Patents by Inventor James M. CLOMBURG
James M. CLOMBURG has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20240182932Abstract: 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 acyloin 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.Type: ApplicationFiled: June 7, 2023Publication date: June 6, 2024Applicant: William Marsh Rice UniversityInventors: Ramon GONZALEZ, James M. CLOMBURG, Seokjung CHEONG
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Patent number: 11697830Abstract: The use of microorganisms to make alpha-functionalized chemicals and fuels, (e.g. alpha-functionalized carboxylic acids, alcohols, hydrocarbons, amines, and their beta-, and omega-functionalized derivatives), by utilizing an iterative carbon chain elongation pathway that uses functionalized extender units. The core enzymes in the pathway include thiolase, dehydrogenase, dehydratase and reductase. Native or engineered thiolases catalyze the condensation of either unsubstituted or functionalized acyl-CoA primers with an alpha-functionalized acetyl-CoA as the extender unit to generate alpha-functionalized ?-keto acyl-CoA. Dehydrogenase converts alpha-functionalized ?-keto acyl-CoA to alpha-functionalized ?-hydroxy acyl-CoA. Dehydratase converts alpha-functionalized ?-hydroxy acyl-CoA to alpha-functionalized enoyl-CoA. Reductase converts alpha-functionalized enoyl-CoA to alpha-functionalized acyl-CoA. The platform can be operated in an iterative manner (i.e.Type: GrantFiled: March 13, 2020Date of Patent: July 11, 2023Inventors: Ramon Gonzalez, James M. Clomburg, Seokjung Cheong
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Publication number: 20220251613Abstract: Methods of using microorganisms to make chemicals and fuels, including carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives are described. Native or engineered thiolases are used condense a growing acyl-ACP and acetyl-ACP in combination with type II fatty acid synthesis. The resulting fatty acid biosynthesis cycle has an ATP yield analogous to the functional reverse ?-oxidation cycle.Type: ApplicationFiled: April 5, 2022Publication date: August 11, 2022Inventors: Ramon GONZALEZ, James M. CLOMBURG
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Patent number: 11319562Abstract: Methods of using microorganisms to make chemicals and fuels, including carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives are described. Native or engineered thiolases are used condense a growing acyl-ACP and acetyl-ACP in combination with type II fatty acid synthesis. The resulting fatty acid biosynthesis cycle has an ATP yield analogous to the functional reverse ?-oxidation cycle.Type: GrantFiled: March 11, 2020Date of Patent: May 3, 2022Inventors: Ramon Gonzalez, James M. Clomburg
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Patent number: 11046978Abstract: 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.Type: GrantFiled: March 15, 2017Date of Patent: June 29, 2021Assignee: WILLIAM MARSH RICE UNIVERSITYInventors: Ramon Gonzalez, James M. Clomburg, Seokjung Cheong
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Publication number: 20200325502Abstract: The use of microorganisms to make alpha-functionalized chemicals and fuels, (e.g. alpha-functionalized carboxylic acids, alcohols, hydrocarbons, amines, and their beta-, and omega-functionalized derivatives), by utilizing an iterative carbon chain elongation pathway that uses functionalized extender units. The core enzymes in the pathway include thiolase, dehydrogenase, dehydratase and reductase. Native or engineered thiolases catalyze the condensation of either unsubstituted or functionalized acyl-CoA primers with an alpha-functionalized acetyl-CoA as the extender unit to generate alpha-functionalized ?-keto acyl-CoA. Dehydrogenase converts alpha-functionalized ?-keto acyl-CoA to alpha-functionalized ?-hydroxy acyl-CoA. Dehydratase converts alpha-functionalized ?-hydroxy acyl-CoA to alpha-functionalized enoyl-CoA. Reductase converts alpha-functionalized enoyl-CoA to alpha-functionalized acyl-CoA. The platform can be operated in an iterative manner (i.e.Type: ApplicationFiled: March 13, 2020Publication date: October 15, 2020Inventors: Ramon GONZALEZ, James M. CLOMBURG, Seokjung CHEONG
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Publication number: 20200277638Abstract: Methods of using microorganisms to make chemicals and fuels, including carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives are described. Native or engineered thiolases are used condense a growing acyl-ACP and acetyl-ACP in combination with type II fatty acid synthesis. The resulting fatty acid biosynthesis cycle has an ATP yield analogous to the functional reverse ?-oxidation cycle.Type: ApplicationFiled: March 11, 2020Publication date: September 3, 2020Inventors: Ramon GONZALEZ, James M. CLOMBURG
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Publication number: 20190352679Abstract: 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.Type: ApplicationFiled: March 15, 2017Publication date: November 21, 2019Inventors: Ramon GONZALEZ, James M. CLOMBURG, Seokjung CHEONG
