GENETIC STUDIES OF PECTINOLYTIC ENZYMES OF BASIDIOMYCETES

Authors

  • P. ZUBYK National Technical University of Ukraine «Igor Sikorsky Kyiv Polytechnic Institute» Author
  • І. KLECHAK National Technical University of Ukraine «Igor Sikorsky Kyiv Polytechnic Institute», Author
  • L. TITOVA National Technical University of Ukraine «Igor Sikorsky Kyiv Polytechnic Institute», Author
  • O.I. YALOVENKO National Technical University of Ukraine «Igor Sikorsky Kyiv Polytechnic Institute» Author

DOI:

https://doi.org/10.31861/biosystems2025.01.059

Keywords:

pectinolytic enzymes, basidiomycetes, sequencing, CAZy

Abstract

The article presents an overview of current ideas about the genetic organisation and functional characteristics of pectinolytic enzyme systems in basidiomycetes. The main families of enzymes involved in the degradation of pectin compounds are analysed, in particular glycosyl hydrolases (GH), polysaccharide lyases (PL) and carbohydrate esterases (CE), as well as the corresponding genes found in representatives of the genera Agaricus, Armillaria, Flammulina, Laccaria, Lentinula, Pleurotus, Schizophyllum and Trametes. A comparative characterisation of the genomes of these fungi is provided in terms of the quantitative indicators of pectinase genes, their structural affiliation and potential functional activity. Methodological approaches to studying pectinolytic potential are considered, in particular sequencing, transcriptomics, biochemical methods and comparative genomics tools. Prospects for further research in the context of the biotechnological application of enzymes of this group are outlined.

References

1. Baldrian, P. (2008). Chapter 2 Enzymes of saprotrophic basidiomycetes (pp. 19–41). https://doi.org/10.1016/S0275-0287(08)80004-5

2. Benoit, I., Coutinho, P. M., Schols, H. A., Gerlach, J. P., Henrissat, B. & de Vries, R. P. (2012). Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin. BMC Genomics, 13(1), 321. https://doi.org/10.1186/1471-2164-13-321

3. Berger, R. G. & Ersoy, F. (2022). Improved Foods Using Enzymes from Basidiomycetes. Processes, 10(4), 726. https://doi.org/10.3390/pr10040726

4. Bonnin, E. & Pelloux, J. (2020). Pectin Degrading Enzymes. In Pectin: Technological and Physiological Properties (pp. 37–60). Springer International Publishing. https://doi.org/10.1007/978-3-030-53421-9_3

5. Danalache, F., Mata, P., Alves, V. D. & Moldão-Martins, M. (2018). Enzyme-Assisted Extraction of Fruit Juices. In Fruit Juices (pp. 183–200). Elsevier. https://doi.org/10.1016/B978-0-12-802230-6.00010-2

6. de Souza, T. S. P. & Kawaguti, H. Y. (2021). Cellulases, Hemicellulases, and Pectinases: Applications in the Food and Beverage Industry. Food and Bioprocess Technology, 14(8), 1446–1477. https://doi.org/10.1007/s11947-021-02678-z

7. Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R. A., Henrissat, B., Martínez, A. T., Otillar, R., Spatafora, J. W., Yadav, J. S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P. M., de Vries, R. P., Ferreira, P., Findley, K., … Hibbett, D. S. (2012). The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes. Science, 336(6089), 1715–1719. https://doi.org/10.1126/science.1221748

8. Gacura, M. D., Sprockett, D. D., Heidenreich, B. & Blackwood, C. B. (2016). Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi. Journal of Microbiological Methods, 123, 108–113. https://doi.org/10.1016/j.mimet.2016.02.013

9. Haile, S. & Ayele, A. (2022). Pectinase from Microorganisms and Its Industrial Applications. The Scientific World Journal, 2022, 1–15. https://doi.org/10.1155/2022/1881305

