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Research Paper

Identification and expression analysis of MAPK cascade gene family in foxtail millet (Setaria italica)

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Article: 2246228 | Received 19 May 2023, Accepted 28 Jul 2023, Published online: 16 Aug 2023

References

  • Zhang T, Liu Y, Yang T, Zhang L, Xu S, Xue L, An L. Diverse signals converge at MAPK cascades in plant. Plant Physiol Biochem. 2006 May-Jun;44(5–6):274–19. doi:10.1016/j.plaphy.2006.06.004.
  • Chen J, Wang L, Yuan M. Update on the roles of rice MAPK cascades. Int J Mol Sci. 2021 Feb 7;22(4):1679. doi:10.3390/ijms22041679.
  • Tena G, Asai T, Chiu WL, Sheen J. Plant mitogen-activated protein kinase signaling cascades. Curr Opin Plant Biol. 2001 Oct;4(5):392–400. doi:10.1016/s1369-5266(00)00191-6.
  • 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 Feb 28;415(6875):977–983. doi:10.1038/415977a.
  • Jonak C, Okrész L, Bögre L, Hirt H. Complexity, cross talk and integration of plant MAP kinase signalling. Curr Opin Plant Biol. 2002 Oct;5(5):415–424. doi:10.1016/s1369-5266(02)00285-6.
  • Lewis TS, Shapiro PS, Ahn NG. Signal transduction through MAP kinase cascades. Adv Cancer Res. 1998;74:49–139. doi:10.1016/s0065-230x(08)60765-4.
  • Kazuya Ichimura, Ichimura K, Shinozaki K, Tena G, Sheen J, Henry Y, Champion A, Kreis M, Zhang S, Hirt H, et al. Mitogen-activated protein kinase cascades in plants: a new nomenclature. Trends Plant Sci. 2002 Jul;7(7):301–308. doi:10.1016/s1360-1385(02)02302-6.
  • Janitza P, Ullrich KK, Quint M. Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom. Front Plant Sci. 2012 Dec 6;3:271. doi:10.3389/fpls.2012.00271.
  • Zhang M, Su J, Zhang Y, Xu J, Zhang S. Conveying endogenous and exogenous signals: MAPK cascades in plant growth and defense. Curr Opin Plant Biol. 2018 Oct;45(Pt A):1–10. doi:10.1016/j.pbi.2018.04.012.
  • Hamel LP, Nicole MC, Sritubtim S, Morency MJ, Ellis M, Ehlting J, Beaudoin N, Barbazuk B, Klessig D, Lee J, et al. Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends Plant Sci. 2006 Apr;11(4):192–198. doi:10.1016/j.tplants.2006.02.007.
  • Chen L, Hu W, Tan S, Wang M, Ma Z, Zhou S, Deng X, Zhang Y, Huang C, Yang G, et al. Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One. 2012;7(10):e46744. doi:10.1371/journal.pone.0046744.
  • Kong X, Pan J, Zhang D, Jiang S, Cai G, Wang L, Li D. Identification of mitogen-activated protein kinase kinase gene family and MKK-MAPK interaction network in maize. Biochem Biophys Res Commun. 2013 Nov 29;441(4):964–969. doi:10.1016/j.bbrc.2013.11.008.
  • Zhan H, Yue H, Zhao X, Wang M, Song W, Nie X. Genome-wide identification and analysis of MAPK and MAPKK gene families in bread wheat (Triticum aestivum L.). Genes (Basel). 2017 Oct 20;8(10):284. doi:10.3390/genes8100284.
  • Goyal RK, Tulpan D, Chomistek N, González-Peña Fundora D, West C, Ellis BE, Frick M, Laroche A, Foroud NA. Analysis of MAPK and MAPKK gene families in wheat and related triticeae species. BMC Genom. 2018 Mar 5;19(1):178. doi:10.1186/s12864-018-4545-9.
  • Cui L, Yang G, Yan J, Pan Y, Nie X. Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley. BMC Genom. 2019 Oct 17;20(1):750. doi:10.1186/s12864-019-6144-9.
