Emergence of a subfamily of xylanase inhibitors within glycoside hydrolase family 18

Identification and expression analysis of XIP gene family members in rice

Xylanase inhibitor proteins (XIP) are widely distributed in the plant kingdom, and also exist in rice. However, a systematic bioinformatics analysis of this gene family in rice (OsXIP) has not been conducted to date. In this study, we identified 32 members of the OsXIP gene family and analyzed their physicochemical properties, chromosomal localization, gene structure, protein structure, expression profiles, and interaction networks. Our results indicated that OsXIP genes exhibit an uneven distribution across eight rice chromosomes. These genes generally feature a low number of introns or are intronless, all family members, except for OsXIP20, contain two highly conserved motifs, namely Motif 8 and Motif 9. In addition, it is worth noting that the promoter regions of OsXIP gene family members feature a widespread presence of abscisic acid response elements (ABRE) and gibberellin response elements (GARE-motif and TATC-box). Quantitative Real-time PCR (qRT-PCR) analysis unveiled that the expression of OsXIP genes exhibited higher levels in leaves and roots, with considerable variation in the expression of each gene in these tissues both prior to and following treatments with abscisic acid (ABA) and gibberellin (GA3). Protein interaction studies and microRNA (miRNA) target prediction showed that OsXIP engages with key elements within the hormone-responsive and drought signaling pathways. The qRT-PCR suggested osa-miR2927 as a potential key regulator in the rice responding to drought stress, functioning as tissue-specific and temporally regulation. This study provides a theoretical foundation for further analysis of the functions within the OsXIP gene family.

Interactive transcriptome analyses of Northern Wild Rice (Zizania palustris L.) and Bipolaris oryzae show convoluted communications during the early stages of fungal brown spot development

Fungal diseases, caused mainly by Bipolaris spp., are past and current threats to Northern Wild Rice (NWR) grain production and germplasm preservation in both natural and cultivated settings. Genetic resistance against the pathogen is scarce. Toward expanding our understanding of the global gene communications of NWR and Bipolaris oryzae interaction, we designed an RNA sequencing study encompassing the first 12 h and 48 h of their encounter. NWR activated numerous plant recognition receptors after pathogen infection, followed by active transcriptional reprogramming of signaling mechanisms driven by Ca2+ and its sensors, mitogen-activated protein kinase cascades, activation of an oxidative burst, and phytohormone signaling-bound mechanisms. Several transcription factors associated with plant defense were found to be expressed. Importantly, evidence of diterpenoid phytoalexins, especially phytocassane biosynthesis, among expression of other defense genes was found. In B. oryzae, predicted genes associated with pathogenicity including secreted effectors that could target plant defense mechanisms were expressed. This study uncovered the early molecular communication between the NWR-B. oryzae pathosystem, which could guide selection for allele-specific genes to boost NWR defenses, and overall aid in the development of more efficient selection methods in NWR breeding through the use of the most virulent fungal isolates.

Characterization of two rice GH18 chitinases belonging to family 8 of plant pathogenesis-related proteins

Two rice GH18 chitinases, Oschib1 and Oschib2, belonging to family 8 of plant pathogenesis-related proteins (PR proteins) were expressed, purified, and characterized. These enzymes, which have the structural features of class IIIb chitinases, preferentially cleaved the second glycosidic linkage from the non-reducing end of substrate chitin oligosaccharides as opposed to rice class IIIa enzymes, OsChib3a and OsChib3b, which mainly cleaved the fourth linkage from the non-reducing end of chitin hexasaccharide [(GlcNAc)₆]. Oschib1 and Oschiab2 inhibited the growth of Fusarium solani, but showed only a weak or no antifungal activity against Aspergillus niger and Trichoderma viride on the agar plates. Structural analysis of Oschib1 and Oschib2 revealed that these enzymes have two large loops extruded from the (β/α)₈ TIM-barrel fold, which are absent in the structures of class IIIa chitinases. The differences in the cleavage site preferences toward chitin oligosaccharides between plant class IIIa and IIIb chitinases are likely attributed to the additional loop structures found in the IIIb enzymes. The class IIIb chitinases, Oschib1 and Oschib2, seem to play important roles for the effective hydrolysis of chitin oligosaccharides released from the cell wall of the pathogenic fungi by the cooperative actions with the extracellular chitinases in rice.

Xylanase Inhibitors: Defense Players in Plant Immunity with Implications in Agro-Industrial Processing

Xylanase inhibitors (XIs) are plant cell wall proteins largely distributed in monocots that inhibit the hemicellulose degrading activity of microbial xylanases. XIs have been classified into three classes with different structures and inhibition specificities, namely Triticum aestivum xylanase inhibitors (TAXI), xylanase inhibitor proteins (XIP), and thaumatin-like xylanase inhibitors (TLXI). Their involvement in plant defense has been established by several reports. Additionally, these inhibitors have considerable economic relevance because they interfere with the activity of xylanases applied in several agro-industrial processes. Previous reviews highlighted the structural and biochemical properties of XIs and hypothesized their role in plant defense. Here, we aimed to update the information on the genomic organization of XI encoding genes, the inhibition properties of XIs against microbial xylanases, and the structural properties of xylanase-XI interaction. We also deepened the knowledge of XI regulation mechanisms in planta and their involvement in plant defense. Finally, we reported the recently studied strategies to reduce the negative impact of XIs in agro-industrial processes and mentioned their allergenicity potential.

