New research explains how HIV avoids getting ZAPped

A previous study from Rockefeller revealed that ZAP grabs onto only one specific sequence of neighboring nucleotides (the building blocks of DNA and RNA): a cytosine followed by a guanine, or a CG dinucleotide. Human RNAs have few CG dinucleotides, and HIV RNA has evolved to mimic this characteristic.

“The main motivation for the study was, ‘How does HIV avoid this antiviral protein?’,” explains Jennifer Meagher, Ph.D., a researcher at the LSI and one of the lead authors of the study. “And because we’re structural biologists, we wanted to determine how ZAP ‘sees’ a CG dinucleotide — and how, structurally, it binds the RNA.”

Using a piece of viral RNA that was genetically altered to include extra CG sequences, Meagher and her colleagues at U-M determined the structure of the ZAP protein bound to RNA, exposing the mechanisms that enable the protein to be so selective.

The researchers discovered that ZAP binds to the viral RNA at only one of the four “zinc fingers” on the protein that they considered potential binding sites. They further demonstrated that even a tiny change to that one binding site — altering just a single atom — hampered ZAP’s binding ability.

Working in cells, researchers from Rockefeller found similar results when they altered ZAP’s composition. They created mutant versions of ZAP that were expressed in cells infected with either normal HIV or a version of the virus enriched with CG sequences. 

The mutant ZAP proteins were less able to recognize CG-enriched regions of the viral RNA in cells. They also exhibited increased binding to areas of the RNA that were not rich in CG dinucleotides, indicating that alterations impair ZAP’s ability to distinguish viral RNA from human RNA.

“Natural selection appears to have shaped the ZAP protein structure in such a way to optimize the discrimination of non-self from self RNA, based on CG dinucleotide content,” says Paul Bieniasz, Ph.D., Howard Hughes Medical Institute investigator and head of the Laboratory of Retrovirology at Rockefeller. “However, successful viruses are often one step ahead in a molecular arms race.” 

“This is the crucial first step in a complicated story of how the cell eventually degrades the virus’s RNA,” adds Janet Smith, Ph.D., a research professor at the U-M LSI and a professor of biological chemistry at the Medical School. “And now we know how the step is executed, and why it is not effective on HIV and other viruses that lack this CG sequence.”