WO2023173066A1

WO2023173066A1 - Biosynthesis of abscisic acid and abscisic acid precursors

Info

Publication number: WO2023173066A1
Application number: PCT/US2023/064106
Authority: WO
Inventors: Josef BOBER; Yangxiaolu CAO; Cinzia FORMIGHIERI; Vasiliki TSAKRAKLIDES
Original assignee: Ginkgo Bioworks, Inc.
Priority date: 2022-03-11
Filing date: 2023-03-10
Publication date: 2023-09-14

Abstract

Described in this application are proteins and host cells involved in methods of producing absisic acid (ABA) precursors and/or ABA.

Description

BIOSYNTHESIS OF ABSCISIC ACID AND ABSCISIC ACID PRECURSORS

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 63/319,213 filed March 11, 2022, entitled “BIOSYNTHESIS OF ABSCISIC ACID AND ABSCISIC ACID PRECURSORS,” the entire disclosure of which is hereby incorporated by reference in its entirety.

REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

The contents of the electronic sequence listing (G091970096WO00-SEQ-FL.xml; Size: 55,128 bytes; and Date of Creation: February 9, 2023) is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present disclosure relates to the production of abscisic acid and abscisic acid precursors in recombinant cells.

JOINT RESEARCH AGREEMENT

The presently claimed invention was made by or on behalf of the below listed parties to a joint research agreement. The collaboration and license agreement was in effect on or before the date the claimed invention was made and the claimed invention was made as a result of activities undertaken within the scope of the collaboration and license agreement. The parties to the joint research agreement are 1) Valent BioSciences LLC, 2) Sumitomo Chemical Co. Ltd., and 3) Ginkgo Bioworks, Inc.

BACKGROUND

Abscisic acid (ABA) is an isoprenoid plant hormone derived from the cleavage of carotenoids in the non-mevalonate pathway (MEP). ABA is naturally synthesized in the seeds, fruits, flowers, leaves, stems, and roots of plants, including Arabidopsis thaliana (A. thaliana), and is also naturally produced in some fungal strains. Although anti-inflammatory and anti-diabetic properties have been ascribed to ABA, characterization of the exact proteins involved in ABA biosynthesis is limited. Furthermore, ABA extraction from plants is labor- intensive and the structural complexity of ABA often hinders de novo chemical synthesis. SUMMARY

Aspects of the present disclosure provide host cells and methods useful for the production of absisic acid (ABA) precursors and absisic acid. In some embodiments, the host cell comprises a heterologous polynucleotide encoding a cytochrome b5 (CB5), wherein the host cell is capable of producing more of an abscisic acid (ABA) precursor or ABA than a control host cell that does not comprise the heterologous polynucleotide, and wherein the CB5 comprises a sequence that is at least 90% identical to SEQ ID NO: 1 or 3.

In some embodiments, the CB5 comprises the sequence of SEQ ID NO: 1 or 3.

In some embodiments, the heterologous polynucleotide encoding the CB5 comprises a sequence that is at least 90% identical to a sequence selected from SEQ ID NO: 10 or 12.

In some embodiments, the heterologous polynucleotide encoding the CB5 comprises a sequence selected from SEQ ID NOs: 10 or 12.

In some embodiments, the host cell further comprises a heterologous polynucleotide encoding an ABA synthesis enzyme.

In some embodiments, the ABA synthesis enzyme comprises a sequence that is at least 90% identical to a sequence selected from SEQ ID NOs: 19-23.

In some embodiments, the ABA synthesis enzyme comprises a sequence selected from SEQ ID NOs: 19-23.

In some embodiments, the heterologous polynucleotide encoding the ABA synthesis enzyme comprises a sequence that is at least 90% identical to a sequence selected from SEQ ID NOs: 24-28.

In some embodiments, the heterologous polynucleotide encoding the ABA synthesis enzyme comprises a sequence selected from SEQ ID NOs: 24-28.

In some embodiments, the host cell is a fungal cell, a bacterial cell, an algal cell, a plant cell, an insect cell, or an animal cell. In some embodiments, the fungal cell is a yeast cell. In some embodiments, the host cell is a yeast cell. In some embodiments, the yeast cell is a Saccharomyces cerevisiae cell. In some embodiments, the yeast cell is a Yarrowia lipolytica cell. In some embodiments, the host cell is a bacterial cell. In some embodiments, the bacterial cell is an Escherichia coli cell.

Further aspects of the present disclosure provide methods of producing an abscisic acid (ABA) precursor comprising culturing any of the host cells disclosed herein.

In some embodiments, the ABA precursor is a-ionylideneethane (a-IE), a- ionylideneacetic acid (a-IAA), or l',4'-trans-dihydroxy-a-ionylideneacetic acid (DH-a-IAA or ABA-diol). Further aspects of the present disclosure provide methods of producing abscisic acid (ABA) comprising culturing any of the host cells disclosed herein.

Further aspects of the present disclosure provide bioreactors for producing an abscisic acid (ABA) precursor or ABA. In some embodiments, the bioreactor comprises any of the host cells disclosed herein.

Each of the limitations of the invention can encompass various embodiments of the invention. It is, therefore, anticipated that each of the limitations of the invention involving any one element or combinations of elements can be included in each aspect of the invention. This invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or of being carried out in various ways.

BRIEF DESCRIPTION OF DRAWINGS

The accompanying drawings are not intended to be drawn to scale. The drawings are illustrative only and are not required for enablement of the disclosure. For purposes of clarity, not every component may be labeled in every drawing. In the drawings:

FIG. 1 shows an abscisic acid (ABA) biosynthesis pathway. FIG. 1 is based on FIG. 1 of Otto et al., Microb Cell Fact. 2019; 18: 205.

FIG. 2 is a graph showing ABA-diol production using a Y. lipolytica parent strain (parent strain 1) that expresses the following three ABA synthesis enzymes: abal, aba2, and aba3. The parent strain was transformed with one of 6 fungal Cb5 candidate genes (mined from Myrothecium indicum) or one of 3 S. grosvenorii Cb5 genes. ABA-diol production by each strain was measured by LC-MS. The parent strain produces ABA-diol.

FIG. 3 is a graph showing abscisic acid (ABA) production using a Y. lipolytica parent strain (parent strain 1) that expresses the following three ABA synthesis enzymes: abal, aba2, and aba3. The parent strain was transformed with one of 6 fungal Cb5 candidate genes (mined from Myrothecium indicum) or one of 3 5. grosvenorii Cb5 genes. Production of the stereoisomer S-ABA by each strain was measured by LC-MS. FIG. 3 depicts data from the same samples analyzed in FIG. 2.

FIG. 4 is a graph showing ABA production using a Y. lipolytica parent strain (parent strain 2) that expresses the following four ABA synthesis enzymes: abal, aba2, aba3, and aba4. The parent strain was transformed with either of two S'. grosvenorii genes encoding CB5 proteins (SEQ ID NO: 1, which is referred to in this application as “alpha” or “CB5 alpha” and SEQ ID NO: 3, which is referred to in this application as “gamma” or “CB5 gamma”). SEQ ID NO: 2 is referred to in this application as “beta” or “CB5 beta.” Production of the stereoisomer S-ABA by each strain was measured by LC-MS. The parent strain produces ABA.

FIG. 5 is a graph showing ABA production using a Y. lipolytica parent strain (parent strain 3) that expresses the following ABA synthesis enzymes: abal, aba2, aba3, and aba4 and also a Cytochrome P450 reductase (Myrothecium indicum CPR). The parent strain was transformed with either of two 5. grosvenorii genes encoding CB5 proteins (SEQ ID NO: 1 or 3). Production of the stereoisomer S-ABA by each strain was measured by LC-MS. The parent strain produces ABA.

DETAILED DESCRIPTION

Synthesis of Abscisic Acid (ABA) and ABA Precursors

FIG. 1 shows a putative ABA biosynthesis pathway in a eukaryotic cell. An early step in the biosynthesis of ABA is the mevalonate pathway. As shown in FIG. 1, the mevalonate pathway converts acetyl-CoA to two five carbon building blocks called isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Two acetyl-CoA molecules are condensed by acetoacetyl-CoA thiolase to yield acetoacetyl-CoA. AcetoacetyLCoA is further condensed by HMG-CoA synthase to yield 3-hydroxy-3-methyl-glutaryl-CoA (HMG- CoA). HMG-CoA is then reduced by HMG-CoA reductase to yield mevalonate. At this juncture, mevalonate is either converted to mevalonate-3-phosphate or mevalonate-5- phosphate. In ABA biosynthesis, mevalonate is phosphorylated twice at the 5-OH position to yield mevalonate-5-phosphate then mevalonate pyrophosphate (MVA-PP). MVA-PP is then decarboxylated by mevalonate pyrophosphate decarboxylase to yield IPP. IPP is isomerized to DMAPP via isopentenyl pyrophosphate isomerase, concluding the mevalonate pathway.

Following the mevalonate pathway, ABA biosynthesis continues when IPP and DMAPP are condensed by geranyl pyrophosphate synthase to yield geranyl pyrophosphate (GPP). GPP is then converted to farnesyl pyrophosphate (FPP), which can enter one of many downstream pathways, including the ABA biosynthesis pathway.

