Identification and Pathogenic Response of Tomato WRKY Transcription Factors

SHUI Deju; SUN Ji; XIONG Zili; XU Huanwen; ZHANG Shengmei; SHI Jianlei

doi:10.19303/j.issn.1008-0384.2023.03.004

Volume 38 Issue 3

Mar. 2023

Turn off MathJax

Article Contents

Abstract

References

Fujian Journal of Agricultural Sciences > 2023 > 38(3): 281-293. > DOI: 10.19303/j.issn.1008-0384.2023.03.004

SHUI D J, SUN J, XIONG Z L, et al. Identification and Pathogenic Response of Tomato WRKY Transcription Factors [J]. Fujian Journal of Agricultural Sciences，2023，38（3）：281−293. DOI: 10.19303/j.issn.1008-0384.2023.03.004

Citation:

PDF (6800 KB)

Identification and Pathogenic Response of Tomato WRKY Transcription Factors

Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang　325006, China

More Information

Received Date: October 24, 2022
Revised Date: January 29, 2023
Available Online: March 27, 2023

Graphical Abstract

Abstract

Abstract

Objective Characteristics and biotic stress response of WRKY transcription factors (TFs) in tomato plants were investigated.
Method The latest available bioinformatics and genomics methods were employed to identify the tomato WRKY TFs. RNA-seq of disease-resistant and susceptible tomato inbred lines before and after artificial Ralstonia solanacearum infection were obtained to identify the TFs associated with the pathogenic resistance of the plants.
Result Eighty-five tomato WRKY TFs were identified and divided into I, IIa+b, IIc, IId+e, and III categories. The IIe group had the highest number of the TFs. The conserved motif of 9 TFs had one single amino acid variation, and WRKYGKK was the dominant mutant. The TFs, especially those in the IIe group, were mainly found on chromosome 5, at the ends, and in clusters. In them, 45.88% showed collinearity and 58.82% (mainly in I and IIc groups) formed 73 pairs of orthologs with those in Arabidopsis and chili pepper at a Ka/Ks ratio below 1. Sixteen of them, mainly belonging to IIa+b and IIc, responded significantly to the biotic stress with expressions largely in the roots. There were 12 differentially expressed WRKY TFs identified mainly in III and IIb. Of which, the interaction between Solyc03g095770.3 (III) and Solyc09g014990.4 (I) played a significant role in the response of the tomato plant to bacterial wilt.
Conclusion The WRKY TFs were identified in tomato plants. Twelve genes responded to the bacterial wilt were isolated.
- Tomato,
- WRKY transcription factor,
- genetic characteristics,
- biotic stress,
- transcriptional expression

FullText(HTML)

References (46)

