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Sequence analysis and gene expression of putative oil palm chitinase and chitinase-like proteins in response to colonization of Ganoderma boninense and Trichoderma harzianum

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Abstract

Chitinases are glycosyl hydrolases that cleave the β-1,4-glycosidic linkages between N-acetylglucosamine residues in chitin which is a major component of fungal cell wall. Plant chitinases hydrolyze fungal chitin to chitin oligosaccharides that serve as elicitors of plant defense system against fungal pathogens. However, plants synthesize many chitinase isozymes and some of them are not pathogenesis-related. In this study, three full-length cDNA sequences encoding a putative chitinase (EgChit3-1) and two chitinase-like proteins (EgChit1-1 and EgChit5-1) have been cloned from oil palm (Elaeis guineensis) by polymerase chain reaction (PCR). The abundance of these transcripts in the roots and leaves of oil palm seedlings treated with Ganoderma boninense (a fungal pathogen) or Trichoderma harzianum (an avirulent symbiont), and a combination of both fungi at 3, 6 and 12 weeks post infection were profiled by real time quantitative reverse-transcription (qRT)-PCR. Our findings showed that the gene expression of EgChit3-1 increased significantly in the roots of oil palm seedlings treated with either G. boninense or T. harzianum and a combination of both; whereas the gene expression of EgChit1-1 in the treated roots of oil palm seedlings was not significantly higher compared to those of the untreated oil palm roots. The gene expression of EgChit5-1 was only higher in the roots of oil palm seedlings treated with T. harzianum compared to those of the untreated oil palm roots. In addition, the gene expression of EgChit1-1 and EgChit3-1 showed a significantly higher gene expression in the leaf samples of oil palm seedlings treated with either G. boninense or T. harzianum.

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Abbreviations

BSR:

Basal stem rot

CBD:

Chitin biding domain

CFU:

Colony forming units

CTAB:

Cetyl trimethylammonium bromide

ESTs:

Expressed sequence tags

G. boninense:

Ganoderma boninense

GH:

Glycosyl hydrolase

MEGA:

Molecular evolutionary genetics analysis

ORF:

Open reading frame

PCR:

Polymerase chain reaction

PR:

Pathogenesis-related

PSA:

Potato sucrose agar

qRT:

Quantitative reverse-transcription

RACE:

Rapid amplification of cDNA-ends

T. harzianum:

Trichoderma harzianum

wpi:

Week post infection

References

  1. Kasprzewska A (2003) Plant chitinases–regulation and function. Cell Mol Biol Lett 8:809–824

    PubMed  CAS  Google Scholar 

  2. Boller T, Gehri A, Mauch F, Vögeli U (1983) Chitinase in bean leaves: induction by ethylene, purification, properties and possible function. Planta 157:22–31

    Article  CAS  Google Scholar 

  3. Henrissat B, Bairoch A (1993) New families in the classification of glycosyl hydrolases based on amino-acid-sequence similarities. Biochem J 293:781–788

    PubMed  CAS  Google Scholar 

  4. Andersen MD, Jensen A, Robertus JD, Skriver K (1997) Heterologous expression and characterization of wild-type and mutant forms of a 26 kDa endochitinase from barley (Hordeum vulgare L.). Biochem J 322:815–822

    PubMed  CAS  Google Scholar 

  5. Funkhouser JD, Aronson NN Jr (2007) Chitinase family GH18: evolutionary insights from the genomic history of a diverse protein family. BMC Evol Biol 7:96

    Article  PubMed  Google Scholar 

  6. Neuhaus JM (1999) Chapter 4. Plant chitinases (PR-3, PR-4, PR-8, PR-11). In: Datta SK, Muthukrishnan S (eds) Pathogenesis-related proteins in plants. CRC Press LLC, Boca Raton, pp 77–105

    Google Scholar 

  7. Neuhaus JM, Fritig B, Linthorst HJM, Meins FJ (1996) A revised nomenclature for chitinase genes. Plant Mol Biol Rep 14:102–104

