蓖麻LEA基因家族的鉴定和铝胁迫响应分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-1255

摘要/Abstract

摘要：

目的从蓖麻全基因组范围内鉴定RcLEA基因家族成员，分析其基因特征和潜在功能，为揭示LEA在调控蓖麻铝胁迫耐受性中的作用奠定基础。方法利用生物信息学方法对蓖麻LEA家族基因进行鉴定，并对其理化性质、系统进化关系、基因结构、保守基序、启动子顺式作用元件，以及该家族部分成员在铝胁迫处理后的表达情况进行分析。结果从蓖麻基因组中共鉴定到52个LEA家族基因成员，根据系统发育分析，其可分为RcLEA_1、RcLEA_2、RcLEA_3、RcLEA_4、RcLEA_5、RcLEA_6、Rc_DHN和Rc_SMP 8个亚族，分布于10条染色体上；家族成员氨基酸数量在91‒406 aa之间；等电点介于4.54‒10.29之间；分子量在9 951.42‒44 515.78 Da之间；大多数LEA蛋白为亲水性蛋白；基序分析显示不同亚家族之间的motif有很大差异，但在同一亚类中是相似的。基因结构分析显示，多数基因有1个或1个以上的内含子；52个基因启动子区域均存在1种或多种与植物激素和逆境响应相关的顺式作用元件；共线性分析显示，鉴定到8对复制基因。另外，实时荧光定量PCR结果显示，RcLEA基因在铝胁迫处理下，与对照相比基因表达量发生变化，推测该家族基因参与铝胁迫应答。结论从蓖麻基因组中共鉴定出52个RcLEA基因，分为8个亚族。对8个亚族部分RcLEA基因进行铝胁迫表达分析，发现大部分基因表达量变化显著，表明这些基因在蓖麻响应铝胁迫中发挥重要作用。

关键词: 蓖麻, LEA基因家族, 生物信息学, 全基因组鉴定, 系统进化, 铝胁迫处理, 表达分析, 铝胁迫应答基因

Abstract:

Objective To identify members of the RcLEA gene family in the Ricinus communis genome and analyze their gene characteristics, potential functions, which lays a foundation for exploring the role of LEA in regulating tolerance to aluminum stress. Method Bioinformatics was used to identify the LEA gene family of R. communis, then their physicochemical properties, phylogenetic relationships, gene structure, conserved motifs, promoter cis-acting elements of its proteins were analyzed, and finally the expressions of some RcLEA genes under aluminum stress was analyzed. Result A total of 52 LEA family gene members were identified from the R. communis genome. By phylogenetic analysis, they were classified into eight subgroups: RcLEA_1, RcLEA_2, RcLEA_3, RcLEA_4, RcLEA_5, RcLEA_6, Rc_DHN, and Rc_SMP, distributed across ten chromosomes. The number of amino acids of family members ranged from 91 to 406, with isoelectric points between 4.54 and 10.29, and molecular weights ranging from 9 951.42 to 44 515.78 Da. Most LEA proteins were hydrophilic. Motif analysis revealed significant variations among different subfamilies, while maintaining similarity within the same subclass. Gene structure analysis indicated that most genes contained one or more introns. Promoter regions of all 52 genes contained one or more cis-acting elements related to plant hormones and stress responses. Collinearity analysis identified eight pairs of duplicated genes. Additionally, real-time quantitative PCR results demonstrated that the expressions of the RcLEA genes changed under aluminum stress treatment compared to the control, suggesting their involvement in the responses to aluminum stress. Conclusion A total of 52 RcLEA genes are identified from the R. communis genome, which are classified into eight subgroups. Expression analysis of selected RcLEA genes from these eight subgroups under aluminum stress reveals significant alterations in the expressions of most genes, indicating their potential crucial roles in R. communis responding to aluminum stress.

Key words: Ricinus communis, LEA gene family, bioinformatics, whole genome identification, system evolution, Al (aluminum) stress treatment, expression analysis, response gene to Al stress

李凯月, 邓晓霞, 殷缘, 杜亚彤, 徐元静, 王竞红, 于耸, 蔺吉祥. 蓖麻LEA基因家族的鉴定和铝胁迫响应分析[J]. 生物技术通报, 2025, 41(7): 128-138.

