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Definitions

• Ammonia is highly toxic and generated during metabolism in all organs (Walker, 2012). Hyperammonemia is caused by the decreased detoxification and/or increased production of ammonia, in mammals, the urea cycle detoxifies ammonia by enzymatica!ly converting ammonia into urea, which is then removed in the urine. Decreased ammonia detoxification may be caused by urea cycle disorders (UCDs) in which urea cycle enzymes are defective, such as argininosuccinic aciduria, arginase deficiency,
• Another aspect of the invention provides methods for selecting or targeting genetically engineered bacteria based on increased levels of ammonia and/or nitrogen consumption, or production of a non-toxic byproduct, e.g., arginine or citruiline.
• the invention also provides pharmaceutical compositions comprising the genetically engineered bacteria, and methods of modulating and treating disorders associated with
• Fig. 4 depicts another embodiment of the invention.
• a construct comprising an ArgR binding site (black bar) in a promoter driving expression of the Tet repressor (TetR) from the tetR gene is linked to a second promoter comprising a TetR binding site (black bar bound to TetR oval) that drives expression of green fluorescent protein ("GFP").
• TetR TetR binding site
• GFP green fluorescent protein
• TetR is expressed and inhibits the expression of GFP.
• ArgR associates with arginine and binds to the ArgR binding site, thereby inhibiting expression of TetR from the tetR gene.
• RNA polymerase binding sites are underlined (Cunin, 1983; Maas, 1994). Bases that are protected from DNA methylation during ArgR binding are highlighted, and bases that are protected from hydroxy! radical attack during ArgR binding are boided (Charlier et a!., 1992). The highlighted and bonded bases are the primary targets for mutations to disrupt ArgR binding.
• F g. 10 depicts a schematic diagram of the argA TO! gene under the control of an exemplary FNR promoter (fnrS) fused to a strong ribosome binding site.
• Fig. 11 depicts another schematic diagram of the argA far gene under the control of an exemplary FNR promoter (nirB) fused to a strong ribosome binding site.
• Other regulatory elements may also be present.
• Fig. 17 depicts a map of the wild-type argG operon E, coii Nissle, and a constitutively expressing mutant thereof. ARG boxes are present in the wild-type operon, but absent from the mutant. ArgG is constitutively expressed under the control of the
• F g. 29 depicts a bar graph of ammonia levels in hyperammonemic spf sh mice. Fifty-six spf stl mice were separated into four groups. Group 1 was fed normal chow., and groups 2-4 were fed 70% protein chow following an initial blood draw. Groups were gavaged twice daily, with water, streptomycin-resistant Nissle control (SYN-UCD103), or SYN-UCD204, and blood was drawn 4 hours following the first gavage.
• SYN-UCD103 streptomycin-resistant Nissle control
• SYN-UCD204 SYN-UCD204
• Fig. 3B depicts another non-limiting embodiment of the disclosure, where an exogenous environmental condition or one or more environmental signals activates expression of a heterologous gene and at least one recombinase from an inducible promoter or inducible promoters.
• the recombinase then flips at least one excision enzyme into an activated conformation.
• the at least one excision enzyme then excises one or more essential genes, leading to senescence, and eventual cell death.
• Fig. 59 depicts an exemplary tryptophan biosynthesis pathway.
• Fig. 61 depicts a synthetic biotic engineered to target urea cycle disorder (UCD) having the kill-switch embodiment described in Fig. 60.
• UCD urea cycle disorder
• the Int recombinanse and the Kid-Kis toxin-antitoxin system are used in a recombinant bacterial cell for treating UCD.
• the recombinant bacterial ceil is engineered to consume excess ammonia to produce beneficial byproducts to improve patient outcomes.
• the recombinant bacterial cell also comprises a highly controlla ble kill switch to ensure safety.
• Fig. 62 depicts another non-limiting embodiment of the disclosure, wherein the expression of a heterologous gene is activated by an exogenous environmental signal.
• the AraC transcription factor adopts a conformation that represses transcription.
• the AraC transcription factor undergoes a conformational change that allows it to bind to and activate the AraBAD promoter, which induces expression of TetR (tet repressor) and an antitoxin.
• TetR tet repressor
• the antitoxin builds up in the recombinant bacterial cell, while TetR prevents expression of a toxin (which is under the control of a promoter having a TetR binding site).
• chromosome multiple copies of any arginine operon, or a gene or regulatory region within an arginine operon, may be present in the bacterium, wherein one or more copies of the operon or gene or regulatory region may be mutated or otherwise altered as described herein.
