Investigation of the characteristics and expression changes of snakin gene family members in different stages of seed development in barley (Hordeum vulgare L.)

Document Type : Research Paper

Authors

1 Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.

2 Professor, Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.

3 Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran

Abstract

Antimicrobial peptides are a part of the innate immune system in plants. They are present in all tissues and a wide range of plant species, and their antimicrobial effect against plant and animal pathogens and cancer cells has been proven. Snakins are a group of low molecular weight cysteine-rich plant antimicrobial peptides involved in the defense against biotic and abiotic stresses, hormone pathways, and plant growth and development. In the present study, laboratory and bioinformatic methods were used to investigate the characteristics of the snakin gene family members and to evaluate their expression changes in four seed development stages (3, 8, 13, and 18 days after pollination) in barley plants. The results showed the presence of 11 snakin genes in the genome of barley. The protein sequences of the identified snakins contained the GASA functional domain. These snakins had a signal peptide and had extracellular accumulation. Due to their high abundance of hydrophobic amino acids, they were hydrophobic and produced complex secondary structures. Phylogenetic analysis was performed between barley, rice, and arabidopsis snakins as two monocot and dicot models, leading to three classes. Also, six disulfide bonds and antimicrobial properties were computationally confirmed in all identified proteins. Expression analysis showed different expression patterns for snakin gene family members in different stages of seed development and also exhibited different trends in each stage. The snakin genes can use to produce transgenic plants and to produce a new generation of natural antibiotic agents to protect humans, plants, and animals.

