Methods and compositions for processing biomass with elevated levels of starch

• US 9,598,700 B2
• Filed: 03/11/2013
• Issued: 03/21/2017
• Est. Priority Date: 06/25/2010
• Status: Active Grant

• Current Assignee: Agrivida, Inc. (Nippon Soda Company Limited)
• Original Assignee: Agrivida, Inc. (Nippon Soda Company Limited)
• Inventors: Lessard, Philip A., Lanahan, Michael, Samoylov, Vladimir, Bougri, Oleg, Emery, Jonas, Raab, R. Michael, Zhang, Dongcheng
• Primary Examiner(s): DEVEAU ROSEN, JASON
• Application Number:
  US13/793,078
• Publication Number:
  US 20130269061A1
• Time in Patent Office: 1,471 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: A23K 10/12 by fermentation of natural products, e.g. of vegetable material, animal waste material or biomass
• CPC Class Codes: A23K 10/30 from material of plant origin, e.g. roots, seeds or hay; from material of fungal origin, e.g. mushrooms obtained by microbiological or biochemical processes, e.g. using yeasts or enzymes, A23K10/10
• CPC Class Codes: A23K 10/38 from distillers' or brewers' waste
• CPC Class Codes: A23K 40/10 by agglomeration; by granulation, e.g. making powders
• CPC Class Codes: A23K 50/10 for ruminants
• CPC Class Codes: A23K 50/30 for swines
• CPC Class Codes: A23K 50/75 for poultry
• CPC Class Codes: C12N 15/8218 Antisense, co-suppression, viral induced gene silencing [VIGS], post-transcriptional induced gene silencing [PTGS]
• CPC Class Codes: C12N 15/8245 involving modified carbohydrate or sugar alcohol metabolism, e.g. starch biosynthesis
• CPC Class Codes: C12N 15/8246 Non-starch polysaccharides, e.g. cellulose, fructans, levans
• CPC Class Codes: C12N 9/1294 Phosphotransferases with paired acceptors (2.7.9)
• CPC Class Codes: C12P 19/14 produced by the action of a carbohydrase (EC 3.2.x), e.g. by alpha-amylase , e.g. by cellulase, hemicellulase
• CPC Class Codes: C12Y 207/09004 Alpha-glucan, water dikinase (2.7.9.4)
• CPC Class Codes: Y02P 20/52 using catalysts, e.g. selective catalysts
• CPC Class Codes: Y02P 60/87 Re-use of by-products of food processing for fodder production

Abstract

Genetically engineered plants having altered levels of one or more starch regulation enzymes and a polysaccharide degrading enzyme are provided. Methods of genetically engineering plants to express products altering expression of one or more starch regulation enzymes and polysaccharide degrading enzymes, and genetic constructs are provided. Methods of agricultural processing and animal feed using the genetically engineered plants are described.

Claims

1. A genetically engineered plant comprising:

a first isolated nucleic acid comprising a sequence of SEQ ID NO;

50 that encodes a ribonucleic acid product that inactivates or inhibits expression of at least one gene encoding a protein involved in mobilization of starch in a plant, and a second isolated nucleic acid that encodes an endo-1,4-beta-xylanase from Thermomyces lanuginosus, a cellobiohydrolase B and an endo-beta 1,4-endoglucanase from Nasutitermes takasagoensis;

wherein the second isolated nucleic acid comprises a sequence of;

SEQ ID NO;

86, SEQ ID NO;

87, and SEQ ID NO;

90.

2. The genetically engineered plant of claim 1 further comprising a promoter operably linked to at least one of the first isolated nucleic acid or the second isolated nucleic acid.

27. The genetically engineered plant of claim 1 comprising the nucleic acid sequence of SEQ ID NO:

139.

3. A genetic construct comprising:

a first isolated nucleic acid comprising a sequence of SEQ ID NO;

50 that encodes a ribonucleic acid product that inactivates or inhibits expression of at least one gene encoding a protein involved in mobilization of starch in a plant, and a second isolated nucleic acid that encodes an endo-1,4-beta-xylanase from Thermomyces lanuginosus, a cellobiohydrolase B and an endo-beta 1,4-endoglucanase from Nasutitermes takasagoensis;

wherein the second isolated nucleic acid comprises a sequence of;

SEQ ID NO;

86, SEQ ID NO;

87, and SEQ ID NO;

90.

4. The genetic construct of claim 3 further comprising a promoter operably linked to at least one of the first isolated nucleic acid or the second isolated nucleic acid.

28. The genetic construct of claim 3 comprising the nucleic acid sequence of SEQ ID NO:

139.

5. A method of agricultural processing or preparing animal feed comprising pretreating a genetically engineered plant with a chemical formulation to form a mixture, wherein the genetically engineered plant comprises:

a first isolated nucleic acid comprising a sequence of SEQ ID NO;

50 that encodes a ribonucleic acid product that inactivates or inhibits expression of at least one gene encoding a protein involved in mobilization of starch in a plant, and a second isolated nucleic acid that encodes an endo-1,4-beta-xylanase from Thermomyces lanuginosus, a cellobiohydrolase B and an endo-beta 1,4-endoglucanase from Nasutitermes takasagoensis;

wherein the second isolated nucleic acid comprises a sequence of;

SEQ ID NO;

86, SEQ ID NO;

87, and SEQ ID NO;

90.