References

[1]	刘强, 张贵友, 陈受宜. 植物转录因子的结构与调控作用 [J]. 科学通报, 2000, 45(14):1465−1474. DOI: 10.3321/j.issn:0023-074X.2000.14.002 LIU Q, ZHANG G Y, CHEN S Y. Structure and regulation of plant transcription factors [J]. Chinese Science Bulletin, 2000, 45(14): 1465−1474.(in Chinese) DOI: 10.3321/j.issn:0023-074X.2000.14.002
[2]	RUSHTON P J, SOMSSICH I E, RINGLER P, et al. WRKY transcription factors [J]. Trends in Plant Science, 2010, 15(5): 247−258. DOI: 10.1016/j.tplants.2010.02.006
[3]	EULGEM T, RUSHTON P J, ROBATZEK S, et al. The WRKY superfamily of plant transcription factors [J]. Trends in Plant Science, 2000, 5(5): 199−206. DOI: 10.1016/S1360-1385(00)01600-9
[4]	AGARWAL P, REDDY M P, CHIKARA J. WRKY: Its structure, evolutionary relationship, DNA-binding selectivity, role in stress tolerance and development of plants [J]. Molecular Biology Reports, 2011, 38(6): 3883−3896. DOI: 10.1007/s11033-010-0504-5
[5]	赵楠楠, 刘立峰. 植物WRKY转录因子及其生物学功能 [J]. 分子植物育种, 2019, 17(21):7040−7046. DOI: 10.13271/j.mpb.017.007040 ZHAO N N, LIU L F. WRKY transcription factors and their biological functions in plants [J]. Molecular Plant Breeding, 2019, 17(21): 7040−7046.(in Chinese) DOI: 10.13271/j.mpb.017.007040
[6]	XIE Z, ZHANG Z L, ZOU X L, et al. Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells [J]. Plant Physiology, 2005, 137(1): 176−189. DOI: 10.1104/pp.104.054312
[7]	BAKSHI M, OELMÜLLER R. WRKY transcription factors: Jack of many trades in plants [J]. Plant Signaling & Behavior, 2014, 9(2): e27700.
[8]	WU K L, GUO Z J, WANG H H, et al. The WRKY family of transcription factors in rice and Arabidopsis and their origins [J]. DNA Research, 2005, 12(1): 9−26. DOI: 10.1093/dnares/12.1.9
[9]	ZHANG Y J, WANG L J. The WRKY transcription factor superfamily: Its origin in eukaryotes and expansion in plants [J]. BMC Evolutionary Biology, 2005, 5(1): 1. DOI: 10.1186/1471-2148-5-1
[10]	CHEN L G, SONG Y, LI S J, et al. The role of WRKY transcription factors in plant abiotic stresses [J]. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2012, 1819(2): 120−128. DOI: 10.1016/j.bbagrm.2011.09.002
[11]	ROSS C A, LIU Y, SHEN Q J. The WRKY gene family in rice (Oryza sativa) [J]. Journal of Integrative Plant Biology, 2007, 49(6): 827−842. DOI: 10.1111/j.1744-7909.2007.00504.x
[12]	WEI K F, CHEN J, CHEN Y F, et al. Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize [J]. DNA Research, 2012, 19(2): 153−164. DOI: 10.1093/dnares/dsr048
[13]	BENCKE-MALATO M, CABREIRA C, WIEBKE-STROHM B, et al. Genome-wide annotation of the soybean WRKY family and functional characterization of genes involved in response to Phakopsora pachyrhizi infection [J]. BMC Plant Biology, 2014, 14: 236. DOI: 10.1186/s12870-014-0236-0
[14]	ZHANG C, WANG D D, YANG C H, et al. Genome-wide identification of the potato WRKY transcription factor family [J]. PLoS One, 2017, 12(7): e0181573. DOI: 10.1371/journal.pone.0181573
[15]	HUANG S X, GAO Y F, LIU J K, et al. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum [J]. Molecular Genetics and Genomics, 2012, 287(6): 495−513. DOI: 10.1007/s00438-012-0696-6
[16]	YANG Y, LIU J, ZHOU X H, et al. Identification of WRKY gene family and characterization of cold stress-responsive WRKY genes in eggplant [J]. PeerJ, 2020, 8: e8777. DOI: 10.7717/peerj.8777
[17]	SCIENCE F I P. Retraction: Genome-wide identification and expression analysis of WRKY gene family in Capsicum annuum L [J]. Frontiers in Plant Science, 2016, 7: 1727.
[18]	LING J, JIANG W J, ZHANG Y, et al. Genome-wide analysis of WRKY gene family in Cucumis sativus [J]. BMC Genomics, 2011, 12: 471. DOI: 10.1186/1471-2164-12-471
[19]	PHUKAN U J, JEENA G S, SHUKLA R K. WRKY transcription factors: Molecular regulation and stress responses in plants [J]. Frontiers in Plant Science, 2016, 7: 760.
[20]	史建磊, 熊自立, 苏世闻, 等. 基于RNA-seq的番茄青枯病响应基因鉴定与表达分析 [J]. 华北农学报, 2022, 37(2):171−182. DOI: 10.7668/hbnxb.20192621 SHI J L, XIONG Z L, SU S W, et al. Identification and expression analysis of bacterial wilt response genes based on RNA-seq in tomato [J]. Acta Agriculturae Boreali-Sinica, 2022, 37(2): 171−182.(in Chinese) DOI: 10.7668/hbnxb.20192621
[21]	CHEN C J, CHEN H, ZHANG Y, et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data [J]. Molecular Plant, 2020, 13(8): 1194−1202. DOI: 10.1016/j.molp.2020.06.009
[22]	ASHBURNER M, BALL C A, BLAKE J A, et al. Gene Ontology: Tool for the unification of biology [J]. Nature Genetics, 2000, 25(1): 25−29. DOI: 10.1038/75556
[23]	KANEHISA M, GOTO S, KAWASHIMA S, et al. The KEGG resource for deciphering the genome [J]. Nucleic Acids Research, 2004, 32(Suppl_1): D277−D280.
[24]	LEE S W, HAN S W, SRIRIYANUM M, et al. A type I–secreted, sulfated peptide triggers XA21-mediated innate immunity [J]. Science, 2009, 326(5954): 850−853. DOI: 10.1126/science.1173438
[25]	张红, 姜景彬, 许向阳, 等. 番茄WRKY基因家族的生物信息学分析 [J]. 分子植物育种, 2016, 14(8):1965−1976. DOI: 10.13271/j.mpb.014.001965 ZHANG H, JIANG J B, XU X Y, et al. Bioinformatics analysis of WRKY gene family in tomato [J]. Molecular Plant Breeding, 2016, 14(8): 1965−1976.(in Chinese) DOI: 10.13271/j.mpb.014.001965
