The hosts-virus arms race reaches the epigenetic level, where silencing of viral chromatin can serve as an innate defense mechanism to restrict invading DNA viruses. However, viruses can code for suppressor proteins to counter epigenetic silencing and escape host surveillance. Thus, the virus-encoded suppressors offer an untapped source of tools for the understanding of pathogenesis and chromatin regulation.
TrAP is a transcription factor encoded by model DNA plant viruses of the family Geminiviridae, which is required for the expression of the virus late genes and for suppression of gene silencing. TrAP is known to interfere with the transcriptional gene-silencing (TGS) pathway by obstructing the methyl cycle in the cytoplasm. Nonetheless, multiple metabolic pathways other than chromatin regulation utilize the methyl donor, and TrAP mainly localizes to the nucleus; furthermore, TrAP is predicted to interact with the transcriptional machinery. Thus, we asked whether TrAP directly suppressed TGS.
We first generated TrAP-stable transgenic plants, and through transcriptome and biochemical assays, we demonstrated that TrAP hampered TGS. We then identified TrAP-interacting partners using a proteomics approach, confirmed by protein interaction experiments in vivo and in vitro. To determine whether these interactions were physiologically relevant, we performed virus infection assays in various host genetic backgrounds.
We demonstrated that TrAP interacts with multiple SET-domain proteins in Arabidopsis. Particularly, the H3K9me2 histone methyltransferase, Su(var)3-9 homolog 4/Kryptonite (SUVH4/KYP) is a bona fide cellular target of TrAP. TrAP expression phenocopies several TGS mutants, reduces the repressive H3K9me2 mark and CHH DNA methylation, and reactivates many endogenous KYP-repressed loci in vivo. KYP binds to the viral chromatin and controls its methylation to combat virus infection. We conclude that TrAP attenuates TGS by inhibiting KYP activity.
Furthermore, we show that TrAP interacts with other proteins, such as the methyl cycle enzymes SAMe-synthetase 2 (SAM2) and the S-adenosyl homocysteine hydrolase 1 (SAHH1), the RNA processing Enhanced silencing phenotype 3 (ESP3), and the chromatin remodeler Relative of early flowering 6 (REF6).
Our findings provide new insight in the host antiviral defense and virus counter- defense at an epigenetic level and provide a model system to study chromatin regulation, and virus infection
