2.A.43 The Lysosomal Cystine Transporter (LCT) Family The LCT family includes proteins that are derived from animals, plants and fungi. They exhibit 7 putative transmembrane α-helical spanners (TMSs) and vary in size between 247 and 487 amino acyl residues although most have between 300 and 400 residues. One of the animal proteins is the lysosomal cystine transporter of humans, also called cystinosin, encoded by the CTNS gene. Mutations in this protein cause nephropathic intermediate cystinosis (Thoene et al., 1999; Zhai et al., 2001). In cystinotic renal proximal tubules (RPTs), defects in cystinosin function results in reduced reabsorption of solutes by apical Na⁺solute cotransport systems, including the Na⁺/Phosphate cotransport system, due to decreased expression of the other transporters (Taub et al., 2011). This family has been reported to have the MtN3 fold (Ferrada and Superti-Furga 2022). Evidence suggests that cystinosin transports cystine out of lysosomes in a pmf-dependent process. The pmf across the lysosomal membrane is generated by a V-type ATPase which hydrolyzes cytoplasmic ATP to pump protons into the lysosomal lumen (Smith et al., 1987). Removal of the C-terminal GYDQL lysosomal sorting motif causes cystinosin to migrate to the plasma membrane with the intralysosomal face of cystinosin facing the extracellular medium (Kalatzis et al., 2001). The cells then take up cystine in a pmf-dependent process. Distant homologues include the Lec15/Lec35 suppressor, SL15, of Chinese hamster ovary cells (Ware and Lehrman, 1996) and ERS1, the ERD suppressor in S. cerevisiae (Hardwick and Pelham, 1990). Both of these suppressors, when overexpressed, have been reported to influence retention of lumenal endoplasmic reticular proteins as well as glycosylation in the Golgi apparatus. The Lec15 and Lec35 mutations are characterized by inefficient synthesis and utilization, respectively, of mannose-P-dolichol for glycolipid biosynthesis (Ware and Lehrman, 1996). All of these proteins are distantly related to the proteins of the microbial rhodopsin (MR) family (TC #3.E.1) (Bieszke et al., 1999; Graul and Sadee, 1999; Zhai et al., 2001) which exhibit an established 7 TMS topology. The reaction believed to be catalyzed by cystinosin is: Cystine (intralysosomal space) + H⁺ (intralysosomal space) → Cystine (cytoplasm) + H⁺ (cytoplasm)
This family belongs to the Transporter-Opsin-G protein-coupled receptor (TOG) Superfamily.
References:
Bieszke, J.A., E.L. Brauir, L.E. Bean, S. Kang, D.O. Natvig, and K.A. Borkovich. (1999). The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to aracheal rhodopsins. Evolution 96: 8034-8039.
Browning, A.C., G.S. Figueiredo, O. Baylis, E. Montgomery, C. Beesley, E. Molinari, F.C. Figueiredo, and J.A. Sayer. (2019). A case of ocular cystinosis associated with two potentially severe CTNS mutations. Ophthalmic Genet 40: 157-160.
Chkioua, L., Y. Amri, C. Saheli, W. Mili, S. Mabrouk, I. Chabchoub, H. Boudabous, W.B. Azzouz, H.B. Turkia, S. Ferchichi, N. Tebib, T. Massoud, M. Ghorbel, and S. Laradi. (2022). Molecular characterization of CTNS mutations in Tunisian patients with ocular cystinosis. Diagn Pathol 17: 44.
Ferrada, E. and G. Superti-Furga. (2022). A structure and evolutionary-based classification of solute carriers. iScience 25: 105096.
Gao, X.D., J. Wang, S. Keppler-Ross, and N. Dean. (2005). ERS1 encodes a functional homologue of the human lysosomal cystine transporter. FEBS J. 272: 2497-2511.
Graul, R.C. and W. Sadee. (1997). Evolutionary relationships among proteins by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsin with the yeast sequence YRO2. Pharm. Res. 11: 1533-1541.
Hardwick, K.G. and H.R.B. Pelham. (1990). ERS1 a seven transmembrane domain protein from Saccharomyces cerevisiae. Nucleic Acids Res. 18: 2177.
Jézégou, A., E. Llinares, C. Anne, S. Kieffer-Jaquinod, S. O'Regan, J. Aupetit, A. Chabli, C. Sagné, C. Debacker, B. Chadefaux-Vekemans, A. Journet, B. André, and B. Gasnier. (2012). Heptahelical protein PQLC2 is a lysosomal cationic amino acid exporter underlying the action of cysteamine in cystinosis therapy. Proc. Natl. Acad. Sci. USA 109: E3434-3443.
Kalatzis, V., S. Cherqui, C. Antignac, and B. Gasnier. (2001). Cystinosin, the protein defective in cystinosis, is a H(+)-driven lysosomal cystine transporter. EMBO J. 20: 5940-5949.
Li, T., D. Hu, and Y. Gong. (2021). Identification of potential lncRNAs and co-expressed mRNAs in gestational diabetes mellitus by RNA sequencing. J Matern Fetal Neonatal Med 1-15. [Epub: Ahead of Print]