LI Kai-yue, DENG Xiao-xia, YIN Yuan, DU Ya-tong, XU Yuan-jing, WANG Jing-hong, YU Song, LIN Ji-xiang. Identification of LEA Gene Family and Analysis on Its Response to Aluminum Stress in Ricinus communis L.[J]. Biotechnology Bulletin, 2025, 41(7): 128-138.

图/表 7

表1 实时荧光定量PCR引物及碱基序列

Table 1 Real-time fluorescent quantitative PCR primers and base sequences

基因 Gene	上游引物 Forward primer （5′‒3′）	下游引物 Reverse primer （5′‒3′）
RcLEA1 RcLEA16	AAGGAGCGTAGGAAGGCAAGAG ACCATGCGATTGAATGCCACTA	GTGGTGGTGTCTCGACTTCTGA TGTGTAGCTGTCCACCGTCAA
RcLEA24	CCTTCCATGTCGGCACAGATG	CCAAACCAACAACTGTCCCTCT
RcLEA36	TGCGTCCTGTAAACCCTAATGC	ATTACCACCACTACCAGCAGCA
RcLEA38	ATGGCTCGCTCTCACTCCTAC	AGTCGCCGAATAGCCTCTCAG
RcLEA40	TGGGTCTGTGCTGAAGAAAGTTG	TCTCATTTACAACATCGTGTGG
RcLEA41 RcLEA43	GGTGGACGTTGCATATGCAGATC TACGATAGAGAGAAAGGAGGAT	TCCGCCCTTCAGCAAGGTGTTC ATAGTAGAAACATCAGCCTCCC
RcLEA45	TGGTGGGAGAAGGAAGAAAGGA	ATGACCGTGTTGTTCTGCTGAA
RcLEA50	GGTTGGTGCGGAGGTTGTTG	CCAGCAGCAGAGTAAGCAGTTG
ACTIN	TCCCTCAGTACGTTCCAGCA	CACCTCCATACTCCTCCCT

图1 蓖麻与拟南芥LEA家族系统进化树

Fig. 1 Phylogenetic tree of LEA familyin R. communis and Arabidopsis

图2 蓖麻RcLEA基因结构（A）和蛋白保守基序（B）分析

Fig. 2 Analysis of RcLEA genes structure (A) and protein conservative motifs (B) in R. communis

图3 蓖麻LEA基因启动子顺式作用元件分析

Fig. 3 Analysis of cis-acting elements of R. communis LEA gene promoter

图4 蓖麻RcLEA基因染色体定位

Fig. 4 Chromosome localization of RcLEA genes in R. communis

图5 蓖麻种内RcLEA基因共线性分析（A）和蓖麻与拟南芥LEA基因同源性分析（B）

Fig. 5 Synteny analysis of RcLEA genes within Ricinus species (A) and homology analysis of LEA genes between R. communis and Arabidopsis (B)

图6 蓖麻LEA基因在铝胁迫处理下的表达量分析不同小写字母表示差异显著（P<0.05）

Fig. 6 Expression analysis of R. communis LEA genes under aluminum stressDifferent lowercase letters indicate significant differences (P<0.05)