  • Wu J, Wang J, Pan C, Guan X, Wang Y, Liu S, He Y, Chen J, Chen L, Lu G, et al. Genome-wide identification of MAPKK and MAPKKK gene families in tomato and transcriptional profiling analysis during development and stress response. PLoS One. 2014 Jul 18;9(7):e103032. doi:10.1371/journal.pone.0103032.
  • Wang Z, Wan Y, Meng X, Zhang X, Yao M, Miu W, Zhu D, Yuan D, Lu K, Li J, et al. Genome-wide identification and analysis of MKK and MAPK gene families in Brassica species and response to stress in Brassica napus. Int J Mol Sci. 2021 Jan 7;22(2):544. doi:10.3390/ijms22020544.
  • Zhang X, Mi X, Chen C, Wang H, Guo W. Identification on mitogen-activated protein kinase signaling cascades by integrating protein interaction with transcriptional profiling analysis in cotton. Sci Rep. 2018 May 25;8(1):8178. doi:10.1038/s41598-018-26400-w.
  • Chen X, Ding Y, Yang Y, Song C, Wang B, Yang S, Guo Y, Gong Z. Protein kinases in plant responses to drought, salt, and cold stress. J Integr Plant Biol. 2021 Jan;63(1):53–78. doi:10.1111/jipb.13061.
  • Smékalová V, Luptovčiak I, Komis G, Šamajová O, Ovečka M, Doskočilová A, Takáč T, Vadovič P, Novák O, Pechan T, et al. Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation and cell division plane orientation. New Phytol. 2014 Sep;203(4):1175–1193. doi:10.1111/nph.12880.
  • Guan Y, Lu J, Xu J, McClure B, Zhang S. Two mitogen-activated protein kinases, MPK3 and MPK6, are required for funicular guidance of pollen tubes in Arabidopsis. Plant Physiol. 2014 Jun;165(2):528–533. doi:10.1104/pp.113.231274.
  • Miao Y, Laun TM, Smykowski A, Zentgraf U. Arabidopsis MEKK1 can take a short cut: it can directly interact with senescence-related WRKY53 transcription factor on the protein level and can bind to its promoter. Plant Mol Biol. 2007 Sep;65(1–2):63–76. doi:10.1007/s11103-007-9198-z.
  • Wang L, Zhao R, Li R, Yu W, Yang M, Sheng M, Shen L. Enhanced drought tolerance in tomato plants by overexpression of SlMAPK1. Plant Cell Tiss Organ Cult. 2018;133(1):27–38. doi:10.1007/s11240-017-1358-5.
  • Zhang Z, Li J, Li F, Liu H, Yang W, Chong K, Xu Y. OsMAPK3 phosphorylates OsbHLH002/OsICE1 and inhibits its ubiquitination to activate OsTPP1 and enhances rice chilling tolerance. Dev Cell. 2017 Dec 18;43(6):731–743.e5. doi:10.1016/j.devcel.2017.11.016.
  • Xiong L, Yang Y. Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase. Plant Cell. 2003 Mar;15(3):745–759. doi:10.1105/tpc.008714.
  • Ma H, Chen J, Zhang Z, Ma L, Yang Z, Zhang Q, Li X, Xiao J, Wang S. MAPK kinase 10.2 promotes disease resistance and drought tolerance by activating different MAPKs in rice. Plant J. 2017 Nov;92(4):557–570. doi:10.1111/tpj.13674.
  • Yu L, Yan J, Yang Y, Zhu W. Overexpression of tomato mitogen-activated protein kinase SlMPK3 in tobacco increases tolerance to low temperature stress. Plant Cell Tiss Organ Cult. 2015;121(1):21–34. doi:10.1007/s11240-014-0675-1.
  • Cai G, Wang G, Wang L, Liu Y, Pan J, Li D. A maize mitogen-activated protein kinase kinase, ZmMKK1, positively regulated the salt and drought tolerance in transgenic Arabidopsis. J Plant Physiol. 2014 Jul 15;171(12):1003–1016. doi:10.1016/j.jplph.2014.02.012.
  • 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 Jul 2;15(1):141–152. doi:10.1016/j.molcel.2004.06.023.