FPP enters the ABA biosynthesis pathway once it undergoes direct cyclization by a- ionylideneethane synthase 3 aba3 to yield a-ionylideneethane (a-IE). AB A3 first converts FPP to P-famesene and allofamesene before cyclizing allofarnesene to yield ot-IE. Following cyclization, a- IE interacts with the P450 monooxygenase ABAI to undergo an oxidation reaction to yield a-ionylideneacetic acid (a-IAA), followed by further oxidation by the P450 monooxygenase aba2 to yield l',4'-trans-dihydroxy-a-ionylideneacetic acid (DH-a-IAA or ABA-diol). Finally, the P450 monooxygenase aba4 oxidizes DH-a-IAA to produce ABA. Overall, FPP undergoes direct cyclization to yield a-IE, followed by three oxidation steps to yield ABA.

ABA precursors include but are not limited to acetyl-CoA, acetoacetyl-CoA, HMG- CoA, mevalonate, mevalonate-5-phosphate, MVA-PP, IPP, DMAPP, GPP, FPP, a-IE, a- IAA, and DH-a-IAA.

In some embodiments, ABA is a compound of Formula 1:

In some embodiments, ABA is S-ABA.

In some embodiments, a host cell comprising one or more proteins described herein (e.g., a cytochrome b5 (CB5), a ABA synthesis enzyme, and/or any proteins associated with the disclosure) is capable of producing at least 0.005 mg/L, at least 0.01 mg/L, at least 0.02 mg/L, at least 0.03 mg/L, at least 0.04 mg/L, at least 0.05 mg/L, at least 0.06 mg/L, at least 0.07 mg/L, at least 0.08 mg/L, at least 0.09 mg/L, at least 0.1 mg/L, at least 0.2 mg/L, at least 0.3 mg/L, at least 0.4 mg/L, at least 0.5 mg/L, at least 0.6 mg/L, at least 0.7 mg/L, at least 0.8 mg/L, at least 0.9 mg/L, at least 1 mg/L, at least 2 mg/L, at least 3 mg/L, at least 4 mg/L, at least 5 mg/L, at least 6 mg/L, at least 7 mg/L, at least 8 mg/L, at least 9 mg/L, at least 10 mg/L, at least 11 mg/L, at least 12 mg/L, at least 13 mg/L, at least 14 mg/L, at least 15 mg/L, at least 16 mg/L, at least 17 mg/L, at least 18 mg/L, at least 19 mg/L, at least 20 mg/L, at least 21 mg/L, at least 22 mg/L, at least 23 mg/L, at least 24 mg/L, at least 25 mg/L, at least 26 mg/L, at least 27 mg/L, at least 28 mg/L, at least 29 mg/L, at least 30 mg/L, at least 31 mg/L, at least 32 mg/L, at least 33 mg/L, at least 34 mg/L, at least 35 mg/L, at least 36 mg/L, at least 37 mg/L, at least 38 mg/L, at least 39 mg/L, at least 40 mg/L, at least 41 mg/L, at least 42 mg/L, at least 43 mg/L, at least 44 mg/L, at least 45 mg/L, at least 46 mg/L, at least 47 mg/L, at least 48 mg/L, at least 49 mg/L, at least 50 mg/L, at least 51 mg/L, at least 52 mg/L, at least 53 mg/L, at least 54 mg/L, at least 55 mg/L, at least 56 mg/L, at least 57 mg/L, at least 58 mg/L, at least 59 mg/L, at least 60 mg/L, at least 61 mg/L, at least 62 mg/L, at least 63 mg/L, at least 64 mg/L, at least 65 mg/L, at least 66 mg/L, at least 67 mg/L, at least 68 mg/L, at least 69 mg/L, at least 70 mg/L, at least 75 mg/L, at least 80 mg/L, at least 85 mg/L, at least 90 mg/L, at least 95 mg/L, at least 100 mg/L, at least 125 mg/L, at least 150 mg/L, at least 175 mg/L, at least 200 mg/L, at least 225 mg/L, at least 250 mg/L, at least 275 mg/L, at least 300 mg/L, at least 325 mg/L, at least 350 mg/L, at least 375 mg/L, at least 400 mg/L, at least 425 mg/L, at least 450 mg/L, at least 475 mg/L, at least 500 mg/L, at least

1,000 mg/L, at least 2,000 mg/L, at least 3,000 mg/L, at least 4,000 mg/L, at least 5,000 mg/L, at least 6,000 mg/L, at least 7,000 mg/L, at least 8,000 mg/L, at least 9,000 mg/L, or at least 10,000 mg/L of ABA or a precursor thereof.

Cytochrome b5 ( CB5 )

Aspects of the present disclosure provide cytochrome b5 (CB5) proteins, which may be useful in promoting production of an ABA precursor and/or ABA . As used herein, a “cytochrome b5” or “CB5” refers to a protein that comprises a lipid binding domain or cytochrome b5-like heme binding domain. In some embodiments, a lipid binding domain is a steroid binding domain.

CB5 proteins are heme- or lipid- binding proteins. For example, a CB5 may be a steroid binding protein. Some have been implicated in electron transport and enzymatic redox reactions. CB5 proteins generally harbor a conserved CB5 domain (e.g., a cytochrome b5-like heme or steroid binding domain). The tertiary structure of the CB5 domain is highly conserved and the domain folds around two hydrophobic residue cores on each side of a beta sheet. Without wishing to be bound by any theory, one hydrophobic core may include the heme or lipid binding domain, while the other hydrophobic core may promote formation of the proper conformation. In some embodiments, a lipid binding domain is a steroid binding domain.

Without being bound by a particular theory, two histidine residues may be required for a CB5 to interact with the iron in heme and CB5s that do not comprise these conserved histidine residues may comprise a lipid binding domain (e.g., a steroid binding domain) instead of a heme-binding domain.

A non-limiting example of a CB5 domain is provided under Pfam Accession No.

PF00173. The CB5 domain may form a majority of the protein’s structure. See e.g., SEQ ID NOs: 1-3. In some embodiments, additional domains such as a fatty acid desaturase and/or a FMN-dependent dehydrogenase are also present. CB5 proteins may serve as an electron transfer component of a redox reaction. For example, a CB5 may function as an obligate electron donor in an oxidative reaction. In some embodiments, a CB5 serves as an electron-delivery partner for a cytochrome P450. In some embodiments, a CB5 catalyzes or promotes electron transfer from NADPH to a cytochrome P450 enzyme.

In some embodiments, a CB5 plays an allosteric role to promote production of ABA and/or an ABA precursor. In some embodiments, a CB5 sterically interacts with the P450 enzyme to support an enzyme conformation that promotes higher activity, without a direct enzymatic role of the CB5 itself.

The rate of an enzymatic redox reaction may be assessed by any suitable method, including determination of the change in product concentration over a period of time. Any suitable method including mass spectrometry may be used to measure the presence of a substrate or product. See also, e.g., Schenkman et al., Pharmacology & Therapeutics 97 (2003) 139- 152; Gou et al., Plant Cell. 2019 Jun;31(6): 1344-1366; Interpro Accession No. IPR001199; Interpro Accession No. IPR018506; Lederer Biochimie. 1994;76(7):674-92; GenBank Accession No. AF332415; UniProt Accession No. P40312.

In some embodiments, a CB5 is 100-300 amino acids in length (e.g., 200-300, 210- 290 amino acids in length, 205-215 amino acids in length, or 275-295 amino acids in length).

In some embodiments, a CB5 of the present disclosure comprises a sequence e.g., nucleic acid or amino acid sequence) that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least

55%, at least 60%, at least 65%, at least 70%, at least 71%, at least 72%, at least 73%, at least

74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least

81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least

88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least

95%, at least 96%, at least 97%, at least 98%, at least 99%, or is 100% identical, including all values in between, to any one of SEQ ID NOs: 1-18. In some embodiments, a CB5 of the present disclosure comprises a sequence that is a conservatively substituted version of any one of SEQ ID NOs: 1-9.

In some embodiments, a CB5 is capable of increasing production of an ABA precursor and/or ABA by a host cell by at least 0.01%, at least 0.05%, at least 1%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, or at least 1000%, including all values in between relative to production of the ABA precursor and/or ABA by a host cell that does not comprise the CB5. In some embodiments, a CB5 is capable of increasing production of a ABA precursor and/or ABA by a host cell at most 5%, at most 10%, at most 15%, at most 20%, at most 25%, at most 30%, at most 35%, at most 40%, at most 45%, at most 50%, at most 55%, at most 60%, at most 65%, at most 70%, at most 75%, at most 80%, at most 85%, at most 90%, at most 95%, at most 100%, at most 150%, at most 200%, at most 250%, at most 300%, at most 350%, at most 400%, at most 450%, at most 500%, at most 550%, at most 600%, at most 650%, at most 700%, at most 750%, at most 800%, at most 850%, at most 900%, at most 950%, or at most 1000%, including all values in between relative to production of the ABA precursor and/or ABA by a host cell that does not comprise the CB5. In some embodiments, a CB5 is capable of increasing production of a ABA precursor and/or ABA by a host cell between 0.01% and 1%, between 1% and 10%, between 10% and 20%, between 10% and 50%, between 50% and 100%, between 100% and 200%, between 200% and 300%, between 300% and 400%, between 400% and 500%, between 500% and 600%, between 600% and 700%, between 700% and 800%, between 800% and 900%, between 900% and 1000%,, between 1% and 50%, between 1% and 100%, between 1% and 500%, or between 1% and 1,000%, including all values in between relative to production of the ABA precursor and/or ABA by a host cell that does not comprise the CB5.

