Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

Zhixuan Du,Junru Fu,Haohua He,Jianzhong Bao,Chuihai Zeng,Zheng Wu,Hang Tu,Jianbin Li,Zhou Huang,Qitao Su

doi:10.1186/s12862-021-01873-y

Abstract

Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

Highlights

Multidrug and toxic compound extrusion (MATE) transporters constitute a class of secondary active transporters widely present in archaea, bacteria, prokaryotic and eukaryotic cells, and rely on the electrochemical potential of sodium or hydrogen ions to excrete compounds for transport activity as part of a secondary active transport mode [18]
Chromosome 3 contains the largest number of MATE genes-a total of 10, and only one of the MATE genes is on chromosome 5 (Fig. 1A)
There are 3 pairs of tandem repeat OsMATE genes (OsMATE21 and OsMATE22, OsMATE39 and OsMATE40, and OsMATE41 and OsMATE42) in rice, which are located on chromosomes 6, 10 and 11, respectively, and there is a high similarity between the protein sequences within each gene cluster

Summary

Introduction

Multidrug and toxic compound extrusion (MATE) transporters constitute a class of secondary active transporters widely present in archaea, bacteria, prokaryotic and eukaryotic cells, and rely on the electrochemical potential of sodium or hydrogen ions to excrete compounds for transport activity as part of a secondary active transport mode [18]. All MATE proteins have approximately 40 % sequence similarity [13]. The NorM protein has twelve transmembrane domains, which are. The first MATE transporter (NorM) was identified from Vibrio paralyticus; this protein expels norfloxacin and ciprofloxacin out of cells in an energy-dependent manner [3, 29]. Mammalian MATE proteins were first identified in humans and mice (MATE1 and MATE2) [34]. Human MATE1 and MATE2 proteins are encoded by the SLC47A1 and SLC47A2 genes, respectively [46], which are mainly expressed in the kidney and liver [50]. Mammalian MATE protein can be used as multispecific and electron-neutral transporters of organic cations, mediating the discharge of various organic cations and cationic drugs [12, 61]

Methods

Results

Discussion

Conclusion