1
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Luo JH, Wang FX, Zhao JW, Yang CL, Rong SJ, Lu WY, Chen QJ, Zhou Q, Xiao J, Wang YN, Luo X, Li Y, Song DN, Chen C, Zhang CL, Chen SH, Yang P, Xiong F, Yu QL, Zhang S, Liu SW, Sun F, Wang CY. PDIA3 defines a novel subset of adipose macrophages to exacerbate the development of obesity and metabolic disorders. Cell Metab 2024; 36:2262-2280.e5. [PMID: 39293433 DOI: 10.1016/j.cmet.2024.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 06/04/2024] [Accepted: 08/26/2024] [Indexed: 09/20/2024]
Abstract
Adipose tissue macrophages (ATMs) play important roles in maintaining adipose tissue homeostasis and orchestrating metabolic inflammation. Given the extensive functional heterogeneity and phenotypic plasticity of ATMs, identification of the authentically pathogenic ATM subpopulation under obese setting is thus necessitated. Herein, we performed single-nucleus RNA sequencing (snRNA-seq) and unraveled a unique maladaptive ATM subpopulation defined as ATF4hiPDIA3hiACSL4hiCCL2hi inflammatory and metabolically activated macrophages (iMAMs), in which PDIA3 is required for the maintenance of their migratory and pro-inflammatory properties. Mechanistically, ATF4 serves as a metabolic stress sensor to transcribe PDIA3, which then imposes a redox control on RhoA activity and strengthens the pro-inflammatory and migratory properties of iMAMs through RhoA-YAP signaling. Administration of Pdia3 small interfering RNA (siRNA)-loaded liposomes effectively repressed adipose inflammation and high-fat diet (HFD)-induced obesity. Together, our data support that strategies aimed at targeting iMAMs by suppressing PDIA3 expression or activity could be a viable approach against obesity and metabolic disorders in clinical settings.
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Affiliation(s)
- Jia-Hui Luo
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fa-Xi Wang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jia-Wei Zhao
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chun-Liang Yang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan-Jie Rong
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wan-Ying Lu
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi-Jie Chen
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Zhou
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Xiao
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Ya-Nan Wang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Xi Luo
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dan-Ni Song
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cai Chen
- Department of Endocrinology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng-Liang Zhang
- Department of Pharmacy, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Su-Hua Chen
- Department of Obstetrics and Gynecology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Yang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Xiong
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi-Lin Yu
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Zhang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shi-Wei Liu
- Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, The Key Laboratory of Endocrine and Metabolic Diseases of Shanxi Province, Taiyuan, China
| | - Fei Sun
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Cong-Yi Wang
- Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, The Key Laboratory of Endocrine and Metabolic Diseases of Shanxi Province, Taiyuan, China; The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Tongji Hospital Research Building, Wuhan, China.
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2
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van de Weijer ML, Samanta K, Sergejevs N, Jiang L, Dueñas ME, Heunis T, Huang TY, Kaufman RJ, Trost M, Sanyal S, Cowley SA, Carvalho P. Tapasin assembly surveillance by the RNF185/Membralin ubiquitin ligase complex regulates MHC-I surface expression. Nat Commun 2024; 15:8508. [PMID: 39353943 PMCID: PMC11445256 DOI: 10.1038/s41467-024-52772-x] [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: 02/21/2024] [Accepted: 09/19/2024] [Indexed: 10/03/2024] Open
Abstract
Immune surveillance by cytotoxic T cells eliminates tumor cells and cells infected by intracellular pathogens. This process relies on the presentation of antigenic peptides by Major Histocompatibility Complex class I (MHC-I) at the cell surface. The loading of these peptides onto MHC-I depends on the peptide loading complex (PLC) at the endoplasmic reticulum (ER). Here, we uncovered that MHC-I antigen presentation is regulated by ER-associated degradation (ERAD), a protein quality control process essential to clear misfolded and unassembled proteins. An unbiased proteomics screen identified the PLC component Tapasin, essential for peptide loading onto MHC-I, as a substrate of the RNF185/Membralin ERAD complex. Loss of RNF185/Membralin resulted in elevated Tapasin steady state levels and increased MHC-I at the surface of professional antigen presenting cells. We further show that RNF185/Membralin ERAD complex recognizes unassembled Tapasin and limits its incorporation into PLC. These findings establish a novel mechanism controlling antigen presentation and suggest RNF185/Membralin as a potential therapeutic target to modulate immune surveillance.
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Affiliation(s)
- Michael L van de Weijer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Krishna Samanta
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Nikita Sergejevs
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - LuLin Jiang
- Degenerative Diseases Program, Genetics, and Aging Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
- Altos Labs-Bay Institute of Science, Redwood City, CA, USA
| | - Maria Emilia Dueñas
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
- Telethon Kids Institute, Perth, Nedlands, WA, 6009, Australia
| | - Tiaan Heunis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Immunocore Ltd, 92 Park Drive, Abingdon, OX14 4RY, UK
| | - Timothy Y Huang
- Degenerative Diseases Program, Genetics, and Aging Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Randal J Kaufman
- Degenerative Diseases Program, Genetics, and Aging Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Matthias Trost
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sally A Cowley
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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3
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Sun Y, Pumroy RA, Mallik L, Chaudhuri A, Wang C, Hwang D, Danon JN, Goli KD, Moiseenkova-Bell V, Sgourakis NG. CryoEM structure of an MHC-I/TAPBPR peptide bound intermediate reveals the mechanism of antigen proofreading. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606663. [PMID: 39211162 PMCID: PMC11361172 DOI: 10.1101/2024.08.05.606663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Class I major histocompatibility complex (MHC-I) proteins play a pivotal role in adaptive immunity by displaying epitopic peptides to CD8+ T cells. The chaperones tapasin and TAPBPR promote the selection of immunogenic antigens from a large pool of intracellular peptides. Interactions of chaperoned MHC-I molecules with incoming peptides are transient in nature, and as a result, the precise antigen proofreading mechanism remains elusive. Here, we leverage a high-fidelity TAPBPR variant and conformationally stabilized MHC-I, to determine the solution structure of the human antigen editing complex bound to a peptide decoy by cryogenic electron microscopy (cryo-EM) at an average resolution of 3.0 Å. Antigen proofreading is mediated by transient interactions formed between the nascent peptide binding groove with the P2/P3 peptide anchors, where conserved MHC-I residues stabilize incoming peptides through backbone-focused contacts. Finally, using our high-fidelity chaperone, we demonstrate robust peptide exchange on the cell surface across multiple clinically relevant human MHC-I allomorphs. Our work has important ramifications for understanding the selection of immunogenic epitopes for T cell screening and vaccine design applications.
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4
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Brunnberg J, Barends M, Frühschulz S, Winter C, Battin C, de Wet B, Cole DK, Steinberger P, Tampé R. Dual role of the peptide-loading complex as proofreader and limiter of MHC-I presentation. Proc Natl Acad Sci U S A 2024; 121:e2321600121. [PMID: 38771881 PMCID: PMC11145271 DOI: 10.1073/pnas.2321600121] [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: 12/08/2023] [Accepted: 04/17/2024] [Indexed: 05/23/2024] Open
Abstract
Antigen presentation via major histocompatibility complex class I (MHC-I) molecules is essential for surveillance by the adaptive immune system. Central to this process is the peptide-loading complex (PLC), which translocates peptides from the cytosol to the endoplasmic reticulum and catalyzes peptide loading and proofreading of peptide-MHC-I (pMHC-I) complexes. Despite its importance, the impact of individual PLC components on the presented pMHC-I complexes is still insufficiently understood. Here, we used stoichiometrically defined antibody-nanobody complexes and engineered soluble T cell receptors (sTCRs) to quantify different MHC-I allomorphs and defined pMHC-I complexes, respectively. Thereby, we uncovered distinct effects of individual PLC components on the pMHC-I surface pool. Knockouts of components of the PLC editing modules, namely tapasin, ERp57, or calreticulin, changed the MHC-I surface composition to a reduced proportion of HLA-A*02:01 presentation compensated by a higher ratio of HLA-B*40:01 molecules. Intriguingly, these knockouts not only increased the presentation of suboptimally loaded HLA-A*02:01 complexes but also elevated the presentation of high-affinity peptides overexpressed in the cytosol. Our findings suggest that the components of the PLC editing module serve a dual role, acting not only as peptide proofreaders but also as limiters for abundant peptides. This dual function ensures the presentation of a broad spectrum of antigenic peptides.
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Affiliation(s)
- Jamina Brunnberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Martina Barends
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Stefan Frühschulz
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Claire Battin
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Ben de Wet
- Immunocore Ltd., AbingdonOX14 4RY, United Kingdom
| | | | - Peter Steinberger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
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5
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Jiang J, Natarajan K, Margulies DH. Chaperone-mediated MHC-I peptide exchange in antigen presentation. IUCRJ 2024; 11:287-298. [PMID: 38656309 PMCID: PMC11067752 DOI: 10.1107/s2052252524002768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
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6
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McWilliam HEG, Villadangos JA. MR1 antigen presentation to MAIT cells and other MR1-restricted T cells. Nat Rev Immunol 2024; 24:178-192. [PMID: 37773272 PMCID: PMC11108705 DOI: 10.1038/s41577-023-00934-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2023] [Indexed: 10/01/2023]
Abstract
MHC antigen presentation plays a fundamental role in adaptive and semi-invariant T cell immunity. Distinct MHC molecules bind antigens that differ in chemical structure, origin and location and present them to specialized T cells. MHC class I-related protein 1 (MR1) presents a range of small molecule antigens to MR1-restricted T (MR1T) lymphocytes. The best studied MR1 ligands are derived from microbial metabolism and are recognized by a major class of MR1T cells known as mucosal-associated invariant T (MAIT) cells. Here, we describe the MR1 antigen presentation pathway: the known types of antigens presented by MR1, the location where MR1-antigen complexes form, the route followed by the complexes to the cell surface, the mechanisms involved in termination of MR1 antigen presentation and the accessory cellular proteins that comprise the MR1 antigen presentation machinery. The current road map of the MR1 antigen presentation pathway reveals potential strategies for therapeutic manipulation of MR1T cell function and provides a foundation for further studies that will lead to a deeper understanding of MR1-mediated immunity.
