Introduction

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The Leukocyte Receptor Complex (LRC) (19q13.4)

The KIR gene family currently consists of 15 gene loci (KIR2DL1, KIR2DL2/L3, KIR2DL4, KIR2DL5A, KIR2DL5B, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, KIR3DL1/S1, KIR3DL2, KIR3DL3 and two pseudogenes, KIR2DP1 and KIR3DP1) encoded within a 100-200 Kb region of the Leukocyte Receptor Complex (LRC) located on chromosome 19 (19q13.4) (1). The LRC constitutes a large, 1 Mb, and dense cluster of rapidly evolving immune genes (2) which contains genes encoding other cell surface molecules with distinctive Ig-like extra-cellular domains. These genes include, from centromere to telomere, Leukocyte Immunoglobulin-like Receptors (LILR) and Leukocyte-Associated Immunoglobulin-like Receptors (LAIR), FcGammaR as well as the Natural cytotoxicity-triggering Receptor 1 (NCR1) (3, 4). In addition the extended LRC contains genes encoding the Sialic acid binding Immunoglobulin-like Lectins (SIGLEC) and the CD66 family members such as the carcino-embryonic antigen (CEA) genes as well as the genes encoding the transmembrane adaptor molecules DAP10 and DAP12 (5, 6).

 

 

Figure 1: The extended Leukocyte Receptor Complex (19q13.4) and a KIR haplotype. KIR genes are encoded within a 150 Kb stretch of the 1 Mb long extended LRC on chromosome 19. The extended LRC also contains the genes encoding DAP adaptor proteins, CD66 antigens as well as SIGLEC, FcGRT, LILR, LAIR, FcAlphaR and NCR1 receptors. A prototypical group A KIR haplotype is shown in the right portion of the figure, where blue boxes indicate framework genes, purple boxes pseudogenes (KIR3DP1 is also a framework gene), red boxes indicate inhibitory KIR and green boxes represent activating KIR genes.

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KIR Gene Organisation

KIR genes vary in length from 4 to 16 Kb (full genomic sequence) and can contain four to nine exons. KIR genes are classified as belonging to one of three groups according to their structural features: 1) Type I KIR2D genes, which encode two extra-cellular domain proteins with a D1 and D2 conformation; 2) The structurally divergent Type II KIR2D genes which encode two extra-cellular domain proteins with a D0 and D2 conformation and finally; 3) KIR3D genes encoding proteins with three extra-cellular Ig-like domains (D0, D1 and D2) (7).

Type I KIR2D genes, which include the pseudogene KIR2DP1 as well as KIR2DL1-3 and KIR2DS1-5 genes, possess eight exons as well as a pseudoexon 3 sequence (8, 9, 10). This pseudoexon is inactivated in Type I KIR2D. In some cases this is due to a nucleotide substitution located on the intron 2-exon 3 splice-site where its nucleotide sequence exhibits a high-degree of identity to KIR3D exon 3 sequences and possesses a characteristic three base pair deletion. In other cases a premature stop codon initiates differential splicing of exon 3 (11). Within the Type I KIR2D group of genes, KIR2DL1 and KIR2DL2 share a common deletion in exon 7 distinguishing them from all other KIR in this exon, which results in a shorter exon 7 sequence. Similarly, within Type I KIR2D, KIR2DL1-3 differ from KIR2DS1-5 only in the length of their cytoplasmic tail encoding region in exon 9. The KIR2DP1 pseudogene structure differs from that of KIR2DL1-3 in that the former has a shorter exon 4 sequence, due to a single base pair deletion (12).

Type II KIR2D genes include KIR2DL4 and KIR2DL5. Unlike KIR3D and Type I KIR2D, Type II KIR2D characteristically have deleted the region corresponding to exon 4 in all other KIR. Additionally, Type II KIR2D genes differ from Type I KIR2D genes in that the former possess a translated exon 3, while Type I KIR2D genes have an untranslated pseudoexon 3 sequence in its place (12, 13). Within the Type II KIR2D genes, KIR2DL4 is further differentiated from KIR2DL5 (as well as from other KIR genes) by the length of its exon 1 sequence. In KIR2DL4, exon 1 was found to be six nucleotides longer and to possess an initiation codon different from those present in the other KIR genes. This initiation codon is in better agreement with the 'Kozak transcription initiation consensus sequence' (14) than the second potential initiation codon in KIR2DL4 that corresponds to the initiation codon present in other KIR genes (12).

