Enzymatic process for production of modified hop products

Abstract

The present invention relates to a process for producing a beer littering agent via enzyme catalyzed bioconversion of hop-derived isoalpha acids to dihydro-(rho)-isoalpha acids.

Claims

1. A process for the preparation of dihydro-(rho)-isoalpha acids, comprising treating isoalpha acids with a ketoreductase enzyme or a microorganism expressing a gene that encodes the ketoreductase, wherein the ketoreductase enzyme comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 414 and SEQ ID NO: 416, or wherein the ketoreductase enzyme or microorganism expressing a gene which encodes the ketoreductase is 99, 95 or 90 percent homologous to the ketoreductase enzyme selected from the group consisting of SEQ ID NO: 414 and SEQ ID NO: 416.

2. The process according to claim 1, wherein the process is carried out in an aqueous system.

3. The process according to claim 2, wherein the process is carried out under mild temperature and pH conditions.

4. The process according to claim 1, comprising addition of the ketoreductase enzyme and NADPH or NADP to a mixture of isoalpha acids followed by incubation.

5. The process according to claim 1, comprising adding the ketoreductase enzyme and NADPH or NADP to a mixture of isoalpha acids in the presence of isopropanol for cofactor recycling, followed by incubation.

6. The process according to claim 1, wherein the concentration of isoalpha acids, i.e. the substrate, is maximized to increase the volumetric productivity of the bioconversion.

7. The process according to claim 1, wherein the concentration of the cofactor NADPH or NADP in the mixture is minimized to improve the economics of the bioconversion.

8. The process according to claim 1, wherein the reaction is carried out in a vessel purged of air using an inert gas such as nitrogen or argon to prevent the production of degradation products.

9. The process according to claim 1, comprising adding the ketoreductase enzyme and NADPH or NADP to a mixture of isoalpha acids in the presence of another enzyme for cofactor recycling, followed by incubation.

10. The process according to claim 1, comprising adding a whole cell biocatalyst, wherein the whole cell biocatalyst is an immobilized microorganism expressing the gene which encodes a ketoreductase, to a mixture of isoalpha acids followed by incubation.

11. The process according to claim 1, comprising treating isoalpha acids with a growing microorganism expressing a gene which encodes the ketoreductase.

12. The process according to claim 1, comprising adding the ketoreductase enzyme, wherein the ketoreductase is thermostable, to an extract of isoalpha acids wherein heat is applied, and the mixture is incubated.

13. The process according to claim 1, wherein the ketoreductase specifically reduces cis-isohumulone, cis-isocohumulone, and cis-isoadhumulone.

14. The process according to claim 1, wherein the ketoreductase specifically reduces trans-isohumulone, trans-isocohumulone, and trans-isoadhumulone.

15. The process according to claim 1, comprising adding a mixture of 2 or more ketoreductase enzymes to reduce a mixture of cis- and trans-isoalpha acids, to their respective dihydroisoalpha acids.

16. The process according to claim 14, wherein the mixture of 2 or more ketoreductase enzymes produces a unique mixture of dihydroisoalpha acids that is distinct from that produced by chemical reducing agents, such as sodium borohydride.

17. The process according to claim 1, wherein the ketoreductase is 99 or 95, percent homologous to the ketoreductase enzyme selected from the group consisting of SEQ ID NO: 414 and SEQ ID NO: 416.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1 shows the enzyme catalyzed reduction of a representative epimer of isoalpha acids.

(2) FIG. 2 shows a UPLC chromatogram for Codexis KRED-P1-B05 (SEQ ID NO: 4) incubated with Isoalpha Acids (acidic solution) for 48 hr at 30° C.

(3) FIG. 3 shows an HPLC chromatogram and peak quantitation for Codexis KRED-P1-B05 (SEQ ID NO: 4) incubated with Isoalpha Acids (acidic solution) for 48 hr at 30° C.

(4) FIG. 4 shows UPLC chromatogram for Codexis KRED-433 incubated with Isoalpha Acids for 24 hr at 30° C.

(5) FIG. 5 shows improved KRED Activity of SEQ ID NO: 80, 104, 100, 136, 116, 132, 162, 150, 152, 144, 146 and 158 at High Substrate and low NADP Concentration.

(6) FIG. 6 shows improved KRED activity of SEQ ID NO: 6, SEQ ID NO: 80, SEQ ID NO: 104, SEQ ID NO: 172, SEQ ID NO: 186, SEQ ID NO: 194, SEQ ID NO: 252, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 286, SEQ ID NO: 328, SEQ ID NO: 330, SEQ ID NO: 346, SEQ ID NO: 414 and SEQ ID NO: 416 compared to SEQ ID NO: 4 where %-conversion increases at increasing concentrations of isoalpha acids (substrate).

DETAILED DESCRIPTION OF THE INVENTION

(7) In this invention, a ketoreductase enzyme replaces the function of sodium borohydride and allows a more natural production method for the beverage additive, dihydro-(rho)-isoalpha acids. The enzyme may be any ketoreductase specifically reducing a ketone group to a hydroxy group of any or all isomers of isoalpha acid (co-, n- ad-, and cis/trans-). The enzyme may be derived from, but not limited to, bacteria, fungi, or plants. The enzyme may be cofactor dependent (NADH or NADPH) or independent.

(8) Herein, “isoalpha acids”, “hop isoalpha acids”, and “hop-derived isoalpha acids” may be used interchangeably.

(9) Isoalpha acid solution is subjected to enzymatic treatment using a purified enzyme or a mixture containing an enzyme and optionally additional enzymes for cofactor recycling. The amount of enzyme depends on the incubation parameters including duration, temperature, amount and concentration of substrate.

