Abstract

Chitinases are glycoside hydrolase (GH) family of proteins having multifaceted roles in plants. It is of interest to identify and characterize chitinase-encoding genes from the popular bulbous plant onion (Allium cepa L.). We have used the EST sequences for onion chitinases to elucidate its functional features using sequence, structure and functional analysis. These contigs belong to the GH19 chitinases family according to domain architecture analysis. They have highly conserved chitinase motifs including motifs exclusive to plant chitinases as implied using the MEME based structural characterization. Estimation of biochemical properties suggested that these proteins have features to form stable and hydrophilic proteins capable of localizing extracellular and in vacuoles. Further, they have multiple cellular processes including defense role as inferred by DeepGO function prediction. Phylogenetic analysis grouped them as class I and class VII plant chitinase, with possible abundance of class I chitinase in onion. These observations help in the isolation and functional validation of onion chitinases.

Highlights

  • Onion (Allium cepa L.) is an important and most widely cultivated bulbous vegetable with great commercial and medicinal significance [1]

  • Sequence homology assessment by consecutive rounds of Basic Local Alignment Search Tool (BLAST) searches resulted in identification of nine (AcCon16, AcCon72, AcCon198, AcCon213, AcCon387, AcCon703, AcCon1214, AcCon2325, and AcCon3094) highly homologous onion contigs with previously reported plant chitinases (Table 1)

  • In Angiosperms, GH19 family chitinases are seen in abundance and their distribution is localized to higher plants

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Summary

Introduction

Onion (Allium cepa L.) is an important and most widely cultivated bulbous vegetable with great commercial and medicinal significance [1]. On one hand the demand for onion is rising and on the other hand the vegetable faces huge crop losses due to pathogen infections majorly from fungal pathogens [3]. Diverse functionality is linked to plant chitinases, based on their sequence conservations of their catalytic domain and mechanism of action, they are classified into two glycoside hydrolase (GH) (GH18 and GH19) families [9]. GH18 family includes some plant chitinases, but mainly consists of chitinases from animals, fungi, bacteria and viruses. Most plant chitinases belong to GH19 family along with a few chitinases from nematodes and bacteria [10]. The functions and localization of different class chitinases differ from one another; for instance, class I chitinase are basic in nature and localize in vacuole, whereas class II are acidic in nature and localize extracellularly [11]

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