scholarly journals New insights of glycosylation role on variable domain of antibody structures

2021 ◽  
Author(s):  
Marcella Nunes Melo-Braga ◽  
Milene Barbosa Carvalho ◽  
Manuela Cristina Emiliano Ferreira ◽  
Liza Felicori
Keyword(s):  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Data Bank ◽  
Variable Domain ◽  
Glycosylation Sites ◽  
Germline Genes ◽  
Hiv Antibodies ◽  
Antigen Antibody ◽  
Antibody Interactions

N-glycosylation at antibody variable domain (FvN-glyco) has emerged as an important modification for antibody function such as stability and antigen recognition, but it is also associated with autoimmune disease and IgE-mediated hypersensitivity reaction. However, the information related to its role and regulation is still scarce. Therefore, we investigated new insights in this regarding using solved antibody structures presenting in the Protein Data Bank (PDB). From 130 FvN-glyco structures, we observed significant findings as a higher prevalence of N-glycosylation in human and mouse antibodies containing IGHV1-8 and IGHV2-2 germline genes, respectively. We also speculate the influence of activation-induced cytidine deaminase (AID) in introducing N-glycosylation sites during somatic hypermutation, specifically on threonine to asparagine substitution. Moreover, we highlight the enrichment of anti-HIV antibodies containing N-glycosylation at antibody variable domain and where we showed a possible important role of N-glycosylation, besides to antigen-antibody interactions, in antibody chain pair and antibody-antibody interactions. These could be a positive secondary effect of glycosylation to enhance antigen binding and further neutralization, including an additional mechanism to form Fab-dimers. Overall, our findings extend the knowledge on the characteristics and diverse role of N-glycosylation at antibody variable domain.

scholarly journals Post-translational regulation of activation-induced cytidine deaminase

2008 ◽  
Vol 364 (1517) ◽  
pp. 667-673 ◽  
Author(s):  
Uttiya Basu ◽  
Andrew Franklin ◽  
Frederick W Alt
Keyword(s):  
Translational Regulation ◽  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Specific Protein ◽  
Antibody Repertoire ◽  
Dna Modification ◽  
Class Switch ◽  
Protein Factor ◽  
Activation Induced Cytidine Deaminase

The assembled immunoglobulin genes in the B cells of mice and humans are altered by distinct processes known as class switch recombination (CSR) and somatic hypermutation, leading to diversification of the antibody repertoire. These two DNA modification processes are initiated by the B cell-specific protein factor activation-induced cytidine deaminase (AID). AID is post-translationally modified by phosphorylation at multiple sites, although functional significance during CSR has been implicated only for phosphorylation at serine-38 (S38). Although multiple laboratories have demonstrated that AID function is regulated via phosphorylation at S38, the precise biological role of S38 phosphorylation has been a topic of debate. Here, we discuss our interpretation of the significance of AID regulation via phosphorylation and also discuss how this form of AID regulation may have evolved in higher organisms.

scholarly journals A/T mutagenesis in hypermutated immunoglobulin genes strongly depends on PCNAK164 modification

2007 ◽  
Vol 204 (8) ◽  
pp. 1989-1998 ◽  
Author(s):  
Petra Langerak ◽  
Anders O.H. Nygren ◽  
Peter H.L. Krijger ◽  
Paul C.M. van den Berk ◽  
Heinz Jacobs
Keyword(s):  
B Cells ◽  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Nuclear Antigen ◽  
Translesion Dna Synthesis ◽  
Class Switch ◽  
Activation Induced Cytidine Deaminase ◽  
Mismatch Recognition ◽  
Proliferating Cell

B cells use translesion DNA synthesis (TLS) to introduce somatic mutations around genetic lesions caused by activation-induced cytidine deaminase. Monoubiquitination at lysine164 of proliferating cell nuclear antigen (PCNAK164) stimulates TLS. To determine the role of PCNAK164 modifications in somatic hypermutation, PCNAK164R knock-in mice were generated. PCNAK164R/K164R mutants are born at a sub-Mendelian frequency. Although PCNAK164R/K164R B cells proliferate and class switch normally, the mutation spectrum of hypermutated immunoglobulin (Ig) genes alters dramatically. A strong reduction of mutations at template A/T is associated with a compensatory increase at G/C, which is a phenotype similar to polymerase η (Polη) and mismatch repair–deficient B cells. Mismatch recognition, monoubiquitinated PCNA, and Polη likely cooperate in establishing mutations at template A/T during replication of Ig genes.