In some embodiments, a host cell comprising a CB5 is capable of producing at least O.Olmg/L, at least 0.05mg/L, at least Img/L, at least 5mg/L, at least lOmg/L, at least 15mg/L, at least 20mg/L, at least 25mg/L, at least 30mg/L, at least 35mg/L, at least 40mg/L, at least 45mg/L, at least 50mg/L, at least 55mg/L, at least 60mg/L, at least 65mg/L, at least 70mg/L, at least 75mg/L, at least 80mg/L, at least 85mg/L, at least 90mg/L, at least 95mg/L, at least lOOmg/L, at least 150mg/L, at least 200mg/L, at least 250mg/L, at least 300mg/L, at least

350mg/L, at least 400mg/L, at least 450mg/L, at least 500mg/L, at least 550mg/L, at least

600mg/L, at least 650mg/L, at least 700mg/L, at least 750mg/L, at least 800mg/L, at least

850mg/L, at least 900mg/L, at least 950mg/L, at least lOOOmg/L, at least 2g/L, at least 3g/L, at least 4g/L, at least 5g/L, at least lOg/L, at least 15g/L, at least 20g/L, at least 25g/L, at least 30g/L, at least 35g/L, at least 40g/L, at least 45g/L, at least 50g/L, at least 55g/L, at least 60g/L, at least 65g/L, at least 70g/L, at least 75g/L, at least 80g/L, at least 85g/L, at least 90g/L, at least 95g/L, at least lOOg/L, at least 150g/L, at least 200g/L, at least 250g/L, at least 300g/L, at least 350g/L, at least 400g/L, at least 450g/L, at least 500g/L, at least 550g/L, at least 600g/L, at least 650g/L, at least 700g/L, at least 750g/L, at least 800g/L, at least 850g/L, at least 900g/L, at least 950g/L, or at least lOOOg/L, including all values of a ABA precursor and/or ABA. In some embodiments, a host cell comprising a CB5 is capable of producing at most 5mg/L, at most lOmg/L, at most 15mg/L, at most 20mg/L, at most 25mg/L, at most 30mg/L, at most 35mg/L, at most 40mg/L, at most 45mg/L, at most 50mg/L, at most 55mg/L, at most 60mg/L, at most 65mg/L, at most 70mg/L, at most 75mg/L, at most 80mg/L, at most 85mg/L, at most 90mg/L, at most 95mg/L, at most lOOmg/L, at most 150mg/L, at most 200mg/L, at most 250mg/L, at most 300mg/L, at most 350mg/L, at most 400mg/L, at most 450mg/L, at most 500mg/L, at most 550mg/L, at most 600mg/L, at most 650mg/L, at most 700mg/L, at most 750mg/L, at most 800mg/L, at most 850mg/L, at most 900mg/L, at most 950mg/L, at most lOOOmg/L, at most Ig/L, at least 2g/L, at least 3g/L, at least 4g/L, at most 5g/L, at most lOg/L, at most 15g/L, at most 20g/L, at most 25g/L, at most 30g/L, at most 35g/L, at most 40g/L, at most 45g/L, at most 50g/L, at most 55g/L, at most 60g/L, at most 65g/L, at most 70g/L, at most 75g/L, at most 80g/L, at most 85g/L, at most 90g/L, at most 95g/L, at most lOOg/L, at most 150g/L, at most 200g/L, at most 250g/L, at most 300g/L, at most 350g/L, at most 400g/L, at most 450g/L, at most 500g/L, at most 550g/L, at most 600g/L, at most 650g/L, at most 700g/L, at most 750g/L, at most 800g/L, at most 850g/L, at most 900g/L, at most 950g/L, or at most lOOOg/L of an ABA precursor and/or ABA. In some embodiments, a host cell comprising a CB5 is capable of producing between O.Olmg/L and Img/L, between Img/L and lOmg/L, between lOmg/L and 20mg/L, between lOmg/L and 50mg/L, between 50mg/L and lOOmg/L, between lOOmg/L and 200mg/L, between 200mg/L and 300mg/L, between 300mg/L and 400mg/L, between 400mg/L and 500mg/L, between 500mg/L and 600mg/L, between 600mg/L and 700mg/L, between 700mg/L and 800mg/L, between 800mg/L and 900mg/L, between 900mg/L and 1000mg/L,, between Img/L and 50mg/L, between Img/L and lOOmg/L, between Img/L and 500mg/L, between Img/L and l,000mg/L, between Ig/L and lOg/L, between lOg/L and 20g/L, between lOg/L and 50g/L, between 50g/L and lOOg/L, between lOOg/L and 200g/L, between 200g/L and 300g/L, between 300g/L and 400g/L, between 400g/L and 500g/L, between 500g/L and 600g/L, between 600g/L and 700g/L, between 700g/L and 800g/L, between 800g/L and 900g/L, between 900g/L and 1000g/L„ between Ig/L and 50g/L, between lg/L and lOOg/L, between Ig/L and 500g/L, or between lg/L and 1,000g /L, including all values in between of an ABA precursor and/or ABA. As a non-limiting example, a CB5 may be capable of increasing production of an ABA precursor and/or ABA by a host cell that comprises one or more ABA synthesis enzymes.

ABA Synthesis Enzymes

Aspects of the present disclosure provide ABA synthesis enzymes. FIG. 1 provides a non-limiting example of an ABA biosynthesis pathway. Non-limiting examples of ABA synthesis enzymes include cytochrome P450s, sesquiterpene synthases, short-chain dehydrogenases (or short-chain reductases), and cytochrome P450 reductases that are useful in the production of ABA or precursors thereof. The first of such enzymes is a- ionylideneethane synthase 3 (aba3). AB A3 is a sesquiterpene synthase that facilitates cyclization of farnesyl pyrophosphate (FPP) to a-ionylideneethane (a-IE). AB A3 dephosphorylates FPP to yield P-famesene, reduces P-famesene to yield allofamesene, then cyclizes allofamesene to yield a-IE. Another enzyme involved in ABA biosynthesis is the P450 monooxygenase abal. ABAI oxidizes a-IE to yield a-IAA. a-IAA is further oxidized by the P450 monooxygenase aba2 to yield l',4'-trans-dihydroxy-a-ionylideneacetic acid (DH-a-IAA). Finally, the short-chain dehydrogenase/reductase aba4 oxidizes DH-a-IAA to produce ABA.

In some embodiments, abal is BcABAl from Botrytis cinerea. In some embodiments, aba2 is BcABA2 from Botrytis cinerea. In some embodiments, aba3 is BcABA3 from Botrytis cinerea. In some embodiments, aba4 is BcABA4 from Botrytis cinerea.

In some embodiments, an ABA synthesis enzyme is abal, aba2, aba3, or aba4. ABA synthesis enzymes abal, aba2, aba3, or aba4 may be referred to as “ABAI,” “ABA2,” “ABA3,” and “ABA4,” respectively in this application. Non-limiting examples of amino acid sequences encoding abal, aba2, aba3, or aba4 are provided as SEQ ID NOs: 19-22, respectively.

In some embodiments, an ABA synthesis enzyme is a cytochrome P450 reductase. Cytochrome P450 reductase is also referred to as NADPHTerrihemoprotein oxidoreductase, NADPH:hemoprotein oxidoreductase, NADPH:P450 oxidoreductase, P450 reductase, POR, CPR, and CYPOR. These reductases can promote cytochrome P450 activity by catalyzing electron transfer from NADPH to a cytochrome p450. SEQ ID NO: 23 is a non-limiting example of an amino acid sequence encoding a cytochrome p450.

ABA synthesis enzymes of the present disclosure may comprise a sequence that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 71%, at least 72%, at least73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% identical, including all values in between, with a sequence set forth as SEQ ID NO: 19-23 or 24-28, or to any ABA synthesis enzyme disclosed in this application or known in the art. In some embodiments, an ABA synthesis enzyme comprises a sequence that is a conservatively substituted version of any one of SEQ ID NOs: 19-23.

In some embodiments, an ABA synthesis enzyme of the present disclosure is capable of promoting oxidation of an ABA precursor e.g., famesyl pyrophosphate, a- ionylideneethane, a-ionylideneacetic acid, or l',4'-trans-dihydroxy-a-ionylideneacetic acid). In some embodiments, an ABA synthesis enzyme of the present disclosure catalyzes the formation of an ABA precursor or ABA.

It should be appreciated that activity (e.g., specific activity) of an ABA synthesis enzyme can be measured by any means known to one of ordinary skill in the art. In some embodiments, activity (e.g., specific activity) of a recombinant ABA synthesis enzyme may be measured as the concentration of an ABA precursor produced or ABA produced per unit enzyme per unit time in the presence of an ABA synthesis enzyme. In some embodiments, an ABA synthesis enzyme of the present disclosure has an activity (e.g., specific activity) of at least 0.0001-0.001 pmol/min/mg, at least 0.001-0.01 pmol/min/mg, at least 0.01-0.1 pmol/min/mg, or at least 0.1-1 pmol/min/mg, including all values in between.

In some embodiments, the activity (e.g., specific activity) of an ABA synthesis enzyme is at least 1.1 fold (e.g., at least 1.3 fold, at least 1.5 fold, at least 1.7 fold, at least 1.9 fold, at least 2 fold, at least 2.5 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 10 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 100 fold, at least 1000 fold or at least 10000 fold, including all values in between) greater than that of a control ABA synthesis enzyme.