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Affiliation(s)
- Hamish E G McWilliam
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
| | - Jose A Villadangos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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7
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Yan T, Boatner LM, Cui L, Tontonoz PJ, Backus KM. Defining the Cell Surface Cysteinome Using Two-Step Enrichment Proteomics. JACS AU 2023; 3:3506-3523. [PMID: 38155636 PMCID: PMC10751780 DOI: 10.1021/jacsau.3c00707] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
The plasma membrane proteome is a rich resource of functionally important and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here, we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of low-density lipoprotein (LDL) particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Lisa M. Boatner
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Liujuan Cui
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Peter J. Tontonoz
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Keriann M. Backus
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- DOE
Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli
and Edythe
Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
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8
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Czaja AJ. Introducing Molecular Chaperones into the Causality and Prospective Management of Autoimmune Hepatitis. Dig Dis Sci 2023; 68:4098-4116. [PMID: 37755606 PMCID: PMC10570239 DOI: 10.1007/s10620-023-08118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
Molecular chaperones influence the immunogenicity of peptides and the activation of effector T cells, and their pathogenic roles in autoimmune hepatitis are unclear. Heat shock proteins are pivotal in the processing and presentation of peptides that activate CD8+ T cells. They can also induce regulatory B and T cells and promote immune tolerance. Tapasin and the transporter associated with antigen processing-binding protein influence the editing and loading of high-affinity peptides for presentation by class I molecules of the major histocompatibility complex. Their over-expression could enhance the autoimmune response, and their deficiency could weaken it. The lysosome-associated membrane protein-2a isoform in conjunction with heat shock cognate 70 supports the importation of cytosolic proteins into lysosomes. Chaperone-mediated autophagy can then process the peptides for activation of CD4+ T cells. Over-expression of autophagy in T cells may also eliminate negative regulators of their activity. The human leukocyte antigen B-associated transcript three facilitates the expression of class II peptide receptors, inhibits T cell apoptosis, prevents T cell exhaustion, and sustains the immune response. Immunization with heat shock proteins has induced immune tolerance in experimental models and humans with autoimmune disease by inducing regulatory T cells. Therapeutic manipulation of other molecular chaperones may promote T cell exhaustion and induce tolerogenic dendritic cells. In conclusion, molecular chaperones constitute an under-evaluated family of ancillary proteins that could affect the occurrence, severity, and outcome of autoimmune hepatitis. Clarification of their contributions to the immune mechanisms and clinical activity of autoimmune hepatitis could have therapeutic implications.
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Affiliation(s)
- Albert J Czaja
- Mayo Clinic College of Medicine and Science, 200 First Street S.W., Rochester, MN, 55905, USA.
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9
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Yan T, Boatner LM, Cui L, Tontonoz P, Backus KM. Defining the Cell Surface Cysteinome using Two-step Enrichment Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562832. [PMID: 37904933 PMCID: PMC10614875 DOI: 10.1101/2023.10.17.562832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
The plasma membrane proteome is a rich resource of functional and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of LDL particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Lisa M. Boatner
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Liujuan Cui
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Peter Tontonoz
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Keriann M. Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095 (USA)
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 (USA)
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095 (USA)
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10
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van Hateren A, Elliott T. Visualising tapasin- and TAPBPR-assisted editing of major histocompatibility complex class-I immunopeptidomes. Curr Opin Immunol 2023; 83:102340. [PMID: 37245412 DOI: 10.1016/j.coi.2023.102340] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/30/2023]
Abstract
Which peptides are selected for presentation by major histocompatibility complex class-I (MHC-I) molecules is a key determinant of successful immune responses. Peptide selection is co-ordinated by the tapasin and TAP Binding PRotein (TAPBPR) proteins, which ensure MHC-I molecules preferentially acquire high-affinity-binding peptides. New structural analyses have offered insight into how tapasin achieves this function within the peptide-loading complex (PLC) (comprising the Transporter associated with Antigen Presentation (TAP) peptide transporter, tapasin-ERp57, MHC-I and calreticulin), and how TAPBPR performs a peptide editing function independently of other molecules. The new structures reveal nuances in how tapasin and TAPBPR interact with MHC-I, and how calreticulin and ERp57 complement tapasin to exploit the plasticity of MHC-I molecules to achieve peptide editing.
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Affiliation(s)
- Andy van Hateren
- Institute for Life Sciences and Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Building 85, Southampton SO17 1BJ, UK
| | - Tim Elliott
- Centre for Immuno-oncology and CAMS-Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK.
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11
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Wong-Benito V, de Rijke J, Dixon B. Antigen presentation in vertebrates: Structural and functional aspects. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104702. [PMID: 37116963 DOI: 10.1016/j.dci.2023.104702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Antigen presentation is a key process of the immune system and is responsible for the activation of T cells. The main characters are the major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules, and accessory proteins that act as chaperones for these glycoproteins. Current knowledge of this process and also the elucidation of the structural features of these proteins, has been extensively reviewed in humans. Unfortunately, this is not the case for non-human species, wherein the function and structural characteristic of the antigen presentation proteins is far from being understood. The majority of previous studies in non-human species, especially in teleost fish and lower vertebrates, are limited to the transcriptomic level, which leads to gaps in the knowledge about the functional process of antigen presentation in these species. This review summarizes what is known so far about antigen presentation pathways in vertebrates from a structural and functional perspective. The focus is not only on the MHC receptors, but also, on the forgotten characters of these pathways such as the proteins of the peptide loading complex, and the MHC-II chaperone invariant chain.
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Affiliation(s)
| | - Jill de Rijke
- Department of Biology, University of Waterloo, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, Canada.
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12
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Margulies DH, Jiang J, Ahmad J, Boyd LF, Natarajan K. Chaperone function in antigen presentation by MHC class I molecules-tapasin in the PLC and TAPBPR beyond. Front Immunol 2023; 14:1179846. [PMID: 37398669 PMCID: PMC10308438 DOI: 10.3389/fimmu.2023.1179846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Peptide loading of MHC-I molecules plays a critical role in the T cell response to infections and tumors as well as to interactions with inhibitory receptors on natural killer (NK) cells. To facilitate and optimize peptide acquisition, vertebrates have evolved specialized chaperones to stabilize MHC-I molecules during their biosynthesis and to catalyze peptide exchange favoring high affinity or optimal peptides to permit transport to the cell surface where stable peptide/MHC-I (pMHC-I) complexes are displayed and are available for interaction with T cell receptors and any of a host of inhibitory and activating receptors. Although components of the endoplasmic reticulum (ER) resident peptide loading complex (PLC) were identified some 30 years ago, the detailed biophysical parameters that govern peptide selection, binding, and surface display have recently been understood better with advances in structural methods including X-ray crystallography, cryogenic electron microscopy (cryo-EM), and computational modeling. These approaches have provided refined mechanistic illustration of the molecular events involved in the folding of the MHC-I heavy chain, its coordinate glycosylation, assembly with its light chain, β2-microglobulin (β2m), its association with the PLC, and its binding of peptides. Our current view of this important cellular process as it relates to antigen presentation to CD8+ T cells is based on many different approaches: biochemical, genetic, structural, computational, cell biological, and immunological. In this review, taking advantage of recent X-ray and cryo-EM structural evidence and molecular dynamics simulations, examined in the context of past experiments, we attempt a dispassionate evaluation of the details of peptide loading in the MHC-I pathway. By critical evaluation of several decades of investigation, we outline aspects of the peptide loading process that are well-understood and indicate those that demand further detailed investigation. Further studies should contribute not only to basic understanding, but also to applications for immunization and therapy of tumors and infections.
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13
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Abstract
ABC transporters are essential for cellular physiology. Humans have 48 ABC genes organized into seven distinct families. Of these genes, 44 (in five distinct families) encode for membrane transporters, of which several are involved in drug resistance and disease pathways resulting from transporter dysfunction. Over the last decade, advances in structural biology have vastly expanded our mechanistic understanding of human ABC transporter function, revealing details of their molecular arrangement, regulation, and interactions, facilitated in large part by advances in cryo-EM that have rendered hitherto inaccessible targets amenable to high-resolution structural analysis. As a result, experimentally determined structures of multiple members of each of the five families of ABC transporters in humans are now available. Here we review this recent progress, highlighting the physiological relevance of human ABC transporters and mechanistic insights gleaned from their direct structure determination. We also discuss the impact and limitations of model systems and structure prediction methods in understanding human ABC transporters and discuss current challenges and future research directions.
