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Wu D, Yan R, Song S, Swansiger AK, Li Y, Prell JS, Zhou Q, Robinson CV. The complete assembly of human LAT1-4F2hc complex provides insights into its regulation, function and localisation. Nat Commun 2024; 15:3711. [PMID: 38697966 PMCID: PMC11065870 DOI: 10.1038/s41467-024-47948-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
The LAT1-4F2hc complex (SLC7A5-SLC3A2) facilitates uptake of essential amino acids, hormones and drugs. Its dysfunction is associated with many cancers and immune/neurological disorders. Here, we apply native mass spectrometry (MS)-based approaches to provide evidence of super-dimer formation (LAT1-4F2hc)2. When combined with lipidomics, and site-directed mutagenesis, we discover four endogenous phosphatidylethanolamine (PE) molecules at the interface and C-terminus of both LAT1 subunits. We find that interfacial PE binding is regulated by 4F2hc-R183 and is critical for regulation of palmitoylation on neighbouring LAT1-C187. Combining native MS with mass photometry (MP), we reveal that super-dimerization is sensitive to pH, and modulated by complex N-glycans on the 4F2hc subunit. We further validate the dynamic assemblies of LAT1-4F2hc on plasma membrane and in the lysosome. Together our results link PTM and lipid binding with regulation and localisation of the LAT1-4F2hc super-dimer.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Siyuan Song
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
| | - Andrew K Swansiger
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Yaning Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - James S Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Qiang Zhou
- Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
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2
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Caprio F, Orefice G, Secondulfo F, Carone Fabiani F, Iervolino A, Capasso G, Simeoni M, Zacchia M, Trepiccione F, Capolongo G. Renal Cystinuria and Immune Cells (T Lymphocytes) Dysfunction: What We Know about? Nephron Clin Pract 2024:1-6. [PMID: 38657578 DOI: 10.1159/000538213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/03/2024] [Indexed: 04/26/2024] Open
Abstract
INTRODUCTION Cystinuria (CYS) is the most common monogenic kidney stone disease. METHODS Starting from an unusual case of CYS associated to primary sclerosing cholangitis, inflammatory bowel disease (IBD), and autoimmune hepatitis in a young male, we carefully review the literature and propose here a working hypothesis regarding the potential risk of cystinuric patients to develop conditions due to immune system dysregulation. To corroborate this hypothesis, we retrospectively evaluate the frequency of dysimmunity in a monocentric cohort including 36 cystinuric patients compared to healthy and disease controls. RESULTS CYS patients have an increased prevalence of atopic disease compared to disease controls (p = 0.03) and 16.7% of CYS subjects were diagnosed with allergic disease to a variety of antigens. CONCLUSION Further studies are needed to define the relationship between proximal tubular transport defect of CYS and dysregulated immunity.
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Affiliation(s)
- Francesca Caprio
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy,
| | - Giuseppe Orefice
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Floriana Secondulfo
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Filippo Carone Fabiani
- University Milano-Bicocca, Department of Economics Management and Statistics, Milan, Italy
| | - Anna Iervolino
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Giovambattista Capasso
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
- Biogem S.c.a.r.l., Ariano Irpino, Italy
| | - Mariadelina Simeoni
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Miriam Zacchia
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Francesco Trepiccione
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
- Biogem S.c.a.r.l., Ariano Irpino, Italy
| | - Giovanna Capolongo
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
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3
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Rullo-Tubau J, Bartoccioni P, Llorca O, Errasti-Murugarren E, Palacín M. HATs meet structural biology. Curr Opin Struct Biol 2022; 74:102389. [DOI: 10.1016/j.sbi.2022.102389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 11/26/2022]
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4
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Ca 2+-mediated higher-order assembly of heterodimers in amino acid transport system b 0,+ biogenesis and cystinuria. Nat Commun 2022; 13:2708. [PMID: 35577790 PMCID: PMC9110406 DOI: 10.1038/s41467-022-30293-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/22/2022] [Indexed: 02/06/2023] Open
Abstract
Cystinuria is a genetic disorder characterized by overexcretion of dibasic amino acids and cystine, causing recurrent kidney stones and kidney failure. Mutations of the regulatory glycoprotein rBAT and the amino acid transporter b0,+AT, which constitute system b0,+, are linked to type I and non-type I cystinuria respectively and they exhibit distinct phenotypes due to protein trafficking defects or catalytic inactivation. Here, using electron cryo-microscopy and biochemistry, we discover that Ca2+ mediates higher-order assembly of system b0,+. Ca2+ stabilizes the interface between two rBAT molecules, leading to super-dimerization of b0,+AT-rBAT, which in turn facilitates N-glycan maturation and protein trafficking. A cystinuria mutant T216M and mutations of the Ca2+ site of rBAT cause the loss of higher-order assemblies, resulting in protein trapping at the ER and the loss of function. These results provide the molecular basis of system b0,+ biogenesis and type I cystinuria and serve as a guide to develop new therapeutic strategies against it. More broadly, our findings reveal an unprecedented link between transporter oligomeric assembly and protein-trafficking diseases.
