Abstract
Feruloyl esterases (FAEs) are a key group of enzymes that hydrolyze ferulic acids ester-linked to plant polysaccharides. The cow’s rumen is a highly evolved ecosystem of complex microbial microflora capable of converting fibrous substances to energy. From direct cloning of the rumen microbial metagenome, we identified seven active phagemids conferring feruloyl esterase activity. The genomic inserts ranged from 1633 to 4143 bp, and the ORFs from 681 to 1359 bp. BLAST search reveals sequence homology to feruloyl esterases and esterases/lipases identified in anaerobes. The seven genes were expressed in Escherichia coli, and the proteins were purified to homogeneity. The FAEs were found to cover types B, C, and D in the feruloyl esterase classification system using model hydroxycinnamic acid esters. The release of ferulic acid (FA) catalyzed by these enzymes was established using natural substrates corn fiber (CF) and wheat insoluble arabinoxylan (WIA). Three of the enzymes were demonstrated to cleave diferulates and hence the capability to break down Araf-FA-FA-Araf cross-links. The wide variation in the sequence, activity, and substrate specificity observed in the FAEs discovered in this study is a confirming evidence that combined actions of a full range of FAE enzymes contribute to the high-efficiency fiber digestion in the rumen microbial ecosystem.
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References
Andreasen MF, Kroon PA, Williamson G, Garcia-Conesa M-T (2001) Intestinal release and uptake of phenolic antioxidant diferulic acids. Free Radic Biol Med 31:304–314. https://doi.org/10.1016/s0891-5849(01)00585-8
Bartolome B, Faulds CB, Kroon PA, Waldron K, Gilbert HJ, Hazlewood G, Williamson G (1997) An Aspergillus niger esterase (ferulic acid esterase III) and a recombinant Pseudomonas fluorescens subsp. Cellulose esterase (XylD) release a 5-5' ferulic dehydrodimer (diferulic acid) from barley and wheat cell walls. Appl Environ Microbiol 63:208–212
Beloqui A, Pita M, Polaina J, Martinez-Arias A, Golyshina OV, Zumarraga M, Yakimov MM, Garcia-Arellano H, Alcalde M, Fernandez VM, Elborough K, Andreu JM, Ballesteros A, Plou FJ, Timmis KN, Ferrer M, Golyshin PN (2006) Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationships. J Biol Chem 281:22933–22942. https://doi.org/10.1074/jbc.M600577200
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing-dye binding. Anal Biochem 72:248–254
Brenner S (1988) The molecular evolution of genes and proteins: a tale of two serines. Nature 334:528–530
Biely P, Singh S, Puchart V (2016) Toward enzymatic breakdown of complex plant xylan structures: State of the art. Biotechnol Adv 34:1260-1274
Carmedy WR (1961) An easily prepared wide range buffer series. J Chem Educ 38:559–560
Crepin VF, Faulds CB, Connerton IF (2003) A non-modular type B feruloyl esterase from Neurospora crassa exhibits concentration-dependent substrate inhibitor. Biochem J 370:417-427
Crepin VF, Faulds CB, Connerton IF (2004) Functional classification of the microbial feruloyl esterases. Appl Microbiol Biotechnol 63:647–652. https://doi.org/10.1007/s00253-003-1476-3
De Vries RP, Kester HCM, Poulsen CH, Benen JAE, Visser J (2000) Synergy between enzymes from Aspergillus involved in the degradation of plant cell wall polysaccharides. Carbohydr Res 327:401–410
