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Title: ERAP1 enzyme-mediated trimming and structural analyses of MHC I–bound precursor peptides yield novel insights into antigen processing and presentation

Abstract

Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 critically shape the major histocompatibility complex I (MHC I) immunopeptidome. The ERAPs remove N-terminal residues from antigenic precursor peptides and generate optimal-length peptides (i.e. 8–10-mers) to fit into the MHC class I groove. It is therefore intriguing that MHC class I molecules can present N-terminally extended peptides on the cell surface that can elicit CD8+ T-cell responses. This observation likely reflects gaps in our understanding of how antigens are processed by the ERAP enzymes. To better understand ERAPs' function in antigen processing, here we generated a nested set of N-terminally extended 10–20-mer peptides (RA)nAAKKKYCL covalently bound to the human leukocyte antigen (HLA)-B*0801. We used X-ray crystallography, thermostability assessments, and an ERAP1-trimming assay to characterize these complexes. The X-ray structures determined at 1.40–1.65 Å resolutions revealed that the residue extensions (RA)n unexpectedly protrude out of the A pocket of HLA-B*0801, whereas the AAKKKYCL core of all peptides adopts similar, bound conformations. HLA-B*0801 residue 62 was critical to open the A pocket. We also show that HLA-B*0801 and antigenic precursor peptides form stable complexes. Finally, ERAP1-mediated trimming of the MHC I–bound peptides required a minimal length of 14 amino acids. We propose a mechanistic modelmore » explaining how ERAP1-mediated trimming of MHC I–bound peptides in cells can generate peptides of canonical as well as noncanonical lengths that still serve as stable MHC I ligands. Our results provide a framework to better understand how the ERAP enzymes influence the MHC I immunopeptidome.« less

Authors:
ORCiD logo [1];  [1]; ORCiD logo [1]
  1. Univ. of Illinois, Chicago, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Inst. of Health
OSTI Identifier:
1591907
Grant/Contract Number:  
R01 AI114467; R01 AI108546
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 294; Journal Issue: 49; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; immunology; antigen presentation; antigen processing; structural biology; endoplasmic reticulum (ER); CD8+ T cells; endoplasmic reticulum aminopeptidase (ERAP); immunopeptidome; major histocompatibility complex I (MHC I); adaptive immunity; HLA-B*0801

Citation Formats

Li, Lenong, Batliwala, Mansoor, and Bouvier, Marlene. ERAP1 enzyme-mediated trimming and structural analyses of MHC I–bound precursor peptides yield novel insights into antigen processing and presentation. United States: N. p., 2019. Web. https://doi.org/10.1074/jbc.RA119.010102.
Li, Lenong, Batliwala, Mansoor, & Bouvier, Marlene. ERAP1 enzyme-mediated trimming and structural analyses of MHC I–bound precursor peptides yield novel insights into antigen processing and presentation. United States. https://doi.org/10.1074/jbc.RA119.010102
Li, Lenong, Batliwala, Mansoor, and Bouvier, Marlene. Thu . "ERAP1 enzyme-mediated trimming and structural analyses of MHC I–bound precursor peptides yield novel insights into antigen processing and presentation". United States. https://doi.org/10.1074/jbc.RA119.010102. https://www.osti.gov/servlets/purl/1591907.
@article{osti_1591907,
title = {ERAP1 enzyme-mediated trimming and structural analyses of MHC I–bound precursor peptides yield novel insights into antigen processing and presentation},
author = {Li, Lenong and Batliwala, Mansoor and Bouvier, Marlene},
abstractNote = {Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 critically shape the major histocompatibility complex I (MHC I) immunopeptidome. The ERAPs remove N-terminal residues from antigenic precursor peptides and generate optimal-length peptides (i.e. 8–10-mers) to fit into the MHC class I groove. It is therefore intriguing that MHC class I molecules can present N-terminally extended peptides on the cell surface that can elicit CD8+ T-cell responses. This observation likely reflects gaps in our understanding of how antigens are processed by the ERAP enzymes. To better understand ERAPs' function in antigen processing, here we generated a nested set of N-terminally extended 10–20-mer peptides (RA)nAAKKKYCL covalently bound to the human leukocyte antigen (HLA)-B*0801. We used X-ray crystallography, thermostability assessments, and an ERAP1-trimming assay to characterize these complexes. The X-ray structures determined at 1.40–1.65 Å resolutions revealed that the residue extensions (RA)n unexpectedly protrude out of the A pocket of HLA-B*0801, whereas the AAKKKYCL core of all peptides adopts similar, bound conformations. HLA-B*0801 residue 62 was critical to open the A pocket. We also show that HLA-B*0801 and antigenic precursor peptides form stable complexes. Finally, ERAP1-mediated trimming of the MHC I–bound peptides required a minimal length of 14 amino acids. We propose a mechanistic model explaining how ERAP1-mediated trimming of MHC I–bound peptides in cells can generate peptides of canonical as well as noncanonical lengths that still serve as stable MHC I ligands. Our results provide a framework to better understand how the ERAP enzymes influence the MHC I immunopeptidome.},
doi = {10.1074/jbc.RA119.010102},
journal = {Journal of Biological Chemistry},
number = 49,
volume = 294,
place = {United States},
year = {2019},
month = {10}
}

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Works referenced in this record:

ERAP1-ERAP2 dimers trim MHC I-bound precursor peptides; implications for understanding peptide editing
journal, August 2016

  • Chen, Hanna; Li, Lenong; Weimershaus, Mirjana
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep28902

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition
journal, December 1991

  • Phillips, Rodney E.; Rowland-Jones, Sarah; Nixon, Douglas F.
  • Nature, Vol. 354, Issue 6353
  • DOI: 10.1038/354453a0

The C-terminal extension landscape of naturally presented HLA-I ligands
journal, April 2018

  • Guillaume, Philippe; Picaud, Sarah; Baumgaertner, Petra
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 20
  • DOI: 10.1073/pnas.1717277115

Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection
journal, March 2007


Tapasin enhances MHC class I peptide presentation according to peptide half-life
journal, July 2004

  • Howarth, M.; Williams, A.; Tolstrup, A. B.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 32
  • DOI: 10.1073/pnas.0306294101

Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle
journal, November 1992

  • Guo, Hwai-Chen; Jardetzky, Theodore S.; Garrettt, Thomas P. J.
  • Nature, Vol. 360, Issue 6402
  • DOI: 10.1038/360364a0

Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation
journal, October 2010


Crystal structure of HLA-B*5801 with a TW10 HIV Gag epitope reveals a novel mode of peptide presentation
journal, May 2017

  • Li, Xiaolong; Lamothe, Pedro A.; Walker, Bruce D.
  • Cellular & Molecular Immunology, Vol. 14, Issue 7
  • DOI: 10.1038/cmi.2017.24

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape
journal, February 2017

  • Pymm, Phillip; Illing, Patricia T.; Ramarathinam, Sri H.
  • Nature Structural & Molecular Biology, Vol. 24, Issue 4
  • DOI: 10.1038/nsmb.3381

HLA Peptide Length Preferences Control CD8 + T Cell Responses
journal, June 2013

  • Rist, Melissa J.; Theodossis, Alex; Croft, Nathan P.
  • The Journal of Immunology, Vol. 191, Issue 2
  • DOI: 10.4049/jimmunol.1300292

Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses
journal, July 2016

  • Rucevic, Marijana; Kourjian, Georgio; Boucau, Julie
  • Journal of Virology, Vol. 90, Issue 19
  • DOI: 10.1128/JVI.00599-16

MHC‐restricted Ag85B‐specific CD8 + T cells are enhanced by recombinant BCG prime and DNA boost immunization in mice
journal, June 2019

  • Komine‐Aizawa, Shihoko; Jiang, Jiansheng; Mizuno, Satoru
  • European Journal of Immunology, Vol. 49, Issue 9
  • DOI: 10.1002/eji.201847988

Mechanisms of Function of Tapasin, a Critical Major Histocompatibility Complex Class I Assembly Factor
journal, March 2010


Naturally Processed Non-canonical HLA-A*02:01 Presented Peptides
journal, December 2014

  • Hassan, Chopie; Chabrol, Eric; Jahn, Lorenz
  • Journal of Biological Chemistry, Vol. 290, Issue 5
  • DOI: 10.1074/jbc.M114.607028

Three-dimensional structure of a peptide extending from one end of a class I MHC binding site
journal, October 1994

  • Collins, Edward J.; Garboczi, David N.; Wiley, Don C.
  • Nature, Vol. 371, Issue 6498
  • DOI: 10.1038/371626a0

Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT
journal, February 2017

  • Remesh, Soumya G.; Andreatta, Massimo; Ying, Ge
  • Journal of Biological Chemistry, Vol. 292, Issue 13
  • DOI: 10.1074/jbc.M117.776542

Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group
journal, October 1998


Structure of the human MHC-I peptide-loading complex
journal, November 2017

  • Blees, Andreas; Januliene, Dovile; Hofmann, Tommy
  • Nature, Vol. 551, Issue 7681
  • DOI: 10.1038/nature24627

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family
journal, October 2010


A Structural Basis for LCMV Immune Evasion
journal, December 2002


Conformational Flexibility of the MHC Class I α1-α2 Domain in Peptide Bound and Free States: A Molecular Dynamics Simulation Study
journal, October 2004


The first step of peptide selection in antigen presentation by MHC class I molecules
journal, January 2015

  • Garstka, Malgorzata A.; Fish, Alexander; Celie, Patrick H. N.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 5
  • DOI: 10.1073/pnas.1416543112

Present Yourself! By MHC Class I and MHC Class II Molecules
journal, November 2016


ERAAP Synergizes with MHC Class I Molecules to Make the Final Cut in the Antigenic Peptide Precursors in the Endoplasmic Reticulum
journal, November 2006


Large Scale Mass Spectrometric Profiling of Peptides Eluted from HLA Molecules Reveals N-Terminal-Extended Peptide Motifs
journal, September 2008

  • Escobar, Hernando; Crockett, David K.; Reyes-Vargas, Eduardo
  • The Journal of Immunology, Vol. 181, Issue 7
  • DOI: 10.4049/jimmunol.181.7.4874

Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance
journal, May 2009

  • Tenzer, Stefan; Wee, Edmund; Burgevin, Anne
  • Nature Immunology, Vol. 10, Issue 6
  • DOI: 10.1038/ni.1728

Conformational Restraints and Flexibility of 14-Meric Peptides in Complex with HLA-B*3501
journal, October 2004

  • Probst-Kepper, Michael; Hecht, Hans-Jürgen; Herrmann, Hanne
  • The Journal of Immunology, Vol. 173, Issue 9
  • DOI: 10.4049/jimmunol.173.9.5610

Two Polymorphisms Facilitate Differences in Plasticity between Two Chicken Major Histocompatibility Complex Class I Proteins
journal, February 2014


Concerted peptide trimming by human ERAP1 and ERAP2 aminopeptidase complexes in the endoplasmic reticulum
journal, May 2005

  • Saveanu, Loredana; Carroll, Oliver; Lindo, Vivian
  • Nature Immunology, Vol. 6, Issue 7
  • DOI: 10.1038/ni1208

The Length Distribution of Class I–Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele–Specific Binding Preference
journal, January 2016

  • Trolle, Thomas; McMurtrey, Curtis P.; Sidney, John
  • The Journal of Immunology, Vol. 196, Issue 4
  • DOI: 10.4049/jimmunol.1501721

HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides.
journal, April 1992

  • Garboczi, D. N.; Hung, D. T.; Wiley, D. C.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 8
  • DOI: 10.1073/pnas.89.8.3429

Structure of the TAPBPR–MHC I complex defines the mechanism of peptide loading and editing
journal, October 2017


Crystal structure of a TAPBPR–MHC I complex reveals the mechanism of peptide editing in antigen presentation
journal, October 2017


Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1
journal, April 2011

  • Nguyen, Tina T.; Chang, Shih-Chung; Evnouchidou, Irini
  • Nature Structural & Molecular Biology, Vol. 18, Issue 5
  • DOI: 10.1038/nsmb.2021

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

An Endogenous HIV Envelope-derived Peptide without the Terminal NH 3 + Group Anchor Is Physiologically Presented by Major Histocompatibility Complex Class I Molecules
journal, October 2003

  • Samino, Yolanda; López, Daniel; Guil, Sara
  • Journal of Biological Chemistry, Vol. 279, Issue 2
  • DOI: 10.1074/jbc.M305343200

Selective loading of high-affinity peptides onto major histocompatibility complex class I molecules by the tapasin-ERp57 heterodimer
journal, July 2007

  • Wearsch, Pamela A.; Cresswell, Peter
  • Nature Immunology, Vol. 8, Issue 8
  • DOI: 10.1038/ni1485

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Cellular peptide composition governed by major histocompatibility complex class I molecules
journal, November 1990

  • Falk, Kirsten; Rötzschke, Olaf; Rammensee, Hans-Georg
  • Nature, Vol. 348, Issue 6298
  • DOI: 10.1038/348248a0

The aminopeptidase ERAAP shapes the peptide repertoire displayed by major histocompatibility complex class I molecules
journal, November 2005

  • Hammer, Gianna Elena; Gonzalez, Federico; Champsaur, Marine
  • Nature Immunology, Vol. 7, Issue 1
  • DOI: 10.1038/ni1286

The Three-Dimensional Structure of Peptide-MHC Complexes
journal, April 1995


Antagonist HIV-1 Gag Peptides Induce Structural Changes in HLA B8
journal, December 1996

  • Reid, Scott W.; McAdam, Steve; Smith, Kathrine J.
  • The Journal of Experimental Medicine, Vol. 184, Issue 6
  • DOI: 10.1084/jem.184.6.2279

Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules
journal, July 1994


ERAAP and Tapasin Independently Edit the Amino and Carboxyl Termini of MHC Class I Peptides
journal, July 2013

  • Kanaseki, Takayuki; Lind, Kristin Camfield; Escobar, Hernando
  • The Journal of Immunology, Vol. 191, Issue 4
  • DOI: 10.4049/jimmunol.1301043

The partial dissociation of MHC class I–bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1
journal, March 2018

  • Papakyriakou, Athanasios; Reeves, Emma; Beton, Mary
  • Journal of Biological Chemistry, Vol. 293, Issue 20
  • DOI: 10.1074/jbc.RA117.000313

Naturally Occurring ERAP1 Haplotypes Encode Functionally Distinct Alleles with Fine Substrate Specificity
journal, June 2013

  • Reeves, Emma; Edwards, Christopher J.; Elliott, Tim
  • The Journal of Immunology, Vol. 191, Issue 1
  • DOI: 10.4049/jimmunol.1300598

Proofreading of Peptide—MHC Complexes through Dynamic Multivalent Interactions
journal, February 2017


NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995

  • Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
  • Journal of Biomolecular NMR, Vol. 6, Issue 3
  • DOI: 10.1007/BF00197809

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove
journal, January 2016


The Energetic Basis Underpinning T-cell Receptor Recognition of a Super-bulged Peptide Bound to a Major Histocompatibility Complex Class I Molecule
journal, February 2012

  • Liu, Yu Chih; Chen, Zhenjun; Burrows, Scott R.
  • Journal of Biological Chemistry, Vol. 287, Issue 15
  • DOI: 10.1074/jbc.M112.344689

ERAP1–ERAP2 Dimerization Increases Peptide-Trimming Efficiency
journal, June 2014

  • Evnouchidou, Irini; Weimershaus, Mirjana; Saveanu, Loredana
  • The Journal of Immunology, Vol. 193, Issue 2
  • DOI: 10.4049/jimmunol.1302855

Peptide trimming by endoplasmic reticulum aminopeptidases: Role of MHC class I binding and ERAP dimerization
journal, May 2019


Have we cut ourselves too short in mapping CTL epitopes?
journal, January 2006

  • Burrows, Scott R.; Rossjohn, Jamie; McCluskey, James
  • Trends in Immunology, Vol. 27, Issue 1
  • DOI: 10.1016/j.it.2005.11.001

Direct Interrogation of Viral Peptides Presented by the Class I HLA of HIV-Infected T Cells
journal, August 2014

  • Yaciuk, J. C.; Skaley, M.; Bardet, W.
  • Journal of Virology, Vol. 88, Issue 22
  • DOI: 10.1128/JVI.01914-14

Human Leukocyte Antigen F Presents Peptides and Regulates Immunity through Interactions with NK Cell Receptors
journal, June 2017


How ERAP1 and ERAP2 Shape the Peptidomes of Disease-Associated MHC-I Proteins
journal, October 2018


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study
journal, August 2015


    Works referencing / citing this record:

    Cutting antigenic peptides down to size
    journal, December 2019

    • Natarajan, Kannan; Margulies, David H.
    • Journal of Biological Chemistry, Vol. 294, Issue 49
    • DOI: 10.1074/jbc.h119.011803