Study of miRNAs involved in drought and salt stress stresses and ontology of target genes in Brassica species

Document Type : Research Paper

Authors

1 MSc Student, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.

2 Assistant Professor, Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.

3 Professor, Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.

Abstract

 
Objective
Abiotic stresses such as drought and salinity significantly affect plant growth and performance. Plants use strategies to adapt and tolerate drought and salt stress that may threaten their survival during their life cycle, one of which is miRNA-mediated post-transcriptional regulation.
Materials and methods
In the current research, miRNAs that showed significant expression during salt and drought stress were selected by checking the references to investigate this phenomenon in rapeseed plants. The phylogenetic tree was constructed to analyze and compare the evolutionary relationships and conservation of MicroRNA effective in drought and salinity stress in Brassica napus, Brassica rapa, and Brassica oleracea species. Target genes for selected miRNAs were identified using psRNATarget online software. Categorization and gene ontology of target genes and identification of biological pathways were accomplished; also, proteins were classified based on molecular function and biological processes. The Protein-protein interaction was analyzed to comprehensively interpret the relationships between the target genes. In the present study, 225 target genes for miRNAs were identified.
Results
After examining the protein interaction network, it was found that there were the most interactions between ribosomal, proteasome subunits and the ubiquitin-proteasome system. This result determined that drought and salinity stress leads to the activation of various biological systems and pathways and changes in gene expression along with the activation of the protein synthesis machine and alterations in protein content. By activating post-transcriptional gene regulation (PTGR) and post-translational modifications (PTMs), the plant regulates the abundance, activities, intracellular distribution, and transport of regulatory proteins involved in various growth processes as well as stress response. 
Conclusion
The results of this study will lead to a broader perspective regarding stress and its effect on the pathways involved in cellular processes and will reveal the wide dimensions of the stress response.

