WO2016053397A2 - Compositions and methods for rapid and dynamic flux control using synthetic metabolic valves - Google Patents

Compositions and methods for rapid and dynamic flux control using synthetic metabolic valves Download PDF

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Publication number
WO2016053397A2
WO2016053397A2 PCT/US2015/035306 US2015035306W WO2016053397A2 WO 2016053397 A2 WO2016053397 A2 WO 2016053397A2 US 2015035306 W US2015035306 W US 2015035306W WO 2016053397 A2 WO2016053397 A2 WO 2016053397A2
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Prior art keywords
controlled
gene
expression
production
genetically modified
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English (en)
French (fr)
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WO2016053397A3 (en
Inventor
Michael David Lynch
Ashley Delanie TRAHAN
Daniel Rodriguez
Zhixia YE
Charlie COOPER
Ahmet BOZDAG
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Duke University
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Duke University
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Priority to JP2016572578A priority Critical patent/JP6730199B2/ja
Priority to ES15845669T priority patent/ES2937642T3/es
Priority to AU2015324564A priority patent/AU2015324564B2/en
Priority to US15/317,768 priority patent/US10662426B2/en
Priority to MYPI2016001993A priority patent/MY187588A/en
Priority to GB1511937.3A priority patent/GB2528177B/en
Priority to EP15845669.9A priority patent/EP3155102B1/en
Priority to DK15845669.9T priority patent/DK3155102T5/da
Priority to BR112016028741A priority patent/BR112016028741A2/pt
Priority to EP22181991.5A priority patent/EP4148127A1/en
Priority to CA2948382A priority patent/CA2948382C/en
Application filed by Duke University filed Critical Duke University
Publication of WO2016053397A2 publication Critical patent/WO2016053397A2/en
Publication of WO2016053397A3 publication Critical patent/WO2016053397A3/en
Priority to IL249191A priority patent/IL249191B/en
Anticipated expiration legal-status Critical
Priority to IL273209A priority patent/IL273209A/en
Priority to US16/849,455 priority patent/US11098307B2/en
Priority to US16/849,441 priority patent/US11142761B2/en
Priority to AU2021203937A priority patent/AU2021203937B2/en
Priority to US17/494,047 priority patent/US20220204969A1/en
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Definitions

  • This invention relates to metabolically engineered microorganisms, such as bacterial and or fungal strains, and bioprocesses utilizing such strains. These strains enable the dynamic control of metabolic pathways.
  • Petroleum is the primary feedstock, not only for the fuels we use, but the majority of the chemicals we consume as well.
  • the chemical industry is heavily reliant on this nonrenewable resource.
  • Replacement of petroleum with renewable feedstocks ensures longer-term viability and environmental sustainability.
  • Novel fermentation based processes to make chemicals have been a contributing technology, enabling the change to renewable feedstocks (Werpy &Peterson, Top Value Added Chemicals from Biomass. Volume I - Results of Screening for Potential Candidates from Sugars and Synthesis Gas., Yixiang et al. "Green” Chemicals from Renewable Agricultural Biomass - A Mini Review. The Open Agriculture Journal, 2008).
  • One solution is the development of platform microbial strains that utilize synthetic metabolic valves (SMVs) that can decouple growth from product formation. These strains enable the dynamic control of metabolic pathways, including those that when altered have negative effects on microorganism growth. Dynamic control over metabolism is accomplished via a combination of methodologies including but not limited to transcriptional silencing and controlled enzyme proteolysis. These microbial strains are utilized in a multi-stage bioprocess encompassing as least two stages, the first stage in which microorganisms are grown and metabolism can be optimized for microbial growth and at least one other stage in which growth can be slowed or stopped, and dynamic changes can be made to metabolism to improve production of desired product, such as a chemical or fuel.
  • SMVs synthetic metabolic valves
  • the transition of growing cultures between stages and the manipulation of metabolic fluxes can be controlled by artificial chemical inducers or preferably by controlling the level of key limiting nutrients.
  • genetic modifications may be made to provide metabolic pathways for the biosynthesis of one or more chemical or fuel products.
  • genetic modifications may be made to enable the utilization of a variety of carbon feedstocks including but not limited sugars such as glucose, sucrose, xylose, arabinose, mannose, and lactose, oils, carbon dioxide, carbon monoxide, methane, methanol and formaldehyde.
  • These synthetic metabolic valves can be used to turn off essential genes and redirect carbon, electrons and energy flux to product formation in a multi-stage fermentation process.
  • One or more of the following enables these synthetic valves: 1) transcriptional gene silencing or repression technologies in combination with 2) inducible enzyme degradation and 3) nutrient limitation to induce a stationary or non-dividing cellular state.
  • SMVs are generalizable to any pathway and microbial host.
  • FIG. 1 A simplified two-stage bioprocess using synthetic metabolic valves is depicted in Figure 1, strains are grown in a minimal media with a single limiting nutrient such as inorganic phosphate. During this growth phase cells are not producing any product other than biomass and as a result are not subject to any possible toxic or unwanted side effects of product formation. Biomass growth and yield can be optimized. As the limiting nutrient is depleted, cell growth is stopped. Simultaneously, these strains will be engineered to contain synthetic metabolic valves, which silence genes and enzymes essential for growth and redirect carbon, electrons and energy to any molecule of interest. This process utilizes a novel combination of a two-stage production and concurrent metabolic engineering strategy.
  • a single limiting nutrient such as inorganic phosphate.
  • Anaerobic growth-coupled product formation enables the use of powerful growth based selections to identify better producers. The faster the cells grow the more product they make. This has allowed for the classical selection of industrial strains for many natural products such as ethanol and isobutanol.
  • the requirement for anaerobic production greatly limits the number and variety of different molecules or products that can be made using synthetic biology. Numerous products would require aerobic metabolism to supply the needed energy and cofactors to allow for a thermodynamically feasible metabolic pathway. In these cases a generic and robust aerobic production platform would greatly simplify the optimization and scale up of a diverse number of products.
  • a controlled multi-stage process, enabled by synthetic metabolic valves, supplies such a platform.
  • Synthetic metabolic valves enable synthetic biologists and metabolic engineers the ability to decouple the complex metabolic and thermodynamic needs of growth from those of product formation. This decoupling also enables the removal of growth based regulatory mechanisms that may inhibit product formation and allows for the silencing of essential metabolic pathways that may detract from or interfere with production. These essential interfering metabolic pathways could include amino acid biosynthesis or the citric acid cycle as well as the biosynthesis of many secondary metabolites, and those pathways involved in maintaining intracellular redox and energy balances. These pathways have traditionally been off limits to many metabolic engineering strategies, as attempts at manipulation have led to growth defects.
  • the invention is directed to methods to construct controllable synthetic metabolic valves.
  • synthetic metabolic valves are used to controllably reduce or eliminate flux through one more metabolic pathways.
  • flux is reduced or eliminated through one or more metabolic pathways whose enzymes are essential for microbial growth in a given environment.
  • the invention is related to genetically modified microorganisms that utilize one or more synthetic metabolic valves thereby enabling dynamic control over metabolic pathways.
  • Other embodiments of the invention are directed to multi-stage bioprocesses that utilize genetically modified microorganism that in turn utilize one or more synthetic metabolic valves that enable dynamic flux control.
  • carbon feedstocks can include, but are not limited to the sugars: glucose, sucrose xylose, arabinose, mannose, lactose, or alternatively carbon dioxide, carbon monoxide, methane, methanol, formaldehyde, or oils.
  • genetic modifications to produce chemical or fuel products from various carbon feedstocks can include metabolic pathways utilizing, but not limited to, the central metabolites acetyl-CoA, malonyl-CoA, pyruvate, oxaloacetate, erthyrose-4-phosphate, xylulose-5-phosphate, alpha-ketoglutarate and citrate.
  • Products that can be derived from these central metabolites include but are not limited to acetate, alcohols (ethanol, butanol, hexanol, and longer n-alcohols), organic acids (3-hydroxyprpionic acid, lactic acid, itaconic acid), amino acids (alanine, serine, valine), fatty acids and there derivatives (fatty acid methyl esters (FAMEs), fatty aldehydes, alkenes, alkanes) and isoprenoids.
  • the increased production of acetate from acetyl-phosphate may occur via the increased expression of an acetate kinase.
  • an acetate kinase A non-limiting example is the acetate kinase from E. coli encoded by the ackA gene.
  • Increased expression of an acetate kinase may optionally be combined with genetic modifications that result decreased activity phosphoacetyltransferase such as that encoded by the pta gene of E. coli.
  • the increased production of ethanol from acetyl-CoA may occur via the increased expression of an oxygen tolerant ethanol dehydrogenase, such as the enzyme from E. coli encoded by the adhE gene with a mutation Glu568Lys as taught by Dellomonaco et al, AEM. August 2010, Vol. 76, No. 15, p 5067. and Holland- Staley et al. JBACs. November 2000, Vol. 182, No. 21, p6049.
  • an oxygen tolerant ethanol dehydrogenase such as the enzyme from E. coli encoded by the adhE gene with a mutation Glu568Lys as taught by Dellomonaco et al, AEM. August 2010, Vol. 76, No. 15, p 5067. and Holland- Staley et al. JBACs. November 2000, Vol. 182, No. 21, p6049.
  • the increased production of butyrate from acetyl-CoA may occur via the increased expression of butyrate pathway enzymes including an acetoacetyl-CoA thiolase, crotonase, crotonyl-CoA reductase, butyrate phospho-transferase and butyrate kinase as taught by Fischer et al, Appl Microbiol Biotechnol. 2010, September, Vol. 88, No.l, p. 265- 275.
  • increased butyrate may be accomplished via the increased expression of butyrate pathway enzymes including an acetoacetyl-CoA synthase, crotonase, crotonyl-CoA reductase and butyryl-CoA thioesterase as taught by PCT/US2012/030209.
  • butyrate pathway enzymes including an acetoacetyl-CoA synthase, crotonase, crotonyl-CoA reductase and butyryl-CoA thioesterase as taught by PCT/US2012/030209.
  • the increased production of n-butanol from acetyl-CoA may occur via the increased expression of n-butanol pathway enzymes including an acetoacetyl- CoA thiolase, crotonase, crotonyl-CoA reductase, butyryl-CoA reductase and butyraldehyde reductase as taught by Atsumi et al, Metabolic Engineering. 2008. November, Vol. 10, No.6, p. 305).
  • the increased production of fatty acids of chain length greater than 4, from acetyl-CoA may occur via the increased expression of a fatty acid synthesis pathway enzymes including an ketoacetyl-CoA synthase, 3-hydroxyacyl-CoA dehydratase, an enoyl-CoA reductase, and a acyl-CoA thioesterase as taught by PCT US2012/030209.
  • a fatty acid synthesis pathway enzymes including an ketoacetyl-CoA synthase, 3-hydroxyacyl-CoA dehydratase, an enoyl-CoA reductase, and a acyl-CoA thioesterase as taught by PCT US2012/030209.
