Solute carrier family explained

The solute carrier (SLC) group of membrane transport proteins include over 400 members organized into 66 families.[1] [2] Most members of the SLC group are located in the cell membrane. The SLC gene nomenclature system was originally proposed by the HUGO Gene Nomenclature Committee (HGNC) and is the basis for the official HGNC names of the genes that encode these transporters. A more general transmembrane transporter classification can be found in TCDB database.

Solutes that are transported by the various SLC group members are extremely diverse and include both charged and uncharged organic molecules as well as inorganic ions and the gas ammonia.

As is typical of integral membrane proteins, SLCs contain a number of hydrophobic transmembrane alpha helices connected to each other by hydrophilic intra- and extra-cellular loops. Depending on the SLC, these transporters are functional as either monomers or obligate homo- or hetero-oligomers. Many SLC families are members of the major facilitator superfamily.

Scope

By convention of the nomenclature system, members within an individual SLC family have greater than 20-25% sequence identity to each other. In contrast, the homology between SLC families is very low to non-existent.[3] Hence, the criteria for inclusion of a family into the SLC group is not evolutionary relatedness to other SLC families but rather functional (i.e., an integral membrane protein that transports a solute).

The SLC group include examples of transport proteins that are:

The SLC series does not include members of transport protein families that have previously been classified by other widely accepted nomenclature systems including:

Subcellular distribution

Most members of the SLC group are located in the cell membrane, but some members are located in mitochondria (the most notable one being SLC family 25) or other intracellular organelles.

Nomenclature system

Names of individual SLC members have the following format:[4]

SLCnXm

where:

For example, is the first isoform of subfamily A of SLC family 1.

An exception occurs with SLC family 21[5] (the organic anion transporting polypeptide transporters), which for historical reasons have names in the format SLCOnXm where n = family number, X = subfamily letter, and m = member number.

While the HGNC only assign nomenclature to human genes, by convention vertebrate orthologs of these genes adopt the same nomenclature (e.g., VGNC-assigned orthologs of SLC10A1). For rodents, the case of the symbols differs from other vertebrates by using title case, i.e. Slc1a1 denotes the rodent ortholog of the human SLC1A1 gene.

Families

The following families are named under SLC:[6]