[26]	SONG H, SUN W H, YANG G F, et al. WRKY transcription factors in legumes [J]. BMC Plant Biology, 2018, 18(1): 243. DOI: 10.1186/s12870-018-1467-2
[27]	MOHANTA T K, PARK Y H, BAE H H. Novel genomic and evolutionary insight of WRKY transcription factors in plant lineage [J]. Scientific Reports, 2016, 6(1): 1−22. DOI: 10.1038/s41598-016-0001-8
[28]	CHEN F, HU Y, VANNOZZI A, et al. The WRKY transcription factor family in model plants and crops [J]. Critical Reviews in Plant Sciences, 2017, 36(5/6): 311−335.
[29]	刁卫平, 王述彬, 刘金兵, 等. 辣椒全基因组WRKY转录因子的分析 [J]. 园艺学报, 2015, 42(11):2183−2196. DIAO W P, WANG S B, LIU J B, et al. Genome-wide analysis of the WRKY transcription factor family in pepper [J]. Acta Horticulturae Sinica, 2015, 42(11): 2183−2196.(in Chinese)
[30]	LIU J L, LIU X L, DAI L Y, et al. Recent progress in elucidating the structure, function and evolution of disease resistance genes in plants [J]. Journal of Genetics and Genomics, 2007, 34(9): 765−776. DOI: 10.1016/S1673-8527(07)60087-3
[31]	ÜLKER B, SOMSSICH I E. WRKY transcription factors: From DNA binding towards biological function [J]. Current Opinion in Plant Biology, 2004, 7(5): 491−498. DOI: 10.1016/j.pbi.2004.07.012
[32]	RINERSON C I, RABARA R C, TRIPATHI P, et al. The evolution of WRKY transcription factors [J]. BMC Plant Biology, 2015, 15: 66. DOI: 10.1186/s12870-015-0456-y
[33]	DESLANDES L, OLIVIER J, THEULIERES F, et al. Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes [J]. Proceedings of the National Academy of Sciences of the United States of America, 2002, 99(4): 2404−2409. DOI: 10.1073/pnas.032485099
[34]	MUKHTAR M S, DESLANDES L, AURIAC M C, et al. The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum [J]. The Plant Journal, 2008, 56(6): 935−947. DOI: 10.1111/j.1365-313X.2008.03651.x
[35]	DANG F F, WANG Y N, YU L, et al. CaWRKY40, a WRKY protein of pepper, plays an important role in the regulation of tolerance to heat stress and resistance to Ralstonia solanacearum infection [J]. Plant, Cell & Environment, 2013, 36(4): 757−774.
[36]	CAI H Y, YANG S, YAN Y, et al. CaWRKY6 transcriptionally activates CaWRKY40, regulates Ralstonia solanacearum resistance, and confers high-temperature and high-humidity tolerance in pepper [J]. Journal of Experimental Botany, 2015, 66(11): 3163−3174. DOI: 10.1093/jxb/erv125
[37]	HUSSAIN A, LI X, WENG Y H, et al. CaWRKY22 acts as a positive regulator in pepper response to RalstoniaSolanacearum by constituting networks with CaWRKY6, CaWRKY27, CaWRKY40, and CaWRKY58 [J]. International Journal of Molecular Sciences, 2018, 19(5): 1426. DOI: 10.3390/ijms19051426
[38]	DANG F F, WANG Y N, SHE J J, et al. Overexpression of CaWRKY27, a subgroup IIe WRKY transcription factor of Capsicum annuum, positively regulates tobacco resistance to Ralstonia solanacearum infection [J]. Physiologia Plantarum, 2014, 150(3): 397−411. DOI: 10.1111/ppl.12093
[39]	YANG S, ZHANG Y W, CAI W W, et al. CaWRKY28 Cys249 is required for interaction with CaWRKY40 in the regulation of pepper immunity to Ralstonia solanacearum [J]. Molecular Plant-Microbe Interactions:MPMI, 2021, 34(7): 733−745. DOI: 10.1094/MPMI-12-20-0361-R
[40]	HUSSAIN A, KHAN M I, ALBAQAMI M, et al. CaWRKY30 positively regulates pepper immunity by targeting CaWRKY40 against Ralstonia solanacearum inoculation through modulating defense-related genes [J]. International Journal of Molecular Sciences, 2021, 22(21): 12091. DOI: 10.3390/ijms222112091
[41]	IFNAN KHAN M, ZHANG Y W, LIU Z Q, et al. CaWRKY40b in pepper acts as a negative regulator in response to Ralstonia solanacearum by directly modulating defense genes including CaWRKY40 [J]. International Journal of Molecular Sciences, 2018, 19(5): 1403. DOI: 10.3390/ijms19051403
[42]	WANG Y N, DANG F F, LIU Z Q, et al. CaWRKY58, encoding a group WRKY transcription factor of Capsicum annuum, negatively regulates resistance to Ralstonia solanacearum infection [J]. Molecular Plant Physiology, 2013, 14(2): 131−144.
[43]	谢政文, 王连军, 陈锦洋, 等. 植物WRKY转录因子及其生物学功能研究进展 [J]. 中国农业科技导报, 2016, 18(3):46−54. DOI: 10.13304/j.nykjdb.2015.605 XIE Z W, WANG L J, CHEN J Y, et al. Studies on WRKY transcription factors and their biological functions in plants [J]. Journal of Agricultural Science and Technology, 2016, 18(3): 46−54.(in Chinese) DOI: 10.13304/j.nykjdb.2015.605
[44]	CHENG Y, ZHOU Y, YANG Y, et al. Structural and functional analysis of VQ motif-containing proteins in Arabidopsis as interacting proteins of WRKY transcription factors [J]. Plant Physiology, 2012, 159(2): 810−825. DOI: 10.1104/pp.112.196816
[45]	PARK C Y, LEE J H, YOO J H, et al. WRKY group IId transcription factors interact with calmodulin [J]. FEBS Letters, 2005, 579(6): 1545−1550. DOI: 10.1016/j.febslet.2005.01.057
[46]	黄幸, 丁峰, 彭宏祥, 等. 植物WRKY转录因子家族研究进展 [J]. 生物技术通报, 2019, 35(12):129−143. DOI: 10.13560/j.cnki.biotech.bull.1985.2019-0626 HUANG X, DING F, PENG H X, et al. Research progress on family of plant WRKY transcription factors [J]. Biotechnology Bulletin, 2019, 35(12): 129−143.(in Chinese) DOI: 10.13560/j.cnki.biotech.bull.1985.2019-0626

