Characterization of a newly identified rice chitinase-like protein (OsCLP) homologous to xylanase inhibitor
© Wu et al.; licensee BioMed Central Ltd. 2013
Received: 2 June 2012
Accepted: 26 December 2012
Published: 18 January 2013
During rice blast fungal attack, plant xylanase inhibitor proteins (XIPs) that inhibit fungal xylanase activity are believed to act as a defensive barrier against fungal pathogens. To understand the role of XIPs in rice, a xylanase inhibitor was cloned from rice. The expression of this gene was examined at the transcriptional/translational levels during compatible and incompatible interactions, and the biochemical activity of this protein was also examined.
Sequence alignment revealed that the deduced amino acid sequence of OsCLP shares a high degree of similarity with that of other plant TAXI-type XIPs. However, recombinant OsCLP did not display inhibitory activity against endo-1,4-β-xylanase enzymes from Aureobasidium pullulans (A. pullulans) or Trichoderma viride (T. viride). Instead, an in-gel activity assay revealed strong chitinase activity. The transcription and translation of OsCLP were highly induced when rice was exposed to pathogens in an incompatible interaction. In addition, exogenous treatment with OsCLP affected the growth of the basidiomycete fungus Rhizoctonia solani through degradation of the hyphal cell wall. These data suggest that OsCLP, which has chitinase activity, may play an important role in plant defenses against pathogens.
Taken together, our results demonstrate that OsCLP may have antifungal activity. This protein may directly inhibit pathogen growth by degrading fungal cell wall components through chitinase activity.
Plants have developed survival strategies, including the strengthening of plant cell walls, to protect themselves from continuous abiotic and biotic stresses. As the first battlefield of the plant-pathogen interaction, plant cell walls, which are mainly composed of various polysaccharides such as cellulose and hemicelluloses, provide tensile strength to plant cells and protect them from biotic invasion [1, 2].
During infection, plant pathogens secrete numerous cell-wall degradation enzymes (CWDE) such as cellulases (e.g., endo-β-1,4-glucanase), pectinases (e.g., pectin lyase, polygalacturonase), and endo-β-1,4-xylanase to degrade the cell wall and allow the pathogen to enter in the cell. The majority of these CWDEs belong to the glycosyl hydrolase (GH) family, based on similarities in amino acid sequence, catalytic domains, protein folds, and overall architecture [3, 4]. Recently, CWDEs have attracted interest because of their utility in biotechnological processes, enhancing processes such as bread making  and animal feed production , as well as their role as pathogenicity factors in plant pathogenic microbes . The microbial GH endoxylanase is an important enzyme in the hydrolysis of xylans, catalyzing the hydrolysis of β-1,4-glycosidic linkages between the xylofuranosyl units in the xylan main chain in both cereals and hardwoods . Comprehensive functional studies based on structural, biochemical, and molecular properties of these enzymes have been reported [9, 10].
At the same time, plants secrete a group of proteinaceous xylanase inhibitors to suppress pathogenic xylanases. These proteins are thought as “defense molecules” that protect plant cells from attack by pathogenic hydrolytic enzymes . Two types of plant xylanase inhibitors have been well studied, i.e., xylanase-inhibiting protein (XIP)-type inhibitors  and Triticum aestivum xylanase inhibitor (TAXI)-type inhibitors [13, 14]. Biochemical analysis revealed that a wheat XIP specifically inhibits the expression of family-10 and −11 xylanases from Aspergillus nidulans and Aspergillus niger, respectively , while a TAXI inhibits the expression of the family-11 xylanase (but not the family-10 xylanase) of A. niger and Bacillus subtilis[13, 16].
Recently, three rice XIPs, including OsXIP, rice XIP, and a putative rice xylanase inhibitor (RIXI), were found to be differentially expressed during various developmental stages and under stress conditions [17–19]. Among these, OsXIP was predicted to be a class III chitinase, based on bioinformatics analysis; however, no chitinase activity was detected for this protein. Instead, the protein showed dosage-dependent xylanase inhibitor activity [17, 20].
In this study, we functionally characterized a chitinase-like protein from rice (OsCLP) that is expressed at both the transcriptional and translational levels during fungal pathogen infection. The recombinant OsCLP protein has strong chitinase activity and can dissolve cell walls, leading to the release of cytosolic contents. This is the first report on TAXI-like molecule with chitinase activity. This work provides new insights into the function of OsCLP in plant defense mechanisms.
Results and discussion
Sequence analysis and characterization of OsCLP
Purification of recombinant OsCLP
Chitinase activity of OsCLP
Recently, it was reported that an XIP identified from coffee, CaclXIP, plays an important role in the inhibition of Asian soybean rust spore germination through the xylanase inhibitor activity, but not the chitinase activity, of this XIP . Like CaclXIP, OsXIP also has xylanase inhibitor activity, although OsXIP was predicted to be a class III chitinase . In contrast to CaclXIP and OsXIP, which lack chitinase activity, we wanted to confirm that OsCLP has chitinase activity by performing an in-gel chitinase activity assay. In this procedure, crude and purified OsCLP induced by IPTG in E. coli, as well as a control with IPTG, were separated by 12.5% SDS-PAGE in a gel containing glycol chitin (Figure 2B). As shown in Figure 2B, strong chitinase activity, in the position in which OsCLP was expressed (Figure 2A), was detected under a UV filter. This suggests that the OsCLP protein displays strong chitinase activity. However, further functional analysis of OsCLP will be required, using biochemical and structural analysis approaches, to understand the different roles played by OsCLP and TAXI-type inhibitors.
Transcriptional and translational levels of OsCLP after fungal infection
Antifungal activity of OsCLP
A close-up view of fungal hyphae after treatment with OsCLP protein was observed through a light microscope to investigate how OsCLP protein suppresses R. solani growth. The release of cytosolic contents occurred within 10 minutes of OsCLP treatment (Figure 5B). These data suggest that OsCLP might exhibit strong biochemical activity to dissolve fungal cell walls.
Plant and fungal growth
Rice (cv. Jinheung) seedlings in the 4–5 leaf stage that were grown under natural light in a greenhouse at 28°C were used for whole-plant inoculations with the blast fungus M. oryzae. For fungal inoculation of rice leaves, a conidial suspension (1 × 105 conidia/mL) of M. oryzae race KJ401 and KJ301 (incompatible and compatible to cv. Jinheung, respectively) was sprayed onto the leaves using an air sprayer. The inoculated plants were kept in a humidity chamber at 28°C and harvested at defined time periods.
Isolation and cloning of OsCLP
The OsCLP coding sequence was amplified from a rice cDNA library, which was synthesized from rice leaves inoculated with M. oryzae race KJ401 (incompatible cv. Jinheung), using PCR with specific primer sets: Forward, 5'-GGATCCATGTCGCTCCACCTCCTCCTC-3'; Reverse, 5'-AAGCTTCTAGGCGGCGAGAGTGAAGT-3', containing BamHI and HindIII restriction enzyme sites (underlined). The amplified fragment was gel purified (PCR Clean-up System, Promega, Madison, WI, USA) and cloned into a pGEM-T easy vector (Promega). The product was digested with BamHI and HindIII and sub-cloned into a pQE30 expression vector. The recombinant plasmid was then transformed into E. coli (strain BL21 DE3.0) for protein purification.
Expression and purification of OsCLP
The E. coli cells were grown in LB medium containing 50 μg/ml of ampicillin until OD600 was 0.6. IPTG, at a final concentration of 0.1 mM, was added for OsCLP protein induction. E. coli cells were cultured at 18°C for 3 days with shaking at 100 × g and harvested by centrifugation at 3,500 × g for 10 min at 4°C. The pellet was resuspended in lysis buffer (50 mM NaH2PO4, 300 mM NaCl, 10 mM imidazole, pH 8.0), followed by sonication of the lysed cells and centrifugation at 10,000 × g for 20 min. The supernatant was collected and incubated with Ni2+- affinity resins at 4°C for 2 h. The collected resins were washed with 5 volumes of washing buffer (50 mM NaH2PO4, 300 mM NaCl, 20 mM imidazole, pH 8.0), and then eluted with elution buffer (50 mM NaH2PO4, 300 mM NaCl, 250 mM imidazole, pH 8.0). The eluted protein was stored at −20°C until further analysis. The purified OsCLP recombinant protein containing 6 × His-tagged was used to raise an antibody in rabbit and for the biochemical assay.
