Genome-wide analysis and expression profiling of half-size ABC protein subgroup G in rice in response to abiotic stress and phytohormone treatments

Abstract

The roles of the proteins encoded by half-size adenosine triphosphate-binding cassette transporter subgroup G (ABCG) genes in abiotic stress responses are starting to be established in the dicot model Arabidopsis thaliana. In the monocot model rice, the functions of most half-size ABCG proteins in abiotic stress responses are unknown. Rcn1/OsABCG5 is an essential transporter for growth and development under abiotic stress, but its molecular function remains largely unclear. Here, we present a comprehensive overview of all 30 half-size ABCG genes in rice, including their gene structures, phylogeny, chromosome locations, and conserved motifs. Phylogenetic analysis revealed that the half-size OsABCG proteins were divided to four classes. All seven rice intronless genes, including Rcn1/OsABCG5, were in Class III, like the 12 intronless ABCG genes of Arabidopsis. The EST and FL-cDNA databases provided expression information for 25 OsABCG genes. Semi-quantitative and quantitative RT-PCR analyses demonstrated that seven OsABCG genes were up-regulated in seedlings, shoots or roots following treatments with abiotic stresses (6, 17, 42 °C, NaCl, or mannitol) and abscisic acid. Another 15 OsABCG genes were up-regulated under at least one of the abiotic stress conditions and other phytohormones besides abscisic acid. Hierarchical clustering analysis of gene expression profiles showed that expression of the OsABCG genes could be classified into four clusters. The Rcn1/OsABCG5 cluster was up-regulated by abscisic acid and included OsABCG2, 3, 13, and 27. The present study will provide a useful reference for further functional analysis of the ABCGs in monocots.

Genetic variability and evolutionary diversification of membrane ABC transporters in plants

“…A total of 995 proteins (Additional file 1 : Table S1) containing one or more ATP-binding cassette domains were identified. Our analysis enlarged number of ABC proteins identified in rice [ 13 ], confirming data on ABCG family refined by Matsuda et al [ 14 ], added 32 novel ABC transporters in V. vinifera , [ 15 ] and provide manual curated ABC protein catalogues for S. lycopersicum, S. tuberosum. Most of these proteins belong to known plant subfamilies (A-I, except H) (Additional file 2 : Table S2 and Additional file 3 ).…”

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress

“…ABC proteins are primary transporters that mediate the energy-driven transport of a large and diverse multitude of substrates across biological membranes. ABC transporters play key roles in many physiological processes, such as plant development and plant nutrition, and in stress response (Moons 2008 ; Matsuda et al 2012 ; Jarzyniak and Jasinski 2014 ; Nguyen et al 2014 ; Saha et al 2015 ). In the rice genome, 133 genes coding for ABC transporters have been identified (Saha et al 2015 ).…”

“…In our study, in 3 h-treated roots, 15 out of the 133 ABC transporter genes were modulated in the same way in the two cultivars, 4 and 7 ABC transporter genes were specifically up-regulated in Eurosis and Loto, respectively, and 14 and 3 ABC transporter genes were specifically down-regulated in Eurosis and Loto, respectively. Among the 4 Eurosis-specific up-regulated genes, the OsABCG22 gene (LOC_Os09g29660) is induced by mannitol and by ABA treatments in rice roots (Matsuda et al 2012 ). Moreover, Nguyen et al ( 2014 ) found that drought stress induced this gene in the leaves.…”

Microarray Analysis of Rice d1 (RGA1) Mutant Reveals the Potential Role of G-Protein Alpha Subunit in Regulating Multiple Abiotic Stresses Such as Drought, Salinity, Heat, and Cold

“…There have been many other whole transcriptome microarray studies in rice under different abiotic stress conditions, but they reported only specific gene families that responded to various stresses. They include the MADS-box transcription factor family (Arora et al, 2007 ), F-Box Proteins (Jain et al, 2007 ), calcium-dependent protein kinase (CDPK) gene family (Ray et al, 2007 ), auxin-responsive genes (Jain and Khurana, 2009 ), protein phosphatase gene family (Singh et al, 2010 ), Sulfotransferase (SOT) gene family (Chen et al, 2012 ), thioredoxin gene family (Nuruzzaman et al, 2012 ), half-size ABC protein subgroup G (Matsuda et al, 2012 ), class III aminotransferase gene family (Sun et al, 2013 ), Ca 2+ ATPases gene family (Kamrul Huda et al, 2013 ), Rice RING E3 Ligase Family (Lim et al, 2013 ) etc.…”