In Silico Screening for Palmitoyl Substrates Reveals a Role for DHHC1/3/10 (zDHHC1/3/11)-mediated Neurochondrin Palmitoylation in Its Targeting to Rab5-positive Endosomes

Protein palmitoylation, a common post-translational lipid modification, plays an important role in protein trafficking and functions. Recently developed palmitoyl-proteomic methods identified many novel substrates. However, the whole picture of palmitoyl substrates has not been clarified. Here, we performed global in silico screening using the CSS-Palm 2.0 program, free software for prediction of palmitoylation sites, and selected 17 candidates as novel palmitoyl substrates. Of the 17 candidates, 10 proteins, including 6 synaptic proteins (Syd-1, transmembrane AMPA receptor regulatory protein (TARP) γ-2, TARP γ-8, cornichon-2, Ca²⁺/calmodulin-dependent protein kinase IIα, and neurochondrin (Ncdn)/norbin), one focal adhesion protein (zyxin), two ion channels (TRPM8 and TRPC1), and one G-protein-coupled receptor (orexin 2 receptor), were palmitoylated. Using the DHHC palmitoylating enzyme library, we found that all tested substrates were palmitoylated by the Golgi-localized DHHC3/7 subfamily. Ncdn, a regulator for neurite outgrowth and synaptic plasticity, was robustly palmitoylated by the DHHC1/10 (zDHHC1/11; z1/11) subfamily, whose substrate has not yet been reported. As predicted by CSS-Palm 2.0, Cys-3 and Cys-4 are the palmitoylation sites for Ncdn. Ncdn was specifically localized in somato-dendritic regions, not in the axon of rat cultured neurons. Stimulated emission depletion microscopy revealed that Ncdn was localized to Rab5-positive early endosomes in a palmitoylation-dependent manner, where DHHC1/10 (z1/11) were also distributed. Knockdown of DHHC1, -3, or -10 (z11) resulted in the loss of Ncdn from Rab5-positive endosomes. Thus, through in silico screening, we demonstrate that Ncdn and the DHHC1/10 (z1/11) and DHHC3/7 subfamilies are novel palmitoyl substrate-enzyme pairs and that Ncdn palmitoylation plays an essential role in its specific endosomal targeting.     

Identification of Neurochondrin as a new interaction partner of the FH3 domain of the Diaphanous-related formin Dia1

Mammalian Diaphanous (Dia)-related formins initiate the assembly of filamentous actin downstream of Rho GTPases to regulate cellular processes such as cytokinesis, cell polarity, cell motility and adhesion. In this work, we show that Neurochondrin (NC) is a novel Dia1 interacting protein. NC specifically binds to the formin homology 3 (FH3), but not to the FH1 or FH2 domain of Dia1. Both proteins show a partial co-localization in dissociated primary rat hippocampal neurons. Ectopic expression of both proteins induced neurite outgrowth in Neuro2A cells. Using a series of deletion mutants of NC we could show that the first 100 amino acids were responsible for its effect on neurite outgrowth, whereas the C-terminal part of NC had no neurite outgrowth promoting activity. Moreover, co-expression of the C terminus of NC with Dia1ΔDAD resulted in a dramatic reduction of Dia1-induced neurite outgrowth. On the basis of actin fractionation assays, SRF-activity assays as well as microtubule stabilization assays, we could demonstrate that the C terminus of NC does not influence the actin polymerizing activity of Dia1, indicating a more specific function of NC in the modulation of Dia1 activity.