Yeast expressing cellulases for simultaneous saccharification and fermentation using cellulose

Patent metadata

Field	Value
Publication number	US-9988652-B2
Application number	US-201514788879-A
Country	US
Kind code	B2
Filing date	Jul 1, 2015
Priority date	Nov 21, 2008
Publication date	Jun 5, 2018
Grant date	Jun 5, 2018

Abstract

The present invention is directed to cellulytic host cells. The host cells of the invention expressing heterologous cellulases and are able to produce ethanol from cellulose. According to the invention, host cells expressing a combination of heterologous cellulases can be used to produce ethanol from cellulose. In addition, multiple host cells expressing different heterologous cellulases can be co-cultured together and used to produce ethanol from cellulose. Furthermore, the invention demonstrates for the first time the ability of Kluveryomyces to produce ethanol from cellulose. The yeast strains and co-cultures of yeast strains of the invention can be used to produce ethanol on their own, or can also be used in combination with externally added cellulases to increase the efficiency of saccharification and fermentation processes.

First claim

What is claimed is:

1. A co-culture comprising at least two yeast host cells wherein
(a) at least one of the host cells comprises a first heterologous polynucleotide comprising a nucleic acid which encodes a cellulase which is an endoglucanase;
(b) at least one of the host cells comprises a second heterologous polynucleotide comprising a nucleic acid which encodes a cellulase which is a β-glucosidase;
(c) at least one of the host cells comprises a third heterologous polynucleotide comprising a nucleic acid which encodes a cellulase which is a first cellobiohydrolase I (CBH1);
(d) at least one of the host cells comprises a fourth heterologous polynucleotide comprising a nucleic acid which encodes a cellulase which is a second cellobiohydrolase II (CBH2);
wherein the first polynucleotide, the second polynucleotide, the third polynucleotide and the fourth polynucleotide are in any combination in at least two or more strains of yeast host cells;
wherein the yeast host cells can grow at a temperature of at least 35° C. or above,
wherein the endoglucanase, β-glucosidase, cellobiohydrolase I, and cellobiohydrolase II are secreted; and
wherein the co-culture is capable of producing ethanol from Avicel.

2. The co-culture of claim 1 , wherein at least one of the host cells is a Saccharomyces cerevisiae cell.

3. The co-culture of claim 1 , wherein at least one of the host cells is a thermotolerant host cell.

4. The co-culture of claim 3 , wherein the thermotolerant host cell is a Issatchenkia orientalis, Pichia mississippiensis, Pichia mexicana, Pichia farinosa, Clavispora opuntiae, Clavispora lusitaniae, Candida mexicana, Hansenula polymorpha or Kluveryomyces host cell.

5. The co-culture of claim 4 , wherein the thermotolerant host cell is a Kluyveromyces host cell.

6. The co-culture of claim 1 , wherein said first or second cellobiohydrolase is cellobiohydrolase I and cellobiohydrolase II are selected from the group consisting of a Humicola grisea CBH1, a Thermoascus aurantiacus CBH1, a Talaromyces emersonii CBH1, a Trichoderma reesei CBH1, a Talaromyces emersonii CBH2, a Chrysosporium lucknowense CBH2 and a Trichoderma reesei CBH2.

7. The co-culture of claim 1 , wherein said polynucleotide comprising a nucleic acid which encodes a first or second cellobiohydrolase I and cellobiohydrolase II, and encodes a fusion protein comprising a cellobiohydrolase and a cellulose binding module (CBM).

8. The co-culture of claim 7 , wherein the CBM is the cellulose binding module (CBM) of Trichoderma reesei Cbh2 comprising amino acids of SEQ ID NO:28.

9. The co-culture of claim 7 , wherein the CBM is the cellulose binding module (CBM) of Trichoderma reesei Cbh1 comprising amino acids of SEQ ID NO:27 or Humicola grisea Cbh1 comprising amino acids of SEQ ID NO:21.

10. The co-culture of claim 7 , wherein the CBM is the cellulose binding module (CBM) of Chrysosporium lucknowense Cbh2b comprising amino acids of SEQ ID NO:25.

11. The co-culture of claim 7 , wherein the CBM is fused to said cellobiohydrolase via a linker sequence.

12. The co-culture of claim 1 , wherein the first cellobiohydryolase cellobiohydrolase I and the second cellobiohydrolase II are a Chrysosporium lucknowense cellobiohydrase comprising the amino acids of SEQ ID NO:25 and a Talaromyces emersonii cellobiohydrolase comprising the amino acids of SEQ ID NO:23.

13. The co-culture of claim 1 , wherein the β-glucosidase is a Saccharomycopsis fibuligera β-glucosidase comprising the amino acid sequence of SEQ ID NO:40.

14. The co-culture of claim 1 , wherein the endoglucanase is a Trichoderma reesei, Coptotermes lacteus, Coptotermes formosanus, Nasulitermes takasagoensis, Coptotermes acinaciformis, Mastotermes darwinensis, Nasutitermes walkeri, Reticulitermes speratus, Aspergillus kmuvachii, Heterodera schachtii, Hypocrea jecorina, Orpinomyces sp., or Irpex lacteus endoglucanase.