  • the increased production of fatty acid methyl esters from acetyl-CoA may occur via the increased expression of fatty acid methyl ester synthesis pathway enzymes including an ketoacetyl-CoA synthase, 3-hydroxyacyl-CoA dehydratase, an enoyl-CoA reductase, and a acyl-CoA wax ester synthase as taught by: PCT US2012/030209 and US 20110146142 Al .
  • the increased production of n-hexanol from acetyl-CoA may occur via the increased expression of a fatty acid synthesis pathway enzymes including an ketoacetyl-CoA thiolases, 3-hydroxyacyl-CoA dehydratase, an enoyl-CoA reductase, and a acyl-CoA thioesterase as taught by Dekishima et al. J Am Chem Soc. 2011. August. Vol.133, No. 30, p. 1139.
  • the increased production of n-alcohols of chain length greater than 4, from acetyl-CoA may occur via the increased expression of a fatty acid synthesis pathway enzymes including an ketoacetyl-CoA synthase, 3-hydroxyacyl-CoA dehydratase, an enoyl-CoA reductase, as taught by PCT/US2012/030209 and a fatty acyl-CoA reductase and fatty aldehyde reductase as taught by Yan-Ning Zheng et al. Microbial Cell Factories. 2012. Vol. 11 :65.
  • the increased production of n-alkenes can be accomplished by first producing n-alcohols as described elsewhere followed by the chemical dehydration of the n-alcohol to an n-alkene by catalytic methods well known in the art.
  • the increased production of n-alkanes can be accomplished by first producing fatty acids as described elsewhere followed by the chemical decarboxylation of the n-alcohol to an alkane by catalytic methods well known in the art.
  • the increased production of isoprene from acetyl-CoA may occur via the increased expression of pathway enzymes including an acetoacetyl-CoA thiolase, hydroxymethylglutaryl-CoA synthase, hydroxymethylglutaryl-CoA reductase, mevalonate kinase, phosphomevalonate kinase, mevalonte diphosphate decarboxylase, isopentenyl- diphosphate isomerase and isoprene synthase as taught by US 20120276603 Al.
  • pathway enzymes including an acetoacetyl-CoA thiolase, hydroxymethylglutaryl-CoA synthase, hydroxymethylglutaryl-CoA reductase, mevalonate kinase, phosphomevalonate kinase, mevalonte diphosphate decarboxylase, isopentenyl- diphosphate isomerase and isoprene synthase as taught
  • the increased production of a product from acetyl-CoA may occur via both the increased expression of an acetyl-CoA carboxylase enzyme which can convert acetyl-CoA into malonyl-CoA and the increased expression of a production pathway comprising multiple pathway enzymes which can convert malonyl-CoA further to a product.
  • the increased production of a product from malonyl-CoA may occur via both the increased activity of an acetyl-CoA carboxylase enzyme which can caused by mutation of one or more fatty acid synthesis enzymes such as is taught by PCT US2012/030209, PCT/US2011/0222790 and 3. UK Patent GB2473755 and the increased expression of a production pathway comprising multiple pathway enzymes which can convert malonyl-CoA further to a product.
  • microorganism capable of producing an acetyl-CoA derived product at a specific rate selected from the rates of greater than 0.05 g/gDCW-hr, 0.08g/gDCW-hr, greater than O.lg/gDCW-hr, greater than 0.13g/gDCW-hr, greater than 0.15 g/gDCW-hr, greater than 0.175g/gDCW-hr, greater than 0.2g/gDCW-hr, greater than 0.25g/gDCW-hr, greater than 0.3g/gDCW-hr, greater than 0.35g/gDCW-hr, greater than 0.4g/gDCW-hr, greater than 0.45g/gDCW-hr, or greater than 0.5g/gDCW-hr.
  • microorganism within the scope of the invention are genetically modified microorganism, wherein the microorganism is capable of producing a product derived from any key metabolic intermediate including but not limited to malonyl-CoA, pyruvate, oxaloacetate, erthyrose-4- phosphate, xylulose-5-phosphate, alpha-ketoglutarate and citrate at a specific rate selected from the rates of greater than 0.05 g/gDCW-hr, 0.08g/gDCW-hr, greater than O.
  • any key metabolic intermediate including but not limited to malonyl-CoA, pyruvate, oxaloacetate, erthyrose-4- phosphate, xylulose-5-phosphate, alpha-ketoglutarate and citrate at a specific rate selected from the rates of greater than 0.05 g/gDCW-hr, 0.08g/gDCW-hr, greater than O.
  • lg/gDCW-hr greater than 0.13g/gDCW-hr, greater than 0.15g/gDCW-hr, greater than 0.175g/gDCW-hr, greater than 0.2g/gDCW-hr, greater than 0.25g/gDCW-hr, greater than 0.3g/gDCW-hr, greater than 0.35g/gDCW-hr, greater than 0.4g/gDCW-hr, greater than 0.45g/gDCW-hr, or greater than 0.5g/gDCW-hr.
  • the invention includes a culture system comprising a carbon source in an aqueous medium and a genetically modified microorganism according to any one of claims herein, wherein said genetically modified organism is present in an amount selected from greater than 0.05 gDCW/L, 0.1 gDCW/L, greater than 1 gDCW/L, greater than 5 gDCW/L, greater than 10 gDCW/L, greater than 15 gDCW/L or greater than 20 gDCW/L, such as when the volume of the aqueous medium is selected from greater than 5 mL, greater than 100 mL, greater than 0.5L, greater than 1L, greater than 2 L, greater than 10 L, greater than 250 L, greater than 1000L, greater than 10,000L, greater than 50,000 L, greater than 100,000 L or greater than 200,000 L, and such as when the volume of the aqueous medium is greater than 250 L and contained within a steel vessel.
  • FIG. 1 depicts an overview of a two-phase fermentation processes utilizing a microbe with synthetic metabolic valves.
  • Top Panel Overview of the fermentation process. Biomass is grown in minimal media with a single limiting macronutrient, such as inorganic phosphate. As the biomass level (black line) or number of cells increases the limiting nutrient (red line) is depleted. When the limiting nutrient is completely consumed, biomass growth is halted. Simultaneously the limitation induces metabolic changes to initiate product biosynthesis through engineered synthetic valves.
  • Lower Panel Metabolic Changes in the Two Phase Process. In correlation with the system level changes, metabolic changes are induced upon depletion of the limiting nutrient.
  • genes encoding metabolic pathways essential for cellular growth are active in the growth phase while genes encoding product biosynthesis “product genes” are silenced. Upon entry into the production phase triggered by nutrient depletion, “growth genes” are silenced and “product genes” are activated.
  • FIG. 2 depicts an overview of a synthetic metabolic valve in E. coli using a combination of CRISPR interference gene silencing and controlled protein degradation.
  • Upper Panel: (LEFT) Constructs are made to express small guide RNAs to target a gene of interest in addition to (RIGHT) the controlled induction of a cascade protein complex such as catalytically inactive Cas9 or dCas9 as well as the controlled induction of the chaperone (clpXP enhancing factor) sspB. Expression can be controlled such as by the controlled ptet promoter induced by aTc.
  • the constructs produce dCas9 and sspB proteins in addition to a targeting sgRNA.
  • the target gene/protein contains a C-terminal DAS4 tag for binding to sspB.
  • dCas9 is targeted to the gene of interest by the targeting sgRNA thereby silencing transcription.
  • the expression of sspB results in the binding of sspB to the DAS4 C-terminal tag of protein that has already been translated.
  • the sspB/DAS4 complex is then targeted for degradation by the clpXP protease.
  • FIG. 3 depicts the production of tetrahydroxynapthalene (THN) by redirecting flux from malonyl-CoA.
  • Upper Panel An overview of redirecting flux from growth to product by controlling fabl (enoyl-coA reductase levels) in E. coli.
  • fabl enoyl-coA reductase levels
  • the key enzyme controlling the rate of lipid synthesis, acetyl-CoA carboxylase, encoded by the accABCD genes, is strongly inhibited by the fatty acid production intermediates, fatty acyl-ACPs.
  • tetrahydroxynapthalene TBN
  • THN tetrahydroxynapthalene
  • Figure 4 depicts increased production of tetrahydroxynapthalene from malonyl-CoA in a two stage process as a result of the controlled inactivation of a temperature sensitive fabl allele. Improved production of THN by redirecting malonyl-CoA flux, using a temperature controlled process to inactivate a temperature sensitive allele oifabl.
  • Plasmids are i) pSMART-HC-Kan- yibD-THNS and ii) pSMART-HC-Kan (control).
  • Figure 5 depicts increased production of tetrahydroxynapthalene from malonyl-CoA in a two stage process as a result of a combination of controlled protein degradation and gene silencing. Improved production of THN by redirecting malonyl-CoA flux, using a synthetic metabolic viae comprising a combination of CRISPR interference gene silencing and controlled proteolysis as outlined in Figure 2. THN production at 4 hrs and 20 hrs is compared for two strains.
  • LEFT Strain BW25113: AldhA, ApflB, ApoxB, AackA-pta, AadhE, AsspB, fabI::DAS4, gentR containing plasmids i) pSMART-HC-Kan-yibD-THNS ii) pdCas9-ptet- sspB and iii) pCDF-control lacking a targeting sgRNA.
  • Figure 6 depicts the low phosphate induction of a GFP reporter with various low phosphate inducible promoters.
  • An ultraviolet excitable, green fluorescent protein (GFPuv) reporter gene was used and relative fluorescent units (RFU) are plotted as a function of time. Growth stops and phosphate depletion begins at about 15-20 hrs.
  • Figure 7 depicts the dynamic control over protein levels in E. coli using the CASCADE System and controlled proteolysis.
  • Strain DLF 0025 (enabling low phosphate DAS+4 degradation) has been modified to constitutive ly express a mCherry protein with a C-terminal DAS+4 degradation tag.
  • the strain has been modified for the low phosphate induction of GFPuv as well as a guide RNA repressing mCherry expression. As cells grow phosphate is depleted, and cells "turn off mCherry and "turn on" GFPuv.
  • Biomass is plotted as grams cell dry weight per liter, GFPuv and mCherry are plotted as relative fluorescence units (RFU) which are normalized to biomass levels.
  • REU relative fluorescence units
  • Figure 9 depicts the production of 3-HP from malonyl-CoA and NADPH at L scale. Biomass and 3-HP titers are plotted as a function of time.
  • Figure 10 depicts the production of alanine from pyruvate and NADPH at mL scale. Biomass and alanine titers are plotted as a function of time.
  • Figure 11 depicts the production of alanine from pyruvate and NADPH at the L scale. Biomass and alanine titers are plotted as a function of time.
  • Figure 12 depicts the production of 2,3-butanediol from pyruvate and NADH at mL scale. Biomass and 2,3-butanediol titers are plotted as a function of time.
  • Figure 13 depicts the production of 2,3-butanediol from pyruvate and NADH at L scale. Biomass and 2,3-butanediol titers are plotted as a function of time.
  • Figure 14 depicts the production of 2,3-butanediol from pyruvate and NADPH at mL scale. Biomass and 2,3-butanediol titers are plotted as a function of time.
