Hexuronate C4-epimerase mutant with improved conversion activity, and method for producing D-tagatose by using same

Abstract

A hexuronate C4-epimerase with improved conversion activity and a method for producing D-tagatose using the hexuronate C4-epimerase. The hexuronate C4-epimerase includes an amino acid sequence set forth in SEQ ID NO: 1, in which serine (S) at position 125, serine (S) at position 185, valine (V) at position 267, serine (S) at position 268, threonine (T) at position 272, tryptophan (W) at position 306, arginine (R) at position 386 and tyrosine (Y) at position 403 from an N-terminal of hexunorate C4-epimerase are mutated.

Claims

1. A hexuronate C4-epimerase variant having the amino acid sequence set forth in SEQ ID NO: 1, in which a serine (S) amino acid residue at position 125 is substituted with cysteine (C), tyrosine (Y), glutamine (Q), glutamic acid (E), threonine (T), asparagine (N), or aspartic acid (D) from an N-terminal of hexuronate C4-epimerase, wherein the variant has an hexuronate C4-epimerase activity.

2. The hexuronate C4-epimerase variant according to claim 1, wherein the serine (S) amino acid residue at position 125 is substituted with aspartic acid (D).

3. The hexuronate C4-epimerase variant according to claim 2, wherein an alanine (A) amino acid residue at position 158 is further substituted with threonine (T).

4. The hexuronate C4-epimerase variant according to claim 3, wherein (i) a glutamine (Q) amino acid residue at position 149 is further substituted with arginine (R), (ii) a valine (V) amino acid residue at position 267 is further substituted with methionine (M), or (iii) a proline (P) amino acid residue at position 351 is further substituted with serine (S).

5. The hexuronate C4-epimerase variant according to claim 2, wherein (i) a glutamine (Q) amino acid residue at position 149 is substituted with arginine (R), and a valine (V) amino acid residue at position 267 is substituted with methionine (M); or (ii) a valine (V) amino acid residue at position 267 is substituted with methionine (M), and a proline (P) amino acid residue at position 351 is further substituted with serine (S).

6. The hexuronate C4-epimerase variant according to claim 2, wherein a lysine (K) amino acid residue at position 164 is substituted with methionine (M), an aspartic acid (D) amino acid residue at position 168 is substituted with glutamic acid (E), and a glutamic acid (E) amino acid residue at position 175 is further substituted with glycine (G); and (i) a leucine (L) amino acid residue at position 140 is substituted with proline (P), and an arginine (R) amino acid residue at position 386 is substituted with valine (V); or (ii) a serine (S) amino acid residue at position 268 is substituted with threonine (T), and a phenylalanine (F) amino acid residue at position 297 is substituted with lysine (K).

7. The hexuronate C4-epimerase variant according to claim 2, wherein a valine (V) amino acid residue at position 267 is substituted with methionine (M), a serine (S) amino acid residue at position 268 is substituted with threonine (T), and a threonine (T) amino acid residue at position 272 is further substituted with aspartic acid (D); and (i) a glutamine (Q) amino acid residue at position 149 is substituted with arginine (R), and an arginine (R) amino acid residue at position 386 is substituted with valine (V); (ii) a proline (P) amino acid residue at position 166 is substituted with arginine (R), and an arginine (R) amino acid residue at position 386 is substituted with valine (V); (iii) a serine (S) amino acid residue at position 185 is substituted with glutamine (Q), and a tyrosine (Y) amino acid residue at position 403 is substituted with threonine (T); or (iv) a proline (P) amino acid residue at position 351 is substituted with serine (S), and an arginine (R) amino acid residue at position 386 is substituted with valine (V).

8. The hexuronate C4-epimerase variant according to claim 2, wherein a valine (V) amino acid at position 267 is substituted with methionine (M), a serine (S) amino acid residue at position 268 is substituted with cysteine (C), a threonine (T) amino acid residue at position 272 is substituted with aspartic acid (D), a serine (S) amino acid residue at position 185 is substituted with glutamine (Q), and a tryptophan (W) amino acid at position 306 is further substituted with methionine (M).

