小鼠耳芥MAPKKK基因家族全基因组鉴定及进化与表达
收稿日期: 2022-08-03
修回日期: 2022-09-18
网络出版日期: 2022-09-30
基金资助
国家自然科学基金项目(32270385);国家自然科学基金项目(U1303302);国家自然科学基金项目(31060149);安徽科技学院学科带头人引进人才启动经费项目(NXYJ202001)
Genome-wide identification, phylogenetic and expression of MAPKKK gene family in Arabidopsis pumila
Received date: 2022-08-03
Revised date: 2022-09-18
Online published: 2022-09-30
Supported by
the National Natural Science Foundation of China(32270385);the National Natural Science Foundation of China(U1303302);the National Natural Science Foundation of China(31060149);the Talent Introduction Start-up Fund Project of Anhui Science and Technology University(NXYJ202001)
丝裂原活化蛋白激酶激酶激酶(Mitogen-activated protein kinase kinase kinases, MAPKKKs)是MAPK级联的重要组成部分，在发育过程和胁迫反应中发挥重要功能。小鼠耳芥(Arabidopsis pumila)是生活在新疆荒漠中的十字花科短命植物，具有很好的耐盐能力。为了探索小鼠耳芥MAPKKK基因家族的进化和功能，本研究通过全基因组分析从小鼠耳芥基因组中鉴定了143个ApMAPKKK基因，分属3个亚族：ZIK (20个)、MEKK (36个)和RAF (87个)。共线性分析表明小鼠耳芥与拟南芥和琴叶拟南芥分别存在74和72个共线性基因，说明该家族在小鼠耳芥基因组中发生了明显的扩张；进化分析表明存在64对复制基因对，Ka/Ks均小于1，以纯化选择为主。利用RNA-seq数据分析ApMAPKKK在盐胁迫和不同组织中的表达特征，结果表明在250 mmol/L NaCl胁迫下，大多数ApMAPKKK基因上调表达，其中ApMAPKKK18-1/2和ApMAPKKK17-1/2显著上调表达；而在8个组织中，ApMAPKKK主要呈现6种表达模式；部分复制基因在盐胁迫和组织中的表达模式存在差异。本研究结果为进一步解析小鼠耳芥MAPKKK基因家族成员响应非生物胁迫信号转导通路的复杂机制奠定了基础。
朱前彬, 甘志承, 李晓翠, 张英杰, 赵合明, 黄先忠 . 小鼠耳芥MAPKKK基因家族全基因组鉴定及进化与表达[J]. 遗传, 2022 , 44(11) : 1044 -1055 . DOI: 10.16288/j.yczz.22-261
Mitogen-activated protein kinase kinase kinases (MAPKKKs) are important components of the MAPK cascade and play crucial roles in development and stress responses. Arabidopsis pumila is an ephemeral Brassicaceae plant growing in Xinjiang desert regions, which possesses salt tolerance. To explore the evolution and function of the MAPKKK gene family in A. pumila, 143 ApMAPKKK genes were identified from A. pumila genome by genome-wide analysis, which were categorized into three subfamilies: ZIK (20), MEKK (36) and RAF (87). There existed 74 and 72 colinear genes between A. thaliana, A. lyrata and A. pumila, respectively, indicating that this gene family expanded obviously in A. pumila genome. Evolutionary analysis revealed that there were 64 duplicated gene pairs with Ka/Ks less than 1, and purifying selection was dominant. RNA-seq data were used to analyze the expression characteristics of ApMAPKKK genes in response to salt stress and in different tissues. The results showed that most ApMAPKKK genes were up-regulated under 250 mmol/L NaCl stress. For example, ApMAPKKK18-1/2 and ApMAPKKK17-1/2 were substantially up-regulated. Tissue expression profiles showed that ApMAPKKK mainly presented six expression patterns. Some duplicated genes were differentially expressed in response to salt stress and in different tissues. These results lay a foundation for further understanding the complex mechanism of MAPKKK gene family transduction pathway in response to abiotic stresses in A. pumila.
