Structural and functional characterization of HSP70 in the common bean (Phaseolus vulgaris) genome: An in sílico analysis
DOI:
https://doi.org/10.33448/rsd-v12i12.44073Keywords:
Structural characterization; Common bean; Heat shock protein.Abstract
The common bean (Phaseolus vulgaris L.) is the most important legume worldwide, with global production estimated at 26.8 million metric tons in 2016, and is cultivated for its green pods as well as its dry seeds. Plants, in general, respond to environmental stresses with a series of physiological and molecular adaptation mechanisms. Heat shock proteins (HSPs) are protective proteins against a wide range of biotic and abiotic stress conditions and are highly conserved proteins that occur in all organisms in nature. HSP70 was first shown to be induced by high temperatures, but in recent years they have been considered as general stress-responsive proteins, which are induced by many abiotic stress conditions. Other studies have found that HSP70s are highly expressed under conditions of heat, cold and drought stress. Therefore, increased tolerance due to high expression of HSP70s has been demonstrated in some plant species. Several computational tools have been used for a broad analysis of the genome in silico and have been used to identify new proteins and genes. Although omics technologies have become significantly popular, there are few studies on the identification and characterization of HSP70 in Phaseolus vulgaris. Therefore, the objective of the present study was to carry out a structural characterization and identification of HSP70 in Phaseolus vulgaris using genome-wide computational methods, namely: phenetic analysis, allergenic potential analysis and three-dimensional modeling of the sequences.
References
of Farm Sciences, 6, 1–5. https://www.indianjournals.com/ijor.aspx?target=ijor:ijfs&volume=6&issue=4&article=001.
Ahuja I., de Vos R. C., Bones A. M., & Hall R. D. (2010) Plant molecular stress responses face climate change. Trends Plant Sci 15(12):664–674. 10.1016/j.tplants.2010.08.002.
Aki, T., Fujikawa, A., Wada, T., Jyo, T., Shigeta, S., Murooka, Y., & Ono, K. (1994). Cloning and expression of cDNA coding for a new allergen from the house dust mite, Dermatophagoides farinae: homology with human heat shock cognate proteins in the heat shock protein 70 family. The Journal of Biochemistry, 115(3), 435-440.
Alvim F. C., Carolino S. M., Cascardo J. C., Nunes C. C., Martinez C. A., Otoni W. C., & Fontes E. P. (2001) Enhanced accumulation of BiP in transgenic plants confers tolerance to water stress. Plant Physiol 126(3):1042–1054. 10.1104/pp.126.3.1042.
Anisimova, O. K., Kochieva, E. Z., Shchennikova, A. V., & Filyushin, M. A. (2022). Thaumatin-like protein (TLP) genes in garlic (Allium sativum L.): Genome-wide identification, characterization, and expression in response to Fusarium proliferatum infection. Plants, 11(6), 748.
Assefa, T., Assibi Mahama, A., Brown, A. V., Cannon, E. K., Rubyogo, J. C., Rao, I. M., & Cannon, S. B. (2019). A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.). Molecular Breeding, 39, 1-23.
Barre, A., Sénéchal, H., Nguyen, C., Granier, C., Poncet, P., & Rougé, P. (2023). Structural Basis for the IgE-Binding Cross-Reacting Epitopic Peptides of Cup s 3, a PR-5 Thaumatin-like Protein Allergen from Common Cypress (Cupressus sempervirens) Pollen. Allergies, 3(1), 11-24.
Blair, M. W. (2013). Mineral biofortification strategies for food staples: the example of common bean. Journal of agricultural and food chemistry, 61(35), 8287-8294.
Boubakri, H., Chihaoui, S. A., Najjar, E., Barhoumi, F., & Jebara, M. (2022). Comprehensive identification, evolutionary patterns and the divergent response of PRX genes in Phaseolus vulgaris under biotic and abiotic interactions. 3 Biotech, 12(8), 175.
Broughton, W. J., Hernández, G., Blair, M., Beebe, S., Gepts, P., & Vanderleyden, J. (2003). Beans (Phaseolus spp.)–model food legumes. Plant and soil, 252, 55-128.
Buruchara, R., Chirwa, R., Sperling, L., Mukankusi, C., Rubyogo, J. C., Mutonhi, R., & Abang, M. M. (2011). Development and delivery of bean varieties in Africa: the Pan-Africa Bean Research Alliance (PABRA) model. African crop science journal, 19(4), 227-245.
Cashikar A.G., Duennwald M., & Lindquist S.L. (2005) A chaperone pathway in protein disaggregation. Hsp26 alters the nature of protein aggregates to facilitate reactivation by Hsp104. J Biol Chem 280(25):23869–23875. 10.1074/jbc.M502854200.
Chen, M., Xu, J., Devis, D., Shi, J., Ren, K., Searle, I., & Zhang, D. (2016). Origin and functional prediction of pollen allergens in plants. Plant physiology, 172(1), 341-357.