Variants

Aspects of the disclosure relate to polynucleotides encoding any of the recombinant polypeptides described, such as CB5s, ABA synthesis enzymes, and any proteins associated with the disclosure. Variants of polynucleotide or amino acid sequences described in this application are also encompassed by the present disclosure. A variant may share at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with a reference sequence, including all values in between.

Unless otherwise noted, the term “sequence identity,” as known in the art, refers to a relationship between the sequences of two polypeptides or polynucleotides, as determined by sequence comparison (alignment). In some embodiments, sequence identity is determined across the entire length of a sequence, while in other embodiments, sequence identity is determined over a region of a sequence.

Identity can also refer to the degree of sequence relatedness between two sequences as determined by the number of matches between strings of two or more residues (e.g., nucleic acid or amino acid residues). Identity measures the percent of identical matches between two or more sequences with gap alignments (if any) addressed by a particular mathematical model, algorithms, or computer program.

Identity of related polypeptides or nucleic acid sequences can be readily calculated by any of the methods known to one of ordinary skill in the art. The “percent identity” of two sequences (e.g., nucleic acid or amino acid sequences) may, for example, be determined using the algorithm of Karlin and Altschul Proc. Natl. Acad. Sci. USA 87:2264-68, 1990, modified as in Karlin and Altschul Proc. Natl. Acad. Sci. USA 90:5873-77, 1993. Such an algorithm is incorporated into the NBLAST® and XBLAST® programs (version 2.0) of Altschul et al., J. Mol. Biol. 215:403-10, 1990. BLAST® protein searches can be performed, for example, with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to the protein molecules of the invention. Where gaps exist between two sequences, Gapped BLAST® can be utilized, for example, as described in Altschul et al., Nucleic Acids Res. 25(17):3389-3402, 1997. When utilizing BLAST® and Gapped BLAST® programs, the default parameters of the respective programs (e.g., XBLAST® and NBLAST®) can be used, or the parameters can be adjusted appropriately as would be understood by one of ordinary skill in the art.

Another local alignment technique which may be used, for example, is based on the Smith- Waterman algorithm (Smith, T.F. & Waterman, M.S. (1981) “Identification of common molecular subsequences.” J. Mol. Biol. 147: 195-197). A general global alignment technique which may be used, for example, is the Needleman-Wunsch algorithm (Needleman, S.B. & Wunsch, C.D. (1970) “A general method applicable to the search for similarities in the amino acid sequences of two proteins.” J. Mol. Biol. 48:443-453), which is based on dynamic programming.

More recently, a Fast Optimal Global Sequence Alignment Algorithm (FOGSAA) was developed that purportedly produces global alignment of nucleic acid and amino acid sequences faster than other optimal global alignment methods, including the Needleman- Wunsch algorithm. In some embodiments, the identity of two polypeptides is determined by aligning the two amino acid sequences, calculating the number of identical amino acids, and dividing by the length of one of the amino acid sequences. In some embodiments, the identity of two nucleic acids is determined by aligning the two nucleotide sequences and calculating the number of identical nucleotides and dividing by the length of one of the nucleic acids.

For multiple sequence alignments, computer programs including Clustal Omega (Sievers et al., Mol Syst Biol. 2011 Oct 11;7:539) may be used.

In preferred embodiments, a sequence, including a nucleic acid or amino acid sequence, is found to have a specified percent identity to a reference sequence, such as a sequence disclosed in this application and/or recited in the claims when sequence identity is determined using the algorithm of Karlin and Altschul Proc. Natl. Acad. Sci. USA 87:2264- 68, 1990, modified as in Karlin and Altschul Proc. Natl. Acad. Sci. USA 90:5873-77, 1993 (e.g., BLAST®, NBLAST®, XBLAST® or Gapped BLAST® programs, using default parameters of the respective programs).

In some embodiments, a sequence, including a nucleic acid or amino acid sequence, is found to have a specified percent identity to a reference sequence, such as a sequence disclosed in this application and/or recited in the claims when sequence identity is determined using the Smith-Waterman algorithm (Smith, T.F. & Waterman, M.S. (1981) “Identification of common molecular subsequences.” J. Mol. Biol. 147:195-197) or the Needleman-Wunsch algorithm (Needleman, S.B. & Wunsch, C.D. (1970) “A general method applicable to the search for similarities in the amino acid sequences of two proteins.” J. Mol. Biol. 48:443- 453).

In some embodiments, a sequence, including a nucleic acid or amino acid sequence, is found to have a specified percent identity to a reference sequence, such as a sequence disclosed in this application and/or recited in the claims when sequence identity is determined using a Fast Optimal Global Sequence Alignment Algorithm (FOGSAA). In some embodiments, a sequence, including a nucleic acid or amino acid sequence, is found to have a specified percent identity to a reference sequence, such as a sequence disclosed in this application and/or recited in the claims when sequence identity is determined using Clustal Omega (Sievers et al., Mol Sy st Biol. 2011 Oct 11;7:539).

As used in this application, a residue (such as a nucleic acid residue or an amino acid residue) in sequence “X” is referred to as corresponding to a position or residue (such as a nucleic acid residue or an amino acid residue) “Z” in a different sequence “Y” when the residue in sequence “X” is at the counterpart position of “Z” in sequence “Y” when sequences X and Y are aligned using amino acid sequence alignment tools known in the art.

Variant sequences may be homologous sequences. As used in this application, homologous sequences are sequences (e.g., nucleic acid or amino acid sequences) that share a certain percent identity (e.g., at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least

60%, at least 65%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least

75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least

82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least

89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least

96%, at least 97%, at least 98%, at least 99%, or 100% percent identity, including all values in between) and include but are not limited to paralogous sequences, orthologous sequences, or sequences arising from convergent evolution. Paralogous sequences arise from duplication of a gene within a genome of a species, while orthologous sequences diverge after a speciation event. Two different species may have evolved independently but may each comprise a sequence that shares a certain percent identity with a sequence from the other species as a result of convergent evolution.

In some embodiments, a polypeptide variant (e.g., CB5, ABA synthesis enzyme variant or variant of any protein associated with the disclosure) comprises a domain that shares a secondary structure (e.g., alpha helix, beta sheet) with a reference polypeptide (e.g., a reference CB5, ABA synthesis enzyme, or any protein associated with the disclosure). In some embodiments, a polypeptide variant (e.g., CB5, ABA synthesis enzyme variant or variant of any protein associated with the disclosure) shares a tertiary structure with a reference polypeptide (e.g., a CB5, ABA synthesis enzyme, or any protein associated with the disclosure). As a non-limiting example, a variant polypeptide may have low primary sequence identity (e.g., less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, or less than 5% sequence identity) compared to a reference polypeptide, but share one or more secondary structures {e.g., including but not limited to loops, alpha helices, or beta sheets, or have the same tertiary structure as a reference polypeptide. For example, a loop may be located between a beta sheet and an alpha helix, between two alpha helices, or between two beta sheets. Homology modeling may be used to compare two or more tertiary structures.

Mutations can be made in a nucleotide sequence by a variety of methods known to one of ordinary skill in the art. For example, mutations can be made by PCR-directed mutation, site-directed mutagenesis according to the method of Kunkel (Kunkel, Proc. Nat. Acad. Sci. U.S.A. 82: 488-492, 1985), by chemical synthesis of a gene encoding a polypeptide, by gene editing tools, or by insertions, such as insertion of a tag (e.g., a HIS tag or a GFP tag). Mutations can include, for example, substitutions, deletions, and translocations, generated by any method known in the art. Methods for producing mutations may be found in in references such as Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Fourth Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2012, or Current Protocols in Molecular Biology, F.M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York, 2010.

In some embodiments, methods for producing variants include circular permutation (Yu and Lutz, Trends Biotechnol. 2011 Jan;29(l):18-25). In circular permutation, the linear primary sequence of a polypeptide can be circularized {e.g., by joining the N-terminal and C- terminal ends of the sequence) and the polypeptide can be severed (“broken”) at a different location. Thus, the linear primary sequence of the new polypeptide may have low sequence identity {e.g., less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less or less than 5%, including all values in between) as determined by linear sequence alignment methods {e.g., Clustal Omega or BLAST). Topological analysis of the two proteins, however, may reveal that the tertiary structure of the two polypeptides is similar or dissimilar. Without being bound by a particular theory, a variant polypeptide created through circular permutation of a reference polypeptide and with a similar tertiary structure as the reference polypeptide can share similar functional characteristics {e.g., enzymatic activity, enzyme kinetics, substrate specificity or product specificity). In some instances, circular permutation may alter the secondary structure, tertiary structure or quaternary structure and produce a protein with different functional characteristics {e.g. , increased or decreased enzymatic activity, different substrate specificity, or different product specificity). See, e.g. , Yu and Lutz, Trends Biotechnol. 2011 Jan;29(l):18-25.

It should be appreciated that in a protein that has undergone circular permutation, the linear amino acid sequence of the protein would differ from a reference protein that has not undergone circular permutation. However, one of ordinary skill in the art would be able to determine which residues in the protein that has undergone circular permutation correspond to residues in the reference protein that has not undergone circular permutation by, for example, aligning the sequences and detecting conserved motifs, and/or by comparing the structures or predicted structures of the proteins, e.g., by homology modeling.