9. The hexuronate C4-epimerase variant according to claim 2, wherein a tyrosine (Y) amino acid residue at position 21 is substituted with phenylalanine (F), a valine (V) amino acid residue at position 62 is substituted with isoleucine (I), a glutamine (Q) amino acid residue at position 149 is substituted with arginine (R), a valine (V) amino acid residue at position 267 is substituted with methionine (M), a leucine (L) amino acid residue at position 316 is substituted with phenylalanine (F), and a proline (P) amino acid residue at position 351 is further substituted with serine (S).

10. A nucleic acid encoding the hexuronate C4-epimerase variant according to claim 1.

11. A transformant comprising the nucleic acid according to claim 10.

12. A composition for producing D-tagatose, comprising the hexuronate C4-epimerase variant according to claim 1.

13. A method for preparing D-tagatose, comprising: epimerizing D-fructose by contacting D-fructose with the hexuronate C4-epimerase variant according to claim 1.

14. The method for preparing D-tagatose according to claim 13, wherein the epimerization is performed in the presence of a metal salt.

15. The method for preparing D-tagatose according to claim 13, further comprising: hydrolyzing sugar using an enzyme to obtain D-fructose or isomerizing glucose using an enzyme before the epimerization step.

16. A method for preparing D-tagatose, comprising: epimerizing D-fructose by contacting D-fructose with the transformant according to claim 11.

17. The method for preparing D-tagatose according to claim 16, wherein the epimerization is performed in the presence of a metal salt.

18. The method for preparing D-tagatose according to claim 16, further comprising: hydrolyzing sugar using an enzyme to obtain D-fructose or isomerizing glucose using an enzyme before the epimerization step.

19. A method for preparing D-tagatose, comprising: epimerizing D-fructose by contacting D-fructose with the composition for producing D-tagatose according to claim 12.

20. The method for preparing D-tagatose according to claim 19, wherein the epimerization is performed in the presence of a metal salt.

Description

EXAMPLES

Example 1

Design and Analysis of Improved Target Site

(1) Based on analysis of active site tertiary model structures of orthologs (homologous genes expected to have the same function in other species of microorganisms) which are expected to possess homology with an amino acid sequence of hexuronate C4-epimerase (hereinafter referred to as wild type) derived from Thermotoga neapolitana, amino acids expected to be functionally important were primarily selected. Based on analysis results of a docking model between the structure refined after alanine-scanning mutagenesis analysis for the selected amino acids and D-fructose, an improved target site to enhance unit activity of C4-epimerization for D-fructose was designed. Detailed description will be explained below.

Example 1-1

Analysis of Orthologs

(2) Orthologs having a homology with an amino acid sequence (SEQ ID NO: 1) of the wild type were selected from GenBank databases (about 60 orthologs having a sequence coverage of 80% or more and a similarity of 50% or more). Through multiple alignment analysis for the selected orthologs, conserved amino acids expected to be functionally important were identified.

Example 1-2

Analysis of Tertiary Structure Model for Enzyme

(3) Since Protein Data Bank databases showed no protein structure having 30% or more amino acid sequence identity with the wild type and orthologs, it was expected that the model structure for the wild type predicted by a homology modeling could be inaccurate. Accordingly, active site structures between models obtained through various structure modeling servers (RaptorX, Robetta, ModWeb, M4T, HHpred, PHYRE2, I-TASSER, SWISS-MODEL and the like) utilizing various algorithms were compared in order to obtain information for commonly expected structural sites, which was utilized in the next step.

Example 1-3

Alanine-Scanning Mutagenesis and Docking Simulation

(4) Amino acids selected from amino acid sequence analysis between orthologs and the tertiary model structure analysis for active sites were subjected to mutagenesis by substituting each amino acid with alanine to produce recombinant variant enzymes in Escherichia coli. Properties of each mutated site were analyzed. Amino acids expected to be functionally important through docking simulation between the model structure refined by alanine-scanning analysis and D-fructose were selected and then an improved target site to enhance unit activity of C4-epimerization for D-fructose was designed. Amino acid residues whose activity was completely eliminated through alanine scanning mutagenesis analysis (suspected to be catalytic metal ion binding residues and catalytic residues involved in deprotonation/protonation) were excluded from the target sites for activity improvement.