scholarly journals Strand-biased defect in C/G transversions in hypermutating immunoglobulin genes in Rev1-deficient mice

2006 ◽  
Vol 203 (2) ◽  
pp. 319-323 ◽  
Author(s):  
Jacob G. Jansen ◽  
Petra Langerak ◽  
Anastasia Tsaalbi-Shtylik ◽  
Paul van den Berk ◽  
Heinz Jacobs ◽  
...  
Keyword(s):  
B Cells ◽  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Translesion Synthesis ◽  
Uracil Dna Glycosylase ◽  
Abasic Sites ◽  
Activation Induced Cytidine Deaminase ◽  
Deficient Mice

Somatic hypermutation of Ig genes enables B cells of the germinal center to generate high-affinity immunoglobulin variants. Key intermediates in somatic hypermutation are deoxyuridine lesions, introduced by activation-induced cytidine deaminase. These lesions can be processed further to abasic sites by uracil DNA glycosylase. Mutagenic replication of deoxyuridine, or of its abasic derivative, by translesion synthesis polymerases is hypothesized to underlie somatic hypermutation. Rev1 is a translesion synthesis polymerase that in vitro incorporates uniquely deoxycytidine opposite deoxyuridine and abasic residues. To investigate a role of Rev1 in mammalian somatic hypermutation we have generated mice deficient for Rev1. Although Rev1−/− mice display transient growth retardation, proliferation of Rev1−/− LPS-stimulated B cells is indistinguishable from wild-type cells. In mutated Ig genes from Rev1−/− mice, C to G transversions were virtually absent in the nontranscribed (coding) strand and reduced in the transcribed strand. This defect is associated with an increase of A to T, C to A, and T to C substitutions. These results indicate that Rev1 incorporates deoxycytidine residues, most likely opposite abasic nucleotides, during somatic hypermutation. In addition, loss of Rev1 causes compensatory increase in mutagenesis by other translesion synthesis polymerases.

Hyper-IgM syndromes: a model for studying the regulation of class switch recombination and somatic hypermutation generation

2002 ◽  
Vol 30 (4) ◽  
pp. 815-818 ◽  
Author(s):  
A. Durandy
Keyword(s):  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Class Switch Recombination ◽  
Humoral Response ◽  
Cd40 Ligand ◽  
Class Switch ◽  
Hyper Igm Syndrome ◽  
Hyper Igm ◽  
Nuclear Factor Kb

Several genetic defects in class switch recombination, which lead to a hyper-IgM syndrome, have been described recently in humans. In addition to the well known role of CD40-ligand-CD40 interaction, these pathologies demonstrate definitively the requirement of CD40-mediated nuclear factor kB activation and the essential role of a recently described molecule, the activationinduced cytidine deaminase in an efficient humoral response, which includes class switch recombination and the production of high-affinity antibodies.

scholarly journals Phosphorylation promotes activation-induced cytidine deaminase activity at the Myc oncogene

2017 ◽  
Vol 214 (12) ◽  
pp. 3543-3552 ◽  
Author(s):  
Yunxiang Mu ◽  
Monika A. Zelazowska ◽  
Kevin M. McBride
Keyword(s):  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Switch Region ◽  
Myc Oncogene ◽  
Class Switch ◽  
Oncogenic Mutations ◽  
Cytidine Deaminase Activity ◽  
Activation Induced Cytidine Deaminase ◽  
Myc Gene

