Genome-Wide Identification of β-1,3-Glucanase Genes in Hevea brasiliensis

Xin Jie Lui; Gincy  P. Thottathil; Sudesh Kumar

doi:10.55230/mabjournal.v52i1.2463

Authors

Xin Jie Lui School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
Gincy P. Thottathil School of Biological Sciences, University Sains Malaysia, 11800 Gelugor, Penang, Malaysia
Sudesh Kumar
ksudesh@usm.my
School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia

Keywords:

β-1,3-glucanase, comparative genomics, disease resistance, Hevea brasiliensis, pathogenesis-related proteins

Abstract

β-1,3-glucanase is one of the pathogenesis-related proteins well-known for their antifungal properties which can be abundantly found in Hevea brasiliensis. Utilization of β-1,3-glucanase in the genetic improvement of H. brasiliensis is very important as the high susceptibility to various fungal infections has challenged the current natural rubber industry. A few nucleotide sequences for β-1,3-glucanase have been reported and their role in biotic stress management has been demonstrated. Being a multigene family, it is necessary to identify and characterize more isoforms of β-1,3-glucanase to select the most suitable isoform to be utilized in genetic improvement. In the current study, we conducted a genome-wide identification of β-1,3-glucanases in H. brasiliensis, their classification based on the functional domains and phylogenetic analysis, using different bioinformatics tools. All publicly available nucleotide sequences were collected and curated by eliminating sequences that lack glycoside hydrolase family 17 (GH 17) domain as well as the partial and closely identical sequences and obtained 14 full-length sequences. The sequences were categorized into 4 distinct classes (I-IV) based on their functional domains and C-terminal extension. Class III and IV which lack the carbohydrate-binding C-terminal X8 domain are the largest classes identified with 5 β-1,3-glucanase each while 4 β-1,3-glucanase contain a variable C-terminal X8 domain. Phylogenetic analysis showed the clustering of β-1,3-glucanases into six major clades (I-VI) based on the domains. Clades I and II were identified as the largest clades with 4 β-1,3-glucanase in each. Several paralogous clusters have been observed for H. brasiliensis indicating the gene family expansion within the species or in the immediate ancestors with possible species-specific function. Further functional characterization is necessary to select the suitable gene to be utilized in genetic improvement and the present study provides a platform for it.

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

Alenius, H., Kalkkinen, N., Reunala, T., Turjanmaa, K. & Palosuo T. 1996. The main IgE-binding epitope of a major latex affergen, prohevein, is present in its N-Terminal 43-Amino acid fragment, hevein. Journal of Immunology, 156(4): 1618−1625. DOI: https://doi.org/10.4049/jimmunol.156.4.1618

Archer, B.L. & Audley, B.G. 1987. New aspects of rubber biosynthesis. Botanical Journal of the Linnean Society, 94(1–2): 181–196. DOI: https://doi.org/10.1111/j.1095-8339.1987.tb01045.x

Barral, P., Suarez, C., Batanero, E., Alfonso, C., Alche, J.D., Rodriguez-Garcia, M., Villalba, M., Rivas, G. & Rodriguez, R. 2005. An olive pollen protein with allergenic activity, Ole e 10, defines a novel family of carbohydrate-binding modules and is potentially implicated in pollen germination. Biochemical Journal, 390(1): 77–84. DOI: https://doi.org/10.1042/BJ20050456

Beffa, R.S., Neuhaus, J.M. & Meins Jr, F. 1993. Physiological compensation in antisense transformants: specific induction of an" ersatz" glucan endo-1, 3-beta-glucosidase in plants infected with necrotizing viruses. Proceedings of the National Academy of Sciences of the United States of America, 90(19): 8792–8796. DOI: https://doi.org/10.1073/pnas.90.19.8792

Boiler, T. 1995. Chemoperception of microbial signals in plant cells. Annual Review of Plant Physiology and Plant Molecular Biology, 46(1): 189–214. DOI: https://doi.org/10.1146/annurev.pp.46.060195.001201

Borner, G.H., Sherrier, D.J., Stevens, T.J., Arkin, I.T. & Dupree, P. 2002. Prediction of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A genomic analysis. Plant Physiology, 129(2): 486–499. DOI: https://doi.org/10.1104/pp.010884

Bucciaglia, P.A. & Smith, A.G. 1994. Cloning and characterization of Tag 1, a tobacco anther β-1,3-glucanase expressed during tetrad dissolution. Plant Molecular Biology, 24(6): 903–914. DOI: https://doi.org/10.1007/BF00014444

Cataldo, F. 2000. Guayule rubber: A new possible world scenario for the production of natural rubber?. Progress in Rubber and Plastics Technology, 16(1): 31–59.

