1
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Kumar Bharathkar S, Stadtmueller BM. Structural and biochemical requirements for secretory component interactions with dimeric Immunoglobulin A. bioRxiv 2024:2023.11.09.566401. [PMID: 38014291 PMCID: PMC10680632 DOI: 10.1101/2023.11.09.566401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Secretory (S) Immunoglobulin (Ig) A is the predominant mucosal antibody that protects host epithelial barriers and promotes microbial homeostasis. SIgA production occurs when plasma cells assemble two copies of monomeric IgA and one joining-chain (JC) to form dimeric (d) IgA, which is bound by the polymeric Ig receptor (pIgR) on the basolateral surface of epithelial cells and transcytosed to the apical surface. There, pIgR is proteolytically cleaved, releasing SIgA, a complex of the dIgA and the pIgR ectodomain, called secretory component (SC). The pIgR's five Ig-like domains (D1-D5) undergo a conformational change upon binding dIgA, ultimately contacting four IgA heavy chains and the JC in SIgA. Here we report structure-based mutational analysis combined with surface plasmon resonance binding assays that identify key residues in mouse SC D1 and D3 that mediate SC binding to dIgA. Residues in D1 CDR3 are likely to initiate binding whereas residues that stabilize the D1-D3 interface are likely to promote the conformation change and stabilize the final SIgA structure. Additionally, we find that the JC's three C-terminal residues play a limited role in dIgA assembly but a significant role in pIgR/SC binding to dIgA. Together results inform new models for the intricate mechanisms underlying IgA transport across epithelia and functions in the mucosa. KEY POINTS The secretory component D1 CDR3 loop plays an important role in binding to dIgA.The formation of SC D1-D3 interface stabilizes SIgA.JC C-terminal residues influence dIgA assembly and mediate pIgR binding to dIgA.
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2
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Lyu M, Malyutin AG, Stadtmueller BM. The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function. Nat Commun 2023; 14:7583. [PMID: 37989996 PMCID: PMC10663602 DOI: 10.1038/s41467-023-43240-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023] Open
Abstract
Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one fragment crystallization (Fc). In addition, many pIgs assemble with a joining-chain (JC); however, the number of monomers and potential to include JC vary with species and heavy chain class. Here, we report the cryo-electron microscopy structure of IgM from a teleost (t) species, which does not encode JC. The structure reveals four tIgM Fcs linked through eight C-terminal tailpieces (Tps), which adopt a single β-sandwich-like domain (Tp assembly) located between two Fcs. Specifically, two of eight heavy chains fold uniquely, resulting in a structure distinct from mammalian IgM, which typically contains five IgM monomers, one JC and a centrally-located Tp assembly. Together with mutational analysis, structural data indicate that pIgs have evolved a range of assembly mechanisms and structures, each likely to support unique antibody effector functions.
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Affiliation(s)
- Mengfan Lyu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrey G Malyutin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
- Takeda Pharmaceuticals, Cambridge, MA, 02139, USA
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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3
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Bharathkar SK, Miller MJ, Stadtmueller BM. Engineered Secretory Immunoglobulin A provides insights on antibody-based effector mechanisms targeting Clostridiodes difficile. bioRxiv 2023:2023.11.08.566291. [PMID: 37986930 PMCID: PMC10659285 DOI: 10.1101/2023.11.08.566291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Secretory (S) Immunoglobin (Ig) A is the predominant mucosal antibody, which mediates host interactions with commensal and pathogenic microbes, including Clostridioides difficile. SIgA adopts a polymeric IgA structure that is bound by secretory component (SC). Despite significance, how SIgA supports diverse effector mechanisms is poorly characterized and SIgA-based therapies nonexistent. We engineered chimeric (c) SIgAs, in which we replaced SC domain D2 with a single domain antibody or a monomeric fluorescent protein, allowing us to investigate and enhance SIgA effector mechanisms. cSIgAs exhibited increased neutralization potency against C. difficile toxins, promoted bacterial clumping and cell rupture, and decreased cytotoxicity. cSIgA also allowed us to visualize and/or quantify C. difficile morphological changes and clumping events. Results reveal mechanisms by which SIgA combats C. difficile infection, demonstrate that cSIgA design can modulate these mechanisms, and demonstrate cSIgA's adaptability to modifications that might target a broad range of antigens and effector mechanisms.
