Evolution of two prototypic T cell lineages

Abstract

Jawless vertebrates, which occupy a unique position in chordate phylogeny, employ leucine-rich repeat (LRR)-based variable lymphocyte receptors (VLR) for antigen recognition. During the assembly of the VLR genes (VLRA, VLRB and VLRC), donor LRR-encoding sequences are copied in a step-wise manner into the incomplete germ-line genes. The assembled VLR genes are differentially expressed by discrete lymphocyte lineages: VLRA- and VLRC-producing cells are T-cell like, whereas VLRB-producing cells are B-cell like. VLRA(+) and VLRC(+) lymphocytes resemble the two principal T-cell lineages of jawed vertebrates that express the αβ or γδ T-cell receptors (TCR). Reminiscent of the interspersed nature of the TCRα/TCRδ locus in jawed vertebrates, the close proximity of the VLRA and VLRC loci facilitates sharing of donor LRR sequences during VLRA and VLRC assembly. Here we discuss the insight these findings provide into vertebrate T- and B-cell evolution, and the alternative types of anticipatory receptors they use for adaptive immunity.

Keywords: Adaptive immunity; Jawless vertebrates; Leucine-rich repeat; Variable lymphocyte receptor; αβ and γδ T-cell receptor.

Figure 1

Evolution of alternative adaptive immune systems in jawless and jawed vertebrates (modified from [89]). The LRR-based VLR genes are found only in the jawless vertebrates, whereas Ig-based BCR, TCR and MHCI/II genes are limited to the extant jawed vertebrates. Neither of these types of antigen recognition receptors has been found in amphioxus and tunicates, suggesting that the LRR-based VLRs and the Ig-based BCRs and TCRs emerged through convergent evolution. The presence of one and the other of these lymphocyte-based adaptive immune systems attests to their survival advantage.

Figure 2

Germline configuration of VLR genes in lampreys and hagfish (modified from [89]). The three pairs of orthologous germline VLRA, VLRC, and VLRB genes are different in lampreys and hagfish. Notably, sea lamprey VLRB has a 5' LRRCT- encoding donor sequence in the large intervening region, whereas the other VLR genes do not and they possess shorter intervening sequences. (not drawn to scale)

Figure 3

Schematic diagram of an VLR gene and the postulated assembly mechanism. (A) Domain organisation of a functional VLR protein. The diversity region is composed of a 3'-end of the N-terminal LRR (LRRNT), LRR1, multiple LRRVs, connecting peptide (CP) and a 5'-end of the C-terminal LRR (LRRCT). (B) Hypothetical scheme of VLR gene assembly process. Multiple LRR cassettes are located upstream and downstream of a pre-assembled germline VLR gene with its non-coding intervening sequence. At the beginning of the gene assembly process, a cytosine deaminase (CDA) converts cytosine (C) to uracil (U) in the germline VLR gene. The uracil is then removed by uracil-DNA glycosylase (UNG), leaving an apurinic (AP) site, blank residue in DNA. The AP site activates nicking activity of AP endonuclease (APE) which leads to a DNA double strand break. To repair this break, homologous recombination starts from the 5'-end and/or 3'-end of the break, based on the sequence homology of 10-30bp between the donor and acceptor LRR cassettes. This process is repeated along with deletion of the intervening sequence until a functional VLR is expressed on the cell surface.

Figure 4

Model of B- cell and T-cell like lineages in jawless vertebrates (modified from [90]). Cognate antigens (Ag) stimulate VLRA⁺, VLRC⁺ and VLRB⁺ lymphocytes, but whether or not VLRA and VLRC see native or processed antigens is unknown. Antigen-stimulated VLRB cells differentiate into VLRB-secreting plasma cells, whereas activated VLRA and VLRC cells do not secrete their receptors.

Figure 5

Structures of the three VLR isotypes. (A) VLRB binds to hen egg lysozyme (HEL) using multiple β-strands on its concave surface and insertion of the LRRCT variable loop into the catalytic cleft. (VLRB.2D, PDB ID: 3G3A) (B) VLRA also binds to HEL using its concave surface, but the LRRCT loop packs against the side of HEL, instead of inserting in the catalytic site. (VLRA.R2.1, PDB ID: 3M18) (C) Unlike VLRA and VLRB, VLRC does not have a protruding loop in the LRRCT, and the LRRCT sequence is almost invariant. (PDB ID: 3WO9, LRRCT is indicated in red and LRRNT in blue)

Figure 6

Schematic diagram of the gemomic organization of sea lamprey VLRA/VLRC locus and its resemblance with TCRα/δ loci of jawed vertebrates (modified from [82]). In lamprey a total of 262 genomic donor cassettes have been identified in sea lampreys [82]. Genomic donor cassettes observed only in VLRA or VLRC assemblies are indicated by purple and green dots, respectively, and donor cassettes shared by both VLRA and VLRC are indicated by orange dots.