参考文献 50

[1]	Salazar-Chavarría V, Sánchez-Nieto S, Cruz-Ortega R. Fagopyrum esculentum at early stages copes with aluminum toxicity by increasing ABA levels and antioxidant system [J]. Plant Physiol Biochem, 2020, 152: 170-176.
[2]	Chandra J, Keshavkant S. Mechanisms underlying the phytotoxicity and genotoxicity of aluminum and their alleviation strategies: a review [J]. Chemosphere, 2021, 278: 130384.
[3]	Wang Y, Yao ZS, Zhan Y, et al. Potential benefits of liming to acid soils on climate change mitigation and food security [J]. Glob Chang Biol, 2021, 27(12): 2807-2821.
[4]	冯晶. 水稻耐铝候选基因生物学功能分析 [D]. 沈阳: 沈阳农业大学, 2023.
	Feng J. Biological function analysis of aluminum-tolerant candidate gene in rice [D]. Shenyang: Shenyang Agricultural University, 2023.
[5]	黄丽媛, 胡光伟, 王琼, 等. 铝胁迫下钙对油茶营养元素吸收积累的影响 [J]. 湖北农业科学, 2022, 61(22): 19-24.
	Huang LY, Hu GW, Wang Q, et al. Effect of calcium on nutrient uptake and accumulation in Camellia oleifera under aluminum stress [J]. Hubei Agric Sci, 2022, 61(22): 19-24.
[6]	周小华, 李昆志, 赵峥, 等. 外源抗坏血酸对水稻抗铝生理指标的影响 [J]. 热带作物学报, 2021, 42(3): 769-776.
	Zhou XH, Li KZ, Zhao Z, et al. Effects of exogenous ascorbic acid on physiological indexes in rice under aluminum stress [J]. Chin J Trop Crops, 2021, 42(3): 769-776.
[7]	刘爱慧. BnaALMT7.2在甘蓝型油菜根系响应铝毒害的作用机制研究 [D]. 重庆: 西南大学, 2021.
	Liu AH. Study on the mechanism of BnaALMT7.2 in the root system of Brassica napus in response to aluminum toxicity [D]. Chongqing: Southwest University, 2021.
[8]	Hundertmark M, Hincha DK. LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana [J]. BMC Genomics, 2008, 9: 118.
[9]	Xiao BZ, Huang YM, Tang N, et al. Over-expression of a LEA gene in rice improves drought resistance under the field conditions [J]. Theor Appl Genet, 2007, 115(1): 35-46.
[10]	Zan T, Li LQ, Li JT, et al. Genome-wide identification and characterization of late embryogenesis abundant protein-encoding gene family in wheat: Evolution and expression profiles during development and stress [J]. Gene, 2020, 736: 144422.
[11]	Liu Y, Wang L, Xing X, et al. ZmLEA3, a multifunctional group 3 LEA protein from maize (Zea mays L.), is involved in biotic and abiotic stresses [J]. Plant Cell Physiol, 2013, 54(6): 944-959.
[12]	Hand SC, Menze MA, Toner M, et al. LEA proteins during water stress: not just for plants anymore [J]. Annu Rev Physiol, 2011, 73: 115-134.
[13]	Stacy RA, Aalen RB. Identification of sequence homology between the internal hydrophilic repeated motifs of group 1 late-embryogenesis-abundant proteins in plants and hydrophilic repeats of the general stress protein GsiB of Bacillus subtilis [J]. Planta, 1998, 206(3): 476-478.
[14]	Close TJ, Lammers PJ. An osmotic stress protein of cyanobacteria is immunologically related to plant dehydrins [J]. Plant Physiol, 1993, 101(3): 773-779.
[15]	Abba' S, Ghignone S, Bonfante P. A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins [J]. BMC Genomics, 2006, 7: 39.
[16]	Iii LD. A repeating 11-mer amino acid motif and plant desiccation [J]. Plant J, 1993, 3(3): 363-369.
[17]	Punta M, Coggill PC, Eberhardt RY, et al. The pfam protein families database [J]. Nucleic Acids Res, 2012, 40(database issue): D290-D301.
[18]	杨洪强, 贾文锁, 张大鹏. 植物水分胁迫信号识别与转导 [J]. 植物生理学通讯, 2001, 37(2): 149-154.
	Yang HQ, Jia WS, Zhang DP. Plant signal perception and transduction response to water stress [J]. Plant Physiol Commun, 2001, 37(2): 149-154.