Keywords

Main Subjects

References

Ahmad, B., Yao, J., Zhang, S., Li, X., Zhang, X., Yadav, V., & Wang, X. (2020). Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development. Int J Mol Sci, 21(3).https://doi.org/10.3390/ijms21031088 Ahmad, M. Z., Sana, A., Jamil, A., Nasir, J. A., Ahmed, S., Hameed, M. U., & Abdullah. (2019). A genome-wide approach to the comprehensive analysis of GASA gene family in Glycine max. Plant Molecular Biology, 100(6), 607-620. https://doi.org/10.1007/s11103-019-00883-1 Apte, A., & Singh, S. (2007). AlleleID: a pathogen detection and identification system. Methods Mol Biol, 402, 329-346. https://doi.org/10.1007/978-1-59745-528-2_17 Bahar, A.A., & Ren, D. (2013). Antimicrobial Peptides. Pharmaceuticals, 6(12), 1543-1575. https://www.mdpi.com/1424-8247/6/12/1543 Bamdad, F., Sun, X., & Chen, L. (2015). Preparation and characterization of antimicrobial cationized peptides from barley (Hordeum vulgare L.) proteins. LWT-Food science and Technology, 63(1), 29-36. Baum, M., Von Korff, M., Guo, P., Lakew, B., Hamwieh, A., Lababidi, S., Udupa, S. M., Sayed, H., Choumane, W., & Grando, S. (2007). Molecular approaches and breeding strategies for drought tolerance in barley. In Genomics-assisted crop improvement (pp. 51-79). Springer. Berrocal-Lobo, M., Segura, A., Moreno, M., López, G., Garcıa-Olmedo, F., & Molina, A. (2002). Snakin-2, an antimicrobial peptide from potato whose gene is locally induced by wounding and responds to pathogen infection. Plant physiology, 128(3), 951-961. Bian, J., Deng, P., Zhan, H., Wu, X., Nishantha, M. D., Yan, Z., Du, X., Nie, X., & Song, W. (2019). Transcriptional dynamics of grain development in barley (Hordeum vulgare L.). International Journal of Molecular Sciences, 20(4), 962. Carvalho, A. O., Machado, O. L. T., Da Cunha, M., Santos, I. S., & Gomes, V. M. (2001). Antimicrobial peptides and immunolocalization of a LTPin Vigna unguiculata seeds. Plant Physiology and Biochemistry, 39(2), 137-146. Castro, M. S., & Fontes, W. (2005). Plant defense and antimicrobial peptides. Protein Pept Lett, 12(1), 13-18. Dai, X., Zhuang, Z., & Zhao, P. X. (2018). psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Research, 46(W1), W49-W54. https://doi.org/10.1093/nar/gky316 Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Elsbach, P. (2003). What is the real role of antimicrobial polypeptides that can mediate several other inflammatory responses? The Journal of clinical investigation, 111(11), 1643-1645. https://doi.org/10.1172/JCI18761 Epand, R. M. (2016). Host Defense Peptides and Their Potential as Therapeutic Agents. Springer. Fan, S., Zhang, D., Zhang, L., Gao, C., Xin, M., Tahir, M. M., Li, Y., Ma, J., & Han, M. (2017). Comprehensive analysis of GASA family members in the Malus domestica genome: identification, characterization, and their expressions in response to apple flower induction. BMC Genomics, 18(1), 827. https://doi.org/10.1186/s12864-017-4213-5 Faraji, S., Mehmood, F., Malik, H. M. T., Ahmed, I., Heidari, P., & Poczai, P. (2021). The GASA Gene Family in Theobroma cacao: Genome Wide Identification and Expression Analyses. bioRxiv. Ferrè, F., & Clote, P. (2005). DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Research, 33(suppl_2), W230-W232. https://doi.org/10.1093/nar/gki412 Filiz, E., & Kurt, F. (2020). Antimicrobial peptides Snakin/GASA gene family in sorghum (Sorghum bicolor): Genome-wide identification and bioinformatics analyses. Gene Reports, 20, 100766. https://doi.org/10.1016/j.genrep.2020.100766 Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., & Sangrador-Vegas, A. (2016). The Pfam protein families database: towards a more sustainable future. Nucleic acids research, 44(D1), D279-D285. Goyal, R. K., & Mattoo, A. K. (2016). Plant Antimicrobial Peptides. In Host Defense Peptides and Their Potential as Therapeutic Agents (pp. 111-136). Springer. Guo, A. Y., Zhu, Q. H., Chen, X., & Luo, J. C. (2007). [GSDS: a gene structure display server]. Yi Chuan, 29(8), 1023-1026. Han, S., Jiao, Z., Niu, M.-X., Yu, X., Huang, M., Liu, C., Wang, H.