Solute carrier family




The solute carrier (SLC) group of membrane transport proteins include over 400 members organized into 65 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.




Contents






  • 1 Scope


  • 2 Subcellular distribution


  • 3 Nomenclature system


  • 4 Families[4]


  • 5 Putative SLCs


  • 6 References


  • 7 External links





Scope


By convention of the nomenclature system, members within an individual SLC family have greater than 20-25% sequence homology 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:




  • facilitative transporters (allow solutes to flow downhill with their electrochemical gradients)


  • secondary active transporters (allow solutes to flow uphill against their electrochemical gradient by coupling to transport of a second solute that flows downhill with its gradient such that the overall free energy change is still favorable)


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




  • primary active transporters (allow flow uphill against electrochemical gradients) such as ABC (ATP Binding Cassette) transporters by coupling transport to an energy releasing event such as ATP hydrolysis

  • ion channels


  • aquaporins (water channels)



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:


  • SLCnXm

where:



  • SLC is the root name (SoLute Carrier)

  • n = an integer representing a family (e.g., 1-52)

  • X = a single letter (A, B, C, ...) denoting a subfamily

  • m = an integer representing an individual family member (isoform).


For example, SLC1A1 is the first isoform of subfamily A of SLC family 1.


An exception occurs with SLC family 21 (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 nomenclature system by definition only includes human genes, the nomenclature system has been informally extended to include rodent species through the use of lowercase letters (e.g., Slc1a1 denotes the rodent ortholog of the human SLC1A1 gene).



Families[4]



  • (1) high-affinity glutamate and neutral amino acid transporter[5]
    • (SLC1A1, SLC1A2, SLC1A3, SLC1A4, SLC1A5, SLC1A6, SLC1A7)


  • (2) facilitative GLUT transporter[6]
    • (SLC2A1, SLC2A2, SLC2A3, SLC2A4, SLC2A5, SLC2A6, SLC2A7, SLC2A8, SLC2A9, SLC2A10, SLC2A11, SLC2A12, SLC2A13, SLC2A14)


  • (3) heavy subunits of heterodimeric amino acid transporters[7]
    • (SLC3A1, SLC3A2)


  • (4) bicarbonate transporter[8]
    • (SLC4A1, SLC4A2, SLC4A3, SLC4A4, SLC4A5, SLC4A6, SLC4A7, SLC4A8, SLC4A9, SLC4A10, SLC4A11)


  • (5) sodium glucose cotransporter[9]
    • (SLC5A1, SLC5A2, SLC5A3, SLC5A4, SLC5A5, SLC5A6, SLC5A7, SLC5A8, SLC5A9, SLC5A10, SLC5A11, SLC5A12)


  • (6) sodium- and chloride-dependent sodium:neurotransmitter symporters[10]
    • (SLC6A1, SLC6A2, SLC6A3, SLC6A4, SLC6A5, SLC6A6, SLC6A7, SLC6A8, SLC6A9, SLC6A10, SLC6A11, SLC6A12, SLC6A13, SLC6A14, SLC6A15, SLC6A16, SLC6A17, SLC6A18, SLC6A19, SLC6A20)


  • (7) cationic amino acid transporter/glycoprotein-associated[11]


    • cationic amino acid transporters (SLC7A1, SLC7A2, SLC7A3, SLC7A4)

    • glycoprotein-associated/light or catalytic subunits of heterodimeric amino acid transporters (SLC7A5, SLC7A6, SLC7A7, SLC7A8, SLC7A9, SLC7A10, SLC7A11, SLC7A13, SLC7A14)



  • (8) Na+/Ca2+ exchanger[12]
    • (SLC8A1, SLC8A2, SLC8A3)


  • (9) Na+/H+ exchanger[13]
    • (SLC9A1, SLC9A2, SLC9A3, SLC9A4, SLC9A5, SLC9A6, SLC9A7, SLC9A8, SLC9A9, SLC9A10, SLC9A11, SLC9B1, SLC9B2)