  1. high-affinity glutamate and neutral amino acid transporter[7]
  2. facilitative GLUT transporter[8]
  3. heavy subunits of heterodimeric amino acid transporters[9]
  4. bicarbonate transporter[10]
  5. sodium glucose cotransporter[11]
  6. sodium- and chloride-dependent [12]
  7. cationic amino acid transporter/glycoprotein-associated[13]
  8. Na+/Ca2+ exchanger[14]
  9. Na+/H+ exchanger[15]
  10. sodium bile salt cotransport[16]
  11. proton coupled metal ion transporter[17]
  12. electroneutral cation-Cl cotransporter[18]
  13. Na+-sulfate/carboxylate cotransporter[19]
  14. urea transporter[20]
  15. proton oligopeptide cotransporter[21]
  16. monocarboxylate transporter[22]
  17. vesicular glutamate transporter[23]
  18. vesicular amine transporter[24]
  19. folate/thiamine transporter[25]
  20. type III Na+-phosphate cotransporter[26]
  21. organic anion transporting[27]
  22. organic cation/anion/zwitterion transporter[28]
  23. Na+-dependent ascorbic acid transporter[29]
  24. Na+/(Ca2+-K+) exchanger[30]
  25. mitochondrial carrier[31]
  26. multifunctional anion exchanger[32]
  27. fatty acid transport proteins[33]
  28. Na+-coupled nucleoside transport[34]
  29. facilitative nucleoside transporter[35]
  30. zinc transporter[36]
  31. copper transporter[37]
  32. vesicular inhibitory amino acid transporter[38]
  33. Acetyl-CoA transporter[39]
  34. type II Na+-phosphate cotransporter[40]
  35. nucleotide-sugar transporter[41]
    • subfamily A (SLC35A1, SLC35A2, SLC35A3, SLC35A4, SLC35A5)
    • subfamily B (SLC35B1, SLC35B2, SLC35B3, SLC35B4)
    • subfamily C (SLC35C1, SLC35C2)
    • subfamily D (SLC35D1, SLC35D2, SLC35D3)
    • subfamily E (SLC35E1, SLC35E2A, SLC35E2B, SLC35E3, SLC35E4)
    • subfamily F (SLC35F1, SLC35F2, SLC35F3, SLC35F4, SLC35F5)
    • subfamily G (SLC35G1, SLC35G3, SLC35G4, SLC35G5, SLC35G6)
  36. proton-coupled amino acid transporter[42]
  37. sugar-phosphate/phosphate exchanger[43]
  38. System A & N, sodium-coupled neutral amino acid transporter[44]
  39. metal ion transporter[45]
  40. basolateral iron transporter[46]
  41. MgtE-like magnesium transporter
  42. Ammonia transporter[47] [48]
  43. Na+-independent, system-L like amino acid transporter
  44. Choline-like transporter
  45. Putative sugar transporter
  46. Folate transporter
  47. multidrug and toxin extrusion
  48. Heme transporter family
    • (SLC48A1)
  49. Heme transporter
  50. Sugar efflux transporters of the SWEET family
  51. Transporters of steroid-derived molecules
  52. Riboflavin transporter family RFVT/SLC52
  53. Phosphate carriers
      1. (XPR1(SLC53A1) Mitochondrial pyruvate carriers
    • (MPC1(SLC54A1), MPC2(SLC54A2), MPC1L(SLC54A3))
  54. Mitochondrial cation/proton exchangers
  55. Sideroflexins
    • (SFXN1(SLC56A1), SFXN2(SLC56A2), SFXN3(SLC56A3), SFXN4(SLC56A4), SFXN5(SLC56A5))
  56. NiPA-like magnesium transporter family
  57. MagT-like magnesium transporter family
  58. Sodium-dependent lysophosphatidylcholine symporter family
    • (MFSD2A(SLC59A1), MFSD2B(SLC59A2))
  59. Glucose transporters
    • (MFSD4A(SLC60A1), MFSD4B(SLC60A2))
  60. Molybdate transporter family
  61. Pyrophosphate transporters
  62. Sphingosine-phosphate transporters
    • (SPNS1(SLC63A1), SPNS2(SLC63A2), SPNS3(SLC63A3))
  63. Golgi Ca2+/H+ exchangers
  64. NPC-type cholesterol transporters
  65. Cationic amino acid exporters

Putative SLCs

Putative SLCs, also called atypical SLCs, are novel, plausible secondary active or facilitative transporter proteins that share ancestral background with the known SLCs. [49] The atypical SLCs of MFS type can, however, be subdivided into 15 Putative MFS Transporter Families (AMTF).

All the putative SLCs are plausible SLC transporters. Some are only "atypical" when it comes to their nomenclature; the genes have an SLC assignment but as an alias, and have retained their already assigned "non-SLC" gene symbol as the approved symbol.

Here are some Putative SLCs listed: OCA2, CLN3, TMEM104, SPNS1, SPNS2, SPNS3, SV2A, SV2B, SV2C, SVOP, SVOPL, MFSD1,[50] MFSD2A, MFSD2B, MFSD3, MFSD4A,[51] MFSD4B, MFSD5,[52] MFSD6, MFSD6L, MFSD8, MFSD9, MFSD10, MFSD11, MFSD12, MFSD13A, MFSD14A,[53] MFSD14B, UNC93A[54] [55] and UNC93B1.