  • Figure 15 depicts the production of mevalonic acid from acetyl-CoA and NADPH at L scale. Biomass and mevalonic acid titers are plotted as a function of time.
  • the present invention is related to various production methods and/or genetically modified microorganisms that have utility for fermentative production of various chemical products, to methods of making such chemical products that utilize populations of these microorganisms in vessels, and to systems for chemical production that employ these microorganisms and methods.
  • Among the benefits of the present invention is the increased ability to reduce or eliminate metabolic pathways required for microbial growth that may interfere with production.
  • reduced enzymatic activity As used herein, “reduced enzymatic activity,” “reducing enzymatic activity,” and the like is meant to indicate that a microorganism cell's, or an isolated enzyme, exhibits a lower level of activity than that measured in a comparable cell of the same species or its native enzyme. That is, enzymatic conversion of the indicated substrate(s) to indicated product(s) under known standard conditions for that enzyme is at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, or at least 90 percent less than the enzymatic activity for the same biochemical conversion by a native (non-modified) enzyme under a standard specified condition. This term also can include elimination of that enzymatic activity.
  • a cell having reduced enzymatic activity of an enzyme can be identified using any method known in the art.
  • enzyme activity assays can be used to identify cells having reduced enzyme activity. See, for example, Enzyme Nomenclature, Academic Press, Inc., New York 2007.
  • heterologous DNA refers to a nucleic acid sequence wherein at least one of the following is true: (a) the sequence of nucleic acids foreign to (i.e., not naturally found in) a given host microorganism; (b) the sequence may be naturally found in a given host microorganism, but in an unnatural (e.g., greater than expected) amount; or (c) the sequence of nucleic acids comprises two or more subsequences that are not found in the same relationship to each other in nature. For example, regarding instance (c), a heterologous nucleic acid sequence that is recombinantly produced will have two or more sequences from unrelated genes arranged to make a new functional nucleic acid, such as an nonnative promoter driving gene expression.
  • heterologous refers to either the use of controlled proteolysis, gene silencing or the combination of both proteolysis and gene silencing to alter metabolic fluxes.
  • heterologous is intended to include the term “exogenous” as the latter term is generally used in the art. With reference to the host microorganism's genome prior to the introduction of a heterologous nucleic acid sequence, the nucleic acid sequence that codes for the enzyme is heterologous (whether or not the heterologous nucleic acid sequence is introduced into that genome).
  • the term "gene disruption,” or grammatical equivalents thereof is intended to mean a genetic modification to a microorganism that renders the encoded gene product as having a reduced polypeptide activity compared with polypeptide activity in or from a microorganism cell not so modified.
  • the genetic modification can be, for example, deletion of the entire gene, deletion or other modification of a regulatory sequence required for transcription or translation, deletion of a portion of the gene which results in a truncated gene product (e.g., enzyme) or by any of various mutation strategies that reduces activity (including to no detectable activity level) the encoded gene product.
  • a disruption may broadly include a deletion of all or part of the nucleic acid sequence encoding the enzyme, and also includes, but is not limited to other types of genetic modifications, e.g., introduction of stop codons, frame shift mutations, introduction or removal of portions of the gene, and introduction of a degradation signal, those genetic modifications affecting mRNA transcription levels and/or stability, and altering the promoter or repressor upstream of the gene encoding the enzyme.
  • Bio-production or Fermentation may be aerobic, microaerobic, or anaerobic.
  • the genetic modification of a gene product i.e., an enzyme
  • the genetic modification is of a nucleic acid sequence, such as or including the gene, that normally encodes the stated gene product, i.e., the enzyme.
  • metabolic flux refers to changes in metabolism that lead to changes in product and/or byproduct formation, including production rates, production titers and production yields from a given substrate.
  • Species and other phylogenic identifications are according to the classification known to a person skilled in the art of microbiology.
  • Enzymes are listed here within, with reference to a Universal Protein Resource (Uniprot) identification number, which would be well known to one skilled in the art (Uniprot is maintained by and available through the UniProt Consortium).
  • Bio-production media which is used in the present invention with recombinant microorganisms must contain suitable carbon sources or substrates for both growth and production stages.
  • suitable substrates may include, but are not limited to glucose, sucrose, xylose, mannose, arabinose, oils, carbon dioxide, carbon monoxide, methane, methanol, formaldehyde and glycerol. It is contemplated that all of the above mentioned carbon substrates and mixtures thereof are suitable in the present invention as a carbon source(s).
  • microorganism selected from the listing herein, or another suitable microorganism, that also comprises one or more natural, introduced, or enhanced product bio-production pathways.
  • the microorganism(s) comprise an endogenous product production pathway (which may, in some such embodiments, be enhanced), whereas in other embodiments the microorganism does not comprise an endogenous product production pathway.
  • suitable microbial hosts for the bio-production of a chemical product generally may include, but are not limited to the organisms described in the Common Methods Section
  • bio-production media In addition to an appropriate carbon source, such as selected from one of the herein- disclosed types, bio-production media must contain suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of the enzymatic pathway necessary for chemical product bio-production under the present invention.
  • Another aspect of the invention regards media and culture conditions that comprise genetically modified microorganisms of the invention and optionally supplements.
  • Suitable cells are grown at a temperature in the range of about 25° C to about 40° C in an appropriate medium, as well as up to 70° C for thermophilic microorganisms.
  • Suitable growth media are well characterized and known in the art.
  • Suitable H ranges for the bio-production are between pH 2.0 to pH 10.0, where pH 6.0 to pH 8.0 is a typical pH range for the initial condition.
  • pH 6.0 to pH 8.0 is a typical pH range for the initial condition.
  • the actual culture conditions for a particular embodiment are not meant to be limited by these pH ranges.
  • Bio-productions may be performed under aerobic, microaerobic or anaerobic conditions with or without agitation.
  • Fermentation systems utilizing methods and/or compositions according to the invention are also within the scope of the invention.
  • any of the recombinant microorganisms as described and/or referred to herein may be introduced into an industrial bio-production system where the microorganisms convert a carbon source into a product in a commercially viable operation.
  • the bio-production system includes the introduction of such a recombinant microorganism into a bioreactor vessel, with a carbon source substrate and bio-production media suitable for growing the recombinant microorganism, and maintaining the bio-production system within a suitable temperature range (and dissolved oxygen concentration range if the reaction is aerobic or microaerobic) for a suitable time to obtain a desired conversion of a portion of the substrate molecules to a selected chemical product.
  • Bio-productions may be performed under aerobic, microaerobic, or anaerobic conditions, with or without agitation. Industrial bio-production systems and their operation are well-known to those skilled in the arts of chemical engineering and bioprocess engineering.
  • the amount of a product produced in a bio-production media generally can be determined using a number of methods known in the art, for example, high performance liquid chromatography (HPLC), gas chromatography (GC), or GC/Mass Spectroscopy (MS).
  • HPLC high performance liquid chromatography
  • GC gas chromatography
  • MS GC/Mass Spectroscopy
  • Embodiments of the present invention may result from introduction of an expression vector into a host microorganism, wherein the expression vector contains a nucleic acid sequence coding for an enzyme that is, or is not, normally found in a host microorganism.
  • the ability to genetically modify a host cell is essential for the production of any genetically modified (recombinant) microorganism.
  • the mode of gene transfer technology may be by electroporation, conjugation, transduction, or natural transformation.
  • a broad range of host conjugative plasmids and drug resistance markers are available.
  • the cloning vectors are tailored to the host organisms based on the nature of antibiotic resistance markers that can function in that host.
  • a genetically modified (recombinant) microorganism may comprise modifications other than via plasmid introduction, including modifications to its genomic DNA.
  • nucleic acid constructs can be prepared comprising an isolated polynucleotide encoding a polypeptide having enzyme activity operably linked to one or more (several) control sequences that direct the expression of the coding sequence in a microorganism, such as E. coli, under conditions compatible with the control sequences.
  • the isolated polynucleotide may be manipulated to provide for expression of the polypeptide. Manipulation of the polynucleotide's sequence prior to its insertion into a vector may be desirable or necessary depending on the expression vector.
  • the techniques for modifying polynucleotide sequences utilizing recombinant DNA methods are well established in the art.
  • the control sequence may be an appropriate promoter sequence, a nucleotide sequence that is recognized by a host cell for expression of a polynucleotide encoding a polypeptide of the present invention.
  • the promoter sequence may contain transcriptional control sequences that mediate the expression of the polypeptide.
  • the promoter may be any nucleotide sequence that shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the host cell.
  • the techniques for modifying and utilizing recombinant DNA promoter sequences are well established in the art.
  • the genetic manipulations may be described to include various genetic manipulations, including those directed to change regulation of, and therefore ultimate activity of, an enzyme or enzymatic activity of an enzyme identified in any of the respective pathways.
  • Such genetic modifications may be directed to transcriptional, trans lational, and post-trans lational modifications that result in a change of enzyme activity and/or selectivity under selected and/or identified culture conditions and/or to provision of additional nucleic acid sequences such as to increase copy number and/or mutants of an enzyme related to product production. Specific methodologies and approaches to achieve such genetic modification are well known to one skilled in the art.
  • a microorganism may comprise one or more gene deletions.
  • Such gene disruptions, including deletions are not meant to be limiting, and may be implemented in
  • a microorganism may comprise one or more synthetic metabolic valves, composed of enzymes targeted for controlled proteolysis, expression silencing or a combination of both controlled proteolysis and expression silencing.
  • one enzyme encoded by one gene or a combination of numerous enzymes encoded by numerous genes in E. coli may be designed as synthetic metabolic valves to alter metabolism and improve product formation.
  • Representative genes in E. coli may include but are not limited to the following: fabl, zwf, gltA, ppc, udhA, Ipd, sucD, aceA, ⁇ , Ion, rpoS, tktA or tktB. It is appreciated that it is well known to one skilled in the art how to identify homologues of these genes and or other genes in additional microbial species.
  • nucleic acid and amino acid sequences provided herein, it is appreciated that conservatively modified variants of these sequences are included, and are within the scope of the invention in its various embodiments.
  • Functionally equivalent nucleic acid and amino acid sequences which may include conservatively modified variants as well as more extensively varied sequences, which are well within the skill of the person of ordinary skill in the art, and microorganisms comprising these, also are within the scope of various embodiments of the invention, as are methods and systems comprising such sequences and/or microorganisms .
  • compositions, methods and systems of the present invention comprise providing a genetically modified microorganism that comprises both a production pathway to make a desired product from a central intermediate in combination with synthetic metabolic valves to redistribute flux.
  • aspects of the invention also regard provision of multiple genetic modifications to improve microorganism overall effectiveness in converting a selected carbon source into a selected product. Particular combinations are shown, such as in the Examples, to increase specific productivity, volumetric productivity, titer and yield substantially over more basic combinations of genetic modifications.
  • genetic modifications including synthetic metabolic valves also are provided to increase the pool and availability of the cofactor NADPH and/or NADH which may be consumed in the production of a product.