Liu, B., H. Du, R. Rutkowski, A. Gartner, and X. Wang. (2012). LAAT-1 is the lysosomal lysine/arginine transporter that maintains amino acid homeostasis. Science 337: 351-354.
Löbel, M., S.P. Salphati, K. El Omari, A. Wagner, S.J. Tucker, J.L. Parker, and S. Newstead. (2022). Structural basis for proton coupled cystine transport by cystinosin. Nat Commun 13: 4845.
Medaer, L., D. David, M. Smits, E. Levtchenko, M. Sampaolesi, and R. Gijsbers. (2024). Residual Cystine Transport Activity for Specific Infantile and Juvenile Mutations in a PTEC-Based Addback Model. Cells 13:.
Ruivo, R., G.C. Bellenchi, X. Chen, G. Zifarelli, C. Sagné, C. Debacker, M. Pusch, S. Supplisson, and B. Gasnier. (2012). Mechanism of proton/substrate coupling in the heptahelical lysosomal transporter cystinosin. Proc. Natl. Acad. Sci. USA 109: E210-217.
Smith, M.L., A.A. Greene, R. Potashnik, S.A. Mendoza, and J.A. Schneider. (1987). Lysosomal cystine transport. J. Biol. Chem. 262: 1244-1253.
Taranta, A., M.A. Elmonem, F. Bellomo, E. De Leo, S. Boenzi, M.J. Janssen, A. Jamalpoor, S. Cairoli, A. Pastore, C. De Stefanis, M. Colucci, L.R. Rega, I. Giovannoni, P. Francalanci, L.P. van den Heuvel, C. Dionisi-Vici, B.M. Goffredo, R. Masereeuw, E. Levtchenko, and F. Emma. (2021). Benefits and Toxicity of Disulfiram in Preclinical Models of Nephropathic Cystinosis. Cells 10:.
Taub, M.L., J.E. Springate, and F. Cutuli. (2011). Reduced phosphate transport in the renal proximal tubule cells in cystinosis is due to decreased expression of transporters rather than an energy defect. Biochem. Biophys. Res. Commun. 407: 355-359.
Thoene, J., R. Lemons, Y. Anikster, J. Mullet, K. Paelicke, C. Lucero, W. Gahl, J. Schneider, S.G. Shu, and T. Campbell. (1999). Mutations of CTNS causing intermediate cystinosis. Mol. Genet. Metabol. 67: 283-293.
Thoene, J.G., M.A. DelMonte, and J. Mullet. (2020). Microvesicle delivery of a lysosomal transport protein to ex vivo rabbit cornea. Mol Genet Metab Rep 23: 100587.
Tian, J., L. Sun, L. Wan, H. Zou, J. Chen, and F. Liu. (2023). TMEM44 as a Novel Prognostic Marker for Kidney Renal Clear Cell Carcinoma is Associated with Tumor Invasion, Migration and Immune Infiltration. Biochem Genet. [Epub: Ahead of Print]
Wang, C., K. Xu, F. Deng, Y. Liu, J. Huang, R. Wang, and X. Guan. (2021). A six-gene signature related with tumor mutation burden for predicting lymph node metastasis in breast cancer. Transl Cancer Res 10: 2229-2246.
Ware, F.E. and M.A. Lehrman. (1996). Expression cloning of a novel suppressor of the Lec15 and Lec35 glycosylation mutations of Chinese hamster ovary cells. J. Biol. Chem. 271: 13935-13938.
Ware, F.E. and M.A. Lehrman. (1998). Expression cloning of a novel suppressor of the Lec15 and Lec35 glycosylation mutations of Chinese hamster ovary cells. J. Biol. Chem. 273: 13366.
Yamamoto, T., K. Fujimura-Kamada, E. Shioji, R. Suzuki, and K. Tanaka. (2017). Cfs1p, a Novel Membrane Protein in the PQ-Loop Family, Is Involved in Phospholipid Flippase Functions in Yeast. G3 (Bethesda) 7: 179-192.
Zhai, Y., W.H.M. Heijne, D.W. Smith, and M.H. Saier, Jr. (2001). Homologues of archaeal rhodopsins in plants, animals and fungi: structural and functional predications for a putative fungal chaperone protein. Biochim. Biophys. Acta 1511: 206-223.
Zhang, Q. and Y. Ye. (2021). Chaperoning transmembrane helices in the lipid bilayer. J. Cell Biol. 220:.
Examples:
TC#	Name	Organismal Type	Example
2.A.43.1.1	Lysosomal cystine transporter, cystinosin (CTNS) of 267 aas and 7 TMSs. It uses a cystine:H⁺ symport mechanism. H⁺ binds to an aspartate residue in one of the two PQ-loops (Ruivo et al., 2012). Several mutations in the CTNS gene gives rise to ocular cystinosis (Browning et al. 2019). Microvesicle delivery of cystinosin to ex vivo corneal keratocytes (corneal fibroblasts) corrects the cystine transport defect and prevents the accumulation of lysosomal cystine (Thoene et al. 2020). Impaired transport of cystine out of lysosomes is associated with mutations in transmembrane domains of cystinosin, resulting from loss of its activity (Chkioua et al. 2022). Cystinosis is characterized by early-onset chronic kidney failure and progressive development of extra-renal complications (Taranta et al. 2021). There is residual cystine transport activity for specific infantile and juvenile CTNS mutations (Medaer et al. 2024).	Animals (homologues in plants and fungi)	Cystinosin or CTNS of Homo sapiens