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Patent number: 10450593Abstract: 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 ?-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 ?-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 ?-, ?-, and ?-functionalized derivatives from renewable carbon sources can be achieved.Type: GrantFiled: January 26, 2015Date of Patent: October 22, 2019Assignee: William Marsh Rice UniversityInventors: Ramon Gonzalez, James M. Clomburg, Jacob E. Vick
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Publication number: 20190002848Abstract: This disclosure generally relates to the use of microorganisms to make various functionalized polyketides through polyketoacyl-CoA thiolase-catalyzed non-decarboxylative condensation reactions instead of decarboxylative reactions catalyzed by polyketide synthases. Native or engineered polyketoacyl-CoA thiolases catalyze the non-decarboxylative Claisen condensation in an iterative manner (i.e. multiple rounds) between two either unsubstituted or functionalized ketoacyl-CoAs (and polyketoacyl-CoAs) serving as the primers and acyl-CoAs serving as the extender unit to generate (and elongate) polyketoacyl-CoAs. Before the next round of polyketoacyl-CoA thiolase reaction, the ?-keto group of the polyketide chain of polyketoacyl-CoA can be reduced and modified step-wise by 3-OH-polyketoacyl-CoA dehydrogenase or polyketoenoyl-CoA hydratase or polyketoenoyl-CoA reductase. Dehydrogenase converts the ?-keto group to ?-hydroxy group. Hydratase converts the ?-hydroxy group to ?-?-double-bond.Type: ApplicationFiled: August 1, 2016Publication date: January 3, 2019Inventors: Ramon GONZALEZ, Seokjung CHEONG, James M. CLOMBURG
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Patent number: 9994881Abstract: 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.Type: GrantFiled: March 6, 2014Date of Patent: June 12, 2018Assignee: William Marsh Rice UniversityInventors: Ramon Gonzalez, James M. Clomburg
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Publication number: 20180142273Abstract: The use of microorganisms to make alpha-functionalized chemicals and fuels, (e.g. alpha-functionalized carboxylic acids, alcohols, hydrocarbons, amines, and their beta-, and omega-functionalized derivatives), by utilizing an iterative carbon chain elongation pathway that uses functionalized extender units. The core enzymes in the pathway include thiolase, dehydrogenase, dehydratase and reductase. Native or engineered thiolases catalyze the condensation of either unsubstituted or functionalized acyl-CoA primers with an alpha-functionalized acetyl-CoA as the extender unit to generate alpha-functionalized ?-keto acyl-CoA. Dehydrogenase converts alpha-functionalized ?-keto acyl-CoA to alpha-functionalized ?-hydroxy acyl-CoA. Dehydratase converts alpha-functionalized ?-hydroxy acyl-CoA to alpha-functionalized enoyl-CoA. Reductase converts alpha-functionalized enoyl-CoA to alpha-functionalized acyl-CoA. The platform can be operated in an iterative manner (i.e.Type: ApplicationFiled: April 15, 2016Publication date: May 24, 2018Inventors: Ramon GONZALEZ, James M. CLOMBURG, Seokjung CHEONG
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Publication number: 20180135059Abstract: The use of microorganisms to make omega- and/or omega-l-functionalized products through an iterative carbon chain elongation pathway that we call a reverse beta oxidation pathway. The pathway uses omega-functionalized CoA thioesters as primers and acetyl-CoA as the extender unit in a non-decarboxylative Claisen condensation, and then uses beta oxidation or fatty acid synthesis enzymes to complete the cycle, via reductase, dehydratase and reductase reactions. Various termination enzymes that act on the functionalized beta-keto acyl-CoA intermediates of the pathway and produce omega or omega-1 functionalized products. The action of termination enzymes on such intermediates yield a large variety of products.Type: ApplicationFiled: October 16, 2017Publication date: May 17, 2018Inventors: Ramon GONZALEZ, Seokjung CHEONG, James M. CLOMBURG
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Publication number: 20180127730Abstract: Methods of using microorganisms to make chemicals and fuels, including carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives are described. Native or engineered thiolases are used condense a growing acyl-ACP and acetyl-ACP in combination with type II fatty acid synthesis. The resulting fatty acid biosynthesis cycle has an ATP yield analogous to the functional reverse ?-oxidation cycle.Type: ApplicationFiled: April 13, 2016Publication date: May 10, 2018Inventors: Ramon GONZALEZ, James M. CLOMBURG
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Publication number: 20160340699Abstract: 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 ?-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 ?-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 ?-, ?-, and ?-functionalized derivatives from renewable carbon sources can be achieved.Type: ApplicationFiled: January 26, 2015Publication date: November 24, 2016Inventors: Ramon Gonzalez, James M. CLOMBURG, Jacob E. VICK
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Publication number: 20140273110Abstract: 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.Type: ApplicationFiled: March 6, 2014Publication date: September 18, 2014Applicant: William Marsh Rice UniversityInventors: Ramon GONZALEZ, James M. CLOMBURG