Unearthing the alleviatory mechanisms of hydrogen sulfide in aluminum toxicity in rice

Hydrogen sulfide (H₂S) improves aluminum (Al) resistance in rice, however, the underlying mechanism remains unclear. In the present study, treatment with 30-μM Al significantly inhibited rice root growth and increased the total Al content, apoplastic and cytoplasm Al concentration in the rice roots. However, pretreatment with NaHS (H₂S donor) reversed these negative effects. Pretreatment with NaHS significantly increased energy production under Al toxicity conditions, such as by increasing the content of ATP and nonstructural carbohydrates. In addition, NaHS stimulated the AsA-GSH cycle to decrease the peroxidation damage induced by Al toxicity. Pretreatment with NaHS significantly inhibited ethylene emissions in the rice and then inhibited pectin synthesis and increased the pectin methylation degree to reduce cell wall Al deposition. The phytohormones indole-3-acetic and brassinolide were also involved in the alleviation of Al toxicity by H₂S. The transcriptome results further confirmed that H₂S alleviates Al toxicity by increasing the pathways relating to material and energy metabolism, redox reactions, cell wall components, and signal transduction. These findings improve our understanding of how H₂S affects rice responses to Al toxicity, which will facilitate further studies on crop safety.

Changes in the Cell Wall Proteome of Leaves in Response to High Temperature Stress in Brachypodium distachyon

High temperature stress leads to complex changes to plant functionality, which affects, i.a., the cell wall structure and the cell wall protein composition. In this study, the qualitative and quantitative changes in the cell wall proteome of Brachypodium distachyon leaves in response to high (40 °C) temperature stress were characterised. Using a proteomic analysis, 1533 non-redundant proteins were identified from which 338 cell wall proteins were distinguished. At a high temperature, we identified 46 differentially abundant proteins, and of these, 4 were over-accumulated and 42 were under-accumulated. The most significant changes were observed in the proteins acting on the cell wall polysaccharides, specifically, 2 over- and 12 under-accumulated proteins. Based on the qualitative analysis, one cell wall protein was identified that was uniquely present at 40 °C but was absent in the control and 24 proteins that were present in the control but were absent at 40 °C. Overall, the changes in the cell wall proteome at 40 °C suggest a lower protease activity, lignification and an expansion of the cell wall. These results offer a new insight into the changes in the cell wall proteome in response to high temperature.

Friend or Foe? Impacts of Dietary Xylans, Xylooligosaccharides, and Xylanases on Intestinal Health and Growth Performance of Monogastric Animals

This paper discusses the structural difference and role of xylan, procedures involved in the production of xylooligosaccharides (XOS), and their implementation into animal feeds. Xylan is non-starch polysaccharides that share a β-(1-4)-linked xylopyranose backbone as a common feature. Due to the myriad of residues that can be substituted on the polymers within the xylan family, more anti-nutritional factors are associated with certain types of xylan than others. XOS are sugar oligomers extracted from xylan-containing lignocellulosic materials, such as crop residues, wood, and herbaceous biomass, that possess prebiotic effects. XOS can also be produced in the intestine of monogastric animals to some extent when exogenous enzymes, such as xylanase, are added to the feed. Xylanase supplementation is a common practice within both swine and poultry production to reduce intestinal viscosity and improve digestive utilization of nutrients. The efficacy of xylanase supplementation varies widely due a number of factors, one of which being the presence of xylanase inhibitors present in common feedstuffs. The use of prebiotics in animal feeding is gaining popularity as producers look to accelerate growth rate, enhance intestinal health, and improve other production parameters in an attempt to provide a safe and sustainable food product. Available research on the impact of xylan, XOS, as well as xylanase on the growth and health of swine and poultry, is also summarized. The response to xylanase supplementation in swine and poultry feeds is highly variable and whether the benefits are a result of nutrient release from NSP, reduction in digesta viscosity, production of short chain xylooligosaccharides or a combination of these is still in question. XOS supplementation seems to benefit both swine and poultry at various stages of production, as well as varying levels of XOS purity and degree of polymerization; however, further research is needed to elucidate the ideal dosage, purity, and degree of polymerization needed to confer benefits on intestinal health and performance in each respective species.

TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity

The ICChI is a 35-kDa, glycosylated protein isolated from the latex of the weed Ipomoea carnea. It displays chitinase and lysozyme activity, which could be important for the defense against pathogenic fungi, insects and bacteria. The ICChI enzyme was crystallized, and a diffraction data set was collected from a single crystal to 1.42 Å resolution. The crystals belong to the primitive tetragonal space group P4₃2₁2, with unit-cell parameters a = b = 57.9, c = 172.0 Å, and α = β = γ = 90°. The structure was elucidated by molecular replacement method using a mixed model of three homologous structures from the N-terminal sequence of ICChI. The refined model consists of 272 amino acid residues and has a R_factor of 18.93% and R_free of 22.42%. The protein consists of a single globular domain with a (α/β)₈ triosephosphate isomerase barrel fold. Three of the consensus sites for N-glycosylation viz., Asn⁴⁵, Asn¹⁷², and Asn¹⁹⁴ containing carbohydrate moieties N-Acetylglucosamine (NAG), mannose, fucose, and xylose. The putative catalytic residues are Asp¹²⁵, Glu¹²⁷, and Tyr¹⁸⁴. The crystal structure may provide fundamental information of GH18 family chitinases.

