Scientia Agricultura Sinica ›› 2018, Vol. 51 ›› Issue (15): 3009-3019.doi: 10.3864/j.issn.0578-1752.2018.15.016

• RESEARCH NOTES • Previous Articles     Next Articles

Genome-Wide Identification and Expression Analysis of SRO Genes Family in Maize

ZHAO QiuFang, MA HaiYang, JIA LiQiang, CHEN Shu, CHEN HongLiang   

  1. South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science/Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, Guangdong
  • Received:2018-02-28 Online:2018-08-01 Published:2018-08-01

RichHTML

25

PDF

1028

Abstract: 【Objective】The SRO (similar to rcd one) is a group of plant-specific proteins which have important functions in plant growth and development, and response to abiotic stress. Based on maize genome information, the SRO family genes were identified, and the sequences, gene localization, protein structure and their evolutionary relationships were analyzed. Meanwhile, the SRO family genes tissue-specific expression profiles and expression pattern under salt and drought stresses of ZmSROs were analyzed. This research can lay a foundation for researching the function of SRO family genes in the growth and response mechanisms of stress in maize. 【Method】The Arabidopsis SRO protein sequences were used as queries to identify SRO in maize genome and download all the SRO gene sequences, which information regarding the maize SRO genes, including CDS sequences , amino acid sequences and chromosome location were obtained from MaizeGDB. The gene structure, protein molecular weight, isoelectric point, secondary structure, subcellular localization, conserved domain, and conserved element were also prospected and analyzed by GSDS2.0, Expasy-protparam, SOPMA, Plant-mPLoc, EMBL-EBI, MEME bioinformatics tools. Meanwhile the homologous sequence alignment and phylogeny were analyzed by Clustalx (1.83) and MEGA6.0 software. The expression levels of ZmSROs genes in different maize tissues and under high salt and drought stresses were analyzed by real-time fluorescence quantitative PCR. 【Result】Six SRO family genes were identified from Maize genome, and designated ZmSRO1a to ZmSRO1f. ZmSROs were mapped on 1, 4, 5 and 9 chromosome, and contained two to five introns. The CDS of 6 ZmSROs varied in length from 1,215 to 1,791 bp, and their predicted protein products ranged from 404 to 596 aa, with corresponding molecular masses of 45.23 kD and 66.78 kD, and with predicted isoelectric points in the range of 7.01 to 9.17. Subcellular localization analysis showed that ZmSRO1a/ZmSRO1b/ZmSRO1c/ZmSRO1d were located in the chloroplast, ZmSRO1e was located in the peroxisome, and ZmSRO1f was located in the nucleus. Phylogentic analysis revealed that ZmSROs can be divided into three subgroups. Subgroup Ⅰ a contains ZmSRO1a/b/c, subgroups Ⅰ b contains ZmSRO1f, and subgroup Ⅰ c contains ZmSRO1d and ZmSRO1e. Conservative structure domain analysis showed that ZmSRO1a/ ZmSRO1b/ ZmSRO1c/ ZmSRO1d/ ZmSRO1e contain the PARP and RST domain, lack the WWE domain. ZmSRO1f contains the PARP and WWE domain, lacks the RST domains. A total 5 motif were identified from ZmSROs proteins，named motif 1—motif 5. ZmSRO1a/ZmSRO1b/ZmSRO1c contain all of motif, ZmSRO1d/ ZmSRO1e lack the motif 3，ZmSRO1f lacks the motif 5. Different tissues expression assay showed that all ZmSROs had specific expressions in root. The expression of ZmSRO1a/ZmSRO1b/ZmSRO1c/ZmSRO1d/ZmSRO1e in root were significantly up-regulated under high salinity treatment for 1 h. ZmSRO1a/ZmSRO1b/ZmSRO1c/ZmSRO1d/ZmSRO1e were down-regulated in shoots, However, the expression of ZmSRO1f in shoot was significantly up-regulated under high salinity treatment for 6 h. ZmSRO1e in root was up-regulated under drought stress for 1 h and that of ZmSRO1f was up-regulated for 24 h. Meanwhile, the expressions of ZmSRO1a/ ZmSRO1b/ZmSRO1d/ZmSRO1e in shoot were down-regulated under drought stress and that of ZmSRO1c and ZmSRO1f had no significant changes in shoot. 【Conclusion】Maize SRO family contains six genes, and ZmSROs genes could be classified into threes subgroups. Six of ZmSROs genes had specific expressions in root and could respond to high salt and drought stresses in varying degrees.

