Genome-wide characterization and expression profiling of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage (Brassica rapa ssp. pekinensis)

Md Abdul Kayum,Hoy-Taek Kim,Gopal Saha,Manosh Kumar Biswas,Ujjal Kumar Nath,Jong-In Park,Ill-Sup Nou

doi:10.1186/s12864-017-4277-2

Abstract

BackgroundProtein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance. PDI family genes are among of them.ResultsWe have identified 32 PDI genes from the Br135K microarray dataset, NCBI and BRAD database, and in silico characterized their sequences. Expression profiling of those genes was performed using cDNA of plant samples imposed to abiotic stresses; cold, salt, drought and ABA (Abscisic Acid) and biotic stress; Fusarium oxysporum f. sp. conglutinans infection. The Chinese cabbage PDI genes were clustered in eleven groups in phylogeny. Among them, 15 PDI genes were ubiquitously expressed in various organs, while 24 PDI genes were up-regulated under salt and drought stress. By contrast, cold and ABA stress responsive gene number were ten and nine, respectively. In case of F. oxysporum f. sp. conglutinans infection 14 BrPDI genes were highly up-regulated. Interestingly, BrPDI1–1 gene was identified as putative candidate against abiotic (salt and drought) and biotic stresses, BrPDI5–2 gene for ABA stress, and BrPDI1–4, 6–1 and 9–2 were putative candidate genes for both cold and chilling injury stresses.ConclusionsOur findings help to elucidate the involvement of PDI genes in stress responses, and they lay the foundation for functional genomics in future studies and molecular breeding of Brassica rapa crops. The stress-responsive PDI genes could be potential resources for molecular breeding of Brassica crops resistant to biotic and abiotic stresses.

Highlights

Protein disulfide isomerase (PDI) and Protein disulfide isomerases (PDIs)-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses
Identification of PDI genes in B. rapa A total of 32 BrPDI genes were identified using SWISSPROT of the B. rapa genomic database (BRAD; [20]); using key word “PDI”, NCBI, and annotations of microarray Br135K dataset from cold-treated B. rapa (Chiifu & Kenshin), removing any duplicates
A high degree of similarity of these 32 BrPDI protein sequences was picked for other plant species

Summary

Introduction

Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Protein disulfide isomerases (PDIs) are enzymes found primarily in the endoplasmic reticulum (ER) in eukaryotes play a vital role in protein folding. PDIs can bind into misfolded or unfolded proteins preventing to produce such aggregates [1]. PDIs are one of the mechanisms, which work through formation and breakage of connections between cysteine residues by producing disulfide bonds, which was described by Anfinsen [3]. These bonds stabilize the folded protein and provide correct structure to perform its particular function

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Conclusion