Study of a functional pathway of miRNAs target genes in response to drought ant salt stresses in canola

Akbudak, M. A., & Filiz, E. (2019). Genome-wide analyses of ATP sulfurylase (ATPS) genes in higher plants and expression profiles in sorghum (Sorghum bicolor) under cadmium and salinity stresses. Genomics, 111(4), 579-589. Ali, M.S., & Baek, K.-H. (2020). Protective Roles of Cytosolic and Plastidal Proteasomes on Abiotic Stress and Pathogen Invasion. Plants, 9(7), 1-17. Alqurashi, M., Chiapello, M., Bianchet, C., Paolocci, F., Lilley, K. S., & Gehring, C. (2018). Early Responses to Severe Drought Stress in the Arabidopsis thaliana Cell Suspension Culture Proteome. Proteomes, 6(4). 38. Amm, I., Sommer, T., & Wolf, D. H. (2014). Protein quality control and elimination of protein waste: The role of the ubiquitin–proteasome system. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1843(1), 182-196. Anjum, N. A., Gill, R., Kaushik, M., Hasanuzzaman, M., Pereira, E., Ahmad, I., ... Gill, S. S. (2015). ATP-sulfurylase, sulfur-compounds, and plant stress tolerance. Frontiers in Plant Science, 6. 210. Aukerman, M. J., & Sakai, H. (2003). Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. The plant cell, 15(11), 2730-2741. Baek, K. H., & Choi, D. I. (2008). Roles of Plant Proteases in Pathogen Defense. Plant Pathol J, 24(4), 367-374. Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. cell, 116(2), 281-297. Bohrer, A. S., Yoshimoto, N., Sekiguchi, A., Rykulski, N., Saito, K., & Takahashi, H. (2014). Alternative translational initiation of ATP sulfurylase underlying dual localization of sulfate assimilation pathways in plastids and cytosol in Arabidopsis thaliana. Front Plant Sci, 5, 750. Chen, Z., Zhao, P. X., Miao, Z. Q., Qi, G. F., Wang, Z., Yuan, Y., ... Xiang, C. B. (2019). SULTR3s Function in Chloroplast Sulfate Uptake and Affect ABA Biosynthesis and the Stress Response. Plant physiology, 180(1), 593-604. Dai, X., Zhuang, Z., & Zhao, P. X. (2018). psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic acids research, 46(1), 49-54. Delauré, S. L., Van Hemelrijck, W., De Bolle, M. F. C., Cammue, B. P. A., & De Coninck, B. M. A. (2008). Building up plant defenses by breaking down proteins. Plant Science,174(4), 375-385. Díaz-Villanueva, J. F., Díaz-Molina, R., & García-González, V. (2015). Protein Folding and Mechanisms of Proteostasis. International Journal of Molecular Sciences, 16(8). 17193-17230. Gu, J., Xia, Z., Luo, Y., Jiang, X., Qian, B., Xie, H., ... Wang, Z.-Y. (2018). Spliceosomal protein U1A is involved in alternative splicing and salt stress tolerance in Arabidopsis thaliana. Nucleic acids research, 46(4), 1777-1792. Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols, 4(1), 44. Hulm, J. L., McIntosh, K. B., & Bonham-Smith, P. C. (2005). Variation in transcript abundance among the four members of the Arabidopsis thaliana RIBOSOMAL PROTEIN S15a gene family. Plant Science, 169(1), 267-278. Jian, H., Wang, J., Wang, T., Wei, L., Li, J., & Liu, L. (2016). Identification of Rapeseed MicroRNAs Involved in Early Stage Seed Germination under Salt and Drought Stresses. Frontiers in Plant Science, 7, 658. Kawasaki, S., Borchert, C., Deyholos, M., Wang, H., Brazille, S., Kawai, K., ... Bohnert, H. J. (2001). Gene expression profiles during the initial phase of salt stress in rice. The Plant cell, 13(4), 889-905. Kawashima, C. G., Matthewman, C. A., Huang, S., Lee, B.-R., Yoshimoto, N., Koprivova, A., ... Kopriva, S. (2011). Interplay of SLIM1 and miR395 in the regulation of sulfate assimilation in Arabidopsis. The Plant Journal, 66(5), 863-876. Kawashima, C. G., Yoshimoto, N., Maruyama-Nakashita, A., Tsuchiya, Y. N., Saito, K., Takahashi, H., & Dalmay, T. (2009). Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. The Plant Journal, 57(2), 313-321. Khan, N. A., Khan, M. I. R., Asgher, M., Fatma, M., & Masood, A. J. J. P. B. P. (2014). Salinity tolerance in plants: revisiting the role of sulfur metabolites. 2(120), 1-18. Kim, K. Y., Park, S. W., Chung, Y. S., Chung, C. H., Kim, J. I., & Lee, J. H. (2004). Molecular cloning of low‐temperature‐inducible ribosomal proteins from soybean. Journal of Experimental Botany, 55(399), 1153-1155. Köster, T., Marondedze, C., Meyer, K., & Staiger, D. (2017). RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome. Trends in Plant Science, 22(6), 512-526. Kurepa, J., Wang, S., Li, Y., & Smalle, J. (2009). Proteasome regulation, plant growth and stress tolerance. Plant Signaling & Behavior, 4(10), 924-927. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., & Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. science, 294(5543), 853-858. Lee, R. C., Feinbaum, R. L., & Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75(5), 843-854. Leustek, T., Murillo, M., & Cervantes, M. (1994). Cloning of a cDNA Encoding ATP Sulfurylase from Arabidopsis thaliana by Functional Expression in Saccharomyces cerevisiae. Plant physiology, 105(3), 897-902. Li, Y., Guo, Q., Liu, P., Huang, J., Zhang, S., Yang, G., ... Yan, K. (2021). Dual roles of the serine/arginine-rich splicing factor SR45a in promoting and interacting with nuclear cap-binding complex to modulate the salt-stress response in Arabidopsis. New Phytologist, 230(2), 641-655. Liang, G., Yang, F., & Yu, D. (2010). MicroRNA395 mediates regulation of sulfate accumulation and allocation in Arabidopsis thaliana. The Plant Journal, 62(6), 1046-1057. Liang, G., & Yu, D. (2010). Reciprocal regulation among miR395, APS and SULTR2;1 in Arabidopsis thaliana. Plant Signaling & Behavior, 5(10), 1257-1259. Liu, X.-D., Xie, L., Wei, Y., Zhou, X., Jia, B., Liu, J., ... Brakhage, A. A. (2014). Abiotic Stress Resistance, a Novel Moonlighting Function of Ribosomal Protein RPL44 in the Halophilic Fungus Aspergillus glaucus. Applied and Environmental Microbiology, 80(14), 4294-4300. Llave, C., Kasschau, K. D., Rector, M. A., & Carrington, J. C. (2002). Endogenous and silencing-associated small RNAs in plants. The plant cell, 14(7), 1605-1619. Marondedze, C., Thomas, L., Lilley, K. S., & Gehring, C. (2020). Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components, 6, 163. Mazahar, M., Achala, B., Anusree, S., & Kirti, P.J.P. (2019). Ribosomal proteins and their extra ribosomal functions in abiotic stress tolerance of plants, 12(7), 1024-1038. Mohsenzadeh Golfazani, M., Pasandideh Arjmand, M., & Samizadeh Lahiji, H. (2022). Bioinformatics identification of hub genes involved in osmotic stress of Arabidopsis. Agricultural Biotechnology Journal, 14(1), 155-174. Mohsenzadeh Golfazani, M., Taghvaei, M. M., Samizadeh Lahiji, H., Ashery, S., & Raza, A. (2022). Investigation of proteins’ interaction network and the expression pattern of genes involved in the ABA biogenesis and antioxidant system under methanol spray in drought-stressed rapeseed. 3 Biotech. 12, 217. Moin, M., Bakshi, A., Madhav, M. S., & Kirti, P. B. (2017). Expression Profiling of Ribosomal Protein Gene Family in Dehydration Stress Responses and Characterization of Transgenic Rice Plants Overexpressing RPL23A for Water-Use Efficiency and Tolerance to Drought and Salt Stresses. Front Chem, 5, 97. Moin, M., Bakshi, A., Saha, A., Dutta, M., Madhav, S. M., & Kirti, P. B. (2016). Rice Ribosomal Protein Large Subunit Genes and Their Spatio-temporal and Stress Regulation. 