BACK TO CONTENTS   |    PDF   |    PREVIOUS   |    NEXT


Title

In silico analysis of onion chitinases using transcriptome data

Authors

Rupesh Kumar Mohapatra1, Satyabrata Nanda1,2*

 

Affiliation

1Center for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha 751003, India;

2State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 311440, China;

 

Email

sbn.satyananda@gmail.com;

 

Article Type

Hypothesis

 

Date

Received August 21, 2018; Revised August 25, 2018; Accepted August 25, 2018; Published August 31, 2018

 

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.

 

Keywords

Chitinases, Glycoside hydrolases (GH), Motifs, Phylogenetic analysis, Allium cepa

 

Citation

Mohapatra & Nanda. Bioinformation 14(8): 440-445 (2018)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.