Plant Single-Stranded DNA Viruses Selectively Re-Purpose the Host DNA Replication Machinery for Their Multiplication

Abstract

Geminiviruses are a family of plant-infecting viruses characterized by twin icosahedral capsids and circular single-stranded (ss) DNA genomes. Members of this family cause devastating diseases in crops worldwide. Geminiviruses replicate in the cell nucleus of the infected plant mainly through a rolling-circle replication (RCR) mechanism. As none of the viral proteins possesses DNA polymerase activity, these viruses heavily rely on the host replication machinery for successful replication. As viral replication is a fundamental step in the infection cycle, the host factors essential for this process can serve as potential targets to develop strategies to control infection. We have previously shown that DNA polymerase α and δ are required for viral replication. However, the composition of the viral replisome remains mostly elusive. The viral replication associated (Rep) protein is highly conserved, and the only virus-encoded protein essential for this process. Here, we used Rep from the geminivirus tomato yellow leaf curl virus (TYLCV) as a bait to capture host factors involved in viral replication in Nicotiana benthamiana via TurboID-based proximity labelling (PL) followed by mass spectrometry (MS) analysis. Our data demonstrate that geminiviruses exploit the molecular machinery mediating eukaryotic leading-strand, but not lagging-strand, DNA synthesis in the bidirectional replication fork. An exception is the DNA polymerases, which are swapped. Furthermore, our findings suggest that the composition of the viral replisome is conserved within the phylum Circular Rep-Encoding Single Stranded (CRESS) DNA viruses. In addition, our work shows that eukaryotic DNA helicase loaders, but not the helicase itself, contribute to the viral genome replication, underscoring a mechanistic divergence in replication initiation between geminiviruses and their plant hosts. Structural prediction indicates that geminiviral Rep assembles into a homo-hexameric complex, analogous to the hetero-hexameric eukaryotic helicase. Taken together, our results demonstrate that geminiviruses selectively repurpose the plant DNA replication machinery to carry out RCR. Collectively, our study provides new insight into viral replication strategies and lays the foundation for the identification of new antiviral targets.