References

SLC Tables. SLCtables

External links

Notes and References

  1. Hediger MA, Romero MF, Peng JB, Rolfs A, Takanaga H, Bruford EA . The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction . Pflügers Archiv . 447 . 5 . 465–468 . February 2004 . 14624363 . 10.1007/s00424-003-1192-y . 1866661 .
  2. Perland E, Fredriksson R . Classification Systems of Secondary Active Transporters . Trends in Pharmacological Sciences . 38 . 3 . 305–315 . March 2017 . 27939446 . 10.1016/j.tips.2016.11.008 .
  3. Höglund PJ, Nordström KJ, Schiöth HB, Fredriksson R . The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species . Molecular Biology and Evolution . 28 . 4 . 1531–1541 . April 2011 . 21186191 . 3058773 . 10.1093/molbev/msq350 .
  4. Hediger MA, Clémençon B, Burrier RE, Bruford EA . The ABCs of membrane transporters in health and disease (SLC series): introduction . Molecular Aspects of Medicine . 34 . 2–3 . 95–107 . 2013 . 23506860 . 3853582 . 10.1016/j.mam.2012.12.009 .
  5. He L, Vasiliou K, Nebert DW . Analysis and update of the human solute carrier (SLC) gene superfamily . Human Genomics . 3 . 2 . 195–206 . January 2009 . 19164095 . 2752037 . 10.1186/1479-7364-3-2-195 . free .
  6. Web site: SLCtables. slc.bioparadigms.org. 2018-03-07.
  7. Kanai Y, Hediger MA . The glutamate/neutral amino acid transporter family SLC1: molecular, physiological and pharmacological aspects . Pflügers Archiv . 447 . 5 . 469–479 . February 2004 . 14530974 . 10.1007/s00424-003-1146-4 . 21564906 .
  8. Uldry M, Thorens B . The SLC2 family of facilitated hexose and polyol transporters . Pflügers Archiv . 447 . 5 . 480–489 . February 2004 . 12750891 . 10.1007/s00424-003-1085-0 . 25539725 .
  9. Palacín M, Kanai Y . The ancillary proteins of HATs: SLC3 family of amino acid transporters . Pflügers Archiv . 447 . 5 . 490–494 . February 2004 . 14770309 . 10.1007/s00424-003-1062-7 . 25808108 .
  10. Romero MF, Fulton CM, Boron WF . The SLC4 family of HCO 3 - transporters . Pflügers Archiv . 447 . 5 . 495–509 . February 2004 . 14722772 . 10.1007/s00424-003-1180-2 . 40609789 .
  11. Wright EM, Turk E . The sodium/glucose cotransport family SLC5 . Pflügers Archiv . 447 . 5 . 510–518 . February 2004 . 12748858 . 10.1007/s00424-003-1063-6 . 41985805 .
  12. Chen NH, Reith ME, Quick MW . Synaptic uptake and beyond: the sodium- and chloride-dependent neurotransmitter transporter family SLC6 . Pflügers Archiv . 447 . 5 . 519–531 . February 2004 . 12719981 . 10.1007/s00424-003-1064-5 . 34991320 .
  13. Verrey F, Closs EI, Wagner CA, Palacin M, Endou H, Kanai Y . CATs and HATs: the SLC7 family of amino acid transporters . Pflügers Archiv . 447 . 5 . 532–542 . February 2004 . 14770310 . 10.1007/s00424-003-1086-z . 11670040 .
  14. Quednau BD, Nicoll DA, Philipson KD . The sodium/calcium exchanger family-SLC8 . Pflügers Archiv . 447 . 5 . 543–548 . February 2004 . 12734757 . 10.1007/s00424-003-1065-4 . 26502273 .
  15. Orlowski J, Grinstein S . Diversity of the mammalian sodium/proton exchanger SLC9 gene family . Pflügers Archiv . 447 . 5 . 549–565 . February 2004 . 12845533 . 10.1007/s00424-003-1110-3 . 5691463 .
