Abstract

Protein kinase D (PKD) controls protein traffic from the trans-Golgi network (TGN) to the plasma membrane of epithelial cells in an isoform-specific manner. However, whether the different PKD isoforms could be selectively regulating the traffic of their specific substrates remains unexplored. We identified the C terminus of the different PKDs that constitutes a postsynaptic density-95/discs large/zonula occludens-1 (PDZ)-binding motif in PKD1 and PKD2, but not in PKD3, to be responsible for the differential control of kinase D-interacting substrate of 220-kDa (Kidins220) surface localization, a neural membrane protein identified as the first substrate of PKD1. A kinase-inactive mutant of PKD3 is only able to alter the localization of Kidins220 at the plasma membrane when its C terminus has been substituted by the PDZ-binding motif of PKD1 or PKD2. This isoform-specific regulation of Kidins220 transport might not be due to differences among kinase activity or substrate selectivity of the PKD isoenzymes but more to the adaptors bound to their unique C terminus. Furthermore, by mutating the autophosphorylation site Ser(916), located at the critical position -2 of the PDZ-binding domain within PKD1, or by phorbol ester stimulation, we demonstrate that the phosphorylation of this residue is crucial for Kidins220-regulated transport. We also discovered that Ser(916) trans-phosphorylation takes place among PKD1 molecules. Finally, we demonstrate that PKD1 association to intracellular membranes is critical to control Kidins220 traffic. Our findings reveal the molecular mechanism by which PKD localization and activity control the traffic of Kidins220, most likely by modulating the recruitment of PDZ proteins in an isoform-specific and phosphorylation-dependent manner.

Highlights

  • 25 Pacific Biosciences Circular consensus (CCS) sequencing, yielding high accuracy single-molecule consensus sequences of large genomic regions

  • Each template molecule in a sample is tagged with a unique molecular identifiers (UMIs) sequence consisting of 10-20 random bases, which can subsequently be used to sort and analyse 40 reads based on their original template molecule

  • 50 Here, we present a simple workflow that combines UMIs with sequencing of long amplicons on the Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) platforms to produce highly accurate single-molecule consensus sequences with a low chimera rate

Read more

Summary

Methods

Source of DNA The ZymoBIOMICS Microbial Community DNA Standard ZRC190811) was 10 obtained from Zymo Research (Irvine, California). The mock community DNA contained genomic material from 10 species (8 bacteria and 2 yeasts): Bacillus subtilis, Cryptococcus neoformans, Enterococcus faecalis, Escherichia coli, Lactobacillus fermentum, Listeria monocytogenes, Pseudomonas aeruginosa, Saccharomyces cerevisiae, Salmonella enterica, Staphylococcus aureus. 2 of the yeast species were not targeted by PCR amplification of 15 rRNA operons based on the primers used (see DNA Sequence Library Preparation). The concentration of DNA in the