Browsing by Author "Clomburg, James M."

Now showing 1 - 8 of 8
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    Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals
    (Cell Press, 2013-01) Clomburg, James M.; Gonzalez, Ramon
    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. This review focuses on current engineering efforts as well as the challenges involved in the utilization of glycerol as a carbon source for the production of fuels and chemicals.
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    Efficient synthesis of L-lactic acid from glycerol by metabolically engineered Escherichia coli
    (BioMed Central, 2013) Mazumdar, Suman; Blankschien, Matthew D.; Clomburg, James M.; Gonzalez, Ramon
    Due to its abundance and low-price, glycerol has become an attractive carbon source for the industrial production of value-added fuels and chemicals. This work reports the engineering of E. coli for the efficient conversion of glycerol into L-lactic acid(L-lactate). Escherichia coli strains have previously been metabolically engineered for the microaerobic production of D-lactic acid from glycerol in defined media by disrupting genes that minimize the synthesis of succinate, acetate, and ethanol, and also overexpressing the respiratory route of glycerol dissimilation (GlpK/GlpD). Here, further rounds of rationale design were performed on these strains for the homofermentative production of L-lactate, not normally produced in E. coli. Specifically, L-lactate production was enabled by: 1), replacing the native D-lactate specific dehydrogenase with Streptococcus bovis L-lactate dehydrogenase (L-LDH), 2) blocking the methylglyoxal bypass pathways to avoid the synthesis of a racemic mixture of D- and L-lactate and prevent the accumulation of toxic intermediate, methylglyoxal, and 3) the native aerobic L-lactate dehydrogenase was blocked to prevent the undesired utilization of L-lactate. The engineered strain produced 50 g/L of L-lactate from 56 g/L of crude glycerol at a yield 93% of the theoretical maximum and with high optical (99.9%) and chemical (97%) purity. This study demonstrates the efficient conversion of glycerol to L-lactate, a microbial process that had not been reported in the literature prior to our work. The engineered biocatalysts produced L-lactate from crude glycerol in defined minimal salts medium at high chemical and optical purity.
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    Functionalized carboxylic acids and alcohols by reverse fatty acid oxidation in engineered microbes
    (2018-06-12) Gonzalez, Ramon; Clomburg, James M.; Rice University; United States Patent and Trademark Office
    Bacteria that run the beta oxidation cycle in reverse anabolic direction are provided, along with many novel primers to start the reverse cycle, pathways to make such primers, and a large variety of products produced thereby. Methods for making desired product by using such primers in the reverse pathway are also disclosed.
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    In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli
    (Wiley, 2022) Clomburg, James M.; Cintolesi, Angela; Gonzalez, Ramon
    Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H2, complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H2 evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H2 evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.
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    Synthesis of isoprenoids and derivatives
    (2021-06-29) Gonzalez, Ramon; Clomburg, James M.; Cheong, Seokjung; Rice University; United States Patent and Trademark Office
    This disclosure generally relates to the use of enzyme combinations or recombinant microbes comprising same to make isoprenoid precursors, isoprenoids and derivatives thereof including prenylated aromatic compounds. Novel metabolic pathways exploiting Claisen, aldol, and acyioin condensations are used instead of the natural mevalonate (MVA) pathway or 1-deoxy-d-xylulose 5-phosphate (DXP) pathways for generating isoprenoid precursors such as isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), and geranyl pyrophosphate (GPP). These pathways have the potential for better carbon and or energy efficiency than native pathways. Both decarboxylative and non-carboxylative condensations are utilized, enabling product synthesis from a number of different starting compounds. These condensation reactions serve as a platform for the synthesis of isoprenoid precursors when utilized in combination with a variety of metabolic pathways and enzymes for carbon rearrangement and the addition/removal of functional groups. Isoprenoid alcohols are key intermediary products for the production of isoprenoid precursors in these novel synthetic metabolic pathways.
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    Type II fatty acid synthesis enzymes in reverse β-oxidation
    (2019-10-22) Gonzalez, Ramon; Clomburg, James M.; Vick, Jacob E.; Rice University; United States Patent and Trademark Office
    This disclosure describes enzymes from the type II (a discrete set of enzymes) fatty acid synthesis (“FAS”) pathway that can be used in combination with thiolases to operate a functional reversal of the β-oxidation cycle. A combination of thiolases with one or more of 3-oxoacyl-[acyl-carrier-protein] reductase (FabG, others), 3-hydroxyacyl-[acp] dehydratase (FabA, FabZ, others), and enoyl-[acyl-carrier-protein] reductase (FabI, FabK, FabL, FabV, others) yields a functional reversal of the β-oxidation cycle. If only one or two enzymes are used, the remaining enzymes will be traditional beta oxidation enzymes. Once this cycle is coupled with the appropriate priming and termination pathways, the production of carboxylic acids, alcohols, hydrocarbons, amines and their α-, β-, and ω-functionalized derivatives from renewable carbon sources can be achieved.