10. Kaczmarska, A., Pieczywek, P. M., Cybulska, J. & Zdunek, A. (2022). Structure and functionality of Rhamnogalacturonan I in the cell wall and in solution: A review. Carbohydrate Polymers, 278, 118909. https://doi.org/10.1016/j.carbpol.2021.118909

11. KC, S., Upadhyaya, J., Joshi, D. R., Lekhak, B., Kumar Chaudhary, D., Raj Pant, B., Raj Bajgai, T., Dhital, R., Khanal, S., Koirala, N. & Raghavan, V. (2020). Production, Characterization, and Industrial Application of Pectinase Enzyme Isolated from Fungal Strains. Fermentation, 6(2), 59. https://doi.org/10.3390/fermentation6020059

12. Kües, U. (2000). Life History and Developmental Processes in the Basidiomycete Coprinus cinereus. Microbiology and Molecular Biology Reviews, 64(2), 316–353. https://doi.org/10.1128/MMBR.64.2.316-353.2000

13. Lara-Espinoza, C., Carvajal-Millán, E., Balandrán-Quintana, R., López-Franco, Y. & Rascón-Chu, A. (2018). Pectin and Pectin-Based Composite Materials: Beyond Food Texture. Molecules, 23(4), 942. https://doi.org/10.3390/molecules23040942

14. Martin, F., Aerts, A., Ahrén, D., Brun, A., Danchin, E. G. J., Duchaussoy, F., Gibon, J., Kohler, A., Lindquist, E., Pereda, V., Salamov, A., Shapiro, H. J., Wuyts, J., Blaudez, D., Buée, M., Brokstein, P., Canbäck, B., Cohen, D., Courty, P. E., … Grigoriev, I. V. (2008). The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature, 452(7183), 88–92. https://doi.org/10.1038/nature06556

15. Moen, V. P., Drageset, J., Eide, G. E. & Gjesdal, S. (2018). Dimensions and predictors of disability—A baseline study of patients entering somatic rehabilitation in secondary care. PLOS ONE, 13(3), e0193761. https://doi.org/10.1371/journal.pone.0193761

16. Morin, E., Kohler, A., Baker, A. R., Foulongne-Oriol, M., Lombard, V., Nagye, L. G., Ohm, R. A., Patyshakuliyeva, A., Brun, A., Aerts, A. L., Bailey, A. M., Billette, C., Coutinho, P. M., Deakin, G., Doddapaneni, H., Floudas, D., Grimwood, J., Hildén, K., Kües, U., … Martin, F. (2012). Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Sciences, 109(43), 17501–17506. https://doi.org/10.1073/pnas.1206847109

17. Ohm, R. A., de Jong, J. F., Lugones, L. G., Aerts, A., Kothe, E., Stajich, J. E., de Vries, R. P., Record, E., Levasseur, A., Baker, S. E., Bartholomew, K. A., Coutinho, P. M., Erdmann, S., Fowler, T. J., Gathman, A. C., Lombard, V., Henrissat, B., Knabe, N., Kües, U., … Wösten, H. A. B. (2010). Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology, 28(9), 957–963. https://doi.org/10.1038/nbt.1643

18. Ozojiofor, U. O. & Rasheed, Z. A. (2023). Pectinases: structure, functions and biotechnological applications. Journal of Natural and Applied Sciences Pakistan, 5(2), 1448–1464.

