Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters

Abstract

Homology search and phylogenetic analysis have commonly been used to annotate gene function, although they are prone to error. We hypothesize that the power of homology search in functional annotation depends on the coupling of sequence variation to functional diversification, and we herein focus on the SoLute Carrier (SLC25) family of mitochondrial metabolite transporters to survey this coupling in a family-wide manner. The SLC25 family is the largest family of mitochondrial metabolite transporters in eukaryotes that translocate ligands of different chemical properties, ranging from nucleotides, amino acids, carboxylic acids and cofactors, presenting adequate experimentally validated functional diversification in ligand transport. Here, we combine phylogenetic analysis to profile SLC25 transporters across common eukaryotic model organisms, from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, to Homo sapiens, and assess their sequence adaptations to the transported ligands within individual subfamilies. Using several recently studied and poorly characterized SLC25 transporters, we discuss the potentials and limitations of phylogenetic analysis in guiding functional characterization.

Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis

“…To explore the regulatory mechanism of A39, we performed amino acid sequence analysis 14,16 and Alphafold structure prediction 17 of A39. In addition to the typical structural fold, the threefold pseudo-symmetrical, six transmembrane α-helices surrounding the central transport cavity, the analysis revealed that A39 contains an extra mitochondrial matrix loop between transmembrane domain 1 and 2 with a low structural prediction confidence score (Fig.…”