Key words: Zea mays, SRO gene, abiotic stress, gene expression

[1]    齐涛. 中国玉米国际竞争力研究[D]. 杨凌: 西北农林科技大学, 2011.
Qi T. The international competitiveness of cron in china [D]. Yangling: Northwest agriculture and forestry university, 2011. (in Chinese)
[2]    Jaspers P, Blomster T, Brosché M, Salojärvi J, Ahlfors R, Vainonen J P, Reddy R A, Immink R, Angenent G, Turck F, Overmyer K, Kangasjärvi J. Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. The Plant Journal, 2009, 60(2): 268-279.
[3]    李保珠, 赵翔, 赵孝亮, 彭雷. 拟南芥SRO蛋白家族的结构及功能分析. 遗传, 2013, 35(10): 1189-1197.
LI B Z, ZHAO X, ZHAO X L, PENG L. Structure and function analysis of Arabidopsis thaliana SRO protein family. Hereditas, 2013, 35(10): 1189-1197. (in Chinese)
[4]    Aravind L. The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation. Trends in Biochemical Sciences, 2001: 26: 273-275.
[5]    Jaspers P, Overmyer K, Wrzaczek M, Vainonen J P, Blomster T, Salojärvi J, Reddy R O, Kangasjärvi J. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. BMC Genomics, 2010, 11: 170.
[6]    Otto H, Reche P A, Bazan F, Dittmar K, Haag F, Koch-Nolte F. In silico characterization of the family of PARP-like poly (ADPribosyl) transferases (pARTs). BMC Genomics, 2005, 6: 139.
[7]    Hassa P O, Haenni S S, Elser M, Hottiger M O. Nuclear ADPribosylation reactions in mammalian cells: where are we today and where are we going? Microbiology and Molecular Biology Reviews, 2006, 70(3): 789-829.
[8]    Ahlfors R, Lang S, Overmyer K, Jaspers P, Brosche M, Tauriainen A, Kollist H, Tuominen H, Belles-Boix E, Piippo M, Inze D, Palva T, Kangasjarvi J. Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses. The Plant Cell, 2004, 16: 1925-1937.
[9]    Ahlfors R, Brosché M, Kollist H, Kangasjärvi J. Nitric oxide modulates ozone‐induced cell death, hormone biosynthesis and gene expression in Arabidopsis thaliana. The Plant Journal, 2009, 58(1): 1-12.
[10]   Katiyar-Agarwal S, Zhu J, Kim K, Agarwal M, Fu X, Huang A, Zhu J K. The plasma membrane Na+/H+ antiporter SOS1 interacts with RCD1 and functions in oxidative stress tolerance in Arabidopsis. Proceedings of the national academy of sciences of the USA, 2006, 103: 18816-18821.
[11]   Fujibe T, Saji H, Arakawa K, Yabe N, Takeuchi Y, Yamamoto K T. A methyl viologen-resistant mutant of Arabidopsis, which is allelic to ozone-sensitive rcd1, is tolerant to supplemental ultraviolet-Birradiation. Plant Physiology, 2004, 134: 275-285.
[12]   Overmyer K, Tuominen H, Kettunen R, Betz C, Langebartels C, Sandermann H, Kangasjärvi J. Ozone-sensitive Arabidopsis rcd1 mutant reveals opposite roles for ethylene and jasmonate signaling pathways in regulating superoxide- dependent cell death. The Plant Cell, 2000, 12(10): 1849-1862.
[13]   Teotia S, Lamb R S. The paralogous genes RADICALINDUCED CELL DEATH 1 and SIMILAR TO RCD ONE 1 have partially redundant functions during Arabidopsis thaliana development. Plant Physiology, 2009, 151(1): 180-198.
[14]   Teotia S, Lamb R S. RCD1 and SRO1 are necessary to maintain meristematic fate in Arabidopsis thaliana. Journal of Experimental Botany, 2011, 62: 1271-1284.
[15]   Borsani O, Zhu J H, Verslues P E, Sunkar R, Zhu J K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell, 2005, 123: 1279-1291.
