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Hyun GH, Cho IH, Yang YY, Jeong DH, Kang YP, Kim YS, Lee SJ, Kwon SW. Mechanisms of interactions in pattern-recognition of common glycostructures across pectin-derived heteropolysaccharides by Toll-like receptor 4. Carbohydr Polym 2023; 314:120921. [PMID: 37173020 DOI: 10.1016/j.carbpol.2023.120921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
Complex pectin, originating from terrestrial plant cell walls has been attracting research attention as a promising source of a new innate immune modulator. Numerous bioactive polysaccharides associated with pectin are newly reported every year, but the general mechanism of their immunological action remains unclear owing to the complexity and heterogeneity of pectin. Herein, we systematically investigated the interactions in pattern-recognition for common glycostructures of pectic heteropolysaccharides (HPSs) by Toll-like receptors (TLRs). The compositional similarity of glycosyl residues derived from pectic HPS was confirmed by conducting systematic reviews, leading to molecular modeling of representative pectic segments. Via structural investigation, the inner concavity of leucine-rich repeats of TLR4 was predicted to act as a binding motif for carbohydrate recognition, and subsequent simulations predicted the binding modes and conformations. We experimentally demonstrated that pectic HPS exhibits the non-canonical and multivalent binding aspects for TLR4 resulting in receptor activation. Furthermore, we showed that pectic HPSs were selectively clustered with TLR4 during endocytosis, inducing downstream signals to cause phenotypic activation of macrophages. Overall, we have presented a better explanation for the pattern recognition of pectic HPS and further proposed an approach to understand the interaction between complex carbohydrates and proteins.
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Affiliation(s)
- Gyu Hwan Hyun
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - In Ho Cho
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoon Young Yang
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Da-Hye Jeong
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Republic of Korea
| | - Yun Pyo Kang
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - You-Sun Kim
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Republic of Korea
| | - Seul Ji Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea.
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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2
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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3
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Raikar SS, Fleischer LC, Moot R, Fedanov A, Paik NY, Knight KA, Doering CB, Spencer HT. Development of chimeric antigen receptors targeting T-cell malignancies using two structurally different anti-CD5 antigen binding domains in NK and CRISPR-edited T cell lines. Oncoimmunology 2017; 7:e1407898. [PMID: 29399409 DOI: 10.1080/2162402x.2017.1407898] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/29/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
Relapsed T-cell malignancies have poor outcomes when treated with chemotherapy, but survival after allogeneic bone marrow transplantation (BMT) approaches 50%. A limitation to BMT is the difficulty of achieving remission prior to transplant. Chimeric antigen receptor (CAR) T-cell therapy has shown successes in B-cell malignancies. This approach is difficult to adapt for the treatment of T-cell disease due to lack of a T-lymphoblast specific antigen and the fratricide of CAR T cells that occurs with T-cell antigen targeting. To circumvent this problem two approaches were investigated. First, a natural killer (NK) cell line, which does not express CD5, was used for CAR expression. Second, CRISPR-Cas9 genome editing technology was used to knockout CD5 expression in CD5-positive Jurkat T cells and in primary T cells, allowing for the use of CD5-negative T cells for CAR expression. Two structurally distinct anti-CD5 sequences were also tested, i) a traditional immunoglobulin-based single chain variable fragment (scFv) and ii) a lamprey-derived variable lymphocyte receptor (VLR), which we previously showed can be used for CAR-based recognition. Our results show i) both CARs yield comparable T-cell activation and NK cell-based cytotoxicity when targeting CD5-positive cells, ii) CD5-edited CAR-modified Jurkat T cells have reduced self-activation compared to that of CD5-positive CAR-modified T cells, iii) CD5-edited CAR-modified Jurkat T cells have increased activation in the presence of CD5-positive target cells compared to that of CD5-positive CAR-modified T cells, and iv) although modest effects were seen, a mouse model using the CAR-expressing NK cell line showed the scFv-CAR was superior to the VLR-CAR in delaying disease progression.
