Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus

Abstract

Cytomegaloviruses (CMVs) are generally unable to cross species barriers, in part because prolonged coevolution with one host species limits their ability to evade restriction factors in other species. However, the limitation in host range is incomplete. For example, rhesus CMV (RhCMV) can replicate in human cells, albeit much less efficiently than in rhesus cells. Previously we reported that the protein kinase R (PKR) antagonist encoded by RhCMV, rTRS1, has limited activity against human PKR but is nonetheless necessary and sufficient to enable RhCMV replication in human fibroblasts (HF). We now show that knockout of PKR in human cells or treatment with the eIF2B agonist ISRIB, which overcomes the translational inhibition resulting from PKR activation, augments RhCMV replication in HF, indicating that human PKR contributes to the inefficiency of RhCMV replication in HF. Serial passage of RhCMV in HF reproducibly selected for viruses with improved ability to replicate in human cells. The evolved viruses contain an inverted duplication of the terminal 6.8 kb of the genome, including rTRS1. The duplication replaces ~11.8 kb just downstream of an internal sequence element, pac1-like, which is very similar to the pac1 cleavage and packaging signal found near the terminus of the genome. Plaque-purified evolved viruses produced at least twice as much rTRS1 as the parental RhCMV and blocked the PKR pathway more effectively in HF. Southern blots revealed that unlike the parental RhCMV, viruses with the inverted duplication isomerize in a manner similar to HCMV and other herpesviruses that have internal repeat sequences. The apparent ease with which this duplication event occurs raises the possibility that the pac1-like site, which is conserved in Old World monkey CMV genomes, may serve a function in facilitating rapid adaptation to evolutionary obstacles.

Does the Zinc Finger Antiviral Protein (ZAP) Shape the Evolution of Herpesvirus Genomes?

“…To achieve this, herpesviruses express multiple accessory proteins, many of which are dedicated to the evasion of host restriction factors [ 6 ]. These viral evasion genes display the characteristic evolutionary signatures of ongoing conflict with host defence [ 7 , 8 ].…”

Cytomegalovirus immediate-early 1 proteins form a structurally distinct protein class with adaptations determining cross-species barriers

“…In contrast, the mechanisms limiting cross-species infection of cytomegaloviruses are less well understood. For instance, a very recent study reported that the replication of rhesus CMV in human cells is considerably enhanced upon duplication of a terminal genomic region which enhances expression of the protein kinase R (PKR) antagonist rTRS1 encoded by rhesus CMV [ 48 ]. This indicates that translational inhibition instituted by human PKR serves as a barrier against cross-species infection with rhesus CMV, which can be overcome by adaptive gene amplification [ 49 ].…”

Engineering, Decoding and Systems-Level Characterization of Chimpanzee Cytomegalovirus

“…3), RL13 and ULb' genes lack any obvious frameshift or translation terminating mutations. Adaptation processes of primate CMVs to human cells can occur in a rapid fashion facilitated by recombination events (Child et al, 2021) or by positive selection of advantageous genetic variants (Mozzi et al, 2020). UL48, which exhibits the second highest number of non-synonymous polymorphisms among all CCMV genes (Fig.…”

“…As a result of prolonged periods of coevolution, CMVs are highly adapted to their specific hosts, making cross-species infections extremely rare events (Burwitz et al, 2016;Child et al, 2021;Murthy et al, 2019). CMVs are very prevalent in their host populations, due to lifelong, mostly asymptomatic infections.…”