(10) Alternatively, an isoalpha acid solution is subjected to enzymatic treatment using a mixture containing a microorganism expressing said enzyme. The invention furthermore provides a process for reducing isoalpha acids according to the invention, which comprises cultivating a ketoreductase-producing microorganism, if appropriate inducing the expression of the ketoreductase, Intact cells can be harvested and added directly to a reaction, in place of isolated enzyme, for the reduction of isoalpha acids as described above. Furthermore, the harvested cells can be immobilized prior to addition to a reduction reaction. The microorganism can be cultivated and fermented by known methods. The microorganism can be bacteria or fungi.

(11) A mixture of cis- and trans-isoalpha acids may be incubated with a single ketoreductase displaying the capacity to reduce both isomers. Alternatively, a mixture of cis- and trans-isoalpha acids may be incubated with 2 or more ketoreductases showing varying specificity where the resulting product is a mixture of cis- and trans-dihydroisoalpha acids.

(12) Alternatively, a solution containing only cis-isoalpha acids may be incubated with a ketoreductase specific for the cis-isomer, and the resulting product is a solution of cis-dihydroisoalpha acids. A solution of only cis-dihydroisoalpha acids may display advantageous bitterness and/or thermal stability properties.

(13) Alternatively, a solution containing only trans-isoalpha acids may be incubated with a ketoreductase specific for the trans-isomer, and the resulting product is a solution of trans-dihydroisoalpha acids. A solution of only trans-dihydroisoalpha acids may display advantageous bitterness properties.

(14) Customized blends of trans- and cis-isoalpha acids may be incubated with 1 or more ketoreductases displaying variable substrate specificity, to produce unique blends of dihydroisoalpha acids otherwise unattainable.

(15) An isoalpha acid mixture may be subjected to an enzymatic reaction using a ketoreductase enzyme in addition to enzymes for catalyzing additional desired modifications, such as but not limited to, dehydrogenases, isomerases, hydratases and lyases. Enzymes of varying activity may be combined in a one pot reaction or added sequentially.

(16) A suitable solvent to use in the enzyme incubation includes water and mixtures of water with another solvent compatible with the enzyme, such as ethanol or isopropanol. Enzymatic activity benefits from buffering of aqueous solutions, Buffering agents include, but are not limited to: tris(hydroxymethyl)aminomethane (aka. Tris), 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid (aka. HEPES), sodium phosphate, and potassium phosphate.

(17) The enzyme and isoalpha acids are incubated within a suitable pH range, for example pH 6 to 10, and temperature range, for example 10 to 90° C., and held at this temperature for a sufficient time to convert isoalpha acids to the desired dihydro-(rho)-isoalpha acids yield. Continuous stirring will ensure a constant temperature and exposure of substrate to enzyme. The reaction duration, typically 24 to 48 hours, will depend on the amount and concentration of the enzyme and substrate, solvent present, and temperature chosen.

(18) Enzyme may be free in solution, immobilized onto beads or similar mixable scaffolds, or immobilized onto a film or resin over which a solution of isoalpha acids is passed. The purity level of the enzyme may vary from 30 to 90+% depending on the purification method.

(19) Enzyme may be removed from the final product via physical filtering or centrifugation, Enzyme may also be rendered inactive by extreme temperature or pH and remain in the final product.

(20) As used herein ketoreductase includes commercially available ketoreductases such as KRED-P1-B05, KRED-P2-B02, KRED-P2-C02, KRED-P2-C11, KRED-P2-D11, KRED-P2-G03, KRED-P2-G09, KRED-101, KRED-119, KRED-130, KRED-NADH-110, KRED-430, KRED-431, KRED-432, KRED-433, KRED-434, KRED-435, and KRED-436 (available from Codexis, Inc., Redwood City, Calif.). The invention also contemplates the foregoing ketoreductase which embody one or more differences in amino acid residues, as well as ketoreductase having 99, 95, 90, 85, 80, 75 and/or 70 percent homology with the foregoing ketoreductases.

(21) The invention also includes ketoreductases purposely produced through known mutagenesis methods displaying variable activity on a single or a mixture of isoalpha acids such as SEQ ID NO: 80, SEQ ID NO: 104, SEQ ID NO: 172, SEQ ID NO: 186, SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 252, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 286, SEQ ID NO: 300, SEQ ID NO: 328, SEQ ID NO: 330, SEQ ID NO: 346, SEQ ID NO: 348 SEQ ID NO: 356, SEQ ID NO: 414, and SEQ ID NO: 416. Some variants are significantly improved in substrate tolerance, temperature tolerance, solvent tolerance, substrate specificity (or lack thereof) and/or turnover compared to commercially available ketoreductases.

(22) As used herein, “percentage of sequence homology,” “percent homology,” and “percent identical” refer to comparisons between polynucleotide sequences or polypeptide sequences, and are determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which either the identical nucleic acid base or amino acid residue occurs in both sequences or a nucleic acid base or amino acid residue is aligned with a gap to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Determination of optimal alignment and percent sequence homology is performed using the BLAST and BLAST 2.0 algorithms (See e.g., Altschul et al., J. Mol. Biol. 215: 403-410 [1990]; and Altschul et al., Nucleic Acids Res. 3389-3402 [1977]). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information website.

EXAMPLES

(23) The following examples illustrate the invention without limiting its scope.

Example 1

E. coli Expression Hosts Containing Recombinant KRED Genes

(24) KRED-encoding genes were cloned into the expression vector pCK110900 (See, FIG. 3 of US Pat. Appln. Publn. No. 2006/0195947), operatively linked to the lac promoter under control of the lac1 repressor. The expression vector also contains the P15a origin of replication and a chloramphenicol resistance gene. The resulting plasmids were transformed into E. coli W3110, using standard methods known in the art. The transformants were isolated by subjecting the cells to chloramphenicol selection, as known in the art (See e.g., U.S. Pat. No. 8,383,346 and WO2010/144103).

Example 2

Preparation of HTP KRED-Containing Wet Cell Pellets

(25) E. coli cells containing recombinant KRED-encoding genes from monoclonal colonies were inoculated into 190 μl Luria-Bertani (LB) broth containing 1% glucose and 30 μg/mL chloramphenicol in the wells of 96-well shallow-well microtiter plates. The plates were sealed with O.sub.2-permeable seals, and cultures were grown overnight at 20° C., 200 rpm, and 85% humidity. Then, 20 μl of each of the cell cultures were transferred into the wells of 96-well deep-well plates containing 380 μL Terrific Broth (TB) and 30 μg/mL chloramphenicol (CAM). The deep-well plates were sealed with O.sub.2-permeable seals and incubated at 30° C., 250 rpm, and 85% humidity until an OD.sub.600 of 0.6-0.8 was reached. The cell cultures were then induced by addition of Isopropyl β-d-1-thiogalactopyranoside (IPTG) to a final concentration of 1 mM and incubated overnight under the same conditions as originally used. The cells were then pelleted using centrifugation at 4° C., 4000 rpm for 10 min. The supernatants were discarded, and the pellets frozen at −80° C. prior to lysis.

Example 3

Preparation of HTP KRED-Containing Cell Lysates

(26) First, the cell pellets that were produced as described in Example 2 were lysed by adding 150 μL lysis buffer containing 100 mM pH 8 triethanolamine*H.sub.2SO.sub.4 with 2 mM MgSO.sub.4 or 100 mM pH 8 Potassium Phosphate with 2 mM MgSO.sub.4, 1 g/L lysozyme, and 0.5 g/L polymixin B sulfate (PMBS). Then, the cell pellets were shaken at room temperature for 2 hours on a bench top shaker. The plates were centrifuged at 4000 rpm, for 15 minutes at 4° C. to remove cell debris. The supernatants were then used in biocatalytic reactions to determine their activity levels.

Example 4

Preparation of Lyophilized Lysates From Shake Flask (SF) Cultures

(27) Shake-flask procedures can be used to generate engineered KRED polypeptide shake-flask powders (SFP), which are useful for secondary screening assays and/or use in the biocatalytic processes described herein. Shake flask powder (SFP) preparation of enzymes provides a more purified preparation (e.g., up to 30% of total protein) of the engineered enzyme, as compared to the cell lysate used in high throughput (HTP) assays and also allows for the use of more concentrated enzyme solutions. To start this, selected HTP cultures grown as described above were plated onto LB agar plates with 1% glucose and 30 μg/ml CAM, and grown overnight at 37° C. A single colony from each culture was transferred to 6 ml of LB with 1% glucose and 30 μg/ml CAM. The cultures were grown for 18 h at 30° C. at 250 rpm, and subcultured approximately 1:50 into 250 ml of TB containing 30 μg/ml CAM, to a final OD.sub.600 of 0.05. The cultures were grown for approximately 3 hours at 30° C. at 250 rpm to an OD600 between 0.8-1.0 and induced with 1 mM IPTG. The cultures were then grown for 20 h at 30° C. at 250 rpm. The cultures were centrifuged (4000 rpm for 20 min at 4° C.). The supernatant was discarded, and the pellets were re-suspended in 35 ml of 50 mM pH 8 Potassium Phosphate with 2 mM MgSO.sub.4. The re-suspended cells were centrifuged (4000 rpm for 20 min at 4° C.). The supernatant was discarded, and the pellets were re-suspended in 6 ml of 50 mM pH 8 Potassium Phosphate with 2 mM MgSO.sub.4, and the cells were lysed using a cell disruptor from Constant Systems (One Shot). The lysates were pelleted (10,000 rpm for 60 min at 4° C.), and the supernatants were frozen and lyophilized to generate shake flask (SF) enzymes.

Example 5

Screening of Commercially Available KRED Enzyme Panel

(28) KRED Screening Assay

(29) A set of commercially available ketoreductases were tested for their ability to reduce isoalpha acids using the commercially available “KRED Screening Kits” (Codexis Inc., Redwood City, Calif.). For a portion of the enzymes in this screening, the enzyme assay was carried out in a 1.5 mL volume tubes, in 1000 μL total volume/tube, which included 10 g/L enzyme powder, 2.9 or 6.9 g/L isoalpha acids substrate, and 0.8 g/L NADP in 30 vol % isopropanol (IPA) in 128 mM pH 7 sodium phosphate with 1.7 mM MgSO.sub.4. The tubes were closed and incubated at 30° C. with shaking at 180 rpm for 24-48 hours. The obtained reaction mixture was filtered to remove enzyme using a 10,000 MWCO centrifugal filtration device. Isoalpha acids and dihydro-(rho)-isoalpha acids were quantified by UPLC. See, for example, the chromatogram for Codexis KRED-433 presented in FIG. 4.

(30) For the other portion of the enzymes in this screening, the enzyme assay was carried out in a 1.5 mL volume tubes, in 1000 μL total volume/tube, which included 10 g/L enzyme powder, 1.5 g/L isoalpha acids substrate, 0.8 g/L NADP, 0.7 g/L NAD, 14.4 g/L D-glucose, and 4.3 U/mL glucose dehydrogenase in 263 mM pH 7 sodium phosphate with 1.7 mM MgSO.sub.4. The tubes were closed and incubated at 30° C. with shaking at 180 rpm for 24-48 hours. The obtained reaction mixture was filtered to remove enzyme using a 10,000 MWCO centrifugal filtration device. Isoalpha acids and dihydro-(rho)-isoalpha acids were quantified by UPLC.

