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TRIM5α provides a cytoplasmic block to retroviral infection, and orthologs encoded by some primates are active against HIV. Here, we present an evolutionary comparison of the  TRIM5  gene to its closest human paralogs:  TRIM22 ,  TRIM34 , and  TRIM6 . We show that  TRIM5  and  TRIM22  have a dynamic history of gene expansion and loss during the evolution of mammals. The cow genome contains an expanded cluster of  TRIM5  genes and no  TRIM22  gene, while the dog genome encodes  TRIM22  but has lost  TRIM5 . In contrast,  TRIM6  and  TRIM34  have been strictly preserved as single gene orthologs in human, dog, and cow. A more focused analysis of primates reveals that, while  TRIM6  and  TRIM34  have evolved under purifying selection,  TRIM22  has evolved under positive selection as was previously observed for  TRIM5 . Based on  TRIM22  sequences obtained from 27 primate genomes, we find that the positive selection of  TRIM22  has occurred episodically for approximately 23 million years, perhaps reflecting the changing pathogenic landscape. However, we find that the evolutionary episodes of positive selection that have acted on  TRIM5  and  TRIM22  are mutually exclusive, with generally only one of these genes being positively selected in any given primate lineage. We interpret this to mean that the positive selection of one gene has constrained the adaptive flexibility of its neighbor, probably due to genetic linkage. Finally, we find a striking congruence in the positions of amino acid residues found to be under positive selection in both TRIM5α and TRIM22, which in both proteins fall predominantly in the β2-β3 surface loop of the B30.2 domain. Astonishingly, this same loop is under positive selection in the multiple cow  TRIM5  genes as well, indicating that this small structural loop may be a viral recognition motif spanning a hundred million years of mammalian evolution.

Discordant Evolution of the Adjacent Antiretroviral Genes TRIM22 and TRIM5 in Mammals