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Affiliation(s)
- Sonya Kumar Bharathkar
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Michael J. Miller
- Carle R. Woese Institute of Genomic Biology
- Department of food science and Human Nutrition, University of Illinois Urbana-Champaign, Illinois 61801 USA
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Carle R. Woese Institute of Genomic Biology
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Liu Q, Stadtmueller BM. SIgA structures bound to Streptococcus pyogenes M4 and human CD89 provide insights into host-pathogen interactions. Nat Commun 2023; 14:6726. [PMID: 37872175 PMCID: PMC10593759 DOI: 10.1038/s41467-023-42469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
Immunoglobulin (Ig) A functions as monomeric IgA in the serum and Secretory (S) IgA in mucosal secretions. Host IgA Fc receptors (FcαRs), including human FcαR1/CD89, mediate IgA effector functions; however, human pathogen Streptococcus pyogenes has evolved surface-protein virulence factors, including M4, that also engage the CD89-binding site on IgA. Despite human mucosa serving as a reservoir for pathogens, SIgA interactions with CD89 and M4 remain poorly understood. Here we report cryo-EM structures of M4-SIgA and CD89-SIgA complexes, which unexpectedly reveal different SIgA-binding stoichiometry for M4 and CD89. Structural data, supporting experiments, and modeling indicate that copies of SIgA bound to S. pyogenes M4 will adopt similar orientations on the bacterium surface and leave one host FcαR binding site open. Results suggest unappreciated functional consequences associated with SIgA binding to host and bacterial FcαRs relevant to understanding host-microbe co-evolution, IgA effector functions and improving the outcomes of group A Streptococcus infection.
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Affiliation(s)
- Qianqiao Liu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA.
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, 61801, USA.
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Donaldson GP, Reis GL, Saad M, Mamede I, Chen G, DelGaudio NL, Zhang D, Aydin B, Harrer CE, Castro TB, Grivennikov S, Reis BS, Stadtmueller BM, Victora GD, Mucida D. Suppression of epithelial proliferation and tumorigenesis by immunoglobulin A. bioRxiv 2023:2023.10.06.561290. [PMID: 37873082 PMCID: PMC10592636 DOI: 10.1101/2023.10.06.561290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Immunoglobulin A (IgA) is the most abundant antibody isotype produced across mammals and plays a specialized role in mucosal homeostasis 1 . Constantly secreted into the lumen of the intestine, IgA binds commensal microbiota to regulate their colonization and function 2,3 , with unclear implications for health. IgA deficiency is common in humans but is difficult to study due to its complex etiology and comorbidities 4-8 . Using genetically and environmentally controlled mice, here we show that IgA-deficient animals have a baseline alteration in the colon epithelium that increases susceptibility to multiple models of colorectal cancer. Transcriptome, imaging, and flow cytometry-based analyses revealed that, in the absence of IgA, colonic epithelial cells induce antibacterial factors and accelerate cell cycling in response to the microbiota. Oral treatment with IgA was sufficient to suppress aberrant epithelial proliferation independently of bacterial binding, suggesting that IgA provides a feedback signal to epithelial cells in parallel with its known roles in microbiome shaping. In a primary colonic organoid culture system, IgA directly suppresses epithelial growth. Conversely, the susceptibility of IgA-deficient mice to colorectal cancer was reversed by Notch inhibition to suppress the absorptive colonocyte developmental program, or by inhibition of the cytokine MIF, the receptor for which was upregulated in stem cells of IgA-deficient animals. These studies demonstrate a homeostatic function for IgA in tempering physiological epithelial responses to microbiota to maintain mucosal health.
