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DeBoer AG, Lei L, Yang C, Martens CA, Anzick SL, Antonioli-Schmit S, Suchland RJ, McClarty G, Caldwell HD, Rockey DD. TargeTron Inactivation of Chlamydia trachomatis gseA Results in a Lipopolysaccharide 3-Deoxy-d-Manno-Oct-2-Ulosonic Acid-Deficient Strain That Is Cytotoxic for Cells. Infect Immun 2023; 91:e0009623. [PMID: 37255490 PMCID: PMC10353364 DOI: 10.1128/iai.00096-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 03/17/2023] [Indexed: 06/01/2023] Open
Abstract
All members of the family Chlamydiaceae have lipopolysaccharides (LPS) that possess a shared carbohydrate trisaccharide antigen, 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) that is functionally uncharacterized. A single gene, genus-specific epitope (gseA), is responsible for attaching the tri-Kdo to lipid IVA. To investigate the function of Kdo in chlamydial host cell interactions, we made a gseA-null strain (L2ΔgseA) by using TargeTron mutagenesis. Immunofluorescence microscopy and immunoblotting with a Kdo-specific monoclonal antibody demonstrated that L2ΔgseA lacked Kdo. L2ΔgseA reacted by immunoblotting with a monoclonal antibody specific for a conserved LPS glucosamine-PO4 epitope, indicating that core lipid A was retained by the mutant. The mutant strain produced a similar number of inclusions as the parental strain but yielded lower numbers of infectious elementary bodies. Transmission electron microscopy of L2ΔgseA-infected cells showed atypical developmental forms and a reduction in the number of elementary bodies. Immunoblotting of dithiothreitol-treated L2ΔgseA-infected cells lysates revealed a marked reduction in outer membrane OmcB disulfide cross-linking, suggesting that the elementary body outer membrane structure was affected by the lack of Kdo. Notably, lactic acid dehydrogenase release by infected cells demonstrated that L2ΔgseA was significantly more cytotoxic to host cells than the wild type. The cytotoxic phenotype may result from an altered outer membrane biogenesis structure and/or function or, conversely, from a direct pathobiological effect of Kdo on an unknown host cell target. These findings implicate a previously unrecognized role for Kdo in host cell interactions that facilitates postinfection host cell survival.
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Affiliation(s)
- Addison G. DeBoer
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lei Lei
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Chunfu Yang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Craig A. Martens
- National Institute of Allergy and Infectious Disease, Rocky Mountain Laboratory, Hamilton, Montana, USA
| | - Sarah L. Anzick
- National Institute of Allergy and Infectious Disease, Rocky Mountain Laboratory, Hamilton, Montana, USA
| | - Sophia Antonioli-Schmit
- National Institute of Allergy and Infectious Disease, Rocky Mountain Laboratory, Hamilton, Montana, USA
| | - Robert J. Suchland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
| | - Grant McClarty
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba Winnipeg, Winnipeg, Manitoba, Canada
| | - Harlan D. Caldwell
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel D. Rockey
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
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2
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Sangesland M, Yousif AS, Ronsard L, Kazer SW, Zhu AL, Gatter GJ, Hayward MR, Barnes RM, Quirindongo-Crespo M, Rohrer D, Lonberg N, Kwon D, Shalek AK, Lingwood D. A Single Human V H-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood. Cell Rep 2021; 32:108065. [PMID: 32846123 PMCID: PMC7446668 DOI: 10.1016/j.celrep.2020.108065] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/05/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023] Open
Abstract
B cell receptors (BCRs) display a combination of variable (V)-gene-encoded complementarity determining regions (CDRs) and adaptive/hypervariable CDR3 loops to engage antigens. It has long been proposed that the former tune for recognition of pathogens or groups of pathogens. To experimentally evaluate this within the human antibody repertoire, we perform immune challenges in transgenic mice that bear diverse human CDR3 and light chains but are constrained to different human VH-genes. We find that, of six commonly deployed VH sequences, only those CDRs encoded by IGHV1-2∗02 enable polyclonal antibody responses against bacterial lipopolysaccharide (LPS) when introduced to the bloodstream. The LPS is from diverse strains of gram-negative bacteria, and the VH-gene-dependent responses are directed against the non-variable and universal saccrolipid substructure of this antigen. This reveals a broad-spectrum anti-LPS response in which germline-encoded CDRs naturally hardwire the human antibody repertoire for recognition of a conserved microbial target.
