Evolutionary Aspects of TRPMLs and TPCs

Abstract

Transient receptor potential (TRP) or transient receptor potential channels are a highly diverse family of mostly non-selective cation channels. In the mammalian genome, 28 members can be identified, most of them being expressed predominantly in the plasma membrane with the exception of the mucolipins or TRPMLs which are expressed in the endo-lysosomal system. In mammalian organisms, TRPMLs have been associated with a number of critical endo-lysosomal functions such as autophagy, endo-lysosomal fusion/fission and trafficking, lysosomal exocytosis, pH regulation, or lysosomal motility and positioning. The related non-selective two-pore cation channels (TPCs), likewise expressed in endosomes and lysosomes, have also been found to be associated with endo-lysosomal trafficking, autophagy, pH regulation, or lysosomal exocytosis, raising the question why these two channel families have evolved independently. We followed TRP/TRPML channels and TPCs through evolution and describe here in which species TRP/TRPMLs and/or TPCs are found, which functions they have in different species, and how this compares to the functions of mammalian orthologs.

Keywords: TPC1; TPC2; TRP; TRPML1; TRPML2; TRPML3; endosome; lysosome.

Figure 1

Phylogenetic tree indicating the number of genes encoding TRPML and TPC proteins. Numbers of TRP, TRPML, and TPC proteins of selected species of the Metazoa, Fungi, and Viridiplantae as well as selected ancestral species. The tree was constructed based on information included in the following resources [2,12,48,50,51,52,53,54,55,56,57,58,59,60,61], and constructed manually based on this information. Branch color coding of the tree indicates a first (orange), second (bright green), and third (blue) gene duplication of TPRML. Full species names can be found in the text.

Figure 2

Main structural differences in loops linking TMD between TRPML ancestors of animal (red), plant (green), and fungi TRPY1 (brown) kingdoms. Amino acid sequences were obtained for Monosiga brevicollis MbTRPML (A9UQ01), Chlamydomonas reinhardtii CrTRPP2 (ABR14113), and Saccharomyces cerevisiae ScTRPY1 (Q12324), and aligned to resolved proteins using SWISS-MODEL (https://swissmodel.expasy.org/). Homology models were constructed using 6BCO (Mus musculus TRPM4) as a template for ScTRPY1, 6T9N (Homo sapiens Polycystin-2) for CrTRPP2 and 6E7P (Homo sapiens TRPML1) for MbTRPML, and visualized using PyMOL. Only MbTRPML aligned well with human TRPML1. Red and green structures indicate the mucolipin or polycystin domains of TRPML and TRPP, respectively, while the TRPY1-unique intracellular domain of ScTRPY1 is colored brown. Having constructed the homology models, we interrogated the possibility of vacuolar channel sorting. Putative lysosomal targeting signals (LTS) were identified using a custom Prosite scan (https://prosite.expasy.org/cgi-bin/prosite/), searching for motifs DxxLL, [DE] xxxL [LI], DxxLM, DxxMV, IMxxYxxL (plant), and YxxL (yeast). Only cytosolic LTS were considered relevant. TRPY1 bears three yeast LTS (Y107-L110, Y293-L296, and Y473-L476, YxxL), while CrTRPP2 bears two yeast and one cross-species LTS (Y44-L47 and Y95-L98, YxxL; E1459-L1464, [DE] xxxL [LI]). MbTRPML bears a single cross-species LTS (E500-I505, [DE] xxxL [LI]).