A comparative proteomic approach to analyse structure, function and evolution of rice chitinases: a step towards increasing plant fungal resistance

Abstract

Glycoside hydrolase family 19 chitinases (EC 3.2.1.14) widely distributed in plants, bacteria and viruses catalyse the hydrolysis of chitin and play a major role in plant defense mechanisms and development. Rice possesses several classes of chitinase, out of which a single structure of class I has been reported in PDB to date. In the present study an attempt was made to gain more insight into the structure, function and evolution of class I, II and IV chitinases of GH family 19 from rice. The three-dimensional structures of chitinases were modelled and validated based on available X-ray crystal structures. The structural study revealed that they are highly α-helical and bilobed in nature. These enzymes are single or multi domain and multi-functional in which chitin-binding domain (CBD) and catalytic domain (CatD) are present in class I and IV whereas class II lacks CBD. The CatD possesses a catalytic triad which is thought to be involved in catalytic process. Loop III, which is common in all three classes of chitinases, reflects that it may play a significant role in their function. Our study also confirms that the absence and presence of different loops in GH family 19 of rice may be responsible for various sized products. Molecular phylogeny revealed chitinases in monocotyledons and dicotyledons differed from each other forming two different clusters and may have evolved differentially. More structural study of this enzyme from different plants is required to enhance the knowledge of catalytic mechanism and substrate binding.

Genome‐wide analysis of salicylic acid and jasmonic acid signalling marker gene families in wheat

“…2010; Sarma et al . 2012). In the PR5 family, proteins encoded by wheat pathogen‐responsive genes were found in all clades with more pathogen‐responsive genes in clade V containing the TLPK and clade VI containing TaPR5‐1 and TaPR5‐2.…”

“…2010; Sarma et al . 2012). The JA biosynthetic gene allene oxide synthase ( AOS ) is a member of the cytochrome p450 CYP74 family and has been studied as a JA‐responsive marker in Arabidopsis (Poncini et al .…”

“…However, the defence-associated plant defensin 1.2 (PDF1.2) and the defence-associated PR4 were also used as markers of the ethylene pathway (Li et al 2004;Poncini et al 2017). PR3 proteins are chitinases from classes I, II, IV, VI and VII, belonging to the glycoside hydrolase family 19 (Tyler et al 2010;Sarma et al 2012). The JA biosynthetic gene allene oxide synthase (AOS ) is a member of the cytochrome p450 CYP74 family and has been studied as a JA-responsive marker in Arabidopsis (Poncini et al 2017;Singh et al 2017), wheat and Brachypodium (Kouzai et al 2016;Liu et al 2016;Debona et al 2017).…”

Plant Chitinases: Molecular Structure, Importance and Utilizations

“…Bu enzim bitki bulunduğu tarihten itibaren bağışıklık cevabını güçlendirmede bir araç olarak kullanılmaktadır (Sharma et al, 2011). Bitki kitinazları; yapıları, substrat spesifiteleri, kataliz mekanizmaları ve inhibitör hassasiyetleri temelinde, GH18 ve GH19 aileleri içinde toplam 7 sınıf (I-VII) altında bulunmaktadırlar (Arie et al, 2000;Sarma et al, 2012). Sınıf I, II, IV, VI ve VII GH19 ailesinde; Sınıf III ve V ise GH18 ailesinin üyelerdir (Adrangi and Faramarzi, 2013).…”

Comparative study of two GH19 chitinase‐like proteins from Hevea brasiliensis, one exhibiting a novel carbohydrate‐binding domain

“…Plants express chitinases and CLPs, which belong to the glycosyl hydrolase GH18 and GH19 families, constitutively in tissues vulnerable to pathogen attack and inducibly as pathogenesis‐related proteins (PRP) . Based on sequence similarity, plant chitinases are classified into seven classes (I–VII) . Classes represented in the GH19 family are I, II, IV, VI and VII, while classes III and V are members of the GH18 family.…”