  16. Hagenbuch B, Dawson P . The sodium bile salt cotransport family SLC10 . Pflügers Archiv . 447 . 5 . 566–570 . February 2004 . 12851823 . 10.1007/s00424-003-1130-z . 35115446 .
  17. Mackenzie B, Hediger MA . SLC11 family of H+-coupled metal-ion transporters NRAMP1 and DMT1 . Pflügers Archiv . 447 . 5 . 571–579 . February 2004 . 14530973 . 10.1007/s00424-003-1141-9 . 7439663 .
  18. Hebert SC, Mount DB, Gamba G . Molecular physiology of cation-coupled Cl- cotransport: the SLC12 family . Pflügers Archiv . 447 . 5 . 580–593 . February 2004 . 12739168 . 10.1007/s00424-003-1066-3 . 21998913 .
  19. Markovich D, Murer H . The SLC13 gene family of sodium sulphate/carboxylate cotransporters . Pflügers Archiv . 447 . 5 . 594–602 . February 2004 . 12915942 . 10.1007/s00424-003-1128-6 . 7609066 .
  20. Shayakul C, Hediger MA . The SLC14 gene family of urea transporters . Pflügers Archiv . 447 . 5 . 603–609 . February 2004 . 12856182 . 10.1007/s00424-003-1124-x . 21071284 .
  21. Daniel H, Kottra G . The proton oligopeptide cotransporter family SLC15 in physiology and pharmacology . Pflügers Archiv . 447 . 5 . 610–618 . February 2004 . 12905028 . 10.1007/s00424-003-1101-4 . 22369521 .
  22. Halestrap AP, Meredith D . The SLC16 gene family-from monocarboxylate transporters (MCTs) to aromatic amino acid transporters and beyond . Pflügers Archiv . 447 . 5 . 619–628 . February 2004 . 12739169 . 10.1007/s00424-003-1067-2 . 15498611 .
  23. Reimer RJ, Edwards RH . Organic anion transport is the primary function of the SLC17/type I phosphate transporter family . Pflügers Archiv . 447 . 5 . 629–635 . February 2004 . 12811560 . 10.1007/s00424-003-1087-y . 9680597 .
  24. Eiden LE, Schäfer MK, Weihe E, Schütz B . The vesicular amine transporter family (SLC18): amine/proton antiporters required for vesicular accumulation and regulated exocytotic secretion of monoamines and acetylcholine . Pflügers Archiv . 447 . 5 . 636–640 . February 2004 . 12827358 . 10.1007/s00424-003-1100-5 . 20764857 .
  25. Ganapathy V, Smith SB, Prasad PD . SLC19: the folate/thiamine transporter family . Pflügers Archiv . 447 . 5 . 641–646 . February 2004 . 14770311 . 10.1007/s00424-003-1068-1 . 7410075 .
  26. Collins JF, Bai L, Ghishan FK . The SLC20 family of proteins: dual functions as sodium-phosphate cotransporters and viral receptors . Pflügers Archiv . 447 . 5 . 647–652 . February 2004 . 12759754 . 10.1007/s00424-003-1088-x . 7737512 .
  27. Hagenbuch B, Meier PJ . Organic anion transporting polypeptides of the OATP/ SLC21 family: phylogenetic classification as OATP/ SLCO superfamily, new nomenclature and molecular/functional properties . Pflügers Archiv . 447 . 5 . 653–665 . February 2004 . 14579113 . 10.1007/s00424-003-1168-y . 21837213 .
  28. Koepsell H, Endou H . The SLC22 drug transporter family . Pflügers Archiv . 447 . 5 . 666–676 . February 2004 . 12883891 . 10.1007/s00424-003-1089-9 . 30419152 .
  29. Takanaga H, Mackenzie B, Hediger MA . Sodium-dependent ascorbic acid transporter family SLC23 . Pflügers Archiv . 447 . 5 . 677–682 . February 2004 . 12845532 . 10.1007/s00424-003-1104-1 . 13018443 .