15. The co-culture of claim 1 , wherein:
(a) said endoglucanase is Coptotermes formosanus endoglucanase II comprising the amino acid sequence of SEQ ID NO:31;
(b) said β-glucosidase is Saccharomycopsis fibuligera β-glucosidase I comprising the amino acid sequence of SEQ ID NO:40;
(c) said first cellobiohydrolase is Trichoderma emersonii cellobiohydrolase I comprising the amino acid sequence of SEQ ID NO:23; and
(d) said second cellobiohydrolase is Chrysosporium lucknowense cellobiohydrase II comprising the amino acid sequence of SEQ ID NO:25.

16. The co-culture of claim 1 , wherein:
(a) said endoglucanase is Hypocrea jecorina endoglucanase 2 comprising the amino acid sequence of SEQ ID NO:54;
(b) said 3-glucosidase is Saccharomycopsis fibuligera β-glucosidase I comprising the amino acid sequence of SEQ ID NO:40;
(c) said first cellobiohydrolase is Trichoderma emersonii cellobiohydrolase I comprising the amino acid sequence of SEQ ID NO:23; and
(d) said second cellobiohydrolase is Chrysosporium lucknowense cellobiohydrase II comprising the amino acid sequence of SEQ ID NO:25.

17. The co-culture of claim 1 , wherein at least one of the first polynucleotide, the second polynucleotide, the third polynucleotide and the fourth polynucleotide is codon optimized.

18. The co-culture of claim 1 , wherein at least one host cell is a xylose-utilizing host cell.

19. The co-culture of claim 18 , wherein the xylose-utilizing host cell heterologously expresses Piromyces sp. E2 XyIA, overexpresses xylulokinase, ribulose 5-phosphate isomerase, ribulose 5-phophate epimerase, transketolase and transaldolase, and does not express the GRE3 gene encoding aldose reductase.

20. The co-culture of claim 1 , wherein the endoglucanase is a Humicola grisea, Thermoascus aurantiacus, Talaromyces emersonii, Trichoderma reesei, Coptotermes lacteus, Coptotermes formosanus, Nasutitermes takasagoensis, Coptotermes acinaciformis, Mastotermes darwinensis, Nasutitermes walkeri, Saccharomycopsis fibuligera, Chrysosporium lucknowense, Reticulitermes speratus, Thermobfida fisca, Clostridum thermocellum, Clostridium cellulolyticum, Clostridumjosui, Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromyces equii, Neocallimastix patricarum, Chaetomium thermophilum, Aspergillus terreus, Neurospora Crassa, Reticulitermes flavipes or Arabidopsis thaliana endoglucanase.

21. The co-culture of claim 1 , wherein the cellobiohydrolase I is a Talaromyces emersonii cellobiohydrolase I comprising the amino acids of SEQ ID NO: 23.

22. The co-culture of claim 1 , wherein the cellobiohydrolase II is a Chrysosporium lucknowense cellobiohydrolase II comprising the amino acid sequence of SEQ ID NO: 25.

23. The co-culture of claim 1 , wherein the endoglucanase is Trichoderma reesei endoglucanase comprising the amino acid sequence of SEQ ID NO: 39.

24. The co-culture of claim 1 , wherein:
(a) said endoglucanase is Trichoderma reesei endoglucanase I comprising the amino acid sequence of SEQ ID NO:39;
(b) said β-glucosidase is Saccharomycopsis fibuligera β-glucosidase I comprising the amino acid sequence of SEQ ID NO:40;
(c) said first cellobiohydrolase is Trichoderma emersonii cellobiohydrolase I comprising the amino acids of SEQ ID NO:23; and
(d) said second cellobiohydrolase is Chrysosporium lucknowense cellobiohydrase II comprising the amino acids of SEQ ID NO:25.

25. The co-culture of claim 1 , wherein the first polynucleotide, the second polynucleotide, th

Assignees

• Lallemand Hungary Liquidity Man Llc
• Univ Stellenbosch

Inventors

• Mcbride John
• Brevnova Elena
• Mellon Mark
• Froehlich Allan
• Deleault Kristen
• Rajgarhia Vineet
• Den Haan Riaan
• Penttila Merja
• Ilmen Marja
• Siika-Aho Matti
• Uusitalo Jaana
• Stonehouse Emily A
• Gilbert Alan
• Xu Haowen
• Willes Deidre
• Bardsley John
• Koivula Anu
• Voutilainen Sanni

Classifications

• Y02E50/10

  Biofuels, e.g. bio-diesel · CPC title

• C12N15/80

  for fungi · CPC title

• C12P7/14

  Multiple stages of fermentation; Multiple types of microorganisms or re-use of microorganisms · CPC title

• C12Y302/01091

  Cellulose 1,4-beta-cellobiosidase (3.2.1.91) · CPC title

• C12N9/2445

  Beta-glucosidase (3.2.1.21) · CPC title