KIR3D genes possess nine exons and include the structurally related KIR3DL1, KIR3DS1, KIR3DL2 and KIR3DL3 genes. KIR3DL2 nucleotide sequences are the longest of all KIR genes and span 16,256 bp in full genomic sequences and 1,368 bp in cDNA. Within the KIR3D group, the four KIR genes differ in the length of the region encoding the cytoplasmic tail in exon 9 (8, 15, 16). The length of the cytoplasmic tail of KIR proteins can vary from 14 amino acid residues long (in some KIR3DS1 alleles) to 108 amino acid residues long (in KIR2DL4 proteins). Additionally, KIR3DS1 differs from KIR3DL1 or KIR3DL2 in that the former has a shorter exon 8 sequence. KIR3DL3 differs from other KIR sequences in that it completely lacks exon 6. The most extreme KIR gene structure difference observed was that of KIR3DP1 (17). This gene fragment completely lacks exons 6 through 9, and occasionally also exon 2. The remaining portions of the gene which are present (exon 1, 3, 4 and 5) share a high level of sequence identity to other KIR3D sequences, in particular to KIR3DL3 sequences.

 

Figure 2: KIR gene organisation. KIR genes sharing similar structural organisation have been grouped accordingly, while KIR genes with structural peculiarities are shown on their own. The coding regions of the exons are represented as blue boxes, their size in base pairs is shown in digits above them. The pseudoexon 3 and the deleted KIR3DP1 exon 2 is shown in red. The brackets at the bottom of the diagram illustrate the way in which the exons code for each protein domain and region.

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KIR Haplotypes

KIR genes are organised into two broad haplotypes termed A and B, which have been shown to exhibit extensive variation in the number and type of KIR genes present. Each A or B KIR haplotype consists of four framework genes which, with very few exceptions, are present in every individual. The KIR gene cluster is flanked by KIR3DL3 at the centromeric end, KIR3DL2 at the telomeric end and KIR3DP1 and KIR2DL4 in the middle (3, 7, 18). These four framework genes limit two regions of variable KIR gene content where the remaining KIR genes are located. All KIR genes are arranged in a head to tail fashion approximately 2.4 Kb apart from each other (5). Many KIR haplotypes have been defined by family segregation studies (19, 20, 21).

Based on their gene content, KIR genotypes can be divided into two broad haplotypes termed A and B. These haplotype groups were originally distinguished using restriction fragment length polymorphism (RFLP), with the presence of a ~24 Kb HindIII fragment indicating a group B haplotype (7, 22). However, these haplotype groups are currently distinguished by the number and combination of KIR genes present. According to this new KIR haplotype group definition, group A haplotypes are generally non-variable in its gene organisation with all four framework genes present plus KIR2DL1, KIR2DL3, KIR3DL1, KIR2DS4 and KIR2DP1. Group B haplotypes show a lot more variation in the number and combination of KIR genes present and are characterized by the presence of one or more of KIR2DL2, KIR2DL5A/B, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS5 and KIR3DS1 genes (23, 24). Group B haplotypes possess a greater variability in the number of genes present. They possess from one to five activating KIR (i.e. KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS5 and KIR3DS1) and can incorporate inhibitory KIR genes which are known to be absent in group A haplotypes (i.e. KIR2DL2 and KIR2DL5) (21). KIR genotyping techniques used in family segregation analysis have defined over 40 distinct group B haplotypes (19, 21, 25, 26). For a diagramatic representation of sequenced KIR haplotypes, please see the Sequenced Haplotypes page.

KIR Gene Motifs

Every KIR haplotype is a combination of a centromeric and a telomeric KIR gene motif. Each of these KIR gene motifs were characterized by sequencing of the complete KIR haplotypes of twelve carefully selected cell lines. In total four centromeric and two telomeric gene motifs have been identified based on the combination of KIR genes present in the centromeric or telomeric segment respectively (27). The centromeric segment is defined as all genes located between KIR3DL3 on the centromeric side and KIR3DP1 on the central part of the KIR gene cluster. The telomeric segment is defined as all genes present between KIR2DL4 on the central part and KIR3DL2 on the telomeric side of the KIR gene cluster (4). One haplotype A specific centromeric and telomeric KIR gene motif were identified. The remaining three centromeric and one telomeric KIR gene motif are all specific for KIR group B haplotypes. A KIR A haplotype will always consist of the A specific centromeric and telomeric gene motifs. A KIR B haplotype consists of any other combination of centromeric and telomeric KIR gene motifs.

