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Although histone H3K9 methylation has been intensively studied in animals and a model plant  Arabidopsis thaliana , little is known about the evolution of the histone methyltransferase and its roles in plant biotic stress response. Here we identified a  Nicotiana benthamiana  homolog of H3K9 histone methyltransferase KRYPTONITE (NbKYP) and demonstrated its fundamental roles on methylation of plant and virus, beside of leading to the suppression of endogenous gene expression and virus replication.  NbKYP  and another gene encoding DNA methyltransferase  CHROMOMETHYLTRANSFERASE 3  ( NbCMT3-1 ) were further identified as the key components of maintenance of transcriptional gene silencing, a DNA methylation involved anti-virus machinery. All three types of DNA methylations (asymmetric CHH and symmetric CHG/CG) were severely affected in  NbKYP- silenced plants, but only severe reduction of CHG methylation found in  NbCMT3-1- silenced plants. Attesting to the importance of plant histone H3K9 methylation immunity to virus, the virulence of geminiviruses requires virus-encoded trans-activator AC2 which inhibits the expression of  KYP  via activation of an EAR-motif-containing transcription repressor  RAV2  ( RELATED TO ABI3 and VP1 ). The reduction of  KYP  was correlated with virulence of various similar geminiviruses. These findings provide a novel mechanism of how virus trans-activates a plant endogenous anti-silencing machinery to gain high virulence.

Attenuation of Histone Methyltransferase KRYPTONITE-mediated transcriptional gene silencing by Geminivirus