6. The method of claim 5, wherein the genetically engineered plant further comprises a promoter operably linked to at least the first isolated nucleic acid or the second isolated nucleic acid.

7. The method of claim 5, wherein the chemical formulation includes at least one moiety comprising an ion selected from the group consisting of:

sulfite, bisulfite, sulfate, carbonate, hydroxide and oxide.

8. The method of claim 7, wherein the at least one moiety further includes a counter ion selected from the group consisting of:

ammonium, sodium, magnesium and calcium.

9. The method of claim 5, wherein the chemical formulation includes a compound selected from the group consisting of:

a sulfuric acid, a base, ammonium bisulfite and ammonium carbonate.

10. The method of claim 5, wherein the mixture has a liquid to solid ratio of 8 to 10.

11. The method of claim 5, wherein the pretreating includes incubating the mixture for a period from 1 hour to 16 hours.

12. The method of claim 5, wherein the pretreating includes a mixture temperature of 40°

C. to 120°

C.

13. The method of claim 5, wherein the pretreating includes a mixture pH ranging from 1.0 to 12.0.

14. The method of claim 13 further comprising hydrolyzing the mixture.

15. The method of claim 14, wherein the step of hydrolyzing includes incubating the mixture for a period from one hour to 144 hours.

16. The method of claim 14, wherein the step of hydrolyzing includes incubating the mixture at a temperature of 40°

C. to 95°

C.

17. The method of claim 16 further comprising hydrolyzing the genetically engineered plant with one or more exogenous enzymes.

18. The method of claim 17, further comprising exposing the genetically engineered plant to a fermenting organism under fermenting conditions to produce a chemical product.

19. The method of claim 17, wherein the one or more exogenous enzymes is selected from the group consisting of:

a glycosidase, an endoglucanase, a cellobiohydrolase, a glycosidase, a β

-xylosidase, a cellulase, a xylanase, an amylase, an invertase, a protease, a phytase, a hydrolytic enzyme, a glucanase, a hemicellulase, an esterase, a laccase, a mannanase, and a peroxidase.

20. The method of claim 5, wherein the genetically engineered plant is made using Agrobacterium-mediated transformation prior to the step of pretreatment.

21. The method of claim 5, wherein the genetically engineered plant is selected from the group consisting of:

corn, soybean, rice, sugar cane, sugar beet, sorghum, switchgrass, miscanthus, eucalyptus, willow and poplar.

22. A method of preparing animal feed comprising at least one procedure selected from the group consisting of:

drying a genetically engineered plant, pelletizing a genetically engineered plant into feed pellets, ensiling a genetically engineered plant to make silage, and combining the genetically engineered plant with distillers grains or with a source of edible fiber, wherein the genetically engineered plant comprises a first isolated nucleic acid comprising a sequence of SEQ ID NO;

50 that encodes a ribonucleic acid product that inactivates or inhibits expression of at least one gene encoding a protein involved in mobilization of starch in a plant, and a second isolated nucleic acid that encodes an endo-1,4-beta-xylanase from Thermomyces lanuginosus, a cellobiohydrolase B and an endo-beta 1,4-endoglucanase from Nasutitermes takasagoensis;

wherein the second isolated nucleic acid comprises a sequence of;

SEQ ID NO;

86, SEQ ID NO;

87, and SEQ ID NO;

90.

23. The method of claim 22, wherein the genetically engineered plant further comprises a promoter operably linked to at least the first isolated nucleic acid or the second isolated nucleic acid.

24. The method of claim 22, wherein the source of edible fiber is selected from the group of plants consisting of:

corn, sorghum, wheat, rye, soybeans, corn grain, sorghum grain, wheat grain, rye grain, soybean meal, corn meal, corn oil, and corn germ.

29. The method of any one of claim 5, 22 or 25, wherein the genetically engineered plant comprises the isolated nucleic acid sequence of SEQ ID NO:

139.

25. A method of agricultural processing comprising feeding an animal with an animal feed comprising a genetically engineered plant to promote animal growth, wherein prior to the step of feeding the animal feed is prepared by at least one procedure selected from the group consisting of:

drying a genetically engineered plant, pelletizing a genetically engineered plant into feed pellets, ensiling a genetically engineered plant to make silage, and combining the genetically engineered plant with distillers grains or with a source of edible fiber, and the genetically engineered plant comprises a first isolated nucleic acid comprising a sequence of SEQ ID NO;

50 that encodes a ribonucleic acid product that inactivates or inhibits expression of at least one gene encoding a protein involved in mobilization of starch in a plant, and a second isolated nucleic acid that encodes an endo-1,4-beta-xylanase from Thermomyces lanuginosus, a cellobiohydrolase B and an endo-beta 1,4-endoglucanase from Nasutitermes takasagoensis;

wherein the second isolated nucleic acid comprises a sequence of;

SEQ ID NO;

86, SEQ ID NO;

87, and SEQ ID NO;

90.

26. The method of claim 25, wherein the animal is selected from the group consisting of:

chicken, swine, and cattle.