Differential inhibition of GH family 11 endo-xylanase by rice xylanase inhibitor and verification by a modified yeast two-hybrid system

Rice xylanase inhibitor (RIXI) is a XIP-type xylanase inhibitor protein that protects rice cells from pathogenic organisms. RIXI inhibits most microbial xylanases and thus decreases their practical application. The recombinant RIXI (rePRIXI) showed evident inhibitory activities against several family 11 endo-xylanases. After interaction with rePRIXI at 50 °C for 40 min, the residual activities of reBaxA50, reBaxA, TfxA_CD214, and TfxA_CD were 55.6%, 30.3%, 30.09%, and 11.20%, respectively. Intrinsic fluorescence of reBaxA50 and TfxA_CD214 was statically quenched after interaction with rePRIXI. rePRIXI decreased hydrolysis of beechwood xylan by reBaxA50 and TfxA_CD214. Molecular dynamics simulations revealed the long loop (residues 144-153) of RIXI inserts into the catalytic cleft of family 11 xylanases. Native PAGE results revealed the formation of RIXI-xylanase complex after their interaction in the test tube. Interactions were also observed between RIXI and xylanases in living yeast cells. The results of inhibitory activity assay and modified yeast two-hybrid revealed that the inhibitory activity of RIXI on family 11 xylanase improved with the interaction strength of the RIXI-xylanase complex, indicating their positive correlation. The modified yeast two-hybrid system is relatively simple and has low cost, and its use may be extended to other studies on protein-protein interactions.

Molecular Cloning and Characterizations of Xylanase Inhibitor Protein from Wheat (Triticum Aestivum)

Xylanase inhibitor proteins (XIPs) were regarded to inhibit the activity of xylanases during baking and gluten-starch separation processes. To avoid the inhibition to xylanases, it is necessary to define the conditions under which the inhibition takes place. In this study, we cloned the XIP gene from 2 different variety of Triticum aestivum, that is, Zhengmai 9023 and Zhengmai 366, and investigated the properties of XIP protein expressed by Pichia pastoris. The results showed that the 2 XIP genes (xip-9023 and xip-366) were highly homologous with only 3 nucleotide differences. XIP-9023 showed the optimal inhibition pH and temperature were 7 °C and 40 °C, respectively. Inhibition of xylanase by XIP-9023 reached the maximum in 40 min. At 50% inhibition of xylanase, the molar ratio of inhibitor: xylanase was 26:1. XIP-9023 was active to various fungal xylanases tested as well as to a bacterial xylanase produced by Paenibacillus sp. isolated from cow rumen.

Transcriptome profiling of Elymus sibiricus, an important forage grass in Qinghai-Tibet plateau, reveals novel insights into candidate genes that potentially connected to seed shattering

BACKGROUND

Elymus sibiricus is an important forage grass in semi-arid regions, but it is difficult to grow for commercial seed production due to high seed shattering. To better understand the underlying mechanism and explore the putative genes related to seed shattering, we conducted a combination of morphological, histological, physiochemical and transcriptome analysis on two E. sibiricus genotypes (XH09 and ZhN03) that have contrasting seed shattering.

RESULTS

The results show that seed shattering is generally caused by a degradation of the abscission layer. Early degradation of abscission layers was associated with the increased seed shattering in high seed shattering genotype XH09. Two cell wall degrading enzymes, cellulase (CE) and polygalacturonase (PG), had different activity in the abscission zone, indicating their roles in differentiation of abscission layer. cDNA libraries from abscission zone tissue of XH09 and ZhN03 at 7 days, 21 days and 28 days after heading were constructed and sequenced. A total of 86,634 unigenes were annotated and 7110 differentially expressed transcripts (DETs) were predicted from "XH09-7 vs ZhN03-7", "XH09-21 vs ZhN03-21" and "XH09-28 vs ZhN03-28", corresponding to 2058 up-regulated and 5052 down-regulated unigenes. The expression profiles of 10 candidate transcripts involved in cell wall-degrading enzymes, lignin biosynthesis and phytohormone activity were validated using quantitative real-time PCR (qRT-PCR), 8 of which were up-regulated in low seed shattering genotype ZhN03, suggesting these genes may be associated with reduction of seed shattering.

CONCLUSIONS

The expression data generated in this study provides an important resource for future molecular biological research in E. sibiricus.

Identification of two transcription factors activating the expression of OsXIP in rice defence response

Background

Xylanase inhibitors have been confirmed to be involved in plant defence. OsXIP is a XIP-type rice xylanase inhibitor, yet its transcriptional regulation remains unknown.

Results

Herbivore infestation, wounding and methyl jasmonate (MeJA) treatment enhanced mRNA levels and protein levels of OsXIP. By analyzing different 5’ deletion mutants of OsXIP promoter exposed to rice brown planthopper Nilaparvata lugens stress, a 562 bp region (–1451 – −889) was finally identified as the key sequence for the herbivores stress response. Using yeast one-hybrid screening, coupled with chromatin immunoprecipitation analysis, a basic helix-loop-helix protein (OsbHLH59) and an APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor OsERF71 directly binding to the 562 bp key sequence to activate the expression of OsXIP were identified, which is further supported by transient expression assay. Moreover, transcriptional analysis revealed that mechanical wounding and treatment with MeJA resulted in an obvious increase in transcript levels of OsbHLH59 and OsERF71 in root and shoot tissues.