    Article  CAS  Google Scholar 

  8. Neuhaus JM, Sticher L, Meins F Jr, Boller T (1991) A short C-terminal sequence is necessary and sufficient for the targeting of chitinases to the plant vacuole. Proc Natl Acad Sci USA 88:10362–10366

    Article  PubMed  CAS  Google Scholar 

  9. Passarinho PA, de Vries AC (2002) Arabidopsis chitinases: a genomic survey. In: Somerville CR, Meyerowitz EM (eds) The Arabidopsis book. American Society of Plant Biologists, Rockville, pp 1–25

    Google Scholar 

  10. Heitz T, Segond S, Kauffmann S, Geoffroy P, Prasad V, Brunner F, Fritig B, Legrand M (1994) Molecular characterization of a novel tobacco pathogenesis-related (PR) protein: a new plant chitinase/lysozyme. Mol Gen Genet 245:246–254

    Article  PubMed  CAS  Google Scholar 

  11. Ponstein AS, Bres-Vloemans SA, Sela-Buurlage MB, van den Elzen PJ, Melchers LS, Cornelissen BJ (1994) A novel pathogen- and wound-inducible tobacco (Nicotiana tabacum) protein with antifungal activity. Plant Physiol 104:109–118

    Article  PubMed  CAS  Google Scholar 

  12. Legrand M, Kauffmann S, Geoffroy P, Fritig B (1987) Biological function of pathogenesis-related proteins: four tobacco pathogenesis-related proteins are chitinases. Proc Natl Acad Sci USA 84:6750–6754

    Article  PubMed  CAS  Google Scholar 

  13. Kombrink E, Schroder M, Hahlbrock K (1988) Several “pathogenesis-related” proteins in potato are 1,3-β -glucanases and chitinases. Proc Natl Acad Sci USA 85:782–786

    Article  PubMed  CAS  Google Scholar 

  14. Hietala AM, Kvaalen H, Schmidt A, Jøhnk N, Solheim H, Fossdal CG (2004) Temporal and spatial profiles of chitinase expression by norway spruce in response to bark colonization by Heterobasidion annosum. Appl Environ Microbiol 70:3948–3953

    Article  PubMed  CAS  Google Scholar 

  15. Liu JJ, Ekramoddoullah AKM, Zamani A (2005) A class IV chitinase is up-regulated by fungal infection and abiotic stresses and associated with slow-canker-growth resistance to Cronartium ribicola in western white pine (Pinus monticola). Phytopathology 95:284–291

    Article  PubMed  CAS  Google Scholar 

  16. Fossdal CG, Hietala AM, Kvaalen H, Solheim H (2006) Changes in host chitinase isoforms in relation to wounding and colonization by Heterobasidion annosum: early and strong defense response in 33-year-old resistant Norway spruce clone. Tree Physiol 26:169–177

    Article  PubMed  CAS  Google Scholar 

  17. Metraux JP, Burkhart W, Moyer M, Dincher S, Middlesteadt W, Williams S, Payne G, Carnes M, Ryals J (1989) Isolation of a complementary DNA encoding a chitinase with structural homology to a bifunctional lysozyme/chitinase. Proc Natl Acad Sci USA 86:896–900

    Article  PubMed  CAS  Google Scholar 

  18. Mauch F, Staehelin LA (1989) Functional implications of the subcellular localization of ethylene-induced chitinase and β-1,3-glucanase in bean leaves. Plant Cell 1:447–457

    PubMed  CAS  Google Scholar 

  19. Silipo A, Erbs G, Shinya T, Dow JM, Parrilli M, Lanzetta R, Shibuya N, Newman MA, Molinaro A (2010) Glyco-conjugates as elicitors or suppressors of plant innate immunity. Glycobiology 20:406–419