(31) Ketoreductase Characterization Assay

(32) Ketoreductases that produced detectable quantities of dihydro-(rho)-isoalpha acids were further characterized under various reaction conditions. For this purpose, the enzyme assays were carried out in 2.0 mL volume tubes, in 1000 μL total volume/tube, which included 10-20 g/L enzyme powder, 1.5-6.0 g/L isoalpha acids substrate, 0.8 g/L NADP (optionally, 0.7 g/L NAD, 14.4 g/L D-glucose, 4.3 U/mL glucose dehydrogenase or 30 vol % Isopropanol) in 100-263 mM pH 7-9 sodium phosphate (or alternatively, Tris HCl) with 1.7 mM MgSO.sub.4. The tubes were closed and incubated at 30-40° C. with shaking at 180 rpm for 24-48 hours. The obtained reaction mixtures were filtered to remove enzyme. Isoalpha acids and dihydro-(rho)-isoalpha acids were detected by UPLC-MS/MS and HPLC.

(33) Results

(34) KRED Screening Results

(35) Several commercially available enzymes from Codexis' “KRED Screening Kits” are capable of reducing isoalpha acids (Table 1). The original kit was composed of 24 ketoreductases (referred to as KREDs) that have been selected (i.e. natural) or engineered for broad substrate range and enhanced activity by the manufacturer. An additional kit was composed of 7 engineered variants based on the backbone of KRED-130.

(36) TABLE-US-00001 TABLE 1 Results from Commercially Available KRED Enzyme Panel Ketoreductase Enzyme Rho Detected?.sup.1 KRED-P1-A04 − KRED-P1-A12 − KRED-P1-B02 − KRED-P1-B05 + KRED-P1-B10 − KRED-P1-B12 − KRED-P1-C01 − KRED-P1-H08 − KRED-P2-B02 + KRED-P2-C02 + KRED-P2-C11 + KRED-P2-D03 − KRED-P2-D11 + KRED-P2-D12 − KRED-P2-G03 + KRED-P2-H07 − KRED-P3-B03 − KRED-P3-G09 + KRED-P3-H12 − KRED-101 + KRED-119 + KRED-130 + KRED-NADH-101 − KRED-NADH-110 + KRED-430 + KRED-431 + KRED-432 + KRED-433 + KRED-434 + KRED-435 + KRED-436 + .sup.1+ = Peaks corresponding to Dihydroisoalpha acids (Rho) observed via UPLC-MS after incubation with enzyme.
Ketoreductase Characterization

(37) Enzymes were determined to reduce isoalpha acids if peaks corresponding to cis/trans-co/ad/n-dihydro-(rho)-isoalpha acid were detected via UPLC at a greater intensity than a control sample lacking enzyme.

(38) KRED-P1-B05 (SEQ ID NO: 4) produced the most dihydro-(rho)-isoalpha acids in a 24 hour period by qualitative comparison of UPLC peak heights (See FIG. 2). KRED-P1-B05 (SEQ ID NO: 4) is derived from an enzyme encoded by a nucleotide (SEQ ID NO: 1) which encodes an amino acid sequence which is a naturally-occurring, wild-type ketoreductase from Lactobacillus kefir (SEQ ID NO: 2). Dihydro-(rho)-isoalpha acids produced by this ketoreductase were present at high enough concentration to be quantified by HPLC. In 24 hour at 30° C., KRED-P1-B05 achieved a yield of 18% dihydro-(rho)-isoalpha acids. The reaction was duplicated with a 48 hour reaction duration, achieving a yield of 42% dihydro-(rho)-isoalpha acids. (See FIG. 3). When the reaction temperature was increased from 30° C. to 37° C. for 48 hours, the yield was 33%.

(39) KRED-P1-B05 activity was initially tested using buffer (128 mM sodium phosphate pH 7 with 1.7 mM magnesium sulfate, 0.8 g/L mM NADP) in addition to 30 vol % isopropanol for cofactor recycling. Multiple reaction conditions (temperature, duration, buffer composition, substrate concentration, etc.) were determined to be adequate for reduction of isoalpha acids.

(40) Substrate Specificity

(41) The ideal ketoreductase for biotransformation purposes shows no substrate specificity for the isohumulone congeners which vary based on side chain composition (conferring n-, ad-, and co-isohumulone). Additionally, the ketoreductase shows no specificity for the isohumulone cis and trans isomers which vary spatially at the C4 tertiary alcohol group proximal to the site of enzymatic reduction. Substrate specificity is dictated by the amino acid sequence and thus the geometry of the substrate binding pocket of an enzyme. Larger binding pockets accommodate larger substrates, as well as a greater variety of substrates, compared to more restricted binding pockets.

(42) Despite the presence of two additional ketone groups on the isoalpha acid molecule, only the desired reduction at the C4 side chain was observed for all characterized ketoreductases.

Example 6

Evolution and Screening of Engineered Polypeptides Derived from SEQ ID NO: 4 for Improved KRED Activity

(43) The enzyme of SEQ ID NO: 4 was selected as the parent enzyme based on the results of screening variants for the reduction of the ene-acid substrate. Libraries of engineered genes were produced using well-established techniques (e.g., saturation mutagenesis, and recombination of previously identified beneficial mutations). The polypeptides encoded by each gene were produced in HTP as described in Example 2, and the soluble lysate was generated as described in Example 3.