  • Li Y, Cai H, Liu P, Wang C, Gao H, Wu C, Yan K, Zhang S, Huang J, Zheng C. Arabidopsis MAPKKK18 positively regulates drought stress resistance via downstream MAPKK3. Biochem Biophys Res Commun. 2017 Mar 4;484(2):292–297. doi:10.1016/j.bbrc.2017.01.104.
  • Shen L, Zhuang B, Wu Q, Zhang H, Nie J, Jing W, Yang L, Zhang W. Phosphatidic acid promotes the activation and plasma membrane localization of MKK7 and MKK9 in response to salt stress. Plant Sci. 2019 Oct;287:110190. doi:10.1016/j.plantsci.2019.110190.
  • Lu C, Han MH, Guevara-Garcia A, Fedoroff NV. Mitogen-activated protein kinase signaling in postgermination arrest of development by abscisic acid. Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15812–15817. doi:10.1073/pnas.242607499.
  • Kandoth PK, Ranf S, Pancholi SS, Jayanty S, Walla MD, Miller W, Howe GA, Lincoln DE, Stratmann JW. Tomato MAPKs LeMPK1, LeMPK2, and LeMPK3 function in the systemin-mediated defense response against herbivorous insects. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12205–12210. doi:10.1073/pnas.0700344104.
  • Jalmi SK, Sinha AK. ROS mediated MAPK signaling in abiotic and biotic stress- striking similarities and differences. Front Plant Sci. 2015 Sep 24;6:769. doi:10.3389/fpls.2015.00769.
  • Kovtun Y, Chiu WL, Tena G, Sheen J. Functional analysis of oxidative stress-activated mitogen-activated protein kinase cascade in plants. Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2940–2945. doi:10.1073/pnas.97.6.2940.
  • Nakagami H, Soukupová H, Schikora A, Zárský V, Hirt H. A mitogen-activated protein kinase kinase kinase mediates reactive oxygen species homeostasis in Arabidopsis. J Biol Chem. 2006 Dec 15;281(50):38697–38704. doi:10.1074/jbc.M605293200.
  • Ortiz-Masia D, Perez-Amador MA, Carbonell J, Marcote MJ. Diverse stress signals activate the C1 subgroup MAP kinases of Arabidopsis. FEBS Lett. 2007 May 1;581(9):1834–1840. doi:10.1016/j.febslet.2007.03.075.
  • Nadeem F, Ahmad Z, Ul Hassan M, Wang R, Diao X, Li X. Adaptation of Foxtail Millet (Setaria italica L.) to abiotic stresses: a special perspective of responses to nitrogen and phosphate limitations. Front Plant Sci. 2020 Feb 28;11:187. doi:10.3389/fpls.2020.00187.
  • Li P, Brutnell TP. Setaria viridis and Setaria italica, model genetic systems for the panicoid grasses. J Exp Bot. 2011 May;62(9):3031–3037. doi:10.1093/jxb/err096.
  • Krishnamurthy L, Upadhyaya HD, Gowda LL, Kashiwagi J, Purushothaman R, Sube S, Vadez V. Large variation for salinity tolerance in the core collection of foxtail millet (Setaria italica (L.) P. Beauv.) germplasm. Crop Pasture Sci. 2013 May;65(4):353–361. doi:10.1071/CP13282.
  • Sudhakar C, Veeranagamallaiah G, Nareshkumar A, Sudhakarbabu O, Sivakumar M, Pandurangaiah M, Kiranmai K, Lokesh U. Polyamine metabolism influences antioxidant defense mechanism in foxtail millet (Setaria italica L.) cultivars with different salinity tolerance. Plant Cell Rep. 2015 Jan;34(1):141–156. doi:10.1007/s00299-014-1695-3.
  • Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. Tbtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020 Aug 3;13(8):1194–1202. doi:10.1016/j.molp.2020.06.009.
  • Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, et al. The pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016 Jan 4;44(D1):D279–D285. doi:10.1093/nar/gkv1344.
  • Kozlowski LP. IPC – isoelectric point calculator. Biol Direct. 2016 Oct 21;11(1):55. doi:10.1186/s13062-016-0159-9.
