马铃薯低温响应的ScmiR390-5p及其靶基因表达与结构分析

doi:10.3864/j.issn.0578-1752.2019.13.009

Abstract

Abstract:

The study was carried out to investigate the mechanism of potato leucine-rich repeat receptor-like protein kinase (LRR-RLK) receptor protein kinase SCLRRK1 regulated by miR390 (ScmiR390-5p) in response to abiotic stress. 【Method】 By sequencing and analyzing potato miRNAs in response to low temperature conditions and predicting target genes, we found that ScmiR390-5p responded to low temperatures by regulating a potential LRR-like receptor protein kinase gene. The expression levels of ScmiR390-5p and SCLRRK1 in response to low temperature stress were verified by quantitative real-time PCR (RT-qPCR). The cleavage site of ScLRR390-5p on SCLRRK1 was determined by using RLM-5'RACE. The DNA sequence and CDS sequence of SCLRRK1 were cloned by PCR and the structure and function of SCLRRK1 were predicted by bioinformatics analysis. The expression levels of ScmiR390-5p/SCLRRK1 in various tissues of potato and under various abiotic stress were analyzed by RT-qPCR. 【Result】 The results of RT-qPCR showed that the expression of ScmiR390-5p was induced by low temperature, while the expression of SCLRRK1 was inhibited. There was a negative correlation between the expression of ScmiR390-5p and scrrk1 under low temperature stress. The result of RLM-5′RACE indicated that cleavage site of ScmiR390-5p on SCLRRK1 was ATTCCT// CCTGAGTT, and potato ScmiR390-5p/SCLRRK1 regulatory module was respond to low temperature. The cloning results indicated that the CDS of SCLRRK1 was 2 685 bp in length, encoding 894 amino acids, and the gene sequence was 3 549 bp containing 1 intron, 2 exons, 3' non-coding region and 5' non-coding region. ScmiR390-5p target site was located at SCLRRK1 CDS (960-981 bp, GGAACTATTCCTCCTGAGTTT). Bioinformatics analysis showed that the SCLRRK1 encoded a leucine-richrepeat (LRR)-like receptor protein kinase, belonging transmembrane secreted protein. RT-qPCR analysis of potato tissue expression pattern showed that the expression level of the ScmiR390-5p was highest in the leaves, followed by roots, and relatively lowers in stem (terrestrial stem, tuber and stolon). Differently, the expression level of SCLRRK1 was the lowest in leaves and the highest in stems. The results under various abiotic stresses showed that the expression of ScmiR390-5p and SCLRRK1 was negatively correlated, and ScmiR390-5p was induced by NaCl stress. Compared with the control, the expression of ScmiR390-5p was decreased and then increased slightly after treatment with ABA and 6-BA. The SCLRRK1 level increased continuously under 6-BA treatment, while the expression of SCLRRK1 increased first and then decreased under ABA treatment. The expression of ScmiR390-5p reached the peak after treatment with GA₃, PEG and IAA for 8 h. The expression of SCLRRK1 was induced by GA3, PEG and IAA, but the change trend was not correlated to ScmiR390-5p. 【Conclusion】 SCLRRK1 had the amino acid sequence and structural basis of nucleic acid to encode LRR-like receptor protein kinase, which was the target gene of ScmiR390-5p; ScmiR390-5p/SCLRRK1 regulatory module had a significant role in potato tissues; ScmiR390-5p responded to low temperature stress by inhibiting the expression of potato SCLRRK1 at the post-transcriptional level, while ScmiR390-5p/SCLRRK1 regulated module played a role in salt and 6-BA stress response. The ScmiR390-5p/SCLRRK1 regulatory module did not respond to ABA, GA₃, IAA and PEG stress, and the ScmiR390-5p and SCLRRK1 were regulated by the above signals at the transcriptional level, respectively.

Key words: potato, ScmiR390-5p, SCLRRK1, quantitative real-time PCR, RLM-5′RACE

XIE Jie,WANG Ming,DING HongYing,LI Qing,WANG WanXing,XIONG XingYao,QIN YuZhi. Expression and Structural Analysis of SC MI390-5p and Its Target Genes in Potato Response to Low Temperature[J].Scientia Agricultura Sinica, 2019, 52(13): 2295-2308.