Example 2

Preparation of Variant Enzymes and Selection of Variant Enzymes with Improved Activity

(5) A single-site saturation mutagenesis library was constructed based on 54 target sites designed in Example 1 (amino acid residues at positions 9, 21, 60, 62, 68, 77, 91, 97, 125, 126, 140, 141, 145, 149, 157, 158, 160, 163, 164, 166, 167, 168, 175, 176, 177, 185, 202, 218, 221, 231, 241, 242, 267, 268, 272, 276, 284, 295, 297, 302, 306, 316, 337, 351, 361, 366, 386, 388, 402, 403, 415, 429, 440 and 441 from the N-terminal of wild type hexuronate C4-epimerase). Thereafter, mutated sites and amino acids having improved unit activity were selected by screening. By incorporating information on the selected improved sites, multiple variant enzymes were prepared. Thereafter, variant enzymes with improved unit activity for D-fructose C4-epimerized conversion were developed.

Example 2-1

Saturation Mutagenesis

(6) A recombinant expression vector prepared for expressing a wild type enzyme gene in Escherichia coli BL21(DE3) (a wild type enzyme gene is introduced into a restriction enzyme site of NdeI and XhoI of pET21a, thereby expressing 6xHis-tag recombinant enzyme at C-terminal) was used as a template for saturation mutagenesis for variant library construction. In view of mutation frequency variation and variant yield and the like, inversed PCR based saturation mutagenesis was used (2014. Anal. Biochem. 449:90-98). In order to minimize scales of screening the constructed variant library (minimize the number of codons introduced for saturation mutagenesis), a mixed primer NDTNMA/ATG/TGG (2012. Biotechniques 52:149-158) in which stop codons were excluded and rare codons for E. coli were minimized was designed and used. Specifically, a mixed primer having a total length of 33 bp was constructed using 15 bp residing at the front side of the mutated site, 3 bp to substitute mutation sites (NDT, VMA, ATG and TGG) and 15 bp residing at the rear side of the mutated site. PCR was performed by repeating 30 cycles consisting of denaturing at 94 C. for 2 minutes, denaturing at 94 C. from 30 minutes, annealing at 60 C. for 30 minutes, and extending at 72 C. for 10 minutes, followed by elongation at 72 C. for 60 minutes. After construction of a saturation mutagenesis library for the selected amino acid sites, variants for each library were randomly selected (<11). Base sequences for the variants were analyzed and evaluated as to amino acid mutation frequency. Based on the results, scales of screening each library were set with sequence coverage of 90% or more (2003. Nucleic Acids Res. 15;31:e30).

Example 2-2

Screening for Variant Enzymes with Improved Activity and Preparation of Multiple Variant Enzymes

(7) In order to perform high throughput screening of variant enzymes with improved activity from the constructed saturation mutagenesis library on a large scale, a colorimetric method capable of specifically quantifying D-fructose was used. Specifically, 70% Folin-Ciocalteu reagent (SIGMA-ALDRICH) was mixed with a reaction liquid as a substrate in a ratio of 15:1, followed by reacting at 80 C. for 5 minutes, and then optical density (OD) at 900 nm was measured. The obtained OD values were compared and analyzed.

(8) When comparing relative activity with wild type enzyme (SEQ ID NO: 1), 54 variant enzymes with improved activity (conversion of D-tagatose into D-fructose) were initially screened. Corresponding genes were sequenced and then analyzed for amino acid variation (Tables 2 to 5).

(9) The initially selected variant enzymes were reacted with D-fructose using purified enzyme liquid (purified by His-tag affinity chromatography), and then the resultant enzyme reaction products were subjected to HPLC analysis (Shodex SUGAR SP-G column, column analysis temperature: 80 C., mobile phase: H.sub.2O, flow rate: 0.6 ml/min, Refractive Index Detector). Based on HPLC analysis results, 222 variant enzymes with increased activity for the production of D-tagatose from D-fructose as compared with a wild type enzyme were finally selected.

Example 3

Comparative Evaluation for Variant Enzymes with Improved Activity

(10) In order to evaluate relative activity of D-fructose C4-epimerization for a variant enzyme at a single site with improved unit activity and a variant enzyme at multiple sites with improved unit activity, each enzyme was expressed in E. coli BL21(DE3), followed by purifying by His-tag affinity chromatography. An enzyme liquid with a concentration of 10 unit/ml was added to a 30% (w/v) D-fructose substrate, followed by reacting at 60 C. and pH 7.0 [50 mM potassium phosphate buffer solution] for two hours, thereby measuring relative activity of D-fructose C4-epimerization for a variant enzyme as compared with Thermotoga neapolitana derived wild type recombinant enzyme (wild type, SEQ ID NO: 1).

(11) TABLE-US-00002 TABLE 2 Mutation Relative name 77 125 149 158 185 267 268 272 351 403 Number Activity WT 100 M1 C 1 193 M2 Y 1 116 M3 Q 1 165 M4 E 1 202 M5 T 1 211 M6 N 1 131 M7 D 1 303 M8 K 1 114 M9 R 1 114 M10 H 1 118 M11 Q 1 107 M12 A 1 102 M13 F 1 104 M14 E 1 120 M15 D 1 121 M16 Q 1 116 M17 S 1 133 M18 V 1 117 M19 R 1 105 M20 K 1 117 M21 S 1 114 M22 T 1 130 M23 Q 1 119 M24 F 1 110 M25 V 1 117 M26 I 1 128 M27 A 1 119 M28 P D 2 479 M29 P D 2 487 M30 R D 2 426 M31 D T 2 494 M32 D K 2 543 M33 D R 2 430 M34 D H 2 493 M35 D Q 2 584 M36 D A 2 447 M37 D G 2 481 M38 D S 2 421 M39 D S 2 377 M40 D T 2 431 M41 D Q 2 371 M42 R D T 3 572 M43 P D T 3 452 M44 P D S 3 473 M45 D R T 3 557 M46 D R M 3 594 M47 D T M 3 608 M48 D T S 3 605 M49 D T S 3 480 M50 D Q C 3 422 M51 D Q C 3 422 M52 D K D 3 638 M53 D K V 3 402 M54 D K I 3 515 M55 D K L 3 506 M56 D K M 3 540 M57 D K Q 3 628 M58 D K T 3 790 M59 D Q T 3 746 M60 D M S 3 613

