Fungal Termoasidofilik GH11 Ksilanazlarının İn Siliko Filojeni, Dizi ve Yapı Analizleri

Termoasidofilik ksilanaz enzimleri, çoğunlukla hayvan yemi katkı maddesi olarak tercih edilmektedir. Bu çalışmada, çeşitli mantar türlerine ait altı termoasidofilik GH11 ksilanazın (Gymnopus androsaceus ksilanazı = GaXyl, Penicilliopsis zonata ksilanazı = PzXyl, Aspergillus neoniger ksilanazı = AnXyl, Calocera viscosa ksilanazı = CvXyl, Acidomyces richmondensis ksilanazı = ArXyl, Oidiodendron maius ksilanazı = OmXyl) in siliko filojeni, dizi, yapı ve enzim-docking kompleks analizleri gerçekleştirilmiştir. Bunu yapmak için, UniProt/TrEMBL veri tabanındaki gözden geçirilmemiş protein girdilerine ait altı mantar termoasidofilik GH11 ksilanazının amino asit dizileri moleküler filojeni ve dizi açısından araştırıldı. Ayrıca, üç boyutlu tahmini enzim modelleri oluşturuldu ve daha sonra çeşitli biyoinformatik programları kullanılarak hesaplamalı olarak doğrulandı. Enzim ve substrat arasındaki etkileşimler, iki substratın (ksilotetraoz = X4 ve ksilopentaoz = X5) varlığında docking programı aracılığıyla analiz edildi. Moleküler filojeni analizine göre, bu enzimlerin üç kümesi oluştu: birinci grup PzXyl, AnXyl ve CvXyl'e sahipti ve ikinci grup GaXyl ve OmXyl'e sahipti ve üçüncü grup ArXyl'i içeriyordu. Çoklu dizi hizalama analizi, beş ksilanazın (ArXyl, OmXyl, CvXyl, PzXyl, AnXyl) daha uzun N-terminal bölgelerine sahip olduğunu gösterdi, bu da GaXyl'e göre daha yüksek termal stabiliteye sahip olduklarını işaret etmiştir. Homoloji modelleme, tahmin edilen tüm model yapılarının büyük ölçüde korunduğunu gösterdi. Docking analizi sonuçları, CvXyl, OmXyl ve AnXyl'in GaXyl, PzXyl ve ArXyl ksilanazlara kıyasla iki substrata daha yüksek bağlanma verimliliğine sahip olduğunu ve CvXyl-X4 docking kompleksinin -9.8 kCal/mol'lük bir bağlanma enerjisiyle en yüksek substrat afinitesine sahip olduğunu gösterdi. CvXyl, OmXyl ve AnXyl enzimleri, daha düşük bağlanma verimliliğine sahip diğer enzimlerden farklı olarak, yaygın olarak B8 β-kolunda iki substrat ile etkileşime giren arjinin içeriyordu. Sonuç olarak, bu üç termoasidofilik ksilanaz enziminin hayvan yemi katkı maddesi olarak daha iyi adaylar olabileceği sonucuna varılmıştır.