19. Park, Y.-J., Jeong, Y.-U. & Kong, W.-S. (2018). Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica. International Journal of Molecular Sciences, 19(8), 2379. https://doi.org/10.3390/ijms19082379

20. Park, Y.-J., Lee, C.-S. & Kong, W.-S. (2019). Genomic Insights into the Fungal Lignocellulolytic Machinery of Flammulina rossica. Microorganisms, 7(10), 421. https://doi.org/10.3390/microorganisms7100421

21. Patidar, M. K., Nighojkar, S., Kumar, A. & Nighojkar, A. (2018). Pectinolytic enzymes-solid state fermentation, assay methods and applications in fruit juice industries: a review. 3 Biotech, 8(4), 199. https://doi.org/10.1007/s13205-018-1220-4

22. Peng, M. & de Vries, R. P. (2021). Machine learning prediction of novel pectinolytic enzymes in Aspergillus niger through integrating heterogeneous (post-) genomics data. Microbial Genomics, 7(12). https://doi.org/10.1099/mgen.0.000674

23. Reina, R., Kellner, H., Hess, J., Jehmlich, N., García-Romera, I., Aranda, E., Hofrichter, M. & Liers, C. (2019). Genome and secretome of Chondrostereum purpureum correspond to saprotrophic and phytopathogenic life styles. PLOS ONE, 14(3), e0212769. https://doi.org/10.1371/journal.pone.0212769

24. Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E. A., Sun, H., LaButti, K. M., Schmutz, J., Jabbour, D., Luo, H., Baker, S. E., Pisabarro, A. G., Walton, J. D., … Grigoriev, I. V. (2014). Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proceedings of the National Academy of Sciences, 111(27), 9923–9928. https://doi.org/10.1073/pnas.1400592111

25. Roman-Benn, A., Contador, C. A., Li, M.-W., Lam, H.-M., Ah-Hen, K., Ulloa, P. E. & Ravanal, M. C. (2023). Pectin: An overview of sources, extraction and applications in food products, biomedical, pharmaceutical and environmental issues. Food Chemistry Advances, 2, 100192. https://doi.org/10.1016/j.focha.2023.100192

26. Ruiz-Dueñas, F. J., Barrasa, J. M., Sánchez-García, M., Camarero, S., Miyauchi, S., Serrano, A., Linde, D., Babiker, R., Drula, E., Ayuso-Fernández, I., Pacheco, R., Padilla, G., Ferreira, P., Barriuso, J., Kellner, H., Castanera, R., Alfaro, M., Ramírez, L., Pisabarro, A. G., … Martínez, A. T. (2021). Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Molecular Biology and Evolution, 38(4), 1428–1446. https://doi.org/10.1093/molbev/msaa301

27. Rytioja, J., Hildén, K., Yuzon, J., Hatakka, A., de Vries, R. P. & Mäkelä, M. R. (2014). Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes. Microbiology and Molecular Biology Reviews, 78(4), 614–649. https://doi.org/10.1128/MMBR.00035-14

28. Safran, J., Tabi, W., Ung, V., Lemaire, A., Habrylo, O., Bouckaert, J., Rouffle, M., Voxeur, A., Pongrac, P., Bassard, S., Molinié, R., Fontaine, J.-X., Pilard, S., Pau-Roblot, C., Bonnin, E., Larsen, D. S., Morel-Rouhier, M., Girardet, J.-M., Lefebvre, V., … Pelloux, J. (2023). Plant polygalacturonase structures specify enzyme dynamics and processivities to fine-tune cell wall pectins. The Plant Cell, 35(8), 3073–3091. https://doi.org/10.1093/plcell/koad134

29. Saharan, R. & Sharma, K. P. (2019). Production, purification and characterization of pectin lyase from Bacillus subtilis isolated from moong beans leaves (Vigna radiata). Biocatalysis and Agricultural Biotechnology, 21, 101306. https://doi.org/10.1016/j.bcab.2019.101306

30. Sahu, N., Indic, B., Wong-Bajracharya, J., Merényi, Z., Ke, H.-M., Ahrendt, S., Monk, T.-L., Kocsubé, S., Drula, E., Lipzen, A., Bálint, B., Henrissat, B., Andreopoulos, B., Martin, F. M., Harder, C. B., Rigling, D., Ford, K. L., Foster, G. D., Pangilinan, J., … Nagy, L. G. (2022). Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen. https://doi.org/10.1101/2022.11.10.515791