    Article  PubMed  CAS  Google Scholar 

  20. Collinge DB, Kragh KM, Mikkelsen JD, Nielsen KK, Rasmussen U, Vad K (1993) Plant chitinases. Plant J 3:31–40

    Article  PubMed  CAS  Google Scholar 

  21. Latgé JP (2007) The cell wall: a carbohydrate armour for the fungal cell. Mol Microbiol 66:279–290

    Article  PubMed  Google Scholar 

  22. Santos P, Fortunato A, Ribeiro A, Pawlowski K (2008) Chitinases in root nodules. Plant Biotech 25:299–307

    Article  CAS  Google Scholar 

  23. Broglie KE, Gaynor JJ, Broglie RM (1986) Ethylene-regulated gene expression: molecular cloning of the genes encoding an endochitinase from Phaseolus vulgaris. Proc Natl Acad Sci USA 83:6820–6824

    Article  PubMed  CAS  Google Scholar 

  24. Ariffin D, Idris AS, Singh G (2000) Status of Ganoderma in oil palm. In: Flood J, Bridge PD, Holderness M (eds) Ganoderma diseases of perennial crops. CABI Publishing, Wallingford, pp 49–68

    Chapter  Google Scholar 

  25. Paterson RRM (2007) Ganoderma disease of oil palm—a white rot perspective necessary for integrated control. Crop Prot 26:1369–1376

    Article  Google Scholar 

  26. Nur Ain Izzati MZ, Faridah A (2008) Disease suppression in Ganoderma-infected oil palm seedlings treated with Trichoderma harzianum. Plant Prot Sci 44:101–107

    Google Scholar 

  27. Shafiquzzaman S, Umi KY, Kausar H, Sarwar J (2009) In vitro studies on the potential Trichoderma harzianum for antagonistic properties against Ganoderma boninense. J Food Agric Environ 7:970–976

    Google Scholar 

  28. Ferreira RB, Monteiro S, Freitas R, Santos CN, Chen ZJ, Batista LM, Duarte J, Borges A, Teixeira AR (2007) The role of plant defense proteins in fungal pathogenesis. Mol Plant Pathol 8:677–700

    Article  PubMed  CAS  Google Scholar 

  29. Siswanto SD, Darmono TW (1998) Chitinase and β-1,3- glucanase activities against Ganoderma sp. in oil palm. In: Tahardi JS, Darmono TW, Siswanto SD, Nataatmadja R (eds) Proceedings of the BTIG Workshop on oil palm improvement through biotechnology. Bogor, Indonesia, pp 104–114

    Google Scholar 

  30. van Hengel AJ, Tadesse Z, Immerzeel P, Schols H, van Kammen A, de Vries SC (2001) N-acetylglucosamine and glucosamine-containing arabinogalactan proteins control somatic embryogenesis. Plant Physiol 125:1880–1890

    Article  PubMed  Google Scholar 

  31. Zhong RQ, Kays SJ, Schroeder BP, Ye ZH (2002) Mutation of a chitinase-like gene causes ectopic deposition of lignin, aberrant cell shapes, and overproduction of ethylene. Plant Cell 14:165–179

    Article  PubMed  CAS  Google Scholar 

  32. Naher L, Ho CL, Tan SG, Umi KY, Faridah A (2011) Cloning of transcripts encoding chitinases from Elaeis guineensis Jacq. and their expression profiles in response to fungal infections. Physiol Mol Plant P 76:96–103

    Article  CAS  Google Scholar 

  33. Ho CL, Kwan YY, Choi MC, Tee SS, Ng WH, Lim KA, Lee YP, Ooi SE, Lee WW, Tee JM, Tan SH, Kulaveerasingam H, Sharifah SRSA, Meilina OA (2007) Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.). BMC Genomics 8:381–392

    Article  PubMed  Google Scholar 

  34. Wang T, Zhang NH, Du LF (2005) Isolation of RNA of high quality and yield from Ginkgo biloba leaves. Biotechnol Lett 27:629–633

    Article  PubMed  Google Scholar 

  35. Altschul SF, Madden TL, Schaffer AA, Zhang I, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  36. 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

    Article  PubMed  CAS  Google Scholar 

  37. Hall TA (1999) Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  38. 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  PubMed  CAS  Google Scholar 

