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Molecular Biology Reports

, Volume 37, Issue 8, pp 3991–4001 | Cite as

Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.)

  • Yijun Wang
  • Dexiang Deng
  • Yunlong Bian
  • Yanping Lv
  • Qin Xie
Article

Abstract

The phytohormone auxin is important in various aspects of organism growth and development. Aux/IAA genes encoding short-lived nuclear proteins are responsive primarily to auxin induction. Despite their physiological importance, systematic analysis of Aux/IAA genes in maize have not yet been reported. In this paper, we presented the isolation and characterization of maize Aux/IAA genes in whole-genome scale. A total of 31 maize Aux/IAA genes (ZmIAA1 to ZmIAA31) were identified. ZmIAA genes are distributed in all the maize chromosomes except chromosome 2. Aux/IAA genes expand in the maize genome partly due to tandem and segmental duplication events. Multiple alignment and motif display results revealed major maize Aux/IAA proteins share all the four conserved domains. Phylogenetic analysis indicated Aux/IAA family can be divided into seven subfamilies. Putative cis-acting regulatory DNA elements involved in auxin response, light signaling transduction and abiotic stress adaption were observed in the promoters of ZmIAA genes. Expression data mining suggested maize Aux/IAA genes have temporal and spatial expression pattern. Collectively, these results will provide molecular insights into the auxin metabolism, transport and signaling research.

Keywords

Maize Auxin Aux/IAA gene family Bioinformatic analysis 

Notes

Acknowledgements

We are grateful to editors and reviewers for their helpful comments. We also thank Dr. Yidan Ouyang (Huazhong Agricultural University) for her help in HMM analysis. This work was supported partly by the Nature Science Foundation of Universities in Jiangsu Province (No. 09KJB180010) and the High-Level Personnel Foundation of Yangzhou University (No. nxy5286).

Supplementary material

11033_2010_58_MOESM1_ESM.doc (86 kb)
Supplementary material 1 (DOC 86 kb)
11033_2010_58_MOESM2_ESM.xls (46 kb)
Supplementary material 2 (XLS 45 kb)
11033_2010_58_MOESM3_ESM.tif (1.1 mb)
Multiple alignment of maize Aux/IAA proteins. Regions I, II, III and IV limited by black boxes represented four conserved domains of Aux/IAA proteins. Two NLSs and one βαα motif were indicated by bidirectional arrows. Phosphorylation sites were emphasized by filled triangles. Identical amino acids were highlighted by filled black columns. Positions of Aux/IAA proteins were showed by figures at both sides of sequences (TIFF 1116 kb)
11033_2010_58_MOESM4_ESM.tif (74 kb)
Phylogeny of Aux/IAA proteins. The phylogenetic tree indicated the relationship of maize, rice and Arabidopsis Aux/IAA proteins. Twelve paris of maize/rice Aux/IAA proteins were in the same clade of the phylogenetic tree. Contrarily, no maize/Arabidopsis Aux/IAA proteins were in the same clade of the dendrogram. Evolutional branches of maize/rice co-orthologs were marked in red in figure (TIFF 74 kb)

