Natural Variation in the ATPS1 Isoform of ATP Sulfurylase Contributes to the Control of Sulfate Levels in Arabidopsis

Abstract

Sulfur is an essential macronutrient for all living organisms. Plants take up inorganic sulfate from the soil, reduce it, and assimilate it into bioorganic compounds, but part of this sulfate is stored in the vacuoles. In our first attempt to identify genes involved in the control of sulfate content in the leaves, we reported that a quantitative trait locus (QTL) for sulfate content in Arabidopsis (Arabidopsis thaliana) was underlain by the APR2 isoform of the key enzyme of sulfate assimilation, adenosine 59-phosphosulfate reductase. To increase the knowledge of the control of this trait, we cloned a second QTL from the same analysis. Surprisingly, the gene underlying this QTL encodes the ATPS1 isoform of the enzyme ATP sulfurylase, which precedes adenosine 59-phosphosulfate reductase in the sulfate assimilation pathway. Plants with the Bay allele of ATPS1 accumulate lower steady-state levels of ATPS1 transcript than those with the Sha allele, which leads to lower enzyme activity and, ultimately, the accumulation of sulfate. Our results show that the transcript variation is controlled in cis. Examination of ATPS1 sequences of Bay-0 and Shahdara identified two deletions in the first intron and immediately downstream the gene in Bay-0 shared with multiple other Arabidopsis accessions. The average ATPS1 transcript levels are lower in these accessions than in those without the deletions, while sulfate levels are significantly higher. Thus, sulfate content in Arabidopsis is controlled by two genes encoding subsequent enzymes in the sulfate assimilation pathway but using different mechanisms, variation in amino acid sequence and variation in expression levels.

Dissection of the Control of Anion Homeostasis by Associative Transcriptomics in Brassica napus

“…Interestingly, the two genes shown to control variation in sulfate levels in Arabidopsis have not been found among the candidate genes. These two genes were shown to underlie QTLs from an analysis of a Bay-0 3 Shahdara population, and they encode isoforms of two consecutive enzymes of the sulfate assimilation pathway, ATP sulfurylase and APR (Loudet et al, 2007;Koprivova et al, 2013). The APR2 gene in Shahdara contained a unique SNP that resulted in an amino acid substitution near the active center and inactivation of the enzyme (Loudet et al, 2007).…”

“…The APR2 gene in Shahdara contained a unique SNP that resulted in an amino acid substitution near the active center and inactivation of the enzyme (Loudet et al, 2007). ATP sulfurylase (ATPS) affects sulfate levels due to variation in transcript levels of the main isoform, ATPS1, caused by a deletion in intron 1 found in a few accessions (Koprivova et al, 2013). Unique or very rare haplotypes, such as the Shahdara allele of APR2, are almost impossible to identify through GWAS, and it is thus no surprise that the gene was not recovered.…”

Variation in Sulfur and Selenium Accumulation Is Controlled by Naturally Occurring Isoforms of the Key Sulfur Assimilation Enzyme ADENOSINE 5′-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis Species Range

“…In the same analysis, a second QTL for leaf sulfate accumulation was described (Loudet et al, 2007). This second QTL was recently established to be driven by an ATPS1 expression-level polymorphism between Bay-0 and Sha, with Bay-0 showing reduced expression of ATPS1 compared with Sha (Koprivova et al, 2013).…”

“…Since sulfate uptake and accumulation is only one step in the complex process of sulfur assimilation in plants, uncovering the genetic architecture of sulfate accumulation, as performed by Loudet et al (2007) and Koprivova et al (2013), could potentially overlook genetic variation in other important aspects of sulfur metabolism. To enable us to identify natural genetic variation in sulfur homeostasis beyond just sulfate accumulation, we chose to quantify total leaf sulfur.…”

“…Both Loudet et al (2007) and Koprivova et al (2013) focused their studies on the genetic architecture of natural variation for leaf sulfate using a single recombinant population created by crossing the Bay-0 and Sha accessions. This recombinant inbred population has proved a powerful tool for the identification of novel alleles controlling several different traits (Loudet et al, 2008;Jiménez-Gómez et al, 2010;Jasinski et al, 2012;Pineau et al, 2012;Anwer et al, 2014).…”