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Paired Ig-Like Receptor Homologs in Birds and Mammals Share a Common Ancestor with Mammalian Fc Receptors

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Paired Ig-Like Receptor Homologs in Birds and Mammals Share a Common Ancestor with Mammalian Fc Receptors Paired Ig-like receptor homologs in birds and mammals share a common ancestor with mammalian Fc receptors Glynn Dennis, Jr.*†, Hiromi Kubagawa*‡, and Max D. Cooper*‡§¶ʈ *Division of Developmental and Clinical Immunology, Departments of †Microbiology, ‡Pathology, and §Pediatrics and Medicine, and ¶Howard Hughes Medical Institute, University of Alabama, Birmingham, AL 35294-3300 Contributed by Max D. Cooper, September 15, 2000 Paired Ig-like receptors (PIR) that can reciprocally modulate cellular also known as mouse activating receptor (MAR)-1 (22) and rat activation have been described in mammals. In the present study, killer cell Ig-like receptor (KILR)-1 [Berg, S. F., Dissen, E., we searched expressed sequence tag databases for PIR relatives to Westgaard, I. H. & Fossum, S. (1998) Direct Submission (Gen- identify chicken expressed sequence tags predictive of Ϸ25% Bank accession no. AF082533)], respectively, have been mapped amino acid identity to mouse PIR. Rapid amplification of cDNA ends to syntenic regions of mouse chromosome 7 and rat chromosome (RACE)-PCR extension of expressed sequence-tag sequences using 1, thereby indicating an LRC-like genomic region in rodents. chicken splenic cDNA as a template yielded two distinct cDNAs, the Surprisingly, extensive investigations have not revealed counter- sequence analysis of which predicted protein products with related parts of other LRC-encoded genes in rodents. The plasticity of extracellular Ig-like domains. Chicken Ig-like receptor (CHIR)-A was LRC-encoded genes is further evidenced by recent studies characterized by its transmembrane segment with a positively indicating that KIRs are a relatively young gene family in charged histidine residue and short cytoplasmic tail, thereby iden- primates, wherein the KIR genes of chimpanzees and humans tifying CHIR-A as a candidate-activating receptor. Conversely, have undergone considerable diversification since the time of CHIR-B was characterized by its nonpolar transmembrane segment their last common ancestor approximately 5 million years ago and cytoplasmic tail with two immunoreceptor tyrosine-based (13, 23). inhibitory motifs, indicating that it may serve as an inhibitory Here, we describe relatives of mammalian PIR genes in the receptor. The use of CHIR amino acid sequences in a search for avian representative, Gallus gallus. The comparative analysis of other PIR relatives led to the recognition of mammalian Fc recep- avian and mammalian PIR sequences has allowed us to begin an tors as distantly related genes. Comparative analyses based on exploration of the evolutionary history of the PIR gene family. amino acid sequences and three-dimensional protein structures Materials and Methods provided molecular evidence for common ancestry of the PIR and Fc receptor gene families. Generation of Full-Length CHIR-A and CHIR-B cDNAs. The chicken splenic ␭ZapII cDNA library used in rapid amplification of IMMUNOLOGY cDNA ends (RACE)-PCR was a kind gift from Dr. Chen-lo he mouse paired Ig-like receptors are expressed as activating Chen (University of Alabama, Birmingham). T3 and T7 vector- T(PIR-A) and inhibitory (PIR-B) isoforms on myeloid, den- specific primers were used for 5Ј- and 3Ј-RACE, respectively. dritic, and B cell lineages, where they may modulate the activity CHIR-specific reverse primers used in 5Ј-RACE were 5Ј- of these cells in innate and adaptive immune responses (1, 2). ATCACTTCCAGGGTCACATTATCCC-3Ј, and CHIR spe- PIR-A and PIR-B have similar extracellular regions containing cific forward primers used in 3Ј-RACE were 5Ј-GGGATAAT- six Ig-like domains that are coupled to distinctive transmem- GTGACCCTGGAAGTGAT-3Ј. Primers used in end-to-end brane and cytoplasmic regions. PIR-A lacks cytoplasmic signal- PCR to generate full-length CHIR-A were forward 5Ј- ing elements but can function as an activating receptor through GCCACGTTGCTCCTGCCTCAT-3Ј and reverse 5Ј-AAAGC- its association with a transmembrane adapter protein, the Fc CATTTAATCTCTTGCCCAC-3Ј. Primers used in end-to-end ␥ receptor common gamma chain (FcR c), which contains immu- PCR to generate full-length CHIR-B were forward 5Ј- noreceptor tyrosine-based activation motifs (ITAM) (3–5). GCCACGTTGCTCCTGCCTCAT-3Ј and reverse 5Ј-TGAG- PIR-B has immunoreceptor tyrosine-based inhibitory motifs CACACCGAGCACACTGGCACTGT-3Ј. Each amplification (ITIM) in its cytoplasmic region, which allows it to function as reaction underwent an initial denaturation at 94°C for 2 min an inhibitory receptor (5–10). Approximately eight Pira genes followed by 35 cycles of denaturation at 94°C for 5 s, annealing and a single Pirb gene reside in