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Hockenberry A, Slack E, Stadtmueller BM. License to Clump: Secretory IgA Structure-Function Relationships Across Scales. Annu Rev Microbiol 2023; 77:645-668. [PMID: 37713459 DOI: 10.1146/annurev-micro-032521-041803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
Secretory antibodies are the only component of our adaptive immune system capable of attacking mucosal pathogens topologically outside of our bodies. All secretory antibody classes are (a) relatively resistant to harsh proteolytic environments and (b) polymeric. Recent elucidation of the structure of secretory IgA (SIgA) has begun to shed light on SIgA functions at the nanoscale. We can now begin to unravel the structure-function relationships of these molecules, for example, by understanding how the bent conformation of SIgA enables robust cross-linking between adjacent growing bacteria. Many mysteries remain, such as the structural basis of protease resistance and the role of noncanonical bacteria-IgA interactions. In this review, we explore the structure-function relationships of IgA from the nano- to the metascale, with a strong focus on how the seemingly banal "license to clump" can have potent effects on bacterial physiology and colonization.
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Affiliation(s)
- Alyson Hockenberry
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
- Department of Environmental Systems Science (D-USYS), ETH Zürich, Zürich, Switzerland;
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland;
- Botnar Research Centre for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Beth M Stadtmueller
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA;
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois, Urbana, Illinois, USA
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7
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Lyu M, Malyutin AG, Stadtmueller BM. The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function. bioRxiv 2023:2023.03.29.534771. [PMID: 37034677 PMCID: PMC10081254 DOI: 10.1101/2023.03.29.534771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one fragment crystallization (Fc). In addition, many pIgs assemble with a joining-chain (JC); however, the number of monomers and potential to include JC varies with species and heavy chain class. Here, we report the cryo-electron microscopy structure of IgM from a teleost (t) species, which does not encode JC. The structure revealed four tIgM Fcs linked through eight C-terminal tailpieces (Tps), which adopt a single β-sandwich-like domain (Tp assembly) located between two Fcs. Remarkably, two of eight heavy chains fold uniquely, resulting in a structure distinct from mammalian IgM, which typically contains five IgM monomers, one JC and a centrally-located Tp assembly. Together with mutational analysis, structural data indicate that pIgs have evolved a range of assembly mechanisms and structures, each likely to support unique antibody effector functions.
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Affiliation(s)
- Mengfan Lyu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Andrey G. Malyutin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125 USA
- Present address, Takeda Development Center Americas, San Diego, California 92121
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
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8
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Liu Q, Stadtmueller BM. The Structures of Secretory IgA in complex with Streptococcus pyogenes M4 and human CD89 provide insights on mucosal host-pathogen interactions. bioRxiv 2023:2023.04.21.537878. [PMID: 37662389 PMCID: PMC10473612 DOI: 10.1101/2023.04.21.537878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Immunoglobulin (Ig) A functions as monomeric IgA in the serum and Secretory (S) IgA in mucosal secretions. Host IgA Fc receptors (FcαRs), including human FcαR1/CD89, mediate IgA effector functions; however human pathogen Streptococcus pyogenes has evolved surface-protein virulence factors, including M4, that also engage the CD89 binding site on IgA. Despite human mucosa serving as a reservoir for pathogens, SIgA interactions with CD89 and M4 remain poorly understood. Here we report cryo-EM structures of M4-SIgA and CD89-SIgA complexes, which unexpectedly reveal different SIgA-binding stoichiometry for M4 and CD89. Structural data, supporting experiments, and modeling indicate that copies of SIgA bound to S. pyogenes M4 will adopt similar orientations on the bacterium surface and leave one host FcαR binding site open. Results suggest unappreciated functional consequences associated with SIgA binding to host and bacterial FcαRs relevant to understanding host-microbe co-evolution, IgA effector functions and to improving the outcomes of group A Streptococcus infection.