In some embodiments, an algorithm that determines the percent identity between a sequence of interest and a reference sequence described in this application accounts for the presence of circular permutation between the sequences. The presence of circular permutation may be detected using any method known in the art, including, for example, RASPODOM (Weiner et al., Bioinformatics. 2005 Apr 1 ;21(7):932-7). In some embodiments, the presence of circulation permutation is corrected for (e.g., the domains in at least one sequence are rearranged) prior to calculation of the percent identity between a sequence of interest and a sequence described in this application. The claims of this application should be understood to encompass sequences for which percent identity to a reference sequence is calculated after taking into account potential circular permutation of the sequence.

Functional variants of the recombinant CB5s, ABA synthesis enzymes, and any other proteins disclosed in this application are also encompassed by the present disclosure. For example, functional variants may bind one or more of the same substrates e.g., ABA or precursors thereof) or produce one or more of the same products (e.g., ABA or precursors thereof). Functional variants may be identified using any method known in the art. For example, the algorithm of Karlin and Altschul Proc. Natl. Acad. Sci. USA 87:2264-68, 1990 described above may be used to identify homologous proteins with known functions.

Putative functional variants may also be identified by searching for polypeptides with functionally annotated domains. Databases including Pfam (Sonnhammer et al., Proteins. 1997 Jul;28(3):405-20) may be used to identify polypeptides with a particular domain.

Homology modeling may also be used to identify amino acid residues that are amenable to mutation without affecting function. A non-limiting example of such a method may include use of position- specific scoring matrix (PSSM) and an energy minimization protocol. See, e.g.^Stormo et al., Nucleic Acids Res . 1982 May 11 ; 10(9):2997-3011. PSSM may be paired with calculation of a Rosetta energy function, which determines the difference between the wild-type and the single-point mutant. Without being bound by a particular theory, potentially stabilizing mutations are desirable for protein engineering (e.g., production of functional homologs). In some embodiments, a potentially stabilizing mutation has a AAGca/c value of less than -0.1 (e.g., less than -0.2, less than -0.3, less than -0.35, less than -0.4, less than -0.45, less than -0.5, less than -0.55, less than -0.6, less than -0.65, less than -0.7, less than -0.75, less than -0.8, less than -0.85, less than -0.9, less than -0.95, or less than -1.0) Rosetta energy units (R.e.u.). See, e.g., Goldenzweig et al., Mol Cell. 2016 Jul 21 ;63(2):337-346. doi: 10.1016/j.molcel.2016.06.012.

In some embodiments, a CB5 or ABA synthesis enzyme coding sequence or coding sequence of any protein associated with the disclosure comprises a mutation at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,

33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,

58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82,

83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 or more than 100 positions corresponding to a reference coding sequence. In some embodiments, the CB5 or ABA synthesis enzyme coding sequence or coding sequence of any protein associated with the disclosure comprises a mutation in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,

43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,

68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,

93, 94, 95, 96, 97, 98, 99, 100 or more codons of the coding sequence relative to a reference coding sequence. As will be understood by one of ordinary skill in the art, a mutation within a codon may or may not change the amino acid that is encoded by the codon due to degeneracy of the genetic code. In some embodiments, the one or more mutations in the coding sequence do not alter the amino acid sequence of the coding sequence relative to the amino acid sequence of a reference polypeptide.

In some embodiments, the one or more mutations in a recombinant CB5 or ABA synthesis enzyme sequence or other recombinant protein sequence associated with the disclosure alter the amino acid sequence of the polypeptide relative to the amino acid sequence of a reference polypeptide. In some embodiments, the one or more mutations alter the amino acid sequence of the recombinant polypeptide relative to the amino acid sequence of a reference polypeptide and alter (enhance or reduce) an activity of the polypeptide relative to the reference polypeptide. The activity, including specific activity, of any of the recombinant polypeptides described in this application may be measured using methods known in the art. As a nonlimiting example, a recombinant polypeptide’ s activity may be determined by measuring its substrate specificity, product(s) produced, the concentration of product(s) produced, or any combination thereof. As used in this application, “specific activity” of a recombinant polypeptide refers to the amount (e.g., concentration) of a particular product produced for a given amount (e.g., concentration) of the recombinant polypeptide per unit time.

Mutations in a recombinant polypeptide coding sequence may result in conservative amino acid substitutions to provide functionally equivalent variants of the recombinant polypeptide, e.g., variants that retain the activities of the polypeptides. As used in this application, a “conservative amino acid substitution” or “conservatively substituted” refers to an amino acid substitution that does not alter the relative charge or size characteristics or functional activity of the protein in which the amino acid substitution is made.

In some instances, an amino acid is characterized by its R group (see, e.g., Table 1). For example, an amino acid may comprise a nonpolar aliphatic R group, a positively charged R group, a negatively charged R group, a nonpolar aromatic R group, or a polar uncharged R group. Non-limiting examples of an amino acid comprising a nonpolar aliphatic R group include alanine, glycine, valine, leucine, methionine, and isoleucine. Non-limiting examples of an amino acid comprising a positively charged R group includes lysine, arginine, and histidine. Non-limiting examples of an amino acid comprising a negatively charged R group include aspartate and glutamate. Non-limiting examples of an amino acid comprising a nonpolar, aromatic R group include phenylalanine, tyrosine, and tryptophan. Non-limiting examples of an amino acid comprising a polar uncharged R group include serine, threonine, cysteine, proline, asparagine, and glutamine.

Non-limiting examples of functionally equivalent variants of polypeptides may include conservative amino acid substitutions in the amino acid sequences of proteins disclosed in this application. Conservative substitutions of amino acids include substitutions made amongst amino acids within the following groups: (a) M, I, L, V; (b) F, Y, W; (c) K, R, H; (d) A, G; (e) S, T; (f) Q, N; and (g) E, D. Additional non-limiting examples of conservative amino acid substitutions are provided in Table 1.

In some embodiments, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more than 20 residues can be changed when preparing variant polypeptides. In some embodiments, amino acids are replaced by conservative amino acid substitutions. Table 1. Non-limiting examples of conservative amino acid substitutions

Amino acid substitutions in the amino acid sequence of a polypeptide to produce a recombinant polypeptide variant having a desired property and/or activity can be made by alteration of the coding sequence of the polypeptide. Similarly, conservative amino acid substitutions in the amino acid sequence of a polypeptide to produce functionally equivalent variants of the polypeptide typically are made by alteration of the coding sequence of the recombinant polypeptide (e.g., CB5, ABA synthesis enzyme, or any protein associated with the disclosure).

Expression of Nucleic Acids in Host Cells

Aspects of the present disclosure relate to the recombinant expression of genes encoding proteins, functional modifications and variants thereof, as well as uses relating thereto. For example, the methods described in this application may be used to produce ABA precursors or ABA.

The term “heterologous” with respect to a polynucleotide, such as a polynucleotide comprising a gene, is used interchangeably with the term “exogenous” and the term “recombinant” and refers to: a polynucleotide that has been artificially supplied to a biological system; a polynucleotide that has been modified within a biological system; or a polynucleotide whose expression or regulation has been manipulated within a biological system. A heterologous polynucleotide that is introduced into or expressed in a host cell may be a polynucleotide that comes from a different organism or species from the host cell, or may be a synthetic polynucleotide, or may be a polynucleotide that is also endogenously expressed in the same organism or species as the host cell. For example, a polynucleotide that is endogenously expressed in a host cell may be considered heterologous when it is: situated non-naturally in the host cell; expressed recombinantly in the host cell, either stably or transiently; modified within the host cell; selectively edited within the host cell; expressed in a copy number that differs from the naturally occurring copy number within the host cell; or expressed in a non-natural way within the host cell, such as by manipulating regulatory regions that control expression of the polynucleotide. In some embodiments, a heterologous polynucleotide is a polynucleotide that is endogenously expressed in a host cell but whose expression is driven by a promoter that does not naturally regulate expression of the polynucleotide. In other embodiments, a heterologous polynucleotide is a polynucleotide that is endogenously expressed in a host cell and whose expression is driven by a promoter that does naturally regulate expression of the polynucleotide, but the promoter or another regulatory region is modified. In some embodiments, the promoter is recombinantly activated or repressed. For example, gene-editing based techniques may be used to regulate expression of a polynucleotide, including an endogenous polynucleotide, from a promoter, including an endogenous promoter. See, e.g., Chavez et al., Nat Methods. 2016 Jul; 13(7): 563-567. A heterologous polynucleotide may comprise a wild-type sequence or a mutant sequence as compared with a reference polynucleotide sequence.

A nucleic acid encoding any of the recombinant polypeptides, such as CB5s, ABA synthesis enzymes, or any proteins associated with the disclosure, described in this application may be incorporated into any appropriate vector through any method known in the art. For example, the vector may be an expression vector, including but not limited to a viral vector (e.g., a lentiviral, retroviral, adenoviral, or adeno-associated viral vector), any vector suitable for transient expression, any vector suitable for constitutive expression, or any vector suitable for inducible expression (e.g., a galactose-inducible or doxycycline-inducible vector).