Key words： MAPKKK; Arabidopsis pumila; ephemeral plant; salt stress; gene expression
| [1] | Zhu JK. Abiotic stress signaling and responses in plants. Cell, 2016, 167(2): 313-324. |
| [2] | Zhang MM, Zhang SQ. Mitogen-activated protein kinase cascades in plant signaling. J Integr Plant Biol, 2022, 64(2): 301-341. |
| [3] | Ichimura K, Shinozaki K, Tena G, Sheen J, Henry Y, Champion A, Kreis M, Zhang SQ, Hirt H, Wilson C, Heberle-Bors E, Ellis BE, Morris PC, Innes RW, Ecker JR, Scheel D, Klessig DF, Machida Y, Mundy J, Ohashi Y, Walker JC. Mitogen-activated protein kinase cascades in plants: a new nomenclature. Trends Plant Sci, 2002, 7(7): 301-308. |
| [4] | Zhang MM, Su JB, Zhang Y, Xu J, Zhang SQ. Conveying endogenous and exogenous signals: MAPK cascades in plant growth and defense. Curr Opin Plant Biol, 2018, 45(Pt A):1-10. |
| [5] | Wang W, Feng BM, Zhou JM, Tang DZ. Plant immune signaling: advancing on two frontiers. J Integr Plant Biol, 2020, 62(1): 2-24. |
| [6] | Jonak C, Okrész L, B?gre L, Hirt H. Complexity, cross talk and integration of plant MAP kinase signalling. Curr Opin Plant Biol, 2002, 5(5): 415-424. |
| [7] | Rao KP, Richa T, Kumar K, Raghuram B, Sinha AK. In silico analysis reveals 75 members of mitogen-activated protein kinase kinase kinase gene family in rice. DNA Res, 2010, 17(3): 139-153. |
| [8] | Wu P, Wang WL, Li Y, Hou XL. Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogenetics. Hortic Res, 2017, 4: 17079. |
| [9] | Rodriguez MCS, Petersen M, Mundy J. Mitogen-activated protein kinase signaling in plants. Annu Rev Plant Biol, 2010, 61: 621-649. |
| [10] | Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, Gomez-Gomez L, Boller T, Ausubel FM, Sheen J. MAP kinase signalling cascade in Arabidopsis innate immunity. Nature, 2002, 415(6875): 977-983. |
| [11] | Matsuoka D, Yasufuku T, Furuya T, Nanmori T. An abscisic acid inducible Arabidopsis MAPKKK, MAPKKK18 regulates leaf senescence via its kinase activity. Plant Mol Biol, 2015, 87(6): 565-575. |
| [12] | Li YY, Cai HX, Liu P, Wang CY, Gao HY, Wu CA, Yan K, Zhang SZ, Huang JG, Zheng CC. Arabidopsis MAPKKK 18 positively regulates drought stress resistance via downstream MAPKK3. Biochem Biophys Res Commun, 2017, 484(2): 292-297. |
| [13] | Shao YM, Yu XX, Xu XW, Li Y, Yuan WX, Xu Y, Mao CZ, Zhang SQ, Xu J. The YDA-MKK4/MKK5-MPK3/MPK6 cascade functions downstream of the RGF1-RGI ligand- receptor pair in regulating mitotic activity in root apical meristem. Mol Plant, 2020, 13(11): 1608-1623. |
| [14] | Soyano T, Nishihama R, Morikiyo K, Ishikawa M, Machida Y. NQK1/NtMEK1 is a MAPKK that acts in the NPK1 MAPKKK-mediated MAPK cascade and is required for plant cytokinesis. Genes Dev, 2003, 17(8): 1055-1067. |
| [15] | Liu YL, Schiff M, Dinesh-Kumar SP. Involvement of MEK1 MAPKK, NTF6 MAPK, WRKY/MYB transcription factors, COI1 and CTR1 in N-mediated resistance to tobacco mosaic virus. Plant J, 2004, 38(5): 800-809. |
| [16] | Li FJ, Li MY, Wang P, Cox KL, Duan LS, Dever JK, Shan LB, Li ZH, He P. Regulation of cotton (Gossypium hirsutum) drought responses by mitogen-activated protein (MAP) kinase cascade-mediated phosphorylation of GhWRKY59. New Phytol, 2017, 215(4): 1462-1475. |
| [17] | Xu R, Duan PG, Yu HY, Zhou ZK, Zhang BL, Wang RC, Li J, Zhang GZ, Zhuang SS, Lyu J, Li N, Chai TY, Tian ZX, Yao SG, Li YH. Control of grain size and weight by the OsMKKK10-OsMKK4-OsMAPK6 signaling pathway in rice. Mol Plant, 2018, 11(6): 860-873. |
| [18] | Guo T, Chen K, Dong NQ, Shi CL, Ye WW, Gao JP, Shan JX, Lin HX. GRAIN SIZE AND NUMBER1 negatively regulates the OsMKKK10-OsMKK4-OsMPK6 cascade to coordinate the trade-off between grain number per panicle and grain size in rice. Plant Cell, 2018, 30(4): 871-888. |
