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(12) Patent Application Publication (10) Pub. No.: US 2017/0101638 A1 Liao Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2017/0101638 A1 Liao Et Al US 201701 01638A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2017/0101638 A1 Liao et al. (43) Pub. Date: Apr. 13, 2017 (54) ACETYL-COA CARBOXYLASES (60) Provisional application No. 61/852.387, filed on Mar. 15, 2013. (71) Applicant: Cargill, Incorporated, Wayzata, MN (US) (72) Inventors: Hans Liao, Superior, CO (US); Publication Classification Christopher Patrick Mercogliano, Minneapolis, MN (US); Travis Robert (51) Int. Cl. Wolter, Denver, CO (US); Michael Tai CI2N 9/00 (2006.01) Man Louie, Broomfield, CO (US); (52) U.S. Cl. Wendy Kathleen Ribble, Arvada, CO CPC ........ CI2N 9/93 (2013.01); C12Y 604/01002 (US); Tanya E. W. Lipscomb, Boulder, (2013.01) CO (US); Eileen Colie Spindler, Lafayette, CO (US); Michael D. Lynch, Durham, NC (US) (57) ABSTRACT (21) Appl. No.: 15/269,382 (22) Filed: Sep. 19, 2016 The present invention provides various combinations of genetic modifications to a transformed host cell that provide Related U.S. Application Data increase conversion of carbon to a chemical product. The (63) Continuation of application No. 14/215,379, filed on present invention also provides methods of fermentation and Mar. 17, 2014, now Pat. No. 9,447,438. methods of making various chemical products. Patent Application Publication US 2017/0101638A1 ['OIH Patent Application Publication US 2017/0101638A1 dH-8.OLEICTÄHEGIT\/II/NESHIV/NOTVINHONOISHEIANOO Z*OIH Patent Application Publication US 2017/0101638A1 vo)-?K1938 US 2017/0101638A1 (Oluod 96) A-A ow Patent Application Publication Apr. 13, 2017. Sheet 5 of 9 US 2017/0101638A1 Patent Application Publication Apr. 13, 2017. Sheet 6 of 9 US 2017/0101638A1 o 2 t O S. O S. d \d 5. fnN CD O c.N U5 O O T hue S. 2 o E C C C C C C C. O O. O. O. O. O. O. n O do to V fa u (Ouluoo 9%) ANOW Patent Application Publication Apr. 13, 2017. Sheet 7 of 9 US 2017/0101638A1 s s s { {} : 8: $3.3 :S x: *8. if ide Patent Application Publication Apr. 13, 2017. Sheet 8 of 9 US 2017/0101638A1 Patent Application Publication Apr. 13, 2017. Sheet 9 of 9 US 2017/0101638A1 6"OIH US 2017/01 01638 A1 Apr. 13, 2017 ACETYL-COA CARBOXYLASES NADPH-dependent, (b) primarily NADH-dependent, (c) primarily flavin-dependent, (d) less susceptible to 3-HP CLAIM OF PRIORITY inhibition at high concentration, and/or (e) catalyzes a 0001. This application is a Continuation of and claims the reaction pathway to 3-HP that is substantially irreversible: benefit of priority to U.S. patent application Ser. No. 14/215. (6) a monofunctional malonyl-CoA reductase enzyme fused 379, Filed on Mar. 17, 2014, which claims the benefit of to one or more malonate semialdehyde dehydrogenase priority to U.S. Provisional Patent Application No. 61/852. enzymes; (7) a malonyl-CoA reductase gene that is mutated 387, filed on Mar. 15, 2013, the benefit of priority of each of to enhance its activity at lower temperatures; (8) salt-tolerant which is claimed hereby, and each of which are incorporated enzymes; (9) a gene that facilitates the exportation of a by reference herein in its entirety. chemical product of interest or the export of an inhibitory chemical from within the cell to the extracellular media; BACKGROUND OF THE INVENTION and/or (10) a gene that facilitates the importation from the extracellular media to within the cell of a reactant, precursor, 0002 There is a need for alternative production methods and/or metabolite used in the organism’s production path of industrial chemicals used for various consumer products way for producing a chemical product of interest. and fuels that are currently made from petroleum. One 0007. The present invention further relates to methods of alternative method is the use of engineered microorganisms producing a chemical product using the genetically modified to produce industrial chemicals. Currently, in the field of organisms of the invention. The present invention further bioproduced chemicals there is a need to improve microbial includes products made from these methods. In accordance enzyme performance, enhanced production rate in order to with certain embodiments that product is acetyl-CoA, malo reach the goal of becoming an at-cost replacement basis for nyl-CoA, malonate semialdehyde, 3-hydroxypropionic acid petro-based chemicals. (3-HP), acrylic acid, 1.3 propanediol, malonic acid, ethyl 0003. A common challenge faced in field of bio-produced 3-HP, propiolactone, acrylonitrile, acrylamide, methyl acry chemicals in microorganisms is that any one modification to late, a polymer including Super absorbent polymers and a host cell may require coordination with other modifica polyacrylic acid, or a consumer product. tions in or r to Successfully enhance chemical bioproduc 0008. The present invention further relates to a method of tion. producing a chemical product from a renewable carbon 0004. The current invention provides methods, systems Source through a bioproduction process that comprises a of fermentation, genetically modified microorganisms, controlled multi-phase production process wherein the ini modified enhanced