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    Understanding Fermentative Glycerol Metabolism and its Application for the Production of Fuels and Chemicals
    (2012-09-05) Clomburg, James M.; Gonzalez, Ramon; Zygourakis, Kyriacos; Bennett, George N.
    Due to its availability, low-price, and higher degree of reduction than lignocellulosic sugars, glycerol has become an attractive carbon source for the production of fuels and reduced chemicals. However, this high degree of reduction of carbon atoms in glycerol also results in significant challenges in regard to its utilization under fermentative conditions. Therefore, in order to unlock the full potential of microorganisms for the fermentative conversion of glycerol into fuels and chemicals, a detailed understanding of the anaerobic fermentation of glycerol is required. The work presented here highlights a comprehensive experimental investigation into fermentative glycerol metabolism in Escherichia coli, which has elucidated several key pathways and mechanisms. The activity of both the fermentative and respiratory glycerol dissimilation pathways was found to be important for maximum glycerol utilization, a consequence of the metabolic cycle and downstream effects created by the essential involvement of PEP-dependent dihydroxyacetone kinase (DHAK) in the fermentative glycerol dissimilation pathway. The decoupling of this cycle is of central importance during fermentative glycerol metabolism, and while multiple decoupling mechanisms were identified, their relative inefficiencies dictated not only their level of involvement, but also implicated the activity of other pathways/enzymes, including fumarate reductase and pyruvate kinase. The central role of the PEP-dependent DHAK, an enzyme whose transcription was found to be regulated by the cyclic adenosine monophosphate (cAMP) receptor protein (CRP)-cAMP complex, was also tied to the importance of multiple fructose 1,6-bisphosphotases (FBPases) encoded by fbp, glpX, and yggF. The activity of these FBPases, and as a result the levels of fructose 1,6-bisphosphate, a key regulatory compound, appear to also play a role in the involvement of several other enzymes during fermentative glycerol metabolism including PEP carboxykinase. Using this improved understanding of fermentative glycerol metabolism as a platform, E. coli has been engineered to produce high yields and titers of ethanol (19.8 g/L, 0.46 g/g), co-produced along with hydrogen, and 1,2-propanediol (5.6 g/L, 0.21 g/g) from glycerol, demonstrating its potential as a carbon source for the production of fuels and reduced chemicals.
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    Volcano-shape glycerol oxidation activity of palladium-decorated gold nanoparticles
    (Royal Society of Chemistry, 2014) Zhao, Zhun; Arentz, Joni; Pretzer, Lori A.; Limpornpipat, Pongsak; Clomburg, James M.; Gonzalez, Ramon; Schweitzer, Neil M.; Wu, Tianpin; Miller, Jeffrey T.; Wong, Michael S.
    Bimetallic PdAu catalysts are more active than monometallic ones for the selective oxidation of alcohols, but the reasons for improvement remain insufficiently detailed. A metal-on-metal material can probe the structure–catalysis relationship more clearly than conventionally prepared bimetallics. In this study, Pd-on-Au nanoparticles with variable Pd surface coverages (sc%) ranging from 10 to 300 sc% were synthesized and immobilized onto carbon (Pd-on-Au/C). Tested for glycerol oxidation at 60 °C, pH 13.5, and 1 atm under flowing oxygen, the series of Pd-on-Au/C materials showed volcano-shape catalytic activity dependence on Pd surface coverage. Increasing surface coverage led to higher catalytic activity, such that initial turnover frequency (TOF) reached a maximum of ̴6000 h−1 at 80 sc%. Activity decreased above 80 sc% mostly due to catalyst deactivation. Pd-on-Au/C at 80 sc% was >10 times more active than monometallic Au/C and Pd/C, with both exhibiting TOF values less than [similar]500 h−1. Glyceric acid was the dominant primary reaction product for all compositions, with its zero-conversion selectivity varying monotonically as a function of Pd surface coverage. Glyceric acid yield from Pd-on-Au/C (80 sc%) was 42%, almost double the yields from Au/C and Pd/C (16% and 22%, respectively). Ex situ X-ray absorption near edge structure analysis of two Pd-on-Au/C materials with comparable activities (60 sc% and 150 sc%) showed that the former had less oxidized Pd ensembles than the latter, and that both catalysts were less oxidized compared to Pd/C. That Au stabilizes the metallic state of surface Pd atoms may be responsible for activity enhancement observed in other PdAu-catalyzed oxidation reactions. Decorating a Au surface with Pd generates a catalyst that has the deactivation resistance of Au, the higher glyceric acid selectivity of Pd, and the synergistically higher activities that neither metal has.