The expression of some KIR genes and alleles is affected by intrinsic genetic defects which lead to their non-transcription, this is the case of the KIR pseudogenes KIR2DP1 and KIR3DP1 and of some KIR2DL5 alleles (12). Furthermore, some structurally intact KIR genes are transcribed but only expressed at low levels on the surface of NK cells for reasons which remain unknown, as happens for KIR3DL3 (28). In addition to this, recent discoveries have shown that amino acid polymorphisms of particular KIR proteins lead to either their cytoplasmic retention or to the formation of soluble variants (as has been shown for the KIR3DL1*004 and KIR2DS4*003 proteins, respectively). KIR3DL1*004 is not expressed in the surface of NK cells due to the presence of an amino acid substitution which disrupts the proper folding of the D0 domain (29). However, KIR2DS4*003 proteins are transcribed but not expressed on the cell surface due to the disruption of their protein sequence (due to a 22 bp deletion in exon 5) after the D2 domain (30, 31). The absence of a transmembrane and cytoplasmic domain together with the high frequency of this allele in human populations has suggested the possibility that this deviant KIR protein might be secreted by NK cells (31, 32).

KIR Proteins

KIR proteins possess characteristic Ig-like domains on their extracellular regions, which in some KIR proteins are involved in HLA class I ligand binding. They also possess transmembrane and cytoplasmic regions which are functionally relevant as they define the type of signal which is transduced to the NK cell. KIR proteins can have two or three Ig-like domains (hence KIR2D or KIR3D) as well as short or long cytoplasmic tails (represented as KIR2DS or KIR2DL). Two domain KIR proteins are subdivided into two groups depending on the origin of the membrane distal Ig-like domains present. Type I KIR2D proteins (KIR2DL1, KIR2DL2, KIR2DL3, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4 and KIR2DS5) possess a membrane-distal Ig-like domain similar in origin to the KIR3D D1 Ig-like domain but lack a D0 domain. This D1 Ig-like domain is encoded mainly by the fourth exon of the corresponding KIR genes. The Type II KIR2D proteins, KIR2DL4 and KIR2DL5, possess a membrane-distal Ig-like domain of similar sequence to the D0 domain present in KIR3D proteins, however, Type II KIR2D lack a D1 domain. Long cytoplasmic tails usually contain two Immune Tyrosine-based Inhibitory Motifs (ITIM) which transduce inhibitory signals to the NK cell. Short cytoplasmic tails possess a positively charged amino acid residue in their transmembrane region which allows them to associate with a DAP12 signalling molecule capable of generating an activation signal (7).

 

 

Figure 3: KIR protein structures. The structural characteristics of two and three Ig-like domain KIR proteins are shown. The association of activating KIR to adaptor molecules is shown in green, whereas the ITIM of inhibitory KIR are shown as red boxes.

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Exceptions to this is KIR2DL4, which contains only one N-terminus ITIM. In addition, KIR2DL4 also possesses a charged residue (arginine) in its transmembrane domain, a feature which allows this receptor to elicit both inhibitory and activating signals (32). KIR control the response of human NK cells by delivering inhibitory or activating signals upon recognition of MHC class I ligands on the surface of potential target cells (10).

KIR proteins vary in length from 306 to 456 amino acid residues. Although the differences in protein length are mostly the consequence of the number of Ig-like domains present, cytoplasmic region length diversity is also an influencing factor. The leader peptide of most KIR proteins is 21 amino acid residues long. However, the presence of a different initiation codon generates a correspondingly longer leader peptide in KIR2DL4 proteins (13).

The D0 Ig-like domain present in Type II KIR2D proteins and KIR3D proteins is approximately 96 amino acid residues in length (8, 9). The D1 domain of Type I KIR2D and of KIR3D proteins is 102 amino acid residues long, while the D2 domain of all KIR proteins is 98 amino acid residues long (8). The length of the stem region varies from the 24 amino acid residues present in most KIR proteins, to only seven amino acid residues in the divergent KIR3DL3 protein (16). The transmembrane region is 20 amino acid residues long for most KIR proteins, but one residue shorter on KIR2DL1 and KIR2DL2 proteins as a result of a three base pair deletion in exon 7 (8, 9). Finally, the cytoplasmic region of KIR proteins exhibits greater length variations, ranging from 23 amino acid residues in some KIR3DS1 alleles to the 96 amino acid residues present in KIR3DL2 proteins (8, 33, 34).

 

Figure 4: Approximate KIR protein domain and region lengths. The main structural characteristics of KIR proteins are shown where the domains and regions are represented as boxes of different colours according to the key at the bottom of the figure. The length of each domain or region is shown in digits above their corresponding box.

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References

All references are linked to the PubMed abstract where possible.

