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MBE Advance Access published online on May 4, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi162
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Published by Oxford University Press 2005.
Accepted April 14, 2005

Research Article

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

Martine Hollyoake 1, R. Duncan Campbell 1, and Begoña Aguado 2*

1 MRC Rosalind Franklin Centre for Genomics Research (formerly MRC UK HGMP Resource Centre), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
2 MRC Rosalind Franklin Centre for Genomics Research (formerly MRC UK HGMP Resource Centre), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK; Centro Nacional de Biotecnología (CNB-CSIC), Campus Cantoblanco, 28049 Madrid, Spain

* To whom correspondence should be addressed.
Begoña Aguado, E-mail: baguado{at}cnb.uam.es


  Abstract

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 non-expressed pseudogene in mouse. Searching databases we have detected alternatively spliced forms of the three NCR members. In addition, we have shown by RT-PCR analysis, that the human NKp30 gene presents differential expression patterns in tissues. However, no ESTs are detected for mouse NKp30, and the genomic sequence contains two premature stop codons, which would encode a severely truncated non-functional 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 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 Ig and intracellular domains. RT-PCR analysis performed on RNA from Mus 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 orthologues, we found similarity to ESTs from a novel rodent TREM family member, which we termed TREM6, and not to any possible NKp44 orthologue.

Keywords: NCR; NKp30; splice forms; pseudogene; Mus caroli; TREM6.
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