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References 40

[1]	谢洁, 王明, 李青, 潘妃, 熊兴耀, 秦玉芝 . 植物miR390的研究进展. 生物技术通报, 2018,34(6):1-10.
	XIE J, WANG M, LI Q, PAN F, XIONG X Y, QIN Y Z . Research progress of plant miR390. Biotechnology Bulletin, 2018,34(6):1-10. (in Chinese)
[2]	马媛媛, 甘睿, 王宁宁 . 植物富含亮氨酸重复序列型类受体蛋白激酶的生物学功能. 分子植物(英文版), 2005,31(4):331-339.
	MA Y Y, GAN R, WANG N N . Biological functions of leucine-rich repeat class of receptor-like protein. Journal of Plant Physiology and Molecular Biology, 2005,31(4):331-339. (in Chinese)
[3]	魏强, 梁永宏, 李广林 . 植物miRNA的进化. 遗传, 2013,35(3):315-323. doi: 10.3724/SP.J.1005.2013.00315
	WEI Q, LIANG Y H, LI G L . Evolution of miRNA in plants. Hereditas, 2013,35(3):315-323. (in Chinese) doi: 10.3724/SP.J.1005.2013.00315
[4]	SUNKAR R, LI Y F, JAGADEESWARAN G . Functions of microRNAs in plant stress responses. Trends in Plant Science, 2012,17(4):196-203.
[5]	KHRAIWESH B, ZHU J Y, ZHU J H . Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochimica Et Biophysica Acta, 2012,1819(2):137-148. doi: 10.1016/j.bbagrm.2011.05.001
[6]	SUNKAR R . MicroRNAs with macro-effects on plant stress responses. Seminars in Cell & Developmental Biology, 2010,21(8):805-811.
[7]	XIA R, XU J, MEYERS B C . The emergence, evolution, and diversification of the miR390-TAS3-ARF pathway in land plants. Plant Cell, 2017,29(6):1232-1247.
[8]	薄维平 . 木薯耐寒相关microRNA的差异表达分析[D]. 海口: 海南大学, 2010.
	BO W P . Analysis of differential expression of cold-tolerance related microRNA in cassava[D]. Haikou: Hainan University, 2010. (in Chinese)
[9]	党春艳 . 高山离子芥低温胁迫调控的miRNAs及其靶基因的表达分析[D]. 兰州: 兰州大学, 2013.
	DANG C Y . Expression anaysis of chilling-stress regulated minRNAs and targets in Chorispora bungeana [D]. Lanzhou: Lanzhou University, 2013. (in Chinese)
[10]	孙润泽, 侯琦, 章文乐 . 甜杨低温响应microRNAs的克隆与分析. 基因组学与应用生物学, 2011,30(2):204-211.
	SUN R Z, HOU Q, ZHANG W L . Cloning and analysis of the low temperature stress-responsive microRNAs from Populus suaveolens. Genomics and Applied Biology, 2011,30(2):204-211. (in Chinese)
[11]	CHEN Q S, LI M, ZHANG Z C, TIE W W, CHEN X, JIN L F, ZHAI N, ZHENG Q X, ZHANG J F, WANG R, XU G Y, ZHANG H, LIU P P, ZHOU H N . Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco. BMC Genomics, 2017,18(1):62-77. doi: 10.1186/s12864-016-3372-0
[12]	翟立红 . 玉米冠根和雄穗中microRNA及Argonaute基因表达的研究[D]. 武汉: 华中农业大学, 2013.
	ZHAI L H . Characterization and expression and analysis of microRNA and argonaute genes in crown roots and tassel of maize[D]. Wuhan: Huazhong Agricultural University, 2013. (in Chinese)
[13]	王宝山, 邹琦 . NaCl胁迫对高粱根、叶鞘和叶片液泡膜ATP酶和焦磷酸酶活性的影响. 植物生理学报, 2000,26(3):181-188.
	WANG B S, ZOU Q . Effects of NaCl stress on the tonoplast ATPase and PPase activity in roots, sheaths and blades of sorghum seedlings. Acta Phytophysiologica Sinica, 2000,26(3):181-188. (in Chinese)
[14]	郭兆奎 . 烟草吸钾相关基因克隆与表达调控研究[D]. 哈尔滨: 哈尔滨工业大学, 2008.
	GUO Z K . The cloning and expression regulation of potassium uptake relative genes in Nicotiana tobacum[D]. Harbin: Harbin Institute of Technology, 2008. (in Chinese)
[15]	王波 . 拟南芥和NaCl生植物灰绿藜液泡膜焦磷酸酶基因与TIR1基因表达相关性分析[D]. 乌鲁木齐: 新疆大学, 2007.
	WANG B . Analysis on gene expression correlation between vacuolar H+-pyrophosphatase and TRANSPORT INHIBITOR RESPONSE1 (TIR1) in Arabidopsis thaliana and halophyte Chenopodium glaucum[D]. Urumqi: Xinjiang University, 2007. (in Chinese)
[16]	佐拉 . 野生大麦与栽培大麦耐NaCl性的生理及遗传差异研究[D]. 杭州: 浙江大学, 2014.
	ZUO L . Physiological and genetic difference in salt stress tolerance in wild and cultivated barleys[D]. Hangzhou: Zhejiang University, 2014. (in Chinese)
[17]	吴冰月, 宋普文, 陈华涛 . 2个大豆RNA依赖的RNA聚合酶基因和的克隆与分析. 南京农业大学学报, 2014,37(3):27-34.
	WU B Y, SONG P W, CHEN H T . Cloning and expression pattern analysis of GmRDR6a and GmRDR6b in soybean. Journal of Nanjing Agricultural University, 2014,37(3):27-34. (in Chinese)
[18]	李贺, 毛健鑫, 戚华彩 . 草莓miR390基因及其启动子的鉴定与表达分析. 果树学报, 2014,31(3):362-336.
	LI H, MAO J X, QI H C . Identification and expression analysis of miR390 gene and its promoter from strawberry. Journal of Fruit Science, 2014,31(3):362-336. (in Chinese)
[19]	YOON E K, YANG J H, LIM J, KIM S H, KIM S K, LEE W S . Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Research, 2010,38:1382-1391.
[20]	DING Y F, YE Y Y, JIANG Z H, WANG Y, ZHU C . MicroRNA390 is involved in cadmium tolerance and accumulation in rice. Frontiers in Plant Science, 2016,7(127):235-244.