Total RNAs isolated from rice tissue and leaves infected with fungus were extracted using a Plant Mini RNA Kit (Qiagen, Valencia, CA, USA). cDNA was synthesized using a SuperScript III First-Strand Synthesis System (Invitrogen, Madison, WI, USA). Primers were designed to generate PCR products of 300–500 bp, and actin transcript was used as an internal control to normalize the concentration of cDNA in each sample. PCR was carried out using gene-specific primer pairs: OsCLP forward, 5'-GGATCTCCCCGGATACTTCA-3'; OsCLP reverse 5'-TTCTCCATCTGGAACCCTCC-3'; actin forward, 5'-AGGAATGGAAGCTGCGGGTAT-3'; actin reverse, 5'-GCAGGAGGACGGCGATAACA-3'. The PCR products were separated on a 1% agarose gel stained with ethidium bromide.
Western blot analysis
Total soluble protein (20 μg) was separated by 12% SDS-PAGE and transferred to a PVDF membrane using a semidry electrophoretic apparatus (Hoefer, Holliston, MA). The blotted membrane was blocked for 4 h at room temperature in 1× TTBS buffer (50 mM Tris–HCl, pH 8.2, 0.1% (v/v) Tween 20, and 150 mM NaCl) with 7% skim milk, followed by incubation for 2 h after the addition of 1/1000 purified OsCLP primary antibody. The membrane was washed three times with 1× TTBS for 15 min each time. A secondary anti-rabbit IgG antibody conjugated with horseradish peroxidase and diluted 1:10,000 in 1× TTBS was used for immunodetection. The antigen-antibody interaction was carried out for 2 h, and cross-reacting proteins were detected by ECL (Perkin Elmer Life Sciences, Boston, MA) using an LAS 4000 imaging system (Fujifilm, Japan).
Xylanase inhibition assay
Standard xylanases from A. pullulans and T. viride were purchased from Sigma-Aldrich corporation. A xylanase inhibition assay for OsCLP was performed in a 1.5% LB agar plate containing 1% (w/v) birchwood xylan substrate. Ten micromoles of xylanase enzyme alone, boiled xylanase alone, xylanase coupled with 10 μg OsCLP protein, xylanase coupled with xylanase inhibitor (15 mM N-bromosuccinimide, Sigma), and xylanase enzyme coupled with 5 μg BSA were incubated in 1 × PBS buffer (pH 8.0) for 1 h at 30°C and pipetted onto separate 0.5 mm filter disks on the LB agar xylan plate. The plate was incubated in the dark for 24 h at 30°C, followed by staining with 1% Congo red solution for 15 min and destaining with 1 M NaCl. The level of xylanase activity was measured with an LAS 4000 imaging system (Fujifilm, Japan) by detecting degraded circles of xylan. All statistical analyses were performed using Student’s t test (P < 0.05).
In-gel chitinase activity assay
Chitinase activity was assayed with glycol chitin as a substrate using previously described methods . Proteins were separated on a 12.5% SDS-PAGE gel containing 0.01% glycol chitin substrate. After incubating the gel in 100 mM sodium acetate buffer (pH 5.0) containing 1% (v/v) Triton X-100 at 37°C for 2 h, the gel was stained with 500 mM Tris–HCl (pH 8.9), 0.01% (w/v) Fluorescent Brightener 28 (Sigma-Aldrich) solution for 10 min. Fluorescent signals were detected under UV using an LAS 4000 system after destaining the gel in distilled water for 20 min.
Antifungal activity of OsCLP
The fungal pathogen Rhizoctonia solani was used for the hyphal growth inhibition assay of the OsCLP protein . R. solani was inoculated on a potato dextrose agar (PDA) plate and cultured at 28°C in the dark. Filter paper was placed onto the PDA plate 5 mm away from the growing hyphae. After placing OsCLP protein or BSA onto the filter paper, the PDA plate was incubated for 4 h at 28°C. Fungal hyphal growth was measured with a digital camera. For a close-up view of degrading hyphae, the growing hyphae on the PDA plate were covered with enzyme and observed until the release of cytosolic contents was detected under a microscope (AX70TRF, Olympus, Japan).
