Glucanases, nucleic acids encoding them and methods for making and using them

Abstract

The invention relates to polypeptides having glucanase, e.g., endoglucanase, mannanase, xylanase activity or a combination of these activities, and polynucleotides encoding them. In one aspect, the glucanase activity is an endoglucanase activity (e.g., endo-1,4-beta-D-glucan 4-glucano hydrolase activity) and comprises hydrolysis of 1,4 -beta-D-glycosidic linkages in cellulose, cellulose derivatives (e.g., carboxy methyl cellulose and hydroxy ethyl cellulose) lichenin, beta-1,4 bonds in mixed beta-1,3 glucans, such as cereal beta-D-glucans or xyloglucans and other plant material containing cellulosic parts. In addition, methods of designing new enzymes and methods of use thereof are also provided. In alternative aspects, the new glucanases e.g., endoglucanases, mannanases, xylanases have increased activity and stability at increased pH and temperature.

What is claimed is: 
     
         1 . An isolated, synthetic, or recombinant polypeptide comprising:
 (i) an amino acid sequence at least 70% or more or complete (100%) sequence identity to SEQ ID NO: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO:100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NO:110, SEQ ID NO:112, SEQ ID NO:114, SEQ ID NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124, SEQ ID NO:126, SEQ ID NO:128, SEQ ID NO:130, SEQ ID NO:132; SEQ ID NO:134; SEQ ID NO:136; SEQ ID NO:138; SEQ ID NO:140; SEQ ID NO:142; SEQ ID NO:144; NO:146, SEQ ID NO:148, SEQ ID NO:150, SEQ ID NO:152, SEQ ID NO:154, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:166, SEQ ID NO:168, SEQ ID NO:170, SEQ ID NO:172, SEQ ID NO:174, SEQ ID NO:176, SEQ ID NO:178, SEQ ID NO:180, SEQ ID NO:182, SEQ ID NO:184, SEQ ID NO:186, SEQ ID NO:188, SEQ ID NO:190, SEQ ID NO:192, SEQ ID NO:194, SEQ ID NO:196, SEQ ID NO:198, SEQ ID NO:200, SEQ ID NO:202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NO:210, SEQ ID NO:212, SEQ ID NO:214, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NO:226, SEQ ID NO:228, SEQ ID NO:230, SEQ ID NO:232, SEQ ID NO:234, SEQ ID NO:236, SEQ ID NO:238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NO:262, SEQ ID NO:264, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:270, SEQ ID NO:272, SEQ ID NO:274, SEQ ID NO:276, SEQ ID NO:278, SEQ ID NO:280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NO:286, SEQ ID NO:288, SEQ ID NO:290, SEQ ID NO:292, SEQ ID NO:294, SEQ ID NO:296, SEQ ID NO:298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NO:308, SEQ ID NO:310, SEQ ID NO:312, SEQ ID NO:314, SEQ ID NO:316, SEQ ID NO:318, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NO:334, SEQ ID NO:336, SEQ ID NO:338, SEQ ID NO:340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:348, SEQ ID NO:350, SEQ ID NO:352, SEQ ID NO:354, SEQ ID NO:356, SEQ ID NO:358, SEQ ID NO:360, SEQ ID NO:362, SEQ ID NO:364, SEQ ID NO:366, SEQ ID NO:368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NO:374, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:382, SEQ ID NO:384, SEQ ID NO:386, SEQ ID NO:388, SEQ ID NO:390, SEQ ID NO:392, SEQ ID NO:394, SEQ ID NO:396, SEQ ID NO:398, SEQ ID NO:400, SEQ ID NO:402, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:418, SEQ ID NO:420, SEQ ID NO:422, SEQ ID NO:424, SEQ ID NO:426, SEQ ID NO:428, SEQ ID NO:430, SEQ ID NO:432, SEQ ID NO:434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NO:442, SEQ ID NO:444, SEQ ID NO:446, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:452, SEQ ID NO:454, SEQ ID NO:456, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:462, SEQ ID NO:464, SEQ ID NO:466, SEQ ID NO:468, SEQ ID NO:470, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:476, SEQ ID NO:478, SEQ ID NO:480, SEQ ID NO:482, SEQ ID NO:484, SEQ ID NO:486, SEQ ID NO:488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NO:496, SEQ ID NO:498, SEQ ID NO:500, SEQ ID NO:502, SEQ ID NO:504, SEQ ID NO:506, SEQ ID NO:508, SEQ ID NO:510, SEQ ID NO:512, SEQ ID NO:514, SEQ ID NO:516 or SEQ ID NO:518, or an enzymatically active fragment thereof, wherein the polypeptide or the enzymatically active fragment has a glucanase activity;   (ii) an amino acid sequence encoded by a nucleic acid having at least 65% sequence identity to SEQ ID NO.: SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:199, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NO:165, SEQ ID NO:167, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:173, SEQ ID NO:175, SEQ ID NO:177, SEQ ID NO:179, SEQ ID NO:181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NO:187, SEQ ID NO:189, SEQ ID NO:191, SEQ ID NO:193, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:199, SEQ ID NO:201, SEQ ID NO:203, SEQ ID NO:205, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:211, SEQ ID NO:213, SEQ ID NO:215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NO:221, SEQ ID NO:223, SEQ ID NO:225, SEQ ID NO:227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NO:233, SEQ ID NO:235, SEQ ID NO:237, SEQ ID NO:239, SEQ ID NO:241, SEQ ID NO:243, SEQ ID NO:245, SEQ ID NO:247, SEQ ID NO:249, SEQ ID NO:251, SEQ ID NO:253, SEQ ID NO:255, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:263, SEQ ID NO:265, SEQ ID NO:267, SEQ ID NO:269, SEQ ID NO:271, SEQ ID NO:273, SEQ ID NO:275, SEQ ID NO:277, SEQ ID NO:279, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:287, SEQ ID NO:289, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:295, SEQ ID NO:297, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:309, SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:315, SEQ ID NO:317, SEQ ID NO:319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NO:325, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:335, SEQ ID NO:337, SEQ ID NO:339, SEQ ID NO:341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347, SEQ ID NO:349, SEQ ID NO:351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357, SEQ ID NO:359, SEQ ID NO:361, SEQ ID NO:363, SEQ ID NO:365, SEQ ID NO:367, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NO:381, SEQ ID NO:383, SEQ ID NO:385, SEQ ID NO:387, SEQ ID NO:389, SEQ ID NO:391, SEQ ID NO:393, SEQ ID NO:395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NO:417, SEQ ID NO:419, SEQ ID NO:421, SEQ ID NO:423, SEQ ID NO:425, SEQ ID NO:427, SEQ ID NO:429, SEQ ID NO:431, SEQ ID NO:433, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:443, SEQ ID NO:445, SEQ ID NO:447, SEQ ID NO:449, SEQ ID NO:451, SEQ ID NO:453, SEQ ID NO:455, SEQ ID NO:457, SEQ ID NO:459, SEQ ID NO:461, SEQ ID NO:463, SEQ ID NO:465, SEQ ID NO:467, SEQ ID NO:469, SEQ ID NO:471, SEQ ID NO:473, SEQ ID NO:475, SEQ ID NO:477, SEQ ID NO:479, SEQ ID NO:481, SEQ ID NO:483, SEQ ID NO:485, SEQ ID NO:487, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:497, SEQ ID NO:499, SEQ ID NO:501, SEQ ID NO:503, SEQ ID NO:505, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:511, SEQ ID NO:513, SEQ ID NO:515 or SEQ ID NO:517, wherein the polypeptide has glucanase activity;   (iii) the amino acid sequence of (i), or (ii), lacking a signal sequence and/or a carbohydrate binding module; or   (iv) the amino acid sequence of (i), (ii), or (iii), further comprising a heterologous sequence.   
     