(12) TABLE-US-00003 TABLE 3 name 9 21 60 62 68 77 91 97 125 140 141 149 158 164 166 168 175 176 WT M42 R D T M43 P D T M44 P D M45 D R T M46 D R M47 D T M48 D T M49 D T M50 D M51 D M52 D M53 D M54 D M55 D M56 D M57 D M58 D M59 D M60 D M61 R D T M62 D M63 D M64 R D T M65 D M66 D M67 D M68 D M69 D M70 Y D P D T M71 G D M72 L D M73 D P M E G M74 D R M75 D M E G M76 D R M77 D M78 D M79 D M80 F I D R M81 F I D R M82 F I D R M83 F I D R M84 W D M85 I D M86 N D M87 D F M88 D M E G M89 D H M90 D F M91 D Y M92 D M93 D M94 D M95 D M96 D M97 D M98 D M99 D M100 D M101 D M102 D M103 D M104 D M105 D M106 D M107 D M108 D M109 D M110 D M111 D M112 D M113 D M114 Mutation Relative name 185 231 267 268 272 297 306 316 351 386 403 415 Number Activity WT 100 M42 3 572 M43 3 452 M44 S 3 473 M45 3 557 M46 M 3 594 M47 M 3 608 M48 S 3 605 M49 S 3 480 M50 Q C 3 422 M51 Q C 3 422 M52 K D 3 638 M53 K V 3 402 M54 K I 3 515 M55 K L 3 506 M56 K M 3 540 M57 K Q 3 628 M58 K T 3 790 M59 Q T 3 746 M60 M S 3 613 M61 T 4 441 M62 Q H M 4 495 M63 Q D M 4 548 M64 V T 5 437 M65 Q C D M 5 526 M66 Q M T D 5 451 M67 R M T D 5 510 M68 M T D V 5 555 M69 M S V T 5 445 M70 E 6 427 M71 Q M M T 6 489 M72 M T D V 6 695 M73 V 6 564 M74 M T D V 6 496 M75 T K 6 498 M76 M T D V 6 592 M77 Q M T D T 6 691 M78 M T D S V 6 553 M79 Q M C D M 6 588 M80 M F S 7 540 M81 M F S 7 454 M82 M F S 7 498 M83 M F s 7 500 M84 Q M T D T 7 478 M85 Q M T D T 7 560 M86 Q M T D T 7 486 M87 Q M T D T 7 496 M88 M C D 7 437 M89 Q M T D I 7 610 M90 Q M T D I 7 539 M91 Q M T D I 7 662 M92 Q M T D M Q 7 822 M93 Q M T D M I 7 1011 M94 Q M T D M L 7 728 M95 Q M T D M A 7 749 M96 Q M T D M P 7 728 M97 Q M T D M V 7 1023 M98 Q M T D M W 7 682 M99 Q M T D M R 7 607 M100 Q M T D M H 7 948 M101 Q M T D M F 7 956 M102 Q M T D M K 7 536 M103 Q M T D M N 7 932 M104 Q M T D M E 7 400 M105 Q M T D M D 7 476 M106 Q M T D M C 7 457 M107 Q M T D M T 7 690 M108 Q M T D M V 7 326 M109 Q M T D V T 7 693 M110 Q M T M V T 7 822 M111 Q M D M V T 7 558 M112 Q T D M V T 7 655 M113 M T D M V T 7 597 M114 Q M T D M V T 7 589

(13) TABLE-US-00004 TABLE 4 name 60 97 125 126 145 163 164 166 168 175 185 202 221 231 241 242 267 268 272 WT M115 D G Q M T D M116 D M E G T M117 D R Q M T D M118 D Q R M T D M119 D Q M T G M120 D Q M T D M121 D Q M T D M122 D Q M T D M123 D Q M T D M124 D Q M T D M125 D Q M T D M126 D Q M T V M127 D Q M T A M128 D Q M C D M129 D Q M T E M130 D Q M T D M131 D Q M T D M132 D Q M T D M133 D M C D M134 D D T F F M T M135 A D Q M T D M136 L D Q M T D M137 D F Q M T D M138 D L Q M T D M139 D P Q M T D M140 D I Q M T D M141 D T Q M T D M142 D A Q M T D M143 D G Q M T D M144 D R Q M T D M145 D A Q M T D M146 D A Q M T D M147 D Q Q M T D M148 D M Q M T D M149 D R Q M T D M150 D Q R M T D M151 D Q N M T D M152 D Q T M T D M153 D Q S M T D M154 D Q M T D M155 D Q M T D M156 D Q M T D M157 D Q M T D M158 D Q M T D M159 D Q M T D M160 D Q M T D M161 D Q M T D M162 D Q M T D M163 D Q M T D M164 D Q M T D M165 D Q M T D M166 D Q M T D M167 D Q M T D M168 D Q M T D Mutation Relative name 276 284 297 306 337 366 386 388 402 403 415 429 440 Number Activity WT 100 M115 V T 8 521 M116 K V T 8 445 M117 M T 8 697 M118 M T 8 640 M119 M V M 8 487 M120 M V M 8 786 M121 M V G 8 808 M122 H V T 8 440 M123 V V T 8 649 M124 F V T 8 740 M125 M V I 8 1006 M126 M V I 8 699 M127 M V I 8 540 M128 M V T 8 495 M129 M V I 8 931 M130 M V G 8 557 M131 M V D 8 625 M132 M V N 8 408 M133 A M T E 8 418 M134 P T 9 643 M135 M V T 9 672 M136 M V T 9 695 M137 M V T 9 661 M138 M V T 9 656 M139 M V T 9 636 M140 M V T 9 667 M141 M V T 9 670 M142 M V T 9 518 M143 M V I 9 682 M144 M V I 9 553 M145 M V T 9 553 M146 M V T 9 664 M147 M V T 9 597 M148 M V T 9 634 M149 M V T 9 752 M150 M V T 9 733 M151 M V I 9 699 M152 M V I 9 697 M153 M V I 9 736 M154 E M V I 9 601 M155 A M V I 9 586 M156 M T V I 9 1093 M157 M Y V I 9 1093 M158 M N V I 9 1489 M159 M P V I 9 1408 M160 M S V I 9 1180 M161 M S V I 9 771 M162 M G V I 9 367 M163 M C V I 9 476 M164 M V F I 9 677 M165 M V C I 9 658 M166 M V Y I 9 644 M167 M V T P 9 585 M168 M V T A 9 764