Anahtar Kelimeler:

Termoasidofilik ksilanaz, Moleküler yerleştirme, GH11 ksilanaz, Hayvan yem katkısı, UniProt/TrEMBL veritabanı

In Silico Phylogeny, Sequence and Structure Analyses of Fungal Thermoacidophilic GH11 Xylanases

Thermoacidophilic xylanase enzymes are mostly preferred for use as animal feed additives. In this study, we performed in silico phylogeny, sequence, structure, and enzyme-docked complex analyses of six thermoacidophilic GH11 xylanases belonging to various fungal species (Gymnopus androsaceus xylanase = GaXyl, Penicilliopsis zonata xylanase = PzXyl, Aspergillus neoniger xylanase = AnXyl, Calocera viscosa xylanase = CvXyl, Acidomyces richmondensis xylanase = ArXyl, Oidiodendron maius xylanase = OmXyl). To do this, amino acid sequences of six fungal thermoacidophilic GH11 xylanases, belonging to unreviewed protein entries in the UniProt/TrEMBL database, were investigated at molecular phylogeny and amino acid sequence levels. In addition, three-dimensional predicted enzyme models were built and then validated by using various bioinformatics programs computationally. The interactions between enzyme and the substrate were analyzed via docking program in the presence of two substrates (xylotetraose = X4 and xylopentaose = X5). According to molecular phylogeny analysis, three clusters of these enzymes occurred: the first group had PzXyl, AnXyl, and CvXyl, and the second group possessed GaXyl and OmXyl, and the third group included ArXyl. Multiple sequence alignment analysis demonstrated that the five xylanases (ArXyl, OmXyl, CvXyl, PzXyl, AnXyl) had longer N-terminal regions, indicating greater thermal stability, relative to the GaXyl. Homology modeling showed that all the predicted model structures were, to a great extent, conserved. Docking analysis results indicated that CvXyl, OmXyl, and AnXyl had higher binding efficiency to two substrates, compared to the GaXyl, PzXyl, and ArXyl xylanases, and CvXyl-X4 docked complex had the highest substrate affinity with a binding energy of -9.8 kCal/mol. CvXyl, OmXyl, and AnXyl enzymes commonly had arginine in B8 β-strand interacted with two substrates, different from the other enzymes having lower binding efficiency. As a result, it was concluded that the three thermoacidophilic xylanase enzymes might be better candidates as the animal feed additive.

Keywords:

Thermoacidophilic xylanase, Molecular docking, GH11 xylanase, Animal feed additive, UniProt/TrEMBL database,

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Alagawany, M., Elnesr, S.S., Farag, M.R. (2018). The role of exogenous enzymes in promoting growth and improving nutrient digestibility in poultry. Iranian Journal of Veterinary Research, 19(3):157-164.
Algan, M., Sürmeli, Y., Şanlı-Mohamed, G. (2021). A novel thermostable xylanase from Geobacillus vulcani GS90: Production, biochemical characterization, and its comparative application in fruit juice enrichment. Journal of Food Biochemistry, 45(5): e13716.
Bajpai, P. (1999). Application of enzymes in the pulp and paper industry. Biotechnology Progress, 15(2): 147–157.
Barbi, F., Kohler, A., Barry, K., Baskaran, P., Daum, C., Fauchery, L., …, Martin, F. (2020). Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers. Environmental Microbiology, 22(3):1089-1103.
Basu, M., Kumar, V., Shukla, P. (2018). Recombinant approaches for microbial xylanases: recent advances and perspectives. Current Protein & Peptide Science, 19: 87–99.
Başkavak, S., Özdüven, M.L., Polat, C., Koç, F. (2008). The effects of lactic acid bacteria+enzyme mixture silage inoculant on wheat silage. Journal of Tekirdag Agricultural Faculty, 5(3):291-296.
Beg, Q.K., Kapoor, M., Mahajan, L., Hoondal, G.S. (2001). Microbial xylanases and their industrial applications: A review. Applied Microbiology and Biotechnology, 56(3–4): 326–338.
Biely, P., Singh, S., Puchart, V. (2016). Towards enzymatic breakdown of complex plant xylan structures: state of the art. Biotechnology Advances, 34:1260–1274.
Boonyapakron, K., Jaruwat, A., Liwnaree, B., Nimchua, T., Champreda, V., Chitnumsub, P. (2017). Structure-based protein engineering for thermostable and alkaliphilic enhancement of endo-β-1,4-xylanase for applications in pulp bleaching. Journal of Biotechnology, 259:95–102.
Bowie, J.U., Lüthy, R., Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253(5016): 164–170.
Chadha, B.S., Kaur, B., Basotra, N., Tsang, A., Pandey, A. (2019). Thermostable xylanases from thermophilic fungi and bacteria: Current perspective. Bioresource Technology, 277: 195–203.