2.A.43.1.2	Cystinosin homolog	Animals	CG17119 of Drosophila melanogaster

2.A.43.1.3	The ERD-1 suppressor, ERS1	Yeast	*ERS1 of Saccharomyces cerevisiae* (P17261)**

2.A.43.1.4	Cystinosin homolog of 270 aas and 6 or 7 TMSs uses the proton gradient to drive cystine export from the lysosome into the cytoplasm. Löbel et al. 2022 presented the crystal structures of cystinosin from Arabidopsis thaliana in both apo and cystine bound states. They establish a mechanism for cystine recognition and proton coupled transport. Mutational mapping and functional characterisation of human cystinosin provided a framework for understanding the molecular impact of disease-causing mutations.	Plants	At5g40670 of Arabidopsis thaliana

2.A.43.1.6	Cystinosin of 355 aas and 7 TMSs.		Cystinosin of Planoprotostelium fungivorum

Examples:
TC#	Name	Organismal Type	Example
2.A.43.2.1	The lysosomal lysine-arginine transporter, LAAT1, SLC66A1, PQ-loop repeat containing protein 2 (PQLC2) (291 aas; 7 TMSs). Also transports L-histidine, L-ornithine, the mixed disulfide of cysteine-cysteamine, a lysine analogue, as well as canavanine, a toxic arginine analogue. Cysteamine is used in the treatment of cystinosis (Liu et al., 2012; Jézégou et al. 2012).	Animals	*PQLC2 of Homo sapiens* (Q6ZP29)**

2.A.43.2.10	The probable vacuolar amino acid transporter YPQ1 of 381 aas and 6 TMSs.		Ypq1 of Sesamum indicum

2.A.43.2.11	The probable vacuolar amino acid transporter Ypq1 of 381 aas and 6 TMSs		Ypq1 of Gossypium raimondii].

2.A.43.2.12	Uncharacterized protein of 282 aas and 7 (3 + 4) TMSs.		UP of Gossypium raimondii

2.A.43.2.13	*Cdc50 supressor, CSF1 of 405 aas and 7 TMSs. Appears to function as a phospholipid flippase or to regulate PL flipping in endosomes or late golgi vesicles (Yamamoto et al.* 2017).**		CSF1 of Saccharomyces cerevisiae

2.A.43.2.14	Uncharacterized PQ loop repeat protein of 228 aas and 6 TMSs.		UP of Entamoeba histolytica

2.A.43.2.15	PQ loop C1 (PQLC1; SLC66A2) protein of 271 aas and 7 TMSs in a 3 + 4 TMS arrangement. It probably transports a variety of amino acids and their derivatives as does PQLC2 (TC# 2.A.43.2.1).		PQLC2 of Homo sapiens

2.A.43.2.16	PQLC2L or SLC66A11L or 304 aas and 7 TMSs.		*PQLC2L of Gallus gallus* (chicken)**

2.A.43.2.2	*The lysosomal lysine-arginine transporter, LAAT1, PQ-loop superfamily member (qx42 gene product; 310aas; 7 TMSs) (Liu et al., 2012).*	Animals	*LAAT1 of Caenorhabditis elegans* (Q95XZ6)**