[19]	Shinozaki K, Yamaguchi-Shinozaki K. Gene expression and signal transduction in water-stress response [J]. Plant Physiol, 1997, 115(2): 327-334.
[20]	李佳琪. 沙地云杉LEA基因家族鉴定及PmLEA25基因抗逆功能分析 [D]. 呼和浩特: 内蒙古农业大学, 2022.
	Li JQ. Identification of LEA gene family of Picea mongolica and analysis of stress resistance function of PmLEA25 gene [D]. Hohhot: Inner Mongolia Agricultural University, 2022.
[21]	刘星辰. 紫花苜蓿MsLEA2基因的克隆及其功能研究 [D]. 上海: 上海交通大学, 2019.
	Liu XC. Cloning and functional analysis of MsLEA2 gene in Alfalfa (Medicago sativa Linn) [D]. Shanghai: Shanghai Jiao Tong University, 2019.
[22]	刘洋. 玉米LEA蛋白基因ZmDHN13,ZmLEA3和ZmLEA5C的分离与功能分析[D]. 泰安: 山东农业大学, 2014.
	Liu Y. Isolation and functional analysis of LEA protein genes, ZmDHN13, ZmLEA3 and ZmLEA5C in Zea mays [D]. Tai'an: Shandong Agricultural University, 2014.
[23]	黄若兰. 花生AhLecRK9和AhLEAs在铝胁迫下的功能研究 [D]. 南宁: 广西大学, 2022.
	Huang RL. Functional analysis of AhLecRK9 and AhLEAs in peanut under aluminum stress [D]. Nanning: Guangxi University, 2022.
[24]	Yu AM, Li F, Liu AZ. Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean [J]. BMC Plant Biol, 2020, 20(1): 48.
[25]	Scarpa A, Guerci A. Various uses of the castor oil plant (Ricinus communis L.). A review [J]. J Ethnopharmacol, 1982, 5(2): 117-137.
[26]	Thanh NC, Narayanan M, Saravanan M, et al. Bio/phyremediation potential of Leptospirillum ferrooxidans and Ricinus communis on metal contaminated mine sludge [J]. Chemosphere, 2023, 339: 139739.
[27]	张涛, 吴心悦, 闫靖芸, 等. 蓖麻SAP基因家族的鉴定及生物信息学分析 [J]. 黑龙江农业科学, 2025(3): 12-21.
	Zhang T, Wu XY, Yan JY, et al. Identification and bioinformatics analysis of SAP gene family in castor [J]. Heilongjiang Agric Sci, 2025(3): 12-21.
[28]	王冬艳, 张春玲, 冯研, 等. 蓖麻bZIP基因家族的全基因组鉴定、生物信息学及表达分析 [J]. 安徽农学通报, 2025, 31(2): 27-35.
	Wang DY, Zhang CL, Feng Y, et al. Genome-wide identification, bioinformatics and expression analysis of bZIP gene family of Ricinus communis [J]. Anhui Agric Sci Bull, 2025, 31(2): 27-35.
[29]	张童劼, 孙一, 杨跃超, 等. 蓖麻CNGC基因家族的鉴定与系统进化分析 [J]. 内蒙古民族大学学报: 自然科学版, 2024, 39(6): 70-75.
	Zhang TJ, Sun Y, Yang YC, et al. Identification and phylogenetic analysis of Ricinus communis L. CNGC gene family [J]. J Inn Mong Minzu Univ Nat Sci Ed, 2024, 39(6): 70-75.
[30]	李艳肖, 向殿军, 满丽莉, 等. 蓖麻NAC基因家族鉴定及表达分析 [J]. 农业生物技术学报, 2023, 31(12): 2519-2534.
	Li YX, Xiang DJ, Man LL, et al. Identification and expression analysis of NAC gene family in castor(Ricinus communis) [J]. J Agric Biotechnol, 2023, 31(12): 2519-2534.
[31]	邹智, 黄启星, 安锋. 蓖麻LEA基因家族的全基因组鉴定、分类及其进化分析 [J]. 中国油料作物学报, 2013, 35(6): 637-643.
	Zou Z, Huang QX, An F. Genome-wide identification, classification and phylogenetic analysis of LEA gene family in castor bean (Ricinus communis L.) [J]. Chin J Oil Crop Sci, 2013, 35(6): 637-643.
[32]	Lu JJ, Pan C, Fan W, et al. A chromosome-level genome assembly of wild castor provides new insights into its adaptive evolution in tropical desert [J]. Genomics Proteomics Bioinformatics, 2022, 20(1): 42-59.
[33]	Chen CJ, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data [J]. Mol Plant, 2020, 13(8): 1194-1202.
[34]	刘浩. 小麦LEA基因家族的鉴定及脱水蛋白WZY2响应干旱胁迫的调节机制 [D]. 杨凌: 西北农林科技大学, 2021.
	Liu H. Genome-wide identification of late embryogenesis abundant (LEA) gene family and regulatory mechanism of dehydrin WZY2 in response to drought stress in wheat [D]. Yangling: Northwest A & F University, 2021.
