Genome-Wide Analysis of the IQM Gene Family in Rice (Oryza sativa L.).

Tian Fan,Changen Tian,Chuping Xie,Tianxiao Lv,Yuping Zhou

doi:10.3390/plants10091949

Abstract

Members of the IQM (IQ-Motif Containing) gene family are involved in plant growth and developmental processes, biotic and abiotic stress response. To systematically analyze the IQM gene family and their expression profiles under diverse biotic and abiotic stresses, we identified 8 IQM genes in the rice genome. In the current study, the whole genome identification and characterization of OsIQMs, including the gene and protein structure, genome localization, phylogenetic relationship, gene expression and yeast two-hybrid were performed. Eight IQM genes were classified into three subfamilies (I–III) according to the phylogenetic analysis. Gene structure and protein motif analyses showed that these IQM genes are relatively conserved within each subfamily of rice. The 8 OsIQM genes are distributed on seven out of the twelve chromosomes, with three IQM gene pairs involved in segmental duplication events. The evolutionary patterns analysis revealed that the IQM genes underwent a large-scale event within the last 20 to 9 million years. In addition, quantitative real-time PCR analysis of eight OsIQMs genes displayed different expression patterns at different developmental stages and in different tissues as well as showed that most IQM genes were responsive to PEG, NaCl, jasmonic acid (JA), abscisic acid (ABA) treatment, suggesting their crucial roles in biotic, and abiotic stress response. Additionally, a yeast two-hybrid assay showed that OsIQMs can interact with OsCaMs, and the IQ motif of OsIQMs is required for OsIQMs to combine with OsCaMs. Our results will be valuable to further characterize the important biological functions of rice IQM genes.

Highlights

As one of the most important intracellular second messenger, Ca2+ plays a prominent role in many essential biological processes of plants, such as numerous developmental processes and responses to various kinds of biotic and abiotic stresses [1]
To identify the IQ motif containing protein (IQM) gene family in rice, the previously reported Arabidopsis IQM proteins and their IQ domain were used as the query sequences to search the RAP-DB
A total of eight putative OsIQM genes contained the conserved IQ calmodulin-binding motif were identified through SMART

Summary

Introduction

As one of the most important intracellular second messenger, Ca2+ plays a prominent role in many essential biological processes of plants, such as numerous developmental processes and responses to various kinds of biotic and abiotic stresses [1]. The spatial and transient changes of cytoplasmic Ca2+ levels in response to various stresses were detected and decoded by specific Ca2+ sensors, which transduce these changes of Ca2+ levels into a series of downstream effects [2,3]. Based on the number of EF hand motifs, four types of Ca2+ sensors were identified in higher plants: calmodulins (CaM), CaM-like proteins (CML), calcineurin B-like proteins (CBL) and calcium-dependent protein kinases (CDPK) [5,6]. Among these Ca2+ sensors, CaM is a highly conserved small, acidic protein and has been getting the most attention in Ca2+ signal transduction [7]. CaM has no enzymatic activity of its own; CaM produces a change in conformation after binding Ca2+, and it can activate a wide range of target proteins named calmodulinbinding proteins (CaMBPs) involved in diverse cellular processes [7,8]

Methods

Results

Conclusion