Dilokpimol A, Makela MR, Aguilar-Ponrwa M, Benoit-Gelber I, Hidden KS, deVries RP (2016) Diversity of fungal feruloyl esterases: updated phylogenetic classification, properties, and industrial applications. Biotechnol Biofuels. https://doi.org/10.1186/s13068-016-0651-6
Doner LW, Johnston DB, Singh V (2001) Analysis and properties of arbinoxylan from discrete corn wet-milling fiber fractions. J Agric Food Chem 49:1266–1269. https://doi.org/10.1021/jf001105o
Faulds CB (2016) What can feruloyl esterases do for us? Phytochem Rev 9:121–132. https://doi.org/10.1007/s11101-009-9156-2
Faulds CB, Molina R, Gonzalez R, Husband F, Juge N, Sanz-Aparicio J, Hermoso JA (2005) Probing the determinant of substrate specificity of a feruloyl esterase, AnFaeA from Aspergillus niger. FEBS J 272:4362-4371. https://doi.org/10.1111/j.1742-4658.2005.04849.x
Ferrer M, Golyshina CV, Chermikova TN, Khachane AN, Reyes-Duarte D, Santos VAPMD, Strompl C, Elborough K, Jarvisl G, Neef A, Yakimov MM, Timmis KN, Golyshin PN (2005) Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Eniviron Microbiol 7:1996–2010. https://doi.org/10.1111/j.1462-2920-2005.00920-x
Gupta Udatha DBRK, Kouskoumvekaki I, Olsson L, Panagiotou G (2011) The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases. Biotechnol Adv 29:94–110. https://doi.org/10.1016/j.biotechadv.2010.09.003
Heald S, Myers S, Walford T, Robbins K, Hill C (2013) Preparation of vanillin from microbial transformation media by extraction by means supercritical fluids or gases. US 8,563,392 B2
Hermoso JA, Sanz-Aparicio J, Molma R, Juge N, Gonzalez R, Faulds CB (2004) The crystal structure of feruloyl esterase A from Aspergillus niger suggests evolutive functional convergence in feruloyl esterase family. J Mol Biol 338:495–507. https://doi.org/10.1016/j-jmb.2004.03.003
Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463–467. https://doi.org/10.1126/science.1200387
Hunt CJ, Antonopoulou L, Tanksale A, Rova U, Christakopoulos P, Haritos VS (2017) Insights into substrate binding of ferulic acid esterases by arabinose and methyl hydroxycinnamate esters and molecular docking. Sci Rep 7:17315. https://doi.org/10.1038/s41598-017-17260-x
Lai KK, Stogios PJ, Vu C, Xu X, Cui H, Molloy S, Savchenko A, Yakunin A, Gonzalez CF (2011) An inserted α/β subdomain shapes the catalytic pocket of Lactobacillus johnsonii cinnamoyl esterase. PLoS One 6(8):e23269. https://doi.org/10.1371/journal.pone.0023269
LaVallie ER, DiBlasio EA, Kovacic S, Grant KL, Schendel PF, McCoy JM (1993) A thioredoxin gene fusion expression system that circumvent inclusion body formation in the E. coli cytoplasm. BioTechnology 11:187–193. https://doi.org/10.1038/nbt0293-187
Morgavi DP, Kelly WJ, Janssen PH, Attwood GT (2013) Rumen microbial genomics and its application to ruminant production. Animal 7(suppl. 1):184–201. https://doi.org/10.1017/s1751731112000419
Ribeiro GO, Gruninger RJ, Badhan A, McAllister TA (2016) Mining the rumen for fibrolytic feed enzymes. Anim Front 6:20–26. https://doi.org/10.2527/af.2016-0019
Schubot FD, Kataeva IA, Blum DL, Shah AK, Ljungdahl IG, Rose JP, Wang B-C (2001) Structural basis for the substrate specificity of the feruloyl esterase domain of the cellulosomal xylanase Z from Clostridium thermocellum. Biochemistry 40:12524–12532. https://doi.org/10.1021/bio11391c
Shang M, Chan VJ, Wong DWS, Liao H (2018) A novel method for rapid and sensitive metagenomic activity screening. MethodsX 5:669–675. https://doi.org/10.1016/j.mex.2018.06.011)
