Histone modification crosstalk between host and pathogen

Abstract

Bacterial pathogens modulate host cell physiology by secreting effector proteins that rewire host signaling pathways. A subset of these effectors directly modify host chromatin to reprogram gene expression and promote infection. While these enzymes are thought to function autonomously, the extent to which the host epigenetic landscape regulates their activity remains largely unknown. RomA and its homolog LegAs4 are Set domain-containing lysine methyltransferases from Legionella pneumophila that methylate histone H3 at lysine 14 (H3K14) to suppress host immune responses and enhance intracellular bacterial replication. Here, we demonstrate that RomA activity is constrained by pre-existing host histone post-translational modifications (PTMs) through multiple layers of histone PTM crosstalk. RomA selectively binds and methylates unmodified histone H3 tails and is inhibited by histone PTMs associated with active transcription, including H3K4 trimethylation, H3K4 acetylation, and H4K12 mono-methylation. We identify both cis- and trans-histone regulatory mechanisms, whereby unmodified H3K4 and H3K14 must reside on the same H3 tail to support RomA activity, while H4K12me1 inhibits RomA across the nucleosome. Notably, cryo-EM analysis and biochemical data reveal that RomA does not engage the nucleosome acidic patch but instead associates flexibly through histone tails. Together, these findings establish the host epigenetic regulation of bacterial effectors as a fundamental and previously unrecognized layer of host-pathogen interactions. SIGNIFICANCEBacterial pathogens reprogram host gene expression by delivering effector proteins that modify chromatin, but it is not known how the host epigenetic environment impacts effector function. Here, we show that the Legionella effector RomA senses and responds to the hosts existing epigenetic landscape and is selectively active only in specific chromatin contexts through mechanisms resembling those used by eukaryotic chromatin regulators. Notably, we uncover that RomA utilizes cis-histone and trans-histone crosstalk mechanisms previously observed only in eukaryotic systems. These reveals an unexpected form of host-pathogen crosstalk in which bacterial effector activity can be constrained by host epigenetic modifications.