Chuang, J. G., Su, S. N., Chiang, B. L., Lee, H. J., & Chow, L. P. (2010). Proteome mining for novel IgE‐binding proteins from the German cockroach (Blattella germanica) and allergen profiling of patients. Proteomics, 10(21), 3854-3867.
Costa, J., Mafra, I., Carrapatoso, I., & Oliveira, M. B. P. (2016). Hazelnut allergens: Molecular characterization, detection, and clinical relevance. Critical reviews in food science and nutrition, 56(15), 2579-2605.
Costa, J., Villa, C., Verhoeckx, K., Cirkovic-Velickovic, T., Schrama, D., Roncada, P., & Holzhauser, T. (2022). Are physicochemical properties shaping the allergenic potency of animal allergens? Clinical Reviews in Allergy & Immunology, 62(1), 1-36.
Daugaard M., Rohde M., & Jaattela M. (2007) The heat shock protein 70 family: highly homologous proteins with overlapping and distinct functions. FEBS Lett 581(19):3702–3710. 10.1016/j.febslet.2007.05.039
Frydman J. (2001) Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70:603–647. 10.1146/annurev.biochem.70.1.603
Guo, W., Zhan, X., Jiang, F., & Xi, Y. (2021). Analysis of allergen components and identification of bioactivity of HSP70 in pollen of Populus deltoides. Proteome science, 19, 1-14.
Guo, Z., Li, Y., & Ding, S. W. (2019). Small RNA-based antimicrobial immunity. Nature Reviews Immunology, 19(1), 31-44.
Hao, M., Xijiri, Zhao, Z., & Che, H. (2022). Identification of allergens in white-and red-fleshed pitaya (Selenicereus undatus and Selenicereus costaricensis) seeds using bottom-up proteomics coupled with immunoinformatics. Nutrients, 14(9), 1962.
Hirano, K., Hino, S., Oshima, K., Nadano, D., Urisu, A., Takaiwa, F., & Matsuda, T. (2016). Evaluation of allergenic potential for rice seed protein components utilizing a rice proteome database and an allergen database in combination with IgE-binding of recombinant proteins. Bioscience, Biotechnology, and Biochemistry, 80(3), 564-573.
Jain, M., Amera, G. M., Muthukumaran, J., & Singh, A. K. (2022). Insights into biological role of plant defense proteins: A review. Biocatalysis and Agricultural Biotechnology, 40, 102293.
Jiang, L., Hu, W., Qian, Y., Ren, Q., & Zhang, J. (2021). Genome-wide identification, classification and expression analysis of the Hsf and Hsp70 gene families in maize. Gene, 770, 145348.
Kajander, T., Sachs, J. N., Goldman, A., & Regan, L. (2009). Electrostatic interactions of Hsp-organizing protein tetratricopeptide domains with Hsp70 and Hsp90: computational analysis and protein engineering. Journal of Biological Chemistry, 284(37), 25364-25374.
Kesici, M., Ipek, A., Ersoy, F., Ergin, S., & Gülen, H. (2020). Genotype-dependent gene expression in strawberry (Fragaria x ananassa) plants under high temperature stress. Biochemical genetics, 58, 848-866.
Kumar, M., Tomar, M., Potkule, J., Punia, S., Dhakane-Lad, J., Singh, S., & Kennedy, J. F. (2022). Functional characterization of plant-based protein to determine its quality for food applications. Food Hydrocolloids, 123, 106986.
Li, Z., & Srivastava, P. (2004). Heat-shock proteins. Current protocols in immunology, Appendix 1. https://doi.org/10.1002/0471142735.ima01ts58.
Liu, J., Han, D., & Shi, Y. (2019). Gene cloning, expression, and antifungal activities of permatin from naked oat (Avena nuda). Probiotics and antimicrobial proteins, 11, 299-309.
Liu, Q., Liang, C., & Zhou, L. (2020). Structural and functional analysis of the Hsp70/Hsp40 chaperone system. Protein Science, 29(2), 378-390.
Liu, X., Chen, H., Li, S., & Wang, L. (2022). Genome-wide identification of the Hsp70 gene family in grape and their expression profile during abiotic stress. Horticulturae, 8(8), 743.
Marcus, J. (2013). Protein Basics: Animal and vegetable proteins in food and health. Culinary nutrition, 189-230.
Panzade, K. P. et al. (2021) Genome-wide analysis of Hsp70 and Hsp100 gene families in Ziziphus jujuba. Cell Stress and Chaperones, 26(2), 341-353
Masand S., & Yadav S.K. (2016) Overexpression of MuHSP70 gene from Macrotyloma uniflorum confers multiple abiotic stress tolerance in transgenic Arabidopsis thaliana. Mol Biol Rep 43(2):53–64. 10.1007/s11033-015-3938-y.
Musidlak, O., Nawrot, R., & Goździcka-Józefiak, A. (2017). Which plant proteins are involved in antiviral defense? Review on in vivo and in vitro activities of selected plant proteins against viruses. International Journal of Molecular Sciences, 18(11), 2300.