  • any subgroup of genetic modifications may be made to decrease cellular production of fermentation product(s) other than the desired fermentation product, selected from the group consisting of acetate, acetoin, acetone, acrylic, malate, fatty acid ethyl esters, isoprenoids, glycerol, ethylene glycol, ethylene, propylene, butylene, isobutylene, ethyl acetate, vinyl acetate, other acetates, 1,4-butanediol, 2,3- butanediol, butanol, isobutanol, sec-butanol, butyrate, isobutyrate, 2-OH-isobutryate, 3-OH- butyrate, ethanol, isopropanol, D-lactate, L-lactate, pyruvate, itaconate, levulinate, glucarate, glutarate, ca
  • the invention describes the construction of synthetic metabolic valves comprising one or more or a combination of the following: controlled gene silencing and controlled proteolysis. It is appreciated that one well skilled in the art is aware of several methodologies for gene silencing and controlled proteolysis. An example of the combination of CRISPR interference based gene silencing and controlled proteolysis is illustrated in Figure 2.
  • the invention describes the use of controlled gene silencing to help enable the control over metabolic fluxes in controlled multi-stage fermentation processes.
  • controlled gene silencing includes mRNA silencing or RNA interference, silencing via transcriptional repressors and CRISPR interference.
  • Methodologies and mechanisms for RNA interference are taught by Agrawal et al. "RNA Interference: Biology, Mechanism, and Applications” Microbiology and Molecular Biology Reviews, December 2003; 67(4) p657-685. DOI: 10.1128/MMBR.67.657-685.2003.
  • Methodologies and mechanisms for CRISRPR interference are taught by Qi et al.
  • the invention describes the use of controlled protein degradation or proteolysis to help enable the control over metabolic fluxes in controlled multi-stage fermentation processes.
  • controlled protein degradation There are several methodologies known in the art for controlled protein degradation, including but not limited to targeted protein cleavage by a specific protease and controlled targeting of proteins for degradation by specific peptide tags.
  • Systems for the use of the E. coli clpXP protease for controlled protein degradation are taught by McGinness et al, "Engineering controllable protein degradation", Mol Cell. June 2006; 22(5) p701-707. This methodology relies upon adding a specific C-terminal peptide tag such as a DAS4 (or DAS+4) tag.
  • Proteins with this tag are not degraded by the clpXP protease until the specificity enhancing chaperone sspB is expressed. sspB induces degradation of DAS4 tagged proteins by the clpXP protease.
  • site specific protease systems are well known in the art. Proteins can be engineered to contain a specific target site of a given protease and then cleaved after the controlled expression of the protease. In some embodiments the cleavage can be expected lead to protein inactivation or degradation. For example Schmidt et al, "ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway" Molecular Microbiology March 2009.
  • N-terminal sequence can be added to a protein of interest in enable clpS dependent clpAP degradation.
  • this sequence can further be masked by an additional N-terminal sequence, which can be controllable cleaved such as by a ULP hydrolase.
  • This allows for controlled N-rule degradation dependent on hydrolase expression. It is therefore possible to tag proteins for controlled proteolysis either at the N-terminus or C- terminus.
  • the preference of using an N-terminal vs. C-terminal tag will largely depend on whether either tag affects protein function prior to the controlled onset of degradation.
  • the invention describes the use of controlled protein degradation or proteolysis to help enable the control over metabolic fluxes in controlled multi-stage fermentation processes, in E. coli.
  • controlled protein degradation in other microbial hosts, including a wide range of gram-negative as well as gram-positive bacteria, yeast and even archaea.
  • systems for controlled proteolysis can be transferred from a native microbial host and used in a non-native host.
  • Grilly et al "A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae" Molecular Systems Biology 3, Article 127. doi:10.1038, teaches the expression and use of the E. coli clpXP protease in the yeast Saccharomyces cerevisiae .
  • Such approaches can be used to transfer the methodology for synthetic metabolic valves to any genetically tractable host.
  • the invention describes the use of synthetic metabolic valves to control metabolic fluxes in multi-stage fermentation processes.
  • methodologies known in the art to induce expression that can be used at the transition between stages in multistage fermentations. These include but are not limited to artificial chemical inducers including: tetracycline, anhydrotetracycline, lactose, IPTG (isopropyl-beta-D-l-thiogalactopyranoside), arabinose, raffinose, tryptophan and numerous others.
  • Systems linking the use of these well known inducers to the control of gene expression silencing and/or controlled proteolysis can be integrated into genetically modified microbial systems to control the transition between growth and production phases in multi-stage fermentation processes.
  • Limiting nutrients can include but are not limited to: phosphate, nitrogen, sulfur and magnesium.
  • Natural gene expression systems that respond to these nutrient limitations can be used to operably link the control of gene expression silencing and/or controlled proteolysis to the transition between growth and production phases in multi-stage fermentation processes.
  • the published resource is specifically incorporated for the teaching(s) indicated by one or more of the title, abstract, and/or summary of the reference. If no such specifically identified teaching and/or other purpose may be so relevant, then the published resource is incorporated in order to more fully describe the state of the art to which the present invention pertains, and/or to provide such teachings as are generally known to those skilled in the art, as may be applicable. However, it is specifically stated that a citation of a published resource herein shall not be construed as an admission that such is prior art to the present invention.
  • Example 1 Dynamic Flux control using temperature sensitive enzymes to improve Malonyl-CoA flux in E. coli.
  • strain BWapldf (BW251 ⁇ 3:AldhA, ApflB, ⁇ , AackA- pta, AadhE) was further genetically modified so that the fabi gene was mutated to contain both a temperature sensitive (ts) mutation (F241S) as well as to incorporate gentamicin resistance cassette a the C-terminus of the fabi gene. This was accomplished using standard recombineering protocols.
  • the strain was further modified to express the tetrahydroxynapthalene (THN) synthase gene (rppA from Steptomyces coelicolor) under phosphate limiting conditions by transformation with the plasmid pSMART-HC-Kan-yibD- THNS (SEQ ID NO: 1).
  • TBN tetrahydroxynapthalene
  • rppA tetrahydroxynapthalene synthase gene
  • rppA tetrahydroxynapthalene synthase gene
  • Example 2 A Synthetic Metabolic Valve to improve Malonyl-CoA flux in E. coli
  • This example describes the increased production of tetrahydroxynaphtalene (THN) in E. coli from the intermediate malonyl-CoA using the controlled repression of fabi using synthetic metabolic valve technology.
  • TBN tetrahydroxynaphtalene
  • a combination of CRISPR interference gene silencing technology and controlled protein degradation was used in a two-stage process. Briefly, strain BWapldf (BW25l l3:AldhA, ApflB, ApoxB, AackA-pta, AadhE) was further genetically modified so that the fabi gene was tagged to contain a C-terminal DAS4 tag as well as to incorporate gentamicin resistance cassette a the C-terminus of the fabi gene.
  • the C- terminal nucleotide sequence encoding the DAS4 tag was integrated as the following sequence: 5'-GCGGCCAACGATGAAAACTATTCTGAAAACTATGCGGATGCGTCT-34. This was accomplished using standard recombineering protocols.
  • the strain was further modified so as to delete the sspB gene. This was also performed with standard recombineering methods.
  • these strains were still further modified to contain three plasmids, the first plasmid expresses the tetrahydroxynapthalene (THN) synthase gene, pSMART-HC-Kan- yibD-THNS (SEQ ID NO: l), as described above.
  • the second plasmid was constructed to express a small guide RNA targeting the fabl gene from a high copy spectinomycin resistance plasmid derived from pCDF-lb, which was obtained from EMD Millipore Biosciences.
  • the plasmid, pCDF-T2-fabIsgR A expresses a small guide RNA to use with S. pyogenes dCas9.
  • the specific fabl T2 targeting sequence is given by 5'- CAGCCTGCTCCGGTCGGACCG-3 ' (SEQ ID NO:47).
  • a control plasmid was also made missing any targeting sequence as described by Qi et al. Cell February 2013; 152(5) pi 173- 1183.
  • pdCas9-ptet-sspB The last plasmid, pdCas9-ptet-sspB (SEQ ID NO:3), was derived from the plasmid pdCas9-bacteria, from Qi et al, which was obtained from Addgene (Cambridge, MA 02139; Plasmid ID 44249). Briefly, pdCas9-bacteria was linearized and the sspB gene was introduced under the control of an additional ptet promoter at the 3' of the catalytically inactive dcas9 gene.
  • anhydrotetracycline (aTc) will induce expression of both dCas9 as well as sspB from this Chloramphenicol resistance conferring plasmid.
  • All plasmids were constructed using standard molecular biology methods and sequences confirmed by DNA sequencing. These strains, as well as controls, were evaluated for THN production using the two-stage protocol as outline in the Common Methods section "Shake Flask Protocol-2". Relative THN production was quantified by measuring the absorbance of the supernatant at 340 nm.
  • Figure 5 summarizes the results.
  • Example 3 General Example
  • Numerous microbial strains such as any of the strains listed in the Common Methods Section, may be genetically modified to express enzymes for the biosynthesis of a product.
  • these modified microbial strains can be further modified to contain a controllable synthetic metabolic valve for the dynamic reduction in enzyme activity of one or more metabolic pathways including those required for growth.
  • These valves may utilize one or a combination of methods including gene silencing and controlled proteolysis.
  • these modified strains may be used in a multistage fermentation process wherein transition between stages is concurrent with controlled activation of these valves.
  • any of these microbial strains may also be further engineered to express a heterologous production pathway enabling the product formation.
  • strain BWapldf (WN25Wi:AldhA, ApflB, ⁇ , AackA-pta, AadhE) was further genetically modified for the deletion of the following genes: arcA, iclR and sspB, to construct strain DLF 0002. This was also performed with standard scarless re combine ering methods. To construct a strain capable of both crispr based gene silencing using the native CASCADE system in E. coli as well as controlled proteolysis, the cas3 gene of E. coli was first deleted.
  • This gene was replaced with a sequence to enable both constitutive expression of the casABCDE-casl ,2 operon enabling CASCADE based gene silencing, as well as a construct allowing for the low phosphate induction of the sspB chaperone.
  • the DNA sequence integrated was ordered as a single synthetic construct: SEQ ID NO:4, and integrated using standard recombineering methodologies.
  • this construct integrates a transcriptional terminator, followed by the low phosphate inducible E. coli ugpB gene promoter and the sspB gene.
  • the sspB gene is followed by another transcriptional terminator and a subsequent constitutive proB promoter adapted from (Davis, JH., Rubin, AJ., and Sauer, RT. NAR. February 2011; 39(3) pl l31-1141. DOI: 10.1093) to drive constant expression of the CASCADE operon.
  • the resulting strain is termed DLF 0025.
  • a derivative of E. coli strain DLF 0025 was constructed to utilize a non-PTS dependent glucose uptake system.
  • PTS phosphotransferase system
  • Alternative uptake has been previously described in E. coli, (Hernandez-Montalvo, V., et al., Biotechnol Bioeng.. September 2003; 83(6) p687-694.), and relies on the overexpression of the E. coli galP permease and glucokinase (glk gene) along with the deletion of the E. coliptsG gene.
