Characteristics of 29 novel atypical SLCs of MFS type : evolutionary conservation, predicted structure and neuronal co-expression

Solute carriers (SLCs) are vital as they are responsible for a major part of the molecular transport over lipid bilayers. At present, there are 430 identified SLCs, of which 28 are called atypical SLCs of major facilitator superfamily (MFS) type. These are MFSD1, 2A, 2B, 3, 4A, 4B, 5, 6, 6L, 7, 8, 9, 10, 11, 12, 13A, 14A, 14B; SV2A, SV2B, SV2C, SVOP, SVOPL; SPNS1, SPNS2, SPNS3; UNC93A and UNC93B1, and we studied their fundamental properties. We also included CLN3, an atypical SLC not yet belonging to any Pfam clan, because its involvement in the same neuronal degenerative disorders as MFSD8. With phylogenetic analyses and bioinformatic sequence comparisons, the proteins were divided into 15 families, denoted Atypical MFS Transporter Families (AMTF1-15). Hidden Markov models were used to identify orthologues from human to D.melanogaster and C.elegans. Topology predictions revealed 12 transmembrane segments (for all except CLN3), corresponding to the common MFS structure. With single-cell RNA sequencing and in situ proximity ligation assay on brain cells, co-expressions of several atypical SLC were identified. Finally, the transcription levels of all genes were analysed in the hypothalamic N25/2 cell line after complete amino acid starvation, showing altered expression levels for several atypical SLCs.