Conclusions

Our data shows that two proteins as direct transcriptional activators of OsXIP responding to stress were identified. These results reveal a coordinated regulatory mechanism of OsXIP, which may probably be involved in defence responses via a JA-mediated signaling pathway.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-017-0344-7) contains supplementary material, which is available to authorized users.

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

The rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-l-arabinofuranosidase, β-d-xylosidase, α-l-arabinanase, and β-d-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides.

Functional Characterization of Novel Chitinase Genes Present in the Sheath Blight Resistance QTL: qSBR11-1 in Rice Line Tetep

Rice sheath blight disease caused by Rhizoctonia solani is one of the most devastating diseases in rice leading to heavy yield losses. Due to the polygenic nature of resistance, no major resistance gene with complete host resistance against R. solani has been reported. In this study, we have performed molecular and functional analysis of the genes associated with the major R. solani-resistance QTL qSBR11-1 in the indica rice line Tetep. Sequence analysis revealed the presence of a set of 11 tandem repeats containing genes with a high degree of homology to class III chitinase defense response genes. Real-time quantitative PCR analysis showed that all the genes are strongly induced 36 h after R. solani infection. Comparison between the resistant Tetep and the susceptible HP2216 lines shows that the induction of the chitinase genes is much higher in the Tetep line. Recombinant protein produced in vitro for six of the eleven genes showed chitinolytic activity in gel assays but we did not detect any xylanase inhibitory activity. All the six in vitro expressed proteins show antifungal activity with a clear inhibitory effect on the growth of the R. solani mycelium. The characterized chitinase genes can provide an important resource for the genetic improvement of R. solani susceptible rice lines for sheath blight resistance breeding.

Structural and functional evolution of chitinase-like proteins from plants

The plant genome contains a large number of sequences that encode catalytically inactive chitinases referred to as chitinase-like proteins (CLPs). Although CLPs share high sequence and structural homology with chitinases of glycosyl hydrolase 18 (TIM barrel domain) and 19 families, they may lack the binding/catalytic activity. Molecular genetic analysis revealed that gene duplication events followed by mutation in the existing chitinase gene have resulted in the loss of activity. The evidences show that adaptive functional diversification of the CLPs has been achieved through alterations in the flexible regions than in the rigid structural elements. The CLPs plays an important role in the defense response against pathogenic attack, biotic and abiotic stress. They are also involved in the growth and developmental processes of plants. Since the physiological roles of CLPs are similar to chitinase, such mutations have led to plurifunctional enzymes. The biochemical and structural characterization of the CLPs is essential for understanding their roles and to develop potential utility in biotechnological industries. This review sheds light on the structure-function evolution of CLPs from chitinases.

Structural basis for carbohydrate binding properties of a plant chitinase-like agglutinin with conserved catalytic machinery

A new chitinase-like agglutinin, RobpsCRA, related to family GH18 chitinases, has previously been identified in black locust (Robinia pseudoacacia) bark. The crystal structure of RobpsCRA at 1.85Å resolution reveals unusual molecular determinants responsible for the lack of its ancestral chitinase activity. Unlike other chitinase-like proteins, which lack chitinase catalytic residues, RobpsCRA has conserved its catalytic machinery. However, concerted rearrangements of loop regions coupled to non-conservative substitutions of aromatic residues central to the chitin-binding groove explain the lack of hydrolytic activity against chitin and the switch toward recognition of high-mannose type N-glycans. Identification of close homologs in flowering plants with conservation of sequence motifs associated to the structural adaptations seen in RobpsCRA defines an emerging class of agglutinins, as emphasized by a phylogenetic analysis, that are likely to share a similar carbohydrate binding specificity for high-mannose type N-glycans. This study illustrates the recent evolution and molecular adaptation of a versatile TIM-barrel scaffold within the ancestral GH18 family.

Depiction of carbohydrate-active enzyme diversity in Caldicellulosiruptor sp. F32 at the genome level reveals insights into distinct polysaccharide degradation features

Diverse and distinctive encoding sequences of CAZyme in the genome of Caldicellulosiruptor sp. F32 enable the deconstruction of unpretreated lignocellulose.

Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome

Background

A critical aspect of plant infection by the majority of pathogens is penetration of the plant cell wall. This process requires the production and secretion of a broad spectrum of pathogen enzymes that target and degrade the many complex polysaccharides in the plant cell wall. As a necessary framework for a study of the expression of cell wall degrading enzymes (CWDEs) produced by the broad host range phytopathogen, Phytophthora parasitica, we have conducted an in-depth bioinformatics analysis of the entire complement of genes encoding CWDEs in this pathogen’s genome.