  • (10) sodium bile salt cotransport[14]
    • (SLC10A1, SLC10A2, SLC10A3, SLC10A4, SLC10A5, SLC10A6, SLC10A7)


  • (11) proton coupled metal ion transporter[15]
    • (SLC11A1, SLC11A2)


  • (12) electroneutral cation-Cl cotransporter[16]
    • (SLC12A1, SLC12A1, SLC12A2, SLC12A3, SLC12A4, SLC12A5, SLC12A6, SLC12A7, SLC12A8, SLC12A9)


  • (13) Na+-sulfate/carboxylate cotransporter[17]
    • (SLC13A1, SLC13A2, SLC13A3, SLC13A4, SLC13A5)


  • (14) urea transporter[18]
    • (SLC14A1, SLC14A2)


  • (15) proton oligopeptide cotransporter[19]
    • (SLC15A1, SLC15A2, SLC15A3, SLC15A4)


  • (16) monocarboxylate transporter[20]
    • (SLC16A1, SLC16A2, SLC16A3, SLC16A4, SLC16A5, SLC16A6, SLC16A7, SLC16A8, SLC16A9, SLC16A10, SLC16A11, SLC16A12, SLC16A13, SLC16A14)


  • (17) vesicular glutamate transporter[21]
    • (SLC17A1, SLC17A2, SLC17A3, SLC17A4, SLC17A5, SLC17A6, SLC17A7, SLC17A8, SLC17A9)


  • (18) vesicular amine transporter[22]
    • (SLC18A1, SLC18A2, SLC18A3)


  • (19) folate/thiamine transporter[23]
    • (SLC19A1, SLC19A2, SLC19A3)


  • (20) type III Na+-phosphate cotransporter[24]
    • (SLC20A1, SLC20A2)


  • (21) organic anion transporting[25]

    • subfamily 1 (SLCO1A2, SLCO1B1, SLCO1B3, SLCO1C1)

    • subfamily 2 (SLCO2A1, SLCO2B1)

    • subfamily 3 (SLCO3A1)

    • subfamily 4 (SLCO4A1, SLCO4C1)

    • subfamily 5 (SLCO5A1)

    • subfamily 6 (SLCO6A1)



  • (22) organic cation/anion/zwitterion transporter[26]
    • (SLC22A1, SLC22A2, SLC22A3, SLC22A4, SLC22A5, SLC22A6, SLC22A7, SLC22A8, SLC22A9, SLC22A10, SLC22A11, SLC22A12, SLC22A13, SLC22A14, SLC22A15, SLC22A16, SLC22A17, SLC22A18, SLC22A18AS, SLC22A19, SLC22A20, SLC22A23, SLC22A24, SLC22A25, SLC22A31)


  • (23) Na+-dependent ascorbic acid transporter[27]
    • (SLC23A1, SLC23A2, SLC23A3, SLC23A4)


  • (24) Na+/(Ca2+-K+) exchanger[28]
    • (SLC24A1, SLC24A2, SLC24A3, SLC24A4, SLC24A5, SLC24A6)


  • (25) mitochondrial carrier[29]
    • (SLC25A1, SLC25A2, SLC25A3, SLC25A4, SLC25A5, SLC25A6, SLC25A7, SLC25A8, SLC25A9, SLC25A10, SLC25A11, SLC25A12, SLC25A13, SLC25A14, SLC25A15, SLC25A16, SLC25A17, SLC25A18, SLC25A19, SLC25A20, SLC25A21, SLC25A22, SLC25A23, SLC25A24, SLC25A25, SLC25A26, SLC25A27, SLC25A28, SLC25A29, SLC25A30, SLC25A31, SLC25A32, SLC25A33, SLC25A34, SLC25A35, SLC25A36, SLC25A37, SLC25A38, SLC25A39, SLC25A40, SLC25A41, SLC25A42, SLC25A43, SLC25A44, SLC25A45, SLC25A46)


