Evaluating the Diversity of Chit18-5 Gene Region across Trichoderma Species for Effective Biocontrol Strategies

Document Type : Original Article

Authors

1 Department of Plant Protection, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.

2 Department of Plant Protection, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

10.22043/MI.2024.363631.1268

Abstract

Trichoderma species are widely used as biological agents to control plant diseases. Chitinases are crucial in mycoparasitism and defense against other fungi or arthropods. In this study, we evaluated 41 amino acid sequences related to the Chit18-5 gene from four sections and 15 Trichoderma species. The conserved domains, motifs, and phylogenetic tree were analyzed using the InterProScan database, COBALT tool, MEME V5.5.1 software, ClustalW algorithm, and MEGA11 software. The results showed that the gene region under investigation can effectively distinguish different Trichoderma species and is an effective tool for optimizing biocontrol strategies. This study highlights the potential of exploring genetic diversity as a means of identifying new solutions for managing pests and diseases in agriculture. The putative motifs of chitinase proteins identified in this study may participate in Trichoderma antagonistic activities

Keywords


Bailey, T.L., Johnson, J., Grant, C.E. and Noble, W.S. 2015. The MEME suite. Nucleic Acids Research 43: 39­-49.
Bolar, J.P., Norelli, J.L., Wong, K.W., Hayes, C.K., Harman, G.E. and Aldwinckle, H.S. 2000. Expression of endochitinase from Trichoderma harzianum in transgenic apples increases resistance to apple scab and reduces vigor. Phytopathology 90: 72-77.
Bononi, L., Chiaramonte, J.B., Pansa, C.C., Moitinho, M.A. and Melo, I.S. 2020. Phosphorus-solubilizing Trichoderma spp. from Amazon soils improves soybean plant growth. Scientific Reports 10: 28-58.
Carsolio, C., Benhamou, N., Haran, S., Cortes, C., Gutierrez, A., Chet, I. and Herrera-Estrella, A. 1999. Role of the Trichoderma harzianum endochitinase gene, ech42, in mycoparasitism. Applied and Environmental Microbiology 65: 929-935.
Cortes, C., Gutierrez, A., Olmedo, V., Inbar, J., Chet, I. and Herrera-Estrella, A. 1998. The expression of genes involved in parasitism by Trichoderma harzianum is triggered by a diffusible factor. Molecular and General Genetics MGG 260: 218-225.
Coudert, E., Gehant, S., de Castro, E., Pozzato, M., Baratin, D., Neto, T., Sigrist, C.J., Redaschi, N. and Bridge, A. 2023. Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinformatics, 39: 1-5.
De La Cruz, J., Hidalgo‐Gallego, A., Lora, J.M., Benitez, T., Pintor‐Toro, J.A. and Llobell, A. 1992. Isolation and characterization of three chitinases from Trichoderma harzianum. European Journal of Biochemistry 206: 859-867.
Druzhinina, I.S., Seidl-Seiboth, V., Herrera-Estrella, A., Horwitz, B.A., Kenerley, C.M., Monte, E., Mukherjee, P.K., Zeilinger, S., Grigoriev, I.V. and Kubicek, C.P. 2011. Trichoderma: the genomics of opportunistic success. Nature Reviews Microbiology 9: 749-759.
Emani, C., Garcia, J.M., Lopata‐Finch, E., Pozo, M.J., Uribe, P., Kim, D.J., Sunilkumar, G., Cook, D.R., Kenerley, C.M. and Rathore, K.S. 2003. Enhanced fungal resistance in transgenic cotton expressing an endochitinase gene from Trichoderma virens. Plant Biotechnology Journal, 1: 321-336.
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap evolution, 39: 783-791.
Fontaine, T., Hartland, R.P., Beauvais, A., Diaquin, M. and Latge, J.P. 1997. Purification and Characterization of an Endo‐1, 3‐β‐Glucanase from Aspergillus fumigatus. European Journal of Biochemistry 243: 315-321.
Garcia, I., Lora, J.M., de la Cruz, J., Benitez, T., Llobell, A. and Pintor-Toro, J.A., 1994. Cloning and characterization of a chitinase (CHIT42) cDNA from the mycoparasitic fungus Trichoderma harzianum. Current genetics 27: 83-89.
Garcia-Rubio, R., de Oliveira, H.C., Rivera, J. and Trevijano-Contador, N., 2020. The fungal cell wall: Candida, Cryptococcus, and Aspergillus species. Frontiers in microbiology 10: 2993.
Gentile, A., Deng, Z., La Malfa, S., Distefano, G., Domina, F., Vitale, A., Polizzi, G., Lorito, M. and Tribulato, E. 2007. Enhanced resistance to Phoma tracheiphila and Botrytis cinerea in transgenic lemon plants expressing a Trichoderma harzianum chitinase gene. Plant Breeding 126: 146-151.
Gow, N.A., Latge, J.P. and Munro, C.A. 2017. The fungal cell wall: structure, biosynthesis, and function. Microbiology Spectrum, 5: 1-25.
Herrera-Estrella, A. and Chet, I. 2003. The biological control agent Trichoderma: from fundamentals to applications. Handbook of Fungal Biotechnology 2: 147-156.