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Affiliation(s)
- Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Samuel W Kazer
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Alex Lee Zhu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - G James Gatter
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Matthew R Hayward
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd., Redwood City, CA 94063-2478, USA
| | | | - Daniel Rohrer
- Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd., Redwood City, CA 94063-2478, USA
| | - Douglas Kwon
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Division of Infectious Diseases, Massachusetts General Hospital. 55 Fruit St., Boston, MA 02114, USA
| | - Alex K Shalek
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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Thakur B, Arora K, Gupta A, Guptasarma P. The DNA-binding protein HU is a molecular glue that attaches bacteria to extracellular DNA in biofilms. J Biol Chem 2021; 296:100532. [PMID: 33713701 PMCID: PMC8063757 DOI: 10.1016/j.jbc.2021.100532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 02/06/2023] Open
Abstract
In biofilms, bacteria that possess a negatively charged surface are embedded within a matrix of polymers consisting mainly of negatively charged extracellular DNA (e-DNA). In all likelihood, a multivalent positively charged substance, for example, a basic protein, exists within biofilms to neutralize charge–charge repulsions and act as a ‘glue’ attaching negatively charged bacteria to negatively charged e-DNA; however, no protein capable of doing so has yet been identified. We decided to investigate whether a highly abundant nucleoid-associated histone-like protein (HU) happens to be the glue in question. In recent years, HU has been shown to possess qualities that could be considered desirable in the proposed glue, for example, (a) availability in association with e-DNA; (b) multivalent DNA binding; (c) non–sequence-specific DNA-binding; (d) enhancement of biofilm formation upon exogenous addition, and (e) disruption of biofilms, upon removal by HU–cognate antibodies. Geometric considerations suggest that basic residues in HU's canonical and noncanonical DNA-binding sites can interact with sugar-linked terminal phosphates in lipopolysaccharide (LPS) molecules in bacterial outer membranes. Here, using genetic, spectroscopic, biophysical–chemical, microscopy-based, and cytometry-based experiments, we demonstrate that HU's DNA-binding sites also bind to LPS, that this facilitates DNA–DNA, DNA–LPS, and LPS–LPS interactions, and that this facilitates bacterial clumping and attachment of bacteria to DNA. Exogenous addition of HU to bacteria in (nonshaken) cultures is shown to cause cells to become engulfed in a matrix of DNA, potentially arising from the lysis of bacteria with vulnerable cell walls (as they strain to grow, divide, and move away from each other, in opposition to the accreting influence of HUs).
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Affiliation(s)
- Bhishem Thakur
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Punjab, India
| | - Kanika Arora
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Punjab, India
| | - Archit Gupta
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Punjab, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Punjab, India.
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Gómez-Redondo M, Ardá A, Gimeno A, Jiménez-Barbero J. Bacterial polysaccharides: conformation, dynamics and molecular recognition by antibodies. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 35-36:1-11. [PMID: 33388123 DOI: 10.1016/j.ddtec.2020.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023]
Abstract
Bacterial infections are the cause of different severe health conditions and new therapies to combat these pathogens have been widely investigated. Carbohydrates, being complex structures covering the surface of bacteria, are considered relevant targets for antibody and vaccine development. The biological activities in pathogenesis of bacterial capsular polysaccharides and lipopolisaccharides and their unique structures have boosted the study of the minimal antigenic binding epitopes and the structural details of antibody-carbohydrate recognition. This review describes the most recent advances on the field, examining the structure, conformation and dynamics of relevant bacterial carbohydrates and their complexes with antibodies. The understanding of key factors governing the recognition process is fundamental for the progress toward the development of specific and efficient bacterial therapeutics.