7, 1284. Moin, M., Bakshi, A., Saha, A., Udaya Kumar, M., Reddy, A. R., Rao, K. V., ... Kirti, P. B. (2016). Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water-use efficiency and abiotic stress tolerance in plants. Plant Cell Environ, 39(11), 2440-2459. Moin, M., Saha, A., Bakshi, A., Madhav, M.S., & Kirti, P. B. (2021). Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants. Gene, 789, 145670. Nishimura, T., Wada, T., & Okada, K. (2004). A key factor of translation reinitiation, ribosomal protein L24, is involved in gynoecium development in Arabidopsis. Biochem Soc Trans, 32(4), 611-613. Pasandideh, M., Samizadeh, H.-A., & Mohsenzadeh, M. (2018). The effect of drought stress on some morphological and physiological characters in canola seedling (Brassica napus). Iranian Journal of Seed Sciences and Research, 5(2), 95-108. Phartiyal, P., Kim, W.-S., Cahoon, R. E., Jez, J. M., & Krishnan, H. B. (2006). Soybean ATP sulfurylase, a homodimeric enzyme involved in sulfur assimilation, is abundantly expressed in roots and induced by cold treatment. Archives of Biochemistry and Biophysics, 450(1), 20-29. Ramezanzadeh Bishegahi, S., Mohsenzadeh, M., & Samizadeh, H. (2021). Effect of methanol foliar application on expression changes of some mitochondrial genes in canola under drought stress. Iranian Journal of Field Crop Science, 52(3), 113-128. Raspor, P., Fujs, Š., Banszky, L., Maraz, A., & Batič, M. (2003). The involvement of ATP sulfurylase in Se(VI) and Cr(VI) reduction processes in the fission yeast Schizosaccharomyces pombe. Applied Microbiology and Biotechnology, 63(1), 89-95. Rogalski, M., Schöttler, M. A., Thiele, W., Schulze, W. X., & Bock, R. (2008). Rpl33, a Nonessential Plastid-Encoded Ribosomal Protein in Tobacco, Is Required under Cold Stress Conditions The Plant cell, 20(8), 2221-2237. Romero, L. C., Domínguez-Solís, J. R., Gutiérrez-Alcalá, G., & Gotor, C. (2001). Salt regulation of O-acetylserine(thiol)lyase in Arabidopsis thaliana and increased tolerance in yeast. Plant Physiology and Biochemistry, 39(7), 643-647. Rosa Téllez, S., Kanhonou, R., Castellote Bellés, C., Serrano, R., Alepuz, P., & Ros, R. (2020). RNA-Binding Proteins as Targets to Improve Salt Stress Tolerance in Crops. Agronomy, 10(2). Sahi, C., Singh, A., Kumar, K., Blumwald, E., & Grover, A. (2006). Salt stress response in rice: genetics, molecular biology, and comparative genomics. Functional & Integrative Genomics, 6(4), 263-284. Sahu, P. P., Sharma, N., Puranik, S., Chakraborty, S., & Prasad, M. (2016). Tomato 26S Proteasome subunit RPT4a regulates ToLCNDV transcription and activates hypersensitive response in tomato. Scientific Reports, 6(1), 27078. Sakamoto, T., Kamiya, T., Sako, K., Yamaguchi, J., Yamagami, M., & Fujiwara, T. (2011). Arabidopsis thaliana 26S Proteasome Subunits RPT2a and RPT5a Are Crucial for Zinc Deficiency-Tolerance. Bioscience, Biotechnology, and Biochemistry, 75(3), 561-567. Seki, M., Kamei, A., Yamaguchi-Shinozaki, K., & Shinozaki, K. (2003). Molecular responses to drought, salinity and frost: common and different paths for plant protection. Current Opinion in Biotechnology, 14(2), 194-199. Shiraku, M. L., Magwanga, R. O., Cai, X., Kirungu, J. N., Xu, Y., Mehari, T. G., ... Liu, F. (2021). Knockdown of 60S ribosomal protein L14-2 reveals their potential regulatory roles to enhance drought and salt tolerance in cotton. Journal of Cotton Research, 4(1), 27. Smalle, J., Kurepa, J., Yang, P., Emborg, T. J., Babiychuk, E., Kushnir, S., & Vierstra, R. D. (2003). The Pleiotropic Role of the 26S Proteasome Subunit RPN10 in Arabidopsis Growth and Development Supports a Substrate-Specific Function in Abscisic Acid Signaling. The Plant cell, 15(4), 965-980. Song, L., Pan, Z., Chen, L., Dai, Y., Wan, J., Ye, H., ... Chen, H. (2020). Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions. Genes, 11(12). 1520. Stone, S. L. (2019). Chapter Three - Role of the Ubiquitin Proteasome System in Plant Response to Abiotic Stress. In L. Galluzzi (Ed.), International Review of Cell and Molecular Biology,343, 65-110. Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., ... Bork, P. (2018). STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic acids research, 47(1), 607-613. Taghvaei, M. M., Lahiji, H. S., & Golfazani, M. M. (2022). Evaluation of expression changes, proteins interaction network, and microRNAs targeting catalase and superoxide dismutase genes under cold stress in rapeseed (Brassica napus L.). OCL, 29. Trippe, R. C., 3rd, & Pilon-Smits, E. A. H. (2021). Selenium transport and metabolism in plants: Phytoremediation and biofortification implications. J Hazard Mater, 404(Pt B), 124178. Verma, S., Nizam, S., & Verma, P. K. (2013). Biotic and Abiotic Stress Signaling in Plants. In M. Sarwat, A. Ahmad, & M. Z. Abdin (Eds.), Stress Signaling in Plants: Genomics and Proteomics Perspective, 1, 25-49. Wang, R., Zou, J., Meng, J., & Wang, J. (2018). Integrative analysis of genome-wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids. Ecol Evol, 8(12), 6034-6052. Wang, S., Kurepa, J., & Smalle, J. A. (2009). The Arabidopsis 26S proteasome subunit RPN1a is required for optimal plant growth and stress responses. Plant & cell physiology, 50(9), 1721-1725. Wang, S., Kurepa, J., & Smalle, J. A. (2009). The Arabidopsis 26S Proteasome Subunit RPN1a is Required for Optimal Plant Growth and Stress Responses. Plant and Cell Physiology, 50(9), 1721-1725. Warner, J. R., & McIntosh, K. B. (2009). How common are extraribosomal functions of ribosomal proteins? Mol Cell, 34(1), 3-11. Watanabe, S., Nakagawa, A., Izumi, S., Shimada, H., & Sakamoto, A. (2010). RNA interference-mediated suppression of xanthine dehydrogenase reveals the role of purine metabolism in drought tolerance in Arabidopsis. FEBS Letters, 584(6), 1181-1186. Yu, X., Wang, H., Lu, Y., de Ruiter, M., Cariaso, M., Prins, M., ... He, Y. (2012). Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. Journal of Experimental Botany, 63(2), 1025-1038. Zhang, B., Pan, X., Cannon, C. H., Cobb, G. P., & Anderson, T. A. (2006). Conservation and divergence of plant microRNA genes. The Plant Journal, 46(2), 243-259. Zhang, C., Chen, J., Huang, W., Song, X., & Niu, J. (2021). Transcriptomics and Metabolomics Reveal Purine and Phenylpropanoid Metabolism Response to Drought Stress in Dendrobium sinense, an Endemic Orchid Species in Hainan Island. Frontiers in Genetics, 12. 692702. Zhang, Y., Zhang, A., Li, X., & Lu, C. (2020). The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress. International Journal of Molecular Sciences, 21(17), 6082. Zolfaghari Khutbehsera, N., Mohsenzadeh Golfazani, M., Taghvaei Mohammad, M., & Samizadeh Lahiji, H. (2022). Study of miRNAs involved in drought and salt stress stresses and ontology of target genes in Brassica species. Agricultural Biotechnology Journal, Accept. Zrenner, R., Stitt, M., Sonnewald, U., & Boldt, R. J. A. R. P. B. (2006). Pyrimidine and purine biosynthesis and degradation in plants. 57, 805-836.