The creation of a complete VLR gene is currently thought to occur during replication of lamprey lymphocyte DNA by a ‘copy-choice’ mechanism that is similar, but not identical, to gene conversion (described in Section 5-20). During DNA replication, LRR units flanking the VLR gene are copied into the VLR gene—presumably when a DNA strand being synthesized switches templates and copies sequences from one of these LRR units. Although final proof is still lacking, this template-switching mechanism may be triggered by enzymes of the AID-APOBEC family that are expressed by lamprey lymphocytes, and whose cytidine deaminase activity (CDA) could cause the single-strand DNA breaks that can start the copy-choice process. Lampreys possess two such enzymes: CDA1, which is expressed in VLRA-lineage lymphocytes, and CDA2, which is expressed in VLRB-lineage lymphocytes. It is not yet known if CDA1 or CDA2 is expressed in VLRC-expressing lymphocytes. The final VLR gene contains a complete amino-terminal capping LRR subunit, followed by the addition of up to seven internal LRR domains, each 24 amino acids long, and the removal of the internal noncoding regions to complete the formation of the carboxy-terminal LRR domain (see Fig. 5.25).
It is estimated that this somatic rearrangement mechanism can generate as much diversity in the VLR proteins as is possible for immunoglobulins. Indeed, the crystal structure of a VLR protein shows that the concave surface formed by the series of LRR repeats interacts with a variable insert in the carboxy-terminal LRR to form a surface capable of interacting with a great diversity of antigens. Thus, the diversity of the anticipatory repertoire of agnathans may be limited not by the numbers of possible receptors they can generate but by the number of lymphocytes present in any individual, as in the adaptive immune system of their evolutionary cousins, the gnathostomes. As noted above, each lamprey lymphocyte rearranges only one of the two germline VLR genes, expressing either a complete VLRA or VLRB or VLRC protein. The first two cell populations seem to have some characteristics of mammalian T and B lymphocytes,
Top panel: an incomplete germline copy of a lamprey VLR gene contains a framework (right) for the complete gene: the portion encoding the signal peptide (SP), part of an amino-terminal LRR unit (NT, dark blue), and a carboxy-terminal LRR unit that is split into two parts (LRR, light red; and CT, red) by intervening noncoding DNA sequences. Nearby flanking regions (left) contain multiple copies of VLR gene-‘cassettes’ with single or double copies of variable LRR domains (green) and cassettes that encode part of the amino-terminal LRR domains (light blue, yellow). Middle panel: somatic recombination causes various LRR units to be copied into the original VLR gene. This creates a complete VLR gene that contains the assembled amino-terminal LRR cassette (LRR NT) and first LRR (yellow), followed by several variable LRR units (green) and the completed carboxy-terminal LRR unit, and ends with the portion that encodes the stalk region of the VLR receptor. The cytidine deaminases PmCDA1 and PmCDA2 from the lamprey