Naikoo, G. A., Mustaqeem, M., Hassan, I. U., Awan, T., Arshad, F., Salim, H., & Qurashi, A. (2021). Bioinspired and green synthesis of nanoparticles from plant extracts with antiviral and antimicrobial properties: A critical review. Journal of Saudi Chemical Society, 25(9), 101304.
Richter, K., Haslbeck, M., & Buchner. J. (2010) The heat shock response: life on the verge of death. Mol Cell 40(2):253–266. 10.1016/j.molcel.2010.10.006.
Rosenzweig, R., Nillegoda, N. B., Mayer, M. P., & Bukau, B. (2019). The Hsp70 chaperone network. Nature reviews molecular cell biology, 20(11), 665-680.
Salas, C. E., Badillo-Corona, J. A., Ramírez-Sotelo, G., & Oliver-Salvador, C. (2015). Biologically active and antimicrobial peptides from plants. BioMed research international, 2015.
Sarkar, N.K., Kim, Y.K., & Grover, A. (2009) Rice sHsp genes: genomic organization and expression profiling under stress and development. BMC Genom 10:393. DOI: 10.1186/1471-2164-10-393.
Shevchenko, M., Servuli, E., Albakova, Z., Kanevskiy, L., & Sapozhnikov, A. (2021). The role of heat shock protein 70 kDa in asthma. Journal of Asthma and Allergy, 757-772.
Tabassum, R., Dosaka, T., Ichida, H., Morita, R., Ding, Y., Abe, T., & Katsube‐Tanaka, T. (2020). FLOURY ENDOSPERM11‐2 encodes plastid HSP70‐2 involved with the temperature‐dependent chalkiness of rice (Oryza sativa L.) grains. The Plant Journal, 103(2), 604-616.
Tabusam, J., Shi, Q., Feng, D., Zulfiqar, S., Shen, S., Ma, W., & Zhao, J. (2022). HSP70 gene family in Brassica rapa: Genome-wide identification, characterization, and expression patterns in response to heat and cold stress. Cells, 11(15), 2316.
Timperio, A.M., Egidi, M.G., & Zolla, L. (2008) Proteomics applied on plant abiotic stresses: role of heat shock proteins (HSP). J proteom 71(4):391–411. DOI: 10.1016/j.jprot.2008.07.005.
Tiroli-Cepeda, A. O., Lima, T. B., Balbuena, T. S., Gozzo, F. C., & Ramos, C. H. (2014). Structural and functional characterization of the chaperone Hsp70 from sugarcane. Insights into conformational changes during cycling from cross-linking/mass spectrometry assays. Journal of proteomics, 104, 48-56.
Tomiczek, B., Delewski, W., Nierzwicki, L., Stolarska, M., Grochowina, I., Schilke, B., & Marszalek, J. (2020). Two-step mechanism of J-domain action in driving Hsp70 function. PLoS Computational Biology, 16(6), e1007913.
Verhoeckx, K., Broekman, H., Knulst, A., & Houben, G. (2016). Allergenicity assessment strategy for novel food proteins and protein sources. Regulatory Toxicology and Pharmacology, 79, 118-124.
Wang, H., Dong, Z., Chen, J., Wang, M., Ding, Y., Xue, Q., & Ding, X. (2022). Genome-wide identification and expression analysis of the Hsp20, Hsp70 and Hsp90 gene family in Dendrobium officinale. Frontiers in Plant Science, 13, 979801.
Wang, W., Vinocur, B., Shoseyov, O., & Altman, A. (2004). Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends in plant science, 9(5), 244–252. DOI: 10.1016/j.tplants.2004.03.006.
Wegele, H., Müller, L., & Buchner, J. (2004). Hsp70 and Hsp90—a relay team for protein folding. Reviews of physiology, biochemistry and pharmacology, 1-44.
Yu, X., Mo, Z., Tang, X., Gao, T., & Mao, Y. (2021). Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): Identification, characterization and expression profiles in response to dehydration stress. BMC Plant Biology, 21, 1-14.
Zhou, S.J., Jing, Z., & Shi, J.L. (2013) Genome-wide identification, characterization, and expression analysis of the MLO gene family in Cucumis sativus. Genet mol res 12(4):6565–6578. 10. 4238/2013.December.11.8.
Zhou, X., Su, L., Tang, R., Dong, Y., Wang, F., Li, R., & Li, H. (2023). Genome-wide analysis of Hsp40 and Hsp70 gene family in four cotton species provides insights into their involvement in response to Verticillium dahliae and abiotic stress. Frontiers in Genetics, 14, 1120861.
Zhu, X., Zhao, X., Burkholder, W. F., Gragerov, A., Ogata, C. M., Gottesman, M. E., & Hendrickson, W. A. (1996). Structural analysis of substrate binding by the molecular chaperone DnaK. Science (New York, N.Y.), 272(5268), 1606–1614. 10.1126/science.272.5268.1606.
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Copyright (c) 2023 Maria Letícia Pereira Aquino; Dalton Ferreira Matos; Genesio José do Amaral Ramos; José Alfredo dos Santos Júnior; José Valdemilson dos Santos Silva; Delma Holanda de Almeida
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