Retrotransposon-Mediated Aluminum Tolerance through Enhanced Expression of the Citrate Transporter OsFRDL4

Abstract

ORCID IDs: 0000-0003-3935-268X (K.Y.); 0000-0003-3411-827X (J.F.M.).High aluminum (Al) tolerance of rice (Oryza sativa) is controlled by multiple tolerance genes, but the regulatory mechanisms underlying the differential expression of these genes are poorly understood. Here, we investigated the factors regulating the expression of OsFRDL4, a gene encoding a citrate efflux transporter involved in Al-induced citrate secretion from the roots. Analysis with chromosome segment substitution lines derived from cv Nipponbare (high OsFRDL4 expression) and cv Kasalath (low OsFRDL4 expression) revealed that the differential expression of OsFRDL4 is responsible for the quantitative trait locus for Al tolerance detected previously on chromosome 1. Comparison of the OsFRDL4 gene structure in cv Nipponbare and cv Kasalath showed that there was no difference in the position of the transcriptional start site, but a 1.2-kb insertion showing high similarity to the solo long terminal repeat of the retrotransposon was found in the promoter region of OsFRDL4 in cv Nipponbare. This insertion showed higher promoter activity and contained nine cis-acting elements for ALUMINUM RESISTANCE TRANSCRIPTION FACTOR1 (ART1). However, this insertion did not alter the spatial expression or cellular localization of OsFRDL4. Furthermore, this insertion was found in most japonica varieties but was largely absent from indica varieties or wild rice species. These results indicate that the 1.2-kb insertion in the OsFRDL4 promoter region in japonica subspecies is responsible for their higher expression level of OsFRDL4 due to the increased number of cis-acting elements of ART1. Our results also suggest that this insertion event happened at the initial stage of domestication of japonica subspecies.

Elevated Carbon Dioxide Alleviates Aluminum Toxicity by Decreasing Cell Wall Hemicellulose in Rice (Oryza sativa)

“…In the present study, Al significantly induced the secretion of citrate (Figure 3A) and up-regulated the expression of OsFRDL4 (Figure 3B), which is able to transport citrate and correlates well with the secretion of citrate in rice (Yokosho et al, 2011, 2016). Elevated CO 2 had no further effect on the secretion of citrate in Al-treated plants (Figure 3A), indicating that citrate efflux does not contribute to the CO 2 -mediated reduction of Al accumulation in rice roots.…”

Genome-wide Association Studies of Agronomic Traits Consisting of Field- and Molecular-based Phenotypes

“…The genes encoding organic acid (OA) transporter have been identified as important Al tolerance genes in various plants, and it has been demonstrated that the ELP of OA transporter caused by cis-element polymorphism is associated with the variation of Al tolerance among the accessions (Hoekenga et al, 2006;Sasaki et al, 2006;Magalhaes et al, 2007;Chen et al, 2013;Yokosho et al, 2016). The higher expression of the OA transporter gene has notably contributed toward high Al tolerance in various crops in the ELP.…”

Aluminum Resistance Transcription Factor 1 (ART1)contributes to natural variation in rice Al resistance

“…OsFRDL4 encodes a Multidrug and Toxin Extrusion (MATE) transporter that mediates root citrate release (Yokosho et al, 2011); Al-activated release of organic acids from the root is a major physiological mechanism of plant Al resistance (Kochian et al, 2015). OsFRDL4 is the major candidate for the gene underlying an Al resistance QTL in a Nipponbare (temperate japonica) x Kasalath (aus) population (Yokosho et al, 2016). The authors of that study also reported a 1.2-Kb insertion in the promoter of OsFRDL4, and demonstrated that a majority of japonica varieties tested carried the insertion, while most indica varieties did not, and suggested that the insertion was associated with higher levels of OsFRDL4 expression under Al stress.…”

“…These "ART1-regulated genes" have received this denomination because they are mis-regulated in the art1 mutant; in other words, their expression is upregulated by Al stress in the wild type, but not in the mutant . It is worth noting that direct binding of the ART1 protein to upstream regulatory regions has so far been experimentally demonstrated only for STAR1 (Tsutsui et al, 2011) and OsFRDL4 (Yokosho et al, 2016).…”