A BAC contig map of the Ly49 gene cluster in 129 mice reveals extensive differences in gene content relative to C57BL/6 mice

Ly49 genes in non-rodent mammals

The Ly49 family of natural killer (NK) receptors is encoded by a highly polymorphic multigene family in the mouse and is also present in multiple copies in the rat. However, this gene exists as a single copy in primates and is mutated to non-function in humans. We recently showed that the cow also likely has only one Ly49 gene, but it is unclear what the Ly49 gene content is for other mammals. We have now isolated Ly49 cDNAs from the domestic cat, dog and pig and show that the corresponding gene appears to be single copy in these three species. The open reading frame is intact in all the genes and the putative proteins contain an immune tyrosine-based inhibition motif (ITIM), suggesting a role as an inhibitory receptor. In contrast to the other mammals, several Ly49-like genes appear to exist in the horse, indicating that amplification of this locus has occurred in a non-rodent lineage. Finally, phylogenetic analysis suggests that the rodent Ly49 genes have evolved more rapidly than their counterparts in mammals where the gene has remained as a single copy.

The NK cell receptor repertoire: formation, adaptation and exploitation

The identification of NK cell receptors specific for MHC class I molecules has greatly improved our knowledge of NK cell reactivity and specificity. Inhibitory receptors prevent NK cell activation directed against cells expressing self-MHC class I molecules. Consequently, diseased cells that do not express self-MHC class I molecules become susceptible to NK cell-mediated attack. Because of the specificity and distribution of inhibitory NK cell receptors, cells that express non-self (allogeneic) MHC class I molecules are also susceptible to NK cell reactions. This feature has been exploited in a clinical setting to treat leukemia patients.

Immune functions encoded by the natural killer gene complex

There has been marked progress in our understanding of the role of natural killer (NK) cells in immune responses, mainly due to the identification of NK-cell receptors and their ligands. The genes encoding many NK-cell receptors are located in the NK-gene complex (NKC). Here, we review the properties of NKC-encoded receptors, and provide a genomic and conceptual framework for an insight into NK-cell function and biology.

The killer cell immunoglobulin-like receptor (KIR) genomic region: gene-order, haplotypes and allelic polymorphism

Recent genetic studies have established that the killer cell immunoglobulin-like receptor (KIR) genomic region displays extensive diversity through variation in gene content and allelic polymorphism within individual KIR genes. It is demonstrated by family segregation analysis, genomic sequencing, and gene order determination that genomic diversity by gene content alone gives rise to more than 20 different KIR haplotypes and at least 40-50 KIR genotypes. In the most reductionist format, KIR haplotypes can be accommodated within one of 10 different prototypes, each with multiple permutations. Our haplotype model considers the KIR haplotype as two separate halves: the centromeric half bordered upstream by KIR3DL3 and downstream by 2DL4, and the telomeric half bordered upstream by 2DL4 and downstream by 3DL2. There are rare KIR haplotypes that do not fit into this model. Recombination, gene duplication, and inversion can however, readily explain these haplotypes. Additional allelic polymorphism imposes extensive individual variability. Accordingly, this segment of the human genome displays a level of diversity similar to the one observed for the human major histocompatibility complex. Recent application of immunogenetic analysis of KIR genes in patient populations implicates these genes as important genetic disease susceptibility factors.

Innate immunity to cytomegalovirus: the Cmv1 locus and its role in natural killer cell function

The identification and characterization of genetic loci that contribute to patterns of susceptibility/resistance to infection provide important insights into the mechanisms of innate and adaptive immunity. Genetic heterogeneity across the population makes the characterization of such traits in humans technically difficult; however, inbred animal models represent an ideal tool for such analyses. This review illustrates the power of mouse genetics as utilized for the identification and characterization of the locus conferring early resistance to murine cytomegalovirus infection, Cmv1. This locus encodes an activating C-type lectin receptor of the Ly49 family that promotes natural killer (NK) cell cytolysis of infected cells. Although NK cells are usually able to detect and destroy virally infected cells via recognition of the downregulation of MHC class I molecules, the Cmv1 locus provides the first example of an NK receptor that is able to mediate clearance of viral infection via direct recognition of a virally encoded protein.

Sequence analysis of the ly49 cluster in C57BL/6 mice: a rapidly evolving multigene family in the immune system

The cytotoxic activity of murine natural killer cells is controlled in part through the action of genes belonging to the Ly49 family. Members of this multigene family are found in a region on mouse chromosome 6 termed the natural killer gene complex. Using data available through public databases, we performed sequence analysis of a 620-kb region in C57Bl/6 (B6) mice that contains the Ly49 genes. The contiguous genomic sequence has allowed us to describe the complete B6 Ly49 gene repertoire, which includes two recently described genes as well as three partial genes. We have shown that the genes in the cluster have evolved through a series of large duplication events involving units of one or more genes and we have attempted to characterize the nature of the duplication end points. Finally, we have used information regarding gene sequence relationships and insertion of repetitive elements to construct a model for the evolution of the gene cluster. Our study illustrates that the Ly49 cluster represents an example of a rapidly evolving gene family, and continued analysis of this region in other strains will undoubtedly provide further insight into mechanisms for generating genomic diversity.

Variable receptors controlling activation and inhibition of NK cells

NK cells are important effector lymphocytes of innate immunity; they kill infected cells and produce cytokines that stimulate other immune effects. Once considered relatively homogeneous, NK cells are now seen to be highly diverse. Within an individual, expression of different combinations of inhibitory and stimulatory receptors creates a diverse NK cell repertoire, which exhibits specificity in the immune response. Rapid evolution of NK cell receptor gene families distinguishes members of a species and causes substantial species-specific differences in NK cell receptor systems. All known ligands for these diverse receptors are MHC class I molecules, or molecules of host or pathogen origin that are homologous to MHC class I.

Aberrant DAP12 signaling in the 129 strain of mice: implications for the analysis of gene-targeted mice

NK cells are implicated in antiviral responses, bone marrow transplantation and tumor immunosurveillance. Their function is controlled, in part, through the Ly49 family of class I binding receptors. Inhibitory Ly49s suppress signaling, while activating Ly49s (i.e., Ly49D) activate NK cells via the DAP12 signaling chain. Activating Ly49 signaling has been studied primarily in C57BL/6 mice, however, 129 substrains are commonly used in gene-targeting experiments. In this study, we show that in contrast to C57BL/6 NK cells, cross-linking of DAP12-coupled receptors in 129/J mice induces phosphorylation of DAP12 but not calcium mobilization or cytokine production. Consistent with poor-activating Ly49 function, 129/J mice reject bone marrow less efficiently than C57BL/6 mice. Sequence analysis of receptors and DAP12 suggests no structural basis for inactivity, and both the 129/J and C57BL/6 receptors demonstrate normal function in a reconstituted receptor system. Most importantly, reconstitution of Ly49D in 129/J NK cells demonstrated that the signaling deficit is within the NK cells themselves. These unexpected findings bring into question any NK analysis of 129/J, 129Sv, or gene-targeted mice derived from these strains before complete backcrossing, and provide a possible explanation for the differences observed in the immune response of 129 mice in a variety of models.