Results

Our bioinformatic analysis indicates that 431 (2%) of the 20,825 predicted proteins encoded by the P. parasitica genome, are carbohydrate-active enzymes (CAZymes) involved in the degradation of cell wall polysaccharides. Of the 431 proteins, 337 contain classical N-terminal secretion signals and 67 are predicted to be targeted to the non-classical secretion pathway. Identification of CAZyme catalytic activity based on primary protein sequence is difficult, nevertheless, detailed comparisons with previously characterized enzymes has allowed us to determine likely enzyme activities and targeted substrates for many of the P. parasitica CWDEs. Some proteins (12%) contain more than one CAZyme module but, in most cases, multiple modules are from the same CAZyme family. Only 12 P. parasitica CWDEs contain both catalytically-active (glycosyl hydrolase) and non-catalytic (carbohydrate binding) modules, a situation that contrasts with that in fungal phytopathogens. Other striking differences between the complements of CWDEs in P. parasitica and fungal phytopathogens are seen in the CAZyme families that target cellulose, pectins or β-1,3-glucans (e.g. callose). About 25% of P. parasitica CAZymes are solely directed towards pectin degradation, with the majority coming from pectin lyase or carbohydrate esterase families. Fungal phytopathogens typically contain less than half the numbers of these CAZymes. The P. parasitica genome, like that of other Oomycetes, is rich in CAZymes that target β-1,3-glucans.

Conclusions

This detailed analysis of the full complement of P. parasitica cell wall degrading enzymes provides a framework for an in-depth study of patterns of expression of these pathogen genes during plant infection and the induction or repression of expression by selected substrates.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-785) contains supplementary material, which is available to authorized users.

Optimization of transplastomic production of hemicellulases in tobacco: effects of expression cassette configuration and tobacco cultivar used as production platform on recombinant protein yields

BACKGROUND

Chloroplast transformation in tobacco has been used extensively to produce recombinant proteins and enzymes. Chloroplast expression cassettes can be designed with different configurations of the cis-acting elements that govern foreign gene expression. With the aim to optimize production of recombinant hemicellulases in transplastomic tobacco, we developed a set of cassettes that incorporate elements known to facilitate protein expression in chloroplasts and examined expression and accumulation of a bacterial xylanase XynA. Biomass production is another important factor in achieving sustainable and high-volume production of cellulolytic enzymes. Therefore, we compared productivity of two tobacco cultivars - a low-alkaloid and a high-biomass - as transplastomic expression platforms.

RESULTS

Four different cassettes expressing XynA produced various mutant phenotypes of the transplastomic plants, affected their growth rate and resulted in different accumulation levels of the XynA enzyme. The most productive cassette was identified and used further to express XynA and two additional fungal xylanases, Xyn10A and Xyn11B, in a high-biomass tobacco cultivar. The high biomass cultivar allowed for a 60% increase in XynA production per plant. Accumulation of the fungal enzymes reached more than 10-fold higher levels than the bacterial enzyme, constituting up to 6% of the total soluble protein in the leaf tissue. Use of a well-characterized translational enhancer with the selected expression cassette revealed inconsistent effects on accumulation of the recombinant xylanases. Additionally, differences in the enzymatic activity of crude plant extracts measured in leaves of different age suggest presence of a specific xylanase inhibitor in the green leaf tissue.

CONCLUSION

Our results demonstrate the pivotal importance of the expression cassette design and appropriate tobacco cultivar for high-level transplastomic production of recombinant proteins.

Characterization of a newly identified rice chitinase-like protein (OsCLP) homologous to xylanase inhibitor

BACKGROUND

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.

RESULTS

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.

CONCLUSIONS

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.

Effects of an exogenous xylanase gene expression on the growth of transgenic rice and the expression level of endogenous xylanase inhibitor gene RIXI

BACKGROUND

Xylanases have attracted considerable interest in recent years owing to their various applications in industry and agriculture. The use of transgenic plants to produce xylanases is a less expensive alternative to biotechnological programmes. The aim of this study was to elucidate whether introducing a foreign xylanase gene ATX into rice had any adverse effect on plant growth and development.

RESULTS

A recombinant xylanase gene ATX was introduced into rice variety Zhonghua 11 through Agrobacterium-mediated transformation. The T₂ generation of transgenic rice was compared with the control (non-transgenic plants). Exogenous xylanase gene ATX was expressed in rice, and all examined transgenic lines exhibited xylanase activity. The transgenic lines (T₂, 'X1-3' and 'X2-5') appeared to grow and develop normally. There were no differences in net photosynthetic rate between transgenic rice lines ('X1-3' and 'X2-5') and wild type (WT) rice plants at the heading/flowering stage. Xylanases are key enzymes in the degradation of plant cell walls. Cell wall composition analysis showed that that there were no changes in cell wall polysaccharides in the root apex but some alterations in leaves in transgenic rice plants. The results also showed that the expression of exogenous xylanase gene ATX in rice would increase the expression of endogenous xylanase inhibitor gene RIXI, which could play a role in plant defence. Thus the stress resistance of transgenic rice plants might be improved.

CONCLUSION

Exogenous xylanase gene ATX could be successfully expressed in rice, and the exogenous protein had no apparent harmful effects on growth and development in transgenic rice plants.

Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)

Background

The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5.

Results

About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions.

Conclusion

Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at http://www.cazy.org/GH5.html.

GH11 xylanases: Structure/function/properties relationships and applications

For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.

A new chitinase-like xylanase inhibitor protein (XIP) from coffee (Coffea arabica) affects Soybean Asian rust (Phakopsora pachyrhizi) spore germination

BACKGROUND

Asian rust (Phakopsora pachyrhizi) is a common disease in Brazilian soybean fields and it is difficult to control. To identify a biochemical candidate with potential to combat this disease, a new chitinase-like xylanase inhibitor protein (XIP) from coffee (Coffea arabica) (CaclXIP) leaves was cloned into the pGAPZα-B vector for expression in Pichia pastoris.

