Alpha-centractin is a novel substrate of SETD3 methyltransferase in vitro

Background The SETD3 enzyme, a protein histidine methyltransferase, catalyzes the Nτ-methylation of the histidine 73 residue in β-actin. This post-translational modification is important for maintaining cytoskeleton integrity, and actin remains the only known substrate of this methyltransferase to date. However, SETD3 was also postulated to play a role in the regulation of processes that are not directly related to actin homeostasis, such as cell cycle control and response to hypoxic conditions. These findings suggest that actin may not be the sole substrate of SETD3 methyltransferase. Here, we demonstrate that SETD3 methylates additional proteins in human cells, and α-centractin (ACTR1A) may be one of them. Methods Three different human SETD3 knockout cell lines (HAP1, HeLa, HEK293T) were generated with the CRISPR/Cas9 method and used as a source of SETD3 substrates. Fluorography was used to detect the SETD3-dependent methylation of proteins present in cell lysates, while the TurboID biotin ligase proximity labeling technique was used to isolate proteins that interact with SETD3. The molecular identity of the proteins was determined by mass spectrometry and the activity of recombinant SETD3 towards potential substrates was tested using a radiochemical assay. Results Fluorography revealed that SETD3 methylates at least five novel proteins besides β-actin in HAP1 cells. TurboID proximity labeling identified α-centractin, a key dynactin subunit, as an SETD3 interactor and an in vitro methylation target, suggesting that SETD3 potentially regulates not only actin cytoskeleton dynamics but also dynein-mediated intracellular transport.