A distal convoluted tubule-specific isoform of murine SLC41A3 extrudes magnesium

The distal convoluted tubule (DCT) plays an indispensable role in magnesium (Mg²⁺) reabsorption in the kidney. Yet, the extrusion mechanism of Mg²⁺ has not been identified. The solute carrier 41A3 (SLC41A3) has been suggested to be involved in Mg²⁺ extrusion, but this has never been conclusively demonstrated.

Using available RNA-sequencing data and real-time quantitative PCR, expression of two alternative Slc41a3 transcripts, encoding isoform (Iso) 1 or 2, were assessed in kidney and isolated DCT tubules. HEK293 or HAP1 cells were transfected with plasmids expressing either of the isoforms, followed by ²⁵Mg²⁺ transport studies. Identification of cis-regulatory elements (CRE) was achieved by combining data from publicly available ATAC sequencing data and luciferase assays.

Gene expression studies revealed a distinct transcript of Slc41a3 in the DCT with an alternative promoter, leading to a protein with a unique N-terminus; SLC41A3-Iso 2. HEK293 cells overexpressing SLC41A3-Iso 2, but not -Iso 1, exhibited 2.7-fold and 1.6-fold higher ²⁵Mg²⁺ uptake and extrusion, compared to mock, respectively. The transport was independent of Na⁺, of the Mg²⁺ channel TRPM7 or of transporters CNNM3 and -4. We identified a CRE accessible in the DCT, ±2.8kb upstream of the transcript. The presence of the CRE increased the Slc41a3-Iso 2 promoter activity 3.8-fold following luciferase assays, indicating the CRE contains an enhancer function.

In conclusion, we identified two alternative transcripts of Slc41a3 in mouse. Slc41a3-Iso 2 is enriched within the DCT using specific gene regulatory elements. We speculate that specifically in the DCT, SLC41A3-Iso 2 orchestrates Mg²⁺ extrusion.