  • 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. Yi Chuan. 2020 Apr 20;42(4):403–421. doi:10.16288/j.yczz.19-388. Chinese.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. mol biol evol. 2013 Dec;30(12):2725–2729. doi:10.1093/molbev/mst197
  • Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012 Apr;40(7):e49. doi:10.1093/nar/gkr1293.
  • Zhang X, Zhang L, Sun Y, Zheng S, Wang J, Zhang T. Hydrogen peroxide is involved in strigolactone induced low temperature stress tolerance in rape seedlings (brassica rapa L.). Plant Physiol Biochem. 2020 Dec;157:402–415. doi:10.1016/j.plaphy.2020.11.006.
  • Ning J, Li X, Hicks L, Xiong L. A Raf-like MAPKKK gene DSM1 mediates drought resistance through reactive oxygen species scavenging in rice. Plant physiol. 2010 Feb;152(2):876–890. doi:10.1104/pp.109.149856.
  • Rodriguez M, Petersen M, Mundy J. Mitogen-activated protein kinase signaling in plants. Annu Rev Plant Biol. 2010 Jun;61(1):621–649. doi:10.1146/annurev-arplant-042809-112252.
  • Bigeard J, Hirt H. Nuclear signaling of plant MAPKs. Front Plant Sci. 2018 Apr 11;9:469. doi:10.3389/fpls.2018.00469.
  • Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H. Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. BMC Genom. 2015 Feb 6;16(1):58. doi:10.1186/s12864-015-1244-7.
  • Akhunov ED, Sehgal S, Liang H, Wang S, Akhunova AR, Kaur G, Li W, Forrest KL, See D, Simková H, et al. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiol. 2013 Jan;161(1):252–265. doi:10.1104/pp.112.205161.
  • Yin Z, Zhu W, Zhang X, Chen X, Wang W, Lin H, Wang J, Ye W. Molecular characterization, expression and interaction of MAPK, MAPKK and MAPKKK genes in upland cotton. Genomics. 2021 Jan;113(1 Pt 2):1071–1086. doi:10.1016/j.ygeno.2020.11.004.
  • Jagodzik P, Tajdel-Zielinska M, Ciesla A, Marczak M, Ludwikow A. Mitogen-activated protein kinase cascades in plant hormone signaling. Front Plant Sci. 2018 Oct 8;9:1387. doi:10.3389/fpls.2018.01387.
  • Yu L, Nie J, Cao C, Jin Y, Yan M, Wang F, Liu J, Xiao Y, Liang Y, Zhang W. Phosphatidic acid mediates salt stress response by regulation of MPK6 in Arabidopsis thaliana. New Phytol. 2010 Nov;188(3):762–773. doi:10.1111/j.1469-8137.2010.03422.x.
  • Colcombet J, Hirt H. Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes. Biochem J. 2008 Jul 15;413(2):217–226. doi:10.1042/BJ20080625.
  • Mishra NS, Tuteja R, Tuteja N. Signaling through MAP kinase networks in plants. Arch Biochem Biophys. 2006 Aug 1;452(1):55–68. doi:10.1016/j.abb.2006.05.001.
  • Raja V, Majeed U, Kang H, Andrabi KI, John R. Abiotic stress: interplay between ROS, hormones and MAPKs. Environ Exp Bot. 2017 May;137:142–157. doi:10.1016/j.envexpbot.2017.02.010.
  • Kong X, Pan J, Zhang M, Xing X, Zhou Y, Liu Y, Li D, Li D. ZmMKK4, a novel group C mitogen-activated protein kinase kinase in maize (Zea mays), confers salt and cold tolerance in transgenic Arabidopsis. Plant, Cell & Environ. 2011 Aug;34(8):1291–1303. doi:10.1111/j.1365-3040.2011.02329.x.
  • Lee SC, Luan S. ABA signal transduction at the crossroad of biotic and abiotic stress responses. Plant, Cell & Environ. 2012 Jan;35(1):53–60. doi:10.1111/j.1365-3040.2011.02426.x.
  • Benková E, Michniewicz M, Sauer M, Teichmann T, Seifertová D, Jürgens G, Friml J. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell. 2003 Nov 26;115(5):591–602. doi:10.1016/s0092-8674(03)00924-3.