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Affiliation(s)
- Qianqiao Liu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
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9
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Diefenbacher M, Tan TJC, Bauer DLV, Stadtmueller BM, Wu NC, Brooke CB. Interactions between Influenza A Virus Nucleoprotein and Gene Segment Untranslated Regions Facilitate Selective Modulation of Viral Gene Expression. J Virol 2022; 96:e0020522. [PMID: 35467364 PMCID: PMC9131868 DOI: 10.1128/jvi.00205-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 11/20/2022] Open
Abstract
The influenza A virus (IAV) genome is divided into eight negative-sense, single-stranded RNA segments. Each segment exhibits a unique level and temporal pattern of expression; however, the exact mechanisms underlying the patterns of individual gene segment expression are poorly understood. We previously demonstrated that a single substitution in the viral nucleoprotein (NP:F346S) selectively modulates neuraminidase (NA) gene segment expression while leaving other segments largely unaffected. Given what is currently known about NP function, there is no obvious explanation for how changes in NP can selectively modulate the replication of individual gene segments. In this study, we found that the specificity of this effect for the NA segment is virus strain specific and depends on the untranslated region (UTR) sequences of the NA segment. While the NP:F346S substitution did not significantly alter the RNA binding or oligomerization activities of NP in vitro, it specifically decreased the ability of NP to promote NA segment viral RNA (vRNA) synthesis. In addition to NP residue F346, we identified two other adjacent aromatic residues in NP (Y385 and F479) capable of similarly regulating NA gene segment expression, suggesting a larger role for this domain in gene-segment specific regulation. Our findings reveal a novel role for NP in selective regulation of viral gene segment replication and provide a framework for understanding how the expression patterns of individual viral gene segments can be modulated during adaptation to new host environments. IMPORTANCE Influenza A virus (IAV) is a respiratory pathogen that remains a significant source of morbidity and mortality. Escape from host immunity or emergence into new host species often requires mutations that modulate the functional activities of the viral glycoproteins hemagglutinin (HA) and neuraminidase (NA), which are responsible for virus attachment to and release from host cells, respectively. Maintaining the functional balance between the activities of HA and NA is required for fitness across multiple host systems. Thus, selective modulation of viral gene expression patterns may be a key determinant of viral immune escape and cross-species transmission potential. We identified a novel mechanism by which the viral nucleoprotein (NP) gene can selectively modulate NA segment replication and gene expression through interactions with the segment UTRs. Our work highlights an unexpected role for NP in selective regulation of expression from the individual IAV gene segments.
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Affiliation(s)
- Meghan Diefenbacher
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Timothy J. C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas C. Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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10
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Tan TJC, Yuan M, Kuzelka K, Padron GC, Beal JR, Chen X, Wang Y, Rivera-Cardona J, Zhu X, Stadtmueller BM, Brooke CB, Wilson IA, Wu NC. Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain. Nat Commun 2021; 12:3815. [PMID: 34155209 PMCID: PMC8217500 DOI: 10.1038/s41467-021-24123-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short complementarity-determining region (CDR) H3. Germline-encoded sequence motifs in heavy chain CDRs H1 and H2 have a major function, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, is not clear. Here, we identify two public clonotypes of IGHV3-53/3-66 RBD antibodies with a 9-residue CDR H3 that pair with different light chains. Distinct sequence motifs on CDR H3 are present in the two public clonotypes that seem to be related to differential light chain pairing. Additionally, we show that Y58F is a common somatic hypermutation that results in increased binding affinity of IGHV3-53/3-66 RBD antibodies with a short CDR H3. These results advance understanding of the antibody response to SARS-CoV-2.
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Affiliation(s)
- Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kaylee Kuzelka
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gilberto C Padron
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jacob R Beal
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joel Rivera-Cardona
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
| | - Nicholas C Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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11
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Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol 2021; 6:830-841. [PMID: 34045711 PMCID: PMC7611113 DOI: 10.1038/s41564-021-00911-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2,3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here, we demonstrate this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: a long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase variation4,5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen-specific immunoglobulin A and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of rationally designed oral vaccines, we induced immunoglobulin A responses blocking all of these trajectories. This selected for Salmonella mutants carrying deletions of the O-antigen polymerase gene wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents or complement) and predation (bacteriophages) and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.
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Affiliation(s)
- Médéric Diard
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Zoology, University of Oxford, Oxford, UK
| | - Verena Lentsch
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | | | | | - Daniel Hoces
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Selma Aslani
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Markus Arnoldini
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Flurina Böhi
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zürich, Zürich, Switzerland
| | - Kathrin Schumann-Moor
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Division of Surgical Research, University Hospital of Zürich, Zürich, Switzerland
| | - Jozef Adamcik
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Donohue
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK.,Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Marjan W van der Woude
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Alyson Hockenberry
- Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland.,Department of Environmental Sciences, ETH Zürich, Zürich, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wüthrich
- Infection Biology, University Hospital of Basel, Basel, Switzerland
| | | | - Claude Loverdo
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Adrian Egli
- Infection Biology, University Hospital of Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Raffaele Mezzenga
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.,Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Otto Holst
- Forschungszentrum Borstel, Borstel, Germany
| | - Beat H Meier
- Institute for Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Emma Slack
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland. .,Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.
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12
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Tan TJ, Yuan M, Kuzelka K, Padron GC, Beal JR, Chen X, Wang Y, Rivera-Cardona J, Zhu X, Stadtmueller BM, Brooke CB, Wilson IA, Wu NC. Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain. bioRxiv 2021:2021.01.26.428356. [PMID: 33532781 PMCID: PMC7852275 DOI: 10.1101/2021.01.26.428356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short CDR H3. Germline-encoded sequence motifs in CDRs H1 and H2 play a major role, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, have not been elucidated. Here, we identify two public clonotypes of IGHV3-53/3-66 RBD antibodies with a 9-residue CDR H3 that pair with different light chains. Distinct sequence motifs on CDR H3 are present in the two public clonotypes that appear to be related to differential light chain pairing. Additionally, we show that Y58F is a common somatic hypermutation that results in increased binding affinity of IGHV3-53/3-66 RBD antibodies with a short CDR H3. Overall, our results advance fundamental understanding of the antibody response to SARS-CoV-2.
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Affiliation(s)
- Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kaylee Kuzelka
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gilberto C. Padron
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jacob R. Beal
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joel Rivera-Cardona
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C. Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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13
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Kumar Bharathkar S, Parker BW, Malyutin AG, Haloi N, Huey-Tubman KE, Tajkhorshid E, Stadtmueller BM. The structures of secretory and dimeric immunoglobulin A. eLife 2020; 9:56098. [PMID: 33107820 PMCID: PMC7707832 DOI: 10.7554/elife.56098] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
Secretory (S) Immunoglobulin (Ig) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that assemble with one joining-chain (JC) to form dimeric (d) IgA that is bound by the polymeric Ig-receptor ectodomain, called secretory component (SC). Here, we report the cryo-electron microscopy structures of murine SIgA and dIgA. Structures reveal two IgAs conjoined through four heavy-chain tailpieces and the JC that together form a β-sandwich-like fold. The two IgAs are bent and tilted with respect to each other, forming distinct concave and convex surfaces. In SIgA, SC is bound to one face, asymmetrically contacting both IgAs and JC. The bent and tilted arrangement of complex components limits the possible positions of both sets of antigen-binding fragments (Fabs) and preserves steric accessibility to receptor-binding sites, likely influencing antigen binding and effector functions.
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Affiliation(s)
- Sonya Kumar Bharathkar
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States
| | - Benjamin W Parker
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States
| | - Andrey G Malyutin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Beckman Institute, California Institute of Technology, Pasadena, United States
| | - Nandan Haloi
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Urbana, United States
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Urbana, United States
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States
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14
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Stadtmueller BM, Bridges MD, Dam KM, Lerch MT, Huey-Tubman KE, Hubbell WL, Bjorkman PJ. DEER Spectroscopy Measurements Reveal Multiple Conformations of HIV-1 SOSIP Envelopes that Show Similarities with Envelopes on Native Virions. Immunity 2018; 49:235-246.e4. [PMID: 30076100 PMCID: PMC6104740 DOI: 10.1016/j.immuni.2018.06.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/15/2018] [Accepted: 06/28/2018] [Indexed: 12/31/2022]
Abstract
HIV-1 Envelope (Env) mediates viral-host membrane fusion after binding host-receptor CD4 and coreceptor. Soluble envelopes (SOSIPs), designed to mimic prefusion conformational states of virion-bound envelopes, are proposed immunogens for eliciting neutralizing antibodies, yet only static structures are available. To evaluate conformational landscapes of ligand-free, CD4-bound, inhibitor-bound, and antibody-bound SOSIPs, we measured inter-subunit distances throughout spin-labeled SOSIPs using double electron-electron resonance (DEER) spectroscopy and compared results to soluble and virion-bound Env structures, and single-molecule fluorescence resonance energy transfer (smFRET)-derived dynamics of virion-bound Envs. Unliganded SOSIP measurements were consistent with closed, neutralizing antibody-bound structures and shielding of non-neutralizing epitopes, demonstrating homogeneity at Env apex, increased flexibility near Env base, and no evidence for the intra-subunit flexibility near Env apex suggested by smFRET. CD4 binding increased inter-subunit distances and heterogeneity, consistent with rearrangements required for coreceptor binding. Results suggest similarities between SOSIPs and virion-bound Envs and demonstrate DEER’s relevance for immunogen design. SOSIP Env apex is 3-fold symmetric and consistent with closed prefusion structures Unliganded Env base and CD4-bound Env apex and base exhibit flexibility SOSIPs retain desired properties of immunogens; e.g., burying non-neutralizing epitopes Results allow interpretation of smFRET studies and SOSIP and virion Env structures
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Affiliation(s)
- Beth M Stadtmueller
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael D Bridges
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Kim-Marie Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael T Lerch
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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15
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Stadtmueller BM, Yang Z, Huey-Tubman KE, Roberts-Mataric H, Hubbell WL, Bjorkman PJ. Biophysical and Biochemical Characterization of Avian Secretory Component Provides Structural Insights into the Evolution of the Polymeric Ig Receptor. J Immunol 2016; 197:1408-14. [PMID: 27412418 PMCID: PMC4976031 DOI: 10.4049/jimmunol.1600463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/11/2016] [Indexed: 12/31/2022]
Abstract
The polymeric Ig receptor (pIgR) transports polymeric Abs across epithelia to the mucosa, where proteolytic cleavage releases the ectodomain (secretory component [SC]) as an integral component of secretory Abs, or as an unliganded protein that can mediate interactions with bacteria. SC is conserved among vertebrates, but domain organization is variable: mammalian SC has five domains (D1-D5), whereas avian, amphibian, and reptilian SC lack the D2 domain, and fish SC lacks domains D2-D4. In this study, we used double electron-electron resonance spectroscopy and surface plasmon resonance binding studies to characterize the structure, dynamics, and ligand binding properties of avian SC, avian SC domain variants, and a human SC (hSC) variant lacking the D2 domain. These experiments demonstrated that, unlike hSC, which adopts a compact or "closed" domain arrangement, unliganded avian SC is flexible and exists in both closed and open states, suggesting that the mammalian SC D2 domain stabilizes the closed conformation observed for hSC D1-D5. Experiments also demonstrated that avian and mammalian pIgR share related, but distinct, mechanisms of ligand binding. Together, our data reveal differences in the molecular recognition mechanisms associated with evolutionary changes in the pIgR protein.
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Affiliation(s)
- Beth M Stadtmueller
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095; and Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Helena Roberts-Mataric
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095; and Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
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16
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Stadtmueller BM, Huey-Tubman KE, López CJ, Yang Z, Hubbell WL, Bjorkman PJ. The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins. eLife 2016; 5. [PMID: 26943617 PMCID: PMC4786434 DOI: 10.7554/elife.10640] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/21/2016] [Indexed: 02/06/2023] Open
Abstract
As a first-line vertebrate immune defense, the polymeric immunoglobulin receptor (pIgR) transports polymeric IgA and IgM across epithelia to mucosal secretions, where the cleaved ectodomain (secretory component; SC) becomes a component of secretory antibodies, or when unliganded, binds and excludes bacteria. Here we report the 2.6Å crystal structure of unliganded human SC (hSC) and comparisons with a 1.7Å structure of teleost fish SC (tSC), an early pIgR ancestor. The hSC structure comprises five immunoglobulin-like domains (D1-D5) arranged as a triangle, with an interface between ligand-binding domains D1 and D5. Electron paramagnetic resonance measurements confirmed the D1-D5 interface in solution and revealed that it breaks upon ligand binding. Together with binding studies of mutant and chimeric SCs, which revealed domain contributions to secretory antibody formation, these results provide detailed models for SC structure, address pIgR evolution, and demonstrate that SC uses multiple conformations to protect mammals from pathogens. DOI:http://dx.doi.org/10.7554/eLife.10640.001 A sticky substance called mucus lines our airways and gut, where it acts as a