[21]	刘凉琴, 宋爱萍, 张永侠 . 马蔺根系响应Cd胁迫的miRNA高通量测序分析. 植物资源与环境学报, 2016,25(3):1-11.
	LIU L Q, SONG A P, ZHANG Y X . High throughput sequencing analysis on miRNA in root of Iris lactea var. chinensis response to Cd stress. Journal of Plant Resources and Environment, 2016,25(3):1-11. (in Chinese)
[22]	DMITRIEV A A, KUDRYAVTSEVA A V, BOLSHEVA N L, ZYABLITSIN A V, ROZHMINA T A, KISHLYAN N V, KRASNOV G S, SPERANSKAYA A S, KRINITSINA A A, SADRITDINOVA A F, SNEZHKINA A V, FEDOROVA M S, YURKEVICH O Y, MURAVENKO O V, BELENIKIN M S , MELNIKOVA N V. miR319, miR390, and miR393 are involved in aluminum response in flax (Linum usitatissimum L.). BioMed Research International, 2017,2017:4975146.
[23]	LEE S C, KIM J Y, KIM S H, KIM S J, LEE K, HAN S K, CHOI H S, JEONG D H, AN G, KIM S R . Trapping and characterization of cold-responsive genes from T-DNA tagging lines in rice. Plant Science, 2004,166(1):69-79. doi: 10.1016/j.plantsci.2003.08.008
[24]	JUNG E H, JUNG H W, LEE S C, HAN S W, HEU S, HWANG B K . Identification of a novel pathogen-induced gene encoding a leucine- rich repeat protein expressed in phloem cells of Capsicum annuum. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression, 2004,1676(3):211-222.
[25]	SUNKAR R, ZHU J K . Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 2004,16(8):2001-2019.
[26]	KHRAIWESH B, ZHU J Y, ZHU J H . Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. BBA-Gene Regulatory Mechanisms, 2012,1819(2):137-148.
[27]	MENG Y J, SHAO C G, MA X X, WANG H Z, CHEN M . Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis. PLoS ONE, 2012,7(11):e50870.
[28]	DING Y F, TAO Y L, ZHU C . Emerging roles of microRNAs in the mediation of drought stress response in plants. Journal of Experimental Botany, 2013,64(11):3077-3086. doi: 10.1093/jxb/ert164
[29]	GARCIA D, COLLIER S A, BYRNE M E, MARTIENSSEN R A . Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Current Biology, 2006,16(9):933-938.
[30]	CHO S H, CORUH C, AXTELL M J . miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens. The Plant Cell, 2012,24(12):4837-4849.
[31]	MARIN E, JOUANNET V, HERZ A, LOKERSE A S, WEIJERS D, VAUCHERET H, NUSSAUME L, CRESPI M D, MAIZEL A . miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. The Plant Cell, 2010,22(4):1104-1117.
[32]	HANKS S K, QUINN A M, HUNTER T . The protein kinase family: Conserved features and deduced phylogeny of the catalytic domains. Science, 1988,241(4861):42-52. doi: 10.1126/science.3291115
[33]	牛吉山 . 植物和小麦蛋白激酶的研究现状. 西北植物学报, 2003,23(1):143-150.
	NIU J S . Studies on plant and wheat protein kinases. Acta Botanica Boreali-Occidentalia Sinica, 2003,23(1):143-150.
[34]	ULLRICH A, SCHLESSINGER J . Signal transduction by receptors with tyrosine kinase activity. Cell, 1990,61(2):203-212. doi: 10.1016/0092-8674(90)90801-K
[35]	STONE J M, WALKER J C . Plant protein kinase families and signal transduction. Plant Physiology, 1995,108(2):451-457. doi: 10.1104/pp.108.2.451
[36]	MIZUNO S, OSAKABE Y, MARUYAMA K, ITO T, OSAKABE K, SATO T, SHINOZAKI K, YAMAGUCHI-SHINOZAKI K . Receptor- like protein kinase 2 (RPK 2) is a novel factor controlling anther development in Arabidopsis thaliana. Plant Journal, 2010,50(5):751-766.
[37]	XU Z S, XIONG T F, NI Z Y, CHEN X P, CHEN M, LI L C, GAO D Y, YU X D, LIU P, MA Y Z . Isolation and identification of two genes encoding leucine-rich repeat (LRR) proteins differentially responsive to pathogen attack and salt stress in tobacco. Plant Science, 2009,176(1):38-45. doi: 10.1016/j.plantsci.2008.09.004
[38]	HAN R, JIAN C, LV J Y, YAN Y, CHI Q, LI Z J, WANG Q, ZHANG J, LIU X L, ZHAO H X . Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics, 2014,15:289.
[39]	余刚, 李敬涛, 孙新华, 刘金亮, 潘洪玉 . 四翅滨藜LRR类受体蛋白激酶基因在酵母中的表达及抗逆分析. 吉林大学学报(理学版), 2012,50(6):1257-1263.
	YU G, LI J T, SUN X H, LIU J L, PAN H Y . Expression and functional characterization of an AcLRR gene from Atriplex canescens in yeast. Journal of Jilin University (Science Edition), 2012,50(6):1257-1263. (in Chinese)
[40]	HONG S W, JON J H, KWAK J M, NAM H G . Identification of a receptor-like protein kinase gene rapidly induced by abscisic acid, dehydration, high salt, and cold treatments in Arabidopsis thaliana. Plant Physiology, 1997,113(4):1203-1212.

