Uric Acid Transporter Gene SLC22A12 is a Chimera of Multiple Ancestral Genes

1. Introduction

Gout is one of the most common types of inflammatory arthritis caused by hyperuricemia. The balance between production of urate and urate excretion pathways determines an individual's serum urate levels [1]. URAT1 is urate-anion exchanger that affects serum urate level via urate reabsorption in human kidneys [2,3,4]. URAT1 is encoded by the SLC22A12 gene, which belongs to the SLC22 protein family [5]. The variants on the SLC22A12 gene have been tested for urate transport activity of URAT1 protein using an in vitro expression system in Xenopus laevis (African clawed frog) oocytes [6,7,8,9,10].

A recent study showed that that Xenopus tropicalis (tropical clawed frog), which is a close relative of X. laevis, appears to lack the full complement of renal urate transporters [11]. This finding raises questions regarding the origin of on the SLC22A12 gene. In this paper, two hypotheses are proposed about the evolutionary history of the SLC22A12 gene. The first hypothesis, termed the URAT1-early hypothesis, posits that SLC22A12 was present in the common ancestor of tetrapods and was subsequently lost in amphibian lineages. The second hypothesis, the URAT1-late hypothesis, suggests that the SLC22A12 gene arose uniquely within the lineage leading to mammals, potentially as a result of gene duplication or fusion events.

The objective of this study is to assess whether the URAT1-early hypothesis or the URAT1-late hypothesis is more plausible through a molecular evolutionary analysis of the SLC22 gene family.

2. Results

2.1. Homology Search and Window Analyses

Homology search revealed that SLC22A1–SLC22A17, SLC22A20P, SLC22A23, and SLC22A25 were homologous to SLC22A12 as shown by Mihaljevic et al. [5]. SLC22A6 and SLC22A20P were selected as the closest candidate genes to SLC22A12 based on the homology search results. SLC22A7 was chosen as an outgroup. SLC22A6 and SLC22A7 encode the OAT1 protein and the OAT2 protein, respectively. SLC22A20P is a pseudogene related to murine Slc22a20, which encodes the mOAT6 protein in mouse. OAT1, OAT2, and mOAT6 are members of a group of membrane proteins that have the function of transporting different organic anions across cell membranes, known as organic anion transporters (OATs).

According to the window analysis, SLC22A12 was found to be similar to different genes in exon 1 and exons 2-10. As shown in Table 1, the proportion of different sites (p-distance) between SLC22A12 and SLC22A6 in exon 1 was 0.398, while the p-distance between SLC22A12 and SLC22A20P in the same region was 0.387. This suggests that SLC22A12 is more closely related to SLC22A20P in this region than to SLC22A6. In exons 2-10, the p-distance between SLC22A12 and SLC22A6 was 0.413, suggesting that in this region, SLC22A12 is evolutionarily closer to SLC22A6 than to SLC22A20P. In exon 1 and exons 2-10, there was a significant difference in both the p-distance between SLC22A12 and SLC22A20P and the p-distance between SLC22A12 and SLC22A6 (Chi-square test, 1 degree of freedom, $\alpha$ = 0.1%).

2.2. Phylogenetic Tree Analysis

The evolutionary history among SLC22A12, SLC22A20P, SLC22A6, and SLC22A7 was inferred by using the ML method