| [19] | Liu ZQ, Mei EY, Tian XJ, He ML, Tang JQ, Xu M, Liu JL, Song L, Li XF, Wang ZY, Guan QJ, Xu QJ, Bu QY. OsMKKK 70 regulates grain size and leaf angle in rice through the OsMKK4-OsMAPK6-OsWRKY53 signaling pathway. J Integr Plant Biol, 2021, 63(12): 2043-2057. |
| [20] | Wang M, Yue H, Feng KW, Deng PC, Song WN, Nie XJ. Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.). BMC Genomics, 2016, 17(1): 668. |
| [21] | Kong XP, Lv W, Zhang D, Jiang SS, Zhang SZ, Li DQ. Genome-wide identification and analysis of expression profiles of maize mitogen-activated protein kinase kinase kinase. PLoS One, 2013, 8(2): e57714. |
| [22] | Zhang JB, Wang XP, Wang YC, Chen YH, Luo JW, Li DD, Li XB. Genome-wide identification and functional characterization of cotton (Gossypium hirsutum) MAPKKK gene family in response to drought stress. BMC Plant Biol, 2020, 20(1): 217. |
| [23] | Huang XZ, Yang LF, Jin YH, Lin J, Liu F. Generation, annotation, and analysis of a large-scale expressed sequence tag library from Arabidopsis pumila to explore salt-responsive genes. Front Plant Sci, 2017, 8: 955. |
| [24] | Yang LF, Jin YH, Huang W, Sun Q, Liu F, Huang XZ. Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress. BMC Genomics, 2018, 19(1): 717. |
| [25] | Li XC, Kang KC, Huang XZ, Fan YB, Song MM, Huang YJ, Ding JJ. Genome-wide identification, phylogenetic analysis and expression profiling of the MKK gene family in Arabidopsis pumila. Hereditas(Beijing), 2020, 42(4): 403-421. |
| [25] | 李晓翠, 康凯程, 黄先忠, 范永斌, 宋苗苗, 黄韵杰, 丁佳佳. 小拟南芥MKK基因家族全基因组鉴定及进化和表达分析. 遗传, 2020, 42(4): 403-421. |
| [26] | Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics, 2002, Chapter 2: Unit 2.3. |
| [27] | Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 2013, 30(12): 2725-2729. |
| [28] | Wang YP, Tang HB, Debarry JD, Tan X, Li JP, Wang XY, Lee TH, Jin HZ, Marler B, Guo H, Kissinger JC, Paterson AH. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 2012, 40(7): e49. |
| [29] | Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, Xia R. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant, 2020, 13(8): 1194-1202. |
| [30] | Tang K, Dong CJ, Liu JY. Genome-wide comparative analysis of the phospholipase D gene families among allotetraploid cotton and its diploid progenitors. PLoS One, 2016, 11(5): e0156281. |
| [31] | Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao- Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol, 2017, 34(12), 3299-3302. |
| [32] | Yadav CB, Bonthala VS, Muthamilarasan M, Pandey G, Khan Y, Prasad M. Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res, 2015, 22(1): 79-90. |
| [33] | Niu XQ, Luo XY, Kang KC, Huang XZ, Hu NB, Sui YH, Ai H. Genome-wide identification, comparative evolution and expression analysis of PEBP gene family from Capsicum annuum. Acta Hortic Sin, 2021, 48(5), 947-959. |
| [33] | 牛西强, 罗潇云, 康凯程, 黄先忠, 胡能兵, 隋益虎, 艾昊. 辣椒PEBP基因家族的全基因组鉴定、比较进化与组织表达分析. 园艺学报, 2021, 48(5), 947-959. |
| [34] | Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) method. Methods, 2001, 25(4): 402- 408. |
| [35] | Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C. Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comput Biol, 2012, 8(5): e1002514. |
| [36] | Mattick JS. Introns: evolution and function. Curr Opin Genet Dev, 1994, 4(6): 823-831. |
| [37] | Ye JQ, Yang H, Shi HT, Wei YX, Tie WW, Ding ZH, Yan Y, Luo Y, Xia ZQ, Wang WQ, Peng M, Li KM, Zhang H, Hu W. The MAPKKK gene family in cassava: genome-wide identification and expression analysis against drought stress. Sci Rep, 2017, 7(1): 14939. |
