Pullulanase variants and polynucleotides encoding same

• US 10,640,755 B2
• Filed: 06/25/2018
• Issued: 05/05/2020
• Est. Priority Date: 01/22/2014
• Status: Active Grant

• Current Assignee: Novozymes A/S (Novozymes)
• Original Assignee: Novozymes A/S (Novozymes)
• Inventors: Matsui, Tomoko, Yamagishi, Akihiko
• Primary Examiner(s): Raghu, Ganapathirama
• Application Number:
  US16/016,950
• Publication Number:
  US 20180298364A1
• Time in Patent Office: 680 Days
• CPC Class Codes: C12N 9/2457 Pullulanase (3.2.1.41)
• CPC Class Codes: C12P 19/02 Monosaccharides 2-ketogulonic acid C12P7/60
• CPC Class Codes: C12P 19/16 produced by the action of an alpha-1, 6-glucosidase, e.g. amylose, debranched amylopectin non-biological hydrolysis of starch C08B30/00
• CPC Class Codes: C12P 2203/00 Fermentation products obtained from optionally pretreated or hydrolyzed cellulosic or lignocellulosic material as the carbon source
• CPC Class Codes: C12P 7/06 Ethanol, i.e. non-beverage
• CPC Class Codes: C12Y 302/01041 Pullulanase (3.2.1.41)
• CPC Class Codes: Y02E 50/10 Biofuels, e.g. bio-diesel

Abstract

The present invention relates to pullulanase variants comprising substitutions of the parent pullulanase at one or more positions corresponding to positions 393, 143, 150, 243, 244, 345, 346, 368, 370, 373, 381, 382, 385, 387, 402, 429, 430, 431, 432, 456, 486, 492, 610, 624, 631, 632, 665 and 699 of the polypeptide of SEQ ID NO: 3. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

Claims

1. A pullulanase variant comprising a substitution at one or more positions corresponding to positions 368, 393, 492, 610, 631, and 632, of the polypeptide of SEQ ID NO:

3, wherein the pullulanase variant has;

(a) pullulanase activity,

(b) at least 85%, but less than 100% sequence identity to the polypeptide of SEQ ID NO;

3,

(c) has increased thermoactivity compared to the pullulanase of SEQ ID NO;

3; and

(d) the substitution is selected from the group consisting of;

(i) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(ii) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(iii) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(iv) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(v) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(vi) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

2. The pullulanase variant of claim 1, comprising at least two of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

3. The pullulanase variant of claim 1, comprising at least three of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

4. The pullulanase variant of claim 1, comprising at least four of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

5. The pullulanase variant of claim 1, comprising at least five of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

6. The pullulanase variant of claim 1, comprising each of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

7. The pullulanase variant of claim 1, which has at least 90% sequence identity to the polypeptide of SEQ ID NO:

3.

8. The pullulanase variant of claim 1, which has at least 95% sequence identity to the polypeptide of SEQ ID NO:

3.

9. A composition comprising a pullulanase variant of claim 1 and one or more enzymes selected from the group consisting of:

alpha-amylase, beta-amylase, glucoamylase, and protease.

10. A process of producing a fermentation product, comprising:

(a) liquefying a starch-containing material in the presence of an alpha amylase;

(b) saccharifying the liquefied material in the presence of a glucoamylase; and

(c) fermenting with a fermenting organism;

wherein step (a) and/or step (b) is carried out in the presence of a pullulanase variant of claim 1.

11. A process of producing a fermentation product, comprising:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature of said starch-containing material using at least a glucoamylase, and a pullulanase variant of claim 1; and

(b) fermenting with a fermenting organism.