[1]	SHI Jianlei, HUANG Shaoyong, CHEN Xianzhi, ZAI Wenshan, XIONG Zili. Re-identification of Tomato AP2/ERF Transcription Factors and Screening of Genes Related to Stress Resistance[J]. Fujian Journal of Agricultural Sciences.
[2]	YANG Yingjie, ZHANG Fukun, MU Jingyi, FU Lufeng, CHEN Zhuo, LI Hua, GUAN Xiayu, LÜ Peitao. Identification and Analysis of NAC Related to Petal Senescence and Stress Responses of Petunia[J]. Fujian Journal of Agricultural Sciences, 2024, 39(6): 700-710. DOI: 10.19303/j.issn.1008-0384.2024.06.009
[3]	AN Zixian, LI Yixuan, ZHENG Youfeng, XIAO Fang, WANG Le, CHEN He, LAI Zhongxiong, MOU Jianmei, LIU Shengcai. Transcriptome-based Identification and Expressions of Amaranth TCP Gene Family[J]. Fujian Journal of Agricultural Sciences, 2022, 37(7): 869-879. DOI: 10.19303/j.issn.1008-0384.2022.007.007
[4]	LIU Jiao, SHUAI Peng. Research Progress on HD-ZIP Transcription Factors in Response to Pathogenic or Abiotic Stresses[J]. Fujian Journal of Agricultural Sciences, 2021, 36(1): 124-134. DOI: 10.19303/j.issn.1008-0384.2021.01.015
[5]	CHEN Rui, CHEN Jian-ming, WU Ming-ji, YANG Shao-hua, HU Chang-quan. Cloning and Expression Analysis of OsPLATZ14 Promoter in Rice (Oryza sativa L.)[J]. Fujian Journal of Agricultural Sciences, 2019, 34(10): 1137-1143. DOI: 10.19303/j.issn.1008-0384.2019.10.004
[6]	XIN Qing-wu, LIU Yi-zhan, ZHU Zhi-ming, LI Li, ZHANG Lin-li, MIAO Zhong-wei, ZHENG Nen-zhu. cDNA Cloning, Tissue Expression Analysis of MITF Gene in Liancheng White Ducks[J]. Fujian Journal of Agricultural Sciences, 2018, 33(12): 1292-1300. DOI: 10.19303/j.issn.1008-0384.2018.12.011
[7]	XIONG Gui-hong, LIU Xiao-juan, YANG Liang, WU Zu-jian. Subcellular Localization Analysis of Rice Protein Kinase Gene OsCIPK5 and Generation of Its RNAi Transgenic Plants[J]. Fujian Journal of Agricultural Sciences, 2017, 32(4): 353-358. DOI: 10.19303/j.issn.1008-0384.2017.04.001
[8]	WANG An-ping, ZHU Shan-yuan, WU Shuang, WANG Yong-juan, ZUO Wei-yong, HONG Wei-ming. Prokaryotic Expression and Antiserum for NP Gene of Duck NDV[J]. Fujian Journal of Agricultural Sciences, 2015, 30(6): 554-557. DOI: 10.19303/j.issn.1008-0384.2015.06.005
[9]	LIAN Ling, HE Wei, CAI Qiu-hua, XU Hui-bin, ZHU Yong-sheng, ZHANG Jian-fu, XIE Hua-an. Cloning and Construct of Over-expression Vector of IPA1 cDNA from Nipponbare[J]. Fujian Journal of Agricultural Sciences, 2012, 27(9): 913-918.
[10]	LIN Guo-qiang, CHEN Zhi-xiong, HU Run-fang, ZHANG Guang-qing, TENG Zhen-yong. Cloning and expression analysis of WRKY transcription factors in soybeans[J]. Fujian Journal of Agricultural Sciences, 2011, 26(1): 29-32.

