Advertisement

Plant Molecular Biology Reporter

, Volume 34, Issue 4, pp 761–776 | Cite as

Functional Characterization of Maize C2H2 Zinc-Finger Gene Family

  • Kaifa Wei
  • Si Pan
  • Yang Li
Original Paper

Abstract

Plant C2H2-type zinc finger proteins (ZFPs) play essential roles in developmental control and stress responses. The whole complement of ZFP genes has been identified in Arabidopsis and rice, while the genome-scale identification and functional analysis of maize ZFPs is not yet reported. Hence, we performed a comprehensive analysis, including gene structure, chromosome location, duplicated event, selective pressure, phylogeny, gene ontology annotation, and expression profiling under developmental stages and abiotic stresses. Phylogenetic analyses suggested that the ZmZFP gene family can be grouped into three classes (A, B, and C). The analysis of differential gene expression in different developmental stages and stress treatments (drought, salt, and cold) was conducted based on microarray and RNA-seq data. A total of 99.05 % (209 genes) of the total ZmZFP genes (211 genes) were detected in 60 different tissues in microarray data. Under drought stress, 13 differentially expressed genes were found in leaf, of which 7 and 6 genes were up-regulated and down-regulated, respectively. For salt stress, crown root (CR), primary root (PR) and seed root (SR) each had one significantly elevated gene, while 2, 1, and 7 genes were obviously down-regulated in CR, PR and SR, respectively. Additionally, 8 and 3 genes were significantly up-regulated and down-regulated, respectively, in the cold-tolerant line ETH-DH7. This study will lay the foundation for understanding the roles of ZFPs in maize growth and stress resistance, contributing to the molecular breeding of maize for food.

Keywords

Maize C2H2 zinc finger protein Development regulation Cold stress Transcript profile 

Notes

Acknowledgments

We are grateful to the providers who submitted microarray and RNA-seq data to the public expression databases, which can be freely applied.

Compliance with Ethical Standards

Conflict of interest

The author declare that they have no conflict of interest.

Funding

The project was supported by the Science and Technology Cooperation Project of Fujian Province, China (Grant No.2015I0006).

Supplementary material

11105_2015_958_MOESM1_ESM.pdf (399 kb)
Figure S1 (PDF 399 kb)
11105_2015_958_MOESM2_ESM.pdf (83 kb)
Figure S2 (PDF 82 kb)
11105_2015_958_MOESM3_ESM.pdf (432 kb)
Figure S3 (PDF 431 kb)
11105_2015_958_MOESM4_ESM.pdf (144 kb)
Figure S4 (PDF 143 kb)
11105_2015_958_MOESM5_ESM.pdf (561 kb)
Figure S5 (PDF 561 kb)
11105_2015_958_MOESM6_ESM.pdf (508 kb)
Figure S6 (PDF 507 kb)
11105_2015_958_MOESM7_ESM.pdf (427 kb)
Figure S7 (PDF 427 kb)
11105_2015_958_MOESM8_ESM.pdf (402 kb)
Figure S8 (PDF 401 kb)
11105_2015_958_MOESM9_ESM.pdf (404 kb)
Figure S9 (PDF 403 kb)
11105_2015_958_MOESM10_ESM.pdf (12 kb)
Table S1 (PDF 12 kb)
11105_2015_958_MOESM11_ESM.pdf (156 kb)
Table S2 (PDF 156 kb)
11105_2015_958_MOESM12_ESM.pdf (99 kb)
Table S3 (PDF 99.1 KB)
11105_2015_958_MOESM13_ESM.pdf (171 kb)
Table S4 (PDF 171 KB)
11105_2015_958_MOESM14_ESM.pdf (453 kb)
Table S5 (PDF 452 kb)
11105_2015_958_MOESM15_ESM.pdf (276 kb)
Table S6 (PDF 275 kb)
11105_2015_958_MOESM16_ESM.pdf (205 kb)
Table S7 (PDF 205 kb)
11105_2015_958_MOESM17_ESM.pdf (91 kb)
Table S8 (PDF 91 kb)
11105_2015_958_MOESM18_ESM.pdf (133 kb)
Table S9 (PDF 133 kb)