physical barrier to prevent bacteria and other microbes from entering the body. Mucus also contains proteins called antibodies that can bind to and neutralize molecules from microbes (known as antigens). The primary antibody found in mucus is called Immunoglobulin A. This antibody is produced by immune cells within the body and must pass through the “epithelial” cells that line the airway or gut to reach the layer of mucus. These epithelial cells have a receptor protein called the polymeric immunoglobulin receptor (plgR) that binds to Immunoglobulin A molecules, transports them across the cell, and then releases them into the mucus layer. The pIgR also releases Immunoglobulin A into breast milk, which protects nursing infants until their own immune system has developed. When released into the mucus layer, the Immunoglobulin A antibodies remain attached to a portion of pIgR known as the secretory component. This part of the receptor serves to stabilize and protect the antibodies from being degraded and helps the antibodies to bind to other host and bacterial proteins. Researchers have noted that the secretory component can be released into the mucus even when it is not attached to an antibody. These “free” secretory components have been shown to help prevent bacteria and the toxins they produce from entering the body. Despite the importance of secretory component in immune responses, the three-dimensional structure of the secretory component and how it interacts with antibodies and bacteria remained unknown. Here, Stadtmueller et al. use a technique called X-ray crystallography to determine a three-dimensional model of the free form of a secretory component from humans, and compare it to an ancestral secretory component protein found in fish. Further experiments on the human protein revealed how the structure of the secretory component changes when antibodies bind to it. Stadtmueller et al. propose a model for how both forms of the secretory component can protect the body from microbes and other external agents. The next challenge is to develop a three-dimensional model of the secretory component when it is bound to Immunoglobulin A. DOI:http://dx.doi.org/10.7554/eLife.10640.002
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Affiliation(s)
- Beth M Stadtmueller
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Carlos J López
- Jules Stein Eye Institute, University of California, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, United States
| | - Zhongyu Yang
- Jules Stein Eye Institute, University of California, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, United States
| | - Wayne L Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, United States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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17
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Stadtmueller BM, Kish-Trier E, Ferrell K, Petersen CN, Robinson H, Myszka DG, Eckert DM, Formosa T, Hill CP. Structure of a proteasome Pba1-Pba2 complex: implications for proteasome assembly, activation, and biological function. J Biol Chem 2012; 287:37371-82. [PMID: 22930756 PMCID: PMC3481334 DOI: 10.1074/jbc.m112.367003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 07/16/2012] [Indexed: 11/06/2022] Open
Abstract
The 20S proteasome is an essential, 28-subunit protease that sequesters proteolytic sites within a central chamber, thereby repressing substrate degradation until proteasome activators open the entrance/exit gate. Two established activators, Blm10 and PAN/19S, induce gate opening by binding to the pockets between proteasome α-subunits using C-terminal HbYX (hydrophobic-tyrosine-any residue) motifs. Equivalent HbYX motifs have been identified in Pba1 and Pba2, which function in proteasome assembly. Here, we demonstrate that Pba1-Pba2 proteins form a stable heterodimer that utilizes its HbYX motifs to bind mature 20S proteasomes in vitro and that the Pba1-Pba2 HbYX motifs are important for a physiological function of proteasomes, the maintenance of mitochondrial function. Other factors that contribute to proteasome assembly or function also act in the maintenance of mitochondrial function and display complex genetic interactions with one another, possibly revealing an unexpected pathway of mitochondrial regulation involving the Pba1-Pba2 proteasome interaction. Our determination of a proteasome Pba1-Pba2 crystal structure reveals a Pba1 HbYX interaction that is superimposable with those of known activators, a Pba2 HbYX interaction that is different from those reported previously, and a gate structure that is disrupted but not sufficiently open to allow entry of even small peptides. These findings extend understanding of proteasome interactions with HbYX motifs and suggest multiple roles for Pba1-Pba2 interactions throughout proteasome assembly and function.
