolytic flux during glycerol fermentation is almost exclusively controlled by the aforementioned glycerol dehydrogenase (encoded by gldA) and dihydroxyacetone kinase (DHAK) (encoded by dhaKLM), and overexpression of these genes was shown to significantly increase glycerol utilization flux under anaerobic conditions (Cintolesi et al., 2012 ). Furthermore, we have established a comprehensive understanding of glycerol utilization under microaerobic conditions in which availability of low amounts of oxygen enables redox balance, in the absence of 1,2-PDO synthesis, while preserving the ability to synthesize reduced products (Durnin et al., 2009 ). These findings have provided a platform for implementing metabolic engineering strategies aimed at the conversion of glycerol into a range of value added products. Targeted production of specific fuel and chemical compounds has utilized combinatorial engineering of glycerol dissimilation pathways and downstream product synthesis pathways. The overexpression of key glycerol utilization pathways to increase the rate of glycerol dissimilation or the availability of specific intermediate metabolites, integrated with specific product synthesis pathways provides overall metabolic engineering strategies for individual product synthesis uniquely tailored to exploiting glycerol as a carbon source. Using this approach, we have demonstrated the high titer production of ethanol (Cintolesi et al., 2012 ; Durnin et al., 2009 ; Yazdani and Gonzalez, 2008 ), 1,2-PDO (Clomburg and Gonzalez, 2011 ), succinic acid (Blankschien et al., 2010 ), D-lactic acid (Mazumdar et al., 2010 ), and L-lactic acid (Mazumdar et al., 2013 ) from glycerol. We are also continually expanding our knowledge base on and use of glycerol as a carbon source for fuel and chemical production, and through the development of novel pathways for advanced fuels and chemicals (i.e. longer carbon chain length) we have demonstrated the synthesis of varying chain length fatty acids (Clomburg et al., 2012 ; Vick et al., 2015 ; Kim et al., 2015 ), n-alcohols (Kim et al., 2015 ), unsaturated carboxylic acids (Kim et al., 2016 ), w-hydroxyacids (Clomburg et al., 2015 ; Cheong et al., 2016 ), and dicarboxylic acids (Clomburg et al., 2015 ; Cheong et al., 2016 ) among other compounds using glycerol as a carbon source. These and continuing efforts are key to diversifying the range of products that can be produced from glycerol, capitalizing on this abundant, low-price feedstock.

Β-OXIDATION REVERSAL AS A PLATFORM FOR SMALL MOLECULE BIOSYNTHESIS Bio-based renewable chemical production is becoming an increasingly important process for the production of industrial bulk and specialty chemicals due to concerns over finite nature of petroleum and other fossil-based resources, as well as the potential net greenhouse gas emissions resulting from the use of these feedstocks, which are thought to have an adverse effect on global climate. Potential advantages related to process safety and green chemistry as well as opportunities to develop value added chemicals not readily obtainable via traditional petrochemical processes are also propelling these trends. Feedstocks for current biocatalytic processes are either C5-C6 sugars, obtained from hydrolytic degradation of starch, cellulose, and hemicellulose, or oils and fats extracted from vegetables and animals. Extensive studies have focused on the development of biochemical pathways to convert sugars into fuels and chemicals. Some products such as hydrogen, ethanol, lactic acid, and succinic acid can be produced directly or be readily synthesized from common compounds within central metabolism. More elaborate pathways such as the fatty acid biosynthesis, isoprenoid, polyketide, and shikimate pathways and more recently β-oxidation reversal (r-BOX) pathway (Dellomonaco et al., 2011 ) have also been employed to produce various value-added chemicals ranging from antibiotics to jet fuels. The r-BOX pathway is usually initiated by thiolase-catalyzed non-decarboxylative Claisen condensation between two acetyl-CoAs. One complete cycle of this pathway consists of four core enzymes: (i) a thiolase (THL) that catalyzes the condensation of acetyl-CoA, which serves as the extender unit for carbon chain elongation, with an acyl-CoA, which serves as the primer, yielding a 3-ketoacyl-CoA; (ii) a hydroxyacyl-CoA dehydrogenase that reduces the 3-ketoacyl-CoA to 3-hydroxyacyl-CoA; (iii) an enoyl-CoA dehydratase that converts the 3-hydroxyacyl-CoA to trans-2-enoyl-CoA; (iv) a trans-enoyl-CoA reductase that generates acyl-CoA two carbon longer than the initial acyl-CoA from enoyl-CoA. This r-BOX platform can utilize fatty acid oxidation pathways to obtain various chemicals. These pathways contain enzymes that allow for the selective functionalization of fatty acids, such as generation of C-C double bonds, additional reactions on the C-C double bond, and functionalization of C-H bond in the alkyl chain leading to microbial synthesis of short-, and medium-chain length aliphatic fatty acids/alcohol, and unsaturated α,β-carboxylic acids (Clomburg et al., 2012 ) (Cintolesi et al., 2014 ) (Kim et al., 2015 ) (Kim et al., 2016 ). Further functionalization can be achieved through usage of different ω and ω-1-functionalized acyl-CoAs as primers and α-functionalized acyl-CoAs as extender units instead of acetyl-CoA, or integration of carbon chain functionalization pathway, such as ω-oxidation pathway, after termination of r-BOX cycle, leading to microbial synthesis of dicarboxylic acids, ω-hydroxy acids, phenylakanoic acids and methyl-branched fatty acids (Clomburg et al., 2015 ) (Cheong et al., 2016 ). Those chemicals can be used for the manufacture of products such as fuels, paints, food additives, resins, foams, lubricants, plasticizers, and cosmetics. Bio-based chemicals, however, suffer from economic competition from much cheaper counterparts derived from conventional fossil-based routes. Nevertheless, 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. While the r-BOX platform is expected to play a crucial role in this effort, one of the major challenges is the selective production of functionalized chemicals with a specific carbon chain length. The r-BOX uses an iterative mechanism to elongate alkyl chains, which in turn can lead to the production of molecules with the same functional groups but various carbon chain lengths. The synthesis of a single product with a specific chain length (as opposed to a mixture of products with various chain lengths) will require the engineering of enzymes with high chain-length specificity, including thiolases, thioesterases, and acyl-CoA or acyl-ACP reductases. Moreover, the efficient operation of platforms like the β-oxidation reversal will also require the engineering of pathways involved in central metabolism to achieve a balanced supply of primers, extender units, and reducing equivalents from a single carbon source. In addition, engineering of pathways will be also required for further diversification of products of the platform.