Chakdar, H., Kumar, M., Pandiyan, K., Singh, A., Nanjappan, K., …, Srivastava, A.K. (2016). Bacterial xylanases: biology to biotechnology. 3 Biotech, 6(2).
Cheng, Y.S., Chen, C.C., Huang, C.H., Ko, T.P., Luo, W., Huang, J.W., …, Guo, R.T. (2014). Structural analysis of a glycoside hydrolase family 11 xylanase from Neocallimastix patriciarum : Insights into the molecular basis of a thermophilic enzyme. Journal of Biological Chemistry, 289: 11020–11028.
Collins, T., Gerday, C., Feller, G. (2005). Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiology Reviews, 29(1):3–23.
de Vries, R.P., Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Uchima, C.A., …, Grigoriev, I.V. (2017). Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology, 18(1): 28.
Debeire-Gosselin, M., Loonis, M., Samain, E., Debeire, P. (1992). Purification and Properties of a 22 kDa Endoxylanase Excreted by a New Strain of Thermophilic Bacillus. In: Visser, J., Beldman, G., van Someren, M. A., Kusters-, Voragen A. G. J., (eds). Xylans and xylanases. Amsterdam, The Netherlands: Elsevier Science Publishers B.V., pp. 463–466.
Decelle, B., Tsang, A., Storms, R.K. (2004). Cloning, functional expression and characterization of three Phanerochaete chrysosporium endo-1,4-β-xylanases. Current Genetics, 46:166–175.
Deng, P., Li, D., Cao, Y., Lu, W., Wang, C. (2006). Cloning of a gene encoding an acidophilic endo-β-1,4-xylanase obtained from Aspergillus niger CGMCC1067 and constitutive expression in Pichia pastoris. Enzyme and Microbial Technology, 39(5):1096-1102.
Drula, E., Garron. M.-L., Dogan, S., Lombard, V., Henrissat, B., Terrapon, N. (2022). The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Research, 50(D1):D571–D577.
Fushinobu, S., Ito, K., Konno, M., Wakagi, T., Matsuzawa, H. (1998). Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Protein Engineering, 11:1121–1128.
Galanopoulou, A.P., Haimala, I., Georgiadou, D.N., Mamma, D., Hatzinikolaou, D.G. (2021). Characterization of the highly efficient acid-stable xylanase and β-xylosidase system from the fungus Byssochlamys spectabilis ATHUM 8891 (Paecilomyces variotii ATHUM 8891). Journal of Fungi, 7(6):430.
Gasteiger, E., Hoogland. C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. In: Walker, J. M. (eds) The Proteomics Protocols Handbook, Springer Protocols Handbooks, Humana Press.
Han, N., Miao, H., Ding, J., Li, J., Mu, Y., Zhou, J., Huang, Z. (2017). Improving the thermostability of a fungal GH11 xylanase via site-directed mutagenesis guided by sequence and structural analysis. Biotechnology for Biofuels, 10:133.
Hakulinen, N., Turunen, O., Jänis, J., Leisola, M., Rouvinen, J. (2003). Three-dimensional structures of thermophilic β-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. FEBS Journal, 270(7):1399–1412.
Harris, G.W., Jenkins, J.A., Connerton, I., Cummings, N., Lo, L.L., Scott, M., …, Pickersgill, R.W. (1994). Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites. Structure, 2(11):1107–1116.
Heinig, M., Frishman, D. (2004). STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Research, 32:W500.
Intasit, R., Cheirsilp, B., Suyotha, W., Boonsawang, P. (2022). Purification and characterization of a highly-stable fungal xylanase from Aspergillus tubingensis cultivated on palm wastes through combined solid-state and submerged fermentation. Preparative Biochemistry & Biotechnology, 52(3): 311-317.
