Analysis of the mouse 129-strain Nkrp1-Clr gene cluster reveals conservation of genomic organization and functional receptor–ligand interactions despite significant allelic polymorphism

Abstract

The Nkrp1 (Klrb) family of NK cell receptors and their genetically linked Clr (Clec2) ligands are conserved between rodents and humans. Nonetheless, certain mouse and rat Nkrp1 genes exhibit significant allelic polymorphism between inbred strains. We previously demonstrated that the Nkrp1-Clr recognition system is genetically and functionally conserved between the B6 and BALB/c strains, with focused sequence divergence evident in certain genes (e.g., Nkrp1b,c). Here, we extend this finding by mapping the 129-strain Nkrp1-Clr gene cluster, which is structurally conserved yet displays significant sequence divergence relative to the B6 haplotype. In addition, we show that 129-strain NK cells possess comparable Nkrp1 and Clr transcript expression, and characterize several NKR-P1:Clr interactions that are functionally conserved between the B6 and 129 strains, including documented and novel receptor-ligand pairs. Thus, despite significant allelic polymorphism observed in the Nkrp1-Clr region, the overall genetic organization and functional repertoire appear to be conserved among mouse strains, in contrast to the striking variation observed in the corresponding Ly49 region. These data extend our knowledge of the complex genetically linked Nkrp1-Clr NK recognition system in mice.

The mouse NKR-P1B:Clr-b recognition system is a negative regulator of innate immune responses

“…12,17,18 The currently known receptor-ligand pairs for these families include NKR-P1B: Clr-b; NKR-P1F:Clr-c,d,g; and NKR-P1G:Clr-d,f,g. 17,18,21,22 We have generated an NKR-P1B-deficient B6 mouse strain to study the role of NKR-P1B in NK cell development and function in vivo. We chose to target NKR-P1B for the following reasons: (1) the NKR-P1B:Clr-b system is well characterized in mice, and appropriate reagents, such as specific monoclonal antibodies (mAbs) and a complementary Clr-b gene-deficient mouse strain, are available 13,23 ; (2) the NKR-P1B:Clr-b system is analogous to the inhibitory NKR-P1A:LLT1 system in humans, although their expression patterns may vary 24,25 ; (3) the existence of 3 significantly different Nkrp1b alleles suggests a possible divergence as a result of pathogen challenge (eg, rat cytomegalovirus encodes a C-type lectinlike protein with homology to rat Clr- 11 [Clec2d11] that protects infected cells from NK recognition via the inhibitory rat NKR-P1B receptor) 26 ; and (4) in contrast to other, tissue-specific Clr family members, Clr-b, like MHC-I, is broadly expressed on hematopoietic cells, and its expression on transfected cells protects them from NK-mediated lysis.…”

“…Notably, NKR-P1G is another inhibitory member of the NKR-P1 receptor family, and NKR-P1F shares overlapping ligand specificity with NKR-P1G. 11,15,21,22,49 A full analysis of Clr-b interactions with other Clr family members remains to be tested.…”

A Viral Immunoevasin Controls Innate Immunity by Targeting the Prototypical Natural Killer Cell Receptor Family

“…Yet to date, NKR-P1C, the prototypical NK1.1 antigen in B6 mice (Glimcher et al, 1977;Koo and Peppard, 1984;Ryan et al, 1992), and NKR-P1A remain orphan-activating receptors with unknown physiological ligands. On the other hand, the paired NKR-P1F and NKR-P1G receptors recognize overlapping ''self'' Clr (Clec2) ligands to balance signals during NK cell education and effector responses, while the inhibitory NKR-P1B receptor recognizes the broadly expressed self Clr-b (Clec2d) ligand (Carlyle et al, 2004;Chen et al, 2011;Iizuka et al, 2003;Kveberg et al, 2009 been shown to be involved in ''missing-self'' recognition under diverse pathological states (Kirkham and Carlyle, 2014), including cancer (Carlyle et al, 2004), genotoxic and cellular stress (Fine et al, 2010), hematopoietic transplantation , immune escape of primary lymphoma cells , and cytomegalovirus and poxvirus infection Voigt et al, 2007;Williams et al, 2012), while the remainder of the self Clr ligands remain less well characterized. Among pathogens recognized by NK cells, cytomegaloviruses (CMV) demonstrate co-evolution with their natural hosts, likely due to cycles of natural selection for viral versus host fitness.…”

Functional characterization of a conserved pair of NKR‐P1 receptors expressed by NK cells and T lymphocytes in liver and gut

“…Even though NKR-P1 receptors and their Clr ligands are less polymorphic than Ly49s and their MHC ligands, there are some allelic variations of both NKR-P1A and NKR-P1B [29]. Some alleles are so divergent they have mistakenly been characterized as novel proteins (rat NKR-P1B PVG as NKR-P1C [15], and mouse NKR-P1B B6 as NKR-P1D [30].…”

“…Rat NKR-P1B is a strong inhibitory receptor that is expressed by a major subset of nonalloreactive Ly49 low NK cells [15], as well as by a characteristic subset of highly responsive, fully differentiated NK cells detected in larger numbers in peripheral blood, liver, and gut-associated lymphoid organs [27]. NKR-P1B is shown to be important for non-MHC-dependent "missing self"-recognition, and downregulation of ligand in response to virus infections and genotoxic stress induces increased sensitivity to NK-mediated killing by the loss of inhibitory signaling in the NK cell [17,28].Even though NKR-P1 receptors and their Clr ligands are less polymorphic than Ly49s and their MHC ligands, there are some allelic variations of both NKR-P1A and NKR-P1B [29]. Some alleles are so divergent they have mistakenly been characterized as novel proteins (rat NKR-P1B PVG as NKR-P1C [15], and mouse NKR-P1B B6 as NKR-P1D [30].…”