NKp30 (NCR3) is a pseudogene in 12 inbred and wild mouse strains, but an expressed gene in Mus caroli

• Published in: Molecular biology and evolution 2005-08, Vol.22 (8), p.1661-1672
• Main Authors: Hollyoake, Martine, Campbell, R Duncan, Aguado, Begoña
• Format: Article
• Language: English
• Subjects: Alternative Splicing - genetics; Animals; Codon, Nonsense - genetics; Expressed Sequence Tags; Gene Expression Regulation - genetics; Membrane Glycoproteins - genetics; Mice; Mice, Inbred C3H; Mus; Mus musculus; Musculus; Natural Cytotoxicity Triggering Receptor 2; Phylogeny; Polymorphism, Single Nucleotide; Pseudogenes - genetics; Rats; Receptors, Immunologic - genetics; Species Specificity
• ISSN: 0737-4038
• DOI: 10.1093/molbev/msi162

Ancient duplications and rearrangements of protein-coding segments have resulted in complex gene family relationships. As a result, gene products may acquire new specificities, altered recognition properties, modified functions, and even loss of functionality. The natural cytotoxicity receptor (NCR) family are natural killer (NK)-activating receptors whose members are NKp46 (NCR1), NKp44 (NCR2), and NKp30 (NCR3). The NCR proteins are putative immunoglobulin superfamily members whose ligands are unknown. The NKp46 gene is present and expressed in human and mouse, NKp44 is only present and expressed in human, and NKp30 is present and expressed in human but is a nonexpressed pseudogene in mouse. By searching databases we have detected alternatively spliced forms of the three NCR members. In addition, we have shown by reverse transcription-polymerase chain reaction (RT-PCR) analysis that the human NKp30 gene presents differential expression patterns in tissues. However, no expressed sequence tags (ESTs) are detected for mouse NKp30, and the genomic sequence contains two premature stop codons, which would encode a severely truncated nonfunctional protein. We have sequenced genomic DNA from 13 mouse inbred and wild strains and discovered that NKp30 is a pseudogene in every mouse strain sequenced except Mus caroli where two single nucleotide polymorphisms (SNPs) abolished the premature stop codons. We observed that the laboratory-inbred strains are, for the exonic sequences, genetically identical, except Mus m. musculus C3H. The Mus musculus strains only have a few SNPs, but the rest of the Mus strains have accumulated gradually several SNPs, mainly in the functional immunoglobulin and intracellular domains. RT-PCR analysis performed on RNA from M. caroli tissue samples identified two transcripts, one of which would encode a putative soluble NKp30 protein, also detected in rat but not in human. We have observed that the intracellular domains of NKp30 (and NKp46) are not conserved among the different species, with the most striking difference when comparing human against mouse and rat. The NKp44 gene is only found in human and shows three different splice forms varying in their "stalk" and intracellular domains. Searching for NKp44 orthologs, we found similarity to ESTs from a novel rodent TREM family member, which we termed TREM6, and not to any possible NKp44 ortholog.