Kataoka, M., Akita, F., Maeno, Y., Inoue, B., Inoue, H., Ishikawa, K. (2014). Crystal structure of Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) GH Family 11 xylanase. Applied Biochemistry and Biotechnology, 174:1599–1612.
Koçyiğit, R., Tüzemen, N. (2012). The effect of probiotic plus enzyme on the fattening performance and feed efficiency ratio of brown Swiss young bulls at two different ages. Journal of Tekirdag Agricultural Faculty, 9(1): 45-50.
Ku, T., Lu, P., Chan, C., Wang, T., Lai, S., Lyu, P., Hsiao, N. (2009). Predicting melting temperature directly from protein sequences. Computational Biology and Chemistry, 33(6):445–450.
Kumar, A., Gautam, A., Dutt, D., Yadav, M., Sehrawat, N., Kumar, P. (2017). Applications of Microbial Technology in Pulp and Paper Industry. ln: Kumar, A., Dutt, D., Yadav, M. (eds), Microbiology and Biotechnology for a Sustainable Environment, 1st edn, Nova Science Publishers, New York, pp 185-206.
Lao, N.T., Schoneveld, O., Mould, R.M., Hibberd, J.M., Gray, J.C., Kavanagh, T.A. (1999). An Arabidopsis gene encoding a chloroplast-targeted beta-amylase. The Plant Journa,l 20(5): 519–527.
Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R., Thornton, J.M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4):477–486.
Li, Z., Zhang, X., Li, C., Kovalevsky, A., Wan, O. (2020). Studying the role of a single mutation of a family 11 glycoside hydrolase using high-resolution x-ray crystallography. The Protein Journal, 39:671–680.
Liao, H., Xu, C., Tan, S., Wei, Z., Ling, N., Yu, G., …, Xu, Y. (2012). Production and characterization of acidophilic xylanolytic enzymes from Penicillium oxalicum GZ-2. Bioresource Technology, 123:117-124.
Madeira, F., Park, Y.M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., …, Lopez, R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research, 47(W1):W636–W641.
Mirdita, M., Von Den Driesch, L., Galiez, C., Martin, M.J., Soding, J., Steinegger, M. (2017). Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research, 45(D1):D170–D176.
Mosier, A.C., Miller, C.S., Frischkorn, K.R., Ohm, R.A., Li, Z., LaButti, K, …, Banfield, J.F. (2016). Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage. Frontiers in Microbiology, 7:238.
Motta, F.L., Andrade, C.C.P., Santana, M.H.A. (2013). A Review of Xylanase Production by the Fermentation of Xylan: classification, Characterization and Applications. ln Chandel, A.K., Da Silva, S.S. (eds) Sustainable Degradation of Lignocellulosic Biomass - Techniques, Applications and Commercialization, IntechOpen, London.
Nagy, L.G., Riley, R., Tritt, A., Adam, C., Daum, C., Floudas, D., …, Hibbett, D.S. (2016). Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities. Molecular Biology and Evolution, 33(4):959-970.
Nordberg Karlsson, E., Schmitz, E., Linares-Pastén, J.A., Adlercreutz, P. (2018). Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties. Applied Microbiology and Biotechnology, 102(21):9081–9088.
Paës, G., Berrin, J.G., Beaugrand, J. (2012). GH11 xylanases: structure/function/properties relationships and applications. Biotechnol Advances, 30(3):564–592.
Pai, C.-K., Wu, Z.-Y., Chen, M.-J., Zeng, Y.-F., Chen, J.-W., Duan, C.-H., …, Liu, J.-R. (2010). Molecular cloning and characterization of a bifunctional xylanolytic enzyme from Neocallimastix patriciarum. Applied Microbiology and Biotechnology, 85:1451–1462.
Park, J., Carey, J.B. (2019). Dietary enzyme supplementation in duck nutrition: a review. Journal of Applied Poultry Research, 28(3):587-597.
Ravindran, V. (2013). Feed enzymes: the science, practice, and metabolic realities. Journal of Applied Poultry Research, 22(3):628-636.
