With Halloween right around the corner at the end of this month, those who choose to participate are given the opportunity to put on costumes and assume a new identity or appearance. Mimicry offers some organisms the same ability by allowing them to externally resemble another organism or object in its surroundings. From the dead leaf mantis that imitates broken and decaying leaves to the Northern Pygmy Owl that has “false eyes” on the back of its head, mimicry incurs upon an organism a survival advantage.
With their small genomes, viruses use mimicry as a strategy to carry out complex life cycles in a host. For example, the Epstein-Barr Virus produces a protein that mimics the cytokine IL-10 in order to suppress an immune response and the Cricket Paralysis Virus adopts a structure in its 5’ untranslated region that mimics tRNA to recruit ribosomes for translation of its viral proteins. In our recent paper, we find that HIV has evolved a dual molecular mimicry system to regulate transcription of its genome.
A unique step in retroviruses like HIV involves integrating a DNA copy of its RNA genome into the host genome, which in principle puts its transcriptional regulation under the control of the host. As such, like some cellular genes, HIV transcription is regulated by transcriptional stalling after RNA polymerase II clears the promoter. Transcription resumes when positive transcriptional elongation factors phosphorylate the stalled polymerase. One of the important elongation factors is pTEFb, a critical commodity that is kept sequestered by forming a ternary complex with the 7SK RNA and HEXIM protein. pTEFb is released only upon receiving signals to resume transcription and is then taken to stalled genes via cellular factors. Such a mechanism then places HIV transcription at the mercy of these cellular factors to bring pTEFb to its stalled transcript, which is an inefficient and nonviable strategy.
In fact, HIV has evolved a very unique strategy. First, its nascent RNA transcript can fold into a stem-loop structure TAR in close proximity to the stalled polymerase. Second, its Tat protein can directly bind pTEFb by displacing HEXIM from 7SK RNA and transferring it onto TAR RNA.
By solving the three-dimensional structure by Nuclear Magnetic Resonance of the various domains involved in HIV transcription, we show that the Tat RNA binding domain mimics the structure of the HEXIM RNA binding domain and that the TAR RNA mimics a structural element present in the 7SK RNA. Briefly, 7SK is peppered with four motifs, termed arginine sandwich motifs, which can interact with arginines in the major groove. Three of these motifs are preformed and ready to dock in arginines whereas one has to be remodeled for arginine intercalation. While HEXIM’s arginine rich RNA binding domain can engage the three preformed motifs, Tat’s RNA binding domain has the added ability to remodel the fourth motif, giving it a competitive advantage to displace HEXIM and hijack pTEFb. The ability to switch 7SK and displace HEXIM comes from a single lysine to arginine substitution in Tat’s RNA binding domain, and the arginine responsible for remodeling 7SK, R52, is the most critical residue for transcriptional regulation.
HIV has also solved the problem of delivering the captured pTEFb precisely to its own transcript by copying the exact remodeled motif from 7SK RNA in its TAR RNA. We show that this mimicry allows Tat to adopt identical bound structures via R52 in both 7SK and TAR. This potentially allows Tat:pTEFb to leave 7SK and bind TAR, bringing pTEFb in close proximity to the stalled polymerase. The dual structural mimicry of viral molecules important in HIV transcription highlights the elegant ways that viruses can co-opt motifs found in cellular factors for their own survival.
A highlight of our study is the first structure that shows a protein capable of interacting with the major groove of RNA over an entire helical turn. This has not been previously observed because RNA major grooves are deep and narrow, making them generally inaccessible for protein interactions. We speculate that the docking of many arginines at intermittent spaces in arginine sandwiching motifs allows for this intimate RNA-protein interaction. Furthermore, we believe that the remodeling of 7SK to displace HEXIM may be used by other cellular factors to similarly capture pTEFb and that this strategy may be important in regulating transcription of cellular genes.