This work was supported by the Ministry of Education, Science, and Technology (2011–0027211 and 2011–0018092) and a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center, PJ008021), Rural Development Administration, Republic of Korea.
- Pennell R: Cell walls: structures and signals. Curr Opin Plant Biol. 1998, 1: 504-551. 10.1016/S1369-5266(98)80043-5.View ArticleGoogle Scholar
- Yoshizawa T, Shimizu T, Yamabe M, Taichi M, Nishiuchi Y, Shichijo N, Unzai S, Hirano H, Sato M, Hashimoto H: Crystal structure of basic 7S globulin, a xyloglucan specific endo-β-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-β-glucanase. FEBS J. 2011, 278: 1944-1954. 10.1111/j.1742-4658.2011.08111.x.View ArticleGoogle Scholar
- Henrissat B: A classification of glycosyl hydrolases based on amino-acid-sequence similarities. Biochem J. 1991, 280: 309-316.View ArticleGoogle Scholar
- Henrissat B, Bairoch A: New families in the classification of glycosyl hydrolases based on amino- acid sequence similarities. Biochem J. 1993, 293: 781-788.View ArticleGoogle Scholar
- Courtin CM, Delcour JA: Relative activity of endoxylanases towards water-extractable and water-unextractable arabinoxylans. J Cereal Sci. 2001, 33: 301-312. 10.1006/jcrs.2000.0354.View ArticleGoogle Scholar
- Bedford MR, Classen HL: The influence of dietary xylanase on intestinal viscosity and molecular weight distribution of carbohydratesin rye fed broiler chicks. Xylans and Xylanases. Edited by: Visser J, Beldman G, Kusters-Van Someren MA, Voragen AGJ. 1992, Amsterdam, The Netherlands: Elsevier, 361-370.Google Scholar
- Kikot GE, Hours RA, Alconana TM: Contribution of cell wall degrading enzymes to pathogenesis of Fusarium graminerum: a review. J Basic Microbiol. 2009, 49: 231-241. 10.1002/jobm.200800231.View ArticleGoogle Scholar
- Reilly PJ: Xylanases: structure and function. 1981, In Trends in the Biology of Fermentation for Fuels and Chemicals. Edited by Hollaender A. Basic Life Sciences: Plenum Press, New York, NY, 111-129.Google Scholar
- Biely P, Vrsanskà M, Tenkanen M, Kluepfel D: Endo-beta-1,4-xylanase families: differences in catalytic properties. J Biotechnol. 1997, 57: 151-166. 10.1016/S0168-1656(97)00096-5.View ArticleGoogle Scholar
- Gilkes NR, Henrissat B, Kilburn DG, Miller RC, Warren RAJ: Domains in microbial β-1,4-glycanases: sequence conservation, function, and enzyme families. Microbiol Rev. 1991, 55: 303-315.Google Scholar
- Misas-Villamil JC, van der Hoorn RA: Enzyme-inhibitor interactions at the plant-pathogen interface. Curr Opin Plant Biol. 2008, 11: 380-388. 10.1016/j.pbi.2008.04.007.View ArticleGoogle Scholar
- McLauchlan WR, Garcia-Conesa MT, Williamson G, Roza M, Ravestein P, Maat J: A novel class of protein from wheat which inhibits xylanases. Biochem J. 1999, 388: 441-446.Google Scholar
- Gebruers K, Debyser W, Goesaert H, Proost P, Van Damme J, Delcour JA: Triticumaestivem L. endoxylanase inhibitor (TAXI) consists of two inhibitors, TAXI I and TAXI II, with different specificities. Biochem J. 2001, 353: 239-244. 10.1042/0264-6021:3530239.View ArticleGoogle Scholar
- Fierens E, Rombouts S, Geruers K, Goesaert H, Brijs K, Beaugrand J, Volckaert G, Van Campenhout S, Proost P, Courtin CM, Delcour JA: TLXI, a novel type of xylanase inhibitor from wheat (Triticum asetivum) belonging to the thaumatin family. Biochem J. 2007, 403: 583-591. 10.1042/BJ20061291.View ArticleGoogle Scholar