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Affiliation(s)
- Amer Alam
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zurich, Switzerland;
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14
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Lan BH, Becker M, Freund C. The mode of action of tapasin on major histocompatibility class I (MHC-I) molecules. J Biol Chem 2023; 299:102987. [PMID: 36758805 PMCID: PMC10040737 DOI: 10.1016/j.jbc.2023.102987] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Tapasin (Tsn) plays a critical role in antigen processing and presentation by major histocompatibility complex class I (MHC-I) molecules. The mechanism of Tsn-mediated peptide loading and exchange hinges on the conformational dynamics governing the interaction of Tsn and MHC-I with recent structural and functional studies pinpointing the critical sites of direct or allosteric regulation. In this review, we highlight these recent findings and relate them to the extensive molecular and cellular data that are available for these evolutionary interdependent proteins. Furthermore, allotypic differences of MHC-I with regard to the editing and chaperoning function of Tsn are reviewed and related to the mechanistic observations. Finally, evolutionary aspects of the mode of action of Tsn will be discussed, a short comparison with the Tsn-related molecule TAPBPR (Tsn-related protein) will be given, and the impact of Tsn on noncanonical MHC-I molecules will be described.
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Affiliation(s)
- By Huan Lan
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Moritz Becker
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany.
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15
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Cassano T, Giamogante F, Calcagnini S, Romano A, Lavecchia AM, Inglese F, Paglia G, Bukke VN, Romano AD, Friuli M, Altieri F, Gaetani S. PDIA3 Expression Is Altered in the Limbic Brain Regions of Triple-Transgenic Mouse Model of Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24033005. [PMID: 36769334 PMCID: PMC9918299 DOI: 10.3390/ijms24033005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
In the present study, we used a mouse model of Alzheimer's disease (AD) (3×Tg-AD mice) to longitudinally analyse the expression level of PDIA3, a protein disulfide isomerase and endoplasmic reticulum (ER) chaperone, in selected brain limbic areas strongly affected by AD-pathology (amygdala, entorhinal cortex, dorsal and ventral hippocampus). Our results suggest that, while in Non-Tg mice PDIA3 levels gradually reduce with aging in all brain regions analyzed, 3×Tg-AD mice showed an age-dependent increase in PDIA3 levels in the amygdala, entorhinal cortex, and ventral hippocampus. A significant reduction of PDIA3 was observed in 3×Tg-AD mice already at 6 months of age, as compared to age-matched Non-Tg mice. A comparative immunohistochemistry analysis performed on 3×Tg-AD mice at 6 (mild AD-like pathology) and 18 (severe AD-like pathology) months of age showed a direct correlation between the cellular level of Aβ and PDIA3 proteins in all the brain regions analysed, even if with different magnitudes. Additionally, an immunohistochemistry analysis showed the presence of PDIA3 in all post-mitotic neurons and astrocytes. Overall, altered PDIA3 levels appear to be age- and/or pathology-dependent, corroborating the ER chaperone's involvement in AD pathology, and supporting the PDIA3 protein as a potential novel therapeutic target for the treatment of AD.
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Affiliation(s)
- Tommaso Cassano
- Department of Medical and Surgical Sciences, University of Foggia, Via L. Pinto 1, 71122 Foggia, Italy
| | - Flavia Giamogante
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Silvio Calcagnini
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Adele Romano
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Angelo Michele Lavecchia
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesca Inglese
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Giuliano Paglia
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Vidyasagar Naik Bukke
- Department of Medical and Surgical Sciences, University of Foggia, Via L. Pinto 1, 71122 Foggia, Italy
| | - Antonino Davide Romano
- Department of Medical and Surgical Sciences, University of Foggia, Via L. Pinto 1, 71122 Foggia, Italy
| | - Marzia Friuli
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Fabio Altieri
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
- Correspondence:
| | - Silvana Gaetani
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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16
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Okuda A, Shimizu M, Inoue R, Urade R, Sugiyama M. Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance. Angew Chem Int Ed Engl 2023; 62:e202214412. [PMID: 36347766 DOI: 10.1002/anie.202214412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 11/10/2022]
Abstract
Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.
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Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
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17
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Bilches Medinas D, Malik S, Yıldız‐Bölükbaşı E, Borgonovo J, Saaranen MJ, Urra H, Pulgar E, Afzal M, Contreras D, Wright MT, Bodaleo F, Quiroz G, Rozas P, Mumtaz S, Díaz R, Rozas C, Cabral‐Miranda F, Piña R, Valenzuela V, Uyan O, Reardon C, Woehlbier U, Brown RH, Sena‐Esteves M, Gonzalez‐Billault C, Morales B, Plate L, Ruddock LW, Concha ML, Hetz C, Tolun A. Mutation in protein disulfide isomerase A3 causes neurodevelopmental defects by disturbing endoplasmic reticulum proteostasis. EMBO J 2022; 41:e105531. [PMID: 34904718 PMCID: PMC8762563 DOI: 10.15252/embj.2020105531] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023] Open
Abstract
Recessive gene mutations underlie many developmental disorders and often lead to disabling neurological problems. Here, we report identification of a homozygous c.170G>A (p.Cys57Tyr or C57Y) mutation in the gene coding for protein disulfide isomerase A3 (PDIA3, also known as ERp57), an enzyme that catalyzes formation of disulfide bonds in the endoplasmic reticulum, to be associated with syndromic intellectual disability. Experiments in zebrafish embryos show that PDIA3C57Y expression is pathogenic and causes developmental defects such as axonal disorganization as well as skeletal abnormalities. Expression of PDIA3C57Y in the mouse hippocampus results in impaired synaptic plasticity and memory consolidation. Proteomic and functional analyses reveal that PDIA3C57Y expression leads to dysregulation of cell adhesion and actin cytoskeleton dynamics, associated with altered integrin biogenesis and reduced neuritogenesis. Biochemical studies show that PDIA3C57Y has decreased catalytic activity and forms disulfide-crosslinked aggregates that abnormally interact with chaperones in the endoplasmic reticulum. Thus, rare disease gene variant can provide insight into how perturbations of neuronal proteostasis can affect the function of the nervous system.
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18
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Crystal structure of the collagen prolyl 4-hydroxylase (C-P4H) catalytic domain complexed with PDI: Toward a model of the C-P4H α 2β 2 tetramer. J Biol Chem 2022; 298:102614. [PMID: 36265586 PMCID: PMC9676403 DOI: 10.1016/j.jbc.2022.102614] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Collagen prolyl 4-hydroxylases (C-P4H) are α2β2 tetramers, which catalyze the prolyl 4-hydroxylation of procollagen, allowing for the formation of the stable triple-helical collagen structure in the endoplasmic reticulum. The C-P4H α-subunit provides the N-terminal dimerization domain, the middle peptide-substrate-binding (PSB) domain, and the C-terminal catalytic (CAT) domain, whereas the β-subunit is identical to the enzyme protein disulfide isomerase (PDI). The structure of the N-terminal part of the α-subunit (N-terminal region and PSB domain) is known, but the structures of the PSB-CAT linker region and the CAT domain as well as its mode of assembly with the β/PDI subunit, are unknown. Here, we report the crystal structure of the CAT domain of human C-P4H-II complexed with the intact β/PDI subunit, at 3.8 Å resolution. The CAT domain interacts with the a, b', and a' domains of the β/PDI subunit, such that the CAT active site is facing bulk solvent. The structure also shows that the C-P4H-II CAT domain has a unique N-terminal extension, consisting of α-helices and a β-strand, which is the edge strand of its major antiparallel β-sheet. This extra region of the CAT domain interacts tightly with the β/PDI subunit, showing that the CAT-PDI interface includes an intersubunit disulfide bridge with the a' domain and tight hydrophobic interactions with the b' domain. Using this new information, the structure of the mature C-P4H-II α2β2 tetramer is predicted. The model suggests that the CAT active-site properties are modulated by α-helices of the N-terminal dimerization domains of both subunits of the α2-dimer.
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19
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Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation. Nat Commun 2022; 13:5470. [PMID: 36115831 PMCID: PMC9482634 DOI: 10.1038/s41467-022-33153-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractLoading of MHC-I molecules with peptide by the catalytic chaperone tapasin in the peptide loading complex plays a critical role in antigen presentation and immune recognition. Mechanistic insight has been hampered by the lack of detailed structural information concerning tapasin–MHC-I. We present here crystal structures of human tapasin complexed with the MHC-I molecule HLA-B*44:05, and with each of two anti-tapasin antibodies. The tapasin-stabilized peptide-receptive state of HLA-B*44:05 is characterized by distortion of the peptide binding groove and destabilization of the β2-microglobulin interaction, leading to release of peptide. Movements of the membrane proximal Ig-like domains of tapasin, HLA-B*44:05, and β2-microglobulin accompany the transition to a peptide-receptive state. Together this ensemble of crystal structures provides insights into a distinct mechanism of tapasin-mediated peptide exchange.
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20
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Müller IK, Winter C, Thomas C, Spaapen RM, Trowitzsch S, Tampé R. Structure of an MHC I–tapasin–ERp57 editing complex defines chaperone promiscuity. Nat Commun 2022; 13:5383. [PMID: 36104323 PMCID: PMC9474470 DOI: 10.1038/s41467-022-32841-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Adaptive immunity depends on cell surface presentation of antigenic peptides by major histocompatibility complex class I (MHC I) molecules and on stringent ER quality control in the secretory pathway. The chaperone tapasin in conjunction with the oxidoreductase ERp57 is crucial for MHC I assembly and for shaping the epitope repertoire for high immunogenicity. However, how the tapasin–ERp57 complex engages MHC I clients has not yet been determined at atomic detail. Here, we present the 2.7-Å crystal structure of a tapasin–ERp57 heterodimer in complex with peptide-receptive MHC I. Our study unveils molecular details of client recognition by the multichaperone complex and highlights elements indispensable for peptide proofreading. The structure of this transient ER quality control complex provides the mechanistic basis for the selector function of tapasin and showcases how the numerous MHC I allomorphs are chaperoned during peptide loading and editing. Adaptive immunity depends on cellular chaperone and quality control systems that are decisive for an effective presentation of foreign antigens via MHC I molecules. Here, the authors present the structure of a key chaperone-MHC I complex.
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21
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Di Risola D, Ricci D, Marrocco I, Giamogante F, Grieco M, Francioso A, Vasco‐Vidal A, Mancini P, Colotti G, Mosca L, Altieri F. ERp57 chaperon protein protects neuronal cells from Aβ-induced toxicity. J Neurochem 2022; 162:322-336. [PMID: 35699375 PMCID: PMC9543391 DOI: 10.1111/jnc.15655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/21/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder whose main pathological hallmark is the accumulation of Amyloid-β peptide (Aβ) in the form of senile plaques. Aβ can cause neurodegeneration and disrupt cognitive functions by several mechanisms, including oxidative stress. ERp57 is a protein disulfide isomerase involved in the cellular stress response and known to be present in the cerebrospinal fluid of normal individuals as a complex with Aβ peptides, suggesting that it may be a carrier protein which prevents aggregation of Aβ. Although several studies show ERp57 involvement in neurodegenerative diseases, no clear mechanism of action has been identified thus far. In this work, we gain insights into the interaction of Aβ with ERp57, with a special focus on the contribution of ERp57 to the defense system of the cell. Here, we show that recombinant ERp57 directly interacts with the Aβ25-35 fragment in vitro with high affinity via two in silico-predicted main sites of interaction. Furthermore, we used human neuroblastoma cells to show that short-term Aβ25-35 treatment induces ERp57 decrease in intracellular protein levels, different intracellular localization, and ERp57 secretion in the cultured medium. Finally, we demonstrate that recombinant ERp57 counteracts the toxic effects of Aβ25-35 and restores cellular viability, by preventing Aβ25-35 aggregation. Overall, the present study shows that extracellular ERp57 can exert a protective effect from Aβ toxicity and highlights it as a possible therapeutic tool in the treatment of AD.
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Affiliation(s)
- Daniel Di Risola
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
| | - Daniela Ricci
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
- Immunobiology of Infection Unit, Institut PasteurParisFrance
| | - Ilaria Marrocco
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Flavia Giamogante
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
- Institute of Oncology Research (IOR), BellinzonaSwitzerland
| | - Maddalena Grieco
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
| | - Antonio Francioso
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
| | | | - Patrizia Mancini
- Department of Experimental MedicineSapienza University of RomaRomeItaly
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology—Italian National Research CouncilRomeItaly
| | - Luciana Mosca
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
| | - Fabio Altieri
- Department of Biochemical SciencesSapienza University of RomaRomeItaly
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22
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Kundu S. TemporalGSSA: a numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets. J Bioinform Comput Biol 2022; 20:2250018. [DOI: 10.1142/s0219720022500184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Shimizu M, Okuda A, Morishima K, Inoue R, Sato N, Yunoki Y, Urade R, Sugiyama M. Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations. Sci Rep 2022; 12:9970. [PMID: 35705644 PMCID: PMC9200744 DOI: 10.1038/s41598-022-13982-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Solving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To examine its practicability, we applied our idea to a multi-domain protein ER-60 and successfully extracted time series longer than 1 micro second from trajectories of coarse-grained molecular dynamics simulations. In the extracted time series, the domain conformation was distributed continuously and smoothly in a conformational space. Preferred domain conformations were also observed. Diversity among scattering curves calculated from each ER-60 structure was interpreted to reflect an open-close motion of the protein. Although our approach did not provide a unique solution for the structural ensemble of the biomolecule, each extracted time series can be an element of the real behavior of ER-60. Considering its low computational cost, our approach will play a key role to identify biomolecular dynamics by integrating SAXS, simulations, and other experiments.
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Affiliation(s)
- Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yasuhiro Yunoki
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
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24
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Critical roles of protein disulfide isomerases in balancing proteostasis in the nervous system. J Biol Chem 2022; 298:102087. [PMID: 35654139 PMCID: PMC9253707 DOI: 10.1016/j.jbc.2022.102087] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 02/08/2023] Open
Abstract
Protein disulfide isomerases (PDIs) constitute a family of oxidoreductases promoting redox protein folding and quality control in the endoplasmic reticulum. PDIs catalyze disulfide bond formation, isomerization, and reduction, operating in concert with molecular chaperones to fold secretory cargoes in addition to directing misfolded proteins to be refolded or degraded. Importantly, PDIs are emerging as key components of the proteostasis network, integrating protein folding status with central surveillance mechanisms to balance proteome stability according to cellular needs. Recent advances in the field driven by the generation of new mouse models, human genetic studies, and omics methodologies, in addition to interventions using small molecules and gene therapy, have revealed the significance of PDIs to the physiology of the nervous system. PDIs are also implicated in diverse pathologies, ranging from neurodevelopmental conditions to neurodegenerative diseases and traumatic injuries. Here, we review the principles of redox protein folding in the ER with a focus on current evidence linking genetic mutations and biochemical alterations to PDIs in the etiology of neurological conditions.
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25
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Xu H, Song K, Da LT. Dynamics of peptide loading into major histocompatibility complex class I molecules chaperoned by TAPBPR. Phys Chem Chem Phys 2022; 24:12397-12409. [PMID: 35575131 DOI: 10.1039/d2cp00423b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Major histocompatibility complex class I (MHC-I) molecules display antigenic peptides on the cell surface for T cell receptor scanning, thereby activating the immune response. Peptide loading into MHC-I molecules is thus a critical step during the antigen presentation process. Chaperone TAP-binding protein related (TAPBPR) plays a critical role in promoting high-affinity peptide loading into MHC-I, by discriminating against the low-affinity ones. However, the complete peptide loading dynamics into TAPBPR-bound MHC-I is still elusive. Here, we constructed kinetic network models based on hundreds of short-time MD simulations with an aggregated simulation time of ∼21.7 μs, and revealed, at atomic level, four key intermediate states of one antigenic peptide derived from melanoma-associated MART-1/Melan-A protein during its loading process into TAPBPR-bound MHC-I. We find that the TAPBPR binding at the MHC-I pocket-F can substantially reshape the distant pocket-B via allosteric regulations, which in turn promotes the following peptide N-terminal loading. Intriguingly, the partially loaded peptide could profoundly weaken the TAPBPR-MHC stability, promoting the dissociation of the TAPBPR scoop-loop (SL) region from the pocket-F to a more solvent-exposed conformation. Structural inspections further indicate that the peptide loading could remotely affect the SL binding site through both allosteric perturbations and direct contacts. In addition, another structural motif of TAPBPR, the jack hairpin region, was also found to participate in mediating the peptide editing. Our study sheds light on the detailed molecular mechanisms underlying the peptide loading process into TAPBPR-bound MHC-I and pinpoints the key structural factors responsible for dictating the peptide-loading dynamics.
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Affiliation(s)
- Honglin Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Kaiyuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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Margulies DH, Taylor DK, Jiang J, Boyd LF, Ahmad J, Mage MG, Natarajan K. Chaperones and Catalysts: How Antigen Presentation Pathways Cope With Biological Necessity. Front Immunol 2022; 13:859782. [PMID: 35464465 PMCID: PMC9022212 DOI: 10.3389/fimmu.2022.859782] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Immune recognition by T lymphocytes and natural killer (NK) cells is in large part dependent on the identification of cell surface MHC molecules bearing peptides generated from either endogenous (MHC I) or exogenous (MHC II) dependent pathways. This review focuses on MHC I molecules that coordinately fold to bind self or foreign peptides for such surface display. Peptide loading occurs in an antigen presentation pathway that includes either the multimolecular peptide loading complex (PLC) or a single chain chaperone/catalyst, TAP binding protein, related, TAPBPR, that mimics a key component of the PLC, tapasin. Recent structural and dynamic studies of TAPBPR reveal details of its function and reflect on mechanisms common to tapasin. Regions of structural conservation among species suggest that TAPBPR and tapasin have evolved to satisfy functional complexities demanded by the enormous polymorphism of MHC I molecules. Recent studies suggest that these two chaperone/catalysts exploit structural flexibility and dynamics to stabilize MHC molecules and facilitate peptide loading.
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Affiliation(s)
- David H Margulies
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Daniel K Taylor
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Jiansheng Jiang
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Lisa F Boyd
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Javeed Ahmad
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Michael G Mage
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
| | - Kannan Natarajan
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Molecular Biology Section, National Institutes of Health, Bethesda, MD, United States
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27
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Characterization of the AGR2 interactome uncovers new players of Protein Disulfide Isomerase network in cancer cells. Mol Cell Proteomics 2021; 21:100188. [PMID: 34929376 PMCID: PMC8816719 DOI: 10.1016/j.mcpro.2021.100188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 12/03/2022] Open
Abstract
Anterior gradient 2 (AGR2) is an endoplasmic reticulum (ER)-resident protein disulfide isomerase (PDI) known to be overexpressed in many human epithelial cancers and is involved in cell migration, cellular transformation, angiogenesis, and metastasis. This protein inhibits the activity of the tumor suppressor p53, and its expression levels can be used to predict cancer patient outcome. However, the precise network of AGR2-interacting partners and clients remains to be fully characterized. Herein, we used label-free quantification and also stable isotope labeling with amino acids in cell culture–based LC–MS/MS analyses to identify proteins interacting with AGR2. Functional annotation confirmed that AGR2 and its interaction partners are associated with processes in the ER that maintain intracellular metabolic homeostasis and participate in the unfolded protein response, including those associated with changes in cellular metabolism, energy, and redox states in response to ER stress. As a proof of concept, the interaction between AGR2 and PDIA3, another ER-resident PDI, was studied in more detail. Pathway analysis revealed that AGR2 and PDIA3 play roles in protein folding in ER, including post-translational modification and in cellular response to stress. We confirmed the AGR2–PDIA3 complex formation in cancer cells, which was enhanced in response to ER stress. Accordingly, molecular docking characterized potential quaternary structure of this complex; however, it remains to be elucidated whether AGR2 rather contributes to PDIA3 maturation in ER, the complex directly acts in cellular signaling, or mediates AGR2 secretion. Our study provides a comprehensive insight into the protein–protein interaction network of AGR2 by identifying functionally relevant proteins and related cellular and biochemical pathways associated with the role of AGR2 in cancer cells. LC–MS/MS analysis of AGR2-interacting proteins in T47D and H1299 cells. About 15 overlapping AGR2 interactors, including PDIA3 and PDIA6, were identified in both cell lines. PDI family members represent the key part of the network. AGR2–PDIA3 interaction is even stronger under ER stress. AGR2–PDIA3 complex formation supports extracellular secretion of AGR2.
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28
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Frozen motion: how cryo-EM changes the way we look at ABC transporters. Trends Biochem Sci 2021; 47:136-148. [PMID: 34930672 DOI: 10.1016/j.tibs.2021.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
ATP-binding cassette (ABC) transporters are widely present molecular machines that transfer substrates across the cell membrane. ABC transporters are involved in numerous physiological processes and are often clinical targets. Structural biology is fundamental to obtain the molecular details underlying ABC transporter function and suggest approaches to modulate it. Until recently, X-ray crystallography has been the only method capable of providing high-resolution structures of ABC transporters. However, modern cryo-electron microscopy (cryo-EM) opens entirely new ways of studying these dynamic membrane proteins. Cryo-EM enables analyses of targets that resist X-ray crystallography, challenging multicomponent complexes, and the exploration of conformational dynamics. These unique capacities have turned cryo-EM into the dominant technique for structural studies of membrane proteins, including ABC transporters.
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29
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Vascular thiol isomerases: Structures, regulatory mechanisms, and inhibitor development. Drug Discov Today 2021; 27:626-635. [PMID: 34757205 DOI: 10.1016/j.drudis.2021.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/15/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Vascular thiol isomerases (VTIs), including PDI, ERp5, ERp57, ERp72, and thioredoxin-related transmembrane protein 1 (TMX1), have important roles in platelet aggregation and thrombosis. Research on VTIs, their substrates in thrombosis, their regulatory mechanisms, and inhibitor development is an emerging and rapidly evolving area in vascular biology. Here, we describe the structures and functions of VTIs, summarize the relationship between the vascular TIs and thrombosis, and focus on the development of VTI inhibitors for antithrombotic applications.
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30
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Paglia G, Antonini L, Cervoni L, Ragno R, Sabatino M, Minacori M, Rubini E, Altieri F. A Comparative Analysis of Punicalagin Interaction with PDIA1 and PDIA3 by Biochemical and Computational Approaches. Biomedicines 2021; 9:biomedicines9111533. [PMID: 34829762 PMCID: PMC8614999 DOI: 10.3390/biomedicines9111533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022] Open
Abstract
In a previous work, it was shown that punicalagin, an active ingredient of pomegranate, is able to bind to PDIA3 and inhibit its disulfide reductase activity. Here we provide evidence that punicalagin can also bind to PDIA1, the main expressed form of protein disulfide isomerase (PDI). In this comparative study, the affinity and the effect of punicalagin binding on each protein were evaluated, and a computational approach was used to identify putative binding sites. Punicalagin binds to either PDIA1 or PDIA3 with a similar affinity, but the inhibition efficacy on protein reductase activity is higher for PDIA3. Additionally, punicalagin differently affects the thermal denaturation profile of both proteins. Molecular docking and molecular dynamics simulations led to propose a punicalagin binding mode on PDIA1 and PDIA3, identifying the binding sites at the redox domains a’ in two different pockets, suggesting different effects of punicalagin on proteins’ structure. This study provides insights to develop punicalagin-based ligands, to set up a rational design for PDIA3 selective inhibitors, and to dissect the molecular determinant to modulate the protein activity.
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Affiliation(s)
- Giuliano Paglia
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (G.P.); (L.C.); (M.M.); (E.R.)
| | - Lorenzo Antonini
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (L.A.); (R.R.); (M.S.)
| | - Laura Cervoni
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (G.P.); (L.C.); (M.M.); (E.R.)
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (L.A.); (R.R.); (M.S.)
| | - Manuela Sabatino
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (L.A.); (R.R.); (M.S.)
| | - Marco Minacori
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (G.P.); (L.C.); (M.M.); (E.R.)
| | - Elisabetta Rubini
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (G.P.); (L.C.); (M.M.); (E.R.)
- Enrico ed Enrica Sovena Foundation, 00199 Rome, Italy
| | - Fabio Altieri
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (G.P.); (L.C.); (M.M.); (E.R.)
- Correspondence:
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31
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Weiß RG, Losfeld ME, Aebi M, Riniker S. N-Glycosylation Enhances Conformational Flexibility of Protein Disulfide Isomerase Revealed by Microsecond Molecular Dynamics and Markov State Modeling. J Phys Chem B 2021; 125:9467-9479. [PMID: 34379416 DOI: 10.1021/acs.jpcb.1c04279] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Secreted proteins of eukaryotes are decorated with branched carbohydrate oligomers called glycans. This fact is only starting to be considered for in silico investigations of protein dynamics. Using all-atom molecular dynamics (MD) simulations and Markov state modeling (MSM), we unveil the influence of glycans on the conformational flexibility of the multidomain protein disulfide isomerase (PDI), which is a ubiquitous chaperone in the endoplasmic reticulum (ER). Yeast PDI (yPDI) from Saccharomyces cerevisiae is glycosylated at asparagine side chains and the knowledge of its five modified sites enables a realistic computational modeling. We compare simulations of glycosylated and unglycosylated yPDI and find that the presence of glycan-glycan and glycan-protein interactions influences the flexibility of PDI in different ways. For example, glycosylation reduces interdomain interactions, shifting the conformational ensemble toward more open, extended structures. In addition, we compare our results on yPDI with structural information of homologous proteins such as human PDI (hPDI), which is natively unglycosylated. Interestingly, hPDI lacks a surface recess that is present in yPDI. We find that glycosylation of yPDI facilitates its catalytic site to reach close to this surface recess. Hence, this might point to a possible functional relevance of glycosylation in yeast to act on substrates, while glycosylation seems redundant for the human homologous protein. We conclude that glycosylation is fundamental for protein dynamics, making it a necessity for a truthful representation of the flexibility and function in in silico studies of glycoproteins.
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Affiliation(s)
- R Gregor Weiß
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Marie-Estelle Losfeld
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, 8093 Zürich, Switzerland
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32
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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33
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Lan H, Abualrous ET, Sticht J, Fernandez LMA, Werk T, Weise C, Ballaschk M, Schmieder P, Loll B, Freund C. Exchange catalysis by tapasin exploits conserved and allele-specific features of MHC-I molecules. Nat Commun 2021; 12:4236. [PMID: 34244493 PMCID: PMC8271027 DOI: 10.1038/s41467-021-24401-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
The repertoire of peptides presented by major histocompatibility complex class I (MHC-I) molecules on the cell surface is tailored by the ER-resident peptide loading complex (PLC), which contains the exchange catalyst tapasin. Tapasin stabilizes MHC-I molecules and promotes the formation of stable peptide-MHC-I (pMHC-I) complexes that serve as T cell antigens. Exchange of suboptimal by high-affinity ligands is catalyzed by tapasin, but the underlying mechanism is still elusive. Here we analyze the tapasin-induced changes in MHC-I dynamics, and find the catalyst to exploit two essential features of MHC-I. First, tapasin recognizes a conserved allosteric site underneath the α2-1-helix of MHC-I, ‘loosening’ the MHC-I F-pocket region that accomodates the C-terminus of the peptide. Second, the scoop loop11–20 of tapasin relies on residue L18 to target the MHC-I F-pocket, enabling peptide exchange. Meanwhile, tapasin residue K16 plays an accessory role in catalysis of MHC-I allotypes bearing an acidic F-pocket. Thus, our results provide an explanation for the observed allele-specificity of catalyzed peptide exchange. Tapasin is part of the peptide loading complex necessary for presenting antigenic peptides on MHC-I for the induction of adaptive immunity. Here the authors show that tapasin interacts with MHC-I in both conserved and allele-specific regions to promote antigen presentation, with tapasin L18 and K16 residues both implicated in this molecular interaction.
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Affiliation(s)
- Huan Lan
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Esam T Abualrous
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Artificial Intelligence for the Sciences, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Core Facility BioSupraMol, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Laura Maria Arroyo Fernandez
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tamina Werk
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Core Facility BioSupraMol, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martin Ballaschk
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Bernhard Loll
- Laboratory of Structural Biology, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.
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Mathematical modeling and stochastic simulations suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into "early"- and "late"-phases. Heliyon 2021; 7:e07466. [PMID: 34286133 PMCID: PMC8278427 DOI: 10.1016/j.heliyon.2021.e07466] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/23/2021] [Accepted: 06/29/2021] [Indexed: 02/01/2023] Open
Abstract
The peptide loading complex (PLC) is a multi-protein complex of the endoplasmic reticulum (ER) which optimizes major histocompatibility I (MHC1)-mediated export of intracellular high-affinity peptides. Whilst, the molecular biology of MHC1-mediated export is well supported by empirical data, the stoichiometry, kinetics and spatio-temporal profile of the participating molecular entities are a matter of considerable debate. Here, a low-affinity peptide-driven (LAPD)-model of MHC1-mediated high-affinity peptide export is formulated, implemented, analyzed and simulated. The model is parameterized in terms of the contribution of the shunt reaction to the concentration of exportable MHC1. Theoretical analyses and simulation studies of the model suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into time-dependent distinct “early”- and “late”-phases. The net exportable MHC1 (eM1β(t)) is a function of the retrograde (rM1β(t))- and anterograde (aM1β(t))-derived fractions. The “early”-phase is dominated by the contribution of the retrograde/recyclable (rM1β≈61%,aM1β≈39%) pathway to exportable MHC1, is characterized by Tapasin-mediated peptide-editing and is ATP-independent. The “late”-phase on the other hand, is characterized by de novo PLC-assembly, rapid disassembly and a significant contribution of the anterograde pathway to exportable MHC1 (rM1β≈21%,aM1β≈79%). The shunt reaction is rate limiting and may integrate peptide translocation with PLC-assembly/disassembly thereby, regulating peptide export under physiological and pathological (viral infections, dysplastic alterations) conditions.
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35
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Truong HV, Sgourakis NG. Dynamics of MHC-I molecules in the antigen processing and presentation pathway. Curr Opin Immunol 2021; 70:122-128. [PMID: 34153556 PMCID: PMC8622473 DOI: 10.1016/j.coi.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 01/07/2023]
Abstract
The endogenous antigen processing and presentation (APP) is a fundamental pathway found in jawed vertebrates, which allows for a set of epitope peptides sampled from the intracellular proteome to be assembled and displayed on class I proteins of the major histocompatibility complex (MHC-I). Peptide/MHC-I antigens enable different aspects of adaptive immunity to emerge, by providing a basis for recognition of self vs. non-self by T cells and Natural Killer (NK) cells. Pioneering studies of pMHC-I molecules and their higher-order protein complexes with molecular chaperones and membrane receptors have gleaned important insights into the peptide loading and antigen recognition mechanisms. While X-ray and cryoEM structures have provided us with static snapshots of different MHC-I assembly stages, complementary biophysical techniques have revealed that MHC-I molecules are highly mobile on a range of biologically relevant timescales, which bears importance for their assembly, peptide repertoire selection, membrane display and turnover. This review summarizes insights gained from experimental and simulation studies aimed at investigating MHC-I dynamics, and their functional implications.
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Affiliation(s)
- Hau V Truong
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA.
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36
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Hafstrand I, Aflalo A, Boyle LH. Why TAPBPR? Implications of an additional player in MHC class I peptide presentation. Curr Opin Immunol 2021; 70:90-94. [PMID: 34052734 DOI: 10.1016/j.coi.2021.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The peptide editor TAPBPR is the newest member of the major histocompatibility complex class I (MHC-I) antigen processing and presentation pathway. Since 2013, studies have explored the functions and mechanisms of action of this tapasin homolog. Here, we review the key insights gained from structural studies of the TAPBPR:MHC-I complex and the involvement of the TAPBPR loop in peptide exchange. However, despite recent advances, the question still remains: why do we need TAPBPR? The recent appreciation that different MHC-I allotypes vary in their ability to interact with TAPBPR, together with a role for TAPBPR in alternative presentation pathways highlights that much remains unknown concerning the biological need for TAPBPR.
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Affiliation(s)
- Ida Hafstrand
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Aure Aflalo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom.
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Shi W, Han H, Zou J, Zhang Y, Li H, Zhou H, Cui G. Identification of dihydrotanshinone I as an ERp57 inhibitor with anti-breast cancer properties via the UPR pathway. Biochem Pharmacol 2021; 190:114637. [PMID: 34062127 DOI: 10.1016/j.bcp.2021.114637] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Salvia miltiorrhiza (Danshen) is a well-known traditional Chinese medicine for treating various diseases, such as breast cancer. However, knowledge regarding its mechanisms is scant. Herein, the active ingredient dihydrotanshinone I (DHT) in Salvia miltiorrhiza extract (SME), which binds ERp57 was identified and verified by an enzymatic solid-phase method combined with LC-MS/MS. DHT potentially inhibited ERp57 activity and suppressed ERp57 expression at both the RNA and protein levels. Molecular docking simulation indicated that DHT could form a hydrogen bond with catalytic site of ERp57. Moreover, ERp57 overexpression decreased DHT-induced cytotoxicity in MDA-MB-231 cells. Thereafter, the signaling pathway downstream of ERp57 was investigated by Western blot analysis. The mechanistic study revealed that DHT treatment resulted in activation of endoplasmic reticulum (ER) stress, the unfolded protein response (UPR), and cellular apoptosis. In conclusion, our data implied that DHT targeted ERp57 for inhibition and induced ER stress and UPR activation, which in turn triggered breast cancer cell apoptosis.
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Affiliation(s)
- Wei Shi
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Han Han
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Jia Zou
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Ying Zhang
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Haitao Li
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Hefeng Zhou
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Guozhen Cui
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China.
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Jantz-Naeem N, Springer S. Venus flytrap or pas de trois? The dynamics of MHC class I molecules. Curr Opin Immunol 2021; 70:82-89. [PMID: 33993034 DOI: 10.1016/j.coi.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
The peptide binding site of major histocompatibility complex (MHC) class I molecules is natively unfolded when devoid of peptides. Peptide binding stabilizes the structure and slows the dynamics, but peptide-specific and subtype-specific motions influence, and are influenced by, interaction with assembly chaperones, the T cell receptor, and other class I-binding proteins. The molecular mechanisms of cooperation between peptide, class I heavy chain, and beta-2 microglobulin are insufficiently known but are being elucidated by nuclear magnetic resonance and other modern methods. It appears that micropolymorphic clusters of charged amino acids, often hidden in the molecule interior, determine the dynamics and thus chaperone dependence, cellular fate, and disease association of class I.
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Affiliation(s)
- Nouria Jantz-Naeem
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany.
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Tanikawa Y, Kanemura S, Ito D, Lin Y, Matsusaki M, Kuroki K, Yamaguchi H, Maenaka K, Lee YH, Inaba K, Okumura M. Ca 2+ Regulates ERp57-Calnexin Complex Formation. Molecules 2021; 26:molecules26102853. [PMID: 34064874 PMCID: PMC8151781 DOI: 10.3390/molecules26102853] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/01/2021] [Accepted: 05/09/2021] [Indexed: 11/20/2022] Open
Abstract
ERp57, a member of the protein disulfide isomerase family, is a ubiquitous disulfide catalyst that functions in the oxidative folding of various clients in the mammalian endoplasmic reticulum (ER). In concert with ER lectin-like chaperones calnexin and calreticulin (CNX/CRT), ERp57 functions in virtually all folding stages from co-translation to post-translation, and thus plays a critical role in maintaining protein homeostasis, with direct implication for pathology. Here, we present mechanisms by which Ca2+ regulates the formation of the ERp57-calnexin complex. Biochemical and isothermal titration calorimetry analyses revealed that ERp57 strongly interacts with CNX via a non-covalent bond in the absence of Ca2+. The ERp57-CNX complex not only promoted the oxidative folding of human leukocyte antigen heavy chains, but also inhibited client aggregation. These results suggest that this complex performs both enzymatic and chaperoning functions under abnormal physiological conditions, such as Ca2+ depletion, to effectively guide proper oxidative protein folding. The findings shed light on the molecular mechanisms underpinning crosstalk between the chaperone network and Ca2+.
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Affiliation(s)
- Yuya Tanikawa
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan; (Y.T.); (S.K.); (H.Y.)
| | - Shingo Kanemura
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan; (Y.T.); (S.K.); (H.Y.)
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan;
| | - Dai Ito
- Department of Brain and Cognitive Science, Daegu Gyeongbuk Institute of Science and Technology, 333 Techno Jungang Daero, Daegu 42988, Korea;
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang, Cheongju 28119, Korea; (Y.L.); (Y.-H.L.)
| | - Motonori Matsusaki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan;
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Kimiko Kuroki
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Nishi 6, Kita 12, Kita-ku, Sapporo 060-0812, Japan; (K.K.); (K.M.)
| | - Hiroshi Yamaguchi
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan; (Y.T.); (S.K.); (H.Y.)
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Nishi 6, Kita 12, Kita-ku, Sapporo 060-0812, Japan; (K.K.); (K.M.)
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences and Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Nishi 6, Kita 12, Kita-ku, Sapporo 060-0812, Japan
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang, Cheongju 28119, Korea; (Y.L.); (Y.-H.L.)
- Research Headquarters, Korea Brain Research Institute, 61 Cheomdan-ro, Dong-gu, Daegu 41068, Korea
- Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan;
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan;
- Fusion Oriented Research for Disruptive Science and Technology, Japan Science Technology Agency, Chiyoda-ku, Tokyo 102-0075, Japan
- Correspondence: ; Tel.: +81-22-795-5764
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40
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Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation. Sci Rep 2021; 11:5655. [PMID: 33707747 PMCID: PMC7952739 DOI: 10.1038/s41598-021-85219-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/25/2021] [Indexed: 11/08/2022] Open
Abstract
Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other.
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Thomas C, Tampé R. MHC I assembly and peptide editing - chaperones, clients, and molecular plasticity in immunity. Curr Opin Immunol 2021; 70:48-56. [PMID: 33689959 DOI: 10.1016/j.coi.2021.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/07/2021] [Indexed: 11/24/2022]
Abstract
Peptides presented on MHC I molecules allow the immune system to detect diseased cells. The displayed peptides typically stem from proteasomal degradation of cytoplasmic proteins and are translocated into the ER lumen where they are trimmed and loaded onto MHC I. Peptide translocation is carried out by the transporter associated with antigen processing, which forms the central building block of a dynamic assembly called the peptide-loading complex (PLC). By coordinating peptide transfer with MHC I loading and peptide optimization, the PLC is a linchpin in the adaptive immune system. Peptide loading and optimization is catalyzed by the PLC component tapasin and the PLC-independent TAPBPR, two MHC I-dedicated enzymes chaperoning empty or suboptimally loaded MHC I and selecting stable peptide-MHC I complexes in a process called peptide editing or proofreading. Recent structural and functional studies of peptide editing have dramatically improved our understanding of this pivotal event in antigen processing/presentation. This review is dedicated to Vincenzo Cerundolo (1959-2020) for his pioneering work in the field of antigen processing/presentation.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
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42
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Alam MN, Yu JQ, Beale P, Huq F. Dose and Sequence Dependent Synergism from the Combination of Oxaliplatin with Emetine and Patulin Against Colorectal Cancer. Anticancer Agents Med Chem 2021; 20:264-273. [PMID: 31736447 DOI: 10.2174/1871520619666191021112042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/29/2019] [Accepted: 10/01/2019] [Indexed: 01/18/2023]
Abstract
BACKGROUND Colorectal cancer is the third most commonly diagnosed cancer in the world, causing many deaths every year. Combined chemotherapy has opened a new horizon in treating colorectal cancer. The objective of the present study is to investigate the activity of oxaliplatin in combination with emetine and patulin against colorectal cancer models. METHODS IC50 values of oxaliplatin, emetine and patulin were determined against human colorectal cancer cell lines (HT-29 and Caco-2) using MTT reduction assay. Synergistic, antagonistic and additive effects from the selected binary combinations were determined as a factor of sequence of administration and added concentrations. Proteomics was carried out to identify the proteins which were accountable for combined drug action applying to the selected drug combination. RESULTS Oxaliplatin in combination with patulin produced synergism against human colorectal cancer models depending on dose and sequence of drug administration. Bolus administration of oxaliplatin with patulin proved to be the best in terms of synergistic outcome. Altered expressions of nine proteins (ACTG, PROF1, PPIA, PDIA3, COF1, GSTP1, ALDOA, TBA1C and TBB5) were considered for combined drug actions of oxaliplatin with patulin. CONCLUSION Bolus administration of oxaliplatin with patulin has the potential to be used in the treatment of colorectal cancer, and would warrant further evaluation using suitable animal model.
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Affiliation(s)
- Md Nur Alam
- Discipline of Pathology, Sydney Medical School, A26-RC Mills Room 105, University of Sydney, Sydney, NSW, Australia
| | - Jun Q Yu
- Discipline of Pathology, Sydney Medical School, A26-RC Mills Room 105, University of Sydney, Sydney, NSW, Australia
| | - Philip Beale
- Sydney Cancer Centre, Concord Hospital, Sydney, NSW 2139, Australia
| | - Fazlul Huq
- Discipline of Pathology, Sydney Medical School, A26-RC Mills Room 105, University of Sydney, Sydney, NSW, Australia
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Roles of Calreticulin in Protein Folding, Immunity, Calcium Signaling and Cell Transformation. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 59:145-162. [PMID: 34050865 DOI: 10.1007/978-3-030-67696-4_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The endoplasmic reticulum (ER) is an organelle that mediates the proper folding and assembly of proteins destined for the cell surface, the extracellular space and subcellular compartments such as the lysosomes. The ER contains a wide range of molecular chaperones to handle the folding requirements of a diverse set of proteins that traffic through this compartment. The lectin-like chaperones calreticulin and calnexin are an important class of structurally-related chaperones relevant for the folding and assembly of many N-linked glycoproteins. Despite the conserved mechanism of action of these two chaperones in nascent protein recognition and folding, calreticulin has unique functions in cellular calcium signaling and in the immune response. The ER-related functions of calreticulin in the assembly of major histocompatibility complex (MHC) class I molecules are well-studied and provide many insights into the modes of substrate and co-chaperone recognition by calreticulin. Calreticulin is also detectable on the cell surface under some conditions, where it induces the phagocytosis of apoptotic cells. Furthermore, mutations of calreticulin induce cell transformation in myeloproliferative neoplasms (MPN). Studies of the functions of the mutant calreticulin in cell transformation and immunity have provided many insights into the normal biology of calreticulin, which are discussed.
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Kanemura S, Matsusaki M, Inaba K, Okumura M. PDI Family Members as Guides for Client Folding and Assembly. Int J Mol Sci 2020; 21:ijms21249351. [PMID: 33302492 PMCID: PMC7763558 DOI: 10.3390/ijms21249351] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/06/2020] [Accepted: 12/06/2020] [Indexed: 12/27/2022] Open
Abstract
Complicated and sophisticated protein homeostasis (proteostasis) networks in the endoplasmic reticulum (ER), comprising disulfide catalysts, molecular chaperones, and their regulators, help to maintain cell viability. Newly synthesized proteins inserted into the ER need to fold and assemble into unique native structures to fulfill their physiological functions, and this is assisted by protein disulfide isomerase (PDI) family. Herein, we focus on recent advances in understanding the detailed mechanisms of PDI family members as guides for client folding and assembly to ensure the efficient production of secretory proteins.
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Affiliation(s)
- Shingo Kanemura
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan;
| | - Motonori Matsusaki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; (M.M.); (K.I.)
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; (M.M.); (K.I.)
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
- Correspondence: ; Tel.: +81-22-217-5628
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45
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Victor P, Sarada D, Ramkumar KM. Crosstalk between endoplasmic reticulum stress and oxidative stress: Focus on protein disulfide isomerase and endoplasmic reticulum oxidase 1. Eur J Pharmacol 2020; 892:173749. [PMID: 33245896 DOI: 10.1016/j.ejphar.2020.173749] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022]
Abstract
Cellular stress and inflammation, establishing as disease pathology, have reached great heights in the last few decades. Stress conditions such as hyperglycemia, hyperlipidemia and lipoproteins are known to disturb proteostasis resulting in the accumulation of unfolded or misfolded proteins, alteration in calcium homeostasis culminating in unfolded protein response. Protein disulfide isomerase and endoplasmic reticulum oxidase-1 are the key players in protein folding. The protein folding process assisted by endoplasmic reticulum oxidase-1 results in the production of reactive oxygen species in the lumen of the endoplasmic reticulum. Production of reactive oxygen species beyond the quenching capacity of the antioxidant systems perturbs ER homeostasis. Endoplasmic reticulum stress also induces the production of cytokines leading to inflammatory responses. This has been proven to be the major causative factor for various pathophysiological states compared to other cellular triggers in diseases, which further manifests to increased oxidative stress, mitochondrial dysfunction, and altered inflammatory responses, deleterious to cellular physiology and homeostasis. Numerous studies have drawn correlations between the progression of several diseases in association with endoplasmic reticulum stress, redox protein folding, oxidative stress and inflammatory responses. This review aims to provide an insight into the role of protein disulfide isomerase and endoplasmic reticulum oxidase-1 in endoplasmic reticulum stress, unfolded protein response, mitochondrial dysfunction, and inflammatory responses, which exacerbate the progression of various diseases.
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Affiliation(s)
- Paul Victor
- Department of Biotechnology, School of Bio-engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, Tamil Nadu, India
| | - Dronamraju Sarada
- Department of Biotechnology, School of Bio-engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, Tamil Nadu, India
| | - Kunka Mohanram Ramkumar
- Department of Biotechnology, School of Bio-engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, Tamil Nadu, India; Life Science Division, SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, Tamil Nadu, India.
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46
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An Ixodes scapularis Protein Disulfide Isomerase Contributes to Borrelia burgdorferi Colonization of the Vector. Infect Immun 2020; 88:IAI.00426-20. [PMID: 32928964 PMCID: PMC7671890 DOI: 10.1128/iai.00426-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/31/2020] [Indexed: 01/06/2023] Open
Abstract
Borrelia burgdorferi causes Lyme disease, the most common tick-transmitted illness in North America. When Ixodes scapularis feed on an infected vertebrate host, spirochetes enter the tick gut along with the bloodmeal and colonize the vector. Here, we show that a secreted tick protein, I. scapularis protein disulfide isomerase A3 (IsPDIA3), enhances B. burgdorferi colonization of the tick gut. I. scapularis ticks in which ispdiA3 has been knocked down using RNA interference have decreased spirochete colonization of the tick gut after engorging on B. burgdorferi-infected mice. Moreover, administration of IsPDIA3 antiserum to B. burgdorferi-infected mice reduced the ability of spirochetes to colonize the tick when feeding on these animals. We show that IsPDIA3 modulates inflammatory responses at the tick bite site, potentially facilitating spirochete survival at the vector-host interface as it exits the vertebrate host to enter the tick gut. These data provide functional insights into the complex interactions between B. burgdorferi and its arthropod vector and suggest additional targets to interfere with the spirochete life cycle.
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47
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Bashirova AA, Viard M, Naranbhai V, Grifoni A, Garcia-Beltran W, Akdag M, Yuki Y, Gao X, O'hUigin C, Raghavan M, Wolinsky S, Bream JH, Duggal P, Martinson J, Michael NL, Kirk GD, Buchbinder SP, Haas D, Goedert JJ, Deeks SG, Fellay J, Walker B, Goulder P, Cresswell P, Elliott T, Sette A, Carlson J, Carrington M. HLA tapasin independence: broader peptide repertoire and HIV control. Proc Natl Acad Sci U S A 2020; 117:28232-28238. [PMID: 33097667 PMCID: PMC7668082 DOI: 10.1073/pnas.2013554117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human leukocyte antigen (HLA) class I allotypes vary in their ability to present peptides in the absence of tapasin, an essential component of the peptide loading complex. We quantified tapasin dependence of all allotypes that are common in European and African Americans (n = 97), which revealed a broad continuum of values. Ex vivo examination of cytotoxic T cell responses to the entire HIV-1 proteome from infected subjects indicates that tapasin-dependent allotypes present a more limited set of distinct peptides than do tapasin-independent allotypes, data supported by computational predictions. This suggests that variation in tapasin dependence may impact the strength of the immune responses by altering peptide repertoire size. In support of this model, we observed that individuals carrying HLA class I genotypes characterized by greater tapasin independence progress more slowly to AIDS and maintain lower viral loads, presumably due to increased breadth of peptide presentation. Thus, tapasin dependence level, like HLA zygosity, may serve as a means to restrict or expand breadth of the HLA-I peptide repertoire across humans, ultimately influencing immune responses to pathogens and vaccines.
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Affiliation(s)
- Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Wilfredo Garcia-Beltran
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Marjan Akdag
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Xiaojiang Gao
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Jay H Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Susan P Buchbinder
- HIV Research Section, San Francisco Department of Public Health, San Francisco, CA 94102
| | - David Haas
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37204
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA 94110
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, OX1 4AJ, United Kingdom
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
- Centre for Cancer Immunology, University of Southampton, Southampton SO16 6YD, United Kingdom
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702;
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
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48
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Li N, Luo X, Yu Q, Yang P, Chen Z, Wang X, Jiang J, Xu J, Gong Q, Eizirik DL, Zhou Z, Zhao J, Xiong F, Zhang S, Wang CY. SUMOylation of Pdia3 exacerbates proinsulin misfolding and ER stress in pancreatic beta cells. J Mol Med (Berl) 2020; 98:1795-1807. [PMID: 33159537 DOI: 10.1007/s00109-020-02006-6] [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] [Received: 07/12/2020] [Revised: 10/16/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
SUMOylation has long been recognized to regulate multiple biological processes in pancreatic beta cells, but its impact on proinsulin disulfide maturation and endoplasmic reticulum (ER) stress remains elusive. Herein, we conducted comparative proteomic analyses of SUMOylated proteins in primary mouse/human islets following proinflammatory cytokine stimulation. Cytokine challenge rendered beta cells to undergo a SUMOylation turnover manifested by the changes of SUMOylation substrates and SUMOylation levels for multiple substrates. Our data support that SUMOylation may play a crucial role to regulate proinsulin misfolding and ER stress at least by targeting Protein Disulfide Isomerase a3 (Pdia3). SUMOylation regulates Pdia3 enzymatic activity, subcellular localization, and protein binding ability. Furthermore, SUMOylation of Pdia3 exacerbated proinsulin misfolding and ER stress, and repressed Stat3 activation. In contrast, disruption of Pdia3 SUMOylation markedly rescued the outcomes. Collectively, our study expands the understanding how SUMOylation regulates ER stress in beta cells, which shed light on developing potential strategies against beta cell dysfunction.
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Affiliation(s)
- Na Li
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Xi Luo
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Qilin Yu
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Ping Yang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Zhishui Chen
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.,Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Tongji Hospital Research Building, Tongji Hospital, Wuhan, China
| | - Xinqiang Wang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.,Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Tongji Hospital Research Building, Tongji Hospital, Wuhan, China
| | - Jipin Jiang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.,Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Tongji Hospital Research Building, Tongji Hospital, Wuhan, China
| | - Jing Xu
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.,Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Tongji Hospital Research Building, Tongji Hospital, Wuhan, China
| | - Quan Gong
- Clinical Molecular Immunology Center, Department of Immunology, School of Medicine, Yangtze University, Jingzhou, 434023, China
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 808 Route de Lennik, B-1070, Brussels, Belgium.,Indiana Biosciences Research Institute (IBRI), Indianapolis, IN, USA
| | - Zhiguang Zhou
- Diabetes Center, the Second Xiangya Hospital, Institute of Metabolism and Endocrinology, Central South University, Changsha, China
| | - Jiajun Zhao
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Fei Xiong
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China. .,Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Tongji Hospital Research Building, Tongji Hospital, Wuhan, China.
| | - Shu Zhang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China. .,Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Tongji Hospital Research Building, Tongji Hospital, Wuhan, China.
| | - Cong-Yi Wang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China. .,Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Tongji Hospital Research Building, Tongji Hospital, Wuhan, China.
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49
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Yang Y, Liu W, Hu D, Su R, Ji M, Huang Y, Shereen MA, Xu X, Luo Z, Zhang Q, Liu F, Wu K, Liu Y, Wu J. HIV-1 Nef Interacts with LMP7 To Attenuate Immunoproteasome Formation and Major Histocompatibility Complex Class I Antigen Presentation. mBio 2020; 11:e02221-19. [PMID: 33109760 PMCID: PMC7593969 DOI: 10.1128/mbio.02221-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/21/2020] [Indexed: 01/03/2023] Open
Abstract
The proteasome is a major protein degradation machinery with essential and diverse biological functions. Upon induction by cytokines, proteasome subunits β1, β2, and β5 are replaced by β1i/LMP2, β2i/MECL-1, and β5i/LMP7, resulting in the formation of an immunoproteasome (iProteasome). iProteasome-degraded products are loaded onto the major histocompatibility complex class I (MHC-I), regulating immune responses and inducing cytotoxic T lymphocytes (CTLs). Human immunodeficiency virus type 1 (HIV-1) is the causal agent of AIDS. HIV-1-specific CTLs represent a critical immune mechanism limiting viral replication. HIV-1 negative regulatory factor (Nef) counteracts host immunity, particularly the response involving MHC-I/CTL. This study identifies a distinct mechanism by which Nef facilitates immune evasion via suppressing the function of iProteasome and MHC-I. Nef interacts with LMP7 on the endoplasmic reticulum (ER), downregulating the incorporation of LMP7 into iProteasome and thereby attenuating its formation. Moreover, Nef represses the iProteasome function of protein degradation, MHC-I trafficking, and antigen presentation.IMPORTANCE The ubiquitin-proteasome system (UPS) is essential for the degradation of damaged proteins, which takes place in the proteasome. Upon activation by cytokines, the catalytic subunits of the proteasome are replaced by distinct isoforms resulting in the formation of an immunoproteasome (iProteasome). iProteasome generates peptides used by major histocompatibility complex class I (MHC-I) for antigen presentation and is essential for immune responses. HIV-1 is the causative agent of AIDS, and HIV-1-specific cytotoxic T lymphocytes (CTLs) provide immune responses limiting viral replication. This study identifies a distinct mechanism by which HIV-1 promotes immune evasion. The viral protein negative regulatory factor (Nef) interacts with a component of iProteasome, LMP7, attenuating iProteasome formation and protein degradation function, and thus repressing the MHC-I antigen presentation activity of MHC-I. Therefore, HIV-1 targets LMP7 to inhibit iProteasome activation, and LMP7 may be used as the target for the development of anti-HIV-1/AIDS therapy.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weiyong Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Rui Su
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Man Ji
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuqing Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Muhammad Adnan Shereen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaodi Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen Luo
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Qi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kailang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
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50
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McWilliam HEG, Mak JYW, Awad W, Zorkau M, Cruz-Gomez S, Lim HJ, Yan Y, Wormald S, Dagley LF, Eckle SBG, Corbett AJ, Liu H, Li S, Reddiex SJJ, Mintern JD, Liu L, McCluskey J, Rossjohn J, Fairlie DP, Villadangos JA. Endoplasmic reticulum chaperones stabilize ligand-receptive MR1 molecules for efficient presentation of metabolite antigens. Proc Natl Acad Sci U S A 2020; 117:24974-24985. [PMID: 32958637 PMCID: PMC7547156 DOI: 10.1073/pnas.2011260117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The antigen-presenting molecule MR1 (MHC class I-related protein 1) presents metabolite antigens derived from microbial vitamin B2 synthesis to activate mucosal-associated invariant T (MAIT) cells. Key aspects of this evolutionarily conserved pathway remain uncharacterized, including where MR1 acquires ligands and what accessory proteins assist ligand binding. We answer these questions by using a fluorophore-labeled stable MR1 antigen analog, a conformation-specific MR1 mAb, proteomic analysis, and a genome-wide CRISPR/Cas9 library screen. We show that the endoplasmic reticulum (ER) contains a pool of two unliganded MR1 conformers stabilized via interactions with chaperones tapasin and tapasin-related protein. This pool is the primary source of MR1 molecules for the presentation of exogenous metabolite antigens to MAIT cells. Deletion of these chaperones reduces the ER-resident MR1 pool and hampers antigen presentation and MAIT cell activation. The MR1 antigen-presentation pathway thus co-opts ER chaperones to fulfill its unique ability to present exogenous metabolite antigens captured within the ER.
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Affiliation(s)
- Hamish E G McWilliam
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia;
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
| | - Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wael Awad
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Matthew Zorkau
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sebastian Cruz-Gomez
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hui Jing Lim
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Yuting Yan
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sam Wormald
- Division of Systems Biology and Personalised Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Laura F Dagley
- Division of Systems Biology and Personalised Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Haiyin Liu
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC 3010, Australia
| | - Scott J J Reddiex
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC 3010, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Justine D Mintern
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, CF14 4XN Cardiff, United Kingdom
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia;
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
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