-L., Zhou, Y., Mao, W., Wang, X., Yin, W., & Xia, X. (2021). Genome-Wide Comprehensive Analysis of the GASA Gene Family in Populus. International journal of molecular sciences, 22(22), 12336. https://www.mdpi.com/1422-0067/22/22/12336 Harris, P. W., Yang, S. H., Molina, A., López, G., Middleditch, M., & Brimble, M. A. (2014). Plant antimicrobial peptides snakin-1 and snakin-2: chemical synthesis and insights into the disulfide connectivity. Chemistry, 20 (17), 5102-5110. https://doi.org/10.1002/chem.201303207 Heidari, P., Mazloomi, F., Nussbaumer, T., & Barcaccia, G. (2020). Insights into the SAM Synthetase Gene Family and Its Roles in Tomato Seedlings under Abiotic Stresses and Hormone Treatments. Plants (Basel), 9(5). https://doi.org/10.3390/plants9050586 Holaskova, E., Galuszka, P., Frebort, I., & Oz, M. T. (2015). Antimicrobial peptide production and plant-based expression systems for medical and agricultural biotechnology. Biotechnology Advances, 33(6,Part 2), 1005-1023. https://doi.org/https://doi.org/10.1016/j.biotechadv.2015.03.007 Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. J Biochem, 88(6), 1895-1898. Kang, H. K., Kim, C., Seo, C. H., & Park, Y. (2017). The therapeutic applications of antimicrobial peptides (AMPs): a patent review. J Microbiol, 55(1), 1-12. https://doi.org/10.1007/s12275-017-6452-1 Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845-858. https://doi.org/10.1038/nprot.2015.053 Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol, 157(1), 105-132. https://doi.org/10.1016/0022-2836(82)90515-0 Lata, S., Sharma, B., & Raghava, G. (2007). Analysis and prediction of antibacterial peptides. BMC bioinformatics, 8(1), 263. Laverty, G., Gorman, S. P., & Gilmore, B. F. (2011). The potential of antimicrobial peptides as biocides. International journal of molecular sciences, 12(10), 6566-6596. Li, Z., Gao, J., Wang, G., Wang, S., Chen, K., Pu, W., Wang, Y., Xia, Q., & Fan, X. (2022). Genome-Wide Identification and Characterization of GASA Gene Family in Nicotiana tabacum [Original Research]. Frontiers in Genetics, 12. https://doi.org/10.3389/fgene.2021.768942 Marchler-Bauer, A., Derbyshire, M. K., Gonzales, N. R., Lu, S., Chitsaz, F., Geer, L. Y., Geer, R. C., He, J., Gwadz, M., & Hurwitz, D. I. (2014). CDD: NCBI's conserved domain database. Nucleic acids research, 43(D1), D222-D226. Muhammad, I., Li, W. Q., Jing, X. Q., Zhou, M. R., Shalmani, A., Ali, M., Wei, X. Y., Sharif, R., Liu, W. T., & Chen, K. M. (2019). A systematic in silico prediction of gibberellic acid stimulated GASA family members: A novel small peptide contributes to floral architecture and transcriptomic changes induced by external stimuli in rice. J Plant Physiol, 234-235, 117-132. https://doi.org/10.1016/j.jplph.2019.02.005 Nahirñak, V., Almasia, N. I., Hopp, H. E., & Vazquez-Rovere, C. (2012). Snakin/GASA proteins: involvement in hormone crosstalk and redox homeostasis. Plant Signal Behav, 7(8), 1004-1008. https://doi.org/10.4161/psb.20813 Nahirñak, V., Rivarola, M., Gonzalez de Urreta, M., Paniego, N., Hopp, H. E., Almasia, N. I., & Vazquez-Rovere, C. (2016). Genome-wide Analysis of the Snakin/GASA Gene Family in Solanum tuberosum cv. Kennebec. American Journal of Potato Research, 93(2), 172-188. https://doi.org/10.1007/s12230-016-9494-8 Olga, K., Marina, K., Alexey, A., Anton, S., Vladimir, Z., & Igor, T. (2020). The role of plant antimicrobial peptides (AMPs) in response to biotic and abiotic environmental factors. Biological Communications, 65(2). Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods, 8(10), 785-786. Porto, W. F., & Franco, O. L. (2013). Theoretical structural insights into the snakin/GASA family. Peptides, 44, 163-167. Qiao, K., Ma, C., Lv, J., Zhang, C., Ma, Q., & Fan, S. (2021). Identification, characterization, and expression profiles of the GASA genes in cotton. Journal of Cotton Research, 4(1), 7. https://doi.org/10.1186/s42397-021-00081-9 Reddy, K., Yedery, R., & Aranha, C. (2004). Antimicrobial peptides: premises and promises. International journal of antimicrobial agents, 24(6), 536-547. Rezaee, S., Ahmadizadeh, M., & Heidari, P. (2020). Genome-wide characterization, expression profiling, and post-transcriptional study of GASA gene family. Gene Reports, 20, 100795. https://doi.org/https://doi.org/10.1016/j.genrep.2020.100795 Sagaram, U. S., Kaur, J., & Shah, D. (2012). Antifungal Plant Defensins: Structure-Activity Relationships, Modes of Action, and Biotech Applications. In Small Wonders: Peptides for Disease Control, 1095, 317-336. American Chemical Society. https://doi.org/doi:10.1021/bk-2012-1095.ch015 bk-2012-1095.ch015/10,1021 Segura, A., Moreno, M., Madueño, F., Molina, A., & García-Olmedo, F. (1999). Snakin-1, a peptide from potato that is active against plant pathogens. Molecular Plant-Microbe Interactions, 12(1), 16-23. Wilkins, M. R., Gasteiger, E., Bairoch, A., Sanchez, J. C., Williams, K. L., Appel, R. D., & Hochstrasser, D. F. (1999). Protein identification and analysis tools in the ExPASy server. Methods Mol Biol, 112, 531-552. https://doi.org/10.1385/1-59259-584-7:531 Zasloff, M. (2006). Defending the epithelium. Nature medicine, 12(6), 607-608. Zimmermann, R., Sakai, H., & Hochholdinger, F. (2009). The Gibberellic Acid Stimulated-Like Gene Family in Maize and Its Role in Lateral Root Development Plant Physiology, 152(1), 356-365. https://doi.org/10.1104/pp.109.149054

Files

Share

How to cite

Statistics