a centromeric region of mouse at 68°C for 15 s, and extension for 4 min. Amplification products chromosome 7 that is syntenic with the leukocyte receptor were visualized by agarose gels containing ethidium bromide and complex (LRC) of genes located in the q13.4 region of human documented with a Bio-Rad Fluro-S Imager. chromosome 19 (1, 11, 12). The human LRC includes a monophyletic gene family that Sequence Analysis. PCR products cloned into pCR2.1 TOPO-TA encodes approximately 24 Ig-like receptors of activating and cloning vectors (Invitrogen) were sequenced on both strands by inhibitory types (13). The closest PIR relatives in the human LRC are the Ig-like transcripts (ILT) (14), also named leukocyte Ig-like receptors (LIR) (15) and monocyte͞macrophage Ig-like Abbreviations: RACE, rapid amplification of cDNA ends; ITAM, immunoreceptor tyrosine- ͞ based activation motifs; ITIM, immunoreceptor tyrosine-based inhibitory motifs; LRC, receptors (MIR) (16). Multiple activating and inhibitory ILT leukocyte receptor complex; SIRP, signal regulatory proteins. LIR͞MIRs possess four or less Ig-like domains that share Data deposition: The sequences reported in this paper have been deposited in the GenBank approximately 60% amino acid identity with mouse PIR. More database [accession nos. AF306851 (CHIR-A) and AF306852 (CHIR-B)]. distant PIR relatives within the human LRC include the natural ʈTo whom reprint requests should be addressed. E-mail: [email protected]. killer cell Ig-like receptors (KIR) (17, 18), an IgA receptor ␣ The publication costs of this article were defrayed in part by page charge payment. This (Fc R) (19), the p46 natural killer cell receptor (NKp46) (20), article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. and leukocyte-associated Ig-like receptors (LAIR) (21). Among §1734 solely to indicate this fact. these genes, NKp46 is the only true homolog, being conserved Article published online before print: Proc. Natl. Acad. Sci. USA, 10.1073͞pnas.230442897. in humans, mice, and rats. The NKp46 genes in mice and rats, Article and publication date are at www.pnas.org͞cgi͞doi͞10.1073͞pnas.230442897 PNAS ͉ November 21, 2000 ͉ vol. 97 ͉ no. 24 ͉ 13245–13250 Downloaded by guest on October 1, 2021 the dideoxy chain-termination method using Thermo Sequenase of identical proteins (0.33 Å) (31). N represents the number of (Amersham Pharmacia) and an automated sequencer (Li-Cor, C␣ carbons used in the rms calculation, and l is the total number Lincoln, NE). Nucleotide sequences were assembled and trans- of C␣ carbons in the shorter of the two structures. Phylogenies lated by the DNASTAR (Madison, WI) software package, and were derived from structural distances by parsimony analysis amino acid sequence alignments were decorated by GENEDOC provided in the PHYLIP software suite, and optimal trees were (www.cris.com/ϳketchup/genedoc/shtml). Multiple sequence estimated by global rearrangements (32). A fibronectin type alignments used in phylogenetic analyses were created by CLUST- III-containing protein, human tissue factor (HTF) (33), was ALX (24) with the Gonnet series substitution matrix (25). Phy- included as a structural relative of the Ig superfamily to serve as logenetic tree topologies derived from amino acid sequences an outgroup. were estimated by neighbor-joining (26) and clustering methods (27) included in the TREECON analysis package (28). Reverse Transcription-PCR. Total RNA was extracted from chicken ␣␤ T cell (UG9 and CU24), ␥␦ T cell (857), and B cell (DT40) DNA Blotting. High molecular weight genomic DNA extracted lines and reverse transcribed into single-stranded cDNA using from nucleated chicken red blood cells was digested to comple- random primed SuperScriptII (Life Technologies, Rockville, tion with restriction endonucleases. DNA digests were resolved MD). Common forward primers 5Ј-GGGATAATGTGACCCT- in 0.8% agarose gels and transferred to nylon filters. A PCR- GGAAGTGAT-3Ј, CHIR-A specific reverse primers 5Ј- generated 600-base pair probe spanning the extracellular region TTCTCTGGGCAACAAGGTGCAAAG-3Ј, and CHIR-B of CHIR-B was [␣-32P]dCTP-labeled and hybridized to filters specific reverse primers 5Ј-GGACACCTGGAACTGCA- overnight. Filters were washed and exposed to x-ray film. CGGCCTC-3Ј amplified products of 158 and 222 bp, respec- Structural Analysis. X-ray crystallographic coordinates for three- tively. Each amplification reaction underwent an initial dimensional protein structures were downloaded from the struc- denaturation at 94°C for 2 min followed by 30 cycles of dena- tural classification of proteins (SCOP) database (29). Structural turation at 94°C for 5 s, annealing at 65°C for 5 s, and extension alignments, decorations, and rms deviation calculations were at 72°C for 30 s followed by a 2-min final extension. Amplified performed using Swiss-pdb Viewer (30). rms deviations were products were visualized
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