[35]	Candat A, Paszkiewicz G, Neveu M, et al. The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress [J]. Plant Cell, 2014, 26(7): 3148-3166.
[36]	李震. 胡麻LEA基因家族的鉴定及其在种子发育过程中的遗传效应 [D]. 北京: 中国农业科学院, 2021.
	Li Z. Identification and genetic effect of LEA genes during seed development in linseed flax [D]. Beijing: Chinese Academy of Agricultural Sciences, 2021.
[37]	王琪. 人参LEA基因家族鉴定分析与PgLEA2-50应答非生物胁迫研究 [D]. 长春: 吉林农业大学, 2024.
	Wang Q. Identification and analysis of LEA gene family in Panax ginseng and the role of PgLEA2-50 in abiotic stress [D]. Changchun: Jilin Agricultural University, 2024.
[38]	陈凯, 佟晓楠, 张晓媛, 等. 枳LEA基因家族鉴定及其对非生物胁迫的响应 [J]. 西北植物学报, 2023, 43(6): 918-928.
	Chen K, Tong XN, Zhang XY, et al. Genome-wide identification and abiotic stress responses of LEA gene family in Poncirus trifoliata [J]. Acta Bot Boreali Occidentalia Sin, 2023, 43(6): 918-928.
[39]	于晓云. 月季LEA基因家族鉴定与弯刺蔷薇低温响应的脱水素基因发掘 [D]. 福州: 福建农林大学, 2022.
	Yu XY. Genome-wide identification of LEA gene family in Rosa chinensis and the mining of cold-response dehydrin genes in R . beggeriana [D]. Fuzhou: Fujian Agriculture and Forestry University, 2022.
[40]	杨剑. 谷子LEA_2基因家族鉴定及SiLEA14参与谷子逆境胁迫响应的功能研究 [D]. 太原: 山西大学, 2023.
	Yang J. Identification of SiLEA_2 gene family and functional analysis of SiLEA14 in Setaria italica stress response [D]. Taiyuan: Shanxi University, 2023.
[41]	贾金山. 顽拗性三七种子LEA基因家族的鉴定与表达分析 [D]. 昆明: 云南农业大学, 2023.
	Jia JS. Identification and expression analysis of the LEA gene family in recalcitrant Panax notoginseng seeds [D]. Kunming: Yunnan Agricultural University, 2023.
[42]	唐晓飞, 刘鑫磊, 薛永国, 等. 大豆LEA-2的家族基因鉴定与表达特征分析 [J/OL]. 分子植物育种, 2023. .
	Tang XF, Liu XL, Xue YG, et al. Genome-wide identification and expression analysis of LEA-2 gene family in soybean [J/OL]. Mol Plant Breed, 2023. .
[43]	付娆, 李佳佳, 单燕, 等. 栽培种花生LEA蛋白基因家族的鉴定及其低温胁迫下表达分析 [J]. 花生学报, 2022, 51(3): 1-12.
	Fu R, Li JJ, Shan Y, et al. Genome-wide identification and expression analysis of the late embryogenesis abundant (LEA) protein gene family in cultivated peanut (Arachis hypogaea L.) on its response to cold stress [J]. J Peanut Sci, 2022, 51(3): 1-12.
[44]	周璇. 垫状卷柏LEA1基因的结构与功能分析 [D]. 昆明: 西南林业大学, 2022.
	Zhou X. Structural and functional analysis of the LEA1 gene in Selaginella pulvinata [D]. Kunming: Southwest Forestry University, 2022.
[45]	Jeffares DC, Penkett CJ, Bähler J. Rapidly regulated genes are intron poor [J]. Trends Genet, 2008, 24(8): 375-378.
[46]	Liang Y, Xiong ZY, Zheng JX, et al. Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus [J]. Sci Rep, 2016, 6: 24265.
[47]	Wu CL, Hu W, Yan Y, et al. The late embryogenesis abundant protein family in cassava (Manihot esculenta crantz): genome-wide characterization and expression during abiotic stress [J]. Molecules, 2018, 23(5): 1196.
[48]	耿伟博. 烟草胚胎发育晚期丰富蛋白(LEA蛋白)基因家族对非生物胁迫反应的鉴定与分析 [D]. 泰安: 山东农业大学, 2022.
	Geng WB. Genome-wide identification and analysis of the tobacco late embryogenesis abundant proteins (LEA proteins) gene family in response to abiotic stresses [D]. Tai'an: Shandong Agricultural University, 2022.
[49]	Sachs M. Alteration of gene expression during environmental stress in plants [J]. Annu Rev Plant Physiol Plant Mol Biol, 37: 363-376.
[50]	Mitchell PJ, Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins [J]. Science, 1989, 245(4916): 371-378.