Activation-induced cytidine deaminase (AID) is a mutator enzyme that targets immunoglobulin (Ig) genes to initiate antibody somatic hypermutation (SHM) and class switch recombination (CSR). Off-target AID association also occurs, which causes oncogenic mutations and chromosome rearrangements. However, AID occupancy does not directly correlate with DNA damage, suggesting that factors beyond AID association contribute to mutation targeting. CSR and SHM are regulated by phosphorylation on AID serine38 (pS38), but the role of pS38 in off-target activity has not been evaluated. We determined that lithium, a clinically used therapeutic, induced high AID pS38 levels. Using lithium and an AID-S38 phospho mutant, we compared the role of pS38 in AID activity at the Ig switch region and off-target Myc gene. We found that deficient pS38 abated AID chromatin association and CSR but not mutation at Myc. Enhanced pS38 elevated Myc translocation and mutation frequency but not CSR or Ig switch region mutation. Thus, AID activity can be differentially targeted by phosphorylation to induce oncogenic lesions.

scholarly journals Switch recombination and somatic hypermutation are controlled by the heavy chain 3′ enhancer region

2009 ◽  
Vol 206 (12) ◽  
pp. 2613-2623 ◽  
Author(s):  
Wesley A. Dunnick ◽  
John T. Collins ◽  
Jian Shi ◽  
Gerwin Westfield ◽  
Clinton Fontaine ◽  
...  
Keyword(s):  
Heavy Chain ◽  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Insertion Site ◽  
Enhancer Region ◽  
Class Switch ◽  
Activation Induced Cytidine Deaminase ◽  
Heavy Chain Constant Region ◽  
Bac Transgene

Both class switch recombination (CSR) and somatic hypermutation (SHM) require transcription and the trans-acting factor activation-induced cytidine deaminase (AID), and must be up-regulated during antigen-dependent differentiation of B lymphocytes. To test the role of the heavy chain 3′ enhancers in both CSR and SHM, we used a BAC transgene of the entire heavy chain constant region locus. Using Cre-loxP recombination to delete a 28-kb region that contains the four known 3′ heavy chain enhancers, we isolated lines of BAC transgenic mice with an intact heavy chain locus and paired lines in the same chromosomal insertion site lacking the 3′ enhancers. Intact heavy chain transgenes undergo CSR to all heavy chain genes and mutate their transgenic VDJ exon. In paired transgenes lacking the 3′ enhancer region, CSR to most heavy chain genes is reduced to ∼1% of the levels for intact heavy chain loci; SHM is also reduced. Finally, we find that in B cells with a transgene lacking the 3′ enhancers, interchromosomal recombination between the transgenic VDJ exon and the endogenous heavy chain C genes is more easily detected than CSR within the transgene.

scholarly journals The Genomic Organisation of the TRA/TRD Locus Validates the Peculiar Characteristics of Dromedary δ-Chain Expression

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 544
Author(s):  
Serafina Massari ◽  
Giovanna Linguiti ◽  
Francesco Giannico ◽  
Pietro D’Addabbo ◽  
Salvatrice Ciccarese ◽  
...  
Keyword(s):  
T Cells ◽  
Somatic Hypermutation ◽  
Genomic Structure ◽  
Mammalian Species ◽  
Γδ T Cells ◽  
Antigen Binding Site ◽  
Germline Genes ◽  
Δ Chain ◽  
Genomic Organisation

The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e., “γδ low species”) with a restricted diversity of γδ T cell receptors (TR). Conversely, artiodactyl species (i.e., “γδ high species”) account for a high proportion of γδ T cells with large γ and δ chain repertoires. The genomic organisation of the TR γ (TRG) and δ (TRD) loci has been determined in sheep and cattle, noting that a wide number of germline genes that encode for γ and δ chains characterise their genomes. Taking advantage of the current improved version of the genome assembly, we have investigated the genomic structure and gene content of the dromedary TRD locus, which, as in the other mammalian species, is nested within the TR α (TRA) genes. The most remarkable finding was the identification of a very limited number of variable germline genes (TRDV) compared to sheep and cattle, which supports our previous expression analyses for which the somatic hypermutation mechanism is able to enlarge and diversify the primary repertoire of dromedary δ chains. Furthermore, the comparison between genomic and expressed sequences reveals that D genes, up to four incorporated in a transcript, greatly contribute to the increased diversity of the dromedary δ chain antigen binding-site.