  • Jammes F, Song C, Shin D, Munemasa S, Takeda K, Gu D, Cho D, Lee S, Giordo R, Sritubtim S, et al. MAP kinases MPK9 and MPK12 are preferentially expressed in guard cells and positively regulate ROS-mediated ABA signaling. Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20520–20525. doi:10.1073/pnas.0907205106.
  • Kim TW, Michniewicz M, Bergmann DC, Wang ZY. Brassinosteroid regulates stomatal development by GSK3-mediated inhibition of a MAPK pathway. Nature. 2012 Feb 5;482(7385):419–422. doi:10.1038/nature10794.
  • Yang Q, Peng Z, Ma W, Zhang S, Hou S, Wei J, Dong S, Yu X, Song Y, Gao W, et al. Melatonin functions in priming of stomatal immunity in Panax notoginseng and Arabidopsis thaliana. Plant Physiol. 2021 Dec 4;187(4):2837–2851. doi:10.1093/plphys/kiab419.
  • Umezawa T, Sugiyama N, Takahashi F, Anderson JC, Ishihama Y, Peck SC, Shinozaki K. Genetics and phosphoproteomics reveal a protein phosphorylation network in the abscisic acid signaling pathway in Arabidopsis thaliana. Sci Signal. 2013 Apr 9;6(270):rs8. doi:10.1126/scisignal.2003509.
  • Wang RS, Pandey S, Li S, Gookin TE, Zhao Z, Albert R, Assmann SM. Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. BMC Genom. 2011 May 9;12(1):216. doi:10.1186/1471-2164-12-216.
  • Menges M, Dóczi R, Ökrész L, Morandini P, Mizzi L, Soloviev M, Murray JAH, Bögre L. Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways. New Phytol. 2008;179(3):643–662. doi:10.1111/j.1469-8137.2008.02552.x.
  • Danquah A, de Zélicourt A, Boudsocq M, Neubauer J, Frei Dit Frey N, Leonhardt N, Pateyron S, Gwinner F, Tamby JP, Ortiz-Masia D, et al. Identification and characterization of an ABA-activated MAP kinase cascade in Arabidopsis thaliana. Plant J. 2015 Apr;82(2):232–244. doi:10.1111/tpj.12808.
  • Wang J, Pan C, Wang Y, Ye L, Wu J, Chen L, Zou T, Lu G. Genome-wide identification of MAPK, MAPKK, and MAPKKK gene families and transcriptional profiling analysis during development and stress response in cucumber. BMC Genom. 2015 May 15;16(1):386. doi:10.1186/s12864-015-1621-2.
  • Zhang X, Wang L, Xu X, Cai C, Guo W. Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton. BMC Plant Biol. 2014 Dec 10;14(1):345. doi:10.1186/s12870-014-0345-9.
  • Lee HY, Back K. Mitogen-activated protein kinase pathways are required for melatonin-mediated defense responses in plants. J Pineal Res. 2016 Apr;60(3):327–335. doi:10.1111/jpi.12314.
  • Lee HY, Back K. The phytomelatonin receptor (PMRT1) Arabidopsis Cand2 is not a bona fide G protein–coupled melatonin receptor. Melatonin Res. 2020 Jun;3(2):177–186. doi:10.32794/mr11250055.
  • Galano A, Reiter RJ. Melatonin and its metabolites vs oxidative stress: from individual actions to collective protection. J Pineal Res. 2018 Aug;65(1):e12514. doi:10.1111/jpi.12514.
  • Du X, Jin Z, Liu D, Yang G, Pei Y. Hydrogen sulfide alleviates the cold stress through MPK4 in Arabidopsis thaliana. Plant Physiol Biochem. 2017 Nov;120:112–119. doi:10.1016/j.plaphy.2017.09.028.
  • Xie G, Kato H, Imai R. Biochemical identification of the OsMKK6-OsMPK3 signalling pathway for chilling stress tolerance in rice. Biochem J. 2012 Apr 1;443(1):95–102. doi:10.1042/BJ20111792.