Bioinformatics analysis of microRNAs related to cold Stress and their effects on proteins associated with fatty acids metabolism in rapeseed (Brassica napus L.)

Document Type : Research Paper

Authors

1 Ph.D. Candidate of Plant Biotechnology, Faculty of Agriculture, University Campus 2 - University of Guilan, Rasht, Iran.

2 Professor, Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran

3 Assistant Professor, Department of Animal and Poultry Sciences, Aburaihan Campus, University of Tehran, Iran

4 Assistant Professor, Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran

Abstract

Rapeseed (Brassica napus) is one of the most important oil plants in the world. Not only it has rich sources of fatty acids, but also contains protein. Cold stress is one of the growth limiting factors for this plant, which causes massive molecular changes inside the plant. In this research miRNAs, bna-miR164a, bra-miR5712, bra-miR5717, bna-miR6029, bna-miR6035, bna-N_miR2, bna-N_miR16 that previously had been studied separately in cold and fatty acid biosynthesis, were selected for investigation of the relationship between microRNAs, Cold stress, Fatty Acids and Lipids. Afterwards, bioinformatics prediction of target genes, investigation of gene ontology and their functional pathway and mapping of protein interactions network were performed. As a result, it was discovered that miRNAs which are effective in cold stress, beside regulation of target genes such as SCRM2, HOS1, STZ, GLP4, PP2CA, which are responsible for cold response and thermal stimulus-response, also have regulatory roles on other target genes such as KAS2, FAD8, FAD4, AAD3, FAD7, FAD2 which are involved in biological processes such as unsaturated fatty acid biosynthesis, unsaturated fatty acid metabolism, fatty acid biosynthesis, fatty acid metabolism, cellular lipid catabolism and lipid metabolism, lipid biosynthesis, cellular lipid metabolism. Evaluation of Protein-Protein Interactions revealed that there was a relation between the target genes involved in fatty acid biosynthesis and the target genes involved in cold stress. The next step for subsequent research is to investigate the expression of these miRNAs and their target genes during cold stress and further experimental verifications to prove the regulatory relationship between them.