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引物 Primer	序列（5′→3′） Sequence (5′→3′)	用途 Use
SCLRRK1 F	ATGACACTTTTGAGGTTTCTGTTAA	SCLRRK1 CDS片段克隆
SCLRRK1 R	TTAGCTTTCCGTGATTTCTTGA	Clone of SCLRRK1 CDS fragments
SCLRRK1 F1	GTTTTCTTCATTTCTTGATATGGC	SCLRRK1DNA全长扩增
SCLRRK1 R1	GTTGAATAGTAGCATTCCCTTAATC	Amplification of Full-length DNA of SCLRRK1
SCLRRK1 F2	GCTTGAGATCCTAACCACCCG	SCLRRK1实时定量PCR
SCLRRK1 R2	TCTTGCAGCATTTCTACCACCTT	Quantitative real-time PCR of SCLRRK1
SCLRRK1 outer F3	GCTGATGGCGATGAATGAATGAACACTG	RLM-5′RACE 分析作用位点
SCLRRK1 outer R3	CAACAAAGACGTTTCCCGCCAGT	Rapid amplification of cDNA 5′ ends
SCLRRK1 inner F4	CGCGGATCCGAACACTGCGTTTGCTGGCTTTGATG	RLM-5′RACE 分析作用位点
SCLRRK1 inner R4	CCTGAGGCAATTTTCCGTGGAGA	Rapid amplification of cDNA 5′ ends
ScmiR390-5p	CCAGCGTGAAGCUCAGGAGGG	ScmiR390-5p实时荧光定量PCR
ScmiR390-5p	CCAGCGTGCGCUAUCCAUCUU	Quantitative real-time PCR of ScmiR390-5p

基因编号 ID	TLX2/CLX2	TLH1/CLH1	基因编号 ID	基因名 Gene name	TLX2/CLX2	TLH1/CLH1
基因编号 ID	上调_下调 Up_down	上调_下调 Up_down	基因编号 ID	基因名 Gene name	上调_下调 Up_down	上调_下调 Up_down
ScmiR390-5p	上调 Up	上调 Up	PGSC0003DMT 400070158 SCLRRK1	Leucine-rich repeat receptor kinase	下调 Down	下调 Down
	上调 Up	上调 Up	PGSC0003DMT 400010618	Receptor protein kinase CLAVATA1	下调 Down	下调 Down
	上调 Up	上调 Up	PGSC0003DMT 400034044	Unknown	下调 Down	下调 Down
	上调 Up	上调 Up	PGSC0003DMT 400009701	Endo-1,3-1,4-beta-d-glucanase	上调 Up	上调 Up

Expression and Structural Analysis of SC MI390-5p and Its Target Genes in Potato Response to Low Temperature

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