Clément-Demange, A., Priyadarshan, P.M., Hoa, T.T, & Venkatachalam, P. 2007. Hevea rubber breeding and genetics. In: Plant Breeding Reviews. J. Janick (Ed.). pp. 177–283. DOI: https://doi.org/10.1002/9780470168035.ch4

Cornish, K. 2001. Similarities and differences in rubber biochemistry among plant species. Phytochemistry, 57(7): 1123–1134. DOI: https://doi.org/10.1016/S0031-9422(01)00097-8

D’Auzac, J., Prevot, J.C. & Jacob, J.L. 1995. What’s new about lutoids? A vacuolar system model from Hevea latex. Plant Physiology and Biochemistry, 33(6): 765−777.

Doxey, A.C., Yaish, M.W.F., Moffatt, B.A., Griffith, M. & McConkey, B.J. 2007. Functional divergence in the Arabidopsis β-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states. Molecular Biology and Evolution, 24(4): 1045–1055. DOI: https://doi.org/10.1093/molbev/msm024

Ebel, J., & Scheel, D. 1992. Elicitor recognition and signal transduction. In: Genes Involved in Plant Defense. T. Boller & F. Meins (Eds.). Springer-Verlag, Vienna. pp. 183–205). DOI: https://doi.org/10.1007/978-3-7091-6684-0_8

Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39(4): 783–791. DOI: https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

Gao, Q.M., Kachroo, A. & Kachroo, P. 2014. Chemical inducers of systemic immunity in plants. Journal of Experimental Botany, 65(7): 1849–1855. DOI: https://doi.org/10.1093/jxb/eru010

Gidrol, X., Chrestin, H., Tan, H.L. & Kush, A. 1994. Hevein, a lectin- like protein from Hevea brasiliensis (rubber tree) is involved in the coagulation of latex. Journal of Biological Chemistry, 269(12): 9278−9283. DOI: https://doi.org/10.1016/S0021-9258(17)37104-1

Hagel, J.M., Yeung, E.C. & Facchini, P.J. 2008. Got milk? The secret life of laticifers. Trends in Plant Science, 13(12): 631−638. DOI: https://doi.org/10.1016/j.tplants.2008.09.005

Hall, T.A. 1999. BioEdit: a user-friendly biological sequences alignment editor and analysis program for Windows 95/95/NT. Nucleic Acids Symposium Series, 41: 95–98.

Henrissat, B. & Davies, G. J. 2000. Glycoside hydrolases and glycosyltransferases. Families, modules, and implications for genomics. Plant Physiology, 124(4): 1515–1519. DOI: https://doi.org/10.1104/pp.124.4.1515

Kanokwiroon, K., Teanpaisan, R., Wititsuwannakul, D., Hooper, A.B. & Wititsuwannakul, R. 2008. Antimicrobial activity of a protein purified from the latex of Hevea brasiliensis on oral microorganisms. Mycoses, 51: 301−307. DOI: https://doi.org/10.1111/j.1439-0507.2008.01490.x

Kurup, V.P., Yeang, H.Y., Sussman, G.L., Bansal, N.K., Beezhold, D.H., Kelly, K.J., Hoffman, D.R., Williams, B. & Fink, J.N. 2000. Detection of immunoglobulin antibodies in the sera of patients using purified latex allergens. Clinical & Experimental Allergy, 30(3): 359-369. DOI: https://doi.org/10.1046/j.1365-2222.2000.00748.x

Lau, N.S., Makita, Y., Kawashima, M., Taylor, T.D., Kondo, S., Othman, A.S., Shu-Chien, A.C. & Matsui, M. 2016. The rubber tree genome shows expansion of gene family associated with rubber biosynthesis. Scientific Reports, 6: 28594. DOI: https://doi.org/10.1038/srep28594

Legentil, L., Paris, F., Ballet, C., Trouvelot, S., Daire, X., Vetvicka, V. & Ferrières, V. 2015. Molecular interactions of β-(1→3)-glucans with their receptors. Molecules, 20(6): 9745–9766. DOI: https://doi.org/10.3390/molecules20069745

Leubner-Metzger, G. & Meins, F. 1999. Functions and regulation of plant ß-1, 3-glucanases (PR-2). In: Pathogenesis-related Proteins in Plants. S.K. Datta and S. Muthukrishnan (Eds.). CRC Press. pp. 49–76. DOI: https://doi.org/10.1201/9781420049299.ch3

Martin, M.N. 1991. The latex of Hevea brasiliensis contains high levels of both chitinases and chitinases/lysozymes. Plant Physiology, 95(2): 469−476. DOI: https://doi.org/10.1104/pp.95.2.469

Men, X., Wang, F., Chen, G.Q., Zhang, H.B. & Xian, M. 2019. Biosynthesis of natural rubber: Current state and perspectives. International Journal of Molecular Sciences, 20(1): 50. DOI: https://doi.org/10.3390/ijms20010050

Mooibroek, H. & Cornish, K. 2000. Alternative sources of natural rubber. Applied Microbiology and Biotechnology, 53(4): 355–365. DOI: https://doi.org/10.1007/s002530051627

Nair, K.P. 2021. Rubber (Hevea brasiliensis). In: Tree Crops. Springer, Cham. pp. 287–332. DOI: https://doi.org/10.1007/978-3-030-62140-7_8

Nei, M. & Kumar, S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.

