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Characterization of a single-chain variable fragment recognizing a linear epitope of aβ: a biotechnical tool for studies on Alzheimer's disease? PLoS One 2013; 8:e59820. [PMID: 23555792 PMCID: PMC3608532 DOI: 10.1371/journal.pone.0059820] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/19/2013] [Indexed: 01/02/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with devastating effects. Currently, therapeutic options are limited to symptomatic treatment. For more than a decade, research focused on immunotherapy for the causal treatment of AD. However, clinical trials with active immunization using Aβ encountered severe complications, for example meningoencephalitis. Consequently, attention focused on passive immunization using antibodies. As an alternative to large immunoglobulins (IgGs), Aβ binding single-chain variable fragments (scFvs) were used for diagnostic and therapeutic research approaches. scFvs can be expressed in E. coli and may provide improved pharmacokinetic properties like increased blood-brain barrier permeability or reduced side-effects in vivo. In this study, we constructed an scFv from an Aβ binding IgG, designated IC16, which binds the N-terminal region of Aβ (Aβ(1-8)). scFv-IC16 was expressed in E. coli, purified and characterized with respect to its interaction with different Aβ species and its influence on Aβ fibril formation. We were able to show that scFv-IC16 strongly influenced the aggregation behavior of Aβ and could be applied as an Aβ detection probe for plaque staining in the brains of transgenic AD model mice. The results indicate potential for therapy and diagnosis of AD.
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Sehlin D, Hedlund M, Lord A, Englund H, Gellerfors P, Paulie S, Lannfelt L, Pettersson FE. Heavy-chain complementarity-determining regions determine conformation selectivity of anti-aβ antibodies. NEURODEGENER DIS 2010; 8:117-23. [PMID: 20714111 DOI: 10.1159/000316530] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 06/03/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND/AIMS Amyloid-β (Aβ) protofibrils are neurotoxic soluble intermediates in the Aβ aggregation process eventually forming senile plaques in Alzheimer's disease. This Aβ species is a potential biomarker for Alzheimer's disease and also a promising target for immunotherapy. In this study, we investigated the characteristics of conformation-dependent Aβ antibodies specific for Aβ protofibrils. METHODS Mice were immunized with Aβ protofibrils to generate hybridomas producing Aβ-specific monoclonal antibodies. Binding of antibodies to different Aβ conformations was investigated with inhibition ELISA. The antibodies' complementarity-determining region (CDR) sequences were determined and compared. RESULTS A majority of the antibodies were of the IgM class, all selectively binding to aggregated Aβ. Two IgG antibodies were generated: one with selective affinity for Aβ protofibrils and the other bound Aβ in all conformations. A high degree of similarity between the heavy-chain CDRs of the conformation-dependent antibodies was found, and all high-affinity Aβ antibodies displayed a high degree of sequence similarity in the light-chain CDRs. CONCLUSION Sequence similarity in the heavy-chain CDRs is associated with conformation selectivity of the antibodies, while sequence similarity in the light-chain CDRs correlates with the affinity for Aβ.
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Affiliation(s)
- Dag Sehlin
- Department of Public Health/Molecular Geriatrics, Rudbeck Laboratory Uppsala University, Uppsala, Sweden
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Magnadottir B, Gudmundsdottir S, Gudmundsdottir BK, Helgason S. Natural antibodies of cod (Gadus morhua L.): Specificity, activity and affinity. Comp Biochem Physiol B Biochem Mol Biol 2009; 154:309-16. [DOI: 10.1016/j.cbpb.2009.07.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 07/02/2009] [Accepted: 07/09/2009] [Indexed: 02/01/2023]
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Hsu E, Criscitiello MF. Diverse immunoglobulin light chain organizations in fish retain potential to revise B cell receptor specificities. THE JOURNAL OF IMMUNOLOGY 2006; 177:2452-62. [PMID: 16888007 PMCID: PMC3129705 DOI: 10.4049/jimmunol.177.4.2452] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have characterized the genomic organization of the three zebrafish L chain isotypes and found they all differed from those reported in other teleost fishes. Two of the zebrafish L chain isotypes are encoded by two loci, each carrying multiple V gene segments. To understand the derivation of these L chain genes and their organizations, we performed phylogenetic analyses and show that IgL organization can diverge considerably among closely related species. Except in zebrafish, the teleost fish IgL each contain only two to four recombinogenic components (one to three V, one J) and exist in multiple copies. BCR heterogeneity can be generated, but this arrangement apparently provides neither combinatorial diversification nor an opportunity for the secondary rearrangements that, in mammals, take place during receptor editing, a process crucial to the promotion of tolerance in developing lymphocytes. Examination of the zebrafish IgL recombination possibilities gave insight into how the suppression of self-reactivity by receptor editing might be managed, including in miniloci. We suggest that, despite the diverse IgL organizations in early and higher vertebrates, two elements essential to generating the Ab repertoire are retained: the numerous genes/loci for ligand-binding diversification and the potential for correcting unwanted specificities that arise.