  1. Trowsdale J.
    Genetic and functional relationships between MHC and NK receptor genes.
    Immunity(2001) 15:363-74 (Abstract)
  2. Khakoo SI, Rajalingam R, Shum BP, Weidenbach K, Flodin L, Muir DG, Canavez F, Cooper SL, Valiante NM, Lanier LL, Parham P.
    Rapid evolution of NK cell receptor systems demonstrated by comparison of chimpanzees and humans.
    Immunity (2000) 12:687-98 (Abstract)
  3. Wilson MJ, Torkar M, Haude A, Milne S, Jones T, Sheer D, Beck S, Trowsdale J.
    Plasticity in the organization and sequences of human KIR/ILT gene families.
    Proc Natl Acad Sci USA (2000) 97:4778-83 (Abstract)
  4. Trowsdale J, Barten R, Haude A, Stewart CA, Beck S, Wilson MJ.
    The genomic context of natural killer receptor extended gene families.
    Immunol Rev (2001) 181:20-38 (Abstract)
  5. Hsu KC, Chida S, Geraghty DE, Dupont B.
    The killer cell immunoglobulin-like receptor (KIR) genomic region: gene-order, haplotypes and allelic polymorphism.
    Immunol Rev (2002) 190:40-52 (Abstract)
  6. Barrow AD, Trowsdale J.
    The extended human leukocyte receptor complex: diverse ways of modulating immune reponses.
    Immunological Reviews (2008) 224:98-123
  7. Vilches C, Parham P.
    KIR: diverse, rapidly evolving receptors of innate and adaptive immunity.
    Annu Rev Immunol (2002) 20:217-51 (Abstract)
  8. Colonna M, Samaridis J.
    Cloning of immunoglobulin-superfamily members associated with HLA-C and HLA-B recognition by human natural killer cells.
    Science (1985) 268:405-8 (Abstract)
  9. Wagtmann N, Biassoni R, Cantoni C, Verdiani S, Malnati MS, Vitale M, Bottino C, Moretta L, Moretta A, and Long EO.
    Molecular clones of the p58 NK cell receptor reveal immunoglobulin-related molecules with diversity in both the extra- and intracellular domains.
    Immunity (1995) 2:439-49 (Abstract)
  10. Vilches C, Gardiner CM, Parham P.
    Gene structure and promoter variation of expressed and nonexpressed variants of the KIR2DL5 gene.
    J Immunol (2000) 165:6416-21 (Abstract)
  11. Vilches C, Pando MJ, Parham P.
    Genes encoding human killer-cell Ig-like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig-like domain.
    Immunogenetics (2000) 51:639-46 (Abstract)
  12. Vilches C, Rajalingam R, Uhrberg M, Gardiner CM, Young NT,Parham P.
    KIR2DL5, a novel killer-cell receptor with a D0-D2 configuration of Ig-like domains.
    J Immunol (2000) 164:5797-804 (Abstract)
  13. Selvakumar A, Steffens U, Dupont B.
    NK cell receptor gene of the KIR family with two IG domains but highest homology to KIR receptors with three IG domains.
    Tissue Antigens (1996) 48:285-94 (Abstract)
  14. Kozak M.
    Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes.
    Cell (1986) 44:283-92 (Abstract)
  15. Dohring C, Samaridis J, Colonna M.
    Alternatively spliced forms of human killer inhibitory receptors.
    Immunogenetics (1996) 44:227-30 (Abstract)
  16. Torkar M, Norgate Z, Colonna M, Trowsdale J, Wilson MJ.
    Isotypic variation of novel immunoglobulin-like transcript/killer cell inhibitory receptor loci in the leukocyte receptor complex.
    Eur J Immunol (1998) 28:3959-67 (Abstract)
  17. Gómez-Lozano N, Estefanía E, Williams F, Halfpenny I, Middleton D, Solís R, Vilches C.
    The silent KIR3DP1 gene (CD158c) is transcribed and might encode a secreted receptor in a minority of humans, in whom the KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1 genes are duplicated.
    Eur J Immunol (2005) 35:16-24
  18. Martin AM, Freitas EM, Witt CS, Christiansen FT.
    The genomic organization and evolution of the natural killer immunoglobulin-like receptor (KIR) gene cluster.
    Immunogenetics (2000) 51:268-80 (Abstract)
  19. Gomez-Lozano N, Gardiner CM, Parham P, Vilches C.
    Some human KIR haplotypes contain two KIR2DL5 genes: KIR2DL5A and KIR2DL5B.