  • the ptsG gene was deleted and replaced with a constitutively expressed glucokinase construct, this construct was ordered as a single synthetic linear DNA construct (SEQ ID NO: 5) and integrated according to standard methodologies.
  • the galP promoter was also replaced via chromosomal replacement using another single synthetic linear DNA construct (SEQ ID NO:6), the resulting strain was called DLF 0286.
  • the proC promoter was used to drive constitutive expression (Davis, JH., Rubin, AJ., and Sauer, RT. NAR. February 2011; 39(3) pl l31-1141. DOI: 10.1093).
  • E. coli strains DLF 0025 and DLF 0286 were further modified for the controlled proteolysis of key enzymes in central metabolism including: 1) enoyl-ACP reductase encoded by the fabl gene, involved in fatty acid biosynthesis, 2) citrate synthase encoded by the gltA gene, involved in citric acid cycle, 3) soluble transhydrogenase encoded by the udhA gene, involved in NADPH metabolism, 4) glucose-6-phosphate-l-dehydrogenase encoded by the zwf gene, involved in the pentose phosphate pathway and 5) the lipoamide dehydrogenase or E3 component of the pyruvate dehydrogenase complex encoded by Ipd gene.
  • C-terminal DAS+4 tags enabling sspB controlled proteolysis were integrated at the 3 ' end of each of the above genes as the following sequence: 5'-
  • DLF_0287 F-, k A(araD-araB)567, AlacZ4787(::rmB-3), rph-1, A(rhaD- rhaB)568, hsdR514, AldhAr.frt, ApoxBr.frt, ApflBr.frt, AackA-pta: :frt, AadhEr.frt, AiclR, AarcA, AsspB, Acas3 : :ugpBp-sspB-pro, AptsGrproC-glk, proC-galP, gltA-DAS+4:zeoR
  • Reporter plasmids linking each promoter to a GFPuv gene reporter were constructed and sequences are as follows: pSMART-amnp-GFPuv (SEQ ID NO:36), pSMART-phoAp-GFPuv (SEQ ID NO:37), pSMART-phoBp-GFPuv (SEQ ID NO:38), pSMART-phoEp-GFPuv (SEQ ID NO:38), pSMART-phoHp-GFPuv (SEQ ID NO:40), pSMART-phoUp-GFPuv (SEQ ID NO:41), pSMART-mipAp-GFPuv (SEQ ID NO:42), pSMART-pstSp-GFPuv (SEQ ID NO:43), pSMART-ugpBp-GFPuv (SEQ ID NO: 12), pSMART-waaHp-GFPuv (SEQ ID NO:44), and pSMART-yd
  • plasmids were transformed into E. coli strain BWapldf (Refer to Example 4). Colonies were used to inoculate 4 mL of SM3 media with kanamycin (Refer to Common Methods Section) and incubated overnight at 37 degrees Celsius and a shaking speed of 225 rpm. After overnight growth, cells were normalized to an optical density at 600nm of 5, and 40 ⁇ . of normalized culture was used to inoculate 760 ⁇ . of fresh FGM3 (Refer to Common Methods Section) medium with kanamycin in wells of a 48 well FlowerPlateTM B which was transferred into a BioLector Microbioreactor both obtained from M2P Labs (Baesweiler, Germany).
  • the BioLector Microbioreactor can continuously measure fluorescence. Cells were incubated in the Microreactor at 37 degrees Celsius and a shaking speed of 1200 rpm for 60 hrs. Growth stopped and phosphate depletion begins at about 15-20 hrs (data not shown for clarity). Fluorescence results for each reporter construct as well as an empty vector control are reported as relative fluorescence units (R.F.U) in Figure 6. All plasmids were constructed using standard Gibson Assembly methodology (Gibson Assembly Master Mix, obtained from New England Biolabs, Ipswich, MA, USA), and synthetic linear double stranded DNA provided as GblocksTM (Integrated DNA Technology, Coralville, IA, USA). Eton Bioscience (Research Triangle Park, NC, USA) was used for plasmid DNA sequence confirmations. Standard codon optimization was performed to optimize constructs for expression in E. coli.
  • pCASCADE-control (SEQ ID NO: 13) was prepared by swapping the tetracycline inducible promoter in pcrRNA plasmid (Luo et al. "Repurposing endogenous type I CRISPR- Cas systems for programmable gene repression” NAR. October 2014; DOI: 10.1093.) with an insulated ugpB promoter.
  • the plasmid was constructed using standard Gibson Assembly methodology (Gibson Assembly Master Mix, obtained from New England Biolabs, Ipswich, MA, USA), and synthetic linear double stranded DNA provided as GblocksTM (Integrated DNA Technology, Coralville, IA, USA). Eton Bioscience (Research Triangle Park, NC, USA) was used for plasmid DNA sequence confirmations.
  • pCASCADE-gltA2 (SEQ ID NO: 14) was prepared using pCASCADE-control as template and the following primers: gltA2-FOR 5'- GGGACAGTTATTAGTTCGAGTTCCCCGCGCCA GCGGGGATAAACCGAAAAAAAAACCCC-3' (SEQ ID NO:49) and gltA2-REV 5'- GAATGAATTGGTCAATACGGTTTATCCCCGCTGGCGCGGGGAACTCGAGGTGGT ACCAGATCT-3 ' (SEQ ID NO:50).
  • Additional pCASCADE plasmids including pCASCADE-fabl (SEQ ID NO:15), pCASCADE-udhA, (SEQ ID NO:16), pCASCADE-zwf (SEQ ID NO:17) and pCASCADE-gltAl (SEQ ID NO:18) were prepared in a similar manner by exchanging the guide RNA targeting sequence using Q5 mutagenesis.
  • pCASCADE-gltA2-udhA SEQ ID NO: 19
  • plasmid was prepared by amplifying gltA2 guide half and udhA guide half from pCASCADE-gltA2 and pCASCADE-udhA respectively using Q5 High-Fidelity 2X Master Mix (NEB, MA).
  • pCASCADE-fabl-udhA (SEQ ID NO:20), pCASCADE-fabl-gltAl (SEQ ID NO:21), pCASCADE-fabI-gltA2 (SEQ ID NO:22), pCASCADE-fabl-zwf (SEQ ID NO:23), pCASCADE-gltAl-udhA (SEQ ID NO:24), pCASCADE-gltA2-udhA (SEQ ID NO:25), pCASCADE-gltAl-zwf (SEQ ID NO:26), pCASCADE-gltA2-zwf (SEQ ID NO:27), were all prepared in a similar way by amplification of each guide and part of the vector backbone followed by Gibson Assembly. All plasmid sequences were confirmed by DNA sequencing (Eton Bioscience, Research Triangle Park, NC, USA).
  • Example 7 Dynamic control over protein levels in E. coli using the CASCADE System and Controlled Proteolysis.
  • All plasmids were constructed using standard Gibson Assembly methodology (Gibson Assembly Master Mix, obtained from New England Biolabs, Ipswich, MA, USA), and synthetic linear double stranded DNA provided as GblocksTM (Integrated DNA Technology, Coralville, IA, USA). Eton Bioscience (Research Triangle Park, NC, USA) was used for plasmid DNA sequence confirmations. Standard codon optimization was performed to optimize constructs for expression in E. coli. First a plasmid expressing a low phosphate inducible (utilizing the low phosphate inducible waaH gene promoter from E.
  • GFPuv ultraviolet excitable, green fluorescent protein
  • pSMART-waaHp-GFPuv SEQ ID NO: 12
  • pBTl-mCherry-DAS+4 SEQ ID NO:28
  • Constitutive expression was achieved using a proD promoter (Davis, JH., Rubin, AJ., and Sauer, RT. NAR. February 2011; 39(3) pi 131-1141. DOI: 10.1093).
  • All plasmids were constructed using standard Gibson Assembly methodology (Gibson Assembly Master Mix, obtained from New England Biolabs, Ipswich, MA, USA), and synthetic linear double stranded DNA provided as GblocksTM (Integrated DNA Technology, Coralville, IA, USA). Eton Bioscience (Research Triangle Park, NC, USA) was used for plasmid DNA sequence confirmations. Standard codon optimization was performed to optimize constructs for expression in E. coli.
  • a plasmid expressing an NADPH dependent 3-hydroxypropionic acid (3-HP) production pathway was constructed as an operon of two genes.
  • the mcr gene from Chloroflexus auranticus (CaMCR), encoding a malonyl-CoA reductase (Uniprot # A9WIU3), and the ydfG gene from E. coli, encoding an NADPH dependent 3-HP dehydrogenase (Uniprot # P39831) were used.
  • a plasmid expressing a malonic acid production pathway was constructed from a single gene encoding a triple mutant (E95N/Q384A/F304R) Pseudomonas fulva (strain 12-X) isobutyryl-CoA thioesterase (Uniprot # F6AA82), with altered specificity (Steen, E., Patent Application PCT US2014/047645).
  • This gene was cloned behind the phosphate dependent waaH gene promoter from E. coli.
  • the gene was then assembled into the pSMART-HC-Kan vector (Lucigen, Middleton WI), resulting in plasmid pSMART-F6AA82M, (SEQ ID NO:31).
  • a plasmid expressing an NADPH dependent L-alanine production pathway was constructed from a single gene encoding a double mutant (Leul97Arg Aspl96Ala) Bacillus subtilis alanine dehydrogenase (AlaDH) (Uniprot # Q08352), with NADPH cofactor specificity (Haas, T., et al. Patent Application PCT/EP2013/057855).
  • This gene was cloned behind the phosphate dependent waaH gene promoter from E. coli. The gene was then assembled into the pSMART-HC-Kan vector (Lucigen, Middleton WI), resulting in plasmid pSMART-Alal, (SEQ ID NO:32).
  • a additional plasmid expressing the same NADPH dependent L-alanine production pathway was constructed using the phosphate dependent ugpB gene promoter from E. coli. The gene was then assembled into the pSMART-HC-Kan vector (Lucigen, Middleton WI), resulting in plasmid pSMART-Ala2, (SEQ ID NO:46).
  • a plasmid expressing a mevalonate production pathway was constructed from two genes assembled into two transcriptional units.
  • the mvaE gene from Enterococcus faecalis encoding a bifunctional acetoacetyl-CoA thiolase, and NADPH dependent HMG- CoA reductase (Uniprot # Q9FD70) was cloned behind an insulated version of the phosphate dependent waaH gene promoter from E. coli.
  • the mvaS gene also from E.
  • faecalis encoding a hydroxymethylglutaryl-CoA synthase (Uniprot # Q9FD71) was cloned behind an insulated version of the phosphate dependent mipA gene promoter from E. coli.
  • the mvaS expression construct was cloned behind the mvaE construct and both assembled into the pSMART-HC-Kan vector, resulting in plasmid pSMART-Mevl, (SEQ ID NO:33).
  • a plasmid expressing an NADH dependent 2,3-butanediol production pathway was constructed as an operon of three genes.