References

  1. Agarwal P, Arora R, Ray S, Singh AK, Singh VP, Takatsuji H, Kapoor S, Tyagi AK (2007) Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Mol Biol 65:467–485CrossRefPubMedGoogle Scholar
  2. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201CrossRefPubMedGoogle Scholar
  3. Chakrabortee S, Boschetti C, Walton LJ, Sarkar S, Rubinsztein DC, Tunnacliffe A (2007) Hydrophilic protein associated with desiccation tolerance exhibits broad protein stabilization function. Proc Natl Acad Sci USA 104:18073–18078CrossRefPubMedPubMedCentralGoogle Scholar
  4. Chinnusamy V, Zhu J, Zhu JK (2007) Cold stress regulation of gene expression in plants. Trends Plant Sci 12:444–451CrossRefPubMedGoogle Scholar
  5. Chinnusamy V, Zhu JK, Sunkar R (2010) Gene regulation during cold stress acclimation in plants. Methods Mol Biol 639:39–55CrossRefPubMedPubMedCentralGoogle Scholar
  6. Ciftci-Yilmaz S, Mittler R (2008) The zinc finger network of plants. Cell Mol Life Sci 65:1150–1160CrossRefPubMedGoogle Scholar
  7. Ciftci-Yilmaz S, Morsy MR, Song L, Coutu A, Krizek BA, Lewis MW, Warren D, Cushman J, Connolly EL, Mittler R (2007) The EAR-motif of the Cys2/His2-type zinc finger protein Zat7 plays a key role in the defense response of Arabidopsis to salinity stress. J Biol Chem 282:9260–9268CrossRefPubMedGoogle Scholar
  8. Colasanti J, Yuan Z, Sundaresan V (1998) The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell 93:593–603CrossRefPubMedGoogle Scholar
  9. Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, Mable BK (2006) The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants. BMC Genomics 7:158CrossRefPubMedPubMedCentralGoogle Scholar
  10. Dathan N, Zaccaro L, Esposito S, Isernia C, Omichinski JG, Riccio A, Pedone C, Di Blasio B, Fattorusso R, Pedone PV (2002) The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif. Nucleic Acids Res 30:4945–4951CrossRefPubMedPubMedCentralGoogle Scholar
  11. Davidson RM, Hansey CN, Gowda M, Childs KL, Lin H, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Jiang N (2011) Utility of RNA sequencing for analysis of maize reproductive transcriptomes. Plant Genome 4:191–203CrossRefGoogle Scholar
  12. Davletova S, Schlauch K, Coutu J, Mittler R (2005) The zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol 139:847–856CrossRefPubMedPubMedCentralGoogle Scholar
  13. Devaiah BN, Nagarajan VK, Raghothama KG (2007) Phosphate homeostasis and root development in Arabidopsis are synchronized by the zinc finger transcription factor ZAT6. Plant Physiol 145:147–159CrossRefPubMedPubMedCentralGoogle Scholar
  14. Dong CH, Agarwal M, Zhang Y, Xie Q, Zhu JK (2006) The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proc Natl Acad Sci USA 103:8281–8286CrossRefPubMedPubMedCentralGoogle Scholar
  15. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) AgriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64–70CrossRefPubMedPubMedCentralGoogle Scholar
  16. Emerson RO, Thomas JH (2009) Adaptive evolution in zinc finger transcription factors. PLoS Genet 5:e1000325CrossRefPubMedPubMedCentralGoogle Scholar
  17. Endo T, Ikeo K, Gojobori T (1996) Large-scale search for genes on which positive selection may operate. Mol Biol Evol 13:685–690CrossRefPubMedGoogle Scholar
  18. Englbrecht CC, Schoof H, Bohm S (2004) Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 5:39CrossRefPubMedPubMedCentralGoogle Scholar
  19. Fernandes J, Morrow DJ, Casati P, Walbot V (2008) Distinctive transcriptome responses to adverse environmental conditions in Zea mays L. Plant Biotechnol J 6:782–798CrossRefPubMedGoogle Scholar
  20. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29–37CrossRefPubMedPubMedCentralGoogle Scholar
  21. Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14:1675–1690CrossRefPubMedPubMedCentralGoogle Scholar
  22. Gan Y, Kumimoto R, Liu C, Ratcliffe O, Yu H, Broun P (2006) GLABROUS INFLORESCENCE STEMS modulates the regulation by gibberellins of epidermal differentiation and shoot maturation in Arabidopsis. Plant Cell 18:1383–1395CrossRefPubMedPubMedCentralGoogle Scholar
  23. Gan Y, Liu C, Yu H, Broun P (2007) Integration of cytokinin and gibberellin signalling by Arabidopsis transcription factors GIS, ZFP8 and GIS2 in the regulation of epidermal cell fate. Development 134:2073–2081CrossRefPubMedGoogle Scholar
  24. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) MiRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–144CrossRefPubMedGoogle Scholar
  25. Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148:993–1003CrossRefPubMedPubMedCentralGoogle Scholar
  26. Huai J, Zheng J, Wang G (2009) Overexpression of a new Cys2/His2 zinc finger protein ZmZF1 from maize confers salt and drought tolerance in transgenic Arabidopsis. Plant Cell Tissue Organ Cult 99:117–124CrossRefGoogle Scholar
  27. Huang J, Yang X, Wang MM, Tang HJ, Ding LY, Shen Y, Zhang HS (2007) A novel rice C2H2-type zinc finger protein lacking DLN-box/EAR-motif plays a role in salt tolerance. Biochim Biophys Acta 1769:220–227CrossRefPubMedGoogle Scholar
  28. Huang XY, Chao DY, Gao JP, Zhu MZ, Shi M, Lin HX (2009) A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev 23:1805–1817CrossRefPubMedPubMedCentralGoogle Scholar
  29. Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ (2006) The PROSITE database. Nucleic Acids Res 34:D227–230CrossRefPubMedGoogle Scholar
  30. Isernia C, Bucci E, Leone M, Zaccaro L, Di Lello P, Digilio G, Esposito S, Saviano M, Di Blasio B, Pedone C, Pedone PV, Fattorusso R (2003) NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein. Chembiochem 4:171–180CrossRefPubMedGoogle Scholar
  31. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467–1483CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kakumanu A, Ambavaram MM, Klumas C, Krishnan A, Batlang U, Myers E, Grene R, Pereira A (2012) Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol 160:846–867CrossRefPubMedPubMedCentralGoogle Scholar
  33. Kam J, Gresshoff PM, Shorter R, Xue GP (2008) The Q-type C2H2 zinc finger subfamily of transcription factors in Triticum aestivum is predominantly expressed in roots and enriched with members containing an EAR repressor motif and responsive to drought stress. Plant Mol Biol 67:305–322CrossRefPubMedGoogle Scholar
  34. Kiełbowicz-Matuk A (2012) Involvement of plant C 2 H 2-type zinc finger transcription factors in stress responses. Plant Sci 185:78–85CrossRefPubMedGoogle Scholar
  35. Klug A, Schwabe JW (1995) Protein motifs 5. Zinc fingers. FASEB J 9:597–604PubMedGoogle Scholar
  36. Kubo K, Sakamoto A, Kobayashi A, Rybka Z, Kanno Y, Nakagawa H, Takatsuji H (1998) Cys2/His2 zinc-finger protein family of petunia: evolution and general mechanism of target-sequence recognition. Nucleic Acids Res 26:608–615CrossRefPubMedPubMedCentralGoogle Scholar
  37. Lee H, Guo Y, Ohta M, Xiong L, Stevenson B, Zhu JK (2002) LOS2, a genetic locus required for cold-responsive gene transcription encodes a bi-functional enolase. EMBO J 21:2692–2702CrossRefPubMedPubMedCentralGoogle Scholar
  38. Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, Reidel EJ, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell TP (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42:1060–1067CrossRefPubMedGoogle Scholar
  39. Lippuner V, Cyert MS, Gasser CS (1996) Two classes of plant cDNA clones differentially complement yeast calcineurin mutants and increase salt tolerance of wild-type yeast. J Biol Chem 271:12859–12866CrossRefPubMedGoogle Scholar
  40. Ma J, Skibbe DS, Fernandes J, Walbot V (2008) Male reproductive development: gene expression profiling of maize anther and pollen ontogeny. Genome Biol 9:R181CrossRefPubMedPubMedCentralGoogle Scholar
  41. Miller J, McLachlan AD, Klug A (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J 4:1609–1614PubMedPubMedCentralGoogle Scholar
  42. Morita MT, Sakaguchi K, Kiyose S, Taira K, Kato T, Nakamura M, Tasaka M (2006) A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems. Plant J 47:619–628CrossRefPubMedGoogle Scholar
  43. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefPubMedGoogle Scholar
  44. Puranik S, Sahu PP, Srivastava PS, Prasad M (2012) NAC proteins: regulation and role in stress tolerance. Trends Plant Sci 17:369–381CrossRefPubMedGoogle Scholar
  45. Qin F, Sakuma Y, Li J, Liu Q, Li YQ, Shinozaki K, Yamaguchi-Shinozaki K (2004) Cloning and functional analysis of a novel DREB1/CBF transcription factor involved in cold-responsive gene expression in Zea mays L. Plant Cell Physiol 45:1042–1052CrossRefPubMedGoogle Scholar
  46. Ren S, Johnston JS, Shippen DE, McKnight TD (2004) TELOMERASE ACTIVATOR1 induces telomerase activity and potentiates responses to auxin in Arabidopsis. Plant Cell 16:2910–2922CrossRefPubMedPubMedCentralGoogle Scholar
  47. Royo J, Gomez E, Barrero C, Muniz LM, Sanz Y, Hueros G (2009) Transcriptional activation of the maize endosperm transfer cell-specific gene BETL1 by ZmMRP-1 is enhanced by two C2H2 zinc finger-containing proteins. Planta 230:807–818CrossRefPubMedGoogle Scholar
  48. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497CrossRefPubMedGoogle Scholar
  49. Sagasser M, Lu GH, Hahlbrock K, Weisshaar B (2002) A. thaliana TRANSPARENT TESTA 1 is involved in seed coat development and defines the WIP subfamily of plant zinc finger proteins. Genes Dev 16:138–149CrossRefPubMedPubMedCentralGoogle Scholar
  50. Saibo NJ, Lourenco T, Oliveira MM (2009) Transcription factors and regulation of photosynthetic and related metabolism under environmental stresses. Ann Bot 103:609–623CrossRefPubMedGoogle Scholar
  51. Sakai H, Medrano LJ, Meyerowitz EM (1995) Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries. Nature 378:199–203CrossRefPubMedGoogle Scholar
  52. Sakamoto H, Maruyama K, Sakuma Y, Meshi T, Iwabuchi M, Shinozaki K, Yamaguchi-Shinozaki K (2004) Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol 136:2734–2746CrossRefPubMedPubMedCentralGoogle Scholar
  53. Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM (2013) Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One 8:e61005CrossRefPubMedPubMedCentralGoogle Scholar
  54. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31:279–292CrossRefPubMedGoogle Scholar
  55. Soderlund C, Bomhoff M, Nelson WM (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res 39:e68CrossRefPubMedPubMedCentralGoogle Scholar
  56. Sugano S, Kaminaka H, Rybka Z, Catala R, Salinas J, Matsui K, Ohme-Takagi M, Takatsuji H (2003) Stress-responsive zinc finger gene ZPT2-3 plays a role in drought tolerance in petunia. Plant J 36:830–841CrossRefPubMedGoogle Scholar
  57. Takatsuji H (1999) Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol Biol 39:1073–1078CrossRefPubMedGoogle Scholar
  58. Takatsuji H, Mori M, Benfey PN, Ren L, Chua NH (1992) Characterization of a zinc finger DNA-binding protein expressed specifically in petunia petals and seedlings. EMBO J 11:241–249PubMedPubMedCentralGoogle Scholar
  59. Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF (2005) Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41:195–211CrossRefPubMedGoogle Scholar
  60. Vollbrecht E, Springer PS, Goh L, Buckler ES, Martienssen R (2005) Architecture of floral branch systems in maize and related grasses. Nature 436:1119–1126CrossRefPubMedGoogle Scholar
  61. Wei K, Pan S (2014) Maize protein phosphatase gene family: identification and molecular characterization. BMC Genomics 15:773CrossRefPubMedPubMedCentralGoogle Scholar
  62. Wei K, Chen J, Wang Y, Chen Y, Chen S, Lin Y, Pan S, Zhong X, Xie D (2012a) Genome-wide analysis of bZIP-encoding genes in maize. DNA Res 19:463–476CrossRefPubMedPubMedCentralGoogle Scholar
  63. Wei KF, Wu LJ, Chen J, Chen YF, Xie DX (2012b) Structural evolution and functional diversification analyses of argonaute protein. J Cell Biochem 113:2576–2585CrossRefPubMedGoogle Scholar
  64. Wei K, Chen Y, Xie D (2013) Genome-scale evolution and phylodynamics of H5N1 influenza virus in China during 1996–2012. Vet Microbiol 167:383–393CrossRefPubMedGoogle Scholar
  65. Wei K, Lin Y, Li Y, Chen Y (2014a) Tracking the evolution in phylogeny, structure and function of H5N1 influenza virus PA gene. Transbound Emerg Dis. doi: 10.1111/tbed.12301 PubMedGoogle Scholar
  66. Wei K, Wang Y, Xie D (2014b) Identification and expression profile analysis of the protein kinase gene superfamily in maize development. Mol Breed 33:155–172CrossRefGoogle Scholar
  67. Wei K, Lin Y, Xie D (2015) Evolutionary and ecological dynamics of transboundary disease caused by H5N1 virus in Southeast Asia. Transbound Emerg Dis 62:315–327CrossRefPubMedGoogle Scholar
  68. Wu C, You C, Li C, Long T, Chen G, Byrne ME, Zhang Q (2008) RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice. Proc Natl Acad Sci USA 105:12915–12920CrossRefPubMedPubMedCentralGoogle Scholar
  69. Xie F, Zhang B (2010) Target-align: a tool for plant microRNA target identification. Bioinformatics 26:3002–3003CrossRefPubMedGoogle Scholar
  70. Yang Z, Gu S, Wang X, Li W, Tang Z, Xu C (2008) Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol 67:266–277CrossRefPubMedGoogle Scholar
  71. Yang S, Vanderbeld B, Wan J, Huang Y (2010) Narrowing down the targets: towards successful genetic engineering of drought-tolerant crops. Mol Plant 3:469–490CrossRefPubMedGoogle Scholar
  72. Zhang H, Liu Y, Wen F, Yao D, Wang L, Guo J, Ni L, Zhang A, Tan M, Jiang M (2014) A novel rice C2H2-type zinc finger protein, ZFP36, is a key player involved in abscisic acid-induced antioxidant defence and oxidative stress tolerance in rice. J Exp Bot 65:5795–5809CrossRefPubMedPubMedCentralGoogle Scholar
  73. Zhao J, Liu M, Jiang L, Ding L, Yan SS, Zhang J, Dong Z, Ren H, Zhang X (2014) Cucumber SUPERMAN has conserved function in stamen and fruit development and a distinct role in floral patterning. PLoS One 9:e86192CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.School of Biological Sciences and BiotechnologyMinnan Normal UniversityZhangzhouChina
  2. 2.School of Life SciencesTsinghua UniversityBeijingChina

Personalised recommendations