• the genetically engineered bacteria are engineered to comprise multiple copies of the same product (e.g.. operon or gene or regulatory region) to enhance copy num ber or to comprise multiple different components of an operon performing multiple different functions.
• ArgR binding to a mutant ARG box and regulatory region of an operon is at least a bout 50% lower, at least a bout 60% lower, at least a bout 70% lower, at least a bout 80% lower, at least a bout 90% lower, or at least a bout 95% lower than ArgR binding to an unmodified ARG box and regulatory region in bacteria of the same su btype under the same conditions.
• a "non-native" nucleic acid sequence refers to a nucleic acid sequence not normally present in a bacterium, e.g., an extra copy of an endogenous sequence, or a heterologous sequence such as a sequence from a different species, strain, or substrain of bacteria, or a sequence that is modified and/or mutated as compared to the unmodified sequence from bacteria of the same subtype.
• the non- native nucleic acid sequence is a synthetic, non-naturaliy occurring sequence ⁇ see, e.g., Purceil et a!., 2013).
• genetically engineered bacteria that "overproduce" arginine or an intermediate byproduct refer to bacteria that comprise a mutant arginine reguion.
• the engineered bacteria may comprise a feedback resistant form of ArgA, and when the arginine feedback resistant ArgA is expressed, are capable of producing more arginine and/or intermediate byproduct than unmodified bacteria of the same subtype under the same conditions.
• the geneticaliy engineered bacteria may alternatively or further comprise a mutant arginine reguion comprising one or more nucleic acid mutations in at least one ARG box for each of the operons that encode the arginine biosynthesis enzymes.
• Probiotic is used to refer to live, non-pathogenic microorganisms, e.g., bacteria, which can confer health benefits to a host organism that contains an appropriate amount of the microorganism.
• the host organism is a mammal.
• the host organism is a human.
• Some species, strains, and/or subtypes of non-pathogenic bacteria are currently recognized as probiotic bacteria.
• the stable bacterium may be a genetically engineered bacterium comprising an orgA tU! gene., in which the plasmid or chromosome carrying the arg,4 J" gene is stably maintained in the bacterium, such that argft can be expressed in the bacterium, and the bacterium is capable of survival and/or growth in vitro and/or in vivo.
• arginine biosynthesis genes i.e., argA, argB, argC, argD, argE, argF, argG, argH, arg!, argj, carA, and carB
• argA, argB, argC, argD, argE, argF, argG, argH, arg!, argj, carA, and carB may he organized, naturally or synthetically, into one or more operons, and such organization may vary between bacterial species, strains, and subtypes ⁇ see, e.g.. Table 2).
• the regulatory region of each operon contains at least one ARG box, and the number of ARG boxes per regulatory region may vary between operons and bacteria,
• the bacterial methionine regulon controls the three-step synthesis of methionine from homoserine (i.e., acylation, sulf rylation, and methy!ation).
• the metJ gene encodes a regulatory protein that, when combined with methionine or a derivative thereof, causes repression of genes within the methionine regulon at the transcriptional level (Saint- Girons et a!., 1984; Shoeman et al,, 1985).
• the genetically engineered bacteria of the invention comprise deleted, disrupted, or mutated metJ.
• Bacteria engineered to comprise a feedback-resistant DHDPS wouid have elevated levels of histidine production, thus increasing ammonia consumption and reducing hyperammonemia.
• lysine production could be optimized by placing one or more genes required for lysine biosynthesis under the control of an inducible promoter, such as a FNR-inducible promoter. Any other suitable modification(s) to the lysine biosynthesis pathway may be used to increase ammonia consumption.
• a fluorophore is added to a sample reaction mixture that may contain arg mRNA, and a thermal cycler is used to illuminate the sample reaction mixture with a specific wavelength of light and detect the subsequent emission by the fluorophore.
• the reaction mixture is heated and cooled to predetermined temperatures for predetermined time periods. In certain embodiments, the heating and cooling is repeated for a predetermined number of cycles.
• a fluorophore is added to a sample reaction mixture that may contain org mRNA, and a thermal cycler is used to illuminate the sample reaction mixture with a specific wavelength of light and detect the subsequent emission by the fluorophore.
• the reaction mixture is heated and cooled to predetermined temperatures for predetermined time periods, in certain embodiments, the heating and cooling is repeated for a predetermined number of cycles.
• the arginine feedback resistant N-acety!g!utamate synthetase protein (argA jbr ) is significantly less sensitive to L-arginine than the enzyme from the feed back sensitive parent strain (see, e.g., Eckhardt et al., 1975; Rajagopal et a!., 1998).
• the feed back resistant argA gene can be present on a plasmid or chromosome.