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Affiliation(s)
- Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA.
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5
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Solem ST, Stenvik J. Antibody repertoire development in teleosts--a review with emphasis on salmonids and Gadus morhua L. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:57-76. [PMID: 16084588 DOI: 10.1016/j.dci.2005.06.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The group of teleosts is highly diverse, comprising more than 23000 extant species. Studies of the teleost antibody repertoire have been conducted in many different species within different orders, though some species and families have been better characterised than others. The Atlantic cod (Gadus morhua L.) and several species within the Salmoninae (e.g. Salmo salar and Oncorynchus mykiss) are among the best-studied teleosts in terms of the antibody repertoire. The estimated size of the repertoire, the organisation of immunoglobulin (IG) gene segments, the expressed IG repertoire, the IgM serum concentration, and the serum antibody responses reveal some fundamental differences between these species. The serum IgM concentration of G. morhua is some ten times higher than that of S. salar, though G. morhua is characterised as a 'low' (or 'non') responder in terms of specific antibody production. In contrast, an antibody response is readily induced in S. salar, although the response is strongly regulated by antigen induced suppression. The IGHD gene of G. morhua has a unique structure, while the IGHM and IGHD genes of S. salar have a characteristic genomic organisation in two parallel loci. In addition, salmonids, express a broad repertoire of IGH and IGI V-region gene segments, while a single V gene family dominates the expressed heavy and light chain repertoire of G. morhua. Little is known about the developing antibody repertoire during ontogeny, in different stages of B-cell maturation, or in separate B-cell subsets. Information on the establishment of the preimmune repertoire, and the possible role of environmental antigens is also sparse.
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Affiliation(s)
- Stein Tore Solem
- Department of Marine Biotechnology, Norwegian College of Fishery Science, Breivika, N-9037 Tromsø, Norway.
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6
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Elemento O, Lefranc MP. IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2003; 27:763-779. [PMID: 12818634 DOI: 10.1016/s0145-305x(03)00078-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international ImMunoGeneTics information system ((R)). IMGT/PhyloGene is strongly associated with the IMGT gene and allele nomenclature and with the IMGT unique numbering for V-REGION, which directly creates standardized alignments from IMGT reference sequences. IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated to a sequence database. Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical tree representations. The resulting IMGT/PhyloGene tree is then used as a support for studying the evolution of particular subregions, such as the CDR-IMGT (Complementarity Determining Regions) or the V-RS (Variable gene Recombination Signals). IMGT/PhyloGene is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Olivier Elemento
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Université Montpellier II, UPR CNRS 1142, Institut de Génétique Humaine (IGH), 141 rue de la Cardonille, 34396 Cedex 5, Montpellier, France
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Zhang YA, Nie P, Luo HY, Wang YP, Sun YH, Zhu ZY. Characterization of cDNA encoding immunoglobulin light chain of the mandarin fish (Siniperca chuatsi). Vet Immunol Immunopathol 2003; 95:81-90. [PMID: 12969639 DOI: 10.1016/s0165-2427(03)00105-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Immunoglobulin light chain cDNA sequences of a perciform fish, the mandarin fish Siniperca chuatsi were amplified from head kidney mRNA by reverse transcription (RT)-PCR and RACE methods using degenerated primer and gene specific ones. In cDNA sequences of the VL region, nucleotide exchanges were present mainly within CDRs, although a lesser degree of variability was also found in FRs. Moreover, the length of CDR1 and CDR3 in the mandarin fish is shorter than in most other fish species. In the middle of S. chuatsi CL region, a microsatellite sequence (AGC)(6-8) was found, which is also present in another perciform species, the spotted wolffish (Anarhichas minor). The comparison of amino acid sequence of the mandarin fish CL domain with those of other vertebrates showed the highest degree of similarity of 94.5% to the spotted wolffish, while the similarity with rainbow trout (Oncorhynchus mykiss) Ig L1 (62.7%) and channel catfish (Ictalurus punctatus) Ig LG (55.9%) isotypes is also higher. However, there is only 50% identity in the VL regions between the mandarin fish and the wolffish. The sequence similarity of the mandarin fish CL domain with those of higher vertebrate did not readily allow it to be classified as kappa or lambda isotype. The phylogenetic analyses also demonstrated that the CL genes of the mandarin fish and most other teleost fish cluster as a separate branch out of the mammal kappa and lambda branches.
