, Volume 208, Issue 1, pp 113–122 | Cite as

The genome wide analysis of GT transcription factors that respond to drought and waterlogging stresses in maize



Trihelix transcription factors (also known as GT transcription factors) are unique to plants and play important roles in abiotic stress. Here, we report the identification of 59 GT factors in maize by the in silico approach. The 59 maize GT factors are classified into five clades: GT-1 (13), GT-2 (7), GTγ (11), SH4 (7), and SIP1 (21). Their amino acid sequence compositions, physical and chemical characteristics, phylogenetic trees, and chromosomal locations are predicted and analyzed. These 59 maize GT factors are distributed on maize chromosomes 1–10 (11, 8, 5, 9, 9, 2, 1, 4, 3 and 7 genes, respectively). The mRNA expression levels of these GT factors in roots are determined using RNA-seq for the waterlogging-tolerant Hz32 maize line. The results showed that the expression levels of 17 of 59 GT factors increase under drought stress, while those of 3 of them decrease. Under waterlogging stress, the mRNA expression levels of 14 of them increase; 8 of these 14 GT factors overlap with the 17 GT factors whose levels increase under drought stress. The spatio-temporal expression patterns of these eight GT factors show that seven of them (SIP1S, GT-2G, GT-2D, GTγG, SIP1F, SIP1D, and SIP1L) are preferentially expressed in leaves, roots, and internodes, indicating that they are the best candidates among the 59 GTs for further study on waterlogging and drought tolerance in maize.


Trihelix transcription factors In silico cloning Maize (Zea mays L.) Abiotic stress RNA sequencing 



We are grateful to Dr. Mawsheng Chern (University of California, Davis) for his critical reading and editing of the manuscript. This work was supported by the National Natural Science Foundation (31271741), the Hubei Province Natural Science Foundation (2011CDB006 and 2012FFA051), and the Foundation of Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education (KF201503).

Supplementary material

10681_2015_1599_MOESM1_ESM.docx (27 kb)
Supplementary material 1 (DOCX 26 kb)