[16]   You J, Zong W, Li X, Ning J, Hu H, Li X, Xiao J, Xiong L. The SNAC1-targeted gene OsSRO1c modulates stomatal closure and oxidative stress tolerance by regulating hydrogen peroxide in rice. Journal of experimental botany, 2012, 64(2): 569-583.
[17]   You J, Zong W, Du H, Hu H, Xiong L. A special member of the rice SRO family, OsSRO1c, mediates responses to multiple abiotic stresses through interaction with various transcription factors. Plant molecular biology, 2014, 84(6): 693-705.
[18]   Liu S, Liu S, Wang M, Wei T, Meng C, Wang M, Xia G. A wheat SIMILAR TO RCD-ONE gene enhances seedling growth and abiotic stress resistance by modulating redox homeostasis and maintaining genomic integrity. The Plant cell, 2014, 26(1): 164-180.
[19]   Babajani G, Effendy J, Plant A L. Sl-SROl1 increases salt tolerance and is a member of the radical-induced cell death 1-similar to RCD1 gene family of tomato. Plant Science, 2009, 176(2): 214-222.
[20]   Li H, Li R, Qu F, Yao J, Hao Y. Identification of the SRO gene family in apples (Malus×domestica) with a functional characterization of MdRCD1. Tree Genetics & Genomes, 2017, 13(5): 94.
[21]   吕有军, 杨卫军, 赵兰杰, 姚金波, 陈伟，李燕，张永山. 陆地棉SRO基因家族的鉴定及表达分析. 作物学报, 2017, 43(10): 1468-1479.
Lü Y J, YANG W J, ZHAO L J, YAO J B, CHEN W, LI Y, ZHANG Y S. Genome-wide identification and expression analysis of SRO genes family in Gossypium hirsutumL.. Acta Agronomica Sinica, 2017, 43(10): 1468-1479. (in Chinese)
[22]   Riechmann J L, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe O J, Samaha R R, Creelman R, Pilgrim M, Broun P, Zhang J Z, Ghandehari D, Sherman B K, Yu G. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000, 290: 2105-2110.
[23]   Olsen A N, Ernst H A, Leggio L L, Skriver K. NAC transcription factors: structurally distinct, functionally diverse. Trends in PlantScience, 2005, 10: 79-87.
[24]   Du H, Huang M, Zhang Z, CHENG S. Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response. Euphytica, 2014, 198(1): 115-126.
[25]   Chen L, Song Y, Li S, Zhang L, Zou C, Yu D. The role of WRKY transcription factors in plant abiotic stresses. Biochimica et Biophysica Acta, 2012, 1819(2): 120-128.
[26]   NOGUERO M, ATIF R M, OCHATT S, THOMPSON R D. The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants. Plant Science, 2013,209, 32-45.
[27]   Wang Y, Deng D, Shi Y, MIAO N, BIAN Y, YIN Z. Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes. Molecular biology reports, 2012, 39(3): 2401-2415.
[1] WANG JiaNuo, CHEN GuiPing, LI Pan, WANG LiPing, NAN YunYou, HE Wei, FAN ZhiLong, HU FaLong, CHAI Qiang, YIN Wen, ZHAO LiaoHao. Photo-Physiological Mechanism at Grain Filling Stage of No-Tillage with Plastic Re-Mulching to Increase Maize Yield in Oasis Irrigation Areas [J]. Scientia Agricultura Sinica, 2026, 59(6): 1189-1202.
[2] CUI ShiYou, CHEN PengJun, MIAO YuanQing, HAN JiJun, SHEN JunMing. Development and Field Evaluation of Glyphosate-Resistant Wheat Germplasm Generated Through EMS Mutagenesis [J]. Scientia Agricultura Sinica, 2026, 59(4): 723-733.
[3] LIAO TingLu, SHI YaFei, XIAO DongHao, SHE YangMengFei, GUO FuCheng, YANG JiuJu, TANG HaiJiang, LUO ChengKe. The Effect of Exogenous Nitroprusside on Sugar Metabolism in Rice Seedlings Under Alkaline Stress [J]. Scientia Agricultura Sinica, 2026, 59(2): 265-277.