Cited By

Cited by

Periodical cited type(4)

1.	乔梦雪，蔡璨，鞠艳，沙伟，张梅娟，彭疑芳，马天意. 铁氧还蛋白在植物逆境响应中的研究进展. 高师理科学刊. 2024(08): 96-101 .
2.	于相丽，刘雅银，李勇慧，周晓君. 金钗石斛AP2/ERF基因家族的鉴定和表达分析. 江苏农业科学. 2024(17): 47-57 .
3.	白龙飞，况勇，肖逸，苏可，甘德芳. 茭白WRKY基因家族鉴定及菰黑粉菌侵染下的表达分析. 安徽农业大学学报. 2024(05): 759-770 .
4.	韩硕，韩晓文，胡义锋，杨静美，陈中义，朱永兴，尹军良. 入侵杂草喜旱莲子草WRKY转录因子家族鉴定及其除草剂胁迫表达特征. 草业科学. 2024(11): 2517-2534 .

Other cited types(1)

Get Citation

PDF

XML

Article Metrics

Article views (962) PDF downloads (44) Cited by(5)

Identification and Pathogenic Response of Tomato WRKY Transcription Factors

Abstract

References

Related Articles

Cited by

Periodical cited type(4)

Other cited types(1)

Catalog

Article Metrics

Related

Identification and Pathogenic Response of Tomato WRKY Transcription Factors

Abstract

References

Related Articles

Cited by

Periodical cited type(4)

Other cited types(1)

Catalog

Article Metrics

Related

Export File

Citation

Format

Content