Arabidopsis Histone Reader EMSY-LIKE 1 Binds H3K36 and Suppresses Geminivirus Infection

Abstract

Histone posttranslational modifications (PTMs) impart information that regulates chromatin structure and activity. Their effects are mediated by histone reader proteins that bind specific PTMs to modify chromatin and/or recruit appropriate effectors to alter the chromatin landscape. Despite their crucial juxtaposition between information and functional outcome, relatively few plant histone readers have been identified, and nothing is known about their impact on viral chromatin and pathogenesis. We used the geminivirus (CaLCuV) as a model to functionally characterize two recently identified reader proteins, EMSY-LIKE 1 (EML1) and EML3, which contain Tudor-like Agenet domains predictive of histone PTM binding function. Here, we show that mutant plants exhibit contrasting hypersusceptible () and tolerant () responses to CaLCuV infection and that EML1 deficiency correlates with RNA polymerase II (Pol II) enrichment on viral chromatin and upregulated viral gene expression. Consistent with reader activity, EML1 and EML3 associate with nucleosomes and with CaLCuV chromatin, suggesting a direct impact on pathogenesis. We also demonstrate that EML1 and EML3 bind peptides containing histone H3 lysine 36 (H3K36), a PTM usually associated with active gene expression. The interaction encompasses multiple H3K36 PTMs, including methylation and acetylation, suggesting nuanced regulation. Furthermore, EML1 and EML3 associate with similar regions of viral chromatin, implying possible competition between the two readers. Regions of EML1 and EML3 association correlate with sites of trimethylated H3K36 (H3K36me3) enrichment, consistent with regulation of geminivirus chromatin by direct EML targeting. Histone PTMs convey information that regulates chromatin compaction and DNA accessibility. Histone reader proteins bind specific PTMs and translate their effects by modifying chromatin and/or by recruiting effectors that alter chromatin structure or activity. In this study, CaLCuV was used to characterize the activities of two Agenet domain histone readers, EML1 and EML3. We show that mutants are hypersusceptible to CaLCuV, whereas plants are more tolerant of infection than wild-type plants. We also demonstrate that EML1 and EML3 associate with histones and viral chromatin and that both proteins bind peptides containing H3K36, a PTM associated with active gene expression. Consistent with antiviral activity, EML1 suppresses CaLCuV gene expression and reduces Pol II access to viral chromatin. By linking EML1 and EML3 to pathogenesis, these studies have expanded our knowledge of histone reader proteins and uncovered an additional level of viral chromatin regulation.

Proteolytic Processing of Plant Proteins by Potyvirus NIa Proteases

“…We confirmed in vivo cleavage of ectopically expressed AtEML2, a nuclear histone reader protein ( 69 – 71 ). The protein was readily cleaved in TuMV-infected plants or in plants that coexpressed the TuMV or PPV proteases ( Fig.…”

“…We chose to test AtEML2, which was efficiently cleaved in vitro by both the PPV and TuMV proteases. AtEML2, a nuclear protein, belongs to a family of histone readers (also including AtEML1, AtEML3, and AtEML4) that have been associated with postfertilization seed development and pathogen resistance, including resistance to geminiviruses ( 69 – 71 ). The cleavage site is not conserved in AtEML1, AtEML3, or AtEML4.…”

Plant Antiviral Immunity Against Geminiviruses and Viral Counter-Defense for Survival

“…Furthermore, transient DEAD35-silencing in a tolerant cultivar results in increased susceptibility to ToLCNDV infection (Pandey et al, 2019). Similarly, Arabidopsis histone reader EML1 (EMSY-LIKE 1) suppresses CabLCV infection by inhibiting the association of RNA polymerase II with viral chromatin and represses viral gene expression (Coursey et al, 2018). Aside from SnRKs and RLKs, plant-derived chromatin modelers have been co-opted as viral resistance factors to defend against geminivirus infections (Figure 5).…”

Manipulation of the Plant Host by the Geminivirus AC2/C2 Protein, a Central Player in the Infection Cycle

“…EMSY-like 1 (EML1), a histone reader protein that binds a mark often present on active chromatin (H3K36 methylation), was recently found to suppress geminivirus infection. Further, EML1 was shown to diminish viral gene expression by inhibiting the association of RNA polymerase II (Pol II) with viral chromatin (Coursey et al, 2018a). Thus, EML1 may bind viral chromatin marked as active and promote changes that render it less accessible to the cellular transcription machinery.…”