  • (26) multifunctional anion exchanger[30]
    • (SLC26A1, SLC26A2, SLC26A3, SLC26A4, SLC26A5, SLC26A6, SLC26A7, SLC26A8, SLC26A9, SLC26A10, SLC26A11)


  • (27) fatty acid transport proteins[31]
    • (SLC27A1, SLC27A2, SLC27A3, SLC27A4, SLC27A5, SLC27A6)


  • (28) Na+-coupled nucleoside transport[32]
    • (SLC28A1, SLC28A2, SLC28A3)


  • (29) facilitative nucleoside transporter[33]
    • (SLC29A1, SLC29A2, SLC29A3, SLC29A4)



  • (30) zinc transporter[34]
    • (SLC30A1, SLC30A2, SLC30A3, SLC30A4, SLC30A5, SLC30A6, SLC30A7, SLC30A8, SLC30A9, SLC30A10)


  • (31) copper transporter[35]
    • (SLC31A1, SLC31A2)


  • (32) vesicular inhibitory amino acid transporter[36]
    • (SLC32A1)


  • (33) Acetyl-CoA transporter[37]
    • (SLC33A1)


  • (34) type II Na+-phosphate cotransporter[38]
    • (SLC34A1, SLC34A2, SLC34A3)


  • (35) nucleotide-sugar transporter[39]

    • 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, SLC35E2, SLC35E3, SLC35E4)

    • subfamily F (SLC35F1, SLC35F2, SLC35F3, SLC35F4, SLC35F5)

    • subfamily G (SLC35G1, SLC35G3, SLC35G4, SLC35G5, SLC35G6)



  • (36) proton-coupled amino acid transporter[40]
    • (SLC36A1, SLC36A2, SLC36A3, SLC36A4)


  • (37) sugar-phosphate/phosphate exchanger[41]
    • (SLC37A1, SLC37A2, SLC37A3, SLC37A4)


  • (38) System A & N, sodium-coupled neutral amino acid transporter[42]
    • (SLC38A1, SLC38A2, SLC38A3, SLC38A4, SLC38A5, SLC38A6, SLC38A7, SLC38A8, SLC38A9, SLC38A10, SLC38A11)


  • (39) metal ion transporter[43]
    • (SLC39A1, SLC39A2, SLC39A3, SLC39A4, SLC39A5, SLC39A6, SLC39A7, SLC39A8, SLC39A9, SLC39A10, SLC39A11, SLC39A12, SLC39A13, SLC39A14)


  • (40) basolateral iron transporter[44]
    • (SLC40A1)


  • (41) MgtE-like magnesium transporter
    • (SLC41A1, SLC41A2, SLC41A3)


  • (42) Ammonia transporter[45][46]
    • (RhAG, RhBG, RhCG)


  • (43) Na+-independent, system-L like amino acid transporter
    • (SLC43A1, SLC43A2, SLC43A3)


  • (44) Choline-like transporter
    • (SLC44A1, SLC44A2, SLC44A3, SLC44A4, SLC44A5)


  • (45) Putative sugar transporter
    • (SLC45A1, SLC45A2, SLC45A3, SLC45A4)


  • (46) Folate transporter
    • (SLC46A1, SLC46A2, SLC46A3)


  • (47) multidrug and toxin extrusion
    • (SLC47A1, SLC47A2)


  • (48) Heme transporter family
    • (SLC48A1)


  • (49) Transporters of the major facilitator superfamily
    • (SLC49A1, SLC49A2, SLC49A3, SLC49A4)


  • (50) Sugar efflux transporters of the SWEET family
    • (SLC50A1)


  • (51) Transporters of steroid-derived molecules
    • (SLC51A, SLC51B)


  • (52) Riboflavin transporter family RFVT/SLC52
    • (SLC52A1, SLC52A2, SLC52A3)


  • (53) Phosphate carriers
    • (SLC53A1)


  • (54) Mitochondrial pyruvate carriers
    • (SLC54A1, SLC54A2, SLC54A3)