Sigoillot C, Camarero S, Vidal T, Record E, Asther M, Perez-Boada M, Martinez KJ, Sigoillot J-C, Asther M, Colom JF, Martinez AT (2005) Comparison of different fungal enzymes for bleaching high-quality paper pulps. J Biotechnol 115:333–343. https://doi.org/10.1016/j.jbiotec.2004.09.006
Suzuki K, Hori A, Kawamoto K, Thangudu RR, Ishida T, Igarashi K, Samejima M, Yamada C, Arakawa T, Wakagi T, Koseki T, Fushinobu S (2014) Crystal structure of a feruloyl esterase belonging to the tannase family: a disulfide bond near a catalytic triad. Proteins 82:2857–2867. https://doi.org/10.1002/prot.24649
Tabka MD, Herpoel-Gimberta I, Monod F, Asther M, Sigoillot JC (2006) Enzymatic saccharification of wheat straw for bioethanol production by a combined cellulase-xylanase and feruloyl esterase treatment. Enzym Microb Technol 39:897–902. https://doi.org/10.1016/j-enzymictec.2006.01.021
Uraji M, Tamura H, Mizohata E, Arima J, Wan K, Ogawa K, Inoue T, Natanaka T (2018) Loop of Streptomyces feruloyl esterase plays an important role in the enzyme's catalyzing the release of ferulic acid from Biomass. Appl Environ Microbiol 84:e02300–e02317. https://doi.org/10.1128/AEM.02300-17
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46(W1):W296–W303. https://doi.org/10.1093/nar/gky427
Wong DWS (2006) Feruloyl esterase-a key enzyme in biomass degradation. Appl Biochem Biotechnol 133:87–112. https://doi.org/10.1385/ABAB.133.2:87
Wong DWS, Chan VJ, Batt SB (2008) Cloning and characterization of a novel exo-α-1,5-L-arabinanase gene and the enzyme. Appl Microbiol Biotechnol 79:941–949. https://doi.org/10.1007/s00253-008-1504-4
Wong DWS, Chan VJ, McCormack AA, Batt SB (2010) A novel xyloglucan-specific endo-β-1,4-glucanase: biochemical properties and inhibition studies. Appl Microbiol Biotechnol 86:1463–1471. https://doi.org/10.1007/s00253-009-2364-2
Wong DWS, Chan VJ, Batt SB, Gauttam S, Liao H (2011) Engineering Saccharomyces cerevisiae to produce feruloyl esterase for the release of ferulic acid from switchgrass. J Ind Microbiol Biotechnol 38:1961–1967. https://doi.org/10.1077/s10295-011-0985-9
Wong DWS, Chan VJ, Liao H, Zidwick MJ (2013a) Cloning of a novel feruloyl esterase gene from rumen microbial metagenome and enzyme characterization in synergism with endoxylanases. J Ind Microbiol Biotechnol 40:287–295. https://doi.org/10.1007/s10295-013-1234-1
Wong DWS, Chan VJ, McCormack AA (2013b) Comparative characterization of a bifunctional endo-1,4-β-mannanase/1,3-1,4-β-glucanase and its individual domains. Protein Pept Lett 20:517–523
Wong DWS, Takeoka G, Chan VJ, Liao H, Murakami MT (2015) Cloning of a novel feruloyl esterase from rumen microbial metagenome for substantial yield of mono- and di-ferulic acids from natural substrates. Protein Pept Lett 22:681–688
Zhao S, Wang J, Bu D, Liu K, Zhu Y, Dong Z, Yu Z (2010) Novel glycoside hydrolases identified by screening a Chinese Hoistein dairy cow rumen-derived metagenome library. Appl Environ Microbiol 76:6701–6705. https://doi.org/10.1128/AEM.00361-10
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Wong, D.W.S., Chan, V.J. & Liao, H. Metagenomic discovery of feruloyl esterases from rumen microflora. Appl Microbiol Biotechnol 103, 8449–8457 (2019). https://doi.org/10.1007/s00253-019-10102-y
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DOI: https://doi.org/10.1007/s00253-019-10102-y