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Comparative analysis of embryo surrounding region (Esr-6) genes in Turkish maize varieties: sequencing and modeling

Abstract

Defensins are cysteine-rich small proteins found in plants and animals. Esr-6 (embryo surrounding region-6), which is a kind of plant defensin gene, plays an important role in nutrition, defense, and signaling of embryo. In this study, Esr-6 genes in three Turkish maize varieties (TMVs) such as Safak, Sakarya, and Seker were sequenced and characterized. Open reading frame (ORF) and protein length of Esr-6 was found as 324 bp and 111 amino acids, respectively. All TMVs contained gamma-thionin family (PF00304) domain, and subcellular localizations were predicted as extracellular. Predicted signal peptide, mature protein, and acidic pro-domain were identified in all TMVs. Four most conserved motifs were identified, but only motif 1 was found to be related with gamma-thionin family. Eight conserved cysteine residues, which are the characteristics of defensins, were detected in all TMVs. In phylogenetic analysis, Esr-6 proteins were clearly diverged from other plant defensins with the highest bootstrap value (100 %). Predicted 3D structures of Esr-6 proteins were similar to each other, including one α-helix and two β-sheets. Conserved cysteine residues, including Cys51, Cys55, Cys66, Cys73, Cys75, and Cys79, were detected in 3D structures of all TMVs. Our study showed that Esr-6 genes and their product are well conserved among TMVs.

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References

  1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. Balandín M, Royo J, Gómez E, Muniz LM, Molina A, Hueros G (2005) A protective role for the embryo surrounding region of the maize endosperm, as evidenced by the characterisation of ZmESR-6, a defensin gene specifically expressed in this region. Plant Mol Biol 58:269–282

    Article  PubMed  Google Scholar 

  3. Bonello JF, Opsahl-Ferstad HG, Perez P, Dumas C, Rogowsky PM (2000) Esr genes show different levels of expression in the same region of maize endosperm. Gene 246:219–227

    CAS  Article  PubMed  Google Scholar 

  4. Cosségal M, Vernoud V, Depège N, Rogowsky PM (2007) The embryo surrounding region. In: Olsen OA (ed) Endosperm, vol 8. Springer, Berlin, pp 57–71

  5. Filiz E, Tombuloglu H, Koc I, Osma E (2014) Characterization of wound-induced serine protease inhibitor (wip1) genes and proteins in Turkish maize varieties. Biochem (Moscow) 79(8):836–844

    CAS  Article  Google Scholar 

  6. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J et al (2014) The Pfam protein families database. Nucleic Acids Res Database Issue 42:D222–D230

    CAS  Article  Google Scholar 

  7. Garcia-Olmedo F, Molina A, Alamillo JM, Rodriguez-Palenzuel P (1998) Plant defense peptides. Biopolymers 47:479–491

    CAS  Article  PubMed  Google Scholar 

  8. Gasteiger E (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana Press, Totowa, pp 571–607

    Chapter  Google Scholar 

  9. Hanks JN, Snyder AK, Graham MA, Shah RK, Blaylock LA, Harrison MJ, Shah DM (2005) Defensin gene family in Medicago truncatula: structure, expression and induction by signal molecules. Plant Mol Biol 58:385–399

    CAS  Article  PubMed  Google Scholar 

  10. Kelley LA, Sternberg MJ (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4:363–371

    CAS  Article  PubMed  Google Scholar 

  11. Kobayashi Y, Sato A, Takashima H, Tamaoki H, Nishimura S, Kyogoku Y, Ikenaka K, Kondo T, Mikroshiba K, Hojo H et al (1991) A new α-helical motif in membrane active peptides. Neurochem Internat 18:525–534

    CAS  Article  Google Scholar 

  12. Lay FT, Anderson MA (2005) Defensins—components of the innate immune system in plants. Curr Prot Pep Sci 6:85–101

    CAS  Article  Google Scholar 

  13. Lay FT, Schirra HJ, Scanlon MJ, Anderson MA, Craik DJ (2003) The three-dimensional solution structure of NaD1, a new floral defensin from Nicotiana alata and its application to a homology model of the crop defense protein alfAFP. J Mol Biol 325:175–188

    CAS  Article  PubMed  Google Scholar 

  14. Lay FT, Poon S, McKenna JA, Connelly AA, Barbeta BL, McGinness BS, Fox JL, Daly NL, Craik DJ, Heath RL et al (2014) The C-terminal propeptide of a plant defensing confers cytoprotective and subcellular targeting functions. BMC Plant Biol 14:41

    Article  PubMed  PubMed Central  Google Scholar 

  15. Opsahl-Ferstad HG, Le Deunff E, Dumas C, Rogowsky PM (1997) Zm Esr, a novel endosperm-specific gene expressed in a restricted region around the maize embryo. Plant J 12:235–246

    CAS  Article  PubMed  Google Scholar 

  16. Sels J, Mathys J, De Coninck BM, Cammue BP, De Bolle MF (2008) Plant pathogenesis-related (PR) proteins: a focus on PR peptides. Plant Physiol Biochem 46:941–950

    CAS  Article  PubMed  Google Scholar 

  17. Sosso D, Wisniewski JP, Khaled AS, Hueros G, Gerentes D, Paul W, Rogowsky PM (2010) The Vpp1, Esr6a, Esr6b and OCL4 promoters are active in distinct domains of maize endosperm. Plant Sci 179:86–96

    CAS  Article  Google Scholar 

  18. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  Google Scholar 

  19. Thomma BPHJ, Cammue BPA, Thevissen K (2002) Plant defensins. Planta 216:193–202

    CAS  Article  PubMed  Google Scholar 

  20. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. Timothy L, Mikael Bodén B, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:202–208

    Article  Google Scholar 

  22. Willard L, Ranjan A, Zhang H, Monzavi H, Boyko RF, Sykes BD, Wishart DS (2003) VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res 31:3316–3319

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Wong JH, Xia L, Ng TB (2007) A review of defensins of diverse origins. Curr Protein Peptide Sci 8:446–459

    CAS  Article  Google Scholar 

  24. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden T (2012) PrimerBLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins 64:643–651

    CAS  Article  PubMed  Google Scholar 

  26. Zhu S, Gao B, Tytgat J (2005) Phylogenetic distribution, functional epitopes and evolution of the CSab superfamily. Cell Mol Life Sci 62:2257–2269

    CAS  Article  PubMed  Google Scholar 

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Correspondence to Ertugrul Filiz.

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Tombuloglu, H., Aydin, M. & Filiz, E. Comparative analysis of embryo surrounding region (Esr-6) genes in Turkish maize varieties: sequencing and modeling. Braz. J. Bot 39, 287–293 (2016). https://doi.org/10.1007/s40415-015-0206-2

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Keywords

  • Bioinformatics
  • Defensin
  • In silico analysis
  • 3D structure