Characterization of HERV-K (HML-2) Rec proteins encoded in the human genome and their post-transcriptional function

Human endogenous retrovirus K (HERV-K) proviruses of the HML-2 subgroup are the most recently integrated retroviral elements within the human genome. The HERV-K Rec protein, a functional homolog of HIV Rev, is essential for the expression of viral mRNAs with retained introns. However, their diversity and functional capacities have remained largely unexplored. We identified Rec coding sequences in the human genome and selected intact Rec proteins from 28 proviral loci for functional characterization. Using a dual-color fluorescent reporter containing the HERV-K Rec-response element and a complementary enzyme-linked immunosorbent assay, we found that Rec proteins from nine proviral genomic loci promoted function at the post-transcriptional level. All but one of these proviruses are insertionally polymorphic in the human genome. In addition, several of the non-functional Rec proteins were trans-dominant negative. Detailed mutational analysis of the most potent inhibitory variant, encoded by the HERV-K provirus 12q14.1, displayed only two amino acid changes (N2H and E34del) relative to the prototypical functional Rec protein encoded by the reconstructed consensus HERV-K. Insertion of a glutamic acid at position 34 in this mutant fully restored the functional activity. Our results unveil an unexpected complexity in HERV-K (HML-2) post-transcriptional regulation, with a few Rec variants showing function, while others are trans-dominant negative. These findings significantly expand our understanding of the various Rec proteins that can be expressed in human cells and how they function at the post-transcriptional level.IMPORTANCEIn this study, we compared Rec sequences from 58 type 2 human endogenous retrovirus K proviruses and showed that only 9 encode Rec proteins that are functional in post-transcriptional regulation of RNAs with retained introns. We also showed that several Rec proteins have trans-dominant negative activity when co-expressed with a functional Rec protein. While previous studies have demonstrated the expression of Rec mRNAs and proteins in human cells, this is the first study to define which loci have the potential to encode either functional or trans-dominant negative Rec proteins. Additionally, our reporter system will also enable future investigations to easily determine whether functional and/or trans-dominant negative Rec proteins are expressed in any cell. These findings are also important for future studies that aim to link Rec post-transcriptional function to physiological or pathological effects.