  1. Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of Arabidopsis MYC and YMB homologs in drought and abscisic acid-regulated gene expression. Plant Cell 9:1859–1868PubMedCentralPubMedGoogle Scholar
  2. Boyer JS, Westgate ME (2004) Grain yields with limited water. J Exp Bot 55(407):2385–2394CrossRefPubMedGoogle Scholar
  3. Brewer PB, Howles PA, Dorian K, Griffith ME, Ishida T, Kaplan-Levy RN, Kilinc A, Smyth DR (2004) PETAL LOSS, a trihelix transcription factor gene, regulates perianth architecture in the Arabidopsis flower. Development 131:4035–4045CrossRefPubMedGoogle Scholar
  4. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500PubMedCentralCrossRefPubMedGoogle Scholar
  5. Fang YJ, Xie KB, Hou X, Hu XH, Xiong LZ (2010) systematic analysis of GT factor family of rice reveals a novel subfamily involved in stress responses. Mol Genet Genomics 283:157–169CrossRefPubMedGoogle Scholar
  6. Fukao T, Bailey-Serres J (2008) Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. PNAS 43:16814–16819CrossRefGoogle Scholar
  7. Gao MJ, Lydiate DJ, Li X, Lui H, Gjetvaj B, Hegedus DD, Rozwadowski K (2009) Repression of seed maturation genes by a trihelix transcriptional repressor in Arabidopsis seedlings. Plant Cell 21:54–71PubMedCentralCrossRefPubMedGoogle Scholar
  8. Green PJ, Kay SA, Chua NH (1987) Sequence-specific inter-actions of a pea nuclear factor with light-responsive elements upstream of the rbcS-3A gene. EMBO J 6:2543–2549PubMedCentralPubMedGoogle Scholar
  9. Guttikonda SK, Valliyodan B, Neelakandan AK, Tran LSP, Kumar R, Quach TN, Voothuluru P, Gutierrez-Gonzalez JJ, Aldrich DL, Pallardy SG, Sharp RE, Ho THD, Nguyen HT (2014) Overexpression of AtDREB1D transcription factor improves drought tolerance in soybean. Mol Biol Rep 41:7995–8008CrossRefPubMedGoogle Scholar
  10. Hattori Y, Nagai K, Furukawa S, Song XJ, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460:1026–1031CrossRefPubMedGoogle Scholar
  11. Hiratsuka K, Wu X, Fukuzawa H, Chua NH (1994) Molecular dissection of GT-1 from Arabidopsis. Plant Cell 6:1805–1813PubMedCentralCrossRefPubMedGoogle Scholar
  12. Kaplan-Levy RN, Brewer PB, Quon T, Smyth DR (2012) The trihelix family of transcription factors-light, stress and development. Trends Plant Sci 17(3):163–171CrossRefPubMedGoogle Scholar
  13. Lee SC, Lan WZ, Buchanan BB, Luan S (2009) A protein kinase-phosphatase pair interacts with an ion channel to regulate ABA signaling in plant guard cells. PNAS 106(50):21419–21424PubMedCentralCrossRefPubMedGoogle Scholar
  14. Licausi F, Dongen JTV, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P (2010) HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J 62:302–315CrossRefPubMedGoogle Scholar
  15. Osorio MB, Bücker-Neto L, Castilhos G, Turchetto-Zolet AC, Wiebke-Strohm B, Bodanese-Zanettini MH, Margis-Pinheiro M (2012) Identification and in silico characterization of soybean trihelix-GT and bHLH transcription factors involved in stress responses. Genet Mol Biol 35(1):233–246PubMedCentralCrossRefPubMedGoogle Scholar
  16. Park HC, Kim ML, Kang YH, Jeon JM, Yoo JH, Kim MC, Park CY, Jeong JC, Moon BC, Lee JH, Yoon HW, Lee SH, Chung WS, Lim CO, Lee SY, Hong JC, Cho MJ (2004) Pathogen-and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor. Plant Physiol 135:2150–2161PubMedCentralCrossRefPubMedGoogle Scholar
  17. Perisic O, Lam E (1992) A tobacco DNA binding protein that interacts with a light-responsive box II element. Plant Cell 4:831–838PubMedCentralCrossRefPubMedGoogle Scholar
  18. Rathore TR, Warsi MZK, Zaidi PH, Singh NN (1997) Waterlogging problem for maize production in Asian region. TAMNET News Lett 4:13–14Google Scholar
  19. Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115CrossRefPubMedGoogle Scholar
  20. Smalle J, Kurepa J, Haegman M, Gielen J, Van Montagu M, Van Der Straeten D (1998) The trihelix DNA-binding motif in higher plants is not restricted to the transcription factors GT-1 and GT-2. PNAS 95:3318–3322PubMedCentralCrossRefPubMedGoogle Scholar
  21. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  22. Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, Inoue H, Takehisa H, Motoyama R, Nagamura Y, Wu JZ, Matsumoto T, Takai T, Okuno K, Yano M (2013) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet 45(9):1097–1102CrossRefPubMedGoogle Scholar
  23. Wang R, Hong G, Han B (2004) Transcript abundance of rml1, encoding a putative GT1-like factor in rice, is un-regulated by Magnaporthe and down-regulated by light. Gene 324:105–115CrossRefPubMedGoogle Scholar
  24. Xie ZM, Zou HF, Wei W, Zhou QY, Niu CF, Liao Y, Tian AG, Ma B, Zhang WK, Zhang JS, Chen SY (2009) Soybean trihelix transcription factors GmGT-2A and GmGT-2B improve plant tolerance to abiotic stresses in transgenic Arabidopsis. PLoS One 4(9):e6898PubMedCentralCrossRefPubMedGoogle Scholar
  25. Xu KN, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailer-Serres J, Ronald PC, Machill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708CrossRefPubMedGoogle Scholar
  26. Yoo CY, Pence HE, Jin JB, Miura K, Gosney MJ, Haseqawa PM, Mickelbart MV (2010) The Arabidopsis GTL1 transcription factor regulates water use efficiency and drought tolerance by modulating stomatal density via transrepression of SDD1. Plant Cell 22:4128–4141PubMedCentralCrossRefPubMedGoogle Scholar
  27. Zhu XY, Xiong LZ (2013) Putative megaenzyme DWA1 plays essential roles in drought resistance by regulating stress-induced was deposition in rice. PNAS 110(44):17790–17795PubMedCentralCrossRefPubMedGoogle Scholar
  28. Zhuang J, Cai B, Peng RH, Zhu B, Jin XF, Xue Y, Gao F, Fu XY, Tian YS, Zhao W, Qiao YS, Zhang Z, Xiong AS, Yao QH (2008) Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem Biophys Res Commun 371:468–474CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of EducationYangtze UniversityJingzhouPeople’s Republic of China
  2. 2.College of Life ScienceYangtze UniversityJingzhouPeople’s Republic of China
  3. 3.Hubei Collaborative Innovation Center for Grain IndustryYangtze UniversityJingzhouPeople’s Republic of China
  4. 4.National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople’s Republic of China

Personalised recommendations