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Bakshi T, Pham D, Kaur R, Sun B. Hidden Relationships between N-Glycosylation and Disulfide Bonds in Individual Proteins. Int J Mol Sci 2022; 23:ijms23073742. [PMID: 35409101 PMCID: PMC8998389 DOI: 10.3390/ijms23073742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
N-Glycosylation (NG) and disulfide bonds (DBs) are two prevalent co/post-translational modifications (PTMs) that are often conserved and coexist in membrane and secreted proteins involved in a large number of diseases. Both in the past and in recent times, the enzymes and chaperones regulating these PTMs have been constantly discovered to directly interact with each other or colocalize in the ER. However, beyond a few model proteins, how such cooperation affects N-glycan modification and disulfide bonding at selective sites in individual proteins is largely unknown. Here, we reviewed the literature to discover the current status in understanding the relationships between NG and DBs in individual proteins. Our results showed that more than 2700 human proteins carry both PTMs, and fewer than 2% of them have been investigated in the associations between NG and DBs. We summarized both these proteins with the reported relationships in the two PTMs and the tools used to discover the relationships. We hope that, by exposing this largely understudied field, more investigations can be encouraged to unveil the hidden relationships of NG and DBs in the majority of membranes and secreted proteins for pathophysiological understanding and biotherapeutic development.
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Affiliation(s)
- Tania Bakshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - David Pham
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Raminderjeet Kaur
- Faculty of Health Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Bingyun Sun
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Correspondence:
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Fort J, Nicolàs-Aragó A, Palacín M. The Ectodomains of rBAT and 4F2hc Are Fake or Orphan α-Glucosidases. Molecules 2021; 26:6231. [PMID: 34684812 PMCID: PMC8537225 DOI: 10.3390/molecules26206231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/22/2022] Open
Abstract
It is known that 4F2hc and rBAT are the heavy subunits of the heteromeric amino acid transporters (HATs). These heavy subunits are N-glycosylated proteins, with an N-terminal domain, one transmembrane domain and a bulky extracellular domain (ectodomain) that belongs to the α-amylase family. The heavy subunits are covalently linked to a light subunit from the SLC7 family, which is responsible for the amino acid transport activity, forming a heterodimer. The functions of 4F2hc and rBAT are related mainly to the stability and trafficking of the HATs in the plasma membrane of vertebrates, where they exert the transport activity. Moreover, 4F2hc is a modulator of integrin signaling, has a role in cell fusion and it is overexpressed in some types of cancers. On the other hand, some mutations in rBAT are found to cause the malfunctioning of the b0,+ transport system, leading to cystinuria. The ectodomains of 4F2hc and rBAT share both sequence and structure homology with α-amylase family members. Very recently, cryo-EM has revealed the structure of several HATs, including the ectodomains of rBAT and 4F2hc. Here, we analyze available data on the ectodomains of rBAT and 4Fhc and their relationship with the α-amylase family. The physiological relevance of this relationship remains largely unknown.
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Affiliation(s)
- Joana Fort
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Adrià Nicolàs-Aragó
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
| | - Manuel Palacín
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
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7
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Ellingsen S, Narawane S, Fjose A, Verri T, Rønnestad I. The zebrafish cationic amino acid transporter/glycoprotein-associated family: sequence and spatiotemporal distribution during development of the transport system b 0,+ (slc3a1/slc7a9). FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1507-1525. [PMID: 34338990 PMCID: PMC8478756 DOI: 10.1007/s10695-021-00984-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/29/2021] [Indexed: 06/12/2023]
Abstract
System b0,+ absorbs lysine, arginine, ornithine, and cystine, as well as some (large) neutral amino acids in the mammalian kidney and intestine. It is a heteromeric amino acid transporter made of the heavy subunit SLC3A1/rBAT and the light subunit SLC7A9/b0,+AT. Mutations in these two genes can cause cystinuria in mammals. To extend information on this transport system to teleost fish, we focused on the slc3a1 and slc7a9 genes by performing comparative and phylogenetic sequence analysis, investigating gene conservation during evolution (synteny), and defining early expression patterns during zebrafish (Danio rerio) development. Notably, we found that slc3a1 and slc7a9 are non-duplicated in the zebrafish genome. Whole-mount in situ hybridization detected co-localized expression of slc3a1 and slc7a9 in pronephric ducts at 24 h post-fertilization and in the proximal convoluted tubule at 3 days post-fertilization (dpf). Notably, both the genes showed co-localized expression in epithelial cells in the gut primordium at 3 dpf and in the intestine at 5 dpf (onset of exogenous feeding). Taken together, these results highlight the value of slc3a1 and slc7a9 as markers of zebrafish kidney and intestine development and show promise for establishing new zebrafish tools that can aid in the rapid screening(s) of substrates. Importantly, such studies will help clarify the complex interplay between the absorption of dibasic amino acids, cystine, and (large) neutral amino acids and the effect(s) of such nutrients on organismal growth.
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Affiliation(s)
- Ståle Ellingsen
- Department of Molecular Biology, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Shailesh Narawane
- Department of Molecular Biology, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Anders Fjose
- Department of Molecular Biology, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Lecce-Monteroni, 73100, Lecce, Italy
| | - Ivar Rønnestad
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway.
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8
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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Structural basis for amino acid exchange by a human heteromeric amino acid transporter. Proc Natl Acad Sci U S A 2020; 117:21281-21287. [PMID: 32817565 DOI: 10.1073/pnas.2008111117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light chain subunit from an SLC7 family member and a heavy chain subunit from the SLC3 family. The light chain constitutes the transport subunit whereas the heavy chain mediates trafficking to the plasma membrane and maturation of the functional complex. Mutation, malfunction, and dysregulation of HATs are associated with a wide range of pathologies or represent the direct cause of inherited and acquired disorders. Here we report the cryogenic electron microscopy structure of the neutral and basic amino acid transport complex (b[0,+]AT1-rBAT) which reveals a heterotetrameric protein assembly composed of two heavy and light chain subunits, respectively. The previously uncharacterized interaction between two HAT units is mediated via dimerization of the heavy chain subunits and does not include participation of the light chain subunits. The b(0,+)AT1 transporter adopts a LeuT fold and is captured in an inward-facing conformation. We identify an amino-acid-binding pocket that is formed by transmembrane helices 1, 6, and 10 and conserved among SLC7 transporters.
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Pandey B, Aarthy M, Sharma M, Singh SK, Kumar V. Computational analysis identifies druggable mutations in human rBAT mediated Cystinuria. J Biomol Struct Dyn 2020; 39:5058-5067. [PMID: 32602810 DOI: 10.1080/07391102.2020.1784792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Culex quinquefasciatus Cqm1 protein acts as the receptor for Lysinibacillus sphaericus mosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary distance between Cqm1 and rBAT, and rBAT ectodomain lacks the sequence motif which serves as binding-site for the BinAB toxin. Thus, BinAB toxin can be expected to remain safe for humans. rBAT (heavy subunit; SLC3A1) and catalytic b0,+AT (light subunit; SLC7A9), linked by single disulfide bond, mediate renal reabsorption of cystine and dibasic amino acids in Na+ independent manner. Mutations in rBAT cause type I Cystinuria disease which shows global prevalence, and rBAT can be thought as an important pharmacological target. However, 3D structures of rBAT and b0,+AT, the two components of b0,+ heteromeric amino acid transporter systems, are not available. We constructed a reliable homology model of rBAT using Cqm1 coordinates and that of transmembrane b0,+AT subunit using LAT1 coordinates. Mapping of pathogenic mutations onto rBAT ectodomain revealed their scattered distribution throughout the rBAT protein. Further, our computational simulations-based scoring of several known deleterious mutations of rBAT revealed that mutations those do not compromise the protein fold and stability, are localized on the same face of the molecule. These residues are expected to interact with the b0,+AT transporter. The present study thus identifies druggable sites on rBAT that could be targeted for the treatment of type I Cystinuria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharati Pandey
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Murali Aarthy
- Computer-aided drug design Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Mahima Sharma
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sanjeev Kumar Singh
- Computer-aided drug design Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Vinay Kumar
- Homi Bhabha National Institute, Mumbai, India
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