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Affiliation(s)
- Y A Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Laboratory of Fish Diseases, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei Province, PR China
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Okamoto K, Ikemura H, Savan R, Sakai M. Cloning, sequence and variability analysis of expressed immunoglobulin light chain genes from yellowtail Seriola quinqueradiata. FISH & SHELLFISH IMMUNOLOGY 2003; 14:55-70. [PMID: 12547626 DOI: 10.1006/fsim.2002.0417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The cDNA clones encoding immunoglobulin (Ig) light (L) chain variable (V) region associated with constant (C) region were isolated from yellowtail (Seriola quinqueradiata) kidney by expressed sequence tag analysis (accession numbers: AB062619-AB062668, AB064322). The sequences of both VL and CL region contain well-conserved cysteine residues important for intra- and inter-domain interaction in mammals. Comparisons of the amino acid sequence of the CL domain with those of other species showed a high degree of similarity, with 88.3%, 59.8%, and 60.6% to those of wolf fish (Anarhichas lupus), rainbow trout IgL I isotype (Oncorhynchus mykiss) and channel catfish G isotype (Ictalurus punctatus), respectively. Multiple sequence alignments of the CL domain with those of higher vertebrates, however, did not readily allow it to be classified as kappa or lambda isotypes. Furthermore, the pI, hydrophobicity and variability of yellowtail VL regions were studied in 65 cDNA clones and the diversity was observed in CDR1, CDR2 and CDR3 regions.
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Affiliation(s)
- Kazuyoshi Okamoto
- Faculty of Agriculture, Miyazaki University, Miyazaki, 889-2125, Japan
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Ramsland PA, Farrugia W. Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products. J Mol Recognit 2002; 15:248-59. [PMID: 12447901 DOI: 10.1002/jmr.585] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sequencing of all human immunoglobulin (Ig) germline gene segments has recently been completed. However, our first glimpses of the recombined products of this combinatorial gene system were in the 1970s, in landmark publications, reporting the crystal structures of two human myeloma proteins, the Mcg lambda light chain dimer and the New IgG1(lambda) Fab. Although numerous crystal structures of murine and human antibodies have now been determined, only a relatively small proportion of the human germline genes have had their corresponding protein three-dimensional structures resolved. Therefore, further structural investigations are required before the inherent diversity of the antibody repertoire can be fully appreciated. We discuss the detailed structural information available for human antibodies with regard to their immune functions. Also discussed, is how the structural information is finding application in the 'humanization' of murine antibodies as part of their development as 'biopharmaceuticals' for the treatment of human disease.
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Affiliation(s)
- Paul A Ramsland
- Structural Biology Laboratory, The Austin Research Institute, Studley Road, Heidelberg, Victoria 3084, Australia.