Keywords

Main Subjects

References

Akhtar MM, Micolucci L, Islam MS, Olivieri F, Procopio AD (2015) Bioinformatic tools for microRNA dissection. Nucleic Acids Res. 44(1): 24-44.
Amid A, Lytovchenko A, Fernie AR, Warren G, Thorlby GJ (2012) The sensitive to freezing3 mutation of Arabidopsis thaliana is a cold-sensitive allele of homomeric acetyl-CoA carboxylase that results in cold-induced cuticle deficiencies. J. Exp. Bot. 63(14): 5289-5299.
Amosova AV, Zoshchuk SA, Volovik VT, Shirokova AV, Horuzhiy NE, Mozgova GV,... Samatadze TE (2019) Phenotypic, biochemical and genomic variability in generations of the rapeseed (Brassica napus L.) mutant lines obtained via chemical mutagenesis. PloS One. 14(8).
Anders S, Samuel T, Anthony J (2002) KAS2 cDNA complements the phenotypes of the Arabidopsis fab1 mutant that differs in a single residue bordering the substrate binding pocket. Plant J.
Andrews C (1987) Low-temperature stress in field and forage crop production–an overview. Can. J. Plant Sci. 67(4): 1121-1133.
Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database. 2013.
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. cell. 116(2): 281-297.
Baud S, Guyon V, Kronenberger J, Wuillème S, Miquel M, Caboche M, . . . Rochat C (2003) Multifunctional acetyl‐CoA carboxylase 1 is essential for very long chain fatty acid elongation and embryo development in Arabidopsis. Plant J. 33(1): 75-86.
Browse J, Somerville C (1991) Glycerolipid synthesis: biochemistry and regulation. Annu. Rev. Plant Biol. 42(1): 467-506.
Chen L, Zhong H, Ren F, Guo Q-Q, Hu X-P, Li X-B (2011) A novel cold-regulated gene, COR25, of Brassica napus is involved in plant response and tolerance to cold stress. Plant Cell Rep. 30(4): 463-471.
Chen M, Thelen JJ (2013) Acyl-lipid desaturase2 is required for chilling and freezing tolerance in Arabidopsis. plant cell. 25(4): 1430-1444.
Chinnusamy V, Zhu J-K, Sunkar R (2010) Gene regulation during cold stress acclimation in plants Plant Stress Tolerance (pp. 39-55): Springer.
Chinnusamy V, Zhu J, Zhu J-K (2007) Cold stress regulation of gene expression in plants. Trends Plant Sci. 12(10): 444-451.
Dai X, Zhuang Z, Zhao PX (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 46(W1): W49-W54.
Gao J, Ajjawi I, Manoli A, Sawin A, Xu C, Froehlich JE, ... Benning C (2009) Fatty acid desaturase4 of Arabidopsis encodes a protein distinct from characterized fatty acid desaturases. Plant J. 60(5): 832-839.
Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc. Natl. Acad. Sci. 103(35): 12987-12992.
Hu H, You J, Fang Y, Zhu X, Qi Z, Xiong L (2008) Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol. Biol. 67(1-2): 169-181.
Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4(1): 44.
Iba K, Gibson S, Nishiuchi T, Fuse T, Nishimura M, Arondel V, Somerville C (1993) A gene encoding a chloroplast omega-3 fatty acid desaturase complements alterations in fatty acid desaturation and chloroplast copy number of the fad7 mutant of Arabidopsis thaliana. J. Biol. Chem. 268(32): 24099-24105.
Ishizaki-Nishizawa O, Fujii T, Azuma M, Sekiguchi K, Murata N, Ohtani T, Toguri T (1996) Low-temperature resistance of higher plants is significantly enhanced by a nonspecific cyanobacterial desaturase. Nat. Biotechnol. 14(8): 1003.
Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell. 14(6): 787-799.
Kodama H, Hamada T, Horiguchi G, Nishimura M, Iba K (1994) Genetic enhancement of cold tolerance by expression of a gene for chloroplast [omega]-3 fatty acid desaturase in transgenic tobacco. Plant Physiol. 105(2): 601-605.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6): 1547-1549.
Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Durrett TP (2013) Acyl-lipid metabolism. The arabidopsis book. 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(2): 741-753.
Long W, Hu M, Gao J, Chen S, Zhang J, Cheng L, Pu H (2018) Identification and functional analysis of two new mutant BnFAD2 alleles that confer elevated oleic acid content in rapeseed. Frontiers in genetics. 9: 399.
Mann M, Wright PR, Backofen R (2017) IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions. Nucleic Acids Res. 45(W1): W435-W439.
Matos AR, Hourton-Cabassa C, Ciçek D, Rezé N, Arrabaça JD, Zachowski A, Moreau F (2007) Alternative oxidase involvement in cold stress response of Arabidopsis thaliana fad2 and FAD3+ cell suspensions altered in membrane lipid composition. Plant Cell Physiol. 48(6): 856-865.
Megha S, Basu U, Joshi RK, Kav NN (2018) Physiological studies and genome-wide microRNA profiling of cold-stressed Brassica napus. Plant Physiol. Biochem. 132: 1-17.
Megha S, Basu U, Kav NN (2018) Regulation of low temperature stress in plants by microRNAs. Plant, Cell Environ. 41(1): 1-15.
Meyers BC, Souret FF, Lu C, Green PJ (2006) Sweating the small stuff: microRNA discovery in plants. Curr. Opin. Biotechnol. 17(2): 139-146.
Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD (2018) PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res. 47(D1): D419-D426.
Min H, Yoon S (2010) Got target?: computational methods for microRNA target prediction and their extension. Exp. Mol. Med. 42(4): 233.
Miquel M, James D, Dooner H (1993) Arabidopsis requires polyunsaturated lipids for low-temperature survival. Proc. Natl. Acad. Sci.  90(13):6028-6212.
