In silico identification and analysis of the protein disulphide isomerases in wheat and rice

Abstract

The protein disulphide isomerases (PDI) typically catalyse the formation and isomerization of disulphide bonds during the folding of nascent proteins. Some PDI isoforms may also have chaperone roles under house-keeping and/or stress conditions. Human PDIs and PDI-like (PDIL) proteins show a diverse array of catalytic and chaperone roles. However, understanding of the diversity and roles of plant PDILs is limited. This work aimed to identify the PDIL superfamilies in the two main cereals, rice and wheat, to identify candidates with potential roles in seed storage protein deposition and stress response processes. Searches of the rice genomic and wheat transcript assembly databases, with the Arabidopsis PDILs as queries, led to the identification of twenty two genomic loci in rice, encoding up to thirty two putative coding sequences, as well as twenty expressed sequence tags in wheat. The gene structures in rice ranged from 3 to 15 exons, the exon lengths ranging from 22 to 1,054 base pairs (bp) and the intron lengths from 74 to 1345 bp. The wheat TAs ranged from 584-2,444 bp and many sequences appeared to be orthologous to some of the rice loci. The putative proteins of both plants exhibited the characteristic thioredoxin active-site motif WCXXC, but significant diversity in the lengths of putative proteins and the composition or positions of functional domains therein. The PDILs thus fell into five major groups: PDIL1 (7 in rice; 4 in wheat); PDIL2 (9 rice; 4 wheat); PDIL5 (7 rice; 10 wheat); QSOXL (2 rice; 1 wheat); APRL (7 rice; 1 wheat). The analysis of the gene and putative protein sequences, the functional domains of the latter, and comparisons to literature have led to identification of a number of sequences with potential enzymatic and/or chaperone roles. Several of these appear to be candidates for key roles in seed storage protein folding, plant development and stress response processes in these important crops.