(14) TABLE-US-00005 TABLE 5 Mutation name 97 125 157 160 163 164 166 167 177 202 218 231 267 268 272 295 302 306 337 361 366 386 403 441 Number Relative Activity WT 100 M169 L D M M T D M V T 10 550 M170 L D R M T D M V T 10 706 M171 L D R M T D M V T 10 613 M172 D R M T D M W V I 10 1268 M173 D L M T D M W V I 10 1429 M174 D F M T D M W V I 10 982 M175 D R M T D M W V I 10 565 M176 D Y M T D M W V I 10 668 M177 D M R M T D M V T 10 617 M178 D A M T D M W V I 10 1803 M179 D W M T D M W V I 10 1854 M180 D I M T D M W V I 10 1678 M181 D K M T D M W V I 10 1432 M182 D M M T D M W V I 10 1770 M183 D V M T D M W V I 10 1351 M184 D S M T D M W V I 10 1951 M185 D Y M T D M W V I 10 911 M186 D H M T D M W V I 10 733 M187 D L M T D M W V I 10 1489 M188 D I M T D M W V I 10 818 M189 D S M T D M W V I 10 1294 M190 D L M T D M W V I 10 1348 M191 D F M T D M W V I 10 1350 M192 D C M T D M W V I 10 1204 M193 D M T D C M W V I 10 1000 M194 D M T D R M W V I 10 485 M195 D M T D Y M W V I 10 1261 M196 D M T D C M W V I 10 1222 M197 D M T D M W K V I 10 966 M198 D M T D M W E V I 10 630 M199 D M T D M W V V I 10 586 M200 D M T D M W W V I 10 783 M201 D M T D M W Y V I 10 781 M202 D M T D M W M V I 10 549 M203 D M T D M W R V I 10 760 M204 D M T D M W Q V I 10 731 M205 D M T D M W L V I 10 638 M206 D M T D M W R V I 10 879 M207 D M T D M W Y V I 10 1428 M208 D M T D M W C V I 10 856 M209 D M T D M W L V I 10 589 M210 D M T D M F S V I 10 1306 M211 D M T D M E S V I 10 1246 M212 D M T D M S S V I 10 1271 M213 D M T D M W S V I 10 1306 M214 D M T D M W V I E 10 1160 M215 D M T D M W V I W 10 1150 M216 D M T D M W V I H 10 1250 M217 D M T D M W V I K 10 1270 M218 D M T D M W V I A 10 1250 M219 D M T D M W V I R 10 1220 M220 D M T D M W V I S 10 1449 M221 D M T D M W V I F 10 1294

(15) As can be seen from the above results, it was confirmed that C4-epimerase variants according to the present invention possess improved D-fructose C4-epimeraization activity as compared to a wild type enzyme, specifically, M184 enzyme variant exhibited about 20 fold increase in D-tagatose production activity as compared to a wild type enzyme.

(16) Although some embodiments have been described herein, it should be understood by those skilled in the art that these embodiments are given by way of illustration only, and that various modifications, variations, and alterations can be made without departing from the spirit and scope of the invention. Therefore, the scope of the invention should be limited only by the accompanying claims and equivalents thereof.