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Affiliation(s)
- Sunil S Raikar
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Lauren C Fleischer
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - Robert Moot
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - Andrew Fedanov
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Na Yoon Paik
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Kristopher A Knight
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Christopher B Doering
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - H Trent Spencer
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, Georgia
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4
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Bulutoglu B, Banta S. Block V RTX Domain of Adenylate Cyclase from Bordetella pertussis: A Conformationally Dynamic Scaffold for Protein Engineering Applications. Toxins (Basel) 2017; 9:E289. [PMID: 28926974 PMCID: PMC5618222 DOI: 10.3390/toxins9090289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/27/2023] Open
Abstract
The isolated Block V repeats-in-toxin (RTX) peptide domain of adenylate cyclase (CyaA) from Bordetella pertussis reversibly folds into a β-roll secondary structure upon calcium binding. In this review, we discuss how the conformationally dynamic nature of the peptide is being engineered and employed as a switching mechanism to mediate different protein functions and protein-protein interactions. The peptide has been used as a scaffold for diverse applications including: a precipitation tag for bioseparations, a cross-linking domain for protein hydrogel formation and as an alternative scaffold for biomolecular recognition applications. Proteins and peptides such as the RTX domains that exhibit natural stimulus-responsive behavior are valuable building blocks for emerging synthetic biology applications.
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Affiliation(s)
- Beyza Bulutoglu
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA.
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5
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Bulutoglu B, Dooley K, Szilvay G, Blenner M, Banta S. Catch and Release: Engineered Allosterically Regulated β-Roll Peptides Enable On/Off Biomolecular Recognition. ACS Synth Biol 2017; 6:1732-1741. [PMID: 28520402 DOI: 10.1021/acssynbio.7b00089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alternative scaffolds for biomolecular recognition are being developed to overcome some of the limitations associated with immunoglobulin domains. The repeat-in-toxin (RTX) domain is a repeat protein sequence that reversibly adopts the β-roll secondary structure motif specifically upon calcium binding. This conformational change was exploited for controlled biomolecular recognition. Using ribosome display, an RTX peptide library was selected to identify binders to a model protein, lysozyme, exclusively in the folded state of the peptide. Several mutants were identified with low micromolar dissociation constants. After concatenation of the mutants, a 500-fold increase in the overall affinity for lysozyme was achieved leading to a peptide with an apparent dissociation constant of 65 nM. This mutant was immobilized for affinity chromatography experiments, and the on/off nature of the molecular recognition was demonstrated as the target is captured from a mixture in the presence of calcium and is released in the absence of calcium as the RTX peptides lose their β-roll structure. This work presents the design of a new stimulus-responsive scaffold that can be used for environmentally responsive specific molecular recognition and self-assembly.
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Affiliation(s)
- Beyza Bulutoglu
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Kevin Dooley
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Géza Szilvay
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Mark Blenner
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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6
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Oldham RAA, Medin JA. Practical considerations for chimeric antigen receptor design and delivery. Expert Opin Biol Ther 2017; 17:961-978. [DOI: 10.1080/14712598.2017.1339687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Robyn A. A. Oldham
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jeffrey A. Medin
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Biochemistry, The Medical College of Wisconsin, Milwaukee, USA
- The Institute of Medical Sciences, University of Toronto, Toronto, Canada
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7
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Moot R, Raikar SS, Fleischer L, Querrey M, Tylawsky DE, Nakahara H, Doering CB, Spencer HT. Genetic engineering of chimeric antigen receptors using lamprey derived variable lymphocyte receptors. MOLECULAR THERAPY-ONCOLYTICS 2016; 3:16026. [PMID: 27933313 PMCID: PMC5142425 DOI: 10.1038/mto.2016.26] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/23/2016] [Indexed: 01/05/2023]
Abstract
Chimeric antigen receptors (CARs) are used to redirect effector cell specificity to selected cell surface antigens. Using CARs, antitumor activity can be initiated in patients with no prior tumor specific immunity. Although CARs have shown promising clinical results, the technology remains limited by the availability of specific cognate cell target antigens. To increase the repertoire of targetable tumor cell antigens we utilized the immune system of the sea lamprey to generate directed variable lymphocyte receptors (VLRs). VLRs serve as membrane bound and soluble immune effectors analogous but not homologous to immunoglobulins. They have a fundamentally different structure than immunoglobulin (Ig)-based antibodies while still demonstrating high degrees of specificity and affinity. To test the functionality of VLRs as the antigen recognition domain of CARs, two VLR-CARs were created. One contained a VLR specific for a murine B cell leukemia and the other contained a VLR specific for the human T cell surface antigen, CD5. The CAR design consisted of the VLR sequence, myc-epitope tag, CD28 transmembrane domain, and intracellular CD3ζ signaling domain. We demonstrate proof of concept, including gene transfer, biosynthesis, cell surface localization, and effector cell activation for multiple VLR-CAR designs. Therefore, VLRs provide an alternative means of CAR-based cancer recognition.