  • (55) Mitochondrial cation/proton exchangers
    • (SLC55A1, SLC55A2, SLC55A3)


  • (56) Sideroflexins
    • (SLC56A1, SLC56A2, SLC56A3, SLC56A4, SLC56A5)


  • (57) NiPA-like magnesium transporter family
    • (SLC57A1, SLC57A2, SLC57A3, SLC57A4, SLC57A5, SLC57A6)


  • (58) MagT-like magnesium transporter family
    • (SLC58A1, SLC58A2)


  • (59) Sodium-dependent lysophosphatidylcholine symporter family
    • (SLC59A1, SLC59A2)


  • (60) Glucose transporters
    • (SLC60A1, SLC60A2)


  • (61) Molybdate transporter family
    • (SLC61A1)


  • (62) Pyrophosphate transporters
    • (SLC62A1)


  • (63) Sphingosine-phosphate transporters
    • (SLC63A1, SLC63A2, SLC63A3)


  • (64) Golgi Ca2+/H+ exchangers
    • (SLC64A1)


  • (65) NPC-type cholesterol transporters
    • (SLC65A1, SLC65A2)




Putative SLCs


Putative SLCs, also called atypical SLCs, are novel, plausible secondary active or facilitative transansporter proteins that share ancestral background with the known SLCs. However, they have not been assigned a name according to the SLC root system, or been classified into any of the existing SLC families.[2][47] The atypical SLCs of MFS type can, however, be subdivided into 15 Putative MFS Transporter Families (AMTF).[47]


All the putative SLCs are plausible SLC transporters. They are only "atypical" when it comes to their names; the genes are not called according to the SLC root system.


Here are some Putative SLCs listed: OCA2, CLN3, TMEM104, SPNS1, SPNS2, SPNS3, SV2A, SV2B, SV2C, SVOP, SVOPL, MFSD1,[48]MFSD2A, MFSD2B, MFSD3,[48]MFSD4A,[49]MFSD4B, MFSD5,[50]MFSD6, MFSD6L, MFSD8, MFSD9,[49]MFSD10, MFSD11,[50]MFSD12, MFSD13A, MFSD14A,[51]MFSD14B,[51]UNC93A[52] and UNC93B1.



References





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  33. ^ Baldwin SA, Beal PR, Yao SY, King AE, Cass CE, Young JD (February 2004). "The equilibrative nucleoside transporter family, SLC29". Pflügers Archiv. 447 (5): 735–43. doi:10.1007/s00424-003-1103-2. PMID 12838422.


  34. ^ Palmiter RD, Huang L (February 2004). "Efflux and compartmentalization of zinc by members of the SLC30 family of solute carriers". Pflügers Archiv. 447 (5): 744–51. doi:10.1007/s00424-003-1070-7. PMID 12748859.


  35. ^ Petris MJ (February 2004). "The SLC31 (Ctr) copper transporter family". Pflügers Archiv. 447 (5): 752–5. doi:10.1007/s00424-003-1092-1. PMID 12827356.


  36. ^ Gasnier B (February 2004). "The SLC32 transporter, a key protein for the synaptic release of inhibitory amino acids". Pflügers Archiv. 447 (5): 756–9. doi:10.1007/s00424-003-1091-2. PMID 12750892.


  37. ^ Hirabayashi Y, Kanamori A, Nomura KH, Nomura K (February 2004). "The acetyl-CoA transporter family SLC33". Pflügers Archiv. 447 (5): 760–2. doi:10.1007/s00424-003-1071-6. PMID 12739170.


  38. ^ Murer H, Forster I, Biber J (February 2004). "The sodium phosphate cotransporter family SLC34". Pflügers Archiv. 447 (5): 763–7. doi:10.1007/s00424-003-1072-5. PMID 12750889.


  39. ^ Ishida N, Kawakita M (February 2004). "Molecular physiology and pathology of the nucleotide sugar transporter family (SLC35)". Pflügers Archiv. 447 (5): 768–75. doi:10.1007/s00424-003-1093-0. PMID 12759756.


