Origin and evolution of the zinc finger antiviral protein

Abstract

The human zinc finger antiviral protein (ZAP) recognizes RNA by binding to CpG dinucleotides. Mammalian transcriptomes are CpG-poor, and ZAP may have evolved to exploit this feature to specifically target non-self viral RNA. Phylogenetic analyses reveal that ZAP and its paralogue PARP12 share an ancestral gene that arose prior to extensive eukaryote divergence, and the ZAP lineage diverged from the PARP12 lineage in tetrapods. Notably, the CpG content of modern eukaryote genomes varies widely, and ZAP-like genes arose subsequent to the emergence of CpG-suppression in vertebrates. Human PARP12 exhibited no antiviral activity against wild type and CpG-enriched HIV-1, but ZAP proteins from several tetrapods had antiviral activity when expressed in human cells. In some cases, ZAP antiviral activity required a TRIM25 protein from the same or related species, suggesting functional co-evolution of these genes. Indeed, a hypervariable sequence in the N-terminal domain of ZAP contributed to species-specific TRIM25 dependence in antiviral activity assays. Crosslinking immunoprecipitation coupled with RNA sequencing revealed that ZAP proteins from human, mouse, bat and alligator exhibit a high degree of CpG-specificity, while some avian ZAP proteins appear more promiscuous. Together, these data suggest that the CpG- rich RNA directed antiviral activity of ZAP-related proteins arose in tetrapods, subsequent to the onset of CpG suppression in certain eukaryote lineages, with subsequent species-specific adaptation of cofactor requirements and RNA target specificity.

S-farnesylation is essential for antiviral activity of the long ZAP isoform against RNA viruses with diverse replication strategies

“…However, many vertebrate viruses, including RNA viruses that do not have a DNA intermediate, show CpG suppression in their genome and introducing CpG dinucleotides into the genomes of diverse viruses inhibits their replication [18,[22][23][24][25][26][27][28][29][30]. While CpG dinucleotides in viral genomes may have multiple deleterious effects on replication [31][32][33], since ZAP has been shown to specifically bind CpG dinucleotides in viral RNA and restrict replication, it has been proposed that ZAP at least partially drives the CpG suppression observed in many vertebrate RNA viruses [18,34,35].…”

“…ZAP restricts HIV-1 replication when CpGs are enriched in the 5’ region of HIV-1 env more efficiently than when CpGs are enriched in other regions of the viral genome and introducing CpGs into this region creates a highly ZAP-sensitive HIV-1 [ 18 , 33 , 35 ]. This model ZAP-sensitive virus has been used to characterize the role of CpG dinucleotides in ZAP-mediated restriction and study its cofactors such as TRIM25 and KHNYN [ 13 , 18 , 19 , 34 ]. While the RNA binding domain (RBD) of ZAP is crucial for its selective antiviral activity [ 7 , 17 , 19 , 20 ], much less is known about the functional relevance of the other domains and motifs.…”

The C-terminal PARP domain of the long ZAP isoform contributes essential effector functions for CpG-directed antiviral activity

“…Similar to ZAP's RBD, the CaaX motif appears to be extremely well conserved in mammals and even birds. A recent study suggested that avian ZAP RBD has lower CpG-specificity than mammalian proteins [29]. It is thus likely that the evolution of CaaX happened after the duplication of genes that gave rise to PARP12 and ZAP, but still preceded the RBD adaptations that enabled efficient CpG-specific viral inhibition.…”

“…ZAP more efficiently targets CpGs in the 5' region of HIV-1 env than other regions of the viral genome and introducing CpGs into this region creates a highly ZAP-sensitive HIV-1 [18][14] [28]. This model ZAP-sensitive virus has been used to discover and characterize ZAP cofactors such as TRIM25 and KHNYN [14] [29].…”

Bioinorganic Chemistry of Zinc in Relation to the Immune System

“…[265] ZAP specifically binds to cytosineguanine (CpG) dinucleotides that are rare in mammals but common in many viruses, possibly as an evolutionary adaptation. [266] The new RNA-ZAP complex conformation enables ribonucleases to degrade the RNA molecule, thus preventing virus replication. [265] During its function, recent studies suggest that ZAP also activate and facilitate cytokine production by T-cells.…”