RESULTS

A cDNA encoding a chitinase-like xylanase inhibitor protein (XIP) from coffee (Coffea arabica) (CaclXIP), was isolated from leaves. The amino acid sequence predicts a (β/α)8 topology common to Class III Chitinases (glycoside hydrolase family 18 proteins; GH18), and shares similarity with other GH18 members, although it lacks the glutamic acid residue essential for catalysis, which is replaced by glutamine. CaclXIP was expressed as a recombinant protein in Pichia pastoris. Enzymatic assay showed that purified recombinant CaclXIP had only residual chitinolytic activity. However, it inhibited xylanases from Acrophialophora nainiana by approx. 60% when present at 12:1 (w/w) enzyme:inhibitor ratio. Additionally, CaclXIP at 1.5 μg/μL inhibited the germination of spores of Phakopsora pachyrhizi by 45%.

CONCLUSIONS

Our data suggests that CaclXIP belongs to a class of naturally inactive chitinases that have evolved to act in plant cell defence as xylanase inhibitors. Its role on inhibiting germination of fungal spores makes it an eligible candidate gene for the control of Asian rust.

Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon

BACKGROUND

Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families.

RESULTS

We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. For several glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51), we present a detailed literature review together with an examination of the family structures. This analysis of individual families revealed both similarities and distinctions between monocots and eudicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within GH families, the Brachypodium and sorghum proteins generally cluster with those from other monocots.

CONCLUSIONS

This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a grass model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.

Proteomic analysis of salicylate-induced proteins of pea (Pisum sativum L.) leaves

The effect of 50 microM salicylic acid on soluble proteins of pea (Pisum sativum L.) leaves was studied by proteomic analysis. Thirty-two salicylate-induced proteins were found, and 13 of these were identified using MALDI TOF MS. Salicylate-induced increased content was shown for the first time for the family 18 glycoside hydrolase, alpha-amylase, 33 kDa protein of photosystem II, lipid-desaturase-like protein, and glutamine amidotransferase. Increased content of protective proteins of direct antipathogenic action such as chitinase and beta-1,3-glucanases was also noted.

Identification of genes associated with growth cessation and bud dormancy entrance using a dormancy-incapable tree mutant

BACKGROUND

In many tree species the perception of short days (SD) can trigger growth cessation, dormancy entrance, and the establishment of a chilling requirement for bud break. The molecular mechanisms connecting photoperiod perception, growth cessation and dormancy entrance in perennials are not clearly understood. The peach [Prunus persica (L.) Batsch] evergrowing (evg) mutant fails to cease growth and therefore cannot enter dormancy under SD. We used the evg mutant to filter gene expression associated with growth cessation after exposure to SD. Wild-type and evg plants were grown under controlled conditions of long days (16 h/8 h) followed by transfer to SD (8 h/16 h) for eight weeks. Apical tissues were sampled at zero, one, two, four, and eight weeks of SD and suppression subtractive hybridization was performed between genotypes at the same time points.

RESULTS

We identified 23 up-regulated genes in the wild-type with respect to the mutant during SD exposure. We used quantitative real-time PCR to verify the expression of the differentially expressed genes in wild-type tissues following the transition to SD treatment. Three general expression patterns were evident: one group of genes decreased at the time of growth cessation (after 2 weeks in SD), another that increased immediately after the SD exposure and then remained steady, and another that increased throughout SD exposure.

CONCLUSIONS

The use of the dormancy-incapable mutant evg has allowed us to reduce the number of genes typically detected by differential display techniques for SD experiments. These genes are candidates for involvement in the signalling pathway leading from photoperiod perception to growth cessation and dormancy entrance and will be the target of future investigations.

Identification of genes associated with growth cessation and bud dormancy entrance using a dormancy-incapable tree mutant

BACKGROUND

In many tree species the perception of short days (SD) can trigger growth cessation, dormancy entrance, and the establishment of a chilling requirement for bud break. The molecular mechanisms connecting photoperiod perception, growth cessation and dormancy entrance in perennials are not clearly understood. The peach [Prunus persica (L.) Batsch] evergrowing (evg) mutant fails to cease growth and therefore cannot enter dormancy under SD. We used the evg mutant to filter gene expression associated with growth cessation after exposure to SD. Wild-type and evg plants were grown under controlled conditions of long days (16 h/8 h) followed by transfer to SD (8 h/16 h) for eight weeks. Apical tissues were sampled at zero, one, two, four, and eight weeks of SD and suppression subtractive hybridization was performed between genotypes at the same time points.

RESULTS

We identified 23 up-regulated genes in the wild-type with respect to the mutant during SD exposure. We used quantitative real-time PCR to verify the expression of the differentially expressed genes in wild-type tissues following the transition to SD treatment. Three general expression patterns were evident: one group of genes decreased at the time of growth cessation (after 2 weeks in SD), another that increased immediately after the SD exposure and then remained steady, and another that increased throughout SD exposure.

CONCLUSIONS

The use of the dormancy-incapable mutant evg has allowed us to reduce the number of genes typically detected by differential display techniques for SD experiments. These genes are candidates for involvement in the signalling pathway leading from photoperiod perception to growth cessation and dormancy entrance and will be the target of future investigations.