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Affiliation(s)
- V K Nguyen
- Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Sint Genesius Rode, 1050 Bruxelles, Belgium
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Ramsland PA, Kaushik A, Marchalonis JJ, Edmundson AB. Incorporation of long CDR3s into V domains: implications for the structural evolution of the antibody-combining site. EXPERIMENTAL AND CLINICAL IMMUNOGENETICS 2002; 18:176-98. [PMID: 11872949 DOI: 10.1159/000049197] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Available data suggest that 'primitive' antibody-combining sites often include longer than average HCDR3s. Long HCDR3 sequences have been reported in diverse vertebrates, including humans, cattle, camels and sharks. These long HCDR3 segments contain unusual sequence features such as stretches of Gly or Pro residues and multiple Cys residues. We examined how longer than average HCDR3s were accommodated in the V domains of human, murine and camel antibodies with known three-dimensional structures. The main conclusions were that (1) HCDR3s longer than 12 residues should protrude outward from the V domains; (2) descending HCDR3 polypeptides may utilize VL (including LCDR3) constituents as a platform, supporting the protruding segments; (3) intra- and inter-HCDR disulfides are frequently formed to rigidify the structure of HCDR3 or the combining site, and (4) V and C domains were possibly more similar in primordial antibodies than they are in their present day counterparts.
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Affiliation(s)
- P A Ramsland
- Crystallography Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
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12
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dos Santos NM, Hermsen T, Rombout JH, Pilström L, Stet RJ. Ig light chain variability in DNP(494)-KLH immunised sea bass (Dicentrarchus labrax L.): evidence for intra-molecular induced suppression. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2001; 25:387-401. [PMID: 11356219 DOI: 10.1016/s0145-305x(01)00002-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The coding sequence of the sea bass light chain was obtained by sequential anchored PCR on a head kidney cDNA library of a DNP(494)-KLH immunised sea bass. The cDNA sequence obtained codes for a leader peptide of 21aa and a mature IgL chain of 223aa. Both the amino acid sequence comparisons and neighbour-joining trees showed that the IgL chain of sea bass obtained is of the L1/G type. To study the variability of the light chain, additional PCRs on the cDNA library and cDNA from pooled head kidneys were performed. Multiple alignment of unique sequences (N=17) could be performed without introducing gaps, and showed extremely low variability in CDR1, and no variability in CDR2 or CDR3. A possible explanation for this low variability of the IgL1 chain might be the enhanced expression of monospecific anti-DNP antibodies. The isolation and characterisation of partial genomic and cDNA IgL sequences, which showed normal variability, corroborate this explanation.
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Affiliation(s)
- N M dos Santos
- Institute for Molecular and Cell Biology-University of Porto, Rua do Campo Alegre, 823 4150, Porto, Portugal
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13
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Lee SS, Greenberg A, Hsu E. Evolution and somatic diversification of immunoglobulin light chains. Curr Top Microbiol Immunol 2000; 248:285-300. [PMID: 10793483 DOI: 10.1007/978-3-642-59674-2_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- S S Lee
- Department of Physiology and Pharmacology, State University of New York, Health Science Center at Brooklyn 11203-2098, USA
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15
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Fleury D, Daniels RS, Skehel JJ, Knossow M, Bizebard T. Structural evidence for recognition of a single epitope by two distinct antibodies. Proteins 2000. [DOI: 10.1002/1097-0134(20000901)40:4<572::aid-prot30>3.0.co;2-n] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Xenopus cDNA sequences encoding the homolog of mammalian kappa (kappa) light (L) chains were isolated from isogenic tadpole and adult individuals to investigate whether there existed stage-specific immunoglobulin L chain expression and somatic diversification. In the course of these studies rearrangements to a sixth J(L) gene segment and a pseudogene (J(L)psi) were found, and it is suggested that the order of these gene segments with respect to the L chain constant (C) region exon is: J(L)6-J(L)1-J(L)2-J(L)3-J(L)4-J(L)5-J(L)psi-C(L). The cDNA junctional diversity was analyzed; few N and P regions were found and almost all the CDR3 were 9 codons in length. There were restricted patterns of recombination site resolution, and this is attributed to some constraint in JL coding end processing.