(44) The engineered polynucleotide of SEQ ID NO: 3 which encodes SEQ ID NO: 4, exhibiting superior KRED activity, was used to generate the further engineered polypeptides of Table 2. These polypeptides displayed improved formation of dihydro-(rho)-isoalpha acids from isoalpha acids, as compared to the starting polypeptide. The engineered polypeptides were generated from the “backbone” amino acid sequence of SEQ ID NO: 4 using directed evolution methods as described above together with the HTP assay and analytical methods described below in Table 2.

(45) TABLE-US-00002 TABLE 2 KRED Variant Activity Relative to SEQ ID NO: 4 SEQ ID NO: Percent Conversion Fold Improvement (nt/aa) (Relative to SEQ ID NO: 4).sup.1 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 + .sup.1Levels of increased activity were determined relative to the reference polypeptide of SEQ ID NO: 4 and defined as follows: “+” > 1.0 but <2.0, “++” ≥ 2 but ≤4, “+++” ≥ 4 but ≤8, “++++” ≥ 8

(46) Directed evolution began with the polynucleotide set forth in SEQ ID NO: 3. Engineered polypeptides were then selected as starting “backbone” gene sequences. Libraries of engineered polypeptides were generated using various well-known techniques (e.g., saturation mutagenesis, recombination of previously identified beneficial amino acid differences) and screened using HTP assay and analysis methods that measured the polypeptides ability to convert the isoalpha acids substrates to the desired dihydro-(rho)-isoalpha acids products.

(47) The enzyme assay was carried out in a 96-well format, in 200 μL total volume/well, which included 50% v/v HTP enzyme lysate, 8 g/L isoalpha acids substrate, and 0.1 g/L NADP in 40 vol % isopropanol (IPA) in 100 mM pH 8 triethanolamine*H.sub.2SO.sub.4 with 2 mM MgSO.sub.4. The plates were sealed and incubated at 40° C. with shaking at 600 rpm for 20-24 hours.

(48) After 20-24 hours, 1000 μL of acetonitrile with 0.1% acetic acid was added. The plates were sealed and centrifuged at 4000 rpm at 4° C. for 10 min. The quenched sample was further diluted 4-5× in 50:50 acetonitrile:water mixture prior to HPLC analysis. The HPLC run parameters are described below in Table 3.

(49) TABLE-US-00003 TABLE 3 HPLC Parameters Instrument Agilent 1100 HPLC Column 30 × 50 mm 2.7 μm Waters XBridge Phenyl column Mobile Phase A: 0.1% acetic acid in water, B: 0.1% acetic acid in acetonitrile Run 42:58 A/B for 1 minute; ramp to 10:90 A/B over 1 parameters minute Flow Rate 1.5 mL/min Run time 2.0 min retention Compound time [min] note Peak Iso-1 0.6 mixture of co-Iso isomers Retention Iso-2 0.7 mixture of n/ad-Iso isomers Times Iso-3 0.8 mixture of n/ad-Iso isomers Rho-1 1.0 mixture of co-Rho isomers Rho-2 1.2 mixture of n/ad-Rho isomers Rho-3 1.4 mixture of n/ad-Rho isomers Column 50° C. Temperature Injection 10 μL Volume Detection 260 nm

Example 7

Evolution and Screening of Engineered Polypeptides Derived from SEQ ID NO: 6 for Improved KRED Activity

(50) Libraries of engineered genes were produced using well-established techniques (e.g., saturation mutagenesis, and recombination of previously identified beneficial mutations). The polypeptides encoded by each gene were produced in HTP as described in Example 2, and the soluble lysate was generated as described in Example 3.

(51) The engineered polynucleotide of SEQ ID NO: 5, which encodes the polypeptide of SEQ ID NO: 6, exhibiting superior KRED activity, was used to generate the further engineered polypeptides of Table 4. These polypeptides displayed improved formation of dihydro-(rho)-isoalpha acid from isoalpha acids as compared to the starting polypeptide. The engineered polypeptides were generated from the “backbone” amino acid sequence of SEQ ID NO: 6 using directed evolution methods as described above together with the HTP assay and analytical methods described in Table 3.

(52) TABLE-US-00004 TABLE 4 KRED Variant Activity Relative to SEQ ID NO: 6 SEQ ID NO: Percent Conversion Fold Improvement (nt/aa) (Relative to SEQ ID NO: 6).sup.1 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 + .sup.1Levels of increased activity were determined relative to the reference polypeptide of SEQ ID NO: 6 and defined as follows: “+” > 1.0 but <2.0, “++” ≥ 2 but ≤4, “+++” ≥ 4 but ≤8, “++++” ≥ 8

(53) Directed evolution began with the polynucleotide set forth in SEQ ID NO: 5. Engineered polypeptides were then selected as starting “backbone” gene sequences. Libraries of engineered polypeptides were generated using various well-known techniques (e.g., saturation mutagenesis, recombination of previously identified beneficial amino acid differences) and screened using HTP assay and analysis methods that measured the polypeptides ability to convert the isoalpha acid substrates to the desired dihydro-(rho)-isoalpha acid products.

(54) The enzyme assay was carried out in a 96-well format, in 200 μL total volume/well, which included 50% v/v HTP enzyme lysate, 16 or 40 g/L of isoalpha acids substrate, and 0.1 g/L NADP in 40 vol % isopropanol (IPA) in 100 mM pH 8 triethanolamine*H2SO4 with 2 mM MgSO4. The plates were sealed and incubated at 40° C. with shaking at 600 rpm for 20-24 hours.