In some embodiments, a vector replicates autonomously in the cell. A vector can contain one or more endonuclease restriction sites that are cut by a restriction endonuclease to insert and ligate a nucleic acid containing a gene described in this application to produce a recombinant vector that is able to replicate in a cell. Vectors can be composed of DNA or RNA. Cloning vectors include, but are not limited to: plasmids, fosmids, phagemids, virus genomes and artificial chromosomes. As used in this application, the terms "expression vector" or "expression construct" refer to a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell, such as a yeast cell. In some embodiments, the nucleic acid sequence of a gene described in this application is inserted into a cloning vector such that it is operably joined to regulatory sequences and, in some embodiments, expressed as an RNA transcript. In some embodiments, the vector contains one or more markers, such as a selectable marker as described in this application, to identify cells transformed or transfected with the recombinant vector. In some embodiments, the nucleic acid sequence of a gene described in this application is codon-optimized. Codon optimization may increase production of the gene product by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100%, including all values in between) relative to a reference sequence that is not codon- optimized.

A coding sequence and a regulatory sequence are “operably joined” or “operably linked” when the coding sequence and the regulatory sequence are covalently linked and the expression or transcription of the coding sequence is under the influence or control of the regulatory sequence.

In some embodiments, the nucleic acid encoding any of the proteins described in this application is under the control of regulatory sequences (e.g., enhancer sequences). In some embodiments, a nucleic acid is expressed under the control of a promoter. In some embodiments, the promoter can be a native promoter, e.g., the promoter of the gene in its endogenous context. Alternatively, a promoter can be a promoter that is different from the native promoter of the gene, e.g., the promoter is different from the promoter of the gene in its endogenous context.

In some embodiments, the promoter is a eukaryotic promoter. Non-limiting examples of eukaryotic promoters include TDH3, PGK1, PKC1, PDC1, TEF1, TEF2, RPL18B, SSA1, TDH2, PYK1,TPI1 GALI, GAL10, GAL7, GAL3, GAL2, MET3, MET25, HXT3, HXT7, ACT1, ADH1, ADH2, CUP1-1, ENO2, and SOD1, as would be known to one of ordinary skill in the art (see, e.g., Addgene website: blog.addgene.org/plasmids-101-the-promoter- region). In some embodiments, the promoter is a prokaryotic promoter (e.g., bacteriophage or bacterial promoter). Non-limiting examples of bacteriophage promoters include Pls Icon, T3, T7, SP6, and PL. Non-limiting examples of bacterial promoters include Pbad, PmgrB, Ptrc2, Plac/ara, Ptac, and Pm.

In some embodiments, the promoter is an inducible promoter. As used in this application, an “inducible promoter” is a promoter controlled by the presence or absence of a molecule. Non-limiting examples of inducible promoters include chemically-regulated promoters and physically -regulated promoters. For chemically-regulated promoters, the transcriptional activity can be regulated by one or more compounds, such as alcohol, tetracycline, galactose, a steroid, a metal, or other compounds. For physically-regulated promoters, transcriptional activity can be regulated by a phenomenon such as light or temperature. Non-limiting examples of tetracycline-regulated promoters include anhydrotetracycline (aTc)-responsive promoters and other tetracycline-responsive promoter systems (e.g., a tetracycline repressor protein (tetR), a tetracycline operator sequence (tetO) and a tetracycline transactivator fusion protein (tTA)). Non-limiting examples of steroid- regulated promoters include promoters based on the rat glucocorticoid receptor, human estrogen receptor, moth ecdysone receptors, and promoters from the steroid/retinoid/thyroid receptor superfamily. Non-limiting examples of metal-regulated promoters include promoters derived from metallothionein (proteins that bind and sequester metal ions) genes. Non-limiting examples of pathogenesis-regulated promoters include promoters induced by salicylic acid, ethylene or benzothiadiazole (BTH). Non-limiting examples of temperature/heat-inducible promoters include heat shock promoters. Non-limiting examples of light-regulated promoters include light responsive promoters from plant cells. In certain embodiments, the inducible promoter is a galactose-inducible promoter. In some embodiments, the inducible promoter is induced by one or more physiological conditions (e.g., pH, temperature, radiation, osmotic pressure, saline gradients, cell surface binding, or concentration of one or more extrinsic or intrinsic inducing agents). Non-limiting examples of an extrinsic inducer or inducing agent include amino acids and amino acid analogs, saccharides and polysaccharides, nucleic acids, protein transcriptional activators and repressors, cytokines, toxins, petroleum-based compounds, metal containing compounds, salts, ions, enzyme substrate analogs, hormones or any combination thereof.

In some embodiments, the promoter is a constitutive promoter. As used in this application, a “constitutive promoter” refers to an unregulated promoter that allows continuous transcription of a gene. Non-limiting examples of a constitutive promoter include TDH3, PGK1, PKC1, PDC1, TEF1, TEF2, RPL18B, SSA1, TDH2, PYK1,TPI1, HXT3, HXT7, ACT1, ADH1, ADH2, EN02, and SODE

Other inducible promoters or constitutive promoters known to one of ordinary skill in the art are also contemplated.

Regulatory sequences for gene expression may also include a terminator sequence. In some embodiments, a terminator sequence marks the end of a gene in DNA during transcription.

The choice and design of one or more appropriate vectors suitable for inducing expression of one or more genes described in this application in a host cell is within the ability and discretion of one of ordinary skill in the art.

Expression vectors containing the necessary elements for expression are commercially available and known to one of ordinary skill in the art (see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Fourth Edition, Cold Spring Harbor Laboratory Press, 2012).

In some embodiments, introduction of a polynucleotide, such as a polynucleotide encoding a recombinant polypeptide, into a host cell results in genomic integration of the polynucleotide. In some embodiments, a host cell comprises at least 1 copy, at least 2 copies, at least 3 copies, at least 4 copies, at least 5 copies, at least 6 copies, at least 7 copies, at least 8 copies, at least 9 copies, at least 10 copies, at least 11 copies, at least 12 copies, at least 13 copies, at least 14 copies, at least 15 copies, at least 16 copies, at least 17 copies, at least 18 copies, at least 19 copies, at least 20 copies, at least 21 copies, at least 22 copies, at least 23 copies, at least 24 copies, at least 25 copies, at least 26 copies, at least 27 copies, at least 28 copies, at least 29 copies, at least 30 copies, at least 31 copies, at least 32 copies, at least 33 copies, at least 34 copies, at least 35 copies, at least 36 copies, at least 37 copies, at least 38 copies, at least 39 copies, at least 40 copies, at least 41 copies, at least 42 copies, at least 43 copies, at least 44 copies, at least 45 copies, at least 46 copies, at least 47 copies, at least 48 copies, at least 49 copies, at least 50 copies, at least 60 copies, at least 70 copies, at least 80 copies, at least 90 copies, at least 100 copies, or more, including any values in between, of a polynucleotide sequence, such as a polynucleotide sequence encoding any of the recombinant polypeptides described in this application, in its genome.

Host Cells

Any of the proteins of the disclosure may be expressed in a host cell. As used in this application, the term “host cell” refers to a cell that can be used to express a polynucleotide, such as a polynucleotide that encodes a protein used in production of ABA precursors or ABA.

Any suitable host cell may be used to produce any of the recombinant polypeptides, including CB5s, ABA synthesis enzymes, and other proteins disclosed in this application, including eukaryotic cells or prokaryotic cells. Suitable host cells include, but are not limited to, fungal cells (e.g., yeast cells), bacterial cells (e.g., E. coli cells), algal cells, plant cells, insect cells, and animal cells, including mammalian cells.

Suitable yeast host cells include, but are not limited to, Candida, Escherichia, Hansenula, Saccharomyces (e.g., S. cerevisiae), Schizosaccharomyces, Pichia, Kluyveromyces (e.g., K. laclis). and Yarrowia (e.g., Y. lipolytica). In some embodiments, the yeast cell is Hansenula polymorpha, Saccharomyces cerevisiae, Saccharomyces carlsbergensis, Saccharomyces diastaticus, Saccharomyces norbensis, Saccharomyces kluyveri, Schizosaccharomyces pombe, Pichia finlandic a, Pichia trehalophila, Pichia kodamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia quercuum, Pichia pijperi, Pichia stipitis, Pichia methanolica, Pichia angusta, Komagataella phaffii, Komagataella pastoris, Kluyveromyces lactis, Candida albicans, or Yarrowia lipolytica.

In some embodiments, the yeast strain is an industrial polyploid yeast strain. Other non-limiting examples of fungal cells include cells obtained from Aspergillus spp., Penicillium spp., Fusarium spp., Rhizopus spp., Acremonium spp., Neurospora spp., Sordaria spp., Magnaporthe spp., Allomyces spp., Ustilago spp., Botrytis spp., Myrothecium spp., and Trichoderma spp.

In certain embodiments, the host cell is an algal cell such as, Chlamydomonas (e.g., C. Reinhardtii) and Phormidium (P. sp. ATCC29409).

In other embodiments, the host cell is a prokaryotic cell. Suitable prokaryotic cells include gram positive, gram negative, and gram-variable bacterial cells. The host cell may be a species of, but not limited to: Agrobacterium, Alicyclobacillus, Anabaena, Anacystis, Acinetobacter, Acidothermus, Arthrobacter, Azobacter, Bacillus, Bifidobacterium, Brevibacterium, Butyrivibrio, Buchnera, Campestris, Camplyobacter, Clostridium, Corynebacterium, Chromatium, Coprococcus, Escherichia, Enterococcus, Enterobacter, Erwinia, Fusobacterium, Faecalibacterium, Francisella, Flavobacterium, Geobacillus, Haemophilus, Helicobacter, Klebsiella, Lactobacillus, Lactococcus, Ilyobacter, Micrococcus, Microbacterium, Mesorhizobium, Methylobacterium, Methylobacterium, Mycobacterium, Neisseria, Pantoea, Pseudomonas, Prochlorococcus, Rhodobacter, Rhodopseudomonas, Rhodopseudomonas, Roseburia, Rhodo spirillum, Rhodococcus, Scenedesmus, Streptomyces, Streptococcus, Synecoccus, Saccharomonospora, Saccharopolyspora, Staphylococcus, Serratia, Salmonella, Shigella, Thermoanaerobacterium, Tropheryma, Tularensis, Temecula, Thermosynechococcus, Thermococcus, Ureaplasma, Xanthomonas, Xylella, Yersinia, and Zymomonas.