  40. ^ Boll M, Daniel H, Gasnier B (February 2004). "The SLC36 family: proton-coupled transporters for the absorption of selected amino acids from extracellular and intracellular proteolysis". Pflügers Archiv. 447 (5): 776–9. doi:10.1007/s00424-003-1073-4. PMID 12748860.


  41. ^ Bartoloni L, Antonarakis SE (February 2004). "The human sugar-phosphate/phosphate exchanger family SLC37". Pflügers Archiv. 447 (5): 780–3. doi:10.1007/s00424-003-1105-0. PMID 12811562.


  42. ^ Mackenzie B, Erickson JD (February 2004). "Sodium-coupled neutral amino acid (System N/A) transporters of the SLC38 gene family". Pflügers Archiv. 447 (5): 784–95. doi:10.1007/s00424-003-1117-9. PMID 12845534.


  43. ^ Eide DJ (February 2004). "The SLC39 family of metal ion transporters". Pflügers Archiv. 447 (5): 796–800. doi:10.1007/s00424-003-1074-3. PMID 12748861.


  44. ^ McKie AT, Barlow DJ (February 2004). "The SLC40 basolateral iron transporter family (IREG1/ferroportin/MTP1)". Pflügers Archiv. 447 (5): 801–6. doi:10.1007/s00424-003-1102-3. PMID 12836025.


  45. ^ Nakhoul NL, Hamm LL (February 2004). "Non-erythroid Rh glycoproteins: a putative new family of mammalian ammonium transporters". Pflügers Archiv. 447 (5): 807–12. doi:10.1007/s00424-003-1142-8. PMID 12920597.


  46. ^ Boron WF (December 2010). "Sharpey-Schafer lecture: gas channels". Experimental Physiology. 95 (12): 1107–30. doi:10.1113/expphysiol.2010.055244. PMC 3003898. PMID 20851859.


  47. ^ ab Perland E, Bagchi S, Klaesson A, Fredriksson R (September 2017). "Characteristics of 29 novel putative solute carriers of major facilitator superfamily type: evolutionary conservation, predicted structure and neuronal co-expression". Open Biology. 7 (9): 170142. doi:10.1098/rsob.170142. PMID 28878041.


  48. ^ ab Perland E, Hellsten SV, Lekholm E, Eriksson MM, Arapi V, Fredriksson R (February 2017). "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. doi:10.1007/s12031-016-0867-8. PMC 5321710. PMID 27981419.


  49. ^ ab Perland E, Hellsten SV, Schweizer N, Arapi V, Rezayee F, Bushra M, Fredriksson R (2017). "Structural prediction of two novel human atypical SLC transporters, MFSD4A and MFSD9, and their neuroanatomical distribution in mice". PLOS One. 12 (10): e0186325. doi:10.1371/journal.pone.0186325. PMC 5648162. PMID 29049335.


  50. ^ ab Perland E, Lekholm E, Eriksson MM, Bagchi S, Arapi V, Fredriksson R (2016). "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. doi:10.1371/journal.pone.0156912. PMC 4896477. PMID 27272503.


  51. ^ ab Lekholm E, Perland E, Eriksson MM, Hellsten SV, Lindberg FA, Rostami J, Fredriksson R (2017). "Putative Membrane-Bound Transporters MFSD14A and MFSD14B Are Neuronal and Affected by Nutrient Availability". Frontiers in Molecular Neuroscience. 10: 11. doi:10.3389/fnmol.2017.00011. PMC 5263138. PMID 28179877.


  52. ^ Ceder MM, Lekholm E, Hellsten SV, Perland E, Fredriksson R (2017). "The Neuronal and Peripheral Expressed Membrane-Bound UNC93A Respond to Nutrient Availability in Mice". Frontiers in Molecular Neuroscience. 10: 351. doi:10.3389/fnmol.2017.00351. PMID 29163028.



SLC Tables. http://slc.bioparadigms.org



External links



  • Outline of families

  • List of proteins at HGNC website










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