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Affiliation(s)
- Marcos Gómez-Redondo
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Ana Ardá
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Ana Gimeno
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain; Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain; Department Organic Chemistry II, Faculty of Science and technology, UPV-EHU, 48940 Leioa, Spain
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Elli S, Alekseeva A, Ramakrishnan B, Koch T, Wollacott A, Viswanathan K, Li K, Delaney JC, Shriver Z, Plante O, Guerrini M. Characterization of an Antibody Recognizing the Conserved Inner Core of Pseudomonas aeruginosa Lipopolysaccharides. Biochemistry 2020; 59:4202-4211. [PMID: 33085893 DOI: 10.1021/acs.biochem.0c00642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial infections are a growing public health threat with carbapenem-resistant Pseudomonas aeruginosa being classified as a Priority 1 critical threat by the World Health Organization. Antibody-based therapeutics can serve as an alternative and in some cases supplement antibiotics for the treatment of bacterial infections. The glycans covering the bacterial cell surface have been proposed as intriguing targets for binding by antibodies; however, antibodies that can engage with high affinity and specificity with glycans are much less common compared to antibodies that engage with protein antigens. In this study, we sought to characterize an antibody that targets a conserved glycan epitope on the surface of Pseudomonas. First, we characterized the breadth of binding of VSX, demonstrating that the VSX is specific to Pseudomonas but can bind across multiple serotypes of the organism. Next, we provide insight into how VSX engages with its target epitope, using a combination of biolayer interferometry and nuclear magnetic resonance, and verify our results using site-directed mutagenesis experiments. We demonstrate that the antibody, with limited somatic hypermutation of the complementarity-determining regions (CDRs) and with a characteristic set of arginines within the CDRs, specifically targets the conserved inner core of Pseudomonas lipopolysaccharides. Our results provide important additional context to antibody-glycan contacts and provide insight useful for the construction of vaccines and therapeutics against Pseudomonas aeruginosa, an important human pathogen.
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Affiliation(s)
- Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", via G. Colombo 81, Milan 20133, Italy
| | - Anna Alekseeva
- Centro Alta Tecnologia Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni" Srl., via G. Colombo 81, Milan 20133, Italy
| | | | - Tyree Koch
- Visterra, Inc., 275 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Andrew Wollacott
- Visterra, Inc., 275 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Karthik Viswanathan
- Visterra, Inc., 275 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Kai Li
- Visterra, Inc., 275 Second Avenue, Waltham, Massachusetts 02451, United States
| | - James C Delaney
- Visterra, Inc., 275 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Zachary Shriver
- Visterra, Inc., 275 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Obadiah Plante
- Visterra, Inc., 275 Second Avenue, Waltham, Massachusetts 02451, United States
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", via G. Colombo 81, Milan 20133, Italy
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Haji-Ghassemi O, Müller-Loennies S, Brooks CL, MacKenzie CR, Caveney N, Van Petegem F, Brade L, Kosma P, Brade H, Evans SV. Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude. Biochemistry 2019; 58:714-726. [PMID: 30571096 DOI: 10.1021/acs.biochem.8b00318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Murine antibodies S25-23, S25-26, and S25-5 derive from a common germ-line origin, and all bind the Chlamydiaceae family-specific epitope αKdo(2→8)αKdo(2→4)αKdo (where Kdo is 3-deoxy-α-d- manno-oct-2-ulosonic acid) with high affinity and specificity. These antibodies recognize the entire trisaccharide antigen in a linkage-dependent manner via a groove composed largely of germ-line residues. Despite sharing identical heavy and light chain genes, S25-23 binds the family-specific epitope with nanomolar affinity, which is an order of magnitude higher than that of S25-26, while S25-5 displays an affinity between those of S25-23 and S25-26. We determined the high-resolution crystal structures of S25-23 and S25-5 antigen binding fragments in complex with a pentasaccharide derived from the LPS of Chlamydia and measured the affinity of S25-5 for chlamydial LPS antigens using isothermal titration microcalorimetry. The 1.75 Å resolution structure of S25-23 shows how subtle conservative mutations Arg(L)-27E to lysine and Ser(H)-56 to threonine lead to an order of magnitude increase in affinity. Importantly, comparison between previous S25-26 structures and the 1.99 and 2.05 Å resolution liganded and unliganded structures of S25-5, respectively, shows how a Ser(L)-27E mutation results in an intermediate affinity due to the reduced enthalpic penalty associated with complex formation that would otherwise be required for arginine in this position. This strategy allows for subtle adjustments in the combining site via affinity maturation that have dramatic consequences for the affinity of an antibody for its antigen.