  30. Schnetkamp PP . The SLC24 Na+/Ca2+-K+ exchanger family: vision and beyond . Pflügers Archiv . 447 . 5 . 683–688 . February 2004 . 14770312 . 10.1007/s00424-003-1069-0 . 37553960 .
  31. Palmieri F . The mitochondrial transporter family (SLC25): physiological and pathological implications . Pflügers Archiv . 447 . 5 . 689–709 . February 2004 . 14598172 . 10.1007/s00424-003-1099-7 . 25304722 .
  32. Mount DB, Romero MF . The SLC26 gene family of multifunctional anion exchangers . Pflügers Archiv . 447 . 5 . 710–721 . February 2004 . 12759755 . 10.1007/s00424-003-1090-3 . 20302398 .
  33. Stahl A . A current review of fatty acid transport proteins (SLC27) . Pflügers Archiv . 447 . 5 . 722–727 . February 2004 . 12856180 . 10.1007/s00424-003-1106-z . 2769738 .
  34. Gray JH, Owen RP, Giacomini KM . The concentrative nucleoside transporter family, SLC28 . Pflügers Archiv . 447 . 5 . 728–734 . February 2004 . 12856181 . 10.1007/s00424-003-1107-y . 24749954 .
  35. Baldwin SA, Beal PR, Yao SY, King AE, Cass CE, Young JD . The equilibrative nucleoside transporter family, SLC29 . Pflügers Archiv . 447 . 5 . 735–743 . February 2004 . 12838422 . 10.1007/s00424-003-1103-2 . 8817821 .
  36. Palmiter RD, Huang L . Efflux and compartmentalization of zinc by members of the SLC30 family of solute carriers . Pflügers Archiv . 447 . 5 . 744–751 . February 2004 . 12748859 . 10.1007/s00424-003-1070-7 . 725350 .
  37. Petris MJ . The SLC31 (Ctr) copper transporter family . Pflügers Archiv . 447 . 5 . 752–755 . February 2004 . 12827356 . 10.1007/s00424-003-1092-1 . 23340930 .
  38. Gasnier B . The SLC32 transporter, a key protein for the synaptic release of inhibitory amino acids . Pflügers Archiv . 447 . 5 . 756–759 . February 2004 . 12750892 . 10.1007/s00424-003-1091-2 . 24669893 .
  39. Hirabayashi Y, Kanamori A, Nomura KH, Nomura K . The acetyl-CoA transporter family SLC33 . Pflügers Archiv . 447 . 5 . 760–762 . February 2004 . 12739170 . 10.1007/s00424-003-1071-6 . 21247182 .
  40. Murer H, Forster I, Biber J . The sodium phosphate cotransporter family SLC34 . Pflügers Archiv . 447 . 5 . 763–767 . February 2004 . 12750889 . 10.1007/s00424-003-1072-5 . 34041192 .
  41. Ishida N, Kawakita M . Molecular physiology and pathology of the nucleotide sugar transporter family (SLC35) . Pflügers Archiv . 447 . 5 . 768–775 . February 2004 . 12759756 . 10.1007/s00424-003-1093-0 . 8690030 .
  42. Boll M, Daniel H, Gasnier B . The SLC36 family: proton-coupled transporters for the absorption of selected amino acids from extracellular and intracellular proteolysis . Pflügers Archiv . 447 . 5 . 776–779 . February 2004 . 12748860 . 10.1007/s00424-003-1073-4 . 25655241 .
  43. Bartoloni L, Antonarakis SE . The human sugar-phosphate/phosphate exchanger family SLC37 . Pflügers Archiv . 447 . 5 . 780–783 . February 2004 . 12811562 . 10.1007/s00424-003-1105-0 . 24776306 .
  44. Mackenzie B, Erickson JD . Sodium-coupled neutral amino acid (System N/A) transporters of the SLC38 gene family . Pflügers Archiv . 447 . 5 . 784–795 . February 2004 . 12845534 . 10.1007/s00424-003-1117-9 . 35457147 .