Prakash, S., Hoque, M.I. & Brinks, T. 2004. Culture media and containers. Low Cost Options for Tissue Culture Technology in Developing Countries. IAEA, Vienna. pp. 29–40.

Priyadarshan, P.M. 2017. Biology of Hevea Rubber. Springer Cham. DOI: https://doi.org/10.1007/978-3-319-54506-6

Radhakrishnan, S., Mathew, S. A., Saleena, A. & Thulaseedharan, A. 2021. New insights into the novel and functional promoter sequences of b-1,3-glucanase gene from Hevea brasiliensis. Journal of Plant Protection Research, 61(1): 28–40.

Rahman, A.Y.A., Usharraj, A.O., Misra, B.B., Thottathil, G.P., Jayasekaran, K., Feng, Y., Hou, S., Ong, S.Y., Ng, F.L., Lee, L.S., Tan, H.S., Muhd Sakaff, M.K L., Teh, B.S., Khoo, B.F., Badai, S.S., Ab Aziz, N., Yuryev, A., Knudsen, B., Dionne-Laporte, A., Mchunu, N.P., Yu, Q., Langston, B.J., Freitas, T.A.K., Young, A.G., Chen, R., Wang, L., Najimudin, N., Saito, J.A. & Alam, M. 2013. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics, 14(1): 1–15. DOI: https://doi.org/10.1186/1471-2164-14-75

Saitou, N. & Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4): 406–425.

Subroto, T., Vries, H., Schuringa, J.J. Soedjanaatmadja, U.S., Hofsteenge, J., Jekel, P.A. & Beintema, J. J. 2001. Enzymic and structural studies on processed proteins from the vacuolar (lutoid-body) fraction of latex of Hevea brasiliensis. Biochem. Plant Physiology and Biochemistry, 39(12): 1047−1055. DOI: https://doi.org/10.1016/S0981-9428(01)01325-0

Sunderasan, E., Samsidar, H., Sharifah, M.A., Ward, H.Y., Yeang, M.J. & Cardosa, J. 1995. Latex B-serum-1,3-Glucanase (Hev b II) and a component of the microhelix (Hev b IV) are major latex allergens. Journal of Natural Rubber Research, 10(2): 82–99.

Tamura, K., Stecher, G. & Sudhir, K. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution, 38(7): 3022–3027. DOI: https://doi.org/10.1093/molbev/msab120

Thanseem, I., Joseph, A. & Thulaseedharan, A. 2005. Induction and differential expression of β-1, 3-glucanase mRNAs in tolerant and susceptible Hevea clones in response to infection by Phytophthora meadii. Tree Physiology, 25(11): 1361–1368. DOI: https://doi.org/10.1093/treephys/25.11.1361

Thompson, J.D., Higgins, D.G. & Gibson, T.J. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighing, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22): 4673–4680. DOI: https://doi.org/10.1093/nar/22.22.4673

Van Beilen, J.B. & Poirier, Y. 2007. Establishment of new crops for the production of natural rubber. Trends in Biotechnology, 25(11): 522–529. DOI: https://doi.org/10.1016/j.tibtech.2007.08.009

Van Parijs, J., Broekaert, W.F., Goldstein, I.J. & Peumans, W.J. 1991. Hevein: An antifungal protein from rubber-tree (Hevea brasiliensis) latex. Planta, 183(2): 258−264. DOI: https://doi.org/10.1007/BF00197797

Wang, X., Shi, M., Wang, D., Chen, Y., Cai, F., Zhang, S., Wang, L., Tong, Z. & Tian, W. M. 2013. Comparative proteomics of primary and secondary lutoids reveals that Chitinase and glucanase play a crucial combined role in rubber particle aggregation in Hevea brasiliensis. Journal of Proteome Research, 12(11): 5146–5159. DOI: https://doi.org/10.1021/pr400378c

Wititsuwannakul, R., Rukseree, K., Kanokwiroon, K. & Wititsuwannakul, D. 2008. A rubber particle protein specific for Hevea latex lectin binding involved in latex coagulation. Phytochemistry, 69(5): 1111−1118. DOI: https://doi.org/10.1016/j.phytochem.2007.12.007

Xu, X., Feng, Y., Fang, S., Xu, J., Wang, X. & Guo, W. 2016. Genome-wide characterization of the β-1,3-glucanase gene family in Gossypium by comparative analysis. Scientific Reports, 6(March): 1–15. DOI: https://doi.org/10.1038/srep29044

Yeang, H.Y., Arif, S.A.M., Yusof, F. & Sunderasan, E. 2002. Allergenic proteins of natural rubber latex. Methods, 27(1): 32–45. DOI: https://doi.org/10.1016/S1046-2023(02)00049-X