(55) After 20-24 hours, 1000 μL of acetonitrile with 0.1% acetic acid was added. The plates were sealed and centrifuged at 4000 rpm at 4° C. for 10 min. The quenched sample was further diluted 10-20× in 50:50 acetonitrile:water mixture prior to HPLC analysis. The HPLC run parameters are described in Table 3.

Example 8

Evolution and Screening of Engineered Polypeptides Derived from SEQ ID NO: 80 for Improved KRED Activity

(56) Libraries of engineered genes were produced using well-established techniques (e.g., saturation mutagenesis, and recombination of previously identified beneficial mutations). The polypeptides encoded by each gene were produced in HTP as described in Example 2, and the soluble lysate was generated as described in Example 3.

(57) The engineered polynucleotide of SEQ ID NO: 79, which encodes the polypeptide of SEQ ID NO: 80, exhibiting superior KRED activity, was used to generate the further engineered polypeptides of Table 5. These polypeptides displayed improved formation of dihydro-(rho)-isoalpha acids from isoalpha acids as compared to the starting polypeptide. The engineered polypeptides were generated from the “backbone” amino acid sequence of SEQ ID NO: 80 using directed evolution methods as described above together with the HTP assay and analytical methods described below in Table 3.

(58) TABLE-US-00005 TABLE 5 KRED Variant Activity Relative to SEQ ID NO: 80 SEQ ID NO: Percent Conversion Fold Improvement (nt/aa) (Relative to SEQ ID NO: 80).sup.1  99/100 ++++ 101/102 ++++ 103/104 +++ 105/106 +++ 107/108 +++ 109/110 +++ 111/112 +++ 113/114 ++ 115/116 ++ 117/118 ++ 119/120 ++ 121/122 ++ 123/124 ++ 125/126 ++ 127/128 ++ 129/130 + 131/132 + 133/134 + 135/136 + 137/138 + 139/140 + 141/142 +

(59) Directed evolution began with the polynucleotide set forth in SEQ ID NO: 79. Engineered polypeptides were then selected as starting “backbone” gene sequences. Libraries of engineered polypeptides were generated using various well-known techniques (e.g., saturation mutagenesis, recombination of previously identified beneficial amino acid differences) and screened using HTP assay and analysis methods that measured the polypeptides ability to convert the isoalpha acid substrates to the desired dihydro-(rho)-isoalpha acid products.

(60) The enzyme assay was carried out in a 96-well format, in 200 μL total volume/well, which included 25% v/v HTP enzyme lysate, 60 or 80 g/L of isoalpha acid substrate, and 0.02 g/L NADP in 40 vol % isopropanol (IPA) in 100 mM pH 8 potassium phosphate with 2 mM MgSO.sub.4. The plates were sealed and incubated at 45° C. with shaking at 600 rpm for 20-24 hours.

(61) After 20-24 hours, 1000 μL of acetonitrile with 0.1% acetic acid was added. The plates were sealed and centrifuged at 4000 rpm at 4° C. for 10 min. The quenched sample was further diluted 20-40× in 50:50 acetonitrile:water mixture prior to HPLC analysis. The HPLC run parameters are described in Table 3.

Example 9

Evolution and Screening of Engineered Polypeptides Derived From SEQ ID NO: 80 for Improved KRED Activity at High Substrate Concentration

(62) Libraries of engineered genes were produced using well-established techniques (e.g., saturation mutagenesis, and recombination of previously identified beneficial mutations). The polypeptides encoded by each gene were produced in HTP as described in Example 2, and the soluble lysate was generated as described in Example 3.

(63) The engineered polynucleotide of SEQ ID NO: 79, which encodes the polypeptide of SEQ ID NO: 80, exhibiting superior KRED activity, was used to generate the further engineered polypeptides of Table 6. These polypeptides displayed improved formation of dihydro-(rho)-isoalpha acids from isoalpha acids as compared to the starting polypeptide. The engineered polypeptides were generated from the “backbone” amino acid sequence of SEQ ID NO: 80 using directed evolution methods as described above and are described below in Table 3.

(64) TABLE-US-00006 TABLE 6 KRED Variant Activity Relative to SEQ ID NO: 80 SEQ ID NO: Percent Conversion Fold Improvement (nt/aa) (Relative to SEQ ID NO: 80).sup.1 143/144 ++++ 145/146 ++++ 147/148 ++++ 149/150 ++++  99/100 ++++ 151/152 +++ 153/154 +++ 155/156 +++ 103/104 ++ 157/158 ++ 159/160 ++ 139/140 + 161/162 +

(65) Directed evolution began with the polynucleotide set forth in SEQ ID NO: 79. Engineered polypeptides were then selected as starting “backbone” gene sequences. Libraries of engineered polypeptides were generated using various well-known techniques (e.g., saturation mutagenesis, recombination of previously identified beneficial amino acid differences) and screened using HTP assay and analysis methods that measured the polypeptides ability to convert the isoalpha acid substrates to the desired dihydro-(rho)-isoalpha acid products.

(66) The enzyme assay was carried out in a 96-well format, in 200 μL total volume/well, which included 10-20% v/v HTP enzyme lysate, 80 or 160 g/L of isoalpha acid substrate, and 0.02 g/L NADP in 40 vol % isopropanol (IPA) in 100 mM pH 8 potassium phosphate with 2 mM MgSO.sub.4. The plates were sealed and incubated at 45° C. with shaking at 600 rpm for 20-24 hours.

(67) After 20-24 hours, 1000 μL of acetonitrile with 0.1% acetic acid was added. The plates were sealed and centrifuged at 4000 rpm at 4° C. for 10 min. The quenched sample was further diluted 20-40× in 50:50 acetonitrile:water mixture prior to HPLC analysis. The HPLC run parameters are described in Table 3.