In some embodiments, the bacterial host cell is of the Agrobacterium species (e.g., A. radiobacter, A. rhizogenes, A. rubi), the Arthrobacterspecies {e.g., A. aurescens, A. citreus, A. globformis, A. hydrocarboglutamicus, A. mysorens, A. nicotianae, A. paraffineus, A. protophonniae, A. roseoparaffinus, A. sulfureus, A. ureafaciens), or the Bacillus species (e.g., B. thuringiensis, B. anthracis, B. megaterium, B. subtilis, B. lentus, B. circulans, B. pumilus, B. lautus, B. coagulans, B. brevis, B. firmus, B. alkaophius, B. licheniformis, B. clausii, B. stearothermophilus, B. halodurans and B. amyloliquefaciens . In particular embodiments, the host cell is an industrial Bacillus strain including but not limited to B. subtilis, B. pumilus, B. licheniformis, B. megaterium, B. clausii, B. stearothermophilus and B. amyloliquefaciens. In some embodiments, the host cell is an industrial Clostridium species (e.g., C. acetobutylicum, C. tetani E88, C. lituseburense, C. saccharobutylicum, C. perfringens, C. beijerinckii). In some embodiments, the host cell is an industrial Corynebacterium species (e.g., C. glutamicum, C. acetoacidophilum). In some embodiments, the host cell is an industrial Escherichia species (e.g., E. coli). In some embodiments, the host cell is an industrial Erwinia species (e.g., E. uredovora, E. carotovora, E. ananas, E. herbicola, E. punctata, E. terreus). In some embodiments, the host cell is an industrial Pantoea species (e.g., P. citrea, P. agglomeransf In some embodiments, the host cell is an industrial Pseudomonas species, (e.g., P. putida, P. aeruginosa, P. mevalonii). In some embodiments, the host cell is an industrial Streptococcus species (e.g., S. equisimiles, S. pyogenes, S. uberisf In some embodiments, the host cell is an industrial Streptomyces species (e.g., S. ambofaciens, S. achromogenes, S. avermitilis, S. coelicolor, S. aureofaciens, S. aureus, S. fungicidicus, S. griseus, S. Uvidans). In some embodiments, the host cell is an industrial Zymomonas species (e.g., Z. mobilis, Z. lipolytica).

The present disclosure is also suitable for use with a variety of animal cell types, including mammalian cells, for example, human (including 293, HeLa, WI38, PER.C6 and Bowes melanoma cells), mouse (including 3T3, NSO, NS1, Sp2/0), hamster (CHO, BHK), monkey (COS, FRhL, Vero), and hybridoma cell lines.

The present disclosure is also suitable for use with a variety of plant cell types. The term “cell,” as used in this application, may refer to a single cell or a population of cells, such as a population of cells belonging to the same cell line or strain. Use of the singular term “cell” should not be construed to refer explicitly to a single cell rather than a population of cells.

In some embodiments, a host cell is modified to reduce or inactivate at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 genes.

In some embodiments, a host cell is modified to reduce or inactivate 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 genes.

Reduction of gene expression and/or gene inactivation may be achieved through any suitable method, including but not limited to deletion of the gene, introduction of a point mutation into the gene, truncation of the gene, introduction of an insertion into the gene, introduction of a tag or fusion into the gene, or selective editing of the gene. For example, polymerase chain reaction (PCR)-based methods may be used (see, e.g., Gardner et al., Methods Mol Biol. 2014;1205:45-78) or well-known gene-editing techniques may be used. As a non-limiting example, genes may be deleted through gene replacement {e.g., with a marker, including a selection marker). A gene may also be truncated through the use of a transposon system (see, e.g., Poussu et al., Nucleic Acids Res. 2005; 33(12): el04).

A vector or nucleic acid encoding any of the recombinant polypeptides described in this application may be introduced into a suitable host cell using any method known in the art. Non-limiting examples of yeast transformation protocols are described in Gietz et al. , Yeast transformation can be conducted by the LiAc/SS Carrier DNA/PEG method. Methods Mol Biol. 2006;313:107-20, which is incorporated by reference in its entirety. Host cells may be cultured under any suitable conditions as would be understood by one of ordinary skill in the art. For example, any media, temperature, and incubation conditions known in the art may be used. For host cells carrying an inducible vector, cells may be cultured with an appropriate inducible agent to promote expression.

Any of the cells disclosed in this application can be cultured in media of any type (rich or minimal) and any composition prior to, during, and/or after contact and/or integration of a nucleic acid. The conditions of the culture or culturing process can be optimized through routine experimentation as would be understood by one of ordinary skill in the art. In some embodiments, the selected media is supplemented with various components. In some embodiments, the concentration and amount of a supplemental component is optimized. In some embodiments, other aspects of the media and growth conditions (e.g., pH, temperature, etc.) are optimized through routine experimentation. In some embodiments, the frequency that the media is supplemented with one or more supplemental components, and the amount of time that the cell is cultured, is optimized.

Culturing of the cells described in this application can be performed in culture vessels known and used in the art. In some embodiments, an aerated reaction vessel (e.g., a stirred tank reactor) is used to culture the cells. In some embodiments, a bioreactor or fermenter is used to culture the cell. Thus, in some embodiments, the cells are used in fermentation. As used in this application, the terms “bioreactor” and “fermenter” are interchangeably used and refer to an enclosure, or partial enclosure, in which a biological, biochemical and/or chemical reaction takes place, involving a living organism, part of a living organism, or purified proteins. A “large-scale bioreactor” or “industrial-scale bioreactor” is a bioreactor that is used to generate a product on a commercial or quasi-commercial scale. Large scale bioreactors typically have volumes in the range of liters, hundreds of liters, thousands of liters, or more.

Non-limiting examples of bioreactors include: stirred tank fermenters, bioreactors agitated by rotating mixing devices, chemostats, bioreactors agitated by shaking devices, airlift fermenters, packed-bed reactors, fixed-bed reactors, fluidized bed bioreactors, bioreactors employing wave induced agitation, centrifugal bioreactors, roller bottles, and hollow fiber bioreactors, roller apparatuses (for example benchtop, cart-mounted, and/or automated varieties), vertically-stacked plates, spinner flasks, stirring or rocking flasks, shaken multi-well plates, MD bottles, T-flasks, Roux bottles, multiple- surface tissue culture propagators, modified fermenters, and coated beads (e.g., beads coated with serum proteins, nitrocellulose, or carboxymethyl cellulose to prevent cell attachment).

In some embodiments, the bioreactor includes a cell culture system where the cell (e.g., yeast cell) is in contact with moving liquids and/or gas bubbles. In some embodiments, the cell or cell culture is grown in suspension. In other embodiments, the cell or cell culture is attached to a solid phase carrier. Non-limiting examples of a carrier system includes microcarriers (e.g., polymer spheres, microbeads, and microdisks that can be porous or non- porous), cross-linked beads (e.g., dextran) charged with specific chemical groups (e.g., tertiary amine groups), 2D microcarriers including cells trapped in nonporous polymer fibers, 3D carriers (e.g., carrier fibers, hollow fibers, multicartridge reactors, and semi-permeable membranes that can comprising porous fibers), microcarriers having reduced ion exchange capacity, encapsulation cells, capillaries, and aggregates. In some embodiments, carriers are fabricated from materials such as dextran, gelatin, glass, or cellulose.

In some embodiments, industrial-scale processes are operated in continuous, semi- continuous or non-continuous modes. Non-limiting examples of operation modes are batch, fed batch, extended batch, repetitive batch, draw/fill, rotating-wall, spinning flask, and/or perfusion mode of operation. In some embodiments, a bioreactor allows continuous or semi- continuous replenishment of the substrate stock, for example a carbohydrate source and/or continuous or semi-continuous separation of the product, from the bioreactor.

In some embodiments, the bioreactor or fermenter includes a sensor and/or a control system to measure and/or adjust reaction parameters. Non-limiting examples of reaction parameters include biological parameters (e.g., growth rate, cell size, cell number, cell density, cell type, or cell state, etc.), chemical parameters (e.g., pH, redox-potential, concentration of reaction substrate and/or product, concentration of dissolved gases, such as oxygen concentration and CO2 concentration, nutrient concentrations, metabolite concentrations, concentration of an oligopeptide, concentration of an amino acid, concentration of a vitamin, concentration of a hormone, concentration of an additive, serum concentration, ionic strength, concentration of an ion, relative humidity, molarity, osmolarity, concentration of other chemicals, for example buffering agents, adjuvants, or reaction byproducts), physical/mechanical parameters e.g., density, conductivity, degree of agitation, pressure, and flow rate, shear stress, shear rate, viscosity, color, turbidity, light absorption, mixing rate, conversion rate, as well as thermodynamic parameters, such as temperature, light intensity/quality, etc.). Sensors to measure the parameters described in this application are well known to one of ordinary skill in the relevant mechanical and electronic arts. Control systems to adjust the parameters in a bioreactor based on the inputs from a sensor described in this application are well known to one of ordinary skill in the art in bioreactor engineering.