Horsch, M., Mayer, C., Sennhauser, U. and Rast, D.M. 1997. β-N-acetylhexosaminidase: a target for the design of antifungal agents. Pharmacology & therapeutics 76: 187-218.
Howell, C.R. 2003. Mechanisms employed by Trichoderma species in the biological control of plant diseases: the history and evolution of current concepts. Plant Disease 87: 4-10.
Ihrmark, K., Asmail, N., Ubhayasekera, W., Melin, P., Stenlid, J. and Karlsson, M. 2010. Comparative molecular evolution of Trichoderma chitinases in response to mycoparasitic interactions. Evolutionary Bioinformatics, 6: 1-26.
Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G. and Pesseat, S. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics, 30: 1236-1240.
Karlsson, M. and Stenlid, J. 2008. Comparative evolutionary histories of the fungal chitinase gene family reveal non-random size expansions and contractions due to adaptive natural selection. Evolutionary Bioinformatics 4: 47-60.
Kubicek, C.P., Herrera-Estrella, A., Seidl-Seiboth, V., Martinez, D.A., Druzhinina, I.S., Thon, M., Zeilinger, S., Casas-Flores, S., Horwitz, B.A., Mukherjee, P.K. and Mukherjee, M. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral lifestyle of Trichoderma. Genome Biology 12: 1-15.
Liu, Y., He, P., He, P., Munir, S., Ahmed, A., Wu, Y., Yang, Y., Lu, J., Wang, J., Yang, J. and Pan, X. 2022. Potential biocontrol efficiency of Trichoderma species against oomycete pathogens. Frontiers in Microbiology 13: 1-11.
Merzendorfer, H. and Zimoch, L. 2003. Chitin metabolism in insects: structure, function, and regulation of chitin synthases and chitinases. Journal of Experimental Biology 206: 4393-4412.
Moxham, S.E. and Buczacki, S.T. 1983. Chemical composition of the resting spore wall of Plasmodiophora brassicae. Transactions of the British Mycological Society 80: 297-304.
Mukherjee, P.K., Mendoza-Mendoza, A., Zeilinger, S. and Horwitz, B.A. 2022. Mycoparasitism as a mechanism of Trichoderma-mediated suppression of plant diseases. Fungal Biology Reviews 39: 15-33.
Papadopoulos, J.S. and Agarwala, R. 2007. COBALT: a constraint-based alignment tool for multiple protein sequences. Bioinformatics 23: 1073-1079.
Rottloff, S., Stieber, R., Maischak, H., Turini, F.G., Heubl, G. and Mithöfer, A. 2011. Functional characterization of a class III acid endochitinase from the traps of the carnivorous pitcher plant genus, Nepenthes. Journal of Experimental Botany 62: 4639-4647.
Ruiz-Herrera, J. and Ortiz-Castellanos, L. 2019. Cell wall glucans of fungi. A review. The Cell Surface, 5: 1-14.
Seidl, V., Huemer, B., Seiboth, B. and Kubicek, C.P. 2005. A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases. The FEBS journal 272: 5923-5939.
Seidl, V., Marchetti, M., Schandl, R., Allmaier, G. and Kubicek, C.P. 2006. Epl1, the major secreted protein of Hypocrea atroviridis on glucose, is a member of a strongly conserved protein family comprising plant defense response elicitors. The FEBS journal 273: 4346-4359.
Seidl, V. 2008. Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions. Fungal Biology Reviews 22: 36-42.
Seidl-Seiboth, V., Ihrmark, K., Druzhinina, I. and Karlsson, M. 2014. Molecular evolution of Trichoderma chitinases. In Biotechnology and biology of Trichoderma 67-78.
Shah, P.A. and Pell, J.K. 2003. Entomopathogenic fungi as biological control agents. Applied microbiology and biotechnology 61: 413-423.
Sharma, V., Salwan, R. and Sharma, P.N. 2017. The comparative mechanistic aspects of Trichoderma and probiotics: scope for future research. Physiological and Molecular Plant Pathology 100: 84-96.
Tamura, K., Stecher, G. and Kumar, S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38: 3022-3027.
Vazquez-Garciduenas, S., Leal-Morales, C.A. and Herrera-Estrella, A. 1998. Analysis of the β-1, 3-glucanolytic system of the biocontrol agent Trichoderma harzianum. Applied and environmental microbiology 64: 1442-1446.
Wang, C. and Zhuang, W.Y. 2019. Evaluating effective Trichoderma isolates for biocontrol of Rhizoctonia solani causing root rot of Vigna unguiculata. Journal of Integrative Agriculture, 18: 2072-2079.
Wang, C. and Zhuang, W.Y. 2020. Carbon metabolic profiling of Trichoderma strains provides insight into potential ecological niches. Mycologia 112: 213-223.
Webster, J. and Weber, R. 2007. Introduction to fungi. Cambridge University Press 1-841.
Weindling, R. 1932. Trichoderma lignorum as a parasite of other soil fungi. Phytopathology, 22: 837-845.
Woo, S.L., Ruocco, M., Vinale, F., Nigro, M., Marra, R., Lombardi, N., Pascale, A., Lanzuise, S., Manganiello, G. and Lorito, M. 2014. Trichoderma-based products and their widespread use in agriculture. The Open Mycology Journal, 8: 71-126