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Affiliation(s)
- Robert Moot
- Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine , Atlanta, Georgia, USA
| | - Sunil S Raikar
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine , Atlanta, Georgia, USA
| | - Lauren Fleischer
- Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine , Atlanta, Georgia, USA
| | - Melissa Querrey
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine , Atlanta, Georgia, USA
| | - Daniel E Tylawsky
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine , Atlanta, Georgia, USA
| | - Hirotomo Nakahara
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, Georgia, USA
| | - Christopher B Doering
- Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, Georgia, USA; Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - H Trent Spencer
- Department of Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, Georgia, USA; Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, Georgia, USA
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8
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Wezner-Ptasinska M, Otlewski J. Selection of specific interactors from phage display library based on sea lamprey variable lymphocyte receptor sequences. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1833-1841. [PMID: 26391289 DOI: 10.1016/j.bbapap.2015.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/06/2015] [Accepted: 09/17/2015] [Indexed: 12/31/2022]
Abstract
Variable lymphocyte receptors (VLRs) are non-immunoglobulin components of adaptive immunity in jawless vertebrates. These proteins composed of leucine-rich repeat modules offer some advantages over antibodies in target binding and therefore are attractive candidates for biotechnological applications. In this paper we report the design and characterization of a phage display library based on a previously proposed dVLR scaffold containing six LRR modules [Wezner-Ptasinska et al., 2011]. Our library was designed based on a consensus approach in which the randomization scheme reflects the frequencies of amino acids naturally occurring in respective positions responsible for antigen recognition. We demonstrate general applicability of the scaffold by selecting dVLRs specific for lysozyme and S100A7 protein with KD values in the micromolar range. The dVLR library could be used as a convenient alternative to antibodies for effective isolation of high affinity binders.
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Affiliation(s)
- Magdalena Wezner-Ptasinska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Jacek Otlewski
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
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9
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Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments. PLoS Comput Biol 2015; 11:e1004327. [PMID: 26132144 PMCID: PMC4489365 DOI: 10.1371/journal.pcbi.1004327] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/14/2015] [Indexed: 11/21/2022] Open
Abstract
The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assessed using a Distance Constraint Model (DCM). We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants. The DCM is an ensemble based statistical mechanical approach that accounts for enthalpy/entropy compensation due to network rigidity, which has been quite successful in elucidating conformational flexibility and Quantitative Stability/Flexibility Relationships (QSFR) in proteins. Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation. The increase in CDR H3 loop rigidity is consistent with other studies in the literature. The redistribution of conformational flexibility is largely controlled by nonspecific changes in the H-bond network, although certain Arg to Asp salt bridges create highly localized rigidity increases. Taken together, these results reveal an intricate flexibility/rigidity response that accompanies affinity maturation. Antibodies are protective proteins used by the immune system to recognize and neutralize foreign objects through interactions with a specific part of the target, called an antigen. Antibody structures are Y-shaped, contain multiple protein chains, and include two antigen-binding sites. The binding sites are located at the end of the Fab fragments, which are the upward facing arms of the Y-structure. The Fab fragments maintain binding affinity by themselves, and are thus often used as surrogates to student antibody-antigen interactions. High affinity antibodies are produced during the course of an immune response by successive mutations to germline gene-encoded antibodies. Germline antibodies are more likely to be polyspecific, whereas the affinity maturation process yields monoclonal antibodies that bind specifically to the target antigen. In this work, we use a computational Distance Constraint Model to characterize how mechanical properties change as three disparate germline antibodies are converted to affinity mature. Our results reveal a rich set of mechanical responses throughout the Fab structure. Nevertheless, increased rigidity in the VH domain is consistently observed, which is consistent with the transition from polyspecificity to monospecificity. That is, flexible antibody structures are able to recognize multiple antigens, while increased affinity and specificity is achieved—in part—by structural rigidification.
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10
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Das S, Li J, Hirano M, Sutoh Y, Herrin BR, Cooper MD. Evolution of two prototypic T cell lineages. Cell Immunol 2015; 296:87-94. [PMID: 25958271 DOI: 10.1016/j.cellimm.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/14/2015] [Accepted: 04/24/2015] [Indexed: 01/06/2023]
Abstract
Jawless vertebrates, which occupy a unique position in chordate phylogeny, employ leucine-rich repeat (LRR)-based variable lymphocyte receptors (VLR) for antigen recognition. During the assembly of the VLR genes (VLRA, VLRB and VLRC), donor LRR-encoding sequences are copied in a step-wise manner into the incomplete germ-line genes. The assembled VLR genes are differentially expressed by discrete lymphocyte lineages: VLRA- and VLRC-producing cells are T-cell like, whereas VLRB-producing cells are B-cell like. VLRA(+) and VLRC(+) lymphocytes resemble the two principal T-cell lineages of jawed vertebrates that express the αβ or γδ T-cell receptors (TCR). Reminiscent of the interspersed nature of the TCRα/TCRδ locus in jawed vertebrates, the close proximity of the VLRA and VLRC loci facilitates sharing of donor LRR sequences during VLRA and VLRC assembly. Here we discuss the insight these findings provide into vertebrate T- and B-cell evolution, and the alternative types of anticipatory receptors they use for adaptive immunity.
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Affiliation(s)
- Sabyasachi Das
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Jianxu Li
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Masayuki Hirano
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Yoichi Sutoh
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Brantley R Herrin
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States.
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11
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Abstract
Leucine-rich repeats (LRRs) are versatile motifs present in more than 6000 proteins throughout the phylogenetic kingdom. Tandem LRRs generate a characteristic horseshoe with a diverse range of functions. Fulfilling a key role in the innate immune system, LRRs form the TLR and NOD-like receptor (NLR) pathogen-recognition domain. Host–pathogen interactions mediated by LRRs drive those involved in ligand recognition to become distinct from their consensus motif. Most LRRs range between 21 and 30 residues; however, large insertions in certain TLRs can generate repeats of over 60 amino acids. LRR variability makes them ideal for species-specific mediation of host-pathogen interactions. Teleost TLRs show large insertions, making cross-species alignments difficult without prior demarcation of their LRR motifs. We present LRRfinder2.0, a webserver for LRR prediction. LRRfinder2.0 utilizes scoring matrices comprising more than 60,000 LRR motifs from more than 200 species. The underlying TLR database tLRRdb contains more than 3500 manually annotated sequences, augmenting identification of irregular LRR motifs.
