Abstract：Lysin motif (LysM) receptor kinases is an important class of receptor-like kinases found in plants and play a key role in plant defense against stress and diseases. The purpose of this study is to explore the members of LysM receptor kinases gene family in Vitis spp. and their functions. Based on the genomic data of Pinot Noir (Vitis vinefera cv. Pinot Noir) from the Eurasian species grapevine and Shanputao (Vitis amurensis) from East Asian species grapevine, VvLysM and VaLysM gene family members were identified using bioinformatic methods, and the protein physicochemical properties, secondary structure, chromosome distribution, conserved motifs, promoter cis-acting elements and other characteristics of these gene family members were compared and analyzed. The expression of VvLysMs under different tissues and abiotic stress were verified by gene chip data and qPCR. The results showed that VvLysM and VaLysM gene family each contained 12 members, and distributed in 9 chromosomes of Pinot Noir and 7 chromosomes of Shanputao, respectively, and the expansion of this family was based on tandem duplication and fragment duplication. The analysis of the physical and chemical properties of the proteins revealed that the amino acid sequence, molecular weight, isoelectric point, fat coefficient and other characteristics of the different members of the two grapevines were different. Most of LysM receptor kinase proteins had poor structural stability, low protein fat solubility, and were hydrophobic; the subcellular location indicated that this gene family was mainly distributed on the plasma membrane, and the secondary structure was dominated by α helix and random coils. According to evolutionary analysis, 24 gene members were divided into 3 subgroups. The quality and distribution characteristics of exons and introns, and the number and distribution of conservative motifs were highly similar among the different genes under the same subgroup. The quantity variation of introns arranged from 0 to 12 presented diversity. The analysis of cis-elements showed that there was a large number of light response elements, hormone response elements and stress response elements in the promoters of these genes members. The expression of VvLysMs in various tissues of grapevine showed obvious tissue expression specificity, especially the expression levels of them were higher in the late development of fruit and flower organs. The results of qPCR showed that different members of this gene family presented different expression patterns due to the types of stress after treatment with exogenous abscisic acid, salicylic acid, methyl jasmonate, low temperature and chitosan especially when VvLysM8 and VvLysM9 were treated with chitosan for 12 h, and VvLysM9 was treated with abscisic acid for 3 h, their relative expression levels were the highest and significantly higher than those of other members under all treatments. VvLysM8 and VvLysM9 could play an important role in abscisic acid signal transduction and chitin induced immune response in plants. This study may provide a reference for further research on the function of grapevine LysM receptor kinase.
褚明宇, 李婉莹, 左存武, 李文芳, 毛娟, 陈佰鸿. 葡萄LysM类受体激酶基因家族的鉴定及表达分析[J]. 农业生物技术学报, 2023, 31(2): 282-297.
CHU Ming-Yu, LI Wan-Ying, ZUO Cun-Wu, LI Wen-Fang, MAO Juan, CHEN Bai-Hong. Identification and Expression Analysis of LysM Receptor Like Kinases Gene Family in Grapevine (Vitis vinefera and Vitis amurensis). 农业生物技术学报, 2023, 31(2): 282-297.