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Affiliation(s)
- Y Ji
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, NY 11203, USA
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Widholm H, Lundbäck AS, Daggfeldt A, Magnadottir B, Warr GW, Pilström L. Light chain variable region diversity in Atlantic cod (Gadus morhua L.). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 1999; 23:231-240. [PMID: 10402210 DOI: 10.1016/s0145-305x(99)00003-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This study was undertaken to determine if a lack of V(L) domain variability could explain, in part, the failure of Atlantic cod to respond to immunization with the production of specific antibodies. The variability of cod V(L) regions was studied in 33 cDNA and two genomic clones. The variability of the CDRs was estimated by the Shannon entropy method and compared with that in other species. It was found to be lowest in the little skate (Raja erinacea), higher in cod, and highest in Xenopus and mouse. While the variability of the CDRs is slightly lower in cod than in Xenopus and mouse, it is spread over broader areas of the amino acid sequence. The length of CDR1 and CDR3 in cod is equal to or exceeds that found in skate, Xenopus, chicken and mammals. Isoelectric points and hydrophobicity vary substantially among the studied Ig light chain domains. Thus, neither the length, nor the variability, nor the physicochemical properties (pI and hydrophobicity) of the L chain CDRs can explain the absence of antibody response to immunization in cod.
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Affiliation(s)
- H Widholm
- Department of Medical Immunology and Microbiology, Uppsala University, Sweden
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Abstract
The immunoglobulin light chains are classified as kappa or lambda in mammals and birds (homeothermic vertebrates), but the traditional criteria for this classification are not applicable to the light chains found in poikilothermic vertebrates. Still it is possible to find some relationships between Ig light chain sequences in these animals and in those of the homeothermic animals. It is generally accepted that the Ig light chains contribute to the antigen binding capacity of antibodies and the variability is approximately similar in all studied vertebrate species except the elasmobranchs. This might be explained by the organisation of the Ig light chain locus in these animals and the fact that the variable and joining DNA segments are joined in the genome. These conclusions are limited by the small number of species studied in this respect.
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Affiliation(s)
- L Pilström
- Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.
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Marchalonis JJ, Schluter SF, Bernstein RM, Shen S, Edmundson AB. Phylogenetic emergence and molecular evolution of the immunoglobulin family. Adv Immunol 1998; 70:417-506. [PMID: 9755343 DOI: 10.1016/s0065-2776(08)60392-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- J J Marchalonis
- Department of Microbiology and Immunology, College of Medicine, University of Arizona, Tucson 85724, USA
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Abstract
Immunoglobulins (Ig) are highly modular proteins, consisting of variable and constant domains, which have clear, conserved sequence patterns. These sequence patterns have allowed T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule domains, as well as some cell adhesion, cell surface receptor and muscle protein domains, to be identified as forming a superfamily of related proteins together with the Ig-domains. The domains of these proteins have been grouped into four sets: variable (V-set), constant-1 (C1-set), constant-2 (C2-set) and intermediate (I-set). X-ray and NMR studies have shown that these domains form a Greek-key beta-sandwich structure with the sets differing in the number of strands in the beta-sheets as well as in their sequence patterns. The conserved sequence elements in the major sets of Ig and Ig-like molecules have previously been reported as general sequence profiles. This work examines the variability within these sets. Detailed sequence profiles and consensus sequences for these sets and groups have been constructed and a novel form of presentation has been developed to overcome some of the drawbacks of current methods of presenting consensus sequences. The profiles that were constructed allow a comparison of the similarities and differences among the sets of Ig and Ig-like sequences and provide a means by which sequences can be tested for compatibility with Ig-like sequence motifs. As well, the sequence separations of the main residues in the characteristic "pin" structure of Ig-like molecules were examined for variation among the groups. From the profiles constructed here, measures of the degree of conservation within the groups of molecules were determined. These measures were used to assist in a reconsideration of possible evolutionary pathways between the major structural groups of the Ig-superfamily.