EXAMPLE 10

Evolution and Screening of Engineered Polypeptides Derived From SEQ ID NO: 80, 104, 100, 136, 116, 132, 162, 150, 152, 144 and 146 for Improved KRED Activity at High Substrate and Low NADP Concentration

(68) A 200 g/L enzyme stock solution was prepared by dissolving 100 mg of enzyme powder in 500 μL of 100 mM pH 8 potassium phosphate buffer with 2 mM MgSO4 and 0.1 g/L of NADP. To a well in a 96 deep-well plate was added 40 μL of the enzyme/NADP stock solution, 80 μL of isopropanol, and 80 μL of 40 wt % aqueous solution of isoalpha acid. The final reaction composition was 40 g/L of enzyme, 160 g/L isoalpha acid, and 0.02 g/L NADP in 40% IPA. The plate was sealed and incubated 40° C. for 24 h and then quenched and analyzed by HPLC-UV. The data are shown in Table 7 and FIG. 5.

(69) TABLE-US-00007 TABLE 7 KRED Activity at High Substrate and Low NADPH Concentration SEQ ID NO: % Conversion (nt/aa) 40 g/L 20 g/L 10 g/L 5 g/L 2.5 g/L 1.25 g/L 79/80 4.2 1.9 0.9 0.5 0.1 0.0 103/104 28.2 16.5 8.7 5.2 2.2 1.2  99/100 23.1 11.2 6.1 3.3 1.3 0.6 135/136 23.6 7.5 2.4 1.2 0.6 0.0 115/116 8.5 3.2 1.2 0.7 0.2 0.0 131/132 5.3 2.2 0.8 0.4 0.1 0.0 161/162 29.1 14.4 5.6 2.1 0.7 0.3 149/150 29.0 14.9 6.0 2.4 1.0 0.2 151/152 30.6 17.9 7.4 3.6 2.0 1.2 143/144 29.1 14.4 5.8 2.4 1.2 0.4 145/146 24.3 12.3 4.7 1.9 0.8 0.1 157/158 3.0 1.1 0.4 0.0 0.0 0.0

Example 11

Enzyme Treatment of Acidified Hop Derived Isoalpha Acids with Cofactor Recycling by Isopropanol Oxidation

(70) Isoalpha acids are treated in a manner described in Example 10, where the source of isoalpha acids is a highly concentrated material (68.9% isoalpha acids) having a pH<7.

Example 12

Enzyme Treatment of Hop Derived Isoalpha Acids With Cofactor Recycling by Glucose Dehydrogenase

(71) Isoalpha acids are treated in a manner described in Example 10, with the exception that isopropanol is replaced with 4.3 U/mL Glucose Dehydrogenase, 0.7 g/L mM NAD, and 14.4 g/L D-glucose.

Example 13

Enzyme Treatment of Hop Derived Isoalpha Acids Without Cofactor Recycling

(72) Isoalpha acids are treated in a manner described in Example 10, with the exception that isopropanol is replaced with an equimolar amount of NADPH as substrate.

Example 14

Enzyme Treatment of Hop Derived Isoalpha Acids With Cofactor Recycling by Ethanol Oxidation

(73) Isoalpha acids are treated in a manner described in Example 10, with the exception that isopropanol is replaced with ethanol.

Example 15

Enzyme Treatment of Hop Derived Isoalpha Acids With Immobilized Ketoreductase via SiO.SUB.2

(74) A ketoreductase is adsorbed on SiO.sub.2 and crosslinked with glutaraldehyde to yield an immobilized ketoreductase material. Isoalpha acids are treated with the immobilized ketoreductase in a manner described in Example 10. The obtained reaction mixture is centrifuged at 10,000 g to remove immobilized enzyme.

Example 16

Enzyme Treatment of Hop Derived Isoalpha Acids With Immobilized Ketoreductase Via DEAE-Cellulose

(75) A ketoreductase is crosslinked with glutaraldehyde and adsorbed onto DEAE-cellulose to yield an immobilized ketoreductase material. Isoalpha acids are treated with the immobilized ketoreductase in a manner described in Example 10. The obtained reaction mixture is centrifuged at 10,000 g to remove immobilized enzyme.

Example 17

Enzyme Treatment of Hop Derived Isoalpha Acids With Immobilized Ketoreductase via PEI-Treated Alumina

(76) A ketoreductase is crosslinked with glutaraldehyde and adsorbed onto polyethylimine (PEI)-treated alumina to yield an immobilized ketoreductase material. Isoalpha acids are treated with the immobilized ketoreductase in a manner described in Example 10. The obtained reaction mixture is centrifuged at 10,000 g to remove immobilized enzyme.

Example 18

Enzyme Treatment of Hop Derived Isoalpha Acids With NADH Cofactor Recycling

(77) Enzyme treatment where the NADPH cofactor is substituted with NADH. Isoalpha acids are treated in a manner described in Example 10 but the NADP is replaced with NAD.

Example 19

Enzyme Treatment of Hop Derived Isoalpha Acids Followed by Extraction

(78) Enzyme treatment followed by extraction to increase final concentration of dihydro-(rho)-isoalpha acids is performed. Isoalpha acids are treated in a manner described in Example 10. The obtained reaction mixture is filtered to remove enzyme and extracted with food-grade solvent to achieve a desired concentration of dihydro-(rho)-isoalpha acids.

Example 20

Enzyme Treatment of Hop Derived Isoalpha Acids Followed by Thermal Inactivation

(79) Isoalpha acids are treated in a manner described in Example 10. The reaction is incubated at 30° C. with orbital shaking at 180 rpm for 24 hours. The obtained reaction mixture is heated at 80-100° C. for 10-30 minutes to inactivate enzyme.