| [38] | Zhang TC, Qiao Q, Novikova PY, Wang Q, Yue JP, Guan YL, Ming SP, Liu TM, De J, Liu YX, Al-Shehbaz IA, Sun H, Van Montagu M, Huang JL, Van de Peer Y, Qiong L. Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude. Proc Natl Acad Sci USA, 2019, 116(14): 7137-7146. |
| [39] | Mao ZM, An ZX, Zhou GL, Yang CY, Han YL, Li XY, Zhang YF. Flora of Xinjiang (vol. 2, part 2). Urumqi: Xinjiang Science and Technology Health Press, 1995, 145-146. |
| [39] | 毛祖美, 安争夕, 周桂玲, 杨昌友, 韩英兰, 李学禹, 张彦福. 《新疆植物志》(第二卷第二分册). 乌鲁木齐: 新疆科技卫生出版社, 1995, 145-146. |
| [40] | Teige M, Scheikl E, Eulgem T, Dóczi R, Ichimura K, Shinozaki K, Dangl JL, Hirt H. The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell, 2004, 15(1): 141-152. |
| [41] | Julkowska MM, Testerink C. Tuning plant signaling and growth to survive salt. Trends Plant Sci, 2015, 20(9): 586-594. |
| [42] | Hong CY, Chao YY, Yang MY, Cheng SY, Cho SC, Kao CH. NaCl-induced expression of glutathione reductase in roots of rice (Oryza sativa L.) seedlings is mediated through hydrogen peroxide but not abscisic acid. Plant Soil, 2009, 320: 103-115. |
| [43] | Bienert GP, Schjoerring JK, Jahn TP. Membrane transport of hydrogen peroxide. Biochim Biophys Acta, 2006, 1758(8): 994-1003. |
| [44] | Choi SW, Lee SB, Na YJ, Jeung SG, Kim SY. Arabidopsis MAP3K16 and other salt-inducible MAP3Ks regulate ABA response redundantly. Mol Cells, 2017, 40(3): 230-242. |
| [45] | Matsuoka D, Soga K, Yasufuku T, Nanmori T.Control of plant growth and development by overexpressing MAP3K17, an ABA-inducible MAP3K, in Arabidopsis. Plant Biotechnol (Tokyo), 2018, 35(2): 171-176. |
| [46] | Virk N, Li DY, Tian LM, Huang L, Hong YB, Li XH, Zhang YF, Liu B, Zhang HJ, Song FM. Arabidopsis Raf-Like mitogen-activated protein kinase kinase kinase gene Raf43 is required for tolerance to multiple abiotic stresses. PLoS One, 2015, 10(7): e0133975. |
| [47] | Kim JM, Woo DH, Kim SH, Lee SY, Park HY, Seok HY, Chung WS, Moon YH. Arabidopsis MKKK 20 is involved in osmotic stress response via regulation of MPK6 activity. Plant Cell Rep, 2012, 31(1): 217-224. |
| [48] | Schmidt R, Mieulet D, Hubberten HM, Obata T, Hoefgen R, Fernie AR, Fisahn J, San Segundo B, Guiderdoni E, Schippers JHM, Mueller-Roeber B. Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice. Plant Cell, 2013, 25(6): 2115-2131. |
| [49] | Kondrashov FA. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci, 2012, 279(1749): 5048-5057. |
| [50] | Zhao CZ, Wang PC, Si T, Hsu CC, Wang L, Zayed O, Yu ZP, Zhu YF, Dong J, Tao WA, Zhu JK. MAP kinase cascades regulate the cold response by modulating ICE1 protein stability. Dev Cell, 2017, 43(5): 618-629.e5. |
| [51] | Qiu JL, Zhou L, Yun BW, Nielsen HB, Fiil BK, Petersen K, Mackinlay J, Loake GJ, Mundy J, Morris PC.Arabidopsis mitogen-activated protein kinase kinases MKK1 and MKK2 have overlapping functions in defense signaling mediated by MEKK1, MPK4, and MKS1. Plant Physiol, 2008, 148(1): 212-222. |
| [52] | Kong Q, Qu N, Gao MH, Zhang ZB, Ding XJ, Yang F, Li YZ, Dong OX, Chen S, Li X, Zhang YL. The MEKK1-MKK1/MKK2-MPK4 kinase cascade negatively regulates immunity mediated by a mitogen-activated protein kinase kinase kinase in Arabidopsis. Plant Cell, 2012, 24(5): 2225-2236. |
| [53] | Xu HY, Zhang C, Li ZC, Wang ZR, Jiang XX, Shi YF, Tian SN, Braun E, Mei Y, Qiu WL, Li S, Wang B, Xu J, Navarre D, Ren DT, Cheng NH, Nakata PA, Graham MA, Whitham SA, Liu JZ. The MAPK kinase kinase GmMEKK1 regulates cell death and defense responses. Plant Physiol, 2018, 178(2): 907-922. |
/
| 〈 |
|
〉 |
www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:
