بررسی بیوانفورماتیکی اعضای خانواده ژنی CBL در گیاه کنجد (Sesamum indicum) تحت تنش خشکی

نوع مقاله : علمی پژوهشی

نویسندگان

1 دانشجوی دکتری بیوتکنولوژی کشاورزی، پژوهشگاه ملی مهندسی ژنتیک و زیست‌فناوری، تهران، ایران.

2 دانشیار گروه بیوتکنولوژی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، ایران.

3 استادیار گروه مهندسی ژنتیک و بیولوژی، پژوهشکده ژنتیک و زیست‌فناوری کشاورزی طبرستان، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ایران.

چکیده

یکی از زیرخانواده‌های ژنی حسگرهای کلسیم، پروتئین‌های شبه‌کالسینئورین B (CBLs) بوده که به‌عنوان یک مولکول پیام‌رسان ثانویه در بسیاری از فرایندهای بیولوژیکی و عملکردهای مولکولی سلول‌های گیاهی نقش ایفا می‌کنند. در این تحقیق، بررسی گستره ژنومی زیرخانواده ژنی CBL در گیاه کنجد مورد بررسی قرار گرفت. تعداد نه ژن SiCBL در ژنوم کنجد شناسایی گردید که بر پایه روابط اورتولوگی با ژن‌های گیاه مدل آرابیدوپسیس، در قالب شش گروه پروتئینی SiCBL1، SiCBL2، SiCBL3، SiCBL4، SiCBL8 و SiCBL10 طبقه‌بندی شدند. وزن مولکولی پروتئین‌های SiCBL در محدوده 4/24 الی 9/37 کیلو دالتون، محدوده pH ایزوالکتریک اسیدی، شاخص ناپایداری 99/33 الی 46/47 درصد و شاخص آلیفاتیک 29/80 الی 89/106 و GRAVY در محدوده 420/0- الی 061/0 متغیر بود. پیش‌بینی تغییرات پس از ترجمه توالی پروتئینی CBL نشان داد موتیف پالمیتوئیلاسیون در همه پروتئین‌های CBL گیاه کنجد مشاهده شد، در حالی‌که اکثر آنها فاقد موتیف میریستویلاسیون بودند. در بررسی ساختار ژنی، 11 درصد ژن‌های SiCBL دارای نه اگزون، 11 درصد دارای هشت اگزون و 77 درصد دارای هفت اگزون بودند. تجزیه و تحلیل الگوی RNA-seq زیرخانواده SiCBL تحت تیمار PEG نشان داد اگرچه اعضای این خانواده در دو رقم حساس و متحمل، الگوی بیان به نسبت مشابه‌ای داشتند ولی هر یک از اعضای این خانواده ژنی به‌دلیل انشقاق عملکردی، از الگوی بیان منحصربفردی برخوردار بودند. مطالعات تکمیلی بیان ژن‌های خانواده ژنی SiCBL و SiCIPK تحت تنش‌های غیر زیستی مختلف در تحقیقات آتی می‌تواند در درک مکانیسم تنظیمات بیان ژن‌های مرتبط با مسیر SOS مفید باشد.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Bioinformatics analysis of CBL gene family members in Sesamum indicum under drought stress

نویسندگان [English]

  • Mozhdeh Arab 1
  • Seyed Kamal Kazemitabar 2
  • Seyyed Hamidreza Hashemi-petroudi 3
1 Ph.D. Student in Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
2 Associate Professor, Department of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
3 Assistant Professors, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
چکیده [English]

Calcineurin B-like proteins (CBLs) are a subfamily of calcium sensors that play a role in various plant cell processes and molecular functions. In sesame (Sesamum indicum), in silico analysis of the CBL gene family was performed to identify CBL proteins involved in calcium signaling. Using their orthologic relationships with Arabidopsis homolog genes, the nine SiCBL genes were identified and subdivided into six groups: SiCBL1, SiCBL2, SiCBL3, SiCBL4, SiCBL8, SiCBL10. The molecular weight of SiCBL proteins ranged from 24.4 to 37.9 kDa, the Isoelectric acid pH range, the instability index ranged from 33.99 to 47.46 percent, the aliphatic index ranged from 80.29 to 10.89, and the GRAVY ranged from -0.420 to 0.061. Prediction of post-translational modifications revealed that palmitoylation motif was observed in all siCBL, however majority of them did not have myristoylaton motif. In term of gene structure, 11% of SiCBL genes had nine exons, 11% had eight exons and 77% had seven exons. The RNA-seq pattern of the SiCBL subfamily under PEG treatment revealed that, whereas members of this gene family had generally similar expression patterns in both susceptible and tolerant cultivars, due to functional Convergence, each member of this gene family had a distinct expression pattern. Future research on the expression of SiCBL and SiCIPK gene family genes under various abiotic conditions could aid in understanding the mechanism of expression control of SOS-related genes.

کلیدواژه‌ها [English]

  • Calcium sensor
  • CBL
  • Gene family
  • PEG
  • Sesame
Arab, M., Najafi Zarrini, H., Nematzadeh, G., & Hashemi-petroudi, S. H. (2021). Comparative study of cis-regulatory elements in the promoter regions of calcineurin B-like genes (CBLs) of Aeluropus, Arabidopsis and rice plants. Crop Biotechnology, 10(34), 93-112. Aslam, M., Fakher, B., Jakada, B. H., Zhao, L., Cao, S., Cheng, Y., & Qin, Y. (2019). Genome-wide identification and expression profiling of CBL-CIPK gene family in pineapple (Ananas comosus) and the role of AcCBL1 in abiotic and biotic stress response. Biomolecules, 9(7), 293. Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., ... & Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic acids research, 37(suppl_2), W202-W208. Dodd, A. N., Kudla, J., & Sanders, D. (2010). The language of calcium signaling. Annual review of plant biology, 61, 593-620. El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., ... & Finn, R. D. (2019). The Pfam protein families database in 2019. Nucleic Acids research, 47(D1), D427-D432. Esfandiari, G. (2001). Stress factors and their relation with general health in students of Kurdistan university of medical sciences in year 1999. Scientific Journal of Kurdistan University of Medical Sciences, 5(2), 17-21. Evrard, A. (2013). Cell type-specific transcriptional responses of plants to salinity. Ph.D. Thesis. Autralian Center for plant functional genomics Adelaide.405 pages. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4), 783-791. Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook, 571-607. Horton, P., Park, K. J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007). WoLF PSORT: protein localization predictor. Nucleic Acids Research, 35(suppl_2), W585-W587. Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics,31(8),1296-1297. Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., De Castro, E., Langendijk-Genevaux, P. S., ... & Sigrist, C. J. (2006). The PROSITE database. Nucleic Acids Research, 34(suppl_1), D227-D230. Jiang, M., Zhao, C., Zhao, M., Li, Y., & Wen, G. (2020). Phylogeny and evolution of Calcineurin B-Like (CBL) gene family in grass and functional analyses of rice CBLs. Journal of Plant Biology, 63(2), 117-130. Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., ... & Hunter, S. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9), 1236-1240. Kaur, A., Pati, P. K., Pati, A. M., & Nagpal, A. K. (2017). In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PloS One, 12(9), e0184523. Kaur, G., & Pati, P. K. (2016). Analysis of cis-acting regulatory elements of Respiratory burst oxidase homolog (Rboh) gene families in Arabidopsis and rice provides clues for their diverse functions. Computational Biology and Chemistry, 62, 104-118. Kim, B. G., Waadt, R., Cheong, Y. H., Pandey, G. K., Dominguez‐Solis, J. R., Schültke, S., ... & Luan, S. (2007). The calcium sensor CBL10 mediates salt tolerance by regulating ion homeostasis in Arabidopsis. The Plant Journal, 52(3), 473-484. Kim, K. N., Cheong, Y. H., Gupta, R., & Luan, S. (2000). Interaction specificity of Arabidopsis calcineurin B-like calcium sensors and their target kinases. Plant Physiology, 124(4), 1844-1853. Kolukisaoglu, U., Weinl, S., Blazevic, D., Batistic, O., & Kudla, J. (2004). Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiology, 134(1), 43-58. Ladan Moghdam, A. (2020). Genome wide bioinformatics analysis BES1 gene family in Vitis vinifera L. Crop Biotechnology, 10(30), 71-86. Lan, W. Z., Lee, S. C., Che, Y. F., Jiang, Y. Q., & Luan, S. (2011). Mechanistic analysis of AKT1 regulation by the CBL–CIPK–PP2CA interactions. Molecular Plant, 4(3), 527-536. Letunic, I., & Bork, P. (2018). 20 years of the SMART protein domain annotation resource. Nucleic Acids Research, 46(D1), D493-D496. Li, J., Jiang, M. M., Ren, L., Liu, Y., & Chen, H. Y. (2016). Identification and characterization of CBL and CIPK gene families in eggplant (Solanum melongena L.). Molecular Genetics and Genomics, 291(4), 1769-1781. Li, R., Zhang, J., Wei, J., Wang, H., Wang, Y., & Ma, R. (2009). Functions and mechanisms of the CBL–CIPK signaling system in plant response to abiotic stress. Progress in Natural Science, 19(6), 667-676. Liu, H., Che, Z., Zeng, X., Zhou, X., Sitoe, H. M., Wang, H., & Yu, D. (2016). Genome-wide analysis of calcium-dependent protein kinases and their expression patterns in response to herbivore and wounding stresses in soybean. Functional & Integrative Genomics, 16(5), 481-493. Lu, T., Zhang, G., Sun, L., Wang, J., & Hao, F. (2017). Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. PeerJ, 5, e3653. Ma, X., Gai, W. X., Qiao, Y. M., Ali, M., Wei, A. M., Luo, D. X., ... & Gong, Z. H. (2019). Identification of CBL and CIPK gene families and functional characterization of CaCIPK1 under Phytophthora capsici in pepper (Capsicum annuum L.). BMC Genomics, 20(1), 1-18. Ma, X., Li, Q. H., Yu, Y. N., Qiao, Y. M., Haq, S. U., & Gong, Z. H. (2020). The CBL–CIPK pathway in plant response to stress signals. International Journal of Molecular Sciences, 21(16), 5668. Mao, D., & Chen, C. (2012). Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway. Martínez-Atienza, J., Jiang, X., Garciadeblas, B., Mendoza, I., Zhu, J. K., Pardo, J. M., & Quintero, F. J. (2007). Conservation of the salt overly sensitive pathway in rice. Plant Physiology, 143(2), 1001-1012. Mohanta, T. K., Kumar, P., & Bae, H. (2017). Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants. BMC Plant Biology, 17(1), 1-19. Monihan, S.M., Magness, C.A., Yadegari, R., Smith, S.E., & Schumaker, K. S. (2016). Arabidopsis CALCINEURIN B-LIKE10 functions independently of the SOS pathway during reproductive development in saline conditions. Plant Physiology, 171(1), 369-379. Nagae, M., Nozawa, A., Koizumi, N., Sano, H., Hashimoto, H., Sato, M., & Shimizu, T. (2003). The crystal structure of the novel calcium-binding protein AtCBL2 from Arabidopsis thaliana. Journal of Biological Chemistry, 278(43), 42240-42246. Rahimi, M., & Gharachorloo, M. (2020). Determination of Some Antinutritional Factors and Heavy Metals in Sesame Oil, Raw and Peeled Sesame (Sesamum indicum L.) Seed of two Varieties Cultivated in Iran. Food Science and Technology, 17(98), 169-181. Roul, B., Mishra, B. K., & Prusty, N. (2017). Natural effect of micronutrient on growth and growth parameter of sesame oilseed crop. Pharmacognosy and Phytochemistry, 6, 1926-1928. Sánchez-Barrena, M. J., Martínez-Ripoll, M., Zhu, J. K., & Albert, A. (2005). The structure of the Arabidopsis thaliana SOS3: molecular mechanism of sensing calcium for salt stress response. Journal of Molecular Biology, 345(5), 1253-1264. Shu, B., Cai, D., Zhang, F., Zhang, D. J., Liu, C. Y., Wu, Q. S., & Luo, C. (2020). Identifying citrus CBL and CIPK gene families and their expressions in response to drought and arbuscular mycorrhizal fungi colonization. Biol. Plant, 64, 773-783. Sigrist, C. J., De Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., ... & Xenarios, I. (2012). New and continuing developments at PROSITE. Nucleic Acids Research, 41(D1), D344-D347. Silva, R. T. D., Oliveira, A. B. D., Lopes, M. D. F. D. Q., Guimarães, M. D. A., & Dutra, A. S. (2016). Physiological quality of sesame seeds produced from plants subjected to water stress. Revista Ciência Agronômica, 47, 643-648. Song, Q., Joshi, M., Wang, S., Johnson, C. D., & Joshi, V. (2021). Comparative analysis of root transcriptome profiles of sesame (Sesamum indicum L.) in response to osmotic stress. Journal of Plant Growth Regulation, 40(4), 1787-1801. Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725-2729. Wang, M., Gu, D., Liu, T., Wang, Z., Guo, X., Hou, W., ... & Wang, G. (2007). Overexpression of a putative maize calcineurin B-like protein in Arabidopsis confers salt tolerance. Plant Molecular Biology, 65(6), 733-746. Wu, Y., Ding, N., Zhao, X., Zhao, M., Chang, Z., Liu, J., & Zhang, L. (2007). Molecular characterization of PeSOS1: the putative Na+/H+ antiporter of Populus Euphratica. Plant molecular Biology, 65(1), 1-11. Yin, X., Wang, Q., Chen, Q., Xiang, N., Yang, Y., & Yang, Y. (2017). Genome-wide identification and functional analysis of the calcineurin B-like protein and calcineurin B-like protein-interacting protein kinase gene families in turnip (Brassica rapa var. rapa). Frontiers in plant science, 8, 1191. Yu, Q., An, L., & Li, W. (2014). The CBL–CIPK network mediates different signaling pathways in plants. Plant Cell Reports, 33(2), 203-214. Zhang, H., Yang, B., Liu, W. Z., Li, H., Wang, L., Wang, B., ... & Jiang, Y. Q. (2014). Identification and characterization of CBL and CIPK gene families in canola (Brassica napus L.). BMC Plant Biology, 14(1), 1-24. Zhao, J., Yu, A., Du, Y., Wang, G., Li, Y., Zhao, G., ... & Wang, Y. (2019). Foxtail millet (Setaria italica (L.) P. Beauv) CIPKs are responsive to ABA and abiotic stresses. PLoS One, 14(11), e0225091.