References

  1. 1.
    Woodward AW, Bartel B (2005) Auxin: regulation, action, and interaction. Ann Bot (Lond) 95(5):707–735. doi: 10.1093/aob/mci083 CrossRefGoogle Scholar
  2. 2.
    De Smet I, Jürgens G (2007) Patterning the axis in plants—auxin in control. Curr Opin Genet Dev 17(4):337–343. doi: 10.1016/j.gde.2007.04.012 CrossRefPubMedGoogle Scholar
  3. 3.
    Kazan K, Manners JM (2009) Linking development to defense: auxin in plant–pathogen interactions. Trends Plant Sci 14(7):373–382. doi: 10.1016/j.tplants.2009.04.005 CrossRefPubMedGoogle Scholar
  4. 4.
    Abel S, Theologis A (1996) Early genes and auxin action. Plant Physiol 111(1):9–17. doi: 10.1104/pp.111.1.9 CrossRefPubMedGoogle Scholar
  5. 5.
    Walker JC, Key JL (1982) Isolation of cloned cDNAs to auxin-responsive poly (A)+ RNAs of elongating soybean hypocotyls. Proc Natl Acad Sci USA 79(23):7185–7189CrossRefPubMedGoogle Scholar
  6. 6.
    Hagen G, Guilfoyle T (2002) Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol 49(3–4):373–385CrossRefPubMedGoogle Scholar
  7. 7.
    Tiwari SB, Hagen G, Guilfoyle TJ (2004) Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell 16(2):533–543. doi: 10.1105/tpc.017384 CrossRefPubMedGoogle Scholar
  8. 8.
    Dreher KA, Brown J, Saw RE, Callisa J (2006) The Arabidopsis Aux/IAA protein family has diversified in degradation and auxin responsiveness. Plant Cell 18(3):699–714. doi: 10.1105/tpc.105.039172 CrossRefPubMedGoogle Scholar
  9. 9.
    Kepinski S, Leyser O (2004) Auxin-induced SCFTIR1-Aux/IAA interaction involves stable modification of the SCFTIR1 complex. Proc Natl Acad Sci USA 101(33):12381–12386. doi: 10.1073/pnas.0402868101 CrossRefPubMedGoogle Scholar
  10. 10.
    Worley CK, Zenser N, Ramos J et al (2000) Degradation of Aux/IAA proteins is essential for normal auxin signalling. Plant J 21(6):553–562. doi: 10.1046/j.1365-313x.2000.00703.x CrossRefPubMedGoogle Scholar
  11. 11.
    Rogg LE, Lasswell J, Bartel B (2001) A gain-of-function mutation in IAA28 suppresses lateral root development. Plant Cell 13(3):465–480. doi: 10.1105/tpc.13.3.465 CrossRefPubMedGoogle Scholar
  12. 12.
    Reed JW (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci 6(9):420–425. doi: 10.1016/S1360-1385(01)02042-8 CrossRefPubMedGoogle Scholar
  13. 13.
    Colón-Carmona A, Chen DL, Yeh KC, Abel S (2000) Aux/IAA proteins are phosphorylated by phytochrome in vitro. Plant Physiol 124(4):1728–1738. doi: 10.1104/pp.124.4.1728 CrossRefPubMedGoogle Scholar
  14. 14.
    Song Y, You J, Xiong L (2009) Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. Plant Mol Biol 70(3):297–309. doi: 10.1007/s11103-009-9474-1 CrossRefPubMedGoogle Scholar
  15. 15.
    Bennetzen JL, Chandler VL, Schnable PS (2001) National science foundation-sponsored workshop report. Maize genome sequencing project. Plant Physiol 127(4):1572–1578. doi: 10.1104/pp.010817 Google Scholar
  16. 16.
    Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115. doi: 10.1126/science.1178534 CrossRefPubMedGoogle Scholar
  17. 17.
    Finn RD, Tate J, Mistry J et al (2008) The Pfam protein families database. Nucleic Acids Res 36(Database issue):D281–D288. doi: 10.1093/nar/gkm960 Google Scholar
  18. 18.
    Eddy SR (2008) A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 4(5):e1000069. doi: 10.1371/journal.pcbi.1000069
  19. 19.
    Letunic I, Copley RR, Schmidt S et al. (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res 32(Database issue):D142–D144. doi: 10.1093/nar/gkh088
  20. 20.
    Hunter S, Apweiler R, Attwood TK et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37(Database issue):D211–D215. doi: 10.1093/nar/gkn785
  21. 21.
    Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan 29(8):1023–1026. doi: 10.1360/yc-007-1023 PubMedGoogle Scholar
  22. 22.
    Bailey TL, Boden M, Buske FA et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37(Web Server issue):W202–W208. doi: 10.1093/nar/gkp335
  23. 23.
    Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948. doi: 10.1093/bioinformatics/btm404 CrossRefPubMedGoogle Scholar
  24. 24.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24(8):1596–1599. doi: 10.1093/molbev/msm092 CrossRefPubMedGoogle Scholar
  25. 25.
    Ouyang Y, Chen J, Xie W, Wang L, Zhang Q (2009) Comprehensive sequence and expression profile analysis of Hsp20 gene family in rice. Plant Mol Biol 70(3):341–357. doi: 10.1007/s11103-009-9477-y CrossRefPubMedGoogle Scholar
  26. 26.
    Maher C, Stein L, Ware D (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res 16(4):510–519. doi: 10.1101/gr.4680506 CrossRefPubMedGoogle Scholar
  27. 27.
    Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27(1):297–300. doi: 10.1093/nar/27.1.297 CrossRefPubMedGoogle Scholar
  28. 28.
    Guilfoyle TJ, Hagen G (2007) Auxin response factors. Curr Opin Plant Biol 10(5):453–460. doi: 10.1016/j.pbi.2007.08.014 CrossRefPubMedGoogle Scholar
  29. 29.
    Ding X, Hou X, Xie K, Xiong L (2009) Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. Planta 230(1):149–163. doi: 10.1007/s00425-009-0929-z CrossRefPubMedGoogle Scholar
  30. 30.
    Ma K, Xiao J, Li X, Zhang Q, Lian X (2009) Sequence and expression analysis of the C3HC4-type RING finger gene family in rice. Gene 444(1–2):33–45. doi: 10.1016/j.gene.2009.05.018 CrossRefPubMedGoogle Scholar
  31. 31.
    Yue G, Hu X, He Y, Yang A, Zhang J (2010) Identification and characterization of two members of the FtsH gene family in maize (Zea mays L.). Mol Biol Rep 37(2):855–863. doi: 10.1007/s11033-009-9691-3 CrossRefPubMedGoogle Scholar
  32. 32.
    Yang L, Zhu H, Guo W, Zhang T (2010) Molecular cloning and characterization of five genes encoding pentatricopeptide repeat proteins from Upland cotton (Gossypium hirsutum L.). Mol Biol Rep 37(2):801–808. doi: 10.1007/s11033-009-9610-7 CrossRefPubMedGoogle Scholar
  33. 33.
    Xu P, Zhu HL, Xu HB et al (2010) Composition and phylogenetic analysis of wheat cryptochrome gene family. Mol Biol Rep 37(2):825–832. doi: 10.1007/s11033-009-9628-x CrossRefPubMedGoogle Scholar
  34. 34.
    Liscum E, Reed JW (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49(3–4):387–400CrossRefPubMedGoogle Scholar
  35. 35.
    Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006) Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genomics 6(1):47–59. doi: 10.1007/s10142-005-0005-0 CrossRefPubMedGoogle Scholar
  36. 36.
    Kalluri UC, Difazio SP, Brunner AM, Tuskan GA (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol 7:59. doi: 10.1186/1471-2229-7-59 CrossRefPubMedGoogle Scholar
  37. 37.
    Jain M, Khurana JP (2009) Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J 276(11):3148–3162. doi: 10.1111/j.1742-4658.2009.07033.x CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Yijun Wang
    • 1
  • Dexiang Deng
    • 1
  • Yunlong Bian
    • 1
  • Yanping Lv
    • 1
  • Qin Xie
    • 1
  1. 1.Key Laboratory of Ministry of Education for Plant Functional Genomics, Key Laboratory of Jiangsu Province for Crop Genetics and PhysiologyYangzhou UniversityYangzhouChina

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