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Affiliation(s)
- Beth M. Stadtmueller
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
| | - Erik Kish-Trier
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
| | - Katherine Ferrell
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
| | - Charisse N. Petersen
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
| | - Howard Robinson
- Department of Biology, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - David G. Myszka
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
| | - Debra M. Eckert
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
| | - Tim Formosa
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
| | - Christopher P. Hill
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650 and
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18
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Abstract
Proteasomes degrade a multitude of protein substrates in the cytosol and nucleus, and thereby are essential for many aspects of cellular function. Because the proteolytic sites are sequestered in a closed barrel-shaped structure, activators are required to facilitate substrate access. Structural and biochemical studies of two activator families, 11S and Blm10, have provided insights to proteasome activation mechanisms, although the biological functions of these factors remain obscure. Recent advances have improved our understanding of the third activator family, including the 19S activator, which targets polyubiquitylated proteins for degradation. Here we present a structural perspective on how proteasomes are activated and how substrates are delivered to the proteolytic sites.
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Affiliation(s)
- Beth M Stadtmueller
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
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19
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Stadtmueller BM, Ferrell K, Whitby FG, Heroux A, Robinson H, Myszka DG, Hill CP. Structural models for interactions between the 20S proteasome and its PAN/19S activators. J Biol Chem 2009; 285:13-7. [PMID: 19889631 DOI: 10.1074/jbc.c109.070425] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteasome activity is regulated by sequestration of its proteolytic centers in a barrel-shaped structure that limits substrate access. Substrates enter the proteasome by means of activator complexes that bind to the end rings of proteasome alpha subunits and induce opening of an axial entrance/exit pore. The PA26 activator binds in a pocket on the proteasome surface using main chain contacts of its C-terminal residues and uses an internal activation loop to trigger gate opening by repositioning the proteasome Pro-17 reverse turn. Subunits of the unrelated PAN/19S activators bind with their C termini in the same pockets but can induce proteasome gate opening entirely from interactions of their C-terminal peptides, which are reported to cause gate opening by inducing a rocking motion of proteasome alpha subunits rather than by directly contacting the Pro-17 turn. Here we report crystal structures and binding studies of proteasome complexes with PA26 constructs that display modified C-terminal residues, including those corresponding to PAN. These findings suggest that PA26 and PAN/19S C-terminal residues bind superimposably and that both classes of activator induce gate opening by using direct contacts to residues of the proteasome Pro-17 reverse turn. In the case of the PAN and 19S activators, a penultimate tyrosine/phenylalanine residue contacts the proteasome Gly-19 carbonyl oxygen to stabilize the open conformation.
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Affiliation(s)
- Beth M Stadtmueller
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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20
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Phillips JD, Whitby FG, Stadtmueller BM, Edwards CQ, Hill CP, Kushner JP. Two novel uroporphyrinogen decarboxylase (URO-D) mutations causing hepatoerythropoietic porphyria (HEP). Transl Res 2007; 149:85-91. [PMID: 17240319 DOI: 10.1016/j.trsl.2006.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 08/07/2006] [Accepted: 08/13/2006] [Indexed: 11/30/2022]
Abstract
Hepatoerythropoietic porphyria (HEP) is a rare form of porphyria in humans. The disorder is caused by homozygosity or compound heterozygosity for mutations of the uroporphyrinogen decarboxylase (URO-D) gene. Subnormal URO-D activity results in accumulation of uroporphyrin in the liver, which ultimately mediates the photosensitivity that clinically characterizes HEP. Two previously undescribed URO-D mutations found in a 2-year-old Caucasian boy with HEP, a maternal nonsense mutation (Gln71Stop), and a paternal missense mutation (Gly168Arg) are reported here. Recombinant Gly168Arg URO-D retained 65% of wild-type URO-D activity and studies in Epstein-Barr Virus (EBV)-transformed lymphoblasts indicated that protein levels are reduced, suggesting that the mutant protein might be subjected to accelerated turnover. The crystal structure of Gly168Arg was determined both as the apo-enzyme and with the reaction product bound. These studies revealed little distortion of the active site, but a loop containing residues 167-172 was displaced, possibly indicating small changes in the catalytic geometry or in substrate binding or increased accessibility to a cellular proteolytic pathway. A second pregnancy occurred in this family, and in utero genotyping revealed a fetus heterozygous for the maternal nonsense mutation (URO-D genotype WT/Gln71Stop). A healthy infant was born with no clinical evidence of porphyria.
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Affiliation(s)
- John D Phillips
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
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