RAMON GONZALEZ Dr. Ramon Gonzalez is the Chief Scientific Officer of MojiaBio (a global biomanufacturing company) and the President of the Society for Industrial Microbiology & Biotechnology (SIMB, founded in 1949). He is an elected Fellow of the American Association for the Advancement of Science (AAAS) and the American Institute for Medical and Biological Engineering (AIMBE). Dr. Gonzalez’s career has spanned the academic, private, and public sectors. Most of his academic work was conducted at Rice University, where he led the laboratory for Metabolic Engineering and Biomanufacturing and rose through the ranks from Assistant Professor to Full Professor. While at Rice, he was the founding director of the Advanced Biomanufacturing Initiative and served as Director of the Energy and Environment Initiative. More recently, Dr. Gonzalez was a Professor and Florida World Class Scholar in the Department of Chemical, Biological and Materials Engineering at the University of South Florida. In addition to his role as Editor-in-Chief of the Journal of Industrial Microbiology & Biotechnology (JIMB) from 2015 to 2023, he has served on the Editorial Boards of Science, Biotechnology Journal, Applied and Environmental Microbiology, Applied Biochemistry and Biotechnology, Food Biotechnology. Dr. Gonzalez also served as Program Director with the Advanced Research Projects Agency-Energy (ARPA-E) of the U.S. Department of Energy and with the U.S. National Science Foundation, as well as on the Board of Directors of SIMB. Dr. Gonzalez has published over 100 papers in prestigious scientific journals, including Nature and its portfolio Journals (Nature Biotechnology , Nature Catalysis , Nature Metabolism , Nature Chemical Biology , Nature Communications ), PNAS , and Science . He is the lead inventor in 25 patents/patent applications and founded/co-founded Glycos Biotechnologies, Creo Ingredients, RBN Bio, and C1Plus Bio. He has advised major industrial bio and Fortune 500 companies and is currently a member of the scientific advisory boards of several companies and research institutions. Dr. Gonzalez has received numerous recognitions, including, Discovery Series Lecture (BioDesign Institute, Arizona State University), Tiangong Forum Lecture (TIB-CAS, China), ‘Inspiring Wisdom’ Distinguished Lecture (SKMML, SJTU, China), AIChE Division 15c Plenary Lecture, ASM Distinguished Lecturer, SDA/NBB Glycerine Innovation Research Award, and NSF CAREER Award. Dr. Gonzalez obtained a Ph.D. in Chemical Engineering from the University of Chile, an M.S. in Biochemical Engineering from the Pontifical Catholic University of Valparaíso (Chile), and a B.S. in Chemical Engineering from the Central University “Marta Abreu” of Las Villas (Cuba). Publications Professional Experience 2018 to 2024 – Professor, Florida 21st Century World Class Scholar, Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, Florida 2015 to 2023 – Editor-in-Chief, Journal of Industrial Microbiology & Biotechnology 2014 to 2018 – Professor, Department of Chemical & Biomolecular Engineering and Department of Bioengineering, Rice University, Houston, Texas 2016 to 2018 – Founding Director, Advanced Biomanufacturing Initiative (iBIO), Rice University, Houston, Texas 2014 to 2016 – Director, Energy and Environment Initiative (EEi), Rice University, Houston, Texas 2012 to 2015 – Program Director, Advanced Research Projects Agency—Energy (ARPA-E), U.S. Department of Energy (DOE), Washington D.C. 2011 to 2014 – Associate Professor, Department of Chemical & Biomolecular Engineering and Department of Bioengineering, Rice University, Houston, Texas 2007 to 2011 – Assistant Professor, Department of Bioengineering, Rice University, Houston, Texas 2005 to 2011 – William W. Akers Assistant Professor, Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 2002 to 2005 – Assistant Professor, Departments of Chemical & Biological Engineering and Food Science & Human Nutrition, Iowa State University, Ames, Iowa 2001 to 2002 – Postdoctoral Associate, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 1994 to 1995 – Process Engineer, Marcelo Salado Sugar Mill (Formerly, Reforma Sugar Mill), MINAZ (Cuba's Sugar Ministry), Caibarien, Cuba 1993 to 1996 – Research Associate and Lecturer, Center for Processes Analysis, Department of Chemical Engineering, Central University of Las Villas, Santa Clara, Cuba Education 2001 – Ph.D., Chemical Engineering, University of Chile 1999 – M.Sc., Biochemical Engineering, Catholic University of Valparaiso, Chile 1993 – B.Sc., Chemical Engineering, Central University of Las Villas, Cuba CONTACT INFORMATION ENB 118 | 4202 E Fowler Ave | Tampa, FL 33620 ramongonzale@usf.edu (813)-974-4653

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