Abstract: Methods for increasing carbon-based chemical product yield in an organism by perturbing redox balance in an organism as well as nonnaturally occurring organisms with perturbed redox balance and methods for their use in producing carbon-based chemical products are provided.

Abstract: Provided herein are methods for generating cellular biomass in continuous aerobic fermentation systems. The biomass yield, and the concentration of polyhydroxyalkanoate within the biomass, are each directed to advantageous levels by operating the continuous fermentation system under particular nutrient limitation conditions. Also provided are biomass produced using the provided methods, and animal feed compositions including the provided biomass.

Abstract: Methods and materials for the production of hydroxy fatty acid anions, including 2-hydroxyisobutyric acid (2-HIBA), and/or derivatives thereof and compounds related thereto are provided. Also provided are products produced in accordance with these methods and materials.

Abstract: Methods and materials for the production of compounds involved in the TCA cycle, and/or derivatives thereof and/or compounds related thereto are provided. Also provided are products produced in accordance with these methods and materials.

Abstract: This document describes biochemical pathways for producing pimeloyl-CoA using a polypeptide having the enzymatic activity of a hydroperoxide lyase to form non-3-enal and 9-oxononanoate from 9-hydroxyperoxyoctadec-10,12-dienoate. Non-3-enal and 9-oxononanoate can be enzymatically converted to pimeloyl-CoA or a salt thereof using one or more polypeptides having the activity of a dehydrogenase, a CoA ligase, an isomerase, a reductase, a thioesterase, a monooxygenase, a hydratase, and/or a thiolase. Pimeloyl-CoA can be enzymatically converted to pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, or 1,7-heptanediol, or corresponding salts thereof. This document also describes recombinant microorganisms producing pimeloyl-CoA, as well as pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, and 1,7-heptanediol, or corresponding salts thereof.

Abstract: This disclosure relates to strategies for in vivo production of certain carbon-based products, for example, aminated aliphatic compounds having a carbon chain length of C5-C19.

Abstract: Systems, networks, methods, compositions and recombinant hosts for biosynthesizing hydrocarbons from a feedstock, such as gas, are provided.

Abstract: Methods for increasing carbon-based chemical product yield in an organism by genetically modifying one or more genes involved in a stringent response and/or in a regulatory network, nonnaturally occurring organisms having increased carbon-based chemical product yield, and methods for use in production of carbon-based chemical products are provided.

Abstract: Methods for increasing carbon-based chemical product yield in an organism by increasing carbon uptake and/or altering a pathway to or from an overflow metabolite in the organism, nonnaturally occurring organisms having increased carbon-based chemical product yield with increased carbon uptake and/or an altered pathway to or from an overflow metabolite, and methods for producing a carbon-based chemical product with these organisms are provided.

Abstract: Provided herein are novel, synthetic polypeptides having, for example, acyl-acyl carrier protein (ACP) thioesterase (TE) activity, including polypeptides that convert pimeloyl-ACP to pimelic acid. In some aspects, the synthetic polypeptides have advantageous enzymatic activity and/or improved substrate specificity relative to a wild type acyl-ACP TE.

Abstract: Disclosed are methods for regulating biosynthesis of at least one of pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, 7-aminoheptanoland 1,7-heptanediol (C7 building blocks) using a pathway having a pimeloyl-ACP intermediate, the method including the step of downregulating the activity of BioF. Also disclosed are recombinant hosts by fermentation in which the above methods are performed. Further disclosed are recombinant hosts for producing pimeloyl-ACP, the recombinant host including a deletion of a bioF gene.

Abstract: Nonnaturally occurring organisms exhibiting improved carbon utilization and methods for production and use of these nonnaturally occurring organisms in chemical production from carbon containing feedstocks are provided.

Abstract: This document describes biochemical pathways for producing a difunctional product having an odd number of carbon atoms in vitro or in a recombinant host, or salts or derivatives thereof, by forming two terminal functional groups selected from carboxyl, amine, formyl, and hydroxyl groups in an aliphatic carbon chain backbone having an odd number of carbon atoms synthesized from (i) acetyl-CoA and propanedioyl-CoA via one or more cycles of methyl ester shielded carbon chain elongation or (ii) propanedioyl-[acp] via one or more cycles of methyl ester shielded carbon chain elongation. The biochemical pathways and metabolic engineering and cultivation strategies described herein rely on enzymes or homologs accepting methyl ester shielded aliphatic carbon chain backbones and maintaining the methyl ester shield for at least one further enzymatic step following one or more cycles of methyl ester shielded carbon chain elongation.

Abstract: This document describes biochemical pathways for producing pimeloyl-CoA using a polypeptide having the enzymatic activity of a hydroperoxide lyase to form non-3-enal and 9-oxononanoate from 9-hydroxyperoxyoctadec-10,12-dienoate. Non-3-enal and 9-oxononanoate can be enzymatically converted to pimeloyl-CoA or a salt thereof using one or more polypeptides having the activity of a dehydrogenase, a CoA ligase, an isomerase, a reductase, a thioesterase, a monooxygenase, a hydratase, and/or a thiolase. Pimeloyl-CoA can be enzymatically converted to pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, or 1,7-heptanediol, or corresponding salts thereof. This document also describes recombinant microorganisms producing pimeloyl-CoA, as well as pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, and 1,7-heptanediol, or corresponding salts thereof.

Abstract: Nonnaturally occurring organisms exhibiting improved carbon utilization and methods for production and use of these nonnaturally occurring organisms in chemical production from carbon containing feedstocks are provided.

Abstract: Methods and compositions for synthesizing dienes and derivative thereof, such as isoprene, in Cupriavidus necator are provided.

Abstract: The disclosure relates to polypeptides having carboxylic acid reductase (CAR) activity, including enzymes that catalyse the irreversible reduction of carboxylic acids, such as pimelic acid and adipic acid, to their respective semialdehydes. The enzymes have been engineered to have higher activity over a corresponding wild type enzyme. Provided herein are novel polypeptides and uses thereof related to the same.

Abstract: Provided herein are novel, synthetic polypeptides having, for example, acyl-acyl carrier protein (ACP) thioesterase (TE) activity, including polypeptides that convert pimeloyl-ACP to pimelic acid. In some aspects, the synthetic polypeptides have advantageous enzymatic activity and/or improved substrate specificity relative to a wild type acyl-ACP TE.

Abstract: Provided herein are methods for increasing the yield of an extracellular product synthesized by an organism cultured in a continuous aerobic fermentation system. The extracellular product yield is increased through the use of an organism modified to decreased production of polyhydroxyalkanoate, to increase production of the extracellular product, and to include promoters that can be inducible in response to nutrient limitation conditions. The extracellular product yield is also increased by operating the continuous fermentation system under particular nutrient limitation conditions. Also provided are non-naturally occurring organisms that have been modified for use with the provided methods, and extracellular products made using the provided methods.

Abstract: This disclosure relates to strategies for in vivo production of certain carbon-based products, for example, aminated aliphatic compounds having a carbon chain length of C5-C19.