Sequence Features of Mitochondrial Transporter Protein Families

Abstract

Mitochondrial carriers facilitate the transfer of small molecules across the inner mitochondrial membrane (IMM) to support mitochondrial function and core cellular processes. In addition to the classical SLC25 (solute carrier family 25) mitochondrial carriers, the past decade has led to the discovery of additional protein families with numerous members that exhibit IMM localization and transporter-like properties. These include mitochondrial pyruvate carriers, sideroflexins, and mitochondrial cation/H⁺ exchangers. These transport proteins were linked to vital physiological functions and disease. Their structures and transport mechanisms are, however, still largely unknown and understudied. Protein sequence analysis per se can often pinpoint hotspots that are of functional or structural importance. In this review, we summarize current knowledge about the sequence features of mitochondrial transporters with a special focus on the newly included SLC54, SLC55 and SLC56 families of the SLC solute carrier superfamily. Taking a step further, we combine sequence conservation analysis with transmembrane segment and secondary structure prediction methods to extract residue positions and sequence motifs that likely play a role in substrate binding, binding site gating or structural stability. We hope that our review will help guide future experimental efforts by the scientific community to unravel the transport mechanisms and structures of these novel mitochondrial carriers.

Keywords: ABC transporter; LETM; MCF; MPC; SLC transporters; SLC25; SLC54; SLC55; SLC56; mitochondrial carriers; protein targeting; sequence analysis; sideroflexin.

Figure 1

Import machinery for mitochondrial transporters. The TOM (orange), TIM23 (purple) and TIM22 (yellow) complexes are depicted, with numbers representing the corresponding Tom/Tim protein names. Proteins with a single transmembrane helix (TMH) and OXA-dependent transporters employ the TIM23 import pathway, while carriers with no mitochondrial targeting sequence (MTS) are imported through TIM22. For details, see text. Figure is based on [11,12,13,17,18,19].

Figure 2

Sequence analysis of human MPC (SLC54) proteins. The diagram above the alignment shows the part of the HMM logo corresponding to the sequence (see text). At each position in the HMM logo, higher columns correspond to higher sequence conservation, and letters are drawn proportional to their frequency of occurrence at that position. Vertical lines in the HMM logo show positions with non-zero insertion frequency. Transmembrane regions predicted by three different methods (HMMTOP, SPOCTOPUS, MEMSAT-SVM) are marked by black lines. Green lines mark transmembrane regions predicted to by pore-lining by MEMSAT-SVM. Secondary structure as predicted by PSIPRED is shown as magenta lines ($\mathsf{\alpha }$-helix) and golden lines ($\mathsf{\beta }$-strand). Uniprot sequence identifiers are shown next to protein names for each sequence.

Figure 3

Sequence analysis of human sideroflexin proteins (SLC56 family). The HMM logo is shown above the sequence alignment (see text). Vertical lines in the HMM logo show positions with non-zero insertion frequency. Transmembrane regions predicted by three different methods (HMMTOP, SPOCTOPUS, MEMSAT-SVM) are marked by black lines. Green lines mark transmembrane regions predicted to by pore-lining by MEMSAT-SVM. Secondary structure as predicted by PSIPRED is shown as magenta lines ($\mathsf{\alpha }$-helix) and golden lines ($\mathsf{\beta }$-strand). Uniprot sequence identifiers are shown next to protein names for each sequence.

Figure 4

Sequence analysis of human LETM proteins (SLC55 family). HMM logo is shown over the alignment, based on the “LETM1” HMM model from Pfam (see text). Only the alignment region covered by the HMM model is shown. Certain non-conserved residue positions with ambiguous matches with the protein sequences have been removed from the HMM logo.