     
         2 . The polypeptide of  claim 1 , wherein the polypeptide comprises at least one glycosylation site; or, wherein the polypeptide comprises at least one N-linked glycosylation site, or, wherein the polypeptide is glycosylated after being expressed in a  P. pastoris  or a  S. pombe.    
     
     
         3 . A protein preparation comprising the polypeptide of  claim 1 , wherein the protein preparation comprises a liquid, a solid or a gel. 
     
     
         4 . An immobilized polypeptide, wherein the polypeptide comprises: (a) the sequence of  claim 1 ; or, (b) the immobilized polypeptide of (a), wherein the polypeptide is immobilized on a cell, a metal, a resin, a polymer, a ceramic, a glass, a microelectrode, a graphitic particle, a bead, a gel, a plate, an array or a capillary tube. 
     
     
         5 . A method for identifying a polypeptide having a glucanase activity comprising:
 (a) providing the polypeptide of  claim 1 ;   (b) providing a glucanase substrate; and   (c) contacting the polypeptide with the substrate of (b) and detecting a decrease in the amount of substrate or an increase in the amount of a reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of the reaction product detects a polypeptide having a glucanase activity.   
     
     
         6 . A method for identifying a glucanase substrate comprising:
 (a) providing the polypeptide of  claim 1 ;   (b) providing a test substrate; and   (c) contacting the polypeptide of (a) with the test substrate of (b) and detecting a decrease in the amount of substrate or an increase in the amount of reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of a reaction product identifies the test substrate as a glucanase substrate.   
     
     
         7 . A method of determining whether a test compound specifically binds to a polypeptide comprising:
 (a) providing the polypeptide of  claim 1 ;   (b) providing a test compound;   (c) contacting the polypeptide with the test compound; and   (d) determining whether the test compound of (b) specifically binds to the polypeptide.   
     
     
         8 . A method for identifying a modulator of a glucanase activity comprising:
 (A) (a) providing the polypeptide of  claim 1 ;
 (b) providing a test compound; 
 (c) contacting the polypeptide of (a) with the test compound of 
   (b) and measuring an activity of the glucanase, wherein a change in the glucanase in the presence of the test compound compared to the activity in the absence of the test compound provides a determination that the test compound modulates the glucanase activity; or   (B) the method of (A), wherein the glucanase activity is measured by providing a glucanase substrate and detecting a decrease in the amount of the substrate or an increase in the amount of a reaction product, or, an increase in the amount of the substrate or a decrease in the amount of a reaction product; or   (C) the method of (B), wherein a decrease in the amount of the substrate or an increase in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an activator of a glucanase activity; or, wherein an increase in the amount of the substrate or a decrease in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an inhibitor of a glucanase.   
     
     
         9 . A method for hydrolyzing, breaking up or disrupting a cellulose-, hemicellulose-, lignin-, or glucan-comprising composition comprising:
 (A) (a) providing the polypeptide having a glucanase activity of  claim 1 ;
 (b) providing a composition comprising a cellulose, hemicellulose, lignin, or glucan; and 
 (c) contacting the polypeptide of (a) with the composition of (b) under conditions wherein the glucanase hydrolyzes, breaks up or disrupts the cellulose-, hemicellulose-, lignin-, or glucan-comprising composition; or 
   (B) the method of (A), wherein the composition comprises a biomass, a plant cell, a bacterial cell, a yeast cell, an insect cell, or an animal cell.   
     
     
         10 . A dough or a bread product comprising the polypeptide of  claim 1 . 
     
     
         11 . A method of dough conditioning comprising contacting a dough or a bread product with at least one polypeptide of  claim 1  under conditions sufficient for conditioning the dough. 
     
     
         12 . A beverage comprising the polypeptide of  claim 1 . 
     
     
         13 . A method of beverage production comprising
 (A) administration of at least one polypeptide of  claim 1  to a beverage or a beverage precursor under conditions sufficient for decreasing the viscosity of the beverage; or   (B) the method of (A), wherein the beverage or beverage precursor is a wort or a beer.   
     
     
         14 . A food, a feed or a nutritional supplement comprising the polypeptide of  claim 1 . 
     