- Flatman R, McLauchlan WR, Juge N, Furniss C, Berrin JG, Hughes RK, Manzanares P, Ladbury JE, O’Brien R, Williamson G: Interactions defining the specificity between fungal xylanases and the xylanase-inhibiting protein XIP-I from wheat. Biochem J. 2002, 365: 773-781.View ArticleGoogle Scholar
- Gebruers K, Brijs K, Courtin CM, Fierens K, Goesaert H: Properties of TAXI-type endoxylanase inhibitors. Biochim Biophys Acta. 2004, 1696: 213-221. 10.1016/j.bbapap.2003.08.013.View ArticleGoogle Scholar
- Takaaki T, Esaka M: Induction of a novel XIP-type xylanase inhibitor by external ascorbic acid treatment and differential expression of XIP-family genes in rice. Plant Cell Physiol. 2007, 48: 700-714. 10.1093/pcp/pcm038.View ArticleGoogle Scholar
- Goesaert H, Gebruers K, Courtin CM, Delcour JA: Purification and characterization of a XIP-type endoxylanase inhibitor from rice (Oryza sativa). J Enzyme Inhib. 2005, 20: 95-101. 10.1080/14756360400002080.View ArticleGoogle Scholar
- Durand A, Hugues R, Roussel A, Flatman R, Henrissat B, Juge N: Emergence of a subfamily of xylanase inhibitos within glycoside hydrolase family 18. FEBS Lett. 2005, 272: 1745-1755.View ArticleGoogle Scholar
- Takaaki T, Miyata Y, Fujikawa Y, Esaka M: RNAi-mediated knockdown of the XIP-type endoxylanase inhibitor gene, OsXIP, has no effect on grain development and germination in rice. Plant Cell Physiol. 2008, 49: 1122-1127. 10.1093/pcp/pcn080.View ArticleGoogle Scholar
- Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A: Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I. J Biol Chem. 2004, 279: 36022-36028. 10.1074/jbc.M404212200.View ArticleGoogle Scholar
- Lovorson J, Chlan CA: Plant chitinase consensus sequences. Plant Mol Biol Rep. 1997, 15: 122-133. 10.1007/BF02812262.View ArticleGoogle Scholar
- Payan F, Flatman R, Porciero S, Williamson G, Juge N, Roussel A: Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var. Soisson). Biochem J. 2003, 372: 399-405. 10.1042/BJ20021802.View ArticleGoogle Scholar
- Vasconcelos EA, Santana CG, Godoy CV, Seixas CD, Silva MS, Moreira LR, Oloveria-Neto OB, Price D, Fitches E, Fiho EX, Mehta A, Gatehouse JA, Grossi-De-Sa MF: A new chitinase-like xylanase inhibitor protein (XIP) from coffee (Coffea arabica) affects Soybean Asian rust (Phakopsora pachyrhizi) spore germination. BMC Biotechnol. 2011, 7: 11-14.Google Scholar
- Igawa T, Ochiai-Fukuda T, Takahashi-Ando N, Ohsato S, Shibata T, Yamaguchi I, Kimura M: New TAXI-type xylanase inhibitor genes are inducible by pathogens and wounding in hexaploid wheat. Plant Cell Physiol. 2004, 45: 1347-1360. 10.1093/pcp/pch195.View ArticleGoogle Scholar
- Trudel J, Asselin A: Detection of chitinase activity after polyacrylamide gel electrophoresis. Anal Biochem. 1989, 178: 362-366. 10.1016/0003-2697(89)90653-2.View ArticleGoogle Scholar
- Dehsetani A, Kazemitabar K, Ahmadian G, Jelodar NB, Salmanian AH, Sezedi M, Rahimian H, Ghasemi S: Chitinolytic and antifungal activity of a Bacillus pumilus chitinase expressed in Arabidopsis. Biotechnol Lett. 2010, 32: 539-546. 10.1007/s10529-009-0192-1.View ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.