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Short KIR haplotypes in pygmy chimpanzee (Bonobo) resemble the conserved framework of diverse human KIR haplotypes.

Rajalingam R, Hong M, Adams EJ, Shum BP, Guethlein LA, Parham P - J. Exp. Med. (2001)

Bottom Line: Five of these genes have orthologs in the common chimpanzee, and three of them (KIRCI, KIR2DL4, and KIR2DL5) also have human orthologs.The remaining two genes are KIR3D paralogous to the human and common chimpanzee major histocompatibility complex A- and/or -B-specific KIRs.Simple patterns on Southern blot were due to inheritance of "short" KIR haplotypes containing only three KIR genes, KIRCI, KIR2DL4, and KIR3D, each of which represents one of the three major KIR lineages.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology, Stanford University, Stanford, California 94305, USA.

ABSTRACT
Some pygmy chimpanzees (also called Bonobos) give much simpler patterns of hybridization on Southern blotting with killer cell immunoglobulin-like receptor (KIR) cDNA probes than do either humans or common chimpanzees. Characterization of KIRs from pygmy chimpanzees having simple and complex banding patterns identified nine different KIRs, representing seven genes. Five of these genes have orthologs in the common chimpanzee, and three of them (KIRCI, KIR2DL4, and KIR2DL5) also have human orthologs. The remaining two genes are KIR3D paralogous to the human and common chimpanzee major histocompatibility complex A- and/or -B-specific KIRs. Within a pygmy chimpanzee family, KIR haplotypes were defined. Simple patterns on Southern blot were due to inheritance of "short" KIR haplotypes containing only three KIR genes, KIRCI, KIR2DL4, and KIR3D, each of which represents one of the three major KIR lineages. These three genes in pygmy chimpanzees or their corresponding genes in humans and common chimpanzees form the conserved "framework" common to all KIR haplotypes in these species and upon which haplotypic diversity is built. The fecundity and health of individual pygmy chimpanzees who are homozygotes for short KIR haplotypes attest to the viability of short KIR haplotypes, indicating that they can provide minimal, essential KIRs for the natural killer and T cells of the hominoid immune system.

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Four of six pygmy chimpanzee KIR cDNA are not orthologous to human or common chimpanzee KIR. The phylogenetic tree was constructed from full-length coding region sequences from cDNA with the exception of human KIRCI for which the coding region sequence was derived from the genomic sequences (reference 42). The tree is unrooted and was derived using the maximum parsimony method (reference 39). Bootstrap values determined by 1,000 replications are given for pairs of branch points (reference 41). Trees with similar topology were obtained by the neighbor-joining method (reference 40) and also when constructed from the amino acid sequences (not shown). The names of the pygmy chimpanzee KIR are boxed. Several variants of Pt-KIR3DL1/2 (Pt-KIR3DL1/2-v1, Pt-KIR3DL1/2v2, and Pt-KIR3DL1/2v3), KIR3DL1 (Nkb1 and Nkat3), KIR3DS1 (3DS1v and Nkat10), and KIR3DL2 (Nkat4, AMC5, and 17.1c) are included in the tree but because of the proximity of the branches they are not individually named (reference 15).
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Figure 3: Four of six pygmy chimpanzee KIR cDNA are not orthologous to human or common chimpanzee KIR. The phylogenetic tree was constructed from full-length coding region sequences from cDNA with the exception of human KIRCI for which the coding region sequence was derived from the genomic sequences (reference 42). The tree is unrooted and was derived using the maximum parsimony method (reference 39). Bootstrap values determined by 1,000 replications are given for pairs of branch points (reference 41). Trees with similar topology were obtained by the neighbor-joining method (reference 40) and also when constructed from the amino acid sequences (not shown). The names of the pygmy chimpanzee KIR are boxed. Several variants of Pt-KIR3DL1/2 (Pt-KIR3DL1/2-v1, Pt-KIR3DL1/2v2, and Pt-KIR3DL1/2v3), KIR3DL1 (Nkb1 and Nkat3), KIR3DS1 (3DS1v and Nkat10), and KIR3DL2 (Nkat4, AMC5, and 17.1c) are included in the tree but because of the proximity of the branches they are not individually named (reference 15).

Mentions: The most abundant KIR cDNA (42 clones) corresponds to the pygmy chimpanzee ortholog of KIR2DL4, which has 96.9 and 98.7% sequence similarity with human KIR2DL4 and common chimpanzee Pt-KIR2DL4, respectively. These relationships are apparent in a phylogenetic tree of chimpanzee and human KIR (Fig. 3). Consequently, this pygmy chimpanzee KIR has been named Pp-KIR2DL4, where Pp signifies P. paniscus. Pp-KIR2DL4 and Pt-KIR2DL4 have identical amino acid sequence in the extracellular domains and differ by just four amino acid substitutions elsewhere: two in the transmembrane region and two in the cytoplasmic tail.