[4] ZHANG TianYu, LI Bai, ZANG JinPing, CAO HongZhe, DONG JinGao, XING JiHong, ZHANG Kang. Genome-Wide Identification and Expression Analysis of HMG Family Genes in Botrytis cinerea [J]. Scientia Agricultura Sinica, 2025, 58(4): 704-718.
[5] ZHANG LinLin, GONG Rui, CUI YanLing, ZHONG XiongHui, LI Ye, LI RanHong, QIAN ZongWei. Effect Analysis of SmWRKY30 in Eggplant Resistance to Ralstonia solanacearum by Virus Induced Gene Silencing (VIGS) [J]. Scientia Agricultura Sinica, 2025, 58(3): 548-563.
[6] ZHANG XiangKun, LI JiaYing, QIAO RuMeng, HE JingLei, WANG Li, SHI XiaoXin, DU GuoQiang. Effects of GFabV Under Different Zn Levels on Photosynthetic Efficiency and Photosynthesis-Related Gene Expression of ‘Shine Muscat’ Grapevine [J]. Scientia Agricultura Sinica, 2025, 58(24): 5190-5200.
[7] DING Ning, QI EnFang, JIA XiaoXia, HUANG Wei, MA LiRong, LI JianWu, YAN RuNan. Screening and Identification of miRNAs in Potato Seedlings in Response to High Temperature Stress [J]. Scientia Agricultura Sinica, 2025, 58(22): 4589-4602.
[8] WU ShuYu, HENG YanFang, YU TaiFei, WANG ShiJia, YU SiJia, LI Yuan, HU Zheng, ZHANG Hui, SUN XianJun, LI Liang, JIANG QiYan. Identification of Salt Tolerance in Maize Natural Populations at the Seedling Stage and Analysis of Salt Tolerance-Associated Genes [J]. Scientia Agricultura Sinica, 2025, 58(20): 4085-4099.
[9] ZHANG Jie, HU ChenXi, QI JianBo, ZHANG YongTai, CHEN YiBo, ZHANG YongJi. Effects of Exogenous Zeatin on Photosynthetic Parameter, Antioxidant System and Expression of Genes Related to Zeatin Synthesis in Pepper Under Low-Temperature Combined with Low-Light Stress [J]. Scientia Agricultura Sinica, 2025, 58(19): 3959-3969.
[10] CHEN BingXian, ZHANG Qi, DAI ZhangYan, ZHOU Xu, LIU Jun. Physiological and Molecular Effects of Salicylic Acid on Rice Seed Germination at Low Temperature [J]. Scientia Agricultura Sinica, 2024, 57(7): 1220-1236.
[11] WANG ChengZe, ZHANG Yan, FU Wei, JIA JingZhe, DONG JinGao, SHEN Shen, HAO ZhiMin. Bioinformatics and Expression Pattern Analysis of Maize ACO Gene Family [J]. Scientia Agricultura Sinica, 2024, 57(7): 1308-1318.
[12] GAO ChenXi, HAO LuYang, HU Yue, LI YongXiang, ZHANG DengFeng, LI ChunHui, SONG YanChun, SHI YunSu, WANG TianYu, LI Yu, LIU XuYang. Analysis of Transposable Element Associated Epigenetic Regulation under Drought in Maize [J]. Scientia Agricultura Sinica, 2024, 57(6): 1034-1048.
[13] SU XiaoYu, TAN ZhengWei, LI ChunMing, LI Lei, LU DanDan, YU YongLiang, DONG Wei, AN SuFang, YANG Qing, SUN Yao, XU LanJie, YANG HongQi, LIANG HuiZhen. Analysis of Genome-Wide Methylation Differences and Associated Gene Expression of Sesame Varieties Under High Temperature Stress [J]. Scientia Agricultura Sinica, 2024, 57(24): 4825-4838.
[14] DU YanWei, YAN XiaoGuang, ZHAO JinFeng, JIA SuQing, WANG GaoHong, YU AiLi, ZHANG Peng. Cloning and Functional Verification of SiCIPK21 Gene in Foxtail Millet [J]. Scientia Agricultura Sinica, 2024, 57(22): 4416-4430.
[15] YANG HaoRong, JIA Fan, HU Xu, MU Rong, LIU WeiNa, LIU ChangYun, WANG ShanZhi, SUN XianChao, MA GuanHua, CHEN GuoKang. BnJAZ7 Promotes Sclerotinia sclerotiorum Infection by Affecting the Antioxidant Pathway in Brassica napus [J]. Scientia Agricultura Sinica, 2024, 57(19): 3799-3809.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd