Skip to main content

Molecular Characterization of an Oomycete-Responsive PR-5 Protein Gene from Zingiber zerumbet


The tropical spice crop ginger (Zingiber officinale Roscoe) is highly susceptible to soft rot disease caused by the necrotrophic oomycete Pythium aphanidermatum (Edson) Fitzp. However, Zingiber zerumbet (L.) Smith, a wild relative of ginger, is resistant to P. aphanidermatum and has been proposed as a potential donor for soft rot resistance to Z. officinale. We identified a member of the pathogenesis-related protein group 5 (PR-5) gene family in Z. zerumbet that is expressed constitutively but upregulated in response to infection by P. aphanidermatum. Expression of this gene was upregulated as early as 1.5 h post inoculation (hpi) with the pathogen, peaked at 6 hpi, declined by 9 hpi, and again peaked at 15 hpi before declining at 48 hpi. A cDNA of this PR-5 gene, designated as ZzPR5, encodes a 226-amino-acid predicted protein with a calculated pI of 5.05. The N terminus of this protein contains a 22-amino-acid signal peptide, suggesting that the protein may show apoplastic accumulation like other acidic PR-5 proteins. Phylogenetic analysis revealed high similarity between ZzPR5 and PR-5 proteins reported from other plant species, especially from other Zingiberales. Molecular modeling of ZzPR5 protein revealed an acidic surface cleft, a feature characteristic of glycoside hydrolases and antifungal PR-5 proteins. In molecular docking studies, a linear polymeric molecule of (1,3)-β-d-glucan, a major constituent of the oomycete cell wall, fitted favorably into the surface cleft of ZzPR5 and interacted with acidic amino acids known to be involved in glucan hydrolysis, suggesting a potential antioomycete activity for ZzPR5 protein. Elucidation of the molecular mechanism of ZzPR5 may provide important insight toward engineering soft rot resistance into the obligatory asexual ginger.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5



hours post inoculation


hypersensitive response




quantitative real-time polymerase chain reaction


rapid amplification of cDNA ends


root mean square deviation


reactive oxygen species


thaumatin-like protein


Zingiber zerumbet pathogenesis-related protein 5


  • Adhikari TB, Balaji B, Breeden J, Goodwin SB (2007) Resistance of wheat to Mycosphaerella graminicola involves early and late peaks of gene expression. Physiol Mol Plant Pathol 71:55–68

    Article  CAS  Google Scholar 

  • Alignan M, Hewezi T, Petitprez M, Dechamp-Guillaume G, Gentzbittel L (2006) A cDNA microarray approach to decipher sunflower (Helianthus annus) responses to the necrotrophic fungus Phoma macdonaldi. New Phytol 170:523–536

    Article  CAS  PubMed  Google Scholar 

  • Asselbergh B, Curvers K, Franca SC, Audenaert K, Vuylsteke M, Breusegem FV, Hofte M (2007) Resistance to Botrytis cinerea in sitiens, an abscisic acid-deficient tomato mutant, involves timely production of hydrogen peroxide and cell wall modifications in the epidermis. Plant Physiol 144:1863–1877

    Article  CAS  PubMed  Google Scholar 

  • Breiteneder H (2004) Thaumatin-like proteins-a new family of pollen and fruit allergens. Allergy 59:479-481

    Article  PubMed  Google Scholar 

  • Campos MA, Ribeiro SG, Rigden DJ, Monte DC, Grossi de Sa MF (2002) Putative pathogenesis-related genes within Solanum nigrum L. var. americanum genome: isolation of two genes coding for PR5-like proteins, phylogenetic and sequence analysis. Physiol Mol Plant Pathol 61:205–216

    Article  CAS  Google Scholar 

  • Chen LR, Chen YJ, Lee CY, Lin TY (2007) MeJA-induced transcriptional changes in adventitious roots of Bupleurum kaoi. Plant Sci 173:12–24

    Article  CAS  Google Scholar 

  • Ellis J, Catanzariti AM, Dodds P (2006) The problem of how fungal and oomycetes avirulence proteins enter plant cells. Trends Plant Sci 11:61–63

    Article  CAS  PubMed  Google Scholar 

  • Fung RWM, Gonzalo M, Fekete C, Kovacs LG, He Y, Marsh E, McIntyre LM, Schachtman DP, Qiu W (2008) Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiol 146:236–249

    Article  CAS  PubMed  Google Scholar 

  • Ge X, Li GJ, Wang SB, Zhu H, Zhu T, Wang X, Xia Y (2007) AtNUDT7, a negative regulator of basal immunity in Arabidopsis, modulates two distinct defense response pathways and is involved in maintaining redox homeostasis. Plant Physiol 145:204–215

    Article  CAS  PubMed  Google Scholar 

  • Ghosh R, Chakrabarti C (2008) Crystal structure analysis of NP24-I: a thaumatin-like protein. Planta 228:883–890

    Article  CAS  PubMed  Google Scholar 

  • Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43:205–227

    Article  CAS  PubMed  Google Scholar 

  • Gomez-Gomez L (2004) Plant perception systems for pathogen recognition and defence. Mol Immunol 41:1055–1062

    Article  CAS  PubMed  Google Scholar 

  • Grenier J, Potvin C, Trudel J, Asselin A (1999) Some thaumatin-like proteins hydrolyse polymeric β-1,3-glucans. Plant J 19:473–480

    Article  CAS  PubMed  Google Scholar 

  • Hardham AR, Takemoto D, White RG (2008) Rapid and dynamic subcellular reorganization following mechanical stimulation of Arabidopsis epidermal cells mimics responses to fungal and oomycete attack. BMC Plant Biol 8:63

    Article  PubMed  Google Scholar 

  • Kavitha PG, Thomas G (2008a) Population genetic structure of the clonal plant Zingiber zerumbet (L.) Smith (Zingiberaceae), a wild relative of cultivated ginger, and its response to Pythium aphanidermatum. Euphytica 160:89–100

    Article  Google Scholar 

  • Kavitha PG, Thomas G (2008b) Defence transcriptome profiling of Zingiber zerumbet (L.) Smith by mRNA differential display. J Biosci 33:81–90

    Article  CAS  PubMed  Google Scholar 

  • Kavitha PG, Thomas G (2008c) Expression analysis of defense-related genes in Zingiber (Zingiberaceae) species with different levels of compatibility to the soft rot pathogen Pythium aphanidermatum. Plant Cell Rep 27:1767–1776

    Article  CAS  PubMed  Google Scholar 

  • Kliebenstein DJ, Rowe HC (2008) Ecological costs of biotrophic versus necrotrophic pathogen resistance, the hypersensitive response and signal transduction. Plant Sci 174:551–556

    Article  CAS  Google Scholar 

  • Koiwa H, Kato H, Nakatsu T, Oda J, Yamada Y, Sato F (1999) Crystal structure of tobacco PR-5d protein at 1.8 Å resolution reveals a conserved acidic cleft structure in antifungal thaumatin-like proteins. J Mol Biol 286:1137–1145

    Article  CAS  PubMed  Google Scholar 

  • Kouwizjer MLCE, Grootenhuis PDJ (1995) Parametrization and application of CHEAT95, an extended atom force field for hydrated oligosaccharides. J Phys Chem 99:13426–13436

    Article  CAS  Google Scholar 

  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemistry of protein structures. J Appl Crystallgr 26:283–291

    Article  CAS  Google Scholar 

  • Latijnhouwers M, de Wit PJGM, Govers F (2003) Oomycetes and fungi: similar weaponry to attack plants. Trends Microbiol 11:462–469

    Article  CAS  PubMed  Google Scholar 

  • Lawrence BM (1984) Major tropical spices—ginger (Zingiber officinale Rosc.). Perfum Flavor 9:1–40

    CAS  Google Scholar 

  • Leone P, Menu-Bouaouiche L, Peumans WJ, Payan F, Barre A, Roussel A, Van Damme EJ, Rougé P (2006) Resolution of the structure of the allergenic and antifungal banana fruit thaumatin-like protein at 1.7 Å. Biochimie 88:45–52

    Article  CAS  PubMed  Google Scholar 

  • Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 19:1639–1662

    Article  CAS  Google Scholar 

  • Okubara PA, Paulitz TC (2005) Root defense responses to fungal pathogens: a molecular perspective. Plant Soil 274:215–226

    Article  CAS  Google Scholar 

  • Osmond RI, Hrmova M, Fontaine F, Imberty A, Fincher GB (2001) Binding interactions between barley thaumatin-like proteins and (1,3)-β-D-glucans. Kinetics, specificity, structural analysis and biological implications. Eur J Biochem 268:4190–4199

    Article  CAS  PubMed  Google Scholar 

  • Pritsch C, Muehlbauer GJ, Bushnell WR, Somers DA, Vance CP (2000) Fungal development and induction of defense response genes during early infection of wheat spikes by Fusarium graminearum. Mol Plant Microbe Interact 13:159–169

    Article  CAS  PubMed  Google Scholar 

  • Salzman RA, Fujita T, Zhu-Salzman K, Hasegawa PM, Bressan RA (1999) An improved RNA isolation method for plant tissues containing high levels of phenolic compounds or carbohydrates. Plant Mol Biol Rep 17:11–17

    Article  CAS  Google Scholar 

  • Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355–362

    Article  CAS  PubMed  Google Scholar 

  • Song J, Win J, Tian M, Schornack S, Kaschani F, Ilyas M, van der Hoorn R, Kamoun S (2009) Apoplastic effectors secreted by two unrelated eukaryotic plant pathogens target the tomato defense protease Rcr3. Proc Natl Acad Sci U S A 106:1654–1659

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  PubMed  Google Scholar 

  • Thompson CE, Fernandes CL, de Souza ON, Salzano FM, Bonatto SL, Freitas LB (2006) Molecular modeling of pathogenesis-related proteins family 5. Cell Biochem Biophys 44:385–394

    Article  CAS  PubMed  Google Scholar 

  • Trudel J, Grenier J, Potvin C, Asselin A (1998) Several thaumatin-like proteins bind to β-1,3-glucans. Plant Physiol 118:1431–1438

    Article  CAS  PubMed  Google Scholar 

  • van Kan JAL (2006) Licensed to kill: the lifestyle of a necrotrophic plant pathogen. Trends Plant Sci 11:247–253

    Article  CAS  PubMed  Google Scholar 

  • van Loon LC, Rep M, Pieterse CMJ (2006) Significance of inducible defense-related proteins in infected plants. Annu Rev Phytopathol 44:135–162

    Article  PubMed  Google Scholar 

  • Vleeshouwers VGAA, Dooijeweert WV, Govers F, Kamoun S, Colon LT (2000) Does basal PR gene expression in Solanum species contribute to non-specific resistance to Phytophthora infestans? Physiol Mol Plant Pathol 57:35–42

    Article  CAS  Google Scholar 

  • Zechel DL, Withers SG (2001) Dissection of nucleophilic and acid-base catalysis in glycosidases. Curr Opin Chem Biol 5:643–649

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Dai Y, Xiong Y, DeFraia C, Li J, Dong X, Mou Z (2007) Overexpression of Arabidopsis MAP kinase kinase 7 leads to activation of plant basal and systemic acquired resistance. Plant J 52:1066–1079

    Article  CAS  PubMed  Google Scholar 

Download references


ANR and KAG gratefully acknowledge the Council for Scientific and Industrial Research (CSIR), Government of India for the research fellowships (F. No. 09/716/(0090)/2007/EMR-I to ANR and F. No. 09/716/(0103)/2008/EMR-I to KAG) and GT gratefully acknowledges the Department of Biotechnology (DBT), Government of India for the research grant (Grant No. BT/PR2211/Agr/08/162/2001).

Author information

Authors and Affiliations


Corresponding author

Correspondence to George Thomas.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Aswati Nair, R., Kiran, A.G., Sivakumar, K.C. et al. Molecular Characterization of an Oomycete-Responsive PR-5 Protein Gene from Zingiber zerumbet . Plant Mol Biol Rep 28, 128–135 (2010).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


  • Ginger
  • Necrotroph
  • PR-5
  • Pythium aphanidermatum
  • Soft rot
  • Zingiber zerumbet