12. A pullulanase variant, which has:

(a) at least 90% sequence identity to the polypeptide of SEQ ID NO;

28, wherein the pullulanase variant has

(b) pullulanase activity,

(c) increased thermoactivity compared to the pullulanase of SEQ ID NO;

3, and

(d) the following amino acid residues at the following positions corresponding to the positions of SEQ ID NO;

3

(i) a glycine residue at position 368,

(ii) an alanine residue at position 393,

(iii) a glutamic acid residue at position 431,

(iv) a phenylalanine residue at position 432,

(v) an alanine or serine residue at position 492,

(vi) an arginine residue at position 610,

(vii) a serine residue at position 624,

(viii) a serine residue at position 631, and

(ix) a cysteine residue at position 632.

13. The pullulanase variant of claim 12, which has at least 95% sequence identity to the polypeptide of SEQ ID NO:

28.

14. The pullulanase variant of claim 12, which comprises SEQ ID NO:

28.

15. A composition comprising a pullulanase variant of claim 12 and one or more enzymes selected from the group consisting of:

alpha-amylase, beta-amylase, glucoamylase, and protease.

16. A process of producing a fermentation product, comprising:

(a) liquefying a starch-containing material in the presence of an alpha amylase;

(b) saccharifying the liquefied material in the presence of a glucoamylase; and

(c) fermenting with a fermenting organism;

wherein step (a) and/or step (b) is carried out in the presence of a pullulanase variant of claim 12.

17. A process of producing a fermentation product, comprising:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature of said starch-containing material using at least a glucoamylase, and a pullulanase variant of claim 12; and

(b) fermenting with a fermenting organism.

18. A pullulanase variant comprising a variant catalytic domain, wherein the variant catalytic domain comprises a substitution at one or more positions corresponding to positions 368, 393, 492, 610, 631, and 632 of the polypeptide of SEQ ID NO:

3, wherein;

(a) the pullulanase variant has pullulanase activity,

(b) the variant catalytic domain at least 85%, but less than 100% sequence identity to amino acids 330 to 828 of SEQ ID NO;

3,

(c) the pullulanase variant has increased thermoactivity compared to the pullulanase of SEQ ID NO;

3; and

(d) the substitution is selected from the group consisting of;

(i) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(ii) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(iii) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(iv) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(v) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(vi) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln Gly, His, Ile Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

19. The pullulanase variant of claim 18, wherein the variant catalytic domain comprises at least two of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

20. The pullulanase variant of claim 18, wherein the variant catalytic domain comprises at least three of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

21. The pullulanase variant of claim 18, wherein the variant catalytic domain comprises at least four of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

22. The pullulanase variant of claim 18, wherein the variant catalytic domain comprises at least five of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

23. The pullulanase variant of claim 18, wherein the variant catalytic domain comprises each of the following substitutions:

(a) a substitution at a position corresponding to position 368 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(b) a substitution at a position corresponding to position 393 with Ala, Arg, Asp, Cyt, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(c) a substitution at a position corresponding to position 492 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(d) a substitution at a position corresponding to position 610 with Ala, Arg, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val,

(e) a substitution at a position corresponding to position 631 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Trp, Tyr or Val,

(f) a substitution at a position corresponding to position 632 with Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Thr, Trp, Tyr or Val.

24. The pullulanase variant of claim 18, wherein the catalytic domain has at least 90% sequence identity to amino acids 330 to 828 of SEQ ID NO:

3.

25. The pullulanase variant of claim 18, wherein the catalytic domain has at least 95% sequence identity to amino acids 330 to 828 of SEQ ID NO:

3.

26. A composition comprising a pullulanase variant of claim 18 and one or more enzymes selected from the group consisting of:

alpha-amylase, beta-amylase, glucoamylase, and protease.

27. A process of producing a fermentation product, comprising:

(a) liquefying a starch-containing material in the presence of an alpha amylase;

(b) saccharifying the liquefied material in the presence of a glucoamylase; and

(c) fermenting with a fermenting organism;

wherein step (a) and/or step (b) is carried out in the presence of a pullulanase variant of claim 18.

28. A process of producing a fermentation product, comprising:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature of said starch-containing material using at least a glucoamylase, and a pullulanase variant of claim 18; and

(b) fermenting with a fermenting organism.