Determination of cDNA and genomic DNA sequences of hevamine, a chitinase from the rubber tree Hevea brasiliensis

Bokma, Evert; Spiering, Marjolein; Chow, Keng See; Mulder, Patty P. M. F. A.; Subroto, Toto; Beintema, Jaap J.

doi:10.1016/s0981-9428(01)01247-5

Cited by 21 publications

(9 citation statements)

References 38 publications

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“…REF is a major protein located on the surface of large rubber particles in latex and is involved in rubber biosynthesis (Priya et al 2008). Hevamine A, a predicted target of miR160, is one of several genes encoding Hevamine, a chitinase/lysozyme activity found in the lutoid (vacuolar) fraction of rubber latex (Bokma et al 2001, 1997; Subroto et al 1996). Hevamine is important for plant defense against various bacterial and fungal pathogens.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing

Lertpanyasampatha

Gao

Kongsawadworakul

et al. 2012

Planta

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MicroRNAs (miRNAs) are short RNAs with essential roles in gene regulation in various organisms including higher plants. In contrast to the vast information on miRNAs from many economically important plants, almost nothing has been reported on the identification or analysis of miRNAs from rubber tree (Hevea brasiliensis L.), the most important natural rubber-producing crop. To identify miRNAs and their target genes in rubber tree, high throughput sequencing combined with a computational approach was performed. Four small RNA libraries were constructed for deep sequencing from mature and young leaves of two rubber tree clones, PB 260 and PB 217, which provide high and low latex yield, respectively. 115 miRNAs belonging to 56 known miRNA families were identified, and northern hybridization validated miRNA expression and revealed developmental stage-dependent and clone-specific expression for some miRNAs. We took advantage of the newly released rubber tree genome assembly and predicted 20 novel miRNAs. Further computational analysis uncovered potential targets of the known and novel miRNAs. Predicted target genes included not only transcription factors but also genes involved in various biological processes including stress responses, primary and secondary metabolism, and signal transduction. In particular, genes with roles in rubber biosynthesis are predicted targets of miRNAs. This study provides a basic catalog of miRNAs and their targets in rubber tree to facilitate future improvement and exploitation of rubber tree.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing

Lertpanyasampatha

Gao

Kongsawadworakul

et al. 2012

Planta

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“…They all show the (β/α) 8 barrel fold and the two consensus regions characteristic of the GH family 18 [10,11]. XIP-I shows 47, 42 and 30 % similarity and 36, 33 and 14 % identity with hevamine [13], concanavalin B [14] and narbonin [15] sequences respectively. Hevamine exhibits both lysozyme and chitinase activity [16], whereas concanavalin B and narbonin [11,12], as also reported for XIP-I [1,7], do not show any chitinase activity.…”

Section: Introductionmentioning

confidence: 99%

Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var. Soisson)

Payan

Flatman

Porciero

et al. 2003

Biochemical Journal

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A novel class of proteinaceous inhibitors exhibiting specificity towards microbial xylanases has recently been discovered in cereals. The three-dimensional structure of xylanase inhibitor protein I (XIP-I) from wheat (Triticum aestivum, var. Soisson) was determined by X-ray crystallography at 1.8 A (1 A=0.1 nm) resolution. The inhibitor possesses a (beta/alpha)(8) barrel fold and has structural features typical of glycoside hydrolase family 18, namely two consensus regions, approximately corresponding to the third and fourth barrel strands, and two non-proline cis -peptide bonds, Ser(36)-Phe and Trp(256)-Asp (in XIP-I numbering). However, detailed structural analysis of XIP-I revealed several differences in the region homologous with the active site of chitinases. The catalytic glutamic acid residue of family 18 chitinases [Glu(127) in hevamine, a chitinase/lysozyme from the rubber tree (Hevea brasiliensis)] is conserved in the structure of the inhibitor (Glu(128)), but its side chain is fully engaged in salt bridges with two neighbouring arginine residues. Gly(81), located in subsite -1 of hevamine, where the reaction intermediate is formed, is replaced by Tyr(80) in XIP-I. The tyrosine side chain fills the subsite area and makes a strong hydrogen bond with the side chain of Glu(190) located at the opposite side of the cleft, preventing access of the substrate to the catalytic glutamic acid. The structural differences in the inhibitor cleft structure probably account for the lack of activity of XIP-I towards chitin.

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“…The existence of several classes of GH18 chitinases in plants was previously suggested [9]. However the general impression was that gene duplications, gene losses and perhaps also translocations resulted in rather unreliable relationships for deriving evolutionary conclusions [10]. In contrast to the abundant genetic information produced from recent sequencing programmes of plant organisms (rice and Arabidopsis), relatively little is known about the enzymatic and structural properties of GH18 plant chitinases.…”

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

et al. 2005

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The xylanase inhibitor protein I (XIP‐I), recently identified in wheat, inhibits xylanases belonging to glycoside hydrolase families 10 (GH10) and 11 (GH11). Sequence and structural similarities indicate that XIP‐I is related to chitinases of family GH18, despite its lack of enzymatic activity. Here we report the identification and biochemical characterization of a XIP‐type inhibitor from rice. Despite its initial classification as a chitinase, the rice inhibitor does not exhibit chitinolytic activity but shows specificities towards fungal GH11 xylanases similar to that of its wheat counterpart. This, together, with an analysis of approximately 150 plant members of glycosidase family GH18 provides compelling evidence that xylanase inhibitors are largely represented in this family, and that this novel function has recently emerged based on a common scaffold. The plurifunctionality of GH18 members has major implications for genomic annotations and predicted gene function. This study provides new information which will lead to a better understanding of the biological significance of a number of GH18 ‘inactivated’ chitinases.

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Determination of cDNA and genomic DNA sequences of hevamine, a chitinase from the rubber tree Hevea brasiliensis

Cited by 21 publications

References 38 publications

Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing

Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing

Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var. Soisson)

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

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