• expression from the plasmid may be useful for increasing argA r expression.
• expression from the chromosome may be useful for increasing sta bility of argA fbr expression.
• the argA' br gene is expressed under the control of a constitutive promoter.
• the argA fbr gene is expressed under the control of a promoter that is induced by exogenous environmental conditions.
• the exogenous environmental conditions are specific to the gut of a mammal.
• exogenous environmental conditions are molecules or metabolites that are specific to the mammalian gut, e.g., propionate or bilirubin.
• the exogenous environmental conditions are low-oxygen or anaerobic conditions, such as the environment of the mammalian gut.
• Non-limiting examples include ArcA/B, ResD/E, NreA/B/C, and AirSR, and others are known in the art.
• insertion sites include, but are not limited to, malE/K, insB/l, araC/BAD, lacZ, dap A, cea, and other shown in F g. 22.
• the genetically engineered bacteria may include four copses of arg r inserted at four different insertion sites, e.g., malE/K, insB/l, araC/BAD, and IacZ,
• the genetically engineered bacteria may include three copies of argA fbr inserted at three different insertion sites, e.g., malE/K, insB/i, and IacZ, and three mutant arginine regulons, e.g., two producing citrulline and one producing arginine, inserted at three different insertion sites dapA, cea, and araC/BAD.
• the mutant arginine regulon comprises argA**" expressed under the control of an oxygen level-dependent promoter, e.g., a FNR promoter, and further comprises wild-type argA without any ARG box mutations.
• essential gene refers to a gene which is necessary to for cell growth and/or survival.
• Bacterial essential genes are well known to one of ordinary skill in the art, and can be identified by directed deletion of genes and/or random
• an ArgR-repressibie promoter comprising wild-type ARG boxes drives the expression of TetR
• a TetR-repressibie promoter drives the expression of at least one gene of interest, e.g., GFP
• GFP Gene of interest
• the at least one recombination event is flipping of an inverted heterologous gene encoding a second recom binase by a first recombinase, followed by the flipping of an inverted heterologous gene encoding a bacterial toxin by the second recombinase.
• the inverted heterologous gene encoding the second recombinase is located between a first forward recombinase recognition sequence and a first reverse recombinase recognition sequence.
• the inverted heterologous gene encoding the bacterial toxin is located between a second forward recom binase recognition sequence and a second reverse recombinase recognition sequence, in one embodiment, the heterologous gene encoding the second recombinase is constitutively expressed after it is flipped by the first recombinase. In one embodiment, the heterologous gene encoding the bacterial toxin is constitutively expressed after it is flipped by the second recombinase. in one embodiment, the genetically engineered bacterium is killed by the bacterial toxin.
• the P araC promoter and the P ARA B D promoter operate as a bidirectional promoter, with the P ARA BAD promoter controlling expression of a heterologous gene(s) in one direction, and the P araC (in close proximity to, and on the opposite strand from the P AI A BAD promoter), controlling expression of a heterologous gene(s) in the other direction, in the presence of ara binose, transcription of both heterologous genes from both promoters is induced .
• the P araC promoter and the P ARA B D promoter operate as a bidirectional promoter, with the P ARA BAD promoter controlling expression of a heterologous gene(s) in one direction, and the P araC (in close proximity to, and on the opposite strand from the P AI A BAD promoter), controlling expression of a heterologous gene(s) in the other direction, in the presence of ara binose, transcription of both heterologous genes from both promoters is induced .
• ara binose transcription of both hetero
• Pressurized aerosol dosage units may be determined by providing a valve to deliver a metered amount.
• Capsules and cartridges e.g., of gelatin
• suitable powder base such as lactose or starch.
• the genetically engineered bacteria of the invention may be administered and formulated as depot preparations. Such long acting formulations may be administered by implantation or by injection.
• Suitable bulking agents include glycine and arginine, either of which can be included at a concentration of 0-0.05 %, and polysorbate-80 (optimally included at a concentration of 0.005-0.01%).
• Additional surfactants include but are not limited to polysorbate 20 and BR!J surfactants.
• the pharmaceutical composition may be prepared as an injectable solution and can further comprise an agent useful as an adjuvant, such as those used to increase absorption or dispersion, e.g., hyaluronidase.
• the pharmaceutical composition may be administered alone or in combination with one or more additional therapeutic agents, including but not limited to, sodium phenyl butyrate, sodium benzoate, and glycerol phenyibutyrate.
• additional therapeutic agents including but not limited to, sodium phenyl butyrate, sodium benzoate, and glycerol phenyibutyrate.
