Isolation of four xylanases capable of hydrolyzing corn fiber xylan from Paenibacillus sp. H2C

References

• Widyaratne GP, Zijlstra RT. Nutritional value of wheat and corn distiller’s dried grain with solubles: digestibility and digestible contents of energy, amino acids and phosphorus, nutrient excretion and growth performance of grower-finisher pigs. Can J Anim Sci. 2007;87:103–114.
   Web of Science ®Google Scholar
• Stein HH, Shurson GC. Boad-invited review: the use and application of distillers dried grains with solubles in swine diets. J Anim Sci. 2009;87:1292–1303.
   PubMed Web of Science ®Google Scholar
• Cowieson AJ, Hruby M, Pierson EEM. Evolving enzyme technology: impact on commercial poultry nutrition. Nutr Res Rev. 2006;19:90–103.
   PubMed Web of Science ®Google Scholar
• Pedersen MB, Dalsgaard S, Knudsen KEB, et al. Compositional profile and variation of distillers dried grains with solubles from various origins with focus on non-starch polysaccharides. Anim Feed Sci Technol. 2014;197:130–141.
   Web of Science ®Google Scholar
• Slominski B. Recent advances in research on enzymes for poultry diets. Poult Sci. 2011;90:2013–2023.
   PubMed Web of Science ®Google Scholar
• Nghiem NP, Montanti J, Johnston DB, et al. Fractionation of corn fiber treated by soaking in aqueous ammonia (SAA) for isolation of hemicellulose B and production of C5 sugars by enzyme hydrolysis. Appl Biochem Biotechnol. 2011;164:1390–1404.
   PubMed Web of Science ®Google Scholar
• Saha BC. Hemicellulose bioconversion. J Ind Microbiol Biotechnol. 2003;30:279–291.
   PubMed Web of Science ®Google Scholar
• Saulnier L, Vigouroux J, Thibault J-F. Isolation and partial characterization of feruloylated oligosaccharides from maize bran. Carbohydr Res. 1995;272:241–253.
   PubMed Web of Science ®Google Scholar
• Saulnier L, Marot C, Chanliaud E, et al. Cell wall polysaccharide interactions in maize bran. Carbohydr Polym. 1995;26:279–287.
   Web of Science ®Google Scholar
• Saulnier L, Thibault JF. Ferulic acid and diferulic acids as components of sugar-beet pectins and maize bran heteroxylans. J Sci Food Agric. 1999;79:396–402.
   Web of Science ®Google Scholar
• Bunzel M, Ralph J, Brüning P, et al. Structural identification of dehydrotriferulic and dehydrotetraferulic acids isolated from insoluble maize bran fiber. J Agric Food Chem. 2006;54:6409–6418.
   PubMed Web of Science ®Google Scholar
• Hespell RB, O’bryan PJ, Moniruzzaman M, et al. Hydrolysis by commercial enzyme mixtures of AFEX-treated corn fiber and isolated xylans. Appl Biochem Biotechnol. 1997;62:87–97.
   Web of Science ®Google Scholar
• Rose DJ, Inglett GE. A method for the determination of soluble arabinoxylan released from insoluble substrates by xylanases. Food Anal Methods. 2011;4:66–72.
   Web of Science ®Google Scholar
• Labourel A, Crouch LI, JLA B, et al. The mechanism by which arabinoxylanases can recognize highly decorated xylans. J Biol Chem. 2016;291:22149–22159.
   PubMed Web of Science ®Google Scholar
• Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Baslé A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN. Glycan complexity dictates microbial resource allocation in the large intestine. Nat Commun. 2015;6:7481.
   Google Scholar
• Biely P, Singh S, Puchart V. Towards enzymatic breakdown of complex plant xylan structures: state of the art. Biotechnol Adv. 2016;34:1260–1274.
   PubMed Web of Science ®Google Scholar
• Agger J, Viksø-Nielsen A, Meyer AS. Enzymatic xylose release from pretreated corn bran arabinoxylan: differential effects of deacetylation and deferuloylation on insoluble and soluble substrate fractions. J Agric Food Chem. 2010;58:6141–6148.
   PubMed Web of Science ®Google Scholar
• Pedersen MB, Dalsgaard S, Arent S, et al. Xylanase and protease increase solubilization of non-starch polysaccharides and nutrient release of corn- and wheat distillers dried grains with solubles. Biochem Eng J. 2015;98:99–106.
   Web of Science ®Google Scholar
• Usui K, Suzuki T, Akisaka T, et al. A cytoplasmic xylanase (XynX) of Aeromonas caviae ME-1 is released from the cytoplasm to the periplasm by osmotic downshock. J Biosci Bioeng. 2003;95:488–495.
   PubMed Web of Science ®Google Scholar
• Mangan D, Cornaggia C, Liadova A, et al. Novel substrates for the automated and manual assay of endo-1,4-β-xylanase. Carbohydr Res. 2017;445:14–22.
   PubMed Web of Science ®Google Scholar
• Barrow GI, Feltham RKA. Cowan and Steel’s manual for the identification of medical bacteria. 3rd ed. Cambridge: Cambridge University Press; 1993.
   Google Scholar
• Chun J, Lee J-H, Jung Y, et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol. 2007;57:2259–2261.