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Affiliation(s)
- Omid Haji-Ghassemi
- Department of Biochemistry and Microbiology , University of Victoria , P.O. Box 3055 STN CSC, Victoria , British Columbia , Canada V8P 3P6
| | - Sven Müller-Loennies
- Research Center Borstel , Leibniz Lung Center , Parkallee 22 , Borstel D-23845 , Germany
| | - Cory L Brooks
- Department of Chemistry , Fresno State University , 2555 East San Ramon Avenue, MS SB70 , Fresno , California 93740 , United States
| | - C Roger MacKenzie
- Human Health Therapeutics Portfolio , National Research Council Canada , 100 Sussex Drive , Ottawa , Ontario , Canada K1A 0R6
| | - Nathanael Caveney
- Department of Biochemistry and Microbiology , University of Victoria , P.O. Box 3055 STN CSC, Victoria , British Columbia , Canada V8P 3P6
| | - Filip Van Petegem
- Department of Chemistry , University of Natural Resources and Life Sciences , A-1190 Vienna , Austria
| | - Lore Brade
- Research Center Borstel , Leibniz Lung Center , Parkallee 22 , Borstel D-23845 , Germany
| | - Paul Kosma
- Department of Chemistry , University of Natural Resources and Life Sciences , A-1190 Vienna , Austria
| | - Helmut Brade
- Research Center Borstel , Leibniz Lung Center , Parkallee 22 , Borstel D-23845 , Germany
| | - Stephen V Evans
- Department of Biochemistry and Microbiology , University of Victoria , P.O. Box 3055 STN CSC, Victoria , British Columbia , Canada V8P 3P6
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Polyspecificity of Anti-lipid A Antibodies and Its Relevance to the Development of Autoimmunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 966:181-202. [PMID: 28887790 DOI: 10.1007/5584_2017_94] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The process of natural selection favours germ-line gene segments that encode CDRs that have the ability to recognize a range of structurally related antigens. This presents an immunological advantage to the host, as it can confer protection against a common pathogen and still cope with new or changing antigens. Cross-reactive and polyspecific antibodies also play a central role in autoimmune responses, and a link has been shown to exist between auto-reactive B cells and certain bacterial infections. Bacterial DNA, lipids, and carbohydrates have been implicated in the progression of autoimmune diseases such as systemic lupus erythematosus. As well, reports of anti-lipid A antibody polyspecificity towards single-stranded DNA together with the observed sequence homology amongst isolated auto- and anti-lipid A antibodies has prompted further study of this phenomenon. Though the lipid A epitope appears cryptic during Gram-negative bacterial infection, there have been several reported instances of lipid A-specific antibodies isolated from human sera, some of which have exhibited polyspecificity for single stranded DNA. In such cases, the breakdown of negative selection through polyspecificity can have the unfortunate consequence of autoimmune disease. This review summarizes current knowledge regarding such antibodies and emphasizes the features of S1-15, A6, and S55-5, anti-lipid A antibodies whose structures were recently determined by X-ray crystallography.
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