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Affiliation(s)
- D K Smith
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Greenberg AS, Hughes AL, Guo J, Avila D, McKinney EC, Flajnik MF. A novel "chimeric" antibody class in cartilaginous fish: IgM may not be the primordial immunoglobulin. Eur J Immunol 1996; 26:1123-9. [PMID: 8647177 DOI: 10.1002/eji.1830260525] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Using a degenerate oligonucleotide primer specific for immunoglobulin (Ig) constant type 1 (C-1 set) domain genes, products were amplified by the reverse transcriptase-polymerase chain reaction from nurse shark spleen cDNA. The deduced protein sequence of one of these clones reveals a novel Ig class in cartilaginous fish. A complete mRNA could encode a mature protein bearing an amino-terminal variable (V) domain, followed by six C-1 set domains, and ending in a carboxy-terminal tail typical of secreted IgM, IgA, and the new antigen receptor (NAR). The two amino-terminal C domains are orthologous to IgX (or IgR), an Ig heavy (H) chain class in the skate, and the last four domains are homologous to the carboxy-terminal four domains of NAR. We designate this "chimeric" Ig class IgNARC for Ig new antigen receptor from cartilaginous fish. Like NAR, but unlike shark IgM, IgNARC is encoded by very few V and C genes which apparently are not closely linked. The number of bands that hybridize with exon-specific probes varies with genomic DNA from individual sharks, suggestive of different numbers of IgNARC genes in different animals. A protein of approximately 95 kDa, which is likely to be the IgNARC H chain, is immunoprecipitated with both light chain-specific monoclonal antibodies and with antisera generated to a peptide comprising the IgNARC carboxy-terminal tail. We conclude that the arsenal of secreted antigen receptors in cartilaginous fish is greater than previously believed. In addition, our data cast doubt on the dogma that IgM is the primordial Ig isotype.
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Affiliation(s)
- A S Greenberg
- Department of Microbiology and Immunology, University of Miami, FL 33101, USA
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Magor KE, Higgins DA, Middleton DL, Warr GW. cDNA sequence and organization of the immunoglobulin light chain gene of the duck, Anas platyrhynchos. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 1994; 18:523-531. [PMID: 7768317 DOI: 10.1016/s0145-305x(06)80006-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A cDNA was cloned which encoded an immunoglobulin (Ig) light (L) chain of the White Pekin duck. The organization of the variable (V) and constant (C) domains was analyzed by genomic Southern blotting. The duck L chain gene has a similar chromosomal organization to that of the chicken, with a single lambda-like C region and multiple VL, hybridizing elements. The amino acid sequence of the VL region of the White Pekin duck L chain showed 88% identity with the Muscovy duck and 87% identity with the chicken, the JL region showed 92% identity with these species, and the CL region showed 88% identity with Muscovy duck and 66% with chicken. The constraints imposed by the gene-conversion mechanism of generating antibody diversity might account for the similarities of the avian V region sequences.
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Affiliation(s)
- K E Magor
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston 29425-2211, USA
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Politou AS, Gautel M, Pfuhl M, Labeit S, Pastore A. Immunoglobulin-type domains of titin: same fold, different stability? Biochemistry 1994; 33:4730-7. [PMID: 8161531 DOI: 10.1021/bi00181a604] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Titin is a 3-MDa protein thought to form a fibrous intracellular system in vertebrate striated muscle and to play an important role in sarcomere alignment during muscle contraction. It has also been implicated as a "molecular ruler", regulating the assembly and the precise length of the thick filaments [Whiting, A. J., Wardale, J., & Trinick, J. (1989) J. Mol. Biol. 205, 163-169]. Partial sequencing of titin-encoding cDNAs suggests that the protein is organized in a modular fashion, containing two classes of approximately 100-residue repeats [Labeit, S., Barlow, D. P., Gautel, M., Gibson, T., Holt, J., Hsieh, C. L., Francke, U., Leonard, K., Wardale, J., Whiting, A., & Trinick, J. (1990) Nature 345, 273-276]. These motifs, referred to as type I and type II modules, show sequence homology to the fibronectin III and immunoglobulin C2 superfamilies, respectively. Since the type II modules represent the most widely occurring motifs along the titin molecule, we expressed in Escherichia coli three domains of this type spanning different regions of the sarcomere (A-band and M-line) and studied their structure and stability. Using circular dichroism, nuclear magnetic resonance, and fluorescence spectroscopy, we showed that all the fragments examined are independently folded in solution and possess a beta-sheet conformation. Furthermore, employing NMR analysis, we identified an overall folding pattern present in all modules and related to the Ig fold, as previously suggested by theoretical predictions. The stability of the modules over a range of conditions was investigated by measuring key thermodynamic parameters for both thermal and chemical denaturation and by monitoring amide proton exchange as a function of time.(ABSTRACT TRUNCATED AT 250 WORDS)
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Bengtén E, Strömberg S, Pilström L. Immunoglobulin VH regions in Atlantic cod (Gadus morhua L.): their diversity and relationship to VH families from other species. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 1994; 18:109-122. [PMID: 8082814 DOI: 10.1016/0145-305x(94)90239-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Variable regions (VH) of Atlantic cod cDNA clones have been isolated by the polymerase chain reaction (PCR) technique, using primers for the first constant domain of heavy chain (CH1) and lambda gt11. Based upon sequence analysis and comparisons these clones have been divided into three different VH families. The approximate number of members in each family was estimated by genomic Southern blot. Comparisons of complementarity determining regions (CDRs) and frameworks (FRs) show that FR2 and the last part of FR3 are the most conserved regions. The CDR3 is very heterogeneous and gives a major contribution to VH diversity. Possible relationships between VH sequences from 17 species are shown graphically. Different VH families are often more conserved between species than within any one species. Two genomic VH clones have been isolated and partially sequenced. The VH genes have an octamer and TATA motif in the 5' region, followed by an 18-amino-acid-long hydrophobic leader, and the mature VH coding region. The characteristics heptamer-nonamer recombination signals for VH to D joining are present 3' of the VH segment.
