Somatic Diversity in CDR3 Loops Allows Single V-Genes To Encode Innate Immunological Memories for Multiple Pathogens

Abstract

The human Ab response to many common pathogens is oligoclonal, with restricted usage of Ig V-genes. Intriguingly, the IGVK3-11 and IGVH3-30 V-genes are repeatedly paired in protective Abs against the 23F polysaccharide of Streptococcus pneumoniae, as well as against the gB envelope protein of human CMV, where germline-encoded amino acids make key contacts with the gB protein. We constructed IgGs encoded by the germline IGVK3-11 and IGVH3-30 V-genes together with DNA encoding the respective CDR3 regions of the L chain and H chain found in a hypermutated anti-23F Ab. These IgGs encoded by germline V-genes bound specifically to 23F pneumococcal capsular polysaccharides with no reactivity to other serotypes of pneumococcal capsular polysaccharides or arrayed glycans and recognized l-rhamnose, a component of the 23F repeating subunit. IgGs encoded by this pair of germline V-genes mediated complement-dependent phagocytosis of encapsulated 23F S. pneumoniae by human neutrophils. Mutations in CDRL3 and CDRH3 had significant effects on binding. Thus, IGKV3-11 and IGHV3-30, depending on with which distinct DNA sequences encoding CDR3 they are recombined, can encode binding sites for protective Abs against chemically distinct Ags and thus, may encode innate immunological memory against human CMV and S. pneumoniae.

Structures of Preferred Human IgV Genes–Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation

“…In the Fab KE5/AD-2S1 complex, as had been seen in the 8F9/AD-2S1 structure (24), many residues encoded by the germline V genes make key contacts with Ag peptide side chains, and affinity maturation serves to support these germline-encoded contacts. A closer inspection of the residues encoded by the L chain V gene IGKV3-11 reveals two key basic and aromatic germline-encoded residues, Arg 91 (L) and Trp 94 (L), which are conserved in all four Fab molecules and make important Ag contacts (10,15,23,24,33,34). The side chain of Arg 91 (L) sits at the base of CDRL3 and CDRH3, forming hydrogen bonds with both the L-rhamnose and AD2-S1 Ags.…”

“…The crystal structures of the complexes of Fab 023.102/RGP and C05/L-rhamnose reveal the basis for the high specificity of these Abs for L-rhamnose, the key antigenic component of the PPS of S. pneumoniae serotype 23F (33)(34)(35) (L) in CDRL3 and stochastically encoded Glu 95 (H) in CDRH3 are placed so that their side chains complement the axial and equatorial L-rhamnose hydroxyls. The CDRH2 loop forms a small pocket to accommodate the C6 methyl group of L-rhamnose engaging the sugar in several van der Waals interactions, thereby elegantly promoting its binding over that of L-mannose (33).…”

Immunoglobulin Polygeny: An Evolutionary Perspective

“…These experiments show that binding site specificity depends on both H and L chains even for antibodies specific for the same hapten since heterologous light chains seldom restore the full binding site (Kranz & Voss, 1981). This mutual dependence is also demonstrated by the non-random pairing found in antibodies of certain specificity such as to the capsular polysaccharides of S. pneumoniae (Thomson et al, 2011). Further evidence for the effect of H-L pairing comes from studies of autoantibodies in a phenomenon called "receptor editing" (deWildt et al, 1999).…”

“…The CDR3 region of the heavy chain, hereafter designated HCDR3, is considered most important to the specificity of the binding site (Amit et al, 1986;Padlan, 1996;Xu & Davis2000;Mageed et al, 2001). In fact the same set of V-genes encoding CDR1 and CDR2 can theoretically and actuallycontribute the binding site for antibodies of quite different specificity in the context of different HCDR3 regions (Thomson et al, 2011;Ichiyoshi & Casali, 1994) as might be envisioned from a comparison of the CDR3 sequences shown in Fig. 8.…”

Molecular characterization and expression analysis of four isotypes of immunoglobulin light chain genes in orange-spotted grouper, Epinephelus coioides

“…The two V regions from IgH and IgL compose the antigen binding site surface of Ig molecules, to which three CDR loops from each V domain contribute. The CDR3 domain is encoded by parts of the V, D H (diversity), and either the J H (joining; in IgH) or J L (in IgL) gene segments; consequently, the CDR3 regions are more variable than CDR1 and CDR2, which are both solely encoded by V genes (Davis, 2004;Thomson et al, 2011). The length of IgL CDRs is considered an important factor for the versatility of the ability to bind antigens.…”