Algerian pearl millet ( Pennisetum glaucum L.) contains XIP but not TAXI and TLXI type xylanase inhibitors

An XIP (xylanase inhibiting protein) type xylanase inhibitor was purified from Algerian pearl millet ( Pennisetum glaucum L.) grains and characterized for the first time. Cation exchange and affinity chromatography with immobilized Trichoderma longibrachiatum glycoside hydrolase (GH) family 11 xylanase resulted in electrophoretically pure protein with a molecular mass of 27-29 kDa and a pI value of 6.7. The experimentally determined N-terminal amino acid sequence of the purified XIP protein is 87.5%, identical to that of sorghum ( Sorghum bicolor L.) XIP and 79.2% identical to that of wheat ( Triticum aestivum L.) XIP-I. The biochemical properties of pearl millet XIP are comparable to those described earlier for sorghum XIP, except for the higher specific activity toward a T. longibrachiatum GH family 11 xylanase. On the basis of immunoblot neither TAXI nor TLXI type xylanase inhibitors were detected in pearl millet grains.

Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora

Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining α-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron α-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. ¹H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining α-galactosidase.

Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice

Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (>100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.

Enzyme-inhibitor interactions at the plant-pathogen interface

The plant apoplast during plant-pathogen interactions is an ancient battleground that holds an intriguing range of attacking enzymes and counteracting inhibitors. Examples are pathogen xylanases and polygalacturonases that are inhibited by plant proteins like TAXI, XIP, and PGIP; and plant glucanases and proteases, which are targeted by pathogen proteins such as GIP1, EPI1, EPIC2B, and AVR2. These seven well-characterized inhibitors have different modes of action and many probably evolved from inactive enzymes themselves. Detailed studies of the structures, sequence variation, and mutated proteins uncovered molecular struggles between these enzymes and their inhibitors, resulting in positive selection for variant residues at the contact surface, where single residues determine the outcome of the interaction.

Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica

Striga hermonthica is a root hemiparasite of cereals that causes devastating loss of yield. Recently, a rice cultivar, Nipponbare, was discovered, which exhibits post-attachment resistance to this parasite and quantitative trait loci (QTL) associated with the resistance were identified. Changes in gene expression in susceptible (IAC 165) and resistant (Nipponbare) rice cultivars were profiled using rice whole-genome microarrays. In addition to a functional categorization of changes in gene expression, genes that were significantly up-regulated within resistance QTL were identified. The resistance reaction was characterized by up-regulation of defence genes, including pathogenesis-related proteins, pleiotropic drug resistance ABC transporters, genes involved in phenylpropanoid metabolism and WRKY transcription factors. These changes in gene expression resemble those associated with resistance to microbial pathogens. Three genes encoding proteins of unknown function, within a major resistance QTL on chromosome 12, were highly up-regulated and are excellent candidate resistance genes. The susceptible interaction was characterized by large-scale down-regulation of gene expression, particularly within the functional categories plant growth regulator signalling and metabolism, biogenesis of cellular components and cell division. Up-regulated genes included nutrient transporters, enzymes of amino acid metabolism and some abiotic stress genes.

RNAi-mediated knockdown of the XIP-type endoxylanase inhibitor gene, OsXIP, has no effect on grain development and germination in rice

OsXIP (Oryza sativa xylanase inhibitor protein) is a XIP-type xylanase inhibitor which was identified as a protein encoded by a wound stress-responsive gene in rice. Although the OsXIP gene was specifically expressed in mature grains under basal conditions, recombinant OsXIP had no effect on rice endogenous xylanases, and OsXIP-suppressed transgenic rice plants did not exhibit any change in grain development and germination, suggesting that rice development may be independent of OsXIP. Analysis using an OsXIP-specific antibody revealed that OsXIP is markedly accumulated in apoplast in rice root cells by wounding. These results reinforced the possibility that OsXIP is involved in plant defense mechanisms against phytopathogens.

Indirect enzyme-antibody sandwich enzyme-linked immunosorbent assay for quantification of TAXI and XIP type xylanase inhibitors in wheat and other cereals

To quantify Triticum aestivum xylanase inhibitor (TAXI) and xylanase inhibiting protein (XIP) type proteins in cereals in general and wheat ( T. aestivum) in particular, a robust enzyme-linked immunosorbent assay (ELISA) using an uncommon enzyme-antibody sandwich format was developed. Bacillus subtilis glycoside hydrolase family (GH) 11 and Aspergillus oryzae GH 10 xylanases were selected for coating ELISA plate wells to capture TAXI and XIP, respectively, prior to probing with antibodies. The detection threshold of the developed ELISA was much lower than that of the currently used xylanase inhibitor assay and the recently described Western blot approach. Because of its broad dynamic range (TAXI, 30-600 ng/mL, and XIP, 3-60 ng/mL), one proper standard extract dilution can be used for analyzing different wheat varieties, whereas for the currently used colorimetric assay, often different dilutions need to be analyzed. The TAXI ELISA for wheat was successfully adapted for barley ( Hordeum vulgare) and could also be used for other cereals.

