Bovine IgM antibodies with exceptionally long complementarity‐determining region 3 of the heavy chain share unique structural properties conferring restricted VH + Vλ pairings

Abstract

Naturally occurring antibody repertoires of cattle (Bos taurus) include a group of IgMlambda antibodies with exceptionally long complementarity-determining region 3 of the heavy chain (CDR3H) segments, containing multiple Cys residues. These massive CDR3H segments will greatly influence the tertiary and quaternary structures of the bovine IgM combining sites. As an antibody's combining site is formed by both heavy and light chains, we have analyzed the nucleotide sequences and structural properties of the lambda-light chains that pair with micro -heavy chains containing exceptionally long CDR3H. There appears to be an exquisite selective pressure for the use of three V(lambda)1 genes (V(lambda)1x and two new V(lambda)1d and V(lambda)1e genes) in IgM with unusually long CDR3H. The V(lambda)1d and V(lambda)1e genes are similar to each other, but diverge from the other V(lambda)1 genes into two closely related subfamilies. The available bovine V(lambda) genes are classified into three V(lambda) gene families: V(lambda)1, V(lambda)2 and V(lambda)3 based on nucleotide similarity >/=80%. Further, analysis of total Ser content and positions of Ser residues in the sequences was found to be sufficient to classify the cattle V(lambda)1 subfamilies. Patterns of Ser residues differ for V(lambda) domains from ruminant species (e.g. cattle, sheep and goats) and other mammals (e.g. humans and mice). These 'Ser signatures' can be used to track divergent evolution in lambda-light chains. Interestingly, Ser90L in complementarity-determining region 3 of the light chain (CDR3L) occurred in all V(lambda) domains that pair with V(H) regions containing exceptionally long CDR3H. A structural role for Ser90L was revealed in homology models of V(lambda) domains, i.e. to hold the ascending polypeptide of CDR3L in a relatively tight space between the N-terminal segment and residues from CDR1L. The CDR3L of V(lambda) domains also occupied smaller volumes if paired to V(H) domains with extremely long CDR3H (>/=48 residues), and were more variable in their conformation and filled larger volumes if CDR3Hs were </=22 residues. Thus, the role of the lambda-light chains in these unusual cattle antibodies is probably to act as a relatively featureless supporting platform for the extremely long CDR3H regions, which undoubtedly are dominantly involved in binding to an antigen.

Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows

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Determining the Epitope Dominance on the Capsid of a Serotype SAT2 Foot-and-Mouth Disease Virus by Mutational Analyses

“…The complementary determining regions (CDRs) of the heavy-and lightchain variable regions of an antibody interact with an antigen, and CDR3 is the most diverse (56,57). Unlike in mouse antibodies, the bovine Ig heavy chain has a very long CDR3, which can be more than 60 residues in length (58,59) and may span a spatial distance of up to 45 Å. As the CDR3 region is the most heterogenous, the three-dimensional structure of the antigen-binding site is influenced by its length (60).…”

Reshaping Antibody Diversity

“…The only known exception to this structural paradigm for antigen recognition is the variable lymphocyte receptor of jawless vertebrates, which use a leucine-rich repeat scaffold with variable loops to bind antigen (Alder et al, 2005; Pancer et al, 2004). Interestingly, some vertebrates, such as Bos taurus , have a very limited diversity of V gene segments (Berens et al, 1997; Lopez et al, 1998; Saini et al, 2003; Sinclair et al, 1997; Zhao et al, 2006), yet maintain a perfectly robust adaptive immune response, suggesting unique diversification mechanisms at work to generate a functional antibody repertoire.…”