  • the budA, budB and budC genes from Enterobacter cloacae subsp. dissolvens SDM, encoding an a-acetolactate decarboxylase, an acetolactate synthase and acetoin reductase, respectively, were cloned behind the phosphate dependent waaH gene promoter from E. coli.
  • the operon was assembled into the pSMART-HC-Kan vector, resulting in plasmid pSMART-2,3-BD01, (SEQ ID NO:34).
  • a plasmid expressing an NADPH dependent 2,3-butanediol production pathway was constructed as an operon of three genes.
  • the budA, budB genes from Enterobacter cloacae subsp. dissolvens SDM, encoding an a-acetolactate decarboxylase, an acetolactate synthase, and a Glu221Ser/Ile222Arg/Ala223Ser triple mutant bdhl gene from S. cerevisiae, encoding an NADPH dependent acetoin reductase (Ehsani, M., Fernandez, MR., Biosca JA and Dequin, S. Biotechnol Bioeng.
  • Example 9 Production of 3-hydroxypropionic acid (3-HP) in E. coli, from malonyl- CoA and NADPH in 96 well plates.
  • E. coli strains were constructed utilizing a combination of host strains as described in Example 5, production pathway plasmids as described in Example 8 and CASCADE based gene silencing constructs such as those described in Example 6. Strains were then evaluated for product formation using the standard 96 well plate evaluation protocol "96 Well Plate Protocol -1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. These strains and the associated production data are given in Table 2.
  • Example 10 Production of 3 -hydroxypropionic acid (3-HP) in E. coli, from malonyl-CoA and NADPH at mL scale
  • E. coli strains were constructed utilizing a combination of host strains as described in Example 5, production pathway plasmids as described in Example 6 and CASCADE based gene silencing constructs such as those described in Example 7. Strains were then evaluated for product formation using the standard mL scale evaluation protocol "Micro24 Protocol -1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Summary metrics are listed in Table 3 and shown in Figure 8.
  • Example 11 Production of 3-hydroxypropionic acid (3-HP) in E. coli , from malonyl-CoA and NADPH L scale
  • E. coli strain 39 from Example 10 was evaluated at 1 L scale using the standard evaluation protocol "1L Fermentation Protocol - 1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Biomass growth and 3-HP production are shown in Figure 9.
  • Example 12 Production of malonic acid in E. coli, from malonyl-CoA in 96 well plates
  • E. coli strains were constructed utilizing a combination of host strains as described in Example 5, production pathway plasmids as described in Example 8 and CASCADE based gene silencing constructs such as those described in Example 6. Strains were then evaluated for product formation using the standard 96 well plate evaluation protocol "96 Well Plate Protocol -1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. These strains and the associated production data are given in Table 4.
  • Example 13 Production of alanine in E. coli, from pyruvate in 96 well plates
  • E. coli strains were constructed utilizing a combination of host strains as described in Example 5, production pathway plasmids as described in Example 8 and CASCADE based gene silencing constructs such as those described in Example 6. Strains were then evaluated for product formation using the standard 96 well plate evaluation protocol "96 Well Plate Protocol -1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. These strains and the associated production data are given in Table 5.
  • Example 14 Production of alanine in E. coli, from pyruvate at mL scale
  • E. coli strain 49 from Example 13 was evaluated at mL scale using the standard evaluation protocol "Micro24 Protocol -1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Biomass growth and alanine production are shown in Figure 10.
  • Example 15 Production of alanine in E. coli, from pyruvate at L scale
  • E. coli strain 60 from Example 13 was evaluated at 1 L scale using the standard evaluation protocol "1L Fermentation Protocol - 1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Biomass growth and alanine production are shown in Figure 11.
  • Example 16 Production of 2,3-butanediol in E. coli, from pyruvate and NADH at mL scale
  • E. coli strain was made by transforming host strain DLF 00165 with both plasmid pSMART-2,3-BD01 and pCASCADE-zwf (Refer to Examples 4, 6 and 8). This strain was evaluated at mL scale using the standard evaluation protocol "Micro24 Protocol -1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Biomass growth and alanine production are shown in Figure 12.
  • Example 17 Production of 2,3-butanediol in E. coli, from pyruvate and NADH at L scale
  • E. coli strain was made by transforming host strain DLF 00165 with both plasmid pSMART-2,3-BD01 and pCASCADE-zwf (Refer to Examples 4, 6 and 8). This strain was evaluated at 1 L scale using the standard evaluation protocol "1L Fermentation Protocol - 1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Biomass growth and alanine production are shown in Figure 13.
  • Example 18 Production of 2,3-butanediol in E. coli, from pyruvate and NADPH at mL scale
  • E. coli strain was made by transforming host strain DLF 00049 with both plasmid pSMART-2,3-BD02 and pC AS CADE-udhA (Refer to Examples 4, 6 and 8). This strain was evaluated at mL scale using the standard evaluation protocol "Micro24 Protocol -1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Biomass growth and alanine production are shown in Figure 14.
  • Example 19 Production of Mevalonic Acid in E. coli, from acetyl-CoA and NADPH at L scale
  • E. coli strain was made by transforming host strain DLF 0004 with plasmid pSMART-Mevl (Refer to Examples 4 and 8). This strain was evaluated at 1 L scale using the standard evaluation protocol "1L Fermentation Protocol - 1" as described in the Common Methods Section. Products levels were then measured using the analytical methods as described in the Common Methods Section. Biomass growth and alanine production are shown in Figure 15. [0160] COMMON METHODS SECTION
  • Microbial species that may be utilized as needed, are as follows:
  • Acinetobacter calcoaceticus (DSMZ # 1139) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Brain Heart Infusion (BHI) Broth (RPI Corp, Mt. Prospect, IL, USA). Serial dilutions of theresuspended calcoaceticus culture are made into BHI and are allowed to grow for aerobically for 48 hours at 37°C at 250 rpm until saturated.
  • BHI Brain Heart Infusion
  • Bacillus subtilis is a gift from the Gill lab (University of Colorado at Boulder) and is obtained as an actively growing culture. Serial dilutions of the actively growing B. subtilis culture are made into Luria Broth (RPI Corp, Mt. Prospect, IL, USA) and are allowed to grow for aerobically for 24 hours at 37°C at 250 rpm until saturated.
  • Chlorobium limicola (DSMZ# 245) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended using Pfennig's Medium I and II (#28 and 29) as described per DSMZ instructions. C. limicola is grown at 25°C under constant vortexing.
  • Citrobacter braakii (DSMZ # 30040) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Brain Heart Infusion(BHI) Broth ( RPI Corp, Mt. Prospect, IL, USA). Serial dilutions of the resuspended C. braakii culture are made into BHI and are allowed to grow for aerobically for 48 hours at 30°C at 250 rpm until saturated.
  • Clostridium acetobutylicum (DSMZ # 792) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Clostridium acetobutylicum medium (#411) as described per DSMZ instructions. C. acetobutylicum is grown anaerobically at 37°C at 250 rpm until saturated.
  • Clostridium aminobutyricum (DSMZ # 2634) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Clostridium aminobutyricum medium (#286) as described per DSMZ instructions. C. aminobutyricum is grown anaerobically at 37°C at 250 rpm until saturated.
  • Clostridium kluyveri (DSMZ #555) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as an actively growing culture. Serial dilutions of C. kluyveri culture are made into Clostridium kluyveri medium (#286) as described per DSMZ instructions. C. kluyveri is grown anaerobically at 37°C at 250 rpm until saturated.
  • Cornyebacterium glutamicum (DSMZ #1412) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as an actively growing culture. Serial dilutions of C. glutamicum culture are made into C. glutamicum medium (#1) as described per DSMZ instructions. C. glutamicum is grown aerobically or anaerobically at 37°C at 250 rpm until saturated.
  • Cupriavidus metallidurans (DMSZ # 2839) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Brain Heart Infusion (BHI) Broth (RPI Corp, Mt. Prospect, IL, USA). Serial dilutions of the resuspended C. metallidurans culture are made into BHI and are allowed to grow for aerobically for 48 hours at 30°C at 250 rpm until saturated.
  • BHI Brain Heart Infusion
  • Cupriavidus necator (DSMZ # 428) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Brain Heart Infusion (BHI) Broth (RPI Corp, Mt. Prospect, IL, USA). Serial dilutions of the resuspended C. necator culture are made into BHI and are allowed to grow for aerobically for 48 hours at 30°C at 250 rpm until saturated. As noted elsewhere, previous names for this species are Alcaligenes eutrophus and Ralstonia eutrophus.
  • Desulfovibrio fructosovorans (DSMZ # 3604) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are thenresuspended in Desulfovibrio fructosovorans medium (#63) as described per DSMZ instructions. D. fructosovorans is grown anaerobically at 37°C at 250 rpm until saturated.
  • Escherichia coli strain BW25113 is obtained from the Yale Genetic Stock Center (New Haven, CT 06520) and is obtained as an actively growing culture. Serial dilutions of the actively growing E. coli K12 culture are made into Luria Broth (RPI Corp, Mt. Prospect, IL, USA) and are allowed to grow for aerobically for 24 hours at 37°C at 250 rpm until saturated.
  • Escherichia coli strain BWapldf ' is a generous gift from George Chen from Tsinghua University in China. Serial dilutions of the actively growing E. coli BWapldf is culture are made into Luria Broth (RPI Corp, Mt. Prospect, IL, USA) and are allowed to grow for aerobically for 24 hours at 37°C at 250 rpm until saturated.
  • Halobacterium salinarum (DSMZ# 1576) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Halobacterium medium (#97) as described per DSMZ instructions. H. salinarum is grown aerobically at 37°C at 250 rpm until saturated.
  • Lactobacillus delbrueckii (#4335) is obtained from WYEAST USA (Odell, OR, USA) as an actively growing culture. Serial dilutions of the actively growing L. delbrueckii culture are made into Brain Heart Infusion (BHI) broth (RPI Corp, Mt. Prospect, IL, USA) and are allowed to grow for aerobically for 24 hours at 30°C at 250 rpm until saturated.
  • BHI Brain Heart Infusion
  • Metallosphaera sedula (DSMZ #5348) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as an actively growing culture. Serial dilutions of M. sedula culture are made into Metallosphaera medium (#485) as described per DSMZ instructions. M. sedula is grown aerobically at 65°C at 250 rpm until saturated.
  • Methylococcus capsulatus Bath (ATCC # 33009) is obtained from the American Type Culture Collection (ATCC) (Manassas, VA 20108 USA) as a vacuum dried culture. Cultures are then resuspended in ATCC ® Medium 1306: Nitrate mineral salts medium (NMS) under a 50% air 50% methane atmosphere (ATCC, Manassas, VA 20108 USA) and are allowed to grow at 45°C .
  • ATCC American Type Culture Collection
  • NMS Nitrate mineral salts medium
  • Methylococcus thermophilus IMV 2 Yu T is obtained.