Identification of multiple highly similar XIP-type xylanase inhibitor genes in hexaploid wheat

In hexaploid wheat, Xip-I is the only XIP-type xylanase inhibitor gene whose expression and function have been characterized in detail. Here we demonstrate the existence of new XIP-type genes with the identification of Xip-R1 and Xip-R2 in the root cDNAs. Southern blot analysis with the Xip-R1 probe revealed that XIP-type genes comprised a significantly greater gene family than previously speculated on in studies with the Xip-I probe. The transcript level of Xip-R genes was increased upon an inoculation with Erysiphe graminis in the leaves, but not with Fusarium graminearum in the spikelets. RT-PCR with the RNA samples followed by extensive sequencing of the cloned amplified products revealed the presence of 12 highly similar Xip-R genes. Among these genes, Xip-R1 was the only predominant Xip-R family member induced to express in response to E. graminis. XIP-R1 was located in the apoplastic space and inhibited family 11 xylanases, but the protein did not show chitinolytic activity. These results suggest that hexaploid wheat has a large family of XIPs in its genome, but that only some of them are expressed for plant defense in limited tissues.

Chitinase family GH18: evolutionary insights from the genomic history of a diverse protein family

Background

Chitinases (EC.3.2.1.14) hydrolyze the β-1,4-linkages in chitin, an abundant N-acetyl-β-D-glucosamine polysaccharide that is a structural component of protective biological matrices such as insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 (GH18) family of chitinases is an ancient gene family widely expressed in archea, prokaryotes and eukaryotes. Mammals are not known to synthesize chitin or metabolize it as a nutrient, yet the human genome encodes eight GH18 family members. Some GH18 proteins lack an essential catalytic glutamic acid and are likely to act as lectins rather than as enzymes. This study used comparative genomic analysis to address the evolutionary history of the GH18 multiprotein family, from early eukaryotes to mammals, in an effort to understand the forces that shaped the human genome content of chitinase related proteins.

Results

Gene duplication and loss according to a birth-and-death model of evolution is a feature of the evolutionary history of the GH18 family. The current human family likely originated from ancient genes present at the time of the bilaterian expansion (approx. 550 mya). The family expanded in the chitinous protostomes C. elegans and D. melanogaster, declined in early deuterostomes as chitin synthesis disappeared, and expanded again in late deuterostomes with a significant increase in gene number after the avian/mammalian split.

Conclusion

This comprehensive genomic study of animal GH18 proteins reveals three major phylogenetic groups in the family: chitobiases, chitinases/chitolectins, and stabilin-1 interacting chitolectins. Only the chitinase/chitolectin group is associated with expansion in late deuterostomes. Finding that the human GH18 gene family is closely linked to the human major histocompatibility complex paralogon on chromosome 1, together with the recent association of GH18 chitinase activity with Th2 cell inflammation, suggests that its late expansion could be related to an emerging interface of innate and adaptive immunity during early vertebrate history.

Mutational analysis of endoxylanases XylA and XylB from the phytopathogen Fusarium graminearum reveals comprehensive insights into their inhibitor insensitivity

Endo-beta-1,4-xylanases (EC 3.2.1.8; endoxylanases), key enzymes in the degradation of xylan, are considered to play an important role in phytopathogenesis, as they occupy a prominent position in the arsenal of hydrolytic enzymes secreted by phytopathogens to breach the cell wall and invade the plant tissue. Plant endoxylanase inhibitors are increasingly being pinpointed as part of a counterattack mechanism. To understand the surprising XIP-type endoxylanase inhibitor insensitivity of endoxylanases XylA and XylB from the phytopathogen Fusarium graminearum, an extensive mutational study of these enzymes was performed. Using combinatorial and site-directed mutagenesis, the XIP insensitivity of XylA as well as XylB was proven to be solely due to amino acid sequence adaptations in the "thumb" structural region. While XylB residues Cys141, Asp148, and Cys149 were shown to prevent XIP interaction, the XIP insensitivity of XylA could be ascribed to the occurrence of only one aberrant residue, i.e., Val151. This study, in addition to providing a thorough explanation for the XIP insensitivity of both F. graminearum endoxylanases at the molecular level, generated XylA and XylB mutants with altered inhibition specificities and pH optima. As this is the first experimental elucidation of the molecular determinants dictating the specificity of the interaction between endoxylanases of phytopathogenic origin and a plant inhibitor, this work sheds more light on the ongoing evolutionary arms race between plants and phytopathogenic fungi involving recognition of endoxylanases.

Microbial endoxylanases: effective weapons to breach the plant cell-wall barrier or, rather, triggers of plant defense systems?

Endo-beta-1,4-xylanases (EC 3.2.1.8) are key enzymes in the degradation of xylan, the predominant hemicellulose in the cell walls of plants and the second most abundant polysaccharide on earth. A number of endoxylanases are produced by microbial phytopathogens responsible for severe crop losses. These enzymes are considered to play an important role in phytopathogenesis, as they provide essential means to the attacking organism to break through the plant cell wall. Plants have evolved numerous defense mechanisms to protect themselves against invading pathogens, amongst which are proteinaceous inhibitors of cell wall-degrading enzymes. These defense mechanisms are triggered when a pathogen-derived elicitor is recognized by the plant. In this review, the diverse aspects of endoxylanases in promoting virulence and in eliciting plant defense systems are highlighted. Furthermore, the role of the relatively recently discovered cereal endoxylanase inhibitor families TAXI (Triticum aestivum xylanase inhibitor) and XIP (xylanase inhibitor protein) in plant defense is discussed.