Short KIR haplotypes in pygmy chimpanzee (Bonobo) resemble the conserved framework of diverse human KIR haplotypes.

Rajalingam R, Hong M, Adams EJ, Shum BP, Guethlein LA, Parham P - J. Exp. Med. (2001)

Four of six pygmy chimpanzee KIR cDNA are not orthologous to human or common chimpanzee KIR. The phylogenetic tree was constructed from full-length coding region sequences from cDNA with the exception of human KIRCI for which the coding region sequence was derived from the genomic sequences (reference 42). The tree is unrooted and was derived using the maximum parsimony method (reference 39). Bootstrap values determined by 1,000 replications are given for pairs of branch points (reference 41). Trees with similar topology were obtained by the neighbor-joining method (reference 40) and also when constructed from the amino acid sequences (not shown). The names of the pygmy chimpanzee KIR are boxed. Several variants of Pt-KIR3DL1/2 (Pt-KIR3DL1/2-v1, Pt-KIR3DL1/2v2, and Pt-KIR3DL1/2v3), KIR3DL1 (Nkb1 and Nkat3), KIR3DS1 (3DS1v and Nkat10), and KIR3DL2 (Nkat4, AMC5, and 17.1c) are included in the tree but because of the proximity of the branches they are not individually named (reference 15).
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2195888&req=5

Figure 3: Four of six pygmy chimpanzee KIR cDNA are not orthologous to human or common chimpanzee KIR. The phylogenetic tree was constructed from full-length coding region sequences from cDNA with the exception of human KIRCI for which the coding region sequence was derived from the genomic sequences (reference 42). The tree is unrooted and was derived using the maximum parsimony method (reference 39). Bootstrap values determined by 1,000 replications are given for pairs of branch points (reference 41). Trees with similar topology were obtained by the neighbor-joining method (reference 40) and also when constructed from the amino acid sequences (not shown). The names of the pygmy chimpanzee KIR are boxed. Several variants of Pt-KIR3DL1/2 (Pt-KIR3DL1/2-v1, Pt-KIR3DL1/2v2, and Pt-KIR3DL1/2v3), KIR3DL1 (Nkb1 and Nkat3), KIR3DS1 (3DS1v and Nkat10), and KIR3DL2 (Nkat4, AMC5, and 17.1c) are included in the tree but because of the proximity of the branches they are not individually named (reference 15).
Mentions: The most abundant KIR cDNA (42 clones) corresponds to the pygmy chimpanzee ortholog of KIR2DL4, which has 96.9 and 98.7% sequence similarity with human KIR2DL4 and common chimpanzee Pt-KIR2DL4, respectively. These relationships are apparent in a phylogenetic tree of chimpanzee and human KIR (Fig. 3). Consequently, this pygmy chimpanzee KIR has been named Pp-KIR2DL4, where Pp signifies P. paniscus. Pp-KIR2DL4 and Pt-KIR2DL4 have identical amino acid sequence in the extracellular domains and differ by just four amino acid substitutions elsewhere: two in the transmembrane region and two in the cytoplasmic tail.

Bottom Line: Five of these genes have orthologs in the common chimpanzee, and three of them (KIRCI, KIR2DL4, and KIR2DL5) also have human orthologs.The remaining two genes are KIR3D paralogous to the human and common chimpanzee major histocompatibility complex A- and/or -B-specific KIRs.Simple patterns on Southern blot were due to inheritance of "short" KIR haplotypes containing only three KIR genes, KIRCI, KIR2DL4, and KIR3D, each of which represents one of the three major KIR lineages.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology, Stanford University, Stanford, California 94305, USA.

ABSTRACT
Some pygmy chimpanzees (also called Bonobos) give much simpler patterns of hybridization on Southern blotting with killer cell immunoglobulin-like receptor (KIR) cDNA probes than do either humans or common chimpanzees. Characterization of KIRs from pygmy chimpanzees having simple and complex banding patterns identified nine different KIRs, representing seven genes. Five of these genes have orthologs in the common chimpanzee, and three of them (KIRCI, KIR2DL4, and KIR2DL5) also have human orthologs. The remaining two genes are KIR3D paralogous to the human and common chimpanzee major histocompatibility complex A- and/or -B-specific KIRs. Within a pygmy chimpanzee family, KIR haplotypes were defined. Simple patterns on Southern blot were due to inheritance of "short" KIR haplotypes containing only three KIR genes, KIRCI, KIR2DL4, and KIR3D, each of which represents one of the three major KIR lineages. These three genes in pygmy chimpanzees or their corresponding genes in humans and common chimpanzees form the conserved "framework" common to all KIR haplotypes in these species and upon which haplotypic diversity is built. The fecundity and health of individual pygmy chimpanzees who are homozygotes for short KIR haplotypes attest to the viability of short KIR haplotypes, indicating that they can provide minimal, essential KIRs for the natural killer and T cells of the hominoid immune system.

Show MeSH
Related in: MedlinePlus