Example 21

Enzyme Treatment of Hop Derived Isoalpha Acids Followed by Chemical Inactivation

(80) Isoalpha acids are treated in a manner described in Example 10. The reaction is incubated at 30° C. with orbital shaking at 180 rpm for 24 hours. Food-grade ethanol is added to a final concentration of >50% to inactivate enzyme.

Example 22

Enzyme Treatment of Hop Derived Isoalpha Acids With Immobilized Ketoreductase Recycling

(81) A ketoreductase is crosslinked with glutaraldehyde and adsorbed onto DEAE-cellulose to yield an immobilized ketoreductase material. Isoalpha acids are then treated with the immobilized ketoreductase in a manner described in Example 10. The obtained reaction mixture is centrifuged at 10,000 g to separate immobilized ketoreductase from the reaction solution. Immobilized ketoreductase is recovered, washed with water or aqueous buffer, and re-used in a new reaction mixture.

Example 23

Isoalpha Acids Reduction Using Engineered Polypeptides Derived From SEQ ID NO: 80, 104, 172, 186, 194, 196, 252, 270, 272, 286, 300, 328, 330, and 346 at High Substrate and Low NADP Concentration

(82) Libraries of engineered genes were produced using well-established techniques (e.g., saturation mutagenesis, and recombination of previously identified beneficial mutations). The polypeptides encoded by each gene were produced in HTP as described in Example 2, and the soluble lysate was generated as described in Example 3e.

(83) The engineered polynucleotide of SEQ ID NO: 103, which encodes the polypeptide of SEQ ID NO: 104, exhibiting superior KRED activity, was used to generate the further engineered polypeptides of Table 8. These polypeptides displayed improved formation of dihydro-(rho)-isoalpha acid from isoalpha acids as compared to the starting polypeptide. The engineered polypeptides were generated from the “backbone” amino acid sequence of SEQ ID NO: 104 using directed evolution methods as described above together with the HTP assay and analytical methods described in Table 3.

(84) The following procedure can use any of the improved variants (SEQ ID NO: 6, SEQ ID NO: 80, SEQ ID NO: 104, SEQ ID NO: 172, SEQ ID NO: 186, SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 252, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 286, SEQ ID NO: 300, SEQ ID NO: 328, SEQ ID NO: 330, SEQ ID NO: 346, SEQ ID NO: 348, SEQ ID NO: 356, SEQ ID NO: 414, and SEQ ID NO: 416) for production of enzymatically reduced isoalpha acids at commercially viable isoalpha acids concentrations (volumetric productivity) and % conversion (yield). The reaction is performed in a glass vessel, temperature controlled, with mixing. The data are shown in Table 8 and FIG. 6.

(85) Reagents a. Isoalpha acids: i. Loading is (up to) 160 g/L; 46.000.318; Lot 1014038 ii. Isoalpha is in the base form (38% by HPLC); iii. Use 4210.5 grams b. Isopropanol (40% by volume) c. RO water d. KRED Enzyme (loading is 10 g/L): 100 grams e. NADP (loading is 0.125 g/L): 1.25 grams f. Magnesium sulfate heptahydrate (91.615, 1 mM in solution; 0.246 g/L; MW=246.4 g/mole): use 2.46 grams g. 15% potassium hydroxide (15% KOH)

(86) Procedure a. Measure out the 40% by volume of water b. Measure out the 40% by volume of isopropanol c. Prepare Isoalpha acid solution by adding 15% KOH to pH 8.5 (+/−0.5) d. Prepare a 10% “solution” of enzyme-NADP-magnesium sulfate heptahydrate in water e. Add enzyme solution to isoalpha acid to start reaction. f. Heat reaction to 40° C. g. Purge vessel with nitrogen. h. Reaction is sampled and pH is recorded at time 0, 24 and 48 hours.

(87) TABLE-US-00008 TABLE 8 KRED Variant Activity Relative to SEQ ID NO: 104 SEQ ID NO: Percent Conversion Fold Improvement (nt/aa) (Relative to SEQ ID NO: 104).sup.1 413/414 ++++ 415/416 ++++ 355/356 ++++ 329/330 ++++ 327/328 ++++ 285/286 ++++ 271/272 +++ 269/270 +++ 251/252 +++ 193/194 +++ 185/186 ++ 171/172 + .sup.1Levels of increased activity were determined relative to the reference polypeptide of SEQ ID NO: 104 and defined as follows: “+” > 1.0 but <10.0, “++” ≥ 10 but ≤20, “+++” ≥ 20 but ≤50, “++++” ≥ 50

Example 24

Isoalpha Acids Reduction Using Engineered Polypeptides Derived From SEQ ID NO: 414 and 416 at Higher Substrate Concentration

(88) Isoalpha acids are treated in a manner described in Example 23, but where the concentration of isoalpha acids present in the reaction can be increased up to 20% w/v.

Conclusions

(89) 208 ketoreductases have been characterized as transforming isoalpha acids into dihydro-(rho)-isoalpha acids. The ketoreductases characterized in this study possess an enzymatic activity that has not been described previously. The ketoreductases characterized in this study all reduce a ketone group into an alcohol and are thus ketoreductases. These results demonstrate that a ketoreductase biocatalyst may be employed to convert isoalpha acids to dihydro-(rho)-isoalpha acids in a novel biotransformation process. The present invention is intended to replace current processes utilizing sodium borohydride.

(90) The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.

(91) All patents, applications, publications, test methods, literature, and other materials cited herein are hereby incorporated by reference.

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