Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica

Abstract

Rice (Oryza sativa L.) is one of the most important cereal crops for one third of the world population. However, the grain quality as well as yield of rice is severely affected by various abiotic stresses. Environmental stresses affect the expression of various microRNAs (miRNAs) which in turn negatively regulate gene expression at the post-transcriptional level either by degrading the target mRNA genes or suppressing translation in plants. Plant homeo-domain (PHD) finger proteins are known to be involved in the plant response to salinity stress. In the present study, we identified 44 putative OsPHD finger genes in Oryza sativa Indica, using Ensembl Plants Database. Using computational approach, potential miRNAs that target OsPHD finger genes were identified. Out of the 44 OsPHD finger genes only three OsPHD finger genes i.e., OsPHD2, OsPHD35 and OsPHD11, were found to be targeted by five newly identified putative miRNAs i.e., ath-miRf10010-akr, ath-miRf10110-akr, osa-miR1857-3p, osa-miRf10863-akr, and osa-miRf11806-akr. This is the first report of these five identified miRNAs on targeting PHD finger in Oryza sativa Indica. Further, expression analysis of 44 PHD finger genes under salinity was also performed using quantitative Real-Time PCR. The expression profile of 8 genes were found to be differentially regulated, among them two genes were significantly up regulated i.e., OsPHD6 and OsPHD12. In silico protein-protein interaction analysis using STRING database showed interaction of the OsPHD finger proteins with other protein partners that are directly or indirectly involved in development and abiotic stress tolerance.

Keywords: Gene expression; Oryza sativa; PHD finger; Protein-protein interaction; Salinity stress; Transcription factor; microRNA.

Fig. 1

Workflow of the identification and characterization of potential miRNAs and their target PHD finger genes in Oryza sativa Indica Group.

Fig. 2

Multiple sequence alignment of PHD finger protein of Indica rice showing characteristic domain feature in red color boxes. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Domain architecture of rice PHD finger protein and their distribution within different groups.

Fig. 4

Phylogenetic tree constructed using NJ method by MEGA X program. Amino acid sequences of all the 44 OsPHD finger proteins were used for tree construction.

Fig. 5

A-F. Mature and precursor sequences and the predicted stem-loop structures of identified miRNAs in Oryza sativa Indica Group- (A) ath-miRf10010-akr, (B) ath-miRf10110-akr, (C) gma-miR4993, (D) osa-miR1857–3p, (E) osa-miRf10863-akr and (F) osa-miRf11806-akr. The mature miRNAs are indicated with bold black line.

Fig. 6

A-D. Expression pattern of 44 OsPHD genes under salinity stress. The expression fold change analysis were examined by qRT-PCR and normalized by the expression of rice actin 1. The Y-axis represents fold change in gene expression. Bar represent standard error of the mean of three biological replicate.

Fig. 7

A-E. Protein-protein interaction network of OsPHDs generated using STRING. Protein interactors as nodes and interactions as edges. Coloured lines between the proteins indicate the various types of interaction evidence. (A) OsPHD6 (B) OsPHD12 (C) OsPHD2 (D) OsPHD11 and (E) OsPHD35.