scholarly journals Adaptive antibody diversification through N-linked glycosylation of the immunoglobulin variable region

2018 ◽  
Vol 115 (8) ◽  
pp. 1901-1906 ◽  
Author(s):  
Fleur S. van de Bovenkamp ◽  
Ninotska I. L. Derksen ◽  
Pleuni Ooijevaar-de Heer ◽  
Karin A. van Schie ◽  
Simone Kruithof ◽  
...  
Keyword(s):  
Amino Acid ◽  
B Cell ◽  
Specific Antibody ◽  
Physiological Role ◽  
Antibody Responses ◽  
Variable Domain ◽  
Antigen Binding ◽  
Antibody Diversification ◽  
Glycosylation Sites

A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N-linked glycans, a process conditional on the introduction of consensus amino acid motifs (N-glycosylation sites) during somatic hypermutation. High levels of variable domain glycans have been associated with autoantibodies in rheumatoid arthritis, as well as certain follicular lymphomas. However, the role of these glycans in the humoral immune response remains poorly understood. Interestingly, studies have reported both positive and negative effects on antibody affinity. Our aim was to elucidate the role of variable domain glycans during antigen-specific antibody responses. By analyzing B-cell repertoires by next-generation sequencing, we demonstrate that N-glycosylation sites are introduced at positions in which glycans can affect antigen binding as a result of a specific clustering of progenitor glycosylation sites in the germline sequences of variable domain genes. By analyzing multiple human monoclonal and polyclonal (auto)antibody responses, we subsequently show that this process is subject to selection during antigen-specific antibody responses, skewed toward IgG4, and positively contributes to antigen binding. Together, these results highlight a physiological role for variable domain glycosylation as an additional layer of antibody diversification that modulates antigen binding.

scholarly journals AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression

2021 ◽  
Vol 11 ◽  
Author(s):  
Pablo Oppezzo ◽  
Marcelo Navarrete ◽  
Nicholas Chiorazzi
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Disease Progression ◽  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Adaptive Immune Response ◽  
Physiological Role ◽  
Enzyme Activation ◽  
Lymphocytic Leukemia ◽  
Leukemic Cells

The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.

scholarly journals Disparate roles of ATR and ATM in immunoglobulin class switch recombination and somatic hypermutation

2006 ◽  
Vol 203 (1) ◽  
pp. 99-110 ◽  
Author(s):  
Qiang Pan-Hammarström ◽  
Aleksi Lähdesmäki ◽  
Yaofeng Zhao ◽  
Likun Du ◽  
Zhihui Zhao ◽  
...  
Keyword(s):  
Ataxia Telangiectasia ◽  
Somatic Hypermutation ◽  
Cytidine Deaminase ◽  
Class Switch Recombination ◽  
End Joining ◽  
Class Switch ◽  
Activation Induced Cytidine Deaminase ◽  
Variable Heavy

Class switch recombination (CSR) and somatic hypermutation (SHM) are mechanistically related processes initiated by activation-induced cytidine deaminase. Here, we have studied the role of ataxia telangiectasia and Rad3-related protein (ATR) in CSR by analyzing the recombinational junctions, resulting from in vivo switching, in cells from patients with mutations in the ATR gene. The proportion of cells that have switched to immunoglobulin (Ig)A and IgG in the peripheral blood seems to be normal in ATR-deficient (ATRD) patients and the recombined S regions show a normal “blunt end-joining,” but impaired end joining with partially complementary (1–3 bp) DNA ends. There was also an increased usage of microhomology at the μ-α switch junctions, but only up to 9 bp, suggesting that the end-joining pathway requiring longer microhomologies (≥10 bp) may be ATR dependent. The SHM pattern in the Ig variable heavy chain genes is altered, with fewer mutations occurring at A and more mutations at T residues and thus a loss of strand bias in targeting A/T pairs within certain hotspots. These data suggest that the role of ATR is partially overlapping with that of ataxia telangiectasia–mutated protein, but that the former is also endowed with unique functional properties in the repair processes during CSR and SHM.

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