Independent birth of a novel TRIMCyp in Tupaia belangeri with a divergent function from its paralog TRIM5.
The origin of novel genes and their evolutionary fates are long-standing questions in evolutionary biology. These questions become more complicated for genes conserved across various lineages, such as TRIM5, an antiretroviral restriction factor and a retrovirus capsid sensor in immune signaling. TRIM5 has been subjected to numerous pathogenic challenges and undergone dynamic evolution, making it an excellent example for studying gene diversification. Previous studies among several species showed that TRIM5 gained genetic and functional novelty in a lineage-specific manner, either through gene duplication or a cyclophilin A retrotransposing into the TRIM5 locus, creating the gene fusion known as TRIM5-Cyclophilin A (TRIMCyp). To date, the general pattern of TRIM5 across the mammalian lineage remains elusive. In this study, we surveyed 36 mammalian genomes to verify a potentially novel TRIM5 pattern that uniquely seems to have occurred in tree shrews (Tupaia belangeri), and found that both gene duplication and retrotransposition worked jointly to form a specific TRIM5/TRIMCyp cluster not found among other mammals. Evolutionary analyses showed that tree shrew TRIMCyp (tsTRIMCyp) originated independently in comparison with previously reported TRIMCyps and underwent strong positive selection, whereas no signal of positive selection was detected for other tree shrew TRIM5 (tsTRIM5) genes. Functional assay results suggest a functional divergence between tsTRIMCyp and its closest paralog TRIM5-4, likely reflecting different fates under diverse evolutionary forces. These findings present a rare example of novel gene origination resulting from a combination of gene duplication, retrotransposition, and exon shuffling processes, providing a new paradigm to study genetic innovations and evolutionary fates of duplicated genes.
['Mu|Dan|D|', 'Yang|Hui|H|', 'Zhu|Jia-Wu|JW|', 'Liu|Feng-Liang|FL|', 'Tian|Ren-Rong|RR|', 'Zheng|Hong-Yi|HY|', 'Han|Jian-Bao|JB|', 'Shi|Peng|P|', 'Zheng|Yong-Tang|YT|']
D000595:Amino Acid Sequence D000818:Animals D001483:Base Sequence D002352:Carrier Proteins D021984:Cyclophilin A D019143:Evolution, Molecular D005091:Exons D016368:Frameshift Mutation D020440:Gene Duplication D015870:Gene Expression D007438:Introns D008969:Molecular Sequence Data D050506:Mutant Chimeric Proteins D018626:Retroelements D012641:Selection, Genetic D016415:Sequence Alignment D014417:Tupaia D016335:Zinc Fingers
TRIMCyp gene duplication tree shrew retrotransposition positive selection functional divergence TRIM5α