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Affiliation(s)
- E Bengtén
- Department of Immunology, Uppsala University, Sweden
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Stewart SE, Du Pasquier L, Steiner LA. Diversity of expressed V and J regions of immunoglobulin light chains in Xenopus laevis. Eur J Immunol 1993; 23:1980-6. [PMID: 8344363 DOI: 10.1002/eji.1830230838] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In Xenopus laevis, two immunoglobulin light chain isotypes, designated L1 or rho and L2 or sigma, have been identified. The genomic organization of the L1 locus has been described previously: a constant (C) gene segment is preceded by a joining (J) gene segment; in addition, there are many cross-hybridizing variable (V) gene segments. To evaluate the extent of sequence diversity of L1 V regions, we screened three cDNA libraries, constructed from mitogen-stimulated Xenopus splenocytes, with probes for the C or the J gene segment. Eighteen cDNA clones that contain complete or truncated V regions were chosen for sequence analysis. The C regions of all clones are identical or nearly identical to the genomic C gene segment; the V regions are greater than 80% identical in nucleotide sequence and are presumably derived from a single family of V gene segments. Although framework regions are nearly identical, complementarity-determining regions are quite diverse. The expressed J segments fall into distinct groups, suggesting the presence of more than one germ-line J segment. Therefore, a genomic library was screened with a J region probe. A clone overlapping with the previously identified J-C clone, and containing four additional J gene segments, was isolated. All five J gene segments are very similar and three are identical in nucleotide sequence. Each of the three distinct germ-line J sequences is represented in the set of cDNA clones, suggesting that combinatorial diversification occurs; imprecision of V-J joining also appears to contribute to variability. Overall, these results suggest that the immunoglobulin repertoire in this species is not significantly restricted by a limitation in the diversity of light chain V regions.
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Affiliation(s)
- S E Stewart
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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Abstract
Sequences of the third complementarity determining region of antibody heavy chains (CDRH3s) are listed according to their length. Human sequences vary from 2 to 26 amino acids residues, but less extensively in other species. When combined with the other five complementarity determining regions, this enormous length variation of CDRH3, together with amino acid substitutions in their sequences, can provide a very large number of antibody specificities and can influence the shape of antibody combining sites.
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Affiliation(s)
- T T Wu
- Department of Biochemistry, Northwestern University, Evanston, Illinois 60208
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Abstract
All vertebrates with jaws (Gnathostomata) have B cells. With the exception of some B cells in cartilaginous fish that express germ-line joined Ig genes, all B cells, irrespective of the organization of their Ig genes (which varies among vertebrates), rearrange the Ig-gene segments somatically. Somatic diversification occurs in all species during rearrangement (junctional diversity) and later by somatic mutation of gene conversion. Somatic mutants are poorly selected in species that lack germinal centers, which may explain the differences in antibody repertoire among vertebrates. The early (larval or neonate) B-cell repertoire is restricted in all species so far studied because of a lack of N-region diversity and in some cases because of a special usage of the D segments of the heavy chain genes.
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