  45. Eide DJ . The SLC39 family of metal ion transporters . Pflügers Archiv . 447 . 5 . 796–800 . February 2004 . 12748861 . 10.1007/s00424-003-1074-3 . 11765308 .
  46. McKie AT, Barlow DJ . The SLC40 basolateral iron transporter family (IREG1/ferroportin/MTP1) . Pflügers Archiv . 447 . 5 . 801–806 . February 2004 . 12836025 . 10.1007/s00424-003-1102-3 . 27340247 .
  47. Nakhoul NL, Hamm LL . Non-erythroid Rh glycoproteins: a putative new family of mammalian ammonium transporters . Pflügers Archiv . 447 . 5 . 807–812 . February 2004 . 12920597 . 10.1007/s00424-003-1142-8 . 24601165 .
  48. Boron WF . Sharpey-Schafer lecture: gas channels . Experimental Physiology . 95 . 12 . 1107–1130 . December 2010 . 20851859 . 3003898 . 10.1113/expphysiol.2010.055244 .
  49. Perland E, Bagchi S, Klaesson A, Fredriksson R . Characteristics of 29 novel atypical solute carriers of major facilitator superfamily type: evolutionary conservation, predicted structure and neuronal co-expression . Open Biology . 7 . 9 . 170142 . September 2017 . 28878041 . 5627054 . 10.1098/rsob.170142 .
  50. Perland E, Hellsten SV, Lekholm E, Eriksson MM, Arapi V, Fredriksson R . The Novel Membrane-Bound Proteins MFSD1 and MFSD3 are Putative SLC Transporters Affected by Altered Nutrient Intake . Journal of Molecular Neuroscience . 61 . 2 . 199–214 . February 2017 . 27981419 . 5321710 . 10.1007/s12031-016-0867-8 .
  51. Perland E, Hellsten SV, Schweizer N, Arapi V, Rezayee F, Bushra M, Fredriksson R . Structural prediction of two novel human atypical SLC transporters, MFSD4A and MFSD9, and their neuroanatomical distribution in mice . PLOS ONE . 12 . 10 . e0186325 . 2017 . 29049335 . 5648162 . 10.1371/journal.pone.0186325 . free . 2017PLoSO..1286325P .
  52. Perland E, Lekholm E, Eriksson MM, Bagchi S, Arapi V, Fredriksson R . The Putative SLC Transporters Mfsd5 and Mfsd11 Are Abundantly Expressed in the Mouse Brain and Have a Potential Role in Energy Homeostasis . PLOS ONE . 11 . 6 . e0156912 . 2016 . 27272503 . 4896477 . 10.1371/journal.pone.0156912 . free . 2016PLoSO..1156912P .
  53. Lekholm E, Perland E, Eriksson MM, Hellsten SV, Lindberg FA, Rostami J, Fredriksson R . Putative Membrane-Bound Transporters MFSD14A and MFSD14B Are Neuronal and Affected by Nutrient Availability . Frontiers in Molecular Neuroscience . 10 . 11 . 2017 . 28179877 . 5263138 . 10.3389/fnmol.2017.00011 . free .
  54. Ceder MM, Lekholm E, Hellsten SV, Perland E, Fredriksson R . The Neuronal and Peripheral Expressed Membrane-Bound UNC93A Respond to Nutrient Availability in Mice . English . Frontiers in Molecular Neuroscience . 10 . 351 . 2017 . 29163028 . 5671512 . 10.3389/fnmol.2017.00351 . free .
  55. Ceder MM, Aggarwal T, Hosseini K, Maturi V, Patil S, Perland E, Williams MJ, Fredriksson R . 6 . CG4928 Is Vital for Renal Function in Fruit Flies and Membrane Potential in Cells: A First In-Depth Characterization of the Putative Solute Carrier UNC93A . English . Frontiers in Cell and Developmental Biology . 8 . 580291 . 2020 . 33163493 . 7591606 . 10.3389/fcell.2020.580291 . free .