Interactome Profiling of a Lysine Deacetylase Trapping Probe Library Uncovers Crosstalk Between HDAC6 and NF‐κB Signaling

Lysine or histone deacetylases (HDACs) remove acetyl groups from lysine residues of numerous proteins, thereby regulating their function and activity. HDAC6 is involved in multiple cellular processes, yet its protein interaction network remains poorly understood. To uncover novel HDAC6 substrates, we performed an acetylome analysis of HDAC6 knockdown cells, which served as a basis for the design of an HDAC6-trapping peptide library containing hydroxamic acids. Most probes enriched HDAC6 from cell lysates stronger than HDAC1. Proteomic profiling of the trapping probes revealed a preferential enrichment of HDAC6 and resulted in the identification of novel putative HDAC6 interaction partners. Among those were several components of the pro-inflammatory transcription factor NF-κB that were independently confirmed as HDAC6 binders. Mechanistically, HDAC6 counteracted NF-κB activity induced upon p300-catalyzed acetylation of NF-κB p50. These findings indicate a potential anti-inflammatory function of HDAC6 in NF-κB signaling.