    Immunogenetics (2002) 54:314-9 (Abstract)
  20. Shilling HG, Guethlein LA, Cheng NW, Gardiner CM, Rodriguez R, Tyan D, Parham P.
    Allelic polymorphism synergizes with variable gene content to individualize human KIR genotype.
    J Immunol (2002) 168: 2307-15 (Abstract)
  21. Uhrberg M, Parham P, Wernet, P.
    Definition of gene content for nine common group B haplotypes of the Caucasoid population: KIR haplotypes contain between seven and eleven KIR genes.
    Immunogenetics (2002) 54:221-9 (Abstract)
  22. Uhrberg M, Valiante NM, Shum BP, Shilling HG, Lienert-Weidenbach K, Corliss B, Tyan D, Lanier LL, Parham P.
    Human diversity in killer cell inhibitory receptor genes.
    Immunity (1997) 7:753-63 (Abstract)
  23. Marsh SGE, Parham P, Dupont B, Geraghty DE, Trowsdale J, Middleton D, Vilches C, Carrington M, Witt C, Guethlein LA, Shilling HG, Garcia CA, Hsu KC, Wain H.
    Killer-cell Immunoglobulin-like Receptors (KIR) Nomenclature Report, 2002.
    Tissue Antigens (2003) 62:79-86 (Abstract)
    Immunogenetics (2003) 55:220-226 (Abstract)
    Human Immunology (2003) 64:648-654 (Abstract)
    European Journal of Immunogenetics (2003) 30:229-234 (Abstract)
    Journal of Immunological Methods (2003) 281:1-8
  24. Martin AM, Kulski JK, Gaudieri S, Witt CS, Freitas EM, Trowsdale J, Christiansen FT.
    Comparative genomic analysis, diversity and evolution of two KIR haplotypes A and B.
    Gene (2004) 335:121-131
  25. Hsu KC, Liu XR, Selvakumar A, Mickelson E, O'Reilly RJ, Dupont B.
    Killer Ig-like receptor haplotype analysis by gene content: evidence for genomic diversity with a minimum of six basic framework haplotypes, each with multiple subsets.
    J Immunol (2002) 169:5118-29 (Abstract)
  26. Khakoo SI, Carrington M
    KIR and disease: a model system or system of models?
    Immunological Reviews (2006) 214:186-201
  27. Pyo CW, Guethlein LA, Vu Q, Wang R, Abi-Rached L, Norman PJ, Marsh SGE, Miller JS, Parham P, Geraghty DE
    Different patterns of evolution in the centromeric and telomeric regions of group A and B haplotypes on the human Killer cell Ig-like Receptor locus.
    PLoS ONE (2010) 5:e15115
  28. Long EO, Barber DF, Burshtyn DN, Faure M, Peterson M, Rajagopalan S, Renard V, Sandusky M, Stebbins CC, Wagtmann N, Watzl C.
    Inhibition of natural killer cell activation signals by killer cell immunoglobulin-like receptors (CD158).
    Immunol Rev (2001) 181:223-33 (Abstract)
  29. Pando MJ, Gardiner CM, Gleimer M, McQueen KL, Parham P.
    The protein made from a common allele of KIR3DL1 (3DL1*004) is poorly expressed at cell surfaces due to substitution at positions 86 in Ig domain 0 and 182 in Ig domain 1.
    J Immunol (2003) 171:6640-9 (Abstract)
  30. Crum KA, Logue SE, Curran MD, Middleton D.
    Development of a PCR-SSOP approach capable of defining the natural killer cell inhibitory receptor (KIR) gene sequence repertoires.
    Tissue Antigens (2000) 56:313-326
  31. Middleton D, Gonzalez A, Gilmore PM.
    Studies on the expression of the deleted KIR2DS4*003 gene product and distribution of KIR2DS4 deleted and nondeleted versions in different populations.
    Hum Immunol (2007) 68:128-134
  32. Maxwell LD, Wallace A, Middleton D, Curran MD.
    A common KIR2DS4 deletion variant in the human that predicts a soluble KIR molecule analogous to the KIR1D molecule observed in the rhesus monkey.
    Tissue Antigens (2002) 60:254-8 (Abstract)
  33. Long EO, Burshtyn DN, Clark WP, Peruzzi M, Rajagopalan S, Rojo S, Wagtmann N, Winter CC.
    Killer cell inhibitory receptors: diversity, specificity, and function.
    Immunol Rev (1997) 155:135-144
  34. Selvakumar A, Steffens U, Dupont B.
    Polymorphism and domain variability of human killer cell inhibitory receptors.
    Immunol Rev (1997) 155:183-96 (Abstract)

IPD-KIR