  • ATCC ® Medium 1306 Nitrate mineral salts medium (NMS) under a 50% air 50% methane atmosphere (ATCC, Manassas, VA 20108 USA ) and are allowed to grow at 50°C .
  • NMS Nitrate mineral salts medium
  • Methylosinus tsporium (ATCC # 35069) is obtained from the American Type Culture Collection (ATCC) (Manassas, VA 20108 USA) as a vacuum dried culture. Cultures are then resuspended in ATCC ® Medium 1306: Nitrate mineral salts medium (NMS) under a 50% air 50%o methane atmosphere (ATCC, Manassas, VA 20108 USA ) and are allowed to grow at 30°C . "ATCC # 35069) is obtained from the American Type Culture Collection (ATCC) (Manassas, VA 20108 USA) as a vacuum dried culture. Cultures are then resuspended in ATCC ® Medium 1306: Nitrate mineral salts medium (NMS) under a 50% air 50%o methane atmosphere (ATCC, Manassas, VA 20108 USA ) and are allowed to grow at 30°C . "ATCC # 35069) is obtained from the American Type Culture Collection (ATCC) (Manassas, VA
  • Pichia pastoris ( Komagataella pastoris) (DSMZ# 70382) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in YPD-medium (#393) as described per DSMZ instructions. Pichia pastoris is grown aerobically at 30°C at 250 rpm until saturated.
  • Propionibacterium freudenreichii subsp. shermanii (DSMZ# 4902) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in PYG-medium (#104) as described per DSMZ instructions. P. freudenreichii subsp. shermanii is grown anaerobically at 30°C at 250 rpm until saturated.
  • Pseudomonas putida is a gift from the Gill lab (University of Colorado at Boulder) and is obtained as an actively growing culture. Serial dilutions of the actively growing P. putida culture are made into Luria Broth (RPI Corp, Mt. Prospect, IL, USA) and are allowed to grow for aerobically for 24 hours at 37°C at 250 rpm until saturated.
  • Saccharomyces cerevisiae strains can be obtained from the American Type Culture Collection (ATCC) (Manassas, VA 20108 USA) as a vacuum dried culture. Cultures are then resuspended in YPD Media and allowed to grow at 30°C.
  • ATCC American Type Culture Collection
  • VA 20108 USA Manassas, VA 20108 USA
  • Streptococcus mutans (DSMZ# 6178) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in Luria Broth (RPI Corp, Mt. Prospect, IL, USA). S. mutans is grown aerobically at 37°C at 250 rpm until saturated.
  • Yarrowia lipolytica (DSMZ# 1345) is obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany) as a vacuum dried culture. Cultures are then resuspended in YPD-medium (#393) as described per DSMZ instructions Yarrowia lipolytica is grown aerobically at 37°C at 250 rpm until saturated.
  • this example is meant to describe a non-limiting approach to genetic modification of a selected microorganism to introduce, remove or alter a nucleic acid sequence of interest.
  • Alternatives and variations are provided within this general example.
  • the methods of this example are conducted to achieve a combination of desired genetic modifications in a selected microorganism species, such as a combination of genetic modifications as described in sections herein, and their functional equivalents, such as in other bacterial and other microorganism species.
  • a gene or other nucleic acid sequence segment of interest is identified in a particular species (such as E. coli as described herein) and a nucleic acid sequence comprising that gene or segment is obtained.
  • each primer is designed to have a sufficient overlap section that hybridizes with such ends or adjacent regions.
  • Such primers may include enzyme recognition sites for restriction digest of transposase insertion that could be used for subsequent vector incorporation or genomic insertion. These sites are typically designed to be outward of the hybridizing overlap sections. Numerous contract services are known that prepare primer sequences to order (e.g., Integrated DNA Technologies, Coralville, IA USA).
  • PCR polymerase chain reaction
  • segment of interest may be synthesized, such as by a commercial vendor, and prepared via PCR, rather than obtaining from a microorganism or other natural source of DNA.
  • the nucleic acid sequences then are purified and separated, such as on an agarose gel via electrophoresis.
  • the region can be validated by standard DNA sequencing methodology and may be introduced into a vector.
  • Any of a number of vectors may be used, which generally comprise markers known to those skilled in the art, and standard methodologies are routinely employed for such introduction. Commonly used vector systems are well known in the art.
  • the vector then is introduced into any of a number of host cells. Commonly used host cells are E. coli strains. Some of these vectors possess promoters, such as inducible promoters, adjacent the region into which the sequence of interest is inserted (such as into a multiple cloning site). The culturing of such plasmid-laden cells permits plasmid replication and thus replication of the segment of interest, which often corresponds to expression of the segment of interest.
  • Various vector systems comprise a selectable marker, such as an expressible gene encoding a protein needed for growth or survival under defined conditions.
  • selectable markers contained on backbone vector sequences include genes that encode for one or more proteins required for antibiotic resistance as well as genes required to complement auxotrophic deficiencies or supply critical nutrients not present or available in a particular culture media.
  • Vectors also comprise a replication system suitable for a host cell of interest.
  • the plasmids containing the segment of interest can then be isolated by routine methods and are available for introduction into other microorganism host cells of interest.
  • Various methods of introduction are known in the art and can include vector introduction or genomic integration.
  • the DNA segment of interest may be separated from other plasmid DNA if the former will be introduced into a host cell of interest by means other than such plasmid.
  • steps of the general prophetic example involve use of plasmids
  • other vectors known in the art may be used instead. These include cosmids, viruses (e.g., bacteriophage, animal viruses, plant viruses), and artificial chromosomes (e.g., yeast artificial chromosomes (YAC) and bacteria artificial chromosomes (BAC)).
  • viruses e.g., bacteriophage, animal viruses, plant viruses
  • artificial chromosomes e.g., yeast artificial chromosomes (YAC) and bacteria artificial chromosomes (BAC)
  • Host cells into which the segment of interest is introduced may be evaluated for performance as to a particular enzymatic step, and/or tolerance or bio-production of a chemical compound of interest. Selections of better performing genetically modified host cells may be made, selecting for overall performance, tolerance, or production or accumulation of the chemical of interest.
  • this procedure may incorporate a nucleic acid sequence for a single gene (or other nucleic acid sequence segment of interest), or multiple genes (under control of separate promoters or a single promoter), and the procedure may be repeated to create the desired heterologous nucleic acid sequences in expression vectors, which are then supplied to a selected microorganism so as to have, for example, a desired complement of enzymatic conversion step functionality for any of the herein-disclosed metabolic pathways.
  • a nucleic acid sequence for a single gene or other nucleic acid sequence segment of interest
  • multiple genes under control of separate promoters or a single promoter
  • Chromosomal modifications can be made to E. coli using one of many methods including phage transduction and recombineering. It is appreciated that one skilled in the art is well versed in these methods. Of particular use are scarless recombineering methods, which allow for the precise deletion or addition of sequences to the chromosome without any unneeded sequences remaining such as that taught by Li, X., et al. "Positive and negative selection using the tetA-sacB cassette: recombineering and PI transduction in Escherichia coli ". Nucleic Acids Res. December 2013. 41(22) doi: 10.1093.
  • Chromosomal modifications can be made to many yeast strains including Saccharomyces cerevisiae. using methods well known in the art for homologous recombination. It is appreciated that one skilled in the art is well versed in these methods.
  • GM25 media GM25 minimal growth media for E. coli contained per liter: 736 mL sterile distilled, deionized water, 2.0 mL of 100X Trace Metals Stock, 100 mL of 10X GM phosphate salts, 2.0 mL of 2M MgS0 4 , 50 mL of 500 g/L glucose, 100 mL of 1 M MOPS buffer, pH 7.4, and 10.0 mL of 100 g/L Yeast Extract.
  • the 100X Trace Metal Stock was prepared in 1.0 L of distilled, deionized water with 10.0 mL of concentrated HCl with 5.0 g CaCl 2 *2H 2 0, 1.00 g FeCl 3 *6H 2 0, 0.05 g CoCl 2 *6H 2 0, 0.3 g CuCl 2 *2H 2 0, 0.02 g ZnCl 2 ,0.02 g Na 2 Mo0 *2H 2 0, 0.01 g H3BO3, and 0.04 g MnCl 2 *4H 2 0 and 0.2 ⁇ sterile-filtered.
  • the 100X Trace Metal Stock was prepared in 1.0 L of distilled, deionized water with 10.0 mL of concentrated HCl with 5.0 g CaCl 2 *2H 2 0, 1.00 g FeCl 3 *6H 2 0, 0.05 g CoCl 2 *6H 2 0, 0.3 g CuCl 2 *2H 2 0, 0.02 g ZnCl 2 ,0.02 g Na 2 Mo0 *2H
  • the 2M MgS0 4 was prepared in 1.0 L of distilled, deionized water with 240.0 g of anhydrous MgS0 4 and 0.2 ⁇ sterile-filtered.
  • the 500 g/L Glucose solution was prepared in 1.0 L of heated distilled, deionized water and 500 g of anhydrous dextrose and 0.2 ⁇ sterile-filtered.
  • the 1 M 4-Morpholinopropanesulfonic acid (MOPS) buffer was prepared in 700.0 mL of distilled, deionized water with 210.0 g MOPS and 30.0 mL 50% KOH solution. The pH was measured with stirring and final adjustments made to pH 7.4 by slowly adding 50%o KOH and Q.S. to a final volume of 1.0 L. The final pH 7.4 solution was 0.2 ⁇ sterile-filtered.
  • MOPS 4-Morpholinopropanesulfonic acid
  • PM25 media PM25 minimal production media for E. coli contained per liter: 636 mL sterile distilled, deionized water, 2.0 mL of 100X Trace Metals Stock, 100 mL of 10X PM phosphate-free salts, 2.0 mL of 2M MgS0 4 , 50 mL of 500 g/L glucose, 200 mL of 1 M MOPS buffer, pH 7.4, and 10 mL of 1 mg/mL Thiamine.
  • the 100X Trace Metal Stock was prepared in 1.0 L of distilled, deionized water with 10.0 mL of concentrated HCl with 5.0 g CaCl 2 *2H 2 0, 1.00 g FeCl 3 *6H 2 0, 0.05 g CoCl 2 *6H 2 0, 0.3 g CuCl 2 *2H 2 0, 0.02 g ZnCl 2 ,0.02 g Na 2 Mo0 *2H 2 0, 0.01 g H3BO3, and 0.04 g MnCl 2 *4H 2 0 and 0.2 ⁇ sterile-filtered.
  • the 10X PM Phosphate-Free Salts were prepared in 1.0 L of distilled, deionized water with 30 g (NH 4 ) 2 S0 4 and 1.5 g Citric Acid (anhydrous) and autoclaved.
  • the 2M MgS0 4 was prepared in 1.0 L of distilled, deionized water with 240.0 g of anhydrous MgS0 4 and 0.2 ⁇ sterile- filtered.
  • the 500 g/L Glucose solution was prepared in 1.0 L of heated distilled, deionized water and 500 g of anhydrous dextrose and 0.2 ⁇ sterile-filtered.
  • the 1 M 4- Morpholinopropanesulfonic acid (MOPS) buffer was prepared in 700.0 mL of distilled, deionized water with 210.0 g MOPS and 30.0 mL 50% KOH solution. The pH was measured with stirring and final adjustments made to pH 7.4 by slowly adding 50%o KOH and Q.S. to a final volume of 1.0 L. The final pH 7.4 solution was 0.2 ⁇ sterile-filtered.
  • MOPS 4- Morpholinopropanesulfonic acid
  • FGM3 Media FGM3 media for E.
  • 96WPM Media 96WPM media for E. coli contained per liter: 638.8 mL sterile distilled, deionized water, 2.0 mL of 100X Trace Metals Stock, 100 mL of 10X Ammonium Citrate 30 Salts, 2mL of 40 mM Fe(II) sulfate, 2.0 mL of 2M MgS0 4 , 5.0mL of 10 mM 2M CaSC , 50 mL of 500 g/L glucose, 200 mL of 1 M MOPS buffer, pH 7.4, and 0.2 mL of 1 mg/mL Thiamine and 10.0 mL of lOOg/L Yeast Extract.
  • Antibiotic concentrations Unless other wise stated standard final concentrations of antibiotic in media are kanamycin (35 ug/mL), ampicillin (100 ug/ml), spectinomycin (100 ug/ml) , chloramphenicol (20 ug/ml) , anhydrotetracycline (50 ng/ml), gentamicin (10 ug/ml), zeocin (50 ug/ml), blasticidin (50 ug/ml). Low salt medium such as low salt LB medium is used when using blasticidin or zeocin as selective antibiotics.
  • Bioproduction is demonstrated at a 50-mL scale using GM25 minimal defined media without phosphate.
  • Cultures are started from single colonies by standard practice into 50 mL of GM25 media containing 3.2 mM phosphate plus appropriate antibiotics and grown to stationary phase overnight at 30°C with rotation at 200 rpm.
  • the optical density ( ⁇ , 1 cm pathlength) of each stationary phase culture is measured and the entire culture is transferred to 50 mL conical tubes and centrifuged at 4,000 rpm for 15 minutes.
  • a 20 optical density resuspension is generated for each culture by calculating the volume of GM25 media to add to the pellet.
  • Bioproduction is demonstrated at a 50-mL scale in GM25 minimal defined media without phosphate.
  • Cultures are started from single colonies by standard practice into 50 mL of GM25 media containing 3.2 mM phosphate plus appropriate antibiotic(s) and grown to stationary phase overnight at 37°C with rotation at 200 rpm.
  • the optical density ( ⁇ , 1 cm pathlength) of each stationary phase culture is measured and the entire culture was transferred to 50 mL conical tubes and centrifuged at 4,000 rpm for 15 minutes.
  • a 20 optical density resuspension is generated for each culture by calculating the volume of GM25 media to add to the pellet.
  • Bioproduction is demonstrated at ⁇ L in minimal medium.
  • Colonies were used to inoculate individual wells in standard 96 well plates, filled with 150 ⁇ L of SM10++ medium with the appropriate antibiotics as needed. Plates were covered with sandwich covers (Model # CR1596 obtained from EnzyScreen, Haarlam, The Netherlands). These covers ensure minimal evaporative loss during incubation. To ensure adequate aeration, the inoculated 96 well plates and sandwich covers were clamped into place into a Mini Shaking Incubator (VWR Catalog # 12620-942, VWR International LLC, Radnor, PA, USA.) at a temperature set to 37 degrees Celsius and a shaking speed of 1100 rpm.
  • VWR Catalog # 12620-942 VWR International LLC, Radnor, PA, USA.
  • the plate clamps used were obtained from Enzyscreen (Model #CR1600, EnzyScreen, Haarlam, The Netherlands). Importantly, the shaker used had an orbit of 0.125 inches or 3mm. This combination of orbit and minimal shaking speed is required to obtain needed mass transfer coefficient and enable adequate culture oxygenation. Cultures were grown for 16 hours.
  • Bioproduction is demonstrated at mL scale in minimal medium. Seeds were prepared as follows._Colonies were used to inoculate 4 mL of SM10 medium, with appropriate antibiotics as needed, into a sterile 14 mL culture tube. Culture tubes were incubated overnight at 37 degrees Celsius in a standard floor model shaking incubator at 225 rpm. After overnight growth, 2.5 mL of these cultures were used to inoculate 50 mL of fresh SM10 medium, plus appropriate antibiotics as needed, in a 250 mL volume disposable and sterile rectangular cell culture flask, such as a CellstarTM Cell Culture Flask (VWR Catalog #82050-856, VWR International LLC, Radnor, PA, USA.).
  • VWR Catalog #82050-856 VWR International LLC, Radnor, PA, USA.
  • the Micro-24TM Microreactor system (Pall Corporation, Exton, PA, USA) was used to evaluate strains at the mL scale.
  • Pall 24-well PERC cassettes (Catalogue #MRT-PRC) were used for cell growth and production along with stainless steel check valve caps (Catalogue # MRT-CAP-E24).
  • the experimental protocol was set up with an initial volume of 3mL of FGM3 medium, with appropriate antibiotics as needed, and an agitation of 1000 rpm. pH control was initially turned off. The temperature was controlled at 37 degrees Celsius, with an environmental temperature of 35 degrees Celsius. Oxygen control was initially turned off with monitoring enabled.
  • Frozen seed vials were thawed on ice and 150 ⁇ was used to inoculate each 3mL culture in each Micro24 cassette well. Samples were collected at inoculation and at regular intervals. Optical density of samples was measured at 600nm, glucose using a YSI biochemistry analyzer was measured as described below. In addition, supematants were collected for subsequent analytical analyses. pH control was turned on for each well at the point at which the culture's optical densities as measured at 600nm was greater than 1.0. pH control was achieved with pressured ammonium hydroxide gas. In addition, oxygen control was turned on for each well when the dissolved oxygen reached below 60%. Glucose boluses of lOg/L were added both 24 and 48 hours post inoculation using a sterile 500g/L stock solution.
  • Bioproduction is demonstrated at L scale in minimal medium. Seeds were prepared as follows._Colonies were used to inoculate 4 mL of SM10 medium, with appropriate antibiotics as needed, into a sterile 14 mL culture tube. Culture tubes were incubated overnight at 37 degrees Celsius in a standard floor model shaking incubator at 225 rpm. After overnight growth, 2.5 mL of these cultures were used to inoculate 50 mL of fresh SM10 medium, plus appropriate antibiotics as needed, in a 250 mL volume disposable and sterile rectangular cell culture flask, such as a CellstarTM Cell Culture Flask (VWR Catalog #82050-856, VWR International LLC, Radnor, PA, USA.).
  • VWR Catalog #82050-856 VWR International LLC, Radnor, PA, USA.
  • An Infors-HT Multifors (Laurel, MD, USA) parallel bioreactor system was used to perform IL fermentations, including three gas connection mass flow controllers configured for air, oxygen and nitrogen gases. Vessels used had a total volume of 1400 mL and a working volume of up to IL. Online pH and p02 monitoring and control were accomplished with Hamilton probes. Offgas analysis was accomplished with a multiplexed Blue-in-One BlueSens gas analyzer (BlueSens. Northbrook, IL, USA). Culture densities were continually monitored using Optek 225 mm OD probes, (Optek , Germantown, WI, USA).
  • the system used was running IrisV6.0 command and control software and integrated with a Seg-flow automated sampling system (Flownamics, Rodeo, CA USA), including FISP cell free sampling probes, a Segmod 4800 and FlowFraction 96 well plate fraction collector.
  • a Seg-flow automated sampling system Flownamics, Rodeo, CA USA
  • FISP cell free sampling probes a Segmod 4800 and FlowFraction 96 well plate fraction collector.
  • Tanks were filled with 800mL of FGM10 Medium, with enough phosphate to target a final E. coli biomass concentration close to lOg dry cell weight per liter. Antibiotics were added as appropriate. Frozen seed vials were thawed on ice and 7mL of seed culture was used to inoculate the tanks. After inoculation, tanks were controlled at 37 degrees Celsius and pH 6.8 using a 10M solution of sodium hydroxide solution as a titrant. The following oxygen control scheme was used to maintain a dissolved oxygen set point of 25%.
  • First gas flow rate was increased from a minimum of 0.3 L/min of air to 0.8 L/min of air, subsequently, if more aeration was needed, agitation was increased from a minimum of 300 rpm to a maximum of 1000 rpm. Finally if more oxygen was required to achieve a 25%o set point, oxygen supplementation was included using the integrated mass flow controllers.
  • a constant concentrated sterile filtered glucose feed 500g/L was added to the tanks at a rate of 2mL/hr, once agitation reached 800rpm. Fermentation runs were extended for up to 70 hrs and samples automatically withdrawn every 2-4 hrs. Samples were saved for subsequent analytical analysis.
  • a reverse phase UPLC-MS/MS method was developed for the simultaneous quantification of organic and amino acids. Chromatographic separation was performed using an Acquity CSH Ci g column (100 mm ⁇ 2.1 i.d., 1.7 ⁇ ; Waters Corp., Milford, MA, USA) at 45 degrees C. The following eluents were used: solvent A: 3 ⁇ 4( , 0.2% formic acid and 0.05%o ammonium (v/v); solvent B: MeOH, 0.1 % formic acid and 0.05%o ammonium (v/v).
  • the gradient elution was as follows: 0-0.2 min isocratic 5% B, 0.2-1.0 min linear from 5% to 90% B, 1.0-1.5 min isocratic 90% B, and 1.5-1.8 min linear from 90% to 5% B, with 1.8-3.0 min for initial conditions of 5% B for column equilibration.
  • the flow rate remained constant at 0.4 ml/min.
  • a 5 ⁇ sample injection volume was used.
  • UPLC method development was carried out using standard aqueous stock solutions of analytes. Separations were performed using an Acquity H-Class UPLC integrated with a XevoTM TQD Mass spectrometer (Waters Corp., Milford, MA. USA).
  • MS/MS parameters including MRM transitions were tuned for each analyte and are listed in Table 6 below.
  • Adipic acid at a concentration of 36mg/L was used as an internal standard for normalization in all samples. Peak integration and further analysis was performed using Mass Lynx v4.1 software. The linear range for all metabolites was 2-50 mg/L. Samples were diluted as needed to be within the accurate linear range.
  • a confirmatory HPLC method was developed for the quantification of 2,3 butanediol stereoisomers. Chromatographic separation was performed using a Biorad Aminex HPX-87H column (300 x 7.8 mm, 1.7 ⁇ ; Biorad, Hercules, California USA). The isocratic separation was run at room temperature with 5mM sulfuric acid as the mobile phase. The flow rate remained constant at 0.4 ml/min for 40 minutes after an injection. A 10 ⁇ sample injection volume was used. Method development was carried out using standard aqueous stock solutions of analytes. Separations were performed using an Acquity H-Class UPLC integrated with an ESAT/IN refractive index (RI) detector. (Waters Corp., Milford, MA.
  • RI refractive index

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