Keywords


عرب پور رق آبادی زهرا، محمدآبادی محمدرضا، خضری امین (1400) الگوی بیانی ژن p32 در بافت‌های ران، دست، راسته و چربی پشت بره کرمانی. مجله بیوتکنولوژی کشاورزی، 13(4)، 183-200.
محسن زاده گلفزانی محمد، پسندیده ارجمند مریم، سمیع زاده لاهیجی حبیب ا.... (1400) شناسایی بیوانفورماتیکی ژن‌های کلیدی دخیل در تنش اسمزی گیاه آرابیدوپسیس. مجله بیوتکنولوژی کشاورزی، 13(1)، 1-22.
محمدآبادی محمدرضا (1399) بیان ژن ESR1 در بز کرکی راینی با استفاده از real time PCR‎. مجله بیوتکنولوژی کشاورزی 12(1)، 192-177.
محمدآبادی محمدرضا (1399) پروفایل بیانیmRNA مختص بافت ژن ESR2 در بز. مجله بیوتکنولوژی کشاورزی 12(4)، 184-169.
محمدآبادی محمدرضا، سفلایی محمد (1399). پروفایل بیانی mRNA مختص بافت ژن BMP15 در بز. مجله بیوتکنولوژی کشاورزی 12(3)، 208-191.
محمدآبادی محمدرضا، کرد محبوبه، نظری محمود (1397) مطالعه بیان ژن لپتین در بافت‌های مختلف گوسفند کرمانی با استفاده از real time PCR. مجله بیوتکنولوژی کشاورزی 10(3)، 122-111.
References
Akdogan G, Tufekci ED, Uranbey S et al. (2016) miRNA-based drought regulation in wheat. Funct Integr Genomics 16, 221-233.
Akhtar MM, Micolucci L, Islam MS et al. (2015) Bioinformatic tools for microRNA dissection. Nucleic Acids Res 44, 24-44.
Arabpour Z, Mohammadabadi M, Khezri A (2021) The expression pattern of p32 gene in femur, humeral muscle, back muscle and back fat tissues of Kermani lambs. Agric Biotechnol J 13 (4), 183-200 (In Persian).
Aravind J, Rinku S, Pooja B et al. (2017) Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds. Front Plant Sci 8, 941.
Baek D, Chun HJ, Kang S et al. (2016) A Role for Arabidopsis miR399f in Salt, Drought, and ABA Signaling. Mol Cells 39, 111-118.
Balakrishnan R, Harris MA, Huntley R et al. (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database bat054.
Barrera-Figueroa BE, Gao L, Wu Z et al. (2012) High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. Plant Biol 12, 132.
Bhardwaj AR, Joshi G, Pandey R et al. (2014) A Genome-Wide Perspective of miRNAome in Response to High Temperature, Salinity and Drought Stresses in Brassica juncea (Czern) L. PLOS ONE 9, e92456.
Carnavale Bottino M, Rosario S, Grativol C et al. (2013) High-Throughput Sequencing of Small RNA Transcriptome Reveals Salt Stress Regulated MicroRNAs in Sugarcane. PLOS ONE 8, e59423.
Cecchetti V, Altamura MM, Falasca G et al. (2008) Auxin regulates Arabidopsis anther dehiscence, pollen maturation, and filament elongation. Plant Cell 20, 1760-1774.
Chung E, Cho C-W, So H-A et al. (2013) Overexpression of VrUBC1, a Mung Bean E2 Ubiquitin-Conjugating Enzyme, Enhances Osmotic Stress Tolerance in Arabidopsis. PLOS ONE 8, e66056.
Cui F, Liu L, Zhao Q et al. (2012) Arabidopsis Ubiquitin Conjugase UBC32 Is an ERAD Component That Functions in Brassinosteroid-Mediated Salt Stress Tolerance.  Plant Cell 24, 233-244.
Dai X, Zhuang Z, Zhao PX (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res 46, 49-54.
Engstrom EM, Andersen CM, Gumulak-Smith J et al. (2011) Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy. Plant Physiol 155, 735-750.
Gaudet P, Livstone MS, Lewis SE et al. (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform 12, 449-462.
Gentile A, Dias LI, Mattos RS et al. (2015) microRNAs and drought responses in sugarcane. Front Plant Sci 6, 58.
Gupta S, Dong Y, Dijkwel PP et al. (2019) Genome-wide analysis of ROS antioxidant genes in resurrection species suggest an involvement of distinct ROS detoxification systems during desiccation. Int J Mol Sci 20, 3101.
Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61, 1041-1052.
Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44.
Huang H-Y, Jiang W-B, Hu Y-W et al. (2013) BR signal influences Arabidopsis ovule and seed number through regulating related genes expression by BZR1. Mol Plant 6, 456-469.
Jian H, Wang J, Wang T et al. (2016) Identification of Rapeseed microRNAs Involved in Early Stage Seed Germination under Salt and Drought Stresses. Front Plant Sci 7, 658.
Jofuku KD, den Boer BG, Van Montagu M et al. (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6, 1211-1225.
Jofuku KD, Omidyar PK, Gee Z et al. (2005) Control of seed mass and seed yield by the floral homeotic gene APETALA2. Proc Natl Acad Sci USA 102, 3117-3122.
Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14, 787-799.
Khraiwesh B, Zhu J-K, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819, 137-148.
Kumar S, Stecher G, Li M et al. (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms.  Mol Biol Evol 35, 1547-1549.
Kunst L, Klenz JE, Martinez-Zapater J et al. (1989) AP2 Gene Determines the Identity of Perianth Organs in Flowers of Arabidopsis thaliana. Plant Cell 1, 1195-1208.
Li G, Siddiqui H, Teng Y et al. (2011) Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol 13, 616-622.
Li Y, Guo Q, Liu P et al. (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 Phytol 230, 641-655.
Liu D, Liu H, Du H et al. (2021) Relationship between polyamines conjugated to mitochondrion membrane and mitochondrion conformation from developing wheat embryos under drought stress.  J Biosci 46, 1-11.
Liu Q, Wang F, Axtell MJ (2014) Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. Plant Cell 26, 741-753.
Lukasik A, Pietrykowska H, Paczek L et al. (2013) High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves. BMC Genomics 14, 801.
Masoudzadeh SH, Mohammadabadi M, Khezri A, et al. (2020) Effects of diets with different levels of fennel (Foeniculum vulgare) seed powder on DLK1 gene expression in brain, adipose tissue, femur muscle and rumen of Kermani lambs. Small Rumin Res 193, e106276.
Meng C, Yang M, Wang Y et al. (2020) SlWHY2 interacts with SlRECA2 to maintain mitochondrial function under drought stress in tomato. Plant Sci 301, 110674.
Mi H, Muruganujan A, Ebert D et al. (2018) PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res 47, 419-426.