Moreno-Pérez AJ, Venegas-Calerón M, Vaistij FE, Salas JJ, Larson TR, Garcés R, . . . Martínez-Force E (2012) Reduced expression of FatA thioesterases in Arabidopsis affects the oil content and fatty acid composition of the seeds. Planta. 235(3): 629-639.
Moreno-Risueno MA, Van Norman JM, Benfey PN (2012) Transcriptional switches direct plant organ formation and patterning Current topics in developmental biology (Vol. 98, pp. 229-257): Elsevier.
Ohlrogge JB, Jaworski JG (1997) Regulation of fatty acid synthesis. Annu. Rev. Plant Biol. 48(1): 109-136.
Pandey B, Gupta OP, Pandey DM, Sharma I, Sharma P (2013) Identification of new stress-induced microRNA and their targets in wheat using computational approach. Plant signaling & behavior. 8(5).e23932
Rehmsmeier M, Steffen P, Höchsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. Rna. 10(10): 1507-1517.
Riffo-Campos Á, Riquelme I, Brebi-Mieville P (2016) Tools for sequence-based miRNA target prediction: what to choose? Int. J. Mol. Sci. 17(12): 1987.
Sanei M, Chen X (2015) Mechanisms of microRNA turnover. Curr. Opin. Plant Biol. 27: 199-206.
Seo J-K, Wu J, Lii Y, Li Y, Jin H (2013) Contribution of small RNA pathway components in plant immunity. Mol. Plant-Microbe Interact. 26(6): 617-625.
Shaner DL (2004) Herbicide safety relative to common targets in plants and mammals. Pest Management Science: formerly Pesticide Science. 60(1): 17-24.
Shepherd T, Wynne Griffiths D (2006) The effects of stress on plant cuticular waxes. New Phytol. 171(3): 469-499.
Steponkus PL (1984) Role of the plasma membrane in freezing injury and cold acclimation. Annu. Rev. Plant Physiol. 35(1): 543-584.
Sunkar R, Zhu JK (2007) Micro RNAs and short‐interfering RNAs in plants. J. Integr. Plant Biol. 49(6): 817-826.
Szklarczyk D, Gable AL, 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 Res. 47(D1): D607-D613.
Takahashi D, Li B, Nakayama T, Kawamura Y, Uemura M (2013) Plant plasma membrane proteomics for improving cold tolerance. Front. Plant Sci. 4: 90.
Tan B-C, Joseph LM, Deng W-T, Liu L, Li Q-B, Cline K, McCarty DR (2003) Molecular characterization of the Arabidopsis 9-cis epoxycarotenoid dioxygenase gene family. Plant J. 35(1): 44-56. doi: 10.1046/j.1365-313X.2003.01786.x
Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu. Rev. Plant Biol. 50(1): 571-599.
Tovuu A, Zulfugarov IS, Wu G, Kang IS, Kim C, Moon BY, Lee C-H (2016) Rice mutants deficient in ω-3 fatty acid desaturase (FAD8) fail to acclimate to cold temperatures. Plant Physiol. Biochem. 109: 525-535.
Uemura M, Joseph RA, Steponkus PL (1995) Cold acclimation of Arabidopsis thaliana (effect on plasma membrane lipid composition and freeze-induced lesions). Plant Physiol. 109(1): 15-30.
Unver T, Namuth-Covert DM, Budak H (2009) Review of current methodological approaches for characterizing microRNAs in plants. Int. J. Plant Genomics. 2009.
Wada H, Combos Z, Murata N (1990) Enhancement of chilling tolerance of a cyanobacterium by genetic manipulation of fatty acid desaturation. Nature.  200(6289):347
Wang J, Jian H, Wang T, Wei L, Li J, Li C, Liu L (2016) Identification of microRNAs actively involved in fatty acid biosynthesis in developing Brassica napus seeds using high-throughput sequencing. Front. Plant Sci. 7: 1570.
Wang Z, Qiao Y, Zhang J, Shi W, Zhang J (2017) Genome wide identification of microRNAs involved in fatty acid and lipid metabolism of Brassica napus by small RNA and degradome sequencing. Gene. 619: 61-70.
Xin H, Xianchao N, Pan X, Wei L, Min Y, Yu K, ... Wei H (2019) Comparative transcriptome analyses revealed conserved and novel responses to cold and freezing stress in Brassica napus L. G3: Genes, Genomes, Genetics: g3. 400229.402019.
Xin Z, Browse J (2000) Cold comfort farm: the acclimation of plants to freezing temperatures. Plant, Cell Environ. 23(9): 893-902.
Xiong L, Lee H, Ishitani M, Zhu J-K (2002) Regulation of Osmotic Stress-responsive Gene Expression by theLOS6/ABA1 Locus in Arabidopsis. Journal of Biological Chemistry. 277(10): 8588-8596.
Xiong L, Schumaker KS, Zhu J-K (2002) Cell signaling during cold, drought, and salt stress. plant cell. 14(suppl 1): S165-S183.
Yang H, Zhang H, Zhu L, Zhang C, Li D (2012) Identification and characterization of microRNAs in Macaca fascicularis by EST analysis. Comparative and functional genomics. 2012.
Yu X, Wang H, Lu Y, de Ruiter M, Cariaso M, Prins M, ... He Y (2011) Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J. Exp. Bot. 63(2): 1025-1038.
Yuan Y, Liang Y, Li B, Zheng Y, Luo X, Dongdong L (2015) Cloning and function characterization of a β-Ketoacyl-acyl-ACP Synthase I from coconut (Cocos nucifera L.) endosperm. Plant Mol. Biol. Rep. 33(4): 1131-1140.
Zhao X, Wei J, He L, Zhang Y, Zhao Y, Xu L, Liu M (2019) Identification of Fatty Acid Desaturases in Maize and Their Differential Responses to Low and High Temperature. Genes. 10(6): 445.
Zhao Y-T, Wang M, Fu S-X, Yang W-C, Qi C-K, Wang X-J (2012) Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production-and development-correlated expression and new small RNA classes. Plant Physiol. 158(2): 813-823.
 
Crop Biotechnology
Volume 9, Issue 1 - Serial Number 27
December 2019
Pages 41-58

Files

Share

How to cite

Statistics