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Affiliation(s)
- Victoria Offord
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Hatfield, UK
| | - Dirk Werling
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Hatfield, UK
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12
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Das S, Hirano M, Tako R, McCallister C, Nikolaidis N. Evolutionary genomics of immunoglobulin-encoding Loci in vertebrates. Curr Genomics 2012; 13:95-102. [PMID: 23024601 PMCID: PMC3308330 DOI: 10.2174/138920212799860652] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/13/2011] [Accepted: 01/14/2012] [Indexed: 11/22/2022] Open
Abstract
Immunoglobulins (or antibodies) are an essential element of the jawed vertebrate adaptive immune response system. These molecules have evolved over the past 500 million years and generated highly specialized proteins that recognize an extraordinarily large number of diverse substances, collectively known as antigens. During vertebrate evolution the diversification of the immunoglobulin-encoding loci resulted in differences in the genomic organization, gene content, and ratio of functional genes and pseudogenes. The tinkering process in the immunoglobulin-encoding loci often gave rise to lineage-specific characteristics that were formed by selection to increase species adaptation and fitness. Immunoglobulin loci and their encoded antibodies have been shaped repeatedly by contrasting evolutionary forces, either to conserve the prototypic structure and mechanism of action or to generate alternative and diversified structures and modes of function. Moreover, evolution favored the development of multiple mechanisms of primary and secondary antibody diversification, which are used by different species to effectively generate an almost infinite collection of diverse antibody types. This review summarizes our current knowledge on the genomics and evolution of the immunoglobulin-encoding loci and their protein products in jawed vertebrates.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, USA
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13
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Cantor JM, Ginsberg MH. CD98 at the crossroads of adaptive immunity and cancer. J Cell Sci 2012; 125:1373-82. [PMID: 22499670 DOI: 10.1242/jcs.096040] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Adaptive immunity, a vertebrate specialization, adds memory and exquisite specificity to the basic innate immune responses present in invertebrates while conserving metabolic resources. In adaptive immunity, antigenic challenge requires extremely rapid proliferation of rare antigen-specific lymphocytes to produce large, clonally expanded effector populations that neutralize pathogens. Rapid proliferation and resulting clonal expansion are dependent on CD98, a protein whose well-conserved orthologs appear restricted to vertebrates. Thus, CD98 supports lymphocyte clonal expansion to enable protective adaptive immunity, an advantage that could account for the presence of CD98 in vertebrates. CD98 supports lymphocyte clonal expansion by amplifying integrin signals that enable proliferation and prevent apoptosis. These integrin-dependent signals can also provoke cancer development and invasion, anchorage-independence and the rapid proliferation of tumor cells. CD98 is highly expressed in many cancers and contributes to formation of tumors in experimental models. Strikingly, vertebrates, which possess highly conserved CD98 proteins, CD98-binding integrins and adaptive immunity, also display propensity towards invasive and metastatic tumors. In this Commentary, we review the roles of CD98 in lymphocyte biology and cancer. We suggest that the CD98 amplification of integrin signaling in adaptive immunity provides survival benefits to vertebrates, which, in turn, bear the price of increased susceptibility to cancer.
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Affiliation(s)
- Joseph M Cantor
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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14
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Das S, Hirano M, McCallister C, Tako R, Nikolaidis N. Comparative genomics and evolution of immunoglobulin-encoding loci in tetrapods. Adv Immunol 2011; 111:143-78. [PMID: 21970954 DOI: 10.1016/b978-0-12-385991-4.00004-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The immunoglobulins (Igs or antibodies) as an integral part of the tetrapod adaptive immune response system have evolved toward producing highly diversified molecules that recognize a remarkably large number of different antigens. Antibodies and their respective encoding loci have been shaped by different and often contrasting evolutionary forces, some of which aim to conserve an established pattern or mechanism and others to generate alternative and diversified structural and functional configurations. The genomic organization, gene content, ratio between functional genes and pseudogenes, number and position of recombining genetic elements, and the different levels of divergence present at the germline of the Ig-encoding loci have been evolutionarily shaped and optimized in a lineage- and, in some cases, species-specific mode aiming to increase organismal fitness. Further, evolution favored the development of multiple mechanisms of primary and secondary antibody diversification, such as V(D)J recombination, class switch recombination, isotype exclusion, somatic hypermutation, and gene conversion. Diverse tetrapod species, based on their specific germline configurations, use these mechanisms in several different combinations to effectively generate a vast array of distinct antibody types and structures. This chapter summarizes our current knowledge on the Ig-encoding loci in tetrapods and discusses the different evolutionary mechanisms that shaped their diversification.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, Atlanta, Georgia, USA
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Heinz DW, Betzel C, Wilmanns M. Highlight: Of Systems and Structures. Biol Chem 2010; 391:717-8. [DOI: 10.1515/bc.2010.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
No abstract available
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