  39. Shamala S, Faridah A, Zainal AMA, Umi KY (2008) Efficacy of single and mixed treatments of Trichoderma harzianum as biocontrol agents of Ganoderma basal stem rot in oil palm. J Oil Palm Res 20:470–483

    Google Scholar 

  40. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:1–12

    Article  Google Scholar 

  41. Kuo CJ, Liao YC, Yang JH, Huang LC, Chang CT, Sung HY (2008) Cloning and characterization of an antifungal class III chitinase from suspension-cultured bamboo (Bambusa oldhamii) cells. J Agric Food Chem 56:11507–11514

    Article  PubMed  CAS  Google Scholar 

  42. Ohnuma T, Numata T, Osawa T, Mizuhara M, Lampela O, Juffer AH, Skriver K, Fukamizo T (2011) A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis. Planta 234:123–137

    Article  PubMed  CAS  Google Scholar 

  43. Kim YS, Lee JH, Yoon GM, Cho HS, Park S-W, Suh MC, Choi D, ha JH, Liu JR, Pai HS (2000) CHRK1, a chitinase-related receptor like kinase in tobacco. Plant Physiol 123:905–915

    Article  PubMed  CAS  Google Scholar 

  44. van Damme EJM, Culerrier R, Barre A, Alvarez R, Rougé P, Peumans WJ (2007) A novel family of lectins evolutionarily related to class V chitinases: an example of neofunctionalization in legumes. Plant Physiol 144:662–672

    Article  PubMed  Google Scholar 

  45. Liu ZH, Yang CP, Qi XT, Xiu LL, Wang YC (2010) Cloning, heterologous expression, and functional characterization of a chitinase gene, Lbchi32, from Limonium bicolor. Biochem Genet 48:669–679

    Article  PubMed  CAS  Google Scholar 

  46. Samac DA, Shah DM (1991) Developmental and pathogen-induced activation of the Arabidopsis acidic chitinase promoter. Plant Cell 3:1063–1072

    PubMed  CAS  Google Scholar 

  47. Lawton KA, Beck J, Potter S, Ward E, Ryals J (1994) Regulation of cucumber class III chitinase gene expression. Mol Plant Microbe Interact 7:48–57

    Article  PubMed  CAS  Google Scholar 

  48. Meier BM, Shaw N, Ślusarenko AJ (1993) Spatial and temporal accumulation of defence gene transcripts in bean (Phaseolus vulgaris) leaves in relation to bacteria-induced hypersensitive cell death. Mol Plant Microbe Interact 6:453–466

    Article  PubMed  CAS  Google Scholar 

  49. Harman GE, Howell CR, Viterbo A, Chet I, Lorito M (2004) Trichoderma species-opportunistic, avirulent plant symbionts. Nat Rev Microbiol 2:43–56

    Article  PubMed  CAS  Google Scholar 

  50. Ebrahim S, Usha K, Singh B (2011) Pathogenesis related (PR) proteins in plant defense mechanism. In: Méndez-Vilas A (ed) Science against microbial pathogens: communicating current research and technological advances. Formatex, Badajoz, pp 1043–1054

    Google Scholar 

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Acknowledgments

We acknowledge the Malaysian Palm Oil Board (MPOB) for funding the research and K. A. Yeoh under the Graduate Studies Assistantship Scheme (GSAS). We thank the Director-General of MPOB for permission to publish this paper, the Pathology Laboratory of MPOB and Mycology Laboratory of UPM for providing us the Ganoderma boninense PER71 and Trichoderma harzianum T32 cultures respectively. We also thank Jugra Palm Oil Mill Sdn. Bhd., Banting for providing us the palm pressed fibres.

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Yeoh, KA., Othman, A., Meon, S. et al. Sequence analysis and gene expression of putative oil palm chitinase and chitinase-like proteins in response to colonization of Ganoderma boninense and Trichoderma harzianum . Mol Biol Rep 40, 147–158 (2013). https://doi.org/10.1007/s11033-012-2043-8

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