   PubMed Web of Science ®Google Scholar
• Zerbino DR, Velvet: BE. Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–829.
   PubMed Web of Science ®Google Scholar
• Nishi T, Ikemura T, Kanaya S. GeneLook: a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences. Gene. 2005;346:115–125.
   PubMed Web of Science ®Google Scholar
• Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970;227:680–685.
   PubMed Web of Science ®Google Scholar
• Mitchell A, Chang HY, Daugherty L, et al. The Interpro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015;43:D213–D221.
   PubMed Web of Science ®Google Scholar
• Yin Y, Mao X, Yang J, et al. A web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40:445–451.
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797.
   PubMed Web of Science ®Google Scholar
• Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 2001;18:691–699.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–1874.
   PubMed Web of Science ®Google Scholar
• Paice MG, Bourbonnais R, Desrochers M, et al. A xylanase gene from Bacillus subtilis: nucleotide sequence and comparison with B. gene. Arch Microbiol. 1986;144:201–206.
   Web of Science ®Google Scholar
• Correia MAS, Mazumder K, JLA B, et al. Structure and function of an arabinoxylan-specific xylanase. J Biol Chem. 2011;286:22510–22520.
   PubMed Web of Science ®Google Scholar
• Lowry OH, Rosebrough NJ, Farr AL, et al. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951;193:265–275.
   PubMed Web of Science ®Google Scholar
• Miller GL. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem. 1959;31:426–428.
   Web of Science ®Google Scholar
• Blumenkrantz N, Asboe-Hansen G. New method for quantitative determination of uronic acids. Anal Biochem. 1973;54:484–489.
   PubMed Web of Science ®Google Scholar
• Huq MA, Kim YJ, Hoang VA, et al. Paenibacillus ginsengiterrae sp. nov., a ginsenoside-hydrolyzing bacteria isolated from soil of ginseng field. Arch Microbiol. 2015;197:389–396.
   PubMed Web of Science ®Google Scholar
• Rivas R, Garciá-Fraile P, Mateos PF, et al. Paenibacillus cellulosilyticus sp. nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera. Int J Syst Evol Microbiol. 2006;56:2777–2781.
   PubMed Web of Science ®Google Scholar
• Shida O, Takagi H, Kadowaki K, et al. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol. 1997;47:289–298.
   PubMedGoogle Scholar
• Aspeborg H, Coutinho PM, Wang Y, et al. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol. 2012;12:186.
   PubMed Web of Science ®Google Scholar
• Boraston AB, Tomme P, Amandoron EA, et al. A novel mechanism of xylan binding by a lectin-like module from Streptomyces lividans xylanase 10A. Biochem J. 2000;350:933–941.
   PubMed Web of Science ®Google Scholar
• Santos CR, Hoffmam ZB, de Matos Martins VP, et al. Molecular mechanisms associated with xylan degradation by Xanthomonas plant pathogens. J Biol Chem. 2014;289:32186–32200.
   PubMed Web of Science ®Google Scholar
• Ma Y, Xue Y, Dou Y, et al. Characterization and gene cloning of a novel β-mannanase from alkaliphilic Bacillus sp. Extremophiles. 2004;8:447–454.
   PubMed Web of Science ®Google Scholar
• Takeda N, Hirasawa K, Uchimura K, et al. Alkaline Mannanase from a Novel Species of Alkaliphilic Bacillus. J Appl Glycosci. 2004;51:229–236.
   Google Scholar
• Li R, Kibblewhite R, Orts WJ, et al. Molecular cloning and characterization of multidomain xylanase from manure library. World J Microbiol Biotechnol. 2009;25:2071–2078.
   Web of Science ®Google Scholar
• Valenzuela SV, Diaz P, Javier Pastor FI. Modular glucuronoxylan-specific xylanase with a family CBM35 carbohydrate-binding module. Appl Environ Microbiol. 2012;78:3923–3931.
   PubMed Web of Science ®Google Scholar
• Sainz-Polo MA, Valenzuela SV, González B, et al. Structural analysis of glucuronoxylan-specific Xyn30D and its attached CBM35 domain gives insights into the role of modularity in specificity. J Biol Chem. 2014;289:31088–31101.
   PubMed Web of Science ®Google Scholar
• Vandermarliere E, Bourgois TM, Rombouts S, et al. Crystallographic analysis shows substrate binding at the −3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-β-xylanases. Biochem J. 2008;410:71–79.
   PubMed Web of Science ®Google Scholar
• Dodd D, Moon YH, Swaminathan K, et al. Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. J Biol Chem. 2010;285:30261–30273.
   PubMed Web of Science ®Google Scholar
• Ä U, Vršanská M, KBR MK, et al. Structural basis for substrate recognition by Erwinia chrysanthemi GH30 glucuronoxylanase. Febs J. 2011;278:2105–2116.
   PubMed Web of Science ®Google Scholar
• Pollet A, Delcour JA, Courtin CM. Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families. Crit Rev Biotechnol. 2010;30:176–191.
   PubMed Web of Science ®Google Scholar
• Khadem A, Lourenço M, Delezie E, et al. Does release of encapsulated nutrients have an important role in the efficacy of xylanase in broilers? Poult. Sci. 2016;95:1066–1076.
   Web of Science ®Google Scholar