[1] 崔力文. 2017. 葡萄管家基因识别与分析[D]. 硕士学位论文, 南京农业大学, 导师: 房经贵, pp. 20. (Cui L W. 2017. The identification and analysis of grape housekeeping gene[D]. Thesis for M.S., Nanjing University, Supervisor: Fang J G, pp. 20.) [2] 李傲. 2018. 葡萄无内含子基因的识别与分析[D]. 硕士学位论文, 南京农业大学, 导师: 房经贵, pp. 2-24. (Li A.2018. The Identification and Analysis of Grape intronless Gene[D]. Thesis for M.S., Nanjing University, Supervisor: Fang J G, pp. 2-24.) [3] 刘艳晶, 孙贵连, 周琴, 等. 2022. 森林草莓FvLysM基因家族的生物信息学分析[J]. 分子植物育种, 20(09): 2864-2875. (Liu Y J, Sun G L, Zhou Q, et al.2022. Bioformatics Analysis of FvLysm Gene Family in Fragaria vesca[J]. Molecular Plant Breeding, 20(09): 2864-2875.) [4] 孙大业,崔素娟,孙颖. 2010. 细胞信号转导[M]. 北京: 科学出版社, pp. 256. (Sun D Y, Cui S J, Sun Y. 2010. Cell Signaling Transduction[M], Sciences press, Beijing, Chian, pp. 256.) [5] 田丽梅. 2016. 番茄IMPα/β和LYK家族基因的鉴定、表达模式分析和功能研究[D]. 硕士学位论文, 浙江大学, 导师: 宋凤鸣, pp. 9-11. (Tian L M.2016. Genome-wide characterization, expression patters and functional analysis of IMPα/β and LYK gene family in tomato[D]. Thesis for M.S., Zhejiang University, Supervisor: Song F M, pp. 9-11.) [6] 张娜. 2021. 中国野生葡萄VqWRKY75调控下游靶基因抗霜霉病的功能研究[D]. 硕士学位论文, 西北农林科技大学, 导师: 徐炎, pp. 15. (Zhang N. 2021. Study on the function of regulating downstream target gene of VqWRKY75 in Chinese wild grape against downy mildew[D]. Thesis for M.S., NorthWest Agriculture and Forestry University, Supervisor: Xu Y, pp. 15.) [7] 左存武, 张卫娜, 毛娟, 等. 2017. 苹果LysM类受体激酶基因家族鉴定与表达分析[J]. 园艺学报, 44(04): 733-742. (Zuo C W, Zhang W N, Mao J, et al.2017. Genome wide identification and expression analysis of LysM receptor-like kinase in apple[J]. Acta Horticulturae Sinica, 44(04): 733-742.) [8] Adam-Blondon A F.2014. Grapevine genome update and beyond[J]. Acta Horticulturae, 1046: 311-318. [9] Bailey T L, Elkan C.1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers[R]. Proceedings/International Conference on Intelligent Systems for Molecular Biology, 2: 28-36. [10] Buendia L, Wang T, Girardin A, et al.2016. The LysM receptor-like kinase SlLYK10 regulates the arbuscular mycorrhizalsymbiosis in tomato[J]. New Phytologist, 210: 184-195. [11] Canaguier A, LePaslier M C, Duchêne E, et al.2018. Development of a new version of the grapevine reference genome as-sembly (12X.v2) based on genetic maps and paired-end sequences[DB]. Portail Data INRAE, V3. [12] Canaguier A, Grimplet J, Scalabrin S, et al.2017. A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)[J]. Genomics Data, 14: 56-62. [13] Cao Y, Liang Y, Tanaka K, et al.2014. The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1[J]. Elife, 3: e03766. [14] Chen C, Chen H, Zhang Y, et al.2020a. TBtools: An Integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 13(8): 1194-1202. [15] Chen Q, Dong C, Sun X, et al.2020b. Overexpression of an apple LysM-containing protein gene, MdCERK1-2, confers improved resistance to the pathogenic fungus, Alternaria alternata, in Nicotiana benthamiana[J]. BMC Plant Biology, 20: 146. [16] Dievart A, Gottin C, Périn C, et al.2020. Origin and diversity of plant receptor-like kinases[J]. Annual Review of Plant Biology, 71(1): 131-156. [17] Fasoli M, Dal Santo S, Zenoni S, et al.2012. The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program[J]. Plant Cell, 24(9): 3489-505. [18] Gamborg O L, Miller R A, Ojima K, 1968. Nutrient requirements of suspension cultures of soybean root cells[J]. Experimental Cell Research, 50(1): 151-158. [19] Gish L A, Clark S E, 2011. The RLK/Pelle family of kinases[J]. The Plant Journal, 66: 117-127. [20] Grimplet J, Van Hemert J, Carbonell-Bejerano P, et al.2012. Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences[J]. BMC Research Notes 5(1): 213-213. [21] Gust A A, Willmann R, Desaki Y, et al.2012. Plant LysM proteins: Modules mediating symbiosis and immunity[J]. Trends Plant Science, 17(8): 495-502. [22] Hu S P, Li J J, Dhar N, et al.2021. Lysin Motif (LysM) proteins: Interlinking manipulation of plant immunity and fungi[J]. International Journal of Molecular Sciences, 22(6): 3114. [23] Jaillon O, Aury J M, Noel B, et al.2007. French-italian public consortium for grapevine genome characterization. the grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla[J]. Nature, 449(7161): 463-467. [24] Kumar S, Stecher G, Li M, et al.2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 35(6): 1547-1549. [25] Lehti-Shiu M D, Zou C, Hanada K, et al.2009. Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes[J]. Plant Physiology, 150(1): 12-26. [26] Limpens E, Franken C, Smit P, et al.2003. LysM domain receptor kinases regulating rhizobial Nod factor-induced infection[J]. Science, 302(5645): 630-633. [27] Liang Z, Duan S, Sheng J, et al.2019. Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses[J]. Nature Communication, 10(1): 1190. [28] Liao D, Sun X, Wang N, et al.2018. Tomato LysM receptor-like kinase SlLYK12 is involved in arbuscular mycorrhizal symbiosis[J]. Frontiers in Plant Science, 9: 1004. [29] Madsen E B, Madsen L H, Radutoiu S, et al.2003. A receptor kinase gene of the LysM type is involved in legume perception of rhizobial signals[J]. Nature, 425(6958): 637-640. [30] Mistry J, Chuguransky S, Williams L, et al.2021. Pfam: The protein families database in 2021[J]. Nucleic Acids Research, 49(D1): D412-D419. [31] Miya A.2007. CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis[J]. Proceedings of the National Academy of Sciences of the USA, 104: 19613-19618. [32] Op den Camp R, Streng A, De Mita S, et al.2011. LysM-type mycorrhizal receptor recruited for Rhizobium symbiosis in nonlegume Parasponia[J]. Science, 331(6019): 909-912. [33] Sakharkar M K, Chow V, Kangueane P.2004. Distributions of exons and introns in the human genome[J]. Silico Biology, 4(4): 387. [34] Shimizu T, Nakano T, Takamizawa D, et al.2010. Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice[J]. Plant Journal, 64: 204-214. [35] Shinya T, Nakagawa T, Kaku H, et al.2015. Chitin-mediated plant-fungal interactions: Catching, hiding and handshaking[J]. Current Opinion in Plant Biology, 26: 64-71. [36] Vitulo N, Forcato C, Carpinelli E C, et al.2014. A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype[J]. BMC Plant Biololgy, 14(1): 99. [37] Wan J, Zhang X C, Neece D, et al.2008. A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis[J], Plant Cell, 20(2): 471-481. [38] Wang Y, Xin H, Fan P, et al.2021. The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine[J]. Plant Journal, 105(6): 1495-1506. [39] Yu C S, Chen Y C, Lu C H.2006. Prediction of protein subcellular localization[J]. Proteins, 64(3): 643-651. [40] Zhang L, Yuan L, Staehelin C, et al.2019. The lysin motif-containingreceptor-like kinase 1 protein of banana is required for perception of pathogenic and symbiotic signals[J]. New Phytologist, 223: 1530-1546. [41] Zhang X C, Wu X, Findley S, et al.2007. Molecular evolution of lysin motif-type receptor-like kinases in plants[J]. Plant Physiology, 144(2): 623-636. [42] Zhu Q, Zhang X L, Nadir S, et al.2017. OsEMSA1A LysM domain-containing gene involved in embryo sac development in rice[J]. Frontiers in Plant Science, 8: 1596.
