The TRIM33 Bromodomain Recognizes Histone Lysine Lactylation.

Abstract

Histone lysine lactylation (Kla) regulates inflammatory gene expression in activated macrophages and mediates the polarization of inflammatory (M1) to reparative (M2) macrophages. However, the molecular mechanisms and key protein players involved in Kla-mediated transcriptional changes are unknown. As Kla is structurally similar to lysine acetylation (Kac), which is bound by bromodomains, we hypothesized that bromodomain-containing proteins bind histone Kla. Here, we screened 28 recombinantly expressed bromodomains for binding to histone Kla peptides via AlphaScreen assays. TRIM33 was the sole bromodomain tested that bound histone Kla peptides. TRIM33 attenuates inflammatory genes during late-stage macrophage activation; thus, TRIM33 provides a potential link between histone Kla and macrophage polarization. Orthogonal biophysical techniques, including isothermal titration calorimetry and protein-detected nuclear magnetic resonance, confirmed the submicromolar binding affinity of the TRIM33 bromodomain to both Kla and Kac histone post-translational modifications. Sequence alignments of human bromodomains revealed a unique glutamic acid residue within the TRIM33 binding pocket that we found confers TRIM33 specificity for binding Kla compared with other bromodomains. Molecular modeling of interactions of Kla with the TRIM33 bromodomain binding pocket and site-directed mutagenesis of glutamic acid confirmed the critical role of this residue in the selective recognition of Kla by TRIM33. Collectively, our findings implicate TRIM33, a bromodomain-containing protein, as a novel reader of histone Kla, potentially bridging the gap between histone Kla and macrophage polarization. This study enhances our understanding of the regulatory role of histone Kla in macrophage-mediated inflammation and offers insights into the underlying structural and biophysical mechanisms.