Min H, Yoon S (2010) Got target?: computational methods for microRNA target prediction and their extension. Exp Mol Med 42, 233.
Mohammadabadi M (2021) Tissue-specific mRNA expression profile of ESR2 gene in goat. Agric Biotechnol J 12 (4), 167-181 (In Persian).
Mohammadabadi M, Masoudzadeh SH, Khezri A, et al. (2021) Fennel (Foeniculum vulgare) seed powder increases Delta-Like Non-Canonical Notch Ligand 1 gene expression in testis, liver, and humeral muscle tissues of growing lambs. Heliyon 7 (12), e08542.
Mohammadabadi M, Soflaei M (2020) Tissue-specific mRNA expression profile of BMP15 gene in goat. Agric Biotechnol J 12, 191-208 (In Persian).
Mohammadabadi MR (2020) Expression of ESR1 gene in Raini Cashmere goat using Real Time PCR. Agric Biotechnol J 12 (1), 177-192 (In Persian).
Mohammadabadi MR, Kord M, Nazari M (2018) Studying expression of leptin gene in different tissues of Kermani Sheep using Real Time PCR. Agric Biotechnol J 10, 111-122 (In Persian).
Mohammadabadi MR, Tohidinejad F (2017) Charachteristics determination of Rheb gene and protein in Raini Cashmere goat. Iran J Appl Anim Sci 7, 289-295.
Mohsenzadeh Golfazani M, Pasandideh Arjmand M, Samizadeh Lahiji HJABJ (2022a) Bioinformatics identification of hub genes involved in osmotic stress of Arabidopsis.  Agric Biotechnol J 14, 155-174. (In Persian).
Mohsenzadeh Golfazani M, Taghvaei MM, Samizadeh Lahiji H et al. (2022b) 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, Saha A, Bakshi A et al. (2021) Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants. Gene 789, 145670.
Nagai S, Koide M, Takahashi S et al. (2007) Induction of isoforms of tetrapyrrole biosynthetic enzymes, AtHEMA2 and AtFC1, under stress conditions and their physiological functions in Arabidopsis. Plant Physiol 144, 1039-1051.
Okonechnikov K, Golosova O, Fursov M et al. (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28, 1166-1167.
Pegler JL, Nguyen DQ, Oultram JMJ et al. (2021) Molecular Manipulation of the MiR396/GRF Expression Module Alters the Salt Stress Response of Arabidopsis thaliana. Agron 11, 1751.
Razi K, Muneer SJCRiB (2021) Drought stress-induced physiological mechanisms, signaling pathways and molecular response of chloroplasts in common vegetable crops. Crit Rev Biotechnol 41 (5), 669-691.
Riechmann JL, Heard J, Martin G et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Sci 290, 2105-2110.
Shahsavari M, Mohammadabadi M, Khezri A, et al. (2021) Correlation between insulin-like growth factor 1 gene expression and fennel (Foeniculum vulgare) seed powder consumption in muscle of sheep. Anim Biotechnol 33, 1-11.
Shannon P, Markiel A, Ozier O et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13 (11), 2498-2504.
Shikata M, Koyama T, Mitsuda N et al. (2009) Arabidopsis SBP-box genes SPL10, SPL11 and SPL2 control morphological change in association with shoot maturation in the reproductive phase. Plant Cell Physiol 50, 2133-2145.
Su T, Yang M, Wang P et al. (2020) Interplay between the Ubiquitin Proteasome System and Ubiquitin-Mediated Autophagy in Plants. Cells 9 (10), 2219.
Sunkar R, Zhu JK (2007) microRNAs and short‐interfering RNAs in plants. J Integr Plant Biol 49, 817-826.
Szklarczyk D, Gable AL, Lyon D et al. (2018) STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47, 607-613.
Taghvaei MM, Lahiji HS, Golfazani MM (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 (3),
Taghvaei MM, Samizadeh Lahiji H, Bakhtiarizadeh MR et al. (2019) Bioinformatics analysis of microRNAs related to cold Stress and their effects on proteins associated with fatty acids metabolism in rapeseed (Brassica napus L.). J Crop Biotech 9, 41-58.
Takahashi H, Watanabe-Takahashi A, Smith FW et al. (2000) The roles of three functional sulphate transporters involved in uptake and translocation of sulphate in Arabidopsis thaliana. Plant J 23(2), 171-182.
Tian Y, Tian Y, Luo X et al. (2014) Identification and characterization of microRNAs related to salt stress in broccoli, using high-throughput sequencing and bioinformatics analysis. BMC Plant Biol 14, 226.
Vidal EA, Araus V, Lu C et al. (2010) Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci USA 107, 4477-4482.
Wang F, Li L, Liu L et al. (2012a) High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Mol Genet Genomics 287, 555-563.
Wang J, Yang X, Xu H et al. (2012b) Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene 505, 300-308.
Wang R, Zou J, Meng J et al. (2018) Integrative analysis of genome-wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids. Ecol Evol 8, 6034-6052.
Würschum T, Gross-Hardt R, Laux T (2006) APETALA2 regulates the stem cell niche in the Arabidopsis shoot meristem. Plant Cell 18, 295-307.
Xing S, Salinas M, Höhmann S et al. (2010) miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis. Plant Cell 22, 3935-3950.
Xu F-Q, Xue H-W (2019) The ubiquitin-proteasome system in plant responses to environments. Plant, Cell Environ 42, 2931-2944.
Yang J, Liu X, Xu B et al. (2013) Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of Brassica juncea. Genomics 14 (9).
Ye B-B, Shang G-D, Pan Y et al. (2020) AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration. Plant Cell 32, 226-241.
Yu X, Wang H, Lu Y et al. (2012) Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 63, 1025-1038.
Zhang B, Pan X, Cannon CH et al. (2006) Conservation and divergence of plant microRNA genes. Plant J 46, 243-259.
Zhang Y, Zhang A, Li X et al. (2020) The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress. Int J Mol Sci 21 (17), 6082.
Zhou G-A, Chang R-Z, Qiu L-J (2010a) Overexpression of soybean ubiquitin-conjugating enzyme gene GmUBC2 confers enhanced drought and salt tolerance through modulating abiotic stress-responsive gene expression in Arabidopsis. Plant Mol Biol 72, 357-367.
Zhou L, Liu Y, Liu Z et al. (2010b) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61, 4157-4168.