     
         15 . A method for utilizing a glucanase nutritional supplement in an animal diet, the method comprising:
 (A) preparing a nutritional supplement containing a polypeptide as set forth in  claim 1 ; and administering the nutritional supplement to an animal to increase utilization of a glucan contained in a feed or a food ingested by the animal;   (B) the method of (A), wherein the animal is a human; or   (C) the method of (A), wherein the animal is a ruminant or a monogastric animal.   
     
     
         16 . An edible enzyme delivery matrix comprising the polypeptide of  claim 1 . 
     
     
         17 . A method for delivering a glucanase to an animal, the method comprising:
 (a) preparing an edible enzyme delivery matrix in the form of pellets comprising a granulate edible carrier and a thermostable recombinant glucanase enzyme, wherein the pellets readily disperse the glucanase enzyme contained therein into aqueous media, and administering the edible enzyme delivery matrix to the animal;   (b) the method of (a), wherein the recombinant glucanase enzyme comprises the polypeptide of  claim 1 ;   (c) the method of (a) or (b), wherein the granulate edible carrier comprises a carrier comprising a grain germ, a grain germ that is spent of oil, a hay, an alfalfa, a timothy, a soy hull, a sunflower seed meal, a wheat midd or a combination thereof;   (d) the method of (a), (b) or (c), wherein the edible carrier comprises grain germ that is spent of oil;   (e) the method of (a), (b), (c) or (d), wherein the glucanase enzyme is glycosylated to provide thermostability at pelletizing conditions;   (f) the method of (a), (b), (c), (d) or (e), wherein the delivery matrix is formed by pelletizing a mixture comprising a grain germ and a glucanase;   (g) the method of (a), (b), (c), (d), (e) or (f), wherein the pelletizing conditions include application of steam.   
     
     
         18 . A cellulose- or cellulose derivative-composition comprising the polypeptide of  claim 1 . 
     
     
         19 . A wood, wood pulp, or wood product comprising the polypeptide of  claim 1 . 
     
     
         20 . A paper, paper pulp, or paper product comprising the polypeptide of  claim 1 . 
     
     
         21 . A method for reducing lignin in a paper, a wood or wood product comprising contacting the paper, wood or wood product with the polypeptide of  claim 1 . 
     
     
         22 . A detergent composition comprising a polypeptide as set forth in  claim 1 . 
     
     
         23 . A method for making a fuel comprising contacting a composition comprising a cellulose, a hemicellulose, a lignin or a glucan with the polypeptide of  claim 1 . 
     
     
         24 . A dairy product comprising:
 (a) the polypeptide of  claim 1 ; or   (b) the dairy product of (a), comprising a milk, an ice cream, a cheese or a yogurt.   
     
     
         25 . A method for improving texture and flavor of a dairy product comprising:
 (a) providing the polypeptide of  claim 1 ;   (b) providing a dairy product; and   (c) contacting the polypeptide of (a) and the dairy product of (b) under conditions wherein the glucanase can improve the texture or flavor of the dairy product.   
     
     
         26 . A composition comprising the polypeptide of  claim 1 . 
     
     
         27 . A fracturing fluid composition comprising the polypeptide of  claim 1 . 
     
     
         28 . A method of treating a subterranean formation comprising use of the polypeptide of  claim 1 . 
     
     
         29 . An expression cassette, a vector or a cloning vehicle comprising a nucleic acid comprising the sequence of  claim 1 ,
 wherein optionally the cloning vehicle comprises a viral vector, a plasmid, a phage, a phagemid, a cosmid, a fosmid, a bacteriophage or an artificial chromosome, or   wherein optionally the cloning vehicle comprises a viral vector comprising an adenovirus vector, a retroviral vector or an adeno-associated viral vector, or   wherein optionally the cloning vehicle comprises a bacterial artificial chromosome (BAC), a plasmid, a bacteriophage P1-derived vector (PAC), a yeast artificial chromosome (YAC), or a mammalian artificial chromosome (MAC).