In some embodiments, the method involves batch fermentation (e.g., shake flask fermentation). General considerations for batch fermentation (e.g., shake flask fermentation) include the level of oxygen and glucose. For example, batch fermentation (e.g., shake flask fermentation) may be oxygen and glucose limited, so in some embodiments, the capability of a strain to perform in a well-designed fed-batch fermentation is underestimated. Also, the final product (e.g., ABA precursor or ABA) may display some differences from the substrate (e.g., another ABA precursor) in terms of solubility, toxicity, cellular accumulation and secretion and in some embodiments can have different fermentation kinetics. The methods described in this application encompass production of the ABA precursors (e.g., a-ionylideneethane (a.- IE), a-ionylideneacetic acid (a-IAA), or l',4'-trans- dihydroxy-a-ionylideneacetic acid (DH-a-IAA or ABA-diol)) or ABA using a recombinant cell, cell lysate or isolated recombinant polypeptides (e.g., CB5, ABA synthesis enzyme, and any proteins associated with the disclosure).

ABA precursors (e.g., a-ionylideneethane (a-IE), a-ionylideneacetic acid (a-IAA), or l',4'-trans-dihydroxy-a-ionylideneacetic acid (DH-a-IAA or ABA-diol)) and ABA produced by any of the recombinant cells disclosed in this application may be identified and extracted using any method known in the art. Mass spectrometry (e.g., LC-MS, GC-MS) is a nonlimiting example of a method for identification and may be used to help extract a compound of interest.

The phraseology and terminology used in this application is for the purpose of description and should not be regarded as limiting. The use of terms such as “including,” “comprising,” “having,” “containing,” “involving,” and/or variations thereof in this application, is meant to encompass the items listed thereafter and equivalents thereof as well as additional items.

The present invention is further illustrated by the following Examples, which in no way should be construed as further limiting. The entire contents of all of the references (including literature references, issued patents, published patent applications, and co pending patent applications) cited throughout this application are hereby expressly incorporated by reference.

EXAMPLES

Example 1. Identification and Functional Characterization of CB5 Proteins that Increase Abscisic Acid (ABA) Production

This Example describes the screening of 3 Siraitia grosvenorii and 6 Myrothecium indicum proteins with homology to Cytochrome b5 (Cb5) proteins to identify proteins that promote abscisic acid (ABA) production in host cells. Y. lipolytica host cell strains engineered to express at least three enzymes within an ABA biosynthetic pathway (e.g., abscisic acid biosynthetic genes abal, aba2, aba3, aba4, and cytochrome P450 reductase (CPR) that includes two Cytochrome P450 (CYP) enzymes (encoded by genes abal and abal)) were used to evaluate the effect of expression of Cb5 proteins. Linear constructs carrying expression cassettes for Cb5 genes codon-optimized for expression in Y. lipolytica were transformed and integrated into the genome of the Y. lipolytica hosts. The hosts (parental strains) lacking any additional Cb5 protein were used as negative controls. Single colonies resulting from transformation were inoculated in culture media and grown in a shaking incubator at 30°C for 48 hours at 1000 rpm. After 48 hours, culture supernatants were analyzed by LC-MS to evaluate sesquiterpene (abscisic acid or ABA-diol) production.

In FIGs. 2-3, a Y. lipolytica parent strain (parent strain 1) that expresses the following three ABA synthesis enzymes: abal, aba2, and aba3 was used. As shown in FIG. 2, parent strain 1 produces the ABA precursor, ABA-diol. Parent strain 1 was transformed with one of six fungal Cb5 candidate genes (mined from Myrothecium indicum) and three A grosvenorii Cb5 genes. ABA-diol production by each strain was measured by LC-MS. Expression of Siraitia grosvenorii CB5 alpha (SEQ ID NO: 1) and Siraitia grosvenorii CB5 gamma (SEQ ID NO: 3) increased ABA-diol production of parent strain 1 (FIG. 2 and Table 2). Notably, CB5s comprising SEQ ID NO: 1 or SEQ ID NO: 3 outperformed fungal CB5s mined from Myrothecium indicum and increased abscisic acid production by parent strain 1 (FIG. 3 and Table 3).

In FIG. 4, a Y. lipolytica parent strain (parent strain 2) that expresses all four of the following ABA synthesis enzymes: abal, aba2, aba3, and aba4 was used. As shown in FIG. 4, parent strain 2 produces ABA. Parent strain 2 was transformed with either of two 5. grosvenorii genes encoding CB5 proteins (alpha and gamma, SEQ ID NOs: 1 and 3, respectively). ABA production was measured by LC-MS. In particular, production of the stereoisomer S-ABA was measured. Expression of Siraitia grosvenorii CB5 alpha (SEQ ID NO: 1) and Siraitia grosvenorii CB5 gamma (SEQ ID NO: 3) increased ABA production of parent strain 2 (FIG. 4 and Table 4).

In FIG. 5, a Y. lipolytica parent strain (strain 3) that expresses all four of the following ABA synthesis enzymes: abal, aba2, aba3, and aba4 and also an accessory Cytochrome P450 Reductase (CPR) from Myrothecium indicum was used. Parent strain 3 was transformed with either of two 5. grosvenorii genes encoding CB5 proteins (alpha and gamma, SEQ ID NOs: 1 and 3, respectively). ABA production was measured by LC-MS. In particular, production of the stereoisomer S-ABA was measured. Expression of Siraitia grosvenorii CB5 alpha (SEQ ID NO: 1) and Siraitia grosvenorii CB5 gamma (SEQ ID NO: 3) increased ABA production of parent strain 3 (FIG. 5 and Table 5).

Table 2. ABA-diol production by parent strain 1 comprising CB5s

Table 3. Abscisic production by parent strain 1 comprising CB5s

Table 4. Abscisic production by parent strain 2 comprising CB5s

Table 5. Abscisic production by parent strain 3 comprising CB5s

Table 6. Non-limiting examples of CBS sequences

Table 7. Additional sequences associated with the disclosure.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described in this application. Such equivalents are intended to be encompassed by the following claims.

All references, including patent documents, disclosed in this application are incorporated by reference in their entirety, particularly for the disclosure referenced in this application.

Claims

1. A host cell that comprises a heterologous polynucleotide encoding a cytochrome b5 (CB5), wherein the host cell is capable of producing more of an abscisic acid (ABA) precursor or ABA than a control host cell that does not comprise the heterologous polynucleotide, and wherein the CB5 comprises a sequence that is at least 90% identical to SEQ ID NO: 1 or 3.

2. The host cell of claim 1, wherein the CB5 comprises the sequence of SEQ ID NO: 1 or 3.

3. The host cell of claim 1 or 2, wherein the heterologous polynucleotide encoding the CB5 comprises a sequence that is at least 90% identical to a sequence selected from SEQ ID NO: 10 or 12.

4. The host cell of claim 3, wherein the heterologous polynucleotide encoding the CB5 comprises a sequence selected from SEQ ID NOs: 10 or 12.

5. The host cell of any one of claims 1-4, wherein the host cell further comprises a heterologous polynucleotide encoding an ABA synthesis enzyme.

6. The host cell of claim 5, wherein the ABA synthesis enzyme comprises a sequence that is at least 90% identical to a sequence selected from SEQ ID NOs: 19-23.

7. The host cell of claim 5 or 6, wherein the ABA synthesis enzyme comprises a sequence selected from SEQ ID NOs: 19-23.

8. The host cell of any one of claims 5-7, wherein the heterologous polynucleotide encoding the ABA synthesis enzyme comprises a sequence that is at least 90% identical to a sequence selected from SEQ ID NOs: 24-28.

9. The host cell of any one of claims 5-8, wherein the heterologous polynucleotide encoding the ABA synthesis enzyme comprises a sequence selected from SEQ ID NOs: 24- 28.

10. The host cell of any one of claims 1-9, wherein the host cell is a fungal cell, a bacterial cell, an algal cell, a plant cell, an insect cell, or an animal cell.

11. The host cell of claim 10, wherein the fungal cell is a yeast cell.

12. The host cell of any one of claims 1-10, wherein the host cell is a yeast cell.

13. The host cell of claim 12, wherein the yeast cell is a Saccharomyces cerevisiae cell.

14. The host cell of claim 12, wherein the yeast cell is a Yarrowia lipolytica cell.

15. The host cell of claim 10, wherein the host cell is a bacterial cell.

16. The host cell of claim 15, wherein the bacterial cell is an Escherichia, coli cell.

17. A method of producing an abscisic acid (ABA) precursor comprising culturing the host cell of any one of claims 1-16.

18. The method of claim 17, wherein the ABA precursor is a-ionylideneethane (a-IE), a- ionylideneacetic acid (a-IAA), or T,4'-trans-dihydroxy-a-ionylideneacetic acid (DH-a-IAA or ABA-diol).

19. A method of producing abscisic acid (ABA) comprising culturing the host cell of any one of claims 1-16.

20. A bioreactor for producing an abscisic acid (ABA) precursor or ABA, wherein the bioreactor comprises a host cell of any one of claims 1-16.