31. Sahu, N., Merényi, Z., Bálint, B., Kiss, B., Sipos, G., Owens, R. A. & Nagy, L. G. (2021). Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species. Microorganisms, 9(1), 149. https://doi.org/10.3390/microorganisms9010149

32. Samreen, P., Mangipudi, M., Grover, S., Rajan, H. & G, S. (2019). Production of Pectinases and Pectinolytic Enzymes: Microorganisms, Cultural Conditions and Substrates. Advances in Biotechnology & Microbiology, 14(2). https://doi.org/10.19080/AIBM.2019.14.555884

33. Shankar Naik, B., Abrar, S. & Krishnappa, M. (2019). Industrially Important Enzymes from Fungal Endophytes (pp. 263–280). https://doi.org/10.1007/978-3-030-10480-1_7

34. Shet, A. R., Desai, S. . & Achappa, S. (2018). Pectinolytic enzymes: classification, production, purification and applications. Life Science Informatics Publications, 4(3), 337. https://doi.org/http://doi.org/10.26479/2018.0403.30

35. Sipos, G., Prasanna, A. N., Walter, M. C., O’Connor, E., Bálint, B., Krizsán, K., Kiss, B., Hess, J., Varga, T., Slot, J., Riley, R., Bóka, B., Rigling, D., Barry, K., Lee, J., Mihaltcheva, S., LaButti, K., Lipzen, A., Waldron, R., … Nagy, L. G. (2017). Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nature Ecology & Evolution, 1(12), 1931–1941. https://doi.org/10.1038/s41559-017-0347-8

36. Voragen, A. G. J., Coenen, G.-J., Verhoef, R. P. & Schols, H. A. (2009). Pectin, a versatile polysaccharide present in plant cell walls. Structural Chemistry, 20(2), 263–275. https://doi.org/10.1007/s11224-009-9442-z

37. Wefers, D., Dong, J., Abdel-Hamid, A. M., Paul, H. M., Pereira, G. V., Han, Y., Dodd, D., Baskaran, R., Mayer, B., Mackie, R. I. & Cann, I. (2017). Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus. Applied and Environmental Microbiology, 83(18). https://doi.org/10.1128/AEM.00794-17

38. Yang, Z. L. (2011). Molecular techniques revolutionize knowledge of basidiomycete evolution. Fungal Diversity, 50(1), 47–58. https://doi.org/10.1007/s13225-011-0121-1

39. Yu, H.-W., Im, J.-H., Kong, W.-S. & Park, Y.-J. (2020). Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome. Microorganisms, 9(1), 20. https://doi.org/10.3390/microorganisms9010020

40. Yüksel, E., Kort, R. & Voragen, A. G. J. (2024). Structure and degradation dynamics of dietary pectin. Critical Reviews in Food Science and Nutrition, 1–20. https://doi.org/10.1080/10408398.2024.2437573

41. Zhang, Y., Wang, J., Yajun, C., Zhou, M., Wang, W., Geng, M., Xu, D. & Xu, Z. (2020). Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes. Mycobiology, 48(2), 104–114. https://doi.org/10.1080/12298093.2020.1725361

42. Zheng, L., Guo, Z., Cao, S. & Zhu, B. (2021). Elucidating the degradation pattern of a new cold-tolerant pectate lyase used for efficient preparation of pectin oligosaccharides. Bioresources and Bioprocessing, 8(1), 121. https://doi.org/10.1186/s40643-021-00475-2

43. Zheng, L., Xu, Y., Li, Q. & Zhu, B. (2021). Pectinolytic lyases: a comprehensive review of sources, category, property, structure, and catalytic mechanism of pectate lyases and pectin lyases. Bioresources and Bioprocessing, 8(1), 79. https://doi.org/10.1186/s40643-021-00432-z

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2025-07-27

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БІОХІМІЯ, БІОТЕХНОЛОГІЯ, МОЛЕКУЛЯРНА ГЕНЕТИКА