• the agent(s) should be compatible with the genetically engineered bacteria of the invention, e.g., the agent(s) must not kill the bacteria
• the pharmaceutical composition is administered with food. In alternate embodiments, the pharmaceutical composition is administered before or after eating food.
• the pharmaceutical composition may be administered in combination with one or more dietary modifications, e.g., low-protein diet and amino acid supplementation.
• the dosage of the pharmaceutical composition and the frequency of administration may be selected based on the severity of the symptoms and the progression of the disorder. The appropriate therapeutically effective dose and/or frequency of administration can be selected by a treating clinician.
• hyperammonemia-associated disorder is a urea cycle disorder.
• urea cycle disorder is argininosuccinic aciduria, arginase deficiency, carbamoylphosphate synthetase deficiency, citru!linemia, N- acetyigiiitamate synthetase deficiency, or ornithine transcarbamylase deficiency.
• the symptoms of the hyperammonemia- associated disorder are selected from the group consisting of seizures, ataxia, stroke-like lesions, coma, psychosis, vision loss, acute encephalopathy, cerebral edema, as well as vomiting, respiratory alkalosis, and hypothermia.
• Lam bda red recom bination is used to make chromosomal modifications, e.g., ARG box mutations.
• Lam bda red is a procedure using recom bination enzymes from a bacteriophage lambda to insert a piece of custom DNA into the chromosome of E. coli.
• a pKD46 plasmid is transformed into the E. co!i Nissie host strain.
• £. coii Nissie cells are grown overnight in LB media. The overnight culture is diluted 1: 100 in 5 mL of LB media and grown until it reaches an OD SO o of 0.4-0.6. All tu bes., solutions, and cuvettes are pre-chilied to 4° C.
• PCR products are analyzed by gel electrophoresis using 10 ⁇ of each amplicon and 2.5 ⁇ 5X dye. The PCR product only forms if the mutation has inserted into the genome.
• the orgA fbr gene is inserted into the bacterial genome at one or more of the following insertion sites in E, coli Nissle: malE/K, araC/BAD, lacZ, thy A, maiP/T. Any suitable insertion site may be used, see, e.g., Fig. 22.
• the insertion site may be anywhere in the genome, e.g., in a gene required for survival and/or growth, such as thy A (to create an auxotroph); in an active area of the genome, such as near the site of genome replication; and/or in between divergent promoters in order to reduce the risk of unintended
• the E. coii Nissle bacteria further comprise an arginine feedback resistant N ⁇ acetylglutamate synthetase (argA jfbr , SEQ ID NO: 28 ⁇ gene expressed under the control of each of the following promoters: tetracycline- inducible promoter, F!MR promoter selected from SEQ ID !MOs: 16-27. As discussed herein, other promoters may be used.
• the arg.A' br gene is expressed on a high-copy piasmid, a low-copy piasmid, or a chromosome.
• ArgR is deleted (AArgR) in each of SYN-UCD201, SYN-UCD202, and SYN- UCD203.
• SYN-UCD201 further comprises wild-type argA, but lacks inducible argA fbr .
• SYN- UCD202 comprises AArgR and argA fbr expressed under the control of a tetracycline-inducible promoter on a high-cop piasmid.
• the plate is heat-sealed with a PierceASeal foil and mixed well, in a V- bottom 96-well polypropylene plate, 5 ⁇ of diluted samples is added to 95 ⁇ of derivatization mix (85 ⁇ . 10m M NaHC0 3 pH 9.7 and ⁇ . lOmg/mL dansyl-chloride (diluted in acetonitrile).
• the plate is heat-sealed with a ThermASeal foil and mixed well.
• the samples are incubated at 60°C for 45 min for derivatization and centrifuged at 4000 rpm for 5 min. in a round-bottom 96-well plate, 20 ⁇ of the derivatized samples are added to 180 ⁇ of water with 0.1% formic acid.
• the plate is heat-sealed with a ClearASeal sheet and mixed well.
• Fig. 24 depicts a bar graph of in vitro arginine levels produced by SY -UCD103, SYN-UCD201, SYN-UCD202, and SYN-UCD203 under inducing (+ATC) and non-inducing (-ATC) fbr
• Intracellular arginine and secreted (supernatant) arginine production in the genetically engineered bacteria in the presence or absence an ATC or anaerobic inducer is measured and compared to control bacteria of the same strain under the same conditions.
• Unmodified E. coii Nissie and the genetically engineered bacteria of the invention may be destroyed, e.g., by defense factors in the gut or blood serum.
• the residence time of bacteria in vivo may be calculated.
• a non-limiting example using a streptomycin- resistant strain of E. coii Nissie is described below.
• residence time is calculated for the genetically engineered bacteria of the invention.

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