Sánchez, Ó.J., Cardona, C.A. (2008).Trends in biotechnological production of fuel ethanol from different feedstocks. Bioresource Technology, 99(13):5270–5295.
Smeets, N., Nuyens, F., Niewold, T., Van Campenhout, L. (2014). Temperature resistance of xylanase inhibitors and the presence of grain-associated xylanases affect the activity of exogenous xylanases added to pelleted wheat-based feeds. Cereal Chemistry, 91:572-577.
Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S.J., Söding, J. (2019). HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics, 20(1):1–15.
Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, R., Haas, J., Schwede, T. (2020). QMEANDisCo—distance constraints applied on model quality estimation. Bioinformatics, 36(8):2647–2647.
Studer, G., Tauriello, G., Bienert, S., Biasini, M., Johner, N., Schwede, T. (2021). ProMod3-A versatile homology modelling toolbox. PLoS Computational Biology, 17(1).
Subramaniyan, S., Prema, P. (2002). Biotechnology of microbial xylanases: enzymology, molecular biology, and application. Critical Reviews in Biotechnology, 22(1):33–64.
Sürmeli, Y. (2022). Comparative investigation of bacterial thermoalkaliphilic GH11 xylanases at molecular phylogeny, sequence and structure level. Biologia, 77:3241–3253.
Tamura, K., Stecher, G., Kumar, S. (2021). MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7):3022–3027.
Törrönen, A., Harkki, A., Rouvinen, J. (1994). Three-dimensional structure of endo-1,4-beta-xylanase II from Trichoderma reesei: two conformational states in the active site. The EMBO Journal, 13(11):2493.
Törrönen, A., Rouvinen, J. (1995). Structural comparison of two major endo-1,4-xylanases from Trichoderma reesei. Biochemistry, 34(3):847-856.
Trott, O., Olson, A.J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31(2):455.
The UniProt Consortium. (2021). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1):D480–D489.
Turunen, O., Etuaho, K., Fenel, F., Vehmaanperä, J., Wu, X., Rouvinen, J., Leisola, L. (2001). A combination of weakly stabilizing mutations with a disul fide bridge in the α-helix region of Trichoderma reesei endo-1,4 -β -xylanase II increases the thermal stability through synergism. Journal of Biotechnology, 88:37–46.
Wakarchuk, W.W., Robert, L., Campbell, R.L., Sung, W.L., Davoodi, J., Yaguchi, M. (1994). Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase. Protein Science, 3: 467–475.
Wang, S., Li, W., Liu, S., Xu, J. (2016). RaptorX-Property: a web server for protein structure property prediction. Nucleic Acids Research, 44(W1):W430-W435.
Wang, X., Ma, R., Xie, X., Liu, W., Tu, T., Zheng, F., …, Luo, H. (2017). Thermostability improvement of a Talaromyces leycettanus xylanase by rational protein engineering. Scientific Reports, 7(1):1–9.
Wiederstein, M., Sippl, M.J. (2007). ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(suppl_2):W407–W410.
Wood, T.M., McCrae, S.I., Bhat, K.M. (1989). The mechanism of fungal cellulase action. Synergism between enzyme components of Penicillium pinophilum cellulase in solubilizing hydrogen bound-ordered cellulose. Biochemical Journal, 260(1):37–43.
Xia, T., Wang, Q. (2009). Directed evolution of Streptomyces lividans xylanase B toward enhanced thermal and alkaline pH stability. World Journal of Microbiology and Biotechnology, 25(1):93–100.
Xiong, H., Fenel, F., Leisola, M., Turunen, O. (2004). Engineering the thermostability of Trichoderma reesei endo-1,4- β-xylanase II by combination of disulphide bridges. Extremophiles, 8:393–400.
Yi, Y., Xu, S., Kovalevsky, A., Zhang, X., Liu, D., Wan, Q. (2021). Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome. Applied Microbiology and Biotechnology, 105:7757–7767.