2.A.43.2.3	Vacuolar (lysosomal) cationic amino acid transporter (YOL092W) (308aas; 7 TMSs), LAAT1. Involved in cationic amino acid homeostasis (Jézégou et al. 2012). It may function as an amino acid exporter of cationic amino acids from the vacuole. The vacuole-associated Rsp5 ubiquitin ligase uses a TMS in the substrate adaptor Ssh4 to recognize membrane helices in Ypq1, which targets this lysine transporter for lysosomal degradation during lysine starvation (Zhang and Ye 2021).	Yeast	*LAAT1 of Saccharomyces cerevisiae* (Q12010)**

2.A.43.2.4	PQ-loop repeat protein (320aas; 7 TMSs)	Amoebozoa	*PQLR protein Entamoeba histolyticus* (C4LT11)**

2.A.43.2.5	PQ-loop repeat protein (288aas; 7 TMSs)	Plants	*PQLR protein of Arabidopsis thaliana* (O49437)**

2.A.43.2.6	7 TMS protein 1 (319aas; 7 TMSs)	Diplomonadida	*7 TMS protein of Giardia lamblia* (E1F7I8)**

2.A.43.2.7	Probable vacuolar (lysosomal) cationic amino acid exporter, RTC2 (Ypq3; Ybr147). Involved in amino acid homeostasis. Up-regulated by addition of ammonia or amino acids to a nitrogen-depleted medium (Jézégou et al. 2012). Resistant to fluconazole. Increased resistance to caspofungin. Suppresses CDC13-1 temperature sensitivity.	Yeast	RTC2 of Saccharomyces cerevisiae

2.A.43.2.8	*Vacuolar (lysosomal) putative cationic amino acid exporter, Ypq2 (Ydr352); involved with cationic amino acid homeostasis (Jézégou et al.* 2012).**	Yeast	Ypq2 of Saccharomyces cerevisiae

2.A.43.2.9	PQ loop protein of 384 aas and 7 (3 + 4) TMSs		PQ-loop protein of Populus trichcarpa

Examples:
TC#	Name	Organismal Type	Example
2.A.43.3.1	The Lec15/Lec35 suppressor, SL15, MPDU1 or SLC66A5, of 247 aas and probably 7 TMSs. It is a suppressor of the Lec15 and Lec35 glycosylation mutations (Ware and Lehrman 1998). The human ortholog is 89% identical to this protein. This protein may be required for normal utilization of mannose-dolichol phosphate (Dol-P-Man) in the synthesis of N-linked and O-linked oligosaccharides and GPI anchors.	Animals	SL15 of Cricetulus griseus

2.A.43.3.2	PQ-loop-containing protein 3 (PQLC3) of 202 aas and 7 closely spaced TMSs. It may play a role in gestational diabetes mellitus (Li et al. 2021). It may also function in tumor mutation burden for predicting lymph node metastasis in breast cancer (Wang et al. 2021).	Animals	*PQLC3 of Mus musculus* (Q8C6U2)**

Examples:
TC#	Name	Organismal Type	Example
2.A.43.4.1	Uncharacterized protein C4C5.03	Yeast	SPAC4C5.03 of Schizosaccharomyces pombe

2.A.43.4.2	Uncharacteerized protein of 308 aas and 7 TMSs.		UP of Entamoeba histolytica

2.A.43.4.3	Uncharacterized protein of 363 aas and 8 TMSs.		UP of Entamoeba histolytica

Examples:
TC#	Name	Organismal Type	Example
2.A.43.5.1	Transmembrane protein 44, TMEM44, of 475 aas and 7 TMSs in a 1 + 2 + 2 + 2 TMS arrangement. TMEM44, as a novel prognostic marker for kidney renal clear cell carcinoma, is associated with tumor invasion, migration and immune infiltration (Tian et al. 2023).		TMEM44 of Homo sapiens

2.A.43.5.2	Uncharacterized protein of 358 aas and 5 N-terminal TMSs.		UP of Austrofundulus limnaeus

2.A.43.5.3	TMEM44 isoform X5 of 360 aas and 7 TMSs in a 1 + 5 + 1 TMS arrangement.		*TMEM44 of Gadus chalcogrammus* (walleye pollock)**

2.A.43.5.4	TMEM44 Isooform 5 of 378 aas and 4 - 6 N-terminal TMSs.		*TMEM44 of Pseudochaenichthys georgianus* (South Georgia icefish)**

2.A.43.5.5	TMEM43 isoform X6 of 399 aas and 7 TMSs in a 4 + 3 arrangement near the N-terminus of the protein.		*TMEM43 of Doryrhamphus excisus* (bluestripe pipefish)**

2.A.43.5.6	Uncharacterized protein isoform X1 of 543 aas and 7 TMSs in a 3 + 1 + 3 TMS arrangement.		UP of Acanthaster planci (crown-of-thorns starfish)