enzymes for chemical production, all of tiation and/or completion of one or more phases of the which may be used in various combinations to increase production process is controlled by genetic modifications to chemical production of a desired chemical product. the organism producing the chemical product and/or is controlled by changes made to the cell environment. In INCORPORATION BY REFERENCE accordance with this aspect of the invention, the bioproduc 0005 All publications, patents, and patent applications tion process may include two or more of the following mentioned in this specification are herein incorporated by phases: (1) growth phase; (2) induction phase; and (3) reference to the same extent as if each individual publica production phase. The present invention further includes tion, patent, or patent application was specifically and indi products made from these methods. vidually indicated to be incorporated by reference. BRIEF DESCRIPTION OF THE DRAWINGS SUMMARY OF THE INVENTION 0009. The novel features of the invention are set forth 0006. The present invention relates to genetically modi with particularity in the appended claims. A better under fied organisms capable of producing an industrial chemical standing of the features and advantages of the present product of interest, wherein the genetic modification invention will be obtained by reference to the following includes introduction of nucleic acid sequences coding for detailed description that sets forth illustrative embodiments, polynucleotides encoding one or more of the following: (1) in which the principles of the invention are utilized, and the an acetyl-CoA carboxylase gene with one or more of its accompanying drawings of which: Subunits fused together in the genetic structure of the 0010 FIG. 1 Depicts some embodiments of the metabolic organism; (2) an acetyl-CoA carboxylase gene having a pathways to produce 3-hydroxypropionic acid. predefined stoichiometric ratio of each of the four ACCase 0011 FIG. 2 Depicts some embodiments of the of various Subunits relative to one another; (3) a monofunctional malo nyl-CoA reductase gene capable of catalyzing the conver equilibrium states in the malonate semialdehyde to 3-HP sion of malonyl-CoA to malonate semialdehyde and one or reaction in a cell environment. more genes encoding one or more of the following enzymes: 0012 FIG. 3 Depicts some embodiments of the reaction ydfG, mmsB, NDSD, ruthE, and nemA; (4) a monofunctional catalyzed by acetyl-CoA carboxylase (ACCase) malonyl-CoA reductase gene capable of catalyzing the con (0013 FIG. 4 Shows the inhibition of ACCase enzyme version of malonyl-CoA to malonate semialdehyde and one activity by high salt concentration. or more genes encoding one or more enzymes capable of 0014 FIG. 5 Depicts some embodiments of the fusion converting malonate semialdehyde keto form to 3-HP, and ACCase subunit gene constructs overexpressed in E. coli. one or more genes encoding one or more enzymes capable CAT-chloramphenicol resistance marker, p15a of converting either the malonate semialdehyde enol form or rep=replication origin; red arrow promoter. the malonate semialdehyde hydrated form to 3-HP; (5) a (0015 FIG. 6 Show improved production of 3-HP in monofunctional malonyl-CoA reductase enzyme fused to a fermentors by genetically modified organism with DA dehydrogenase enzyme that is either: (a) primarily not fusion ACCase. US 2017/01 01638 A1 Apr. 13, 2017 0016 FIG. 7 Shows improved production of 3-HP in that this concept is well-understood in the art. Further, it is fermentors by genetically modified organism with overex appreciated that nucleic acid sequences may be varied and pression of rhtA exporter. still provide a functional enzyme, and Such variations are 0017 FIG. 8 Shows various embodiments of the genetic within the scope of the present invention. The term “enzyme modules used for optimizing expression in host cells. homolog' can also mean a functional variant. 0018 FIG. 9 Shows various chemical products that can 0027. The term "Functional homolog” means a polypep made from various embodiments of the invention. tide that is determined to possess an enzymatic activity and 0019 Table 1 Lists the accession numbers for genes specificity of an enzyme of interest but which has an amino encoding ACCase Subunits from Halomonas elongate. acid sequence different from Such enzyme of interest. A 0020 Table 2 Depicts some embodiments of the RBS corresponding "homolog nucleic acid sequence' may be sequences used to enhance expression of H. elongate constructed that is determined to encode such an identified ACCase subunits. enzymatic functional variant. 0021 Table 3 Shows the improvement in 3-HP produc 0028. The term “3-HP means 3-hydroxypropionic acid. tion by RBS-optimized expression of H. elongata ACCase (0029. The term “heterologous DNA,” “heterologous Subunits. nucleic acid sequence,” and the like as used herein refers to 0022 Table 4 Shows some embodiments of ACCase a nucleic acid sequence wherein at least one of the following Subunit fusions that increase and ACCase enzyme complex is true: (a) the sequence of nucleic acids is foreign to (i.e., activity.
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