1
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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2
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Probing the Conformational States of Thimet Oligopeptidase in Solution. Int J Mol Sci 2022; 23:ijms23137297. [PMID: 35806299 PMCID: PMC9266445 DOI: 10.3390/ijms23137297] [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: 05/23/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
Thimet oligopeptidase (TOP) is a metallopeptidase involved in the metabolism of oligopeptides inside and outside cells of various tissues. It has been proposed that substrate or inhibitor binding in the TOP active site induces a large hinge-bending movement leading to a closed structure, in which the bound ligand is enclosed. The main goal of the present work was to study this conformational change, and fluorescence techniques were used. Four active TOP mutants were created, each equipped with a single-Trp residue (fluorescence donor) and a p-nitro-phenylalanine (pNF) residue as fluorescence acceptor at opposite sides of the active site. pNF was biosynthetically incorporated with high efficiency using the amber codon suppression technology. Inhibitor binding induced shorter Donor-Acceptor (D-A) distances in all mutants, supporting the view that a hinge-like movement is operative in TOP. The activity of TOP is known to be dependent on the ionic strength of the assay buffer and D-A distances were measured at different ionic strengths. Interestingly, a correlation between the D-A distance and the catalytic activity of TOP was observed: the highest activities corresponded to the shortest D-A distances. In this study for the first time the hinge-bending motion of a metallopeptidase in solution could be studied, yielding insight about the position of the equilibrium between the open and closed conformation. This information will contribute to a more detailed understanding of the mode of action of these enzymes, including therapeutic targets like neurolysin and angiotensin-converting enzyme 2 (ACE2).
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3
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Henriques BS, Gomes B, da Costa SG, Moraes CDS, Mesquita RD, Dillon VM, Garcia EDS, Azambuja P, Dillon RJ, Genta FA. Genome Wide Mapping of Peptidases in Rhodnius prolixus: Identification of Protease Gene Duplications, Horizontally Transferred Proteases and Analysis of Peptidase A1 Structures, with Considerations on Their Role in the Evolution of Hematophagy in Triatominae. Front Physiol 2017; 8:1051. [PMID: 29326597 PMCID: PMC5736985 DOI: 10.3389/fphys.2017.01051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/30/2017] [Indexed: 12/27/2022] Open
Abstract
Triatominae is a subfamily of the order Hemiptera whose species are able to feed in the vertebrate blood (i.e., hematophagy). This feeding behavior presents a great physiological challenge to insects, especially in Hemipteran species with a digestion performed by lysosomal-like cathepsins instead of the more common trypsin-like enzymes. With the aim of having a deeper understanding of protease involvement in the evolutionary adaptation for hematophagy in Hemipterans, we screened peptidases in the Rhodnius prolixus genome and characterized them using common blast (NCBI) and conserved domain analyses (HMMER/blast manager software, FAT, plus PFAM database). We compared the results with available sequences from other hemipteran species and with 18 arthropod genomes present in the MEROPS database. Rhodnius prolixus contains at least 433 protease coding genes, belonging to 71 protease families. Seven peptidase families in R. prolixus presented higher gene numbers when compared to other arthropod genomes. Further analysis indicated that a gene expansion of the protease family A1 (Eukaryotic aspartyl protease, PF00026) might have played a major role in the adaptation to hematophagy since most of these peptidase genes seem to be recently acquired, are expressed in the gut and present putative secretory pathway signal peptides. Besides that, most R. prolixus A1 peptidases showed high frequencies of basic residues at the protein surface, a typical structural signature of Cathepsin D-like proteins. Other peptidase families expanded in R. prolixus (i.e., C2 and M17) also presented significant differences between hematophagous (higher number of peptidases) and non-hematophagous species. This study also provides evidence for gene acquisition from microorganisms in some peptidase families in R. prolixus: (1) family M74 (murein endopeptidase), (2) family S29 (Hepatitis C virus NS3 protease), and (3) family S24 (repressor LexA). This study revealed new targets for studying the adaptation of these insects for digestion of blood meals and their competence as vectors of Chagas disease.
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Affiliation(s)
- Bianca S Henriques
- Laboratory of Insect Physiology and Biochemistry, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (IOC-FIOCRUZ), Rio de Janeiro, Brazil
| | - Bruno Gomes
- Laboratory of Insect Physiology and Biochemistry, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (IOC-FIOCRUZ), Rio de Janeiro, Brazil
| | - Samara G da Costa
- Laboratory of Insect Physiology and Biochemistry, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (IOC-FIOCRUZ), Rio de Janeiro, Brazil
| | - Caroline da Silva Moraes
- Laboratory of Insect Physiology and Biochemistry, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (IOC-FIOCRUZ), Rio de Janeiro, Brazil
| | - Rafael D Mesquita
- National Institute of Science and Technology for Molecular Entomology (INCT-EM), Cidade Universitária, Rio de Janeiro, Brazil.,Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viv M Dillon
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Eloi de Souza Garcia
- Laboratory of Insect Physiology and Biochemistry, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (IOC-FIOCRUZ), Rio de Janeiro, Brazil.,National Institute of Science and Technology for Molecular Entomology (INCT-EM), Cidade Universitária, Rio de Janeiro, Brazil
| | - Patricia Azambuja
- Laboratory of Insect Physiology and Biochemistry, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (IOC-FIOCRUZ), Rio de Janeiro, Brazil.,National Institute of Science and Technology for Molecular Entomology (INCT-EM), Cidade Universitária, Rio de Janeiro, Brazil
| | - Roderick J Dillon
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Fernando A Genta
- Laboratory of Insect Physiology and Biochemistry, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (IOC-FIOCRUZ), Rio de Janeiro, Brazil.,National Institute of Science and Technology for Molecular Entomology (INCT-EM), Cidade Universitária, Rio de Janeiro, Brazil
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4
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Roche DB, Villain E, Kajava AV. Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms. Protein Sci 2017; 26:1864-1869. [PMID: 28685932 DOI: 10.1002/pro.3225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 01/08/2023]
Abstract
There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional importance. To evaluate these methods, several datasets have been compiled. Typically, aggregation-prone regions of proteins, which form aggregates or amyloids in vivo, are more than 15 residues long and intrinsically disordered. However, the number of such experimentally established amyloid forming and non-forming sequences are limited, not exceeding one hundred entries in existing databases. In this work, we parsed all available NMR-resolved protein structures from the PDB and assembled a new, sevenfold larger, dataset of unfolded sequences, soluble at high concentrations. We proposed to use these sequences as a negative set for evaluating methods for predicting aggregation in vivo. We also present the results of benchmarking cutting edge tools for the prediction of aggregation versus solubility propensity.
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Affiliation(s)
- Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France.,University ITMO, 49 Kronverksky Pr, 197101, St. Petersburg, Russia
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5
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Appolaire A, Colombo M, Basbous H, Gabel F, Girard E, Franzetti B. TET peptidases: A family of tetrahedral complexes conserved in prokaryotes. Biochimie 2015; 122:188-96. [PMID: 26546839 DOI: 10.1016/j.biochi.2015.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
Abstract
The TET peptidases are large polypeptide destruction machines present among prokaryotes. They form 12-subunits hollow tetrahedral particles, and belong to the family of M42 metallo-peptidases. Structural characterization of various archaeal and bacterial complexes has revealed a unique mechanism of internal compartmentalization and peptide trafficking that distinguishes them from the other oligomeric peptidases. Different versions of the TET complex often co-exist in the cytosol of microorganisms. In depth enzymatic studies have revealed that they are non-processive cobalt-activated aminopeptidases and display contrasting substrate specificities based on the properties of the catalytic chambers. Recent studies have shed light on the assembly mechanism of homo and hetero-dodecameric TET complexes and shown that the activity of TET aminopeptidase towards polypeptides is coupled with its assembly process. These findings suggested a functional regulation based on oligomerization control in vivo. This review describes a current knowledge on M42 TET peptidases biochemistry and discuss their possible physiological roles. This article is a part of the Special Issue entitled: «A potpourri of proteases and inhibitors: from molecular toolboxes to signalling scissors».
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Affiliation(s)
- Alexandre Appolaire
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Matteo Colombo
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Hind Basbous
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Frank Gabel
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - E Girard
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Bruno Franzetti
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France.
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6
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Zachova K, Krupka M, Raska M. Antigen Cross-Presentation and Heat Shock Protein-Based Vaccines. Arch Immunol Ther Exp (Warsz) 2015; 64:1-18. [DOI: 10.1007/s00005-015-0370-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/31/2015] [Indexed: 12/15/2022]
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7
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Jallow S, Leligdowicz A, Kramer HB, Onyango C, Cotten M, Wright C, Whittle HC, McMichael A, Dong T, Kessler BM, Rowland-Jones SL. The presence of prolines in the flanking region of an immunodominant HIV-2 gag epitope influences the quality and quantity of the epitope generated. Eur J Immunol 2015; 45:2232-42. [PMID: 26018465 PMCID: PMC4832300 DOI: 10.1002/eji.201545451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/02/2015] [Accepted: 05/22/2015] [Indexed: 12/31/2022]
Abstract
Both the recognition of HIV‐infected cells and the immunogenicity of candidate CTL vaccines depend on the presentation of a peptide epitope at the cell surface, which in turn depends on intracellular antigen processing. Differential antigen processing maybe responsible for the differences in both the quality and the quantity of epitopes produced, influencing the immunodominance hierarchy of viral epitopes. Previously, we showed that the magnitude of the HIV‐2 gag‐specific T‐cell response is inversely correlated with plasma viral load, particularly when responses are directed against an epitope, 165DRFYKSLRA173, within the highly conserved Major Homology Region of gag‐p26. We also showed that the presence of three proline residues, at positions 119, 159 and 178 of gag‐p26, was significantly correlated with low viral load. Since this proline motif was also associated with stronger gag‐specific CTL responses, we investigated the impact of these prolines on proteasomal processing of the protective 165DRFYKSLRA173 epitope. Our data demonstrate that the 165DRFYKSLRA173 epitope is most efficiently processed from precursors that contain two flanking proline residues, found naturally in low viral‐load patients. Superior antigen processing and enhanced presentation may account for the link between infection with HIV‐2 encoding the “PPP‐gag” sequence and both strong gag‐specific CTL responses as well as lower viral load.
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Affiliation(s)
- Sabelle Jallow
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, UK
| | | | - Holger B Kramer
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | | | | | - Cynthia Wright
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | | | - Andrew McMichael
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, UK
| | - Tao Dong
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, UK
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Sarah L Rowland-Jones
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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8
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Ahmed AB, Znassi N, Château MT, Kajava AV. A structure-based approach to predict predisposition to amyloidosis. Alzheimers Dement 2014; 11:681-90. [PMID: 25150734 DOI: 10.1016/j.jalz.2014.06.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/22/2014] [Accepted: 06/06/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Neurodegenerative diseases and other amyloidoses are linked to the formation of amyloid fibrils. It has been shown that the ability to form these fibrils is coded by the amino acid sequence. Existing methods for the prediction of amyloidogenicity generate an unsatisfactory high number of false positives when tested against sequences of the disease-related proteins. METHODS Recently, it has been shown that the three-dimensional structure of a majority of disease-related amyloid fibrils contains a β-strand-loop-β-strand motif called β-arch. Using this information, we have developed a novel bioinformatics approach for the prediction of amyloidogenicity. RESULTS The benchmark results show the superior performance of our method over the existing programs. CONCLUSIONS As genome sequencing becomes more affordable, our method provides an opportunity to create individual risk profiles for the neurodegenerative, age-related, and other diseases ushering in an era of personalized medicine. It will also be used in the large-scale analysis of proteomes to find new amyloidogenic proteins.
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Affiliation(s)
- Abdullah B Ahmed
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Nadia Znassi
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; Institut de Biologie Computationnelle, Montpellier, France
| | - Marie-Thérèse Château
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; UFR des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237, CNRS, Université Montpellier 1 et 2, Montpellier, France; Institut de Biologie Computationnelle, Montpellier, France.
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9
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Duprez K, Scranton MA, Walling LL, Fan L. Structure of tomato wound-induced leucine aminopeptidase sheds light on substrate specificity. ACTA ACUST UNITED AC 2014; 70:1649-58. [PMID: 24914976 DOI: 10.1107/s1399004714006245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/20/2014] [Indexed: 11/10/2022]
Abstract
The acidic leucine aminopeptidase (LAP-A) from tomato is induced in response to wounding and insect feeding. Although LAP-A shows in vitro peptidase activity towards peptides and peptide analogs, it is not clear what kind of substrates LAP-A hydrolyzes in vivo. In the current study, the crystal structure of LAP-A was determined to 2.20 Å resolution. Like other LAPs in the M17 peptidase family, LAP-A is a dimer of trimers containing six monomers of bilobal structure. Each monomer contains two metal ions bridged by a water or a hydroxyl ion at the active site. Modeling of different peptides or peptide analogs in the active site of LAP-A reveals a spacious substrate-binding channel that can bind peptides of five or fewer residues with few geometric restrictions. The sequence specificity of the bound peptide is likely to be selected by the structural and chemical restrictions on the amino acid at the P1 and P1' positions because these two amino acids have to bind perfectly at the active site for hydrolysis of the first peptide bond to occur. The hexameric assembly results in the merger of the open ends of the six substrate-binding channels from the LAP-A monomers to form a spacious central cavity allowing the hexameric LAP-A enzyme to simultaneously hydrolyze six peptides containing up to six amino acids each. The hexameric LAP-A enzyme may also hydrolyze long peptides or proteins if only one such substrate is bound to the hexamer because the substrate can extend through the central cavity and the two major solvent channels between the two LAP-A trimers.
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Affiliation(s)
- Kevin Duprez
- Department of Biochemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Melissa A Scranton
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Linda L Walling
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Li Fan
- Department of Biochemistry, University of California-Riverside, Riverside, CA 92521, USA
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10
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Hsu HT, Janßen L, Lawand M, Kim J, Perez-Arroyo A, Culina S, Gdoura A, Burgevin A, Cumenal D, Fourneau Y, Moser A, Kratzer R, Wong FS, Springer S, van Endert P. Endoplasmic reticulum targeting alters regulation of expression and antigen presentation of proinsulin. THE JOURNAL OF IMMUNOLOGY 2014; 192:4957-66. [PMID: 24778449 DOI: 10.4049/jimmunol.1300631] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptide ligands presented by MHC class I (MHC-I) molecules are produced by degradation of cytosolic and nuclear, but also endoplasmic reticulum (ER)-resident, proteins by the proteasome. However, Ag processing of ER proteins remains little characterized. Studying processing and presentation of proinsulin, which plays a pivotal role in autoimmune diabetes, we found that targeting to the ER has profound effects not only on how proinsulin is degraded, but also on regulation of its cellular levels. While proteasome inhibition inhibited degradation and presentation of cytosolic proinsulin, as expected, it reduced the abundance of ER-targeted proinsulin. This targeting and protein modifications modifying protein half-life also had profound effects on MHC-I presentation and proteolytic processing of proinsulin. Thus, presentation of stable luminal forms was inefficient but enhanced by proteasome inhibition, whereas that of unstable luminal forms and of a cytosolic form were more efficient and compromised by proteasome inhibitors. Distinct stability of peptide MHC complexes produced from cytosolic and luminal proinsulin suggests that different proteolytic activities process the two Ag forms. Thus, both structural features and subcellular targeting of Ags can have strong effects on the processing pathways engaged by MHC-I-restricted Ags, and on the efficiency and regulation of their presentation.
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Affiliation(s)
- Hsiang-Ting Hsu
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Linda Janßen
- Biochemistry and Cell Biology, Molecular Life Science Center, Jacobs University Bremen, 28759 Bremen, Germany; and
| | - Myriam Lawand
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Jessica Kim
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Alicia Perez-Arroyo
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Slobodan Culina
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Abdel Gdoura
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Anne Burgevin
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Delphine Cumenal
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Yousra Fourneau
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Anna Moser
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Roland Kratzer
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - F Susan Wong
- Centre for Endocrine and Diabetes Science, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Sebastian Springer
- Biochemistry and Cell Biology, Molecular Life Science Center, Jacobs University Bremen, 28759 Bremen, Germany; and
| | - Peter van Endert
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France;
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11
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Culina S, Mauvais FX, Hsu HT, Burgevin A, Guénette S, Moser A, van Endert P. No major role for insulin-degrading enzyme in antigen presentation by MHC molecules. PLoS One 2014; 9:e88365. [PMID: 24516642 PMCID: PMC3917890 DOI: 10.1371/journal.pone.0088365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/06/2014] [Indexed: 12/27/2022] Open
Abstract
Antigen presentation by MHC class I molecules requires degradation of epitope source proteins in the cytosol. Although the preeminent role of the proteasome is clearly established, evidence suggesting a significant role for proteasome-independent generation of class I ligands has been reported repeatedly. However, an enzyme responsible for such a role has not been identified. Recently insulin-degrading enzyme (IDE) was shown to produce an antigenic peptide derived from the tumor antigen MAGE-A3 in an entirely proteasome-independent manner, raising the question of the global impact of IDE in MHC class I antigen processing. Here we report that IDE knockdown in human cell lines, or knockout in two different mouse strains, has no effect on cell surface expression of various MHC class I molecules, including allomorphs such as HLA-A3 and HLA-B27 suggested to be loaded in an at least a partly proteasome-independent manner. Moreover, reduced or absent IDE expression does not affect presentation of five epitopes including epitopes derived from beta amyloid and proinsulin, two preferred IDE substrates. Thus, IDE does not play a major role in MHC class I antigen processing, confirming the dominant and almost exclusive role of the proteasome in cytosolic production of MHC class I ligands.
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Affiliation(s)
- Slobodan Culina
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - François-Xavier Mauvais
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Hsiang-Ting Hsu
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Anne Burgevin
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Suzanne Guénette
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United States of America
| | - Anna Moser
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
- * E-mail:
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12
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Robinson PC, Brown MA. Genetics of ankylosing spondylitis. Mol Immunol 2013; 57:2-11. [PMID: 23916070 DOI: 10.1016/j.molimm.2013.06.013] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 02/08/2023]
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory arthritis that affects the spine and sacroiliac joints. It causes significant disability and is associated with a number of other features including peripheral arthritis, anterior uveitis, psoriasis and inflammatory bowel disease (IBD). Significant progress has been made in the genetics of AS have in the last five years, leading to new treatments in trial, and major leaps in understanding of the aetiopathogenesis of the disease.
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Affiliation(s)
- Philip C Robinson
- University of Queensland Diamantina Institute, Translational Research Institute, 37 Kent Road, Princess Alexandra Hospital, Brisbane, Australia
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13
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Ahmed AB, Kajava AV. Breaking the amyloidogenicity code: methods to predict amyloids from amino acid sequence. FEBS Lett 2012; 587:1089-95. [PMID: 23262221 DOI: 10.1016/j.febslet.2012.12.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 12/11/2012] [Accepted: 12/11/2012] [Indexed: 11/18/2022]
Abstract
Numerous studies have shown that the ability to form amyloid fibrils is an inherent property of the polypeptide chain. This has lead to the development of several computational approaches to predict amyloidogenicity by amino acid sequences. Here, we discuss the principles governing these methods, and evaluate them using several datasets. They deliver excellent performance in the tests made using short peptides (~6 residues). However, there is a general tendency towards a high number of false positives when tested against longer sequences. This shortcoming needs to be addressed as these longer sequences are linked to diseases. Recent structural studies have shown that the core element of the majority of disease-related amyloid fibrils is a β-strand-loop-β-strand motif called β-arch. This insight provides an opportunity to substantially improve the prediction of amyloids produced by natural proteins, ushering in an era of personalized medicine based on genome analysis.
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Affiliation(s)
- Abdullah B Ahmed
- Centre de Recherches de Biochimie Macromoléculaire, UMR5237 CNRS, Montpellier 1 et 2, 1919, Route de Mende, 34293 Montpellier Cédex 5, France
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14
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Stadler LKJ, Hoffmann T, Tomlinson DC, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner SD, Knowles MA, Davis JJ, Keegan N, Ferrigno PK. Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant. Protein Eng Des Sel 2011; 24:751-63. [PMID: 21616931 DOI: 10.1093/protein/gzr019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Constrained binding peptides (peptide aptamers) may serve as tools to explore protein conformations and disrupt protein-protein interactions. The quality of the protein scaffold, by which the binding peptide is constrained and presented, is of crucial importance. SQT (Stefin A Quadruple Mutant-Tracy) is our most recent development in the Stefin A-derived scaffold series. Stefin A naturally uses three surfaces to interact with its targets. SQT tolerates peptide insertions at all three positions. Peptide aptamers in the SQT scaffold can be expressed in bacterial, yeast and human cells, and displayed as a fusion to truncated pIII on phage. Peptides that bind to CDK2 can show improved binding in protein microarrays when presented by the SQT scaffold. Yeast two-hybrid libraries have been screened for binders to the POZ domain of BCL-6 and to a peptide derived from PBP2', specific to methicillin-resistant Staphylococcus aureus. Presentation of the Noxa BH3 helix by SQT allows specific interaction with Mcl-1 in human cells. Together, our results show that Stefin A-derived scaffolds, including SQT, can be used for a variety of applications in cellular and molecular biology. We will henceforth refer to Stefin A-derived engineered proteins as Scannins.
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Affiliation(s)
- Lukas Kurt Josef Stadler
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds, UK
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15
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Seliger B, Dressler SP, Massa C, Recktenwald CV, Altenberend F, Bukur J, Marincola FM, Wang E, Stevanovic S, Lichtenfels R. Identification and characterization of human leukocyte antigen class I ligands in renal cell carcinoma cells. Proteomics 2011; 11:2528-41. [PMID: 21595034 DOI: 10.1002/pmic.201000486] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 03/07/2011] [Accepted: 03/28/2011] [Indexed: 02/01/2023]
Abstract
The presentation of tumor antigen-derived peptides by human leukocyte antigen (HLA) class I surface antigens on tumor cells is a key prerequisite to trigger effective T-cell responses in cancer patients. Multiple complementary strategies like cDNA and serological expression cloning, reverse immunology and different 'ome'-based methods have been employed to identify potential T-cell targets. This report focuses on a ligandomic profiling approach leading to the identification of 49 naturally processed HLA class I peptide ligands presented on the cell surface of renal cell carcinoma (RCC) cells. The source proteins of the defined HLA ligands are classified according to their biological function and subcellular localization. Previously established cDNA microarray data of paired tissue specimen of RCC and renal epithelium assessed the transcriptional regulation for 28 source proteins. In addition, HLA-A2-restricted, peptide-specific T cells directed against a HLA ligand derived from sulfiredoxin-1 (SRXN1) were generated, which were able to recognize and lyse ligand-presenting target cells in a HLA class I-restricted manner. Furthermore, tumor-infiltrating T cells isolated from a RCC patient were also able to kill SRXN1 expressing tumor cells. Thus, this experimental strategy might be suited to define potential candidate biomarkers and novel targets for T-cell-based immunotherapies of this disease.
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Affiliation(s)
- Barbara Seliger
- Institute of Medical Immunology, Martin-Luther University Halle-Wittenberg, Halle, Germany.
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16
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van Endert P. Post-proteasomal and proteasome-independent generation of MHC class I ligands. Cell Mol Life Sci 2011; 68:1553-67. [PMID: 21390545 PMCID: PMC11115176 DOI: 10.1007/s00018-011-0662-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 12/18/2022]
Abstract
Peptide ligands presented by MHC class I molecules are produced by intracellular proteolysis, which often involves multiple steps. Initial antigen degradation seems to rely almost invariably on the proteasome, although tripeptidyl peptidase II (TPP II) and insulin-degrading enzyme (IDE) may be able to substitute for the proteasome in rare cases. Recent evidence suggests that the net effect of cytosolic aminopeptidases is destruction of potential class I ligands, although a positive role in selected cases has been documented. This may apply particularly to the trimming of long precursors by TPP II. In contrast, trimming of ligand precursors in the endoplasmic reticulum is essential for the generation of suitable peptides and has a substantial impact on the repertoire of ligands presented. Trimming by the ER aminopeptidase (ERAP) enzymes most likely acts on free precursors and is adapted to the needs of class I molecules by way of a molecular ruler mechanism. Trimming by ERAP enzymes also occurs for cross-presented ligands, which can alternatively be processed in a special endosomal compartment by insulin-regulated aminopeptidase.
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Affiliation(s)
- Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris 75015, France.
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17
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Zhang J, Wong J, Gao G, Luo H. Tripeptidyl peptidase II serves as an alternative to impaired proteasome to maintain viral growth in the host cells. FEBS Lett 2010; 585:261-5. [PMID: 21134372 PMCID: PMC7164062 DOI: 10.1016/j.febslet.2010.11.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 11/25/2010] [Accepted: 11/30/2010] [Indexed: 12/11/2022]
Abstract
The ubiquitin-proteasome system is known to be utilized by coxsackievirus to facilitate its propagation within the host cells. The present study explores the role of tripeptidyl peptidase II (TPPII), a serine peptidase contributing to protein turnover by acting downstream of the proteasome, in regulating coxsackievirus infection. Inhibition of TPPII does not affect virus replication in cells with functional proteasome. However, when the proteasome is impaired, TPPII appears to serve as an alternative to maintain low levels of virus infection. Our results suggest an important function of TPPII in the maintenance of viral growth and may have implications for anti-viral therapy.
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Affiliation(s)
- Jingchun Zhang
- James Hogg Research Center, Providence Heart+Lung Institute, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
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18
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Wasbrough ER, Dorus S, Hester S, Howard-Murkin J, Lilley K, Wilkin E, Polpitiya A, Petritis K, Karr TL. The Drosophila melanogaster sperm proteome-II (DmSP-II). J Proteomics 2010; 73:2171-85. [DOI: 10.1016/j.jprot.2010.09.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 09/07/2010] [Accepted: 09/07/2010] [Indexed: 01/07/2023]
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19
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Hoffmann T, Stadler LKJ, Busby M, Song Q, Buxton AT, Wagner SD, Davis JJ, Ko Ferrigno P. Structure-function studies of an engineered scaffold protein derived from stefin A. I: Development of the SQM variant. Protein Eng Des Sel 2010; 23:403-13. [PMID: 20179045 PMCID: PMC2851446 DOI: 10.1093/protein/gzq012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-antibody scaffold proteins are used for a range of applications, especially the assessment of protein-protein interactions within human cells. The search for a versatile, robust and biologically neutral scaffold previously led us to design STM (stefin A triple mutant), a scaffold derived from the intracellular protease inhibitor stefin A. Here, we describe five new STM-based scaffold proteins that contain modifications designed to further improve the versatility of our scaffold. In a step-by-step approach, we introduced restriction sites in the STM open reading frame that generated new peptide insertion sites in loop 1, loop 2 and the N-terminus of the scaffold protein. A second restriction site in 'loop 2' allows substitution of the native loop 2 sequence with alternative oligopeptides. None of the amino acid changes interfered significantly with the folding of the STM variants as assessed by circular dichroism spectroscopy. Of the five scaffold variants tested, one (stefin A quadruple mutant, SQM) was chosen as a versatile, stable scaffold. The insertion of epitope tags at varying positions showed that inserts into loop 1, attempted here for the first time, were generally well tolerated. However, N-terminal insertions of epitope tags in SQM had a detrimental effect on protein expression.
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Affiliation(s)
- Toni Hoffmann
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett St, Leeds LS97TF, UK.
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20
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Kajava AV, Baxa U, Steven AC. Beta arcades: recurring motifs in naturally occurring and disease-related amyloid fibrils. FASEB J 2009; 24:1311-9. [PMID: 20032312 DOI: 10.1096/fj.09-145979] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Amyloid fibrils are filamentous protein aggregates that accumulate in diseases such as Alzheimer's or type II diabetes. The amyloid-forming protein is disease specific. Amyloids may also be formed in vitro from many other proteins, after first denaturing them. Unlike the diverse native folds of these proteins, their amyloids are fundamentally similar in being rigid, smooth-sided, and cross-beta-structured, that is, with beta strands running perpendicular to the fibril axis. In the absence of high-resolution fibril structures, increasingly credible models are being derived by integrating data from a crossfire of experimental techniques. Most current models of disease-related amyloids invoke "beta arcades," columnar structures produced by in-register stacking of "beta arches." A beta arch is a strand-turn-strand motif in which the two beta strands interact via their side chains, not via the polypeptide backbone as in a conventional beta hairpin. Crystal structures of beta-solenoids, a class of proteins with amyloid-like properties, offer insight into the beta-arc turns found in beta arches. General conformational and thermodynamic considerations suggest that complexes of 2 or more beta arches may nucleate amyloid fibrillogenesis in vivo. The apparent prevalence of beta arches and their components have implications for identifying amyloidogenic sequences, elucidating fibril polymorphisms, predicting the locations and conformations of beta arcs within amyloid fibrils, and refining existing fibril models.
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Affiliation(s)
- Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier 1 and 2, Montpellier, France
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21
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Polge C, Jaquinod M, Holzer F, Bourguignon J, Walling L, Brouquisse R. Evidence for the Existence in Arabidopsis thaliana of the Proteasome Proteolytic Pathway: ACTIVATION IN RESPONSE TO CADMIUM. J Biol Chem 2009; 284:35412-24. [PMID: 19822524 PMCID: PMC2790970 DOI: 10.1074/jbc.m109.035394] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 10/09/2009] [Indexed: 11/06/2022] Open
Abstract
Heavy metals are known to generate reactive oxygen species that lead to the oxidation and fragmentation of proteins, which become toxic when accumulated in the cell. In this study, we investigated the role of the proteasome during cadmium stress in the leaves of Arabidopsis thaliana plants. Using biochemical and proteomics approaches, we present the first evidence of an active proteasome pathway in plants. We identified and characterized the peptidases acting sequentially downstream from the proteasome in animal cells as follows: tripeptidyl-peptidase II, thimet oligopeptidase, and leucine aminopeptidase. We investigated the proteasome proteolytic pathway response in the leaves of 6-week-old A. thaliana plants grown hydroponically for 24, 48, and 144 h in the presence or absence of 50 mum cadmium. The gene expression and proteolytic activity of the proteasome and the different proteases of the pathway were found to be up-regulated in response to cadmium. In an in vitro assay, oxidized bovine serum albumin and lysozyme were more readily degraded in the presence of 20 S proteasome and tripeptidyl-peptidase II than their nonoxidized form, suggesting that oxidized proteins are preferentially degraded by the Arabidopsis 20 S proteasome pathway. These results show that, in response to cadmium, the 20 S proteasome proteolytic pathway is up-regulated at both RNA and activity levels in Arabidopsis leaves and may play a role in degrading oxidized proteins generated by the stress.
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Affiliation(s)
- Cécile Polge
- From the Laboratoires de Physiologie Cellulaire Végétale, CEA, IRTSV, UMR5168 CNRS/CEA/INRA, Université Joseph Fourier and
| | - Michel Jaquinod
- Etude de la Dynamique des Protéomes, F-38054 Grenoble, France and
| | - Frances Holzer
- the Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521-0124
| | - Jacques Bourguignon
- From the Laboratoires de Physiologie Cellulaire Végétale, CEA, IRTSV, UMR5168 CNRS/CEA/INRA, Université Joseph Fourier and
| | - Linda Walling
- the Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521-0124
| | - Renaud Brouquisse
- From the Laboratoires de Physiologie Cellulaire Végétale, CEA, IRTSV, UMR5168 CNRS/CEA/INRA, Université Joseph Fourier and
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22
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Role of tripeptidyl peptidase II in the processing of Listeria monocytogenes-derived MHC class I-presented antigenic peptides. Microbes Infect 2009; 11:795-802. [PMID: 19426827 DOI: 10.1016/j.micinf.2009.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 04/17/2009] [Accepted: 04/19/2009] [Indexed: 11/23/2022]
Abstract
The effective control of the infection of mice with the facultatively intracellular bacterium Listeria monocytogenes requires CD8 T cells which recognize bacterial antigenic peptides presented in the context of host MHC class I molecules. It is generally accepted that bacterial antigens are processed by the proteasome, a proteolytic cytoplasmic multiprotein complex. We observed that presentation of the L. monocytogenes-derived CD8 T cell epitope LLO 91-99 by infected cells can not be totally suppressed by inhibitors of the proteasome alone. Further analysis revealed that inhibitors of the cytoplasmic tripeptidyl peptidase II suppressed the presentation of the epitopes LLO 91-99 and p60 449-457. While significant suppression of the presentation of LLO 91-99 required the simultaneous inhibition of the proteasome and tripeptidyl peptidase II, presentation of p60 449-457 was suppressed by inhibitors of either the proteasome or TPPII alone. Thus, these data indicate that both, the proteasome and tripeptidyl protease II play a role in the processing of L. monocytogenes-derived antigenic peptides.
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23
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Berkers CR, de Jong A, Ovaa H, Rodenko B. Transpeptidation and reverse proteolysis and their consequences for immunity. Int J Biochem Cell Biol 2008; 41:66-71. [PMID: 18817889 DOI: 10.1016/j.biocel.2008.08.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 08/29/2008] [Accepted: 08/29/2008] [Indexed: 11/27/2022]
Abstract
Reverse proteolysis and transpeptidation lead to the generation of polypeptide sequences that cannot be inferred directly from genome sequences as they are post-translational phenomena. These phenomena have so far received little attention although the physiological consequences may reach far. The protease-mediated synthesis of several immunodominant MHC class I antigens was recently reported, underscoring its importance to immunity. Reverse proteolytic and transpeptidation mechanisms as well as conditions that favor successful protease-catalyzed synthetic events are discussed here.
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Affiliation(s)
- Celia R Berkers
- Division of Cellular Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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24
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Endert PV. Role of tripeptidyl peptidase II in MHC class I antigen processing - the end of controversies? Eur J Immunol 2008; 38:609-13. [PMID: 18286570 DOI: 10.1002/eji.200838181] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Peptide ligands presented by MHC class I molecules are generated in a cascade of proteolytic events starting with the proteasome in the cytosol and frequently terminating with trimming aminopeptidases in the endoplasmic reticulum. Several cytosolic proteases can carry out intermediate proteolytic steps between these start and endpoints. Among these, tripeptidyl peptidase II (TPP II), an exceptionally large homo-oligomeric protease, has been proposed to be involved in the generation of many or most MHC class I ligands by cleaving long precursor peptides. In this issue of the European Journal of Immunology, the effect of pharmacological or genetic TPP II inhibition on peptide loading of HLA-B27 and other HLA class I molecules is examined, and no evidence for a role of TPP II in this process is detected. Although further studies using more efficient inhibitors and focusing on HLA class I alleles such as HLA-A3 are warranted, these results, together with other recently published data, suggest that the role of TPP II in MHC class I processing may be much more limited than previously appreciated.
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Affiliation(s)
- Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 580, Paris, France.
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25
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Kanaseki T, Blanchard N, Hammer GE, Gonzalez F, Shastri N. ERAAP synergizes with MHC class I molecules to make the final cut in the antigenic peptide precursors in the endoplasmic reticulum. Immunity 2006; 25:795-806. [PMID: 17088086 PMCID: PMC2746443 DOI: 10.1016/j.immuni.2006.09.012] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 08/31/2006] [Accepted: 09/13/2006] [Indexed: 10/23/2022]
Abstract
The major histocompatibility complex class I molecules display peptides (pMHC I) on the cell surface for immune surveillance by CD8(+) T cells. These peptides are generated by proteolysis of intracellular polypeptides by the proteasome in the cytoplasm and then in the endoplasmic reticulum (ER) by the ER aminopeptidase associated with antigen processing (ERAAP). To define the unknown mechanism of ERAAP function in vivo, we analyzed naturally processed peptides in cells with or without appropriate MHC I and ERAAP. In the absence of MHC I, ERAAP degraded the antigenic precursors in the ER. However, MHC I molecules could bind proteolytic intermediates and were essential for generation of the final peptide by ERAAP. Thus, ERAAP synergizes with MHC I to generate the final pMHC I repertoire.
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Affiliation(s)
- Takayuki Kanaseki
- Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Nicolas Blanchard
- Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Gianna Elena Hammer
- Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Federico Gonzalez
- Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Nilabh Shastri
- Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
- Correspondence:
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26
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Hammer GE, Gonzalez F, James E, Nolla H, Shastri N. In the absence of aminopeptidase ERAAP, MHC class I molecules present many unstable and highly immunogenic peptides. Nat Immunol 2006; 8:101-8. [PMID: 17128277 DOI: 10.1038/ni1409] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 10/13/2006] [Indexed: 12/11/2022]
Abstract
Immunosurveillance by cytotoxic T cells requires that cells generate a diverse spectrum of peptides for presentation by major histocompatibility complex (MHC) class I molecules. Those peptides are generated by proteolysis, which begins in the cytoplasm and continues in the endoplasmic reticulum by the unique aminopeptidase ERAAP. The overall extent to which trimming by ERAAP modifies the peptide pool and the immunological consequences of ERAAP deficiency are unknown. Here we show that the peptide-MHC repertoire of ERAAP-deficient mice was missing many peptides. Furthermore, ERAAP-deficient cells presented many unstable and structurally unique peptide-MHC complexes, which elicited potent CD8+ T cell and B cell responses. Thus, ERAAP is a 'quintessential editor' of the peptide-MHC repertoire and, paradoxically, its absence enhances immunogenicity.
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Affiliation(s)
- Gianna Elena Hammer
- Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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27
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Altrich-VanLith ML, Ostankovitch M, Polefrone JM, Mosse CA, Shabanowitz J, Hunt DF, Engelhard VH. Processing of a Class I-Restricted Epitope from Tyrosinase Requires Peptide N-Glycanase and the Cooperative Action of Endoplasmic Reticulum Aminopeptidase 1 and Cytosolic Proteases. THE JOURNAL OF IMMUNOLOGY 2006; 177:5440-50. [PMID: 17015730 DOI: 10.4049/jimmunol.177.8.5440] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although multiple components of the class I MHC processing pathway have been elucidated, the participation of nonproteasomal cytosolic enzymes has been largely unexplored. In this study, we provide evidence for multiple cytosolic mechanisms in the generation of an HLA-A*0201-associated epitope from tyrosinase. This epitope is presented in two isoforms containing either Asn or Asp, depending on the structure of the tyrosinase precursor. We show that deamidation of Asn to Asp is dependent on glycosylation in the endoplasmic reticulum (ER), and subsequent deglycosylation by peptide-N-glycanase in the cytosol. Epitope precursors with N-terminal extensions undergo a similar process. This is linked to an inability of ER aminopeptidase 1 to efficiently remove N-terminal residues, necessitating processing by nonproteasomal peptidases in the cytosol. Our work demonstrates that processing of this tyrosinase epitope involves recycling between the ER and cytosol, and an obligatory interplay between enzymes involved in proteolysis and glycosylation/deglycosylation located in both compartments.
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Affiliation(s)
- Michelle L Altrich-VanLith
- Carter Immunology Center and Department of Microbiology, University of Virginia, Charlottesville, VA 22908-1386, USA
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28
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López D, Calero O, Jiménez M, García-Calvo M, Del Val M. Antigen processing of a short viral antigen by proteasomes. J Biol Chem 2006; 281:30315-8. [PMID: 16861221 DOI: 10.1074/jbc.m605973200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mass spectrometry (MS)-based methods coupled to reverse phase chromatography separation are a useful technology to analyze complex peptide pools that are comprised of different peptides with unrelated sequences. In antigen presentation, proteasomes generate a set of short peptides that are closely related and overlapping and in some instances may even have identical retention times and identical masses. In these situations, micro-liquid chromatography-MS/MS focused on each theoretical parent ion followed by manual interpretation optimizes the identification of generated peptides. The results suggest that the degradation of short antigens by the proteasome occurs by sequential cleavage.
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Affiliation(s)
- Daniel López
- Unidad de Proteómica, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain.
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29
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Holst J, Vignali KM, Burton AR, Vignali DAA. Rapid analysis of T-cell selection in vivo using T cell-receptor retrogenic mice. Nat Methods 2006; 3:191-7. [PMID: 16489336 DOI: 10.1038/nmeth858] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 01/20/2006] [Indexed: 01/09/2023]
Abstract
Although T-cell receptor (TCR) transgenic as well as knockout and knockin mice have had a large impact on our understanding of T-cell development, signal transduction and function, the need to cross these mice delays experiments considerably. Here we provide a methodology for the rapid expression of TCRs in mice using 2A peptide-linked multicistronic retroviral vectors to transduce stem cells of any background before adoptive transfer into RAG-1(-/-) mice. For simplicity, we refer to these as retrogenic mice. We demonstrate that these retrogenic mice are comparable to transgenic mice expressing three commonly used TCRs (OT-I, OT-II [corrected] and AND). We also show that retrogenic mice expressing male antigen-specific TCRs (HY, MataHari and Marilyn) facilitated the analysis of positive and negative selection in female and male mice, respectively. We examined various tolerance mechanisms in epitope-coupled TCR retrogenic mice. This powerful resource could expedite the identification of proteins involved in T-cell development and function.
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Affiliation(s)
- Jeff Holst
- Department of Immunology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, Tennessee 38105, USA
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Wherry EJ, Golovina TN, Morrison SE, Sinnathamby G, McElhaugh MJ, Shockey DC, Eisenlohr LC. Re-evaluating the Generation of a “Proteasome-Independent” MHC Class I-Restricted CD8 T Cell Epitope. THE JOURNAL OF IMMUNOLOGY 2006; 176:2249-61. [PMID: 16455981 DOI: 10.4049/jimmunol.176.4.2249] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The proteasome is primarily responsible for the generation of MHC class I-restricted CTL epitopes. However, some epitopes, such as NP(147-155) of the influenza nucleoprotein (NP), are presented efficiently in the presence of proteasome inhibitors. The pathways used to generate such apparently "proteasome-independent" epitopes remain poorly defined. We have examined the generation of NP(147-155) and a second proteasome-dependent NP epitope, NP(50-57), using cells adapted to growth in the presence of proteasome inhibitors and also through protease overexpression. We observed that: 1) Ag processing and presentation proceeds in proteasome-inhibitor adapted cells but may become more dependent, at least in part, on nonproteasomal protease(s), 2) tripeptidyl peptidase II does not substitute for the proteasome in the generation of NP(147-155), 3) overexpression of leucine aminopeptidase, thymet oligopeptidase, puromycin-sensitive aminopeptidase, and bleomycin hydrolase, has little impact on the processing and presentation of NP(50-57) or NP(147-155), and 4) proteasome-inhibitor treatment altered the specificity of substrate cleavage by the proteasome using cell-free digests favoring NP(147-155) epitope preservation. Based on these results, we propose a central role for the proteasome in epitope generation even in the presence of proteasome inhibitors, although such inhibitors will likely alter cleavage patterns and may increase the dependence of the processing pathway on postproteasomal enzymes.
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Affiliation(s)
- E John Wherry
- Department of Microbiology and Immunology, Jefferson Medical College and Kimmel Cancer Institute, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA 19107, USA
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Chang SC, Momburg F, Bhutani N, Goldberg AL. The ER aminopeptidase, ERAP1, trims precursors to lengths of MHC class I peptides by a "molecular ruler" mechanism. Proc Natl Acad Sci U S A 2005; 102:17107-12. [PMID: 16286653 PMCID: PMC1287962 DOI: 10.1073/pnas.0500721102] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an IFN-gamma-induced aminopeptidase in the endoplasmic reticulum that trims longer precursors to the antigenic peptides presented on MHC class I molecules. We recently reported that purified ERAP1 trimmed N-extended precursors but spared peptides of 8-9 residues, the length required for binding to MHC class I molecules. Here, we show another remarkable property of ERAP1: that it strongly prefers substrates 9-16 residues long, the lengths of peptides transported efficiently into the ER by the transporter associated with antigen processing (TAP) transporter. This aminopeptidase rapidly degraded a model 13-mer to a 9-mer and then stopped, even though the substrate and the product had identical N- and C-terminal sequences. No other aminopeptidase, including the closely related ER-aminopeptidase ERAP2, showed a similar length preference. Unlike other aminopeptidases, the activity of ERAP1 depended on the C-terminal residue of the substrate. ERAP1, like most MHC class I molecules, prefers peptides with hydrophobic C termini and shows low affinity for peptides with charged C termini. Thus, ERAP1 is specialized to process precursors transported by TAP to peptides that can serve as MHC class I epitopes. Its "molecular ruler" mechanism involves binding the hydrophobic C terminus of the substrate 9-16 residues away from the active site.
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Affiliation(s)
- Shih-Chung Chang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Shastri N, Cardinaud S, Schwab SR, Serwold T, Kunisawa J. All the peptides that fit: the beginning, the middle, and the end of the MHC class I antigen-processing pathway. Immunol Rev 2005; 207:31-41. [PMID: 16181325 DOI: 10.1111/j.0105-2896.2005.00321.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The end result of the antigen-processing pathway is the display of peptide-bound major histocompatibility complex I (pMHC I) molecules. The pMHC I molecules are expressed on the cell surface where they can be surveyed by CD8(+) T cells for abnormal proteins. MHC I molecules present a large repertoire of peptides that fit perfectly in their binding grooves and represent the otherwise hidden intracellular contents. Many peptides originate as defective ribosomal products in the cytoplasm. In a stepwise manner, the antigen-processing pathway generates and protects the proteolytic intermediates until they yield the final peptides that can fit the MHC I in the endoplasmic reticulum.
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Affiliation(s)
- Nilabh Shastri
- Department of Molecular and Cell Biology, Division of Immunology, University of California, Berkeley, CA 94720, USA.
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Saveanu L, Carroll O, Hassainya Y, van Endert P. Complexity, contradictions, and conundrums: studying post-proteasomal proteolysis in HLA class I antigen presentation. Immunol Rev 2005; 207:42-59. [PMID: 16181326 DOI: 10.1111/j.0105-2896.2005.00313.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The vast majority of the peptides produced during protein degradation by the cytosolic proteasome-ubiquitin system are consecutively hydrolyzed to single amino acids by multiple cytosolic peptidases preferring intermediate length or short substrates. The small fraction of peptides surviving the aggressive cytosolic environment can be recruited for presentation by major histocompatibility complex (MHC) class I molecules. However, such peptides may frequently have to be adapted to the strict MHC class I-binding requirements by one or several N-terminal-trimming steps. A recent model proposes that an initial step, in which peptides of 15 or more residues are shortened by cytosolic tripeptidylpeptidase II, is followed by additional trimming by cytosolic or endoplasmic reticulum (ER) aminopeptidases. In humans, at least two ER resident aminopeptidases, ERAP1 and ERAP2, contribute to trimming of human leukocyte antigen class I ligands. These interferon-gamma-regulated metallopeptidases show distinct substrate preferences and may have to act in a concerted fashion to remove some complex or longer N-terminal extensions and to trim the full spectrum of precursor peptides. This task is likely facilitated by the formation of presumably heterodimeric ERAP1-2 complexes. RNA interference experiments suggest that both enzymes are important for normal antigen presentation, but precise determination of the extent and the cellular context of their requirement will be left to future experimentation.
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Drozina G, Kohoutek J, Jabrane-Ferrat N, Peterlin BM. Expression of MHC II genes. Curr Top Microbiol Immunol 2005; 290:147-70. [PMID: 16480042 DOI: 10.1007/3-540-26363-2_7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Innate and adaptive immunity are connected via antigen processing and presentation (APP), which results in the presentation of antigenic peptides to T cells in the complex with the major histocompatibility (MHC) determinants. MHC class II (MHC II) determinants present antigens to CD4+ T cells, which are the main regulators of the immune response. Their genes are transcribed from compact promoters that form first the MHC II enhanceosome, which contains DNA-bound activators and then the MHC II transcriptosome with the addition of the class II transactivator (CIITA). CIITA is the master regulator of MHC II transcription. It is expressed constitutively in dendritic cells (DC) and mature B cells and is inducible in most other cell types. Three isoforms of CIITA exist, depending on cell type and inducing signals. CIITA is regulated at the levels of transcription and post-translational modifications, which are still not very clear. Inappropriate immune responses are found in several diseases, including cancer and autoimmunity. Since CIITA regulates the expression of MHC II genes, it is involved directly in the regulation of the immune response. The knowledge of CIITA will facilitate the manipulation of the immune response and might contribute to the treatment of these diseases.
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Affiliation(s)
- G Drozina
- Department of Medicine, Rosalind Russell Medical Research Center, University of California, San Francisco 94143, USA.
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35
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Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A. The design and implementation of the immune epitope database and analysis resource. Immunogenetics 2005; 57:326-36. [PMID: 15895191 PMCID: PMC4780685 DOI: 10.1007/s00251-005-0803-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 04/22/2005] [Indexed: 01/13/2023]
Abstract
Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, "The Immune Epitope Database and Analysis Resource." We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide.
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Affiliation(s)
- Bjoern Peters
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - John Sidney
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Phil Bourne
- San Diego Supercomputer Center, P.O.Box 85608 San Diego, CA, 92186-5608, USA
| | - Huynh-Hoa Bui
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Soeren Buus
- University of Copenhagen, Panum Building 18.3.22, Bleadamsvei 3, 220 Copenhagen, Denmark
| | - Grace Doh
- SH Grace Consulting, A-402 Hannam Riverhill, 390 Hannam-dong, Youngsan-ku, Seoul, 140-210, South Korea
| | - Ward Fleri
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Mitch Kronenberg
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Ralph Kubo
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Ole Lund
- BioCentrum-DTU, Technical University of Denmark, Building 208, Lyngby, 2800, Denmark
| | - David Nemazee
- Department of Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, IMM-29, La Jolla, CA, 92037, USA
| | | | - Muthu Sathiamurthy
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Stephen P. Schoenberger
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Scott Stewart
- Science Applications International Corporation, 9455 Towne Center Drive, MS-W2, San Diego, CA, 92121, USA
| | - Pamela Surko
- Science Applications International Corporation, 9455 Towne Center Drive, MS-W2, San Diego, CA, 92121, USA
| | - Scott Way
- Science Applications International Corporation, 9455 Towne Center Drive, MS-W2, San Diego, CA, 92121, USA
| | - Steve Wilson
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
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Kloetzel PM. The proteasome and MHC class I antigen processing. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1695:225-33. [PMID: 15571818 DOI: 10.1016/j.bbamcr.2004.10.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
By generating peptides from intracellular antigens, which are then presented to T cells, the ubiquitin/26S proteasome system plays a central role in the cellular immune response. Under the control of interferon-gamma the proteolytic properties of the proteasome are adapted to the requirements of the immune system. Interferon-gamma induces the formation of immunoproteasomes and the synthesis of the proteasome activator PA28. Both alter the proteolytic properties of the proteasome complex and enhance proteasomal function in antigen presentation. Thus, a combination of several of regulatory events tunes the proteasome system for maximal efficiency in the generation of MHC class I antigens.
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Affiliation(s)
- Peter-M Kloetzel
- Institut für Biochemie, Charité, Medizinische Fakultät der Humboldt-Universität zu Berlin, Monbijoust.2, 10117 Berlin, Germany.
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Craven RA, Stanley AJ, Hanrahan S, Totty N, Jackson DP, Popescu R, Taylor A, Frey J, Selby PJ, Patel PM, Banks RE. Identification of proteins regulated by interferon-? in resistant and sensitive malignant melanoma cell lines. Proteomics 2004; 4:3998-4009. [PMID: 15449380 DOI: 10.1002/pmic.200400870] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Treatment of patients with malignant melanoma with interferon-alpha achieves a response in a small but significant subset of patients. Currently, although much is known about interferon biology, little is known about either the particular mechanisms of interferon-alpha activity that are crucial for response or why only some patients respond to interferon-alpha therapy. Two melanoma cell lines (MeWo and MM418) that are known to differ in their response to the antiproliferative activity of interferon-alpha, have been used as a model system to investigate interferon-alpha action. Using a proteomics approach based on two-dimensional polyacrylamide gel electrophoresis and mass spectrometry, several proteins induced in response to interferon-alpha have been identified. These include a number of gene products previously known to be type I interferon responsive (tryptophanyl tRNA synthetase, leucine aminopeptidase, ubiquitin cross-reactive protein, gelsolin, FUSE binding protein 2 and hPNPase) as well as a number of proteins not previously reported to be induced by type I interferon (cathepsin B, proteasomal activator 28alpha and alpha-SNAP). Although the proteins upregulated by interferon-alpha were common between the cell lines when examined at the level of Western blotting, the disparity in the basal level of cathepsin B was striking, raising the possibility that the higher level in MM418 may contribute to the sensitivity of this cell line to interferon-alpha treatment.
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Affiliation(s)
- Rachel A Craven
- Cancer Research UK Clinical Centre, St. James's University Hospital, Leeds, UK
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39
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Petrovsky N, Brusic V. Virtual models of the HLA class I antigen processing pathway. Methods 2004; 34:429-35. [PMID: 15542368 DOI: 10.1016/j.ymeth.2004.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2004] [Indexed: 11/24/2022] Open
Abstract
Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class I binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify HLA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies.
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Affiliation(s)
- Nikolai Petrovsky
- Autoimmunity Research Unit, The Canberra Hospital, ACT 2606, Australia.
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40
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Doytchinova I, Hemsley S, Flower DR. Transporter Associated with Antigen Processing Preselection of Peptides Binding to the MHC: A Bioinformatic Evaluation. THE JOURNAL OF IMMUNOLOGY 2004; 173:6813-9. [PMID: 15557175 DOI: 10.4049/jimmunol.173.11.6813] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
TAP is responsible for the transit of peptides from the cytosol to the lumen of the endoplasmic reticulum. In an immunological context, this event is followed by the binding of peptides to MHC molecules before export to the cell surface and recognition by T cells. Because TAP transport precedes MHC binding, TAP preferences may make a significant contribution to epitope selection. To assess the impact of this preselection, we have developed a scoring function for TAP affinity prediction using the additive method, have used it to analyze and extend the TAP binding motif, and have evaluated how well this model acts as a preselection step in predicting MHC binding peptides. To distinguish between MHC alleles that are exclusively dependent on TAP and those exhibiting only a partial dependence on TAP, two sets of MHC binding peptides were examined: HLA-A*0201 was selected as a representative of partially TAP-dependent HLA alleles, and HLA-A*0301 represented fully TAP-dependent HLA alleles. TAP preselection has a greater impact on TAP-dependent alleles than on TAP-independent alleles. The reduction in the number of nonbinders varied from 10% (TAP-independent) to 33% (TAP-dependent), suggesting that TAP preselection is an important component in the successful in silico prediction of T cell epitopes.
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Affiliation(s)
- Irini Doytchinova
- Edward Jenner Institute for Vaccine Research, Compton, Berkshire, United Kingdom
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Kim R, Emi M, Tanabe K, Uchida Y, Toge T. The role of Fas ligand and transforming growth factor beta in tumor progression: molecular mechanisms of immune privilege via Fas-mediated apoptosis and potential targets for cancer therapy. Cancer 2004; 100:2281-91. [PMID: 15160330 DOI: 10.1002/cncr.20270] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the fact that expression of Fas ligand (FasL) in cytotoxic T lymphocytes (CTLs) and in natural killer (NK) cells plays an important role in Fas-mediated tumor killing, During tumor progression FasL-expressing tumor cells are involved in counterattacking to kill tumor-infiltrating lymphocytes (TILs). Soluble FasL levels also increase with tumor progression in solid tumors, and this increase inhibits Fas-mediated tumor killing by CTLs and NK cells. The increased expression of FasL in tumor cells is associated with decreased expression of Fas; and the promoter region of the FASL gene is regulated by transcription factors, such as neuronal factor kappaB (NF-kappaB) and AP-1, in the tumor microenvironment. Although the ratio of FasL expression to Fas expression in tumor cells is not strongly related to the induction of apoptosis in TILs, increased expression of FasL is associated with decreased Fas levels in tumor cells that can escape immune surveillance and facilitate tumor progression and metastasis. Transforming growth factor beta (TGF-beta) is a potent growth inhibitor and has tumor-suppressing activity in the early phases of carcinogenesis. During subsequent tumor progression, the increased secretion of TGF-beta by both tumor cells and, in a paracrine fashion, stromal cells, is involved in the enhancement of tumor invasion and metastasis accompanied by immunosuppression. Herein, the authors review the clinical significance of FasL and TGF-beta expression patterns as features of immune privilege accompanying tumor progression in the tumor microenvironment. Potential strategies for identifying which molecules can serve as targets for effective antitumor therapy also are discussed.
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Affiliation(s)
- Ryungsa Kim
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.
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42
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Hickman HD, Luis AD, Buchli R, Few SR, Sathiamurthy M, VanGundy RS, Giberson CF, Hildebrand WH. Toward a definition of self: proteomic evaluation of the class I peptide repertoire. THE JOURNAL OF IMMUNOLOGY 2004; 172:2944-52. [PMID: 14978097 DOI: 10.4049/jimmunol.172.5.2944] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
MHC class I molecules present host- and pathogen-derived peptides for immune surveillance. Much attention is given to the search for viral and tumor nonself peptide epitopes, yet the question remains, "What is self?" Analyses of Edman motifs and of small sets of individual peptides suggest that the class I self repertoire consists of thousands of different peptides. However, there exists no systematic characterization of this self-peptide backdrop, causing the definition of class I-presented self to remain largely hypothetical. To better understand the breadth and nature of self proteins sampled by class I HLA, we sequenced >200 endogenously loaded HLA-B*1801 peptides from a human B cell line. Peptide-source proteins, ranging from actin-related protein 6 to zinc finger protein 147, possessed an assortment of biological and molecular functions. Major categories included binding proteins, catalytic proteins, and proteins involved in cell metabolism, growth, and maintenance. Genetically, peptides encoded by all chromosomes were presented. Statistical comparison of proteins presented by class I vs the human proteome provides empiric evidence that the range of proteins sampled by class I is relatively unbiased, with the exception of RNA-binding proteins that are over-represented in the class I peptide repertoire. These data show that, in this cell line, class I-presented self peptides represent a comprehensive and balanced summary of the proteomic content of the cell. Importantly, virus- and tumor-induced changes in virtually any cellular compartment or to any chromosome can be expected to be presented by class I molecules for immune recognition.
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Affiliation(s)
- Heather D Hickman
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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43
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Wang HX, Wang HM, Li QL, Lin HY, Qian D, Zhu C. Expression of proteasome subunits low molecular mass polypeptide (LMP) 2 and LMP7 in the endometrium and placenta of rhesus monkey (Macaca mulatta) during early pregnancy. Biol Reprod 2004; 71:1317-24. [PMID: 15201202 DOI: 10.1095/biolreprod.104.030213] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Previous studies have demonstrated that the ubiquitin-proteasome pathway plays an important role in embryo implantation. Low molecular mass polypeptide (LMP) 2 and LMP7 are the two subunits of 20S proteasome, which are critical for proteasome activity. To further elucidate the roles of LMP2 and LMP7 in embryo implantation during early pregnancy, we cloned partial sequences of the LMP2 and LMP7 genes and studied the spatiotemporal expression of LMP2 and LMP7 in rhesus monkey (Macaca mulatta) uteri on Days 12, 18, and 26 of pregnancy. The results showed that the 349-base pair (bp) LMP2 fragment and the 340-bp LMP7 fragment were 97% and 99% identical, respectively, to those of human homologues. From the statistical results of reverse transcription-polymerase chain reaction, in situ hybridization, and immunohistochemistry, we found that the expression levels of LMP2 and LMP7 significantly increased with the elongation of pregnancy. The LMP2 and LMP7 mRNAs were mainly expressed in the luminal and glandular epithelium on Day 12 of pregnancy. On Days 18 and 26 of pregnancy, strong signals of LMP2 and LMP7 mRNAs were detected in the placental villi, trophoblastic column, and arterial endothelial cells close to the implantation site, and moderate expressions were found in the trophoblastic shell and glandular epithelium. The LMP2 and LMP7 mRNAs were extensively distributed in the stroma on Day 26 of pregnancy. The expression patterns of LMP2 and LMP7 proteins were similar to those of their transcripts, but weak immunostaining of LMP2 and LMP7 proteins was detected in stroma at all stages of pregnancy. These results suggest that LMP2 and LMP7 may be involved in some key processes of trophoblastic invasion, angiogenesis, degradation of the extracellular matrix, immune tolerance, and glandular secretion.
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Affiliation(s)
- Hong-Xing Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
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44
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Chen L, Jondal M. Endolysosomal Processing of Exogenous Antigen into Major Histocompatibility Complex Class I-Binding Peptides. Scand J Immunol 2004; 59:545-52. [PMID: 15182249 DOI: 10.1111/j.1365-3083.2004.01426.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An alternative endolysosomal pathway has recently been suggested for the processing of MHC-I-binding peptides, and peptide/MHC-I complexes have been demonstrated in this compartment. However, it remains unclear where in the antigen-presenting cells such peptides are processed, in the endolysosomes themselves or in the proteasomal complex. Here, we have investigated this using monoclonal antibodies specific for the immunodominant SIINFEKL/Kb complex (25-D1) or for the carbohydrate part of Db- or Kb-binding glycopeptides in combination with inhibitors for classical and endolysosomal MHC-I-processing pathways. Alternative processing was detected in both wt and TAP1(-/-) immature DC (iDC) as the expression of SIINFEKL/Kb complexes on the surface of OVA-treated cells in the presence of Brefeldin A (BFA) or lactacystin and their absence in the presence of the lysosomotropic amines ammonium chloride, chloroquine and methylamine. Internalized Db- and Kb-binding glycopeptides, detected with high specificity using an anti-galabiose (Gal2) monoclonal antibody, were found to appear on the cell surface of BFA-treated cells after intracellular MHC-I-binding. Peptide exchange in Kb was demonstrated as the gradual appearance of SIINFEKL/Kb complexes on BFA-treated cells which earlier had been saturated with another Kb-binding peptide. Our data support the presence of a fully functional endolysosomal processing pathway in iDC guided by the chaperone function of MHC-I molecules.
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Affiliation(s)
- L Chen
- Microbiology and Tumor Biology Center, Karolinska Institutet, Stockholm, Sweden
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Teoh CY, Davies KJA. Potential roles of protein oxidation and the immunoproteasome in MHC class I antigen presentation: the 'PrOxI' hypothesis. Arch Biochem Biophys 2004; 423:88-96. [PMID: 14871471 DOI: 10.1016/j.abb.2003.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Revised: 12/01/2003] [Indexed: 10/26/2022]
Abstract
The major histocompatibility complex (MHC) class I (MHC-I) antigen presentation system is responsible for the cell-surface presentation of self-proteins and intracellular viral proteins. This pathway is important in screening between self, and non-self or infected cells. In this pathway, proteins are partially degraded to peptides in the cytosol and targeted to the cell surface bound to an MHC-I receptor protein. At the cell surface, T cells bypass cells displaying self-peptides but destroy others displaying foreign antigens. Cells contain several isoforms of the proteasome, but it is thought that the immunoproteasome is the major form involved in generating peptides for the MHC-I pathway. How all intracellular proteins are targeted for MHC-I processing is unclear. Oxidative stress is experienced by all cells, and all proteins are exposed to oxidation. We propose that oxidative modification makes proteins susceptible to degradation by the immunoproteasome. This could be called the protein oxidation and immunoproteasome or 'PrOxI' hypothesis of MHC-I antigen processing. Protein oxidation may, thus, be a universal mechanism for peptide generation and presentation in the MHC-I pathway.
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Affiliation(s)
- Cheryl Y Teoh
- Ethel Percy Andrus Gerontology Center and Division of Molecular and Computational Biology, The University of Southern California, Los Angeles, CA 90089-0191, USA
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Atkins D, Breuckmann A, Schmahl GE, Binner P, Ferrone S, Krummenauer F, Störkel S, Seliger B. MHC class I antigen processing pathway defects, ras mutations and disease stage in colorectal carcinoma. Int J Cancer 2004; 109:265-73. [PMID: 14750179 DOI: 10.1002/ijc.11681] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Colorectal tumorigenesis has been associated with the progressive acquisition of a variety of genetic alterations. These include mutations of the Ki-ras proto-oncogene in codons 12 and 13, which account for 85% of genetic changes in colorectal cancer. In murine in vitro models of oncogenic transformation, an association between ras-mediated transformation and downregulation of different components of the MHC class I antigen processing machinery (APM) has been described. In order to investigate whether this association also exists in human tumors, 10 cases of high-grade intraepithelial neoplasia (HIN), as well as primary tumors and autologous lymph node metastases from 42 patients with colorectal carcinoma, were monitored by allele-specific restriction analysis for Ki-ras mutations. In parallel, APM component expression and tumor cell proliferation were analyzed by immunohistochemistry. In comparison to autologous colorectal mucosa, TAP1, LMP2 and tapasin loss was found in 68%, 67% and 80% of HIN, respectively. In contrast, impaired TAP1, LMP2 and tapasin expression was found in 42%, 42% and 63% of primary adenocarcinomas of stage III disease and in 63%, 47% and 79% of the matched lymph node metastases, respectively. More than 60% of colorectal tumor lesions with TAP1, LMP2 and/or tapasin defects displayed Ki-ras mutations. The frequency of TAP1, LMP2 and tapasin loss varied between 33% of primary adenocarcinomas, 40% of HIN to approximately 67% of metastases. These data suggest that i) APM component deficiencies occur more frequently in Ki-ras-mutated colorectal carcinoma lesions and ii) APM abnormalities in conjunction with Ki-ras mutations appear to be associated with disease stage. These findings support the hypothesis that Ki-ras mutations may contribute to immune escape mechanisms of tumors by downregulating the MHC class I APM component expression.
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Affiliation(s)
- Derek Atkins
- Johannes Gutenberg-University, Third Department of Internal Medicine, Mainz, Germany.
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Krüger E, Kuckelkorn U, Sijts A, Kloetzel PM. The components of the proteasome system and their role in MHC class I antigen processing. Rev Physiol Biochem Pharmacol 2004; 148:81-104. [PMID: 12687403 DOI: 10.1007/s10254-003-0010-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
By generating peptides from intracellular antigens which are then presented to T cells, the ubiquitin/26S proteasome system plays a central role in the cellular immune response. The proteolytic properties of the proteasome are adapted to the requirements of the immune system by proteasome components whose synthesis is under the control of interferon-gamma. Among these are three subunits with catalytic sites that are incorporated into the enzyme complex during its de novo synthesis. Thus, the proteasome assembly pathway and the formation of immunoproteasomes play a critical regulatory role in the regulation of the proteasome's catalytic properties. In addition, interferon-gamma also induces the synthesis of the proteasome activator PA28 which, as part of the so-called hybrid proteasome, exerts a more selective function in antigen presentation. Consequently, the combination of a number of regulatory events tunes the proteasome system to gain maximal efficiency in the generation of peptides with regard to their quality and quantity.
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Affiliation(s)
- E Krüger
- Institut für Biochemie, Medizinische Fakultät, Humboldt-Universität zu Berlin, Charité, Monbijoust 2, 10117 Berlin, Germany
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48
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Abstract
As torrents of new data now emerge from microbial genomics, bioinformatic prediction of immunogenic epitopes remains challenging but vital. In silico methods often produce paradoxically inconsistent results: good prediction rates on certain test sets but not others. The inherent complexity of immune presentation and recognition processes complicates epitope prediction. Two encouraging developments - data driven artificial intelligence sequence-based methods for epitope prediction and molecular modeling methods based on three-dimensional protein structures - offer hope for the future.
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Affiliation(s)
- Darren R Flower
- Edward Jenner Institute for Vaccine Research, Compton, RG20 7NN, Berkshire, UK.
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Bland FA, Lemberg MK, McMichael AJ, Martoglio B, Braud VM. Requirement of the proteasome for the trimming of signal peptide-derived epitopes presented by the nonclassical major histocompatibility complex class I molecule HLA-E. J Biol Chem 2003; 278:33747-52. [PMID: 12821659 DOI: 10.1074/jbc.m305593200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nonclassical major histocompatibility complex class I molecule HLA-E acts as a ligand for CD94/NKG2 receptors on the surface of natural killer cells and a subset of T cells. HLA-E presents closely related nonameric peptide epitopes derived from the highly conserved signal sequences of classical major histocompatibility complex class I molecules as well as HLA-G. Their generation requires cleavage of the signal sequence by signal peptidase followed by the intramembrane-cleaving aspartic protease, signal peptide peptidase. In this study, we have assessed the subsequent proteolytic requirements leading to generation of the nonameric HLA-E peptide epitopes. We show that proteasome activity is required for further processing of the peptide generated by signal peptide peptidase. This constitutes the first example of capture of a naturally derived short peptide by the proteasome, producing a class I peptide ligand.
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Affiliation(s)
- Felicity A Bland
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
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Tanioka T, Hattori A, Masuda S, Nomura Y, Nakayama H, Mizutani S, Tsujimoto M. Human leukocyte-derived arginine aminopeptidase. The third member of the oxytocinase subfamily of aminopeptidases. J Biol Chem 2003; 278:32275-83. [PMID: 12799365 DOI: 10.1074/jbc.m305076200] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study we report the cloning and characterization of a novel human aminopeptidase, which we designate leukocyte-derived arginine aminopeptidase (L-RAP). The sequence encodes a 960-amino acid protein with significant homology to placental leucine aminopeptidase and adipocyte-derived leucine aminopeptidase. The predicted L-RAP contains the HEXXH(X)18E zinc-binding motif, which is characteristic of the M1 family of zinc metallopeptidases. Phylogenetic analysis indicates that L-RAP forms a distinct subfamily with placental leucine aminopeptidase and adipocyte-derived leucine aminopeptidase in the M1 family. Immunocytochemical analysis indicates that L-RAP is located in the lumenal side of the endoplasmic reticulum. Among various synthetic substrates tested, L-RAP revealed a preference for arginine, establishing that the enzyme is a novel arginine aminopeptidase with restricted substrate specificity. In addition to natural hormones such as angiotensin III and kallidin, L-RAP cleaved various N-terminal extended precursors to major histocompatibility complex class I-presented antigenic peptides. Like other proteins involved in antigen presentation, L-RAP is induced by interferon-gamma. These results indicate that L-RAP is a novel aminopeptidase that can trim the N-terminal extended precursors to antigenic peptides in the endoplasmic reticulum.
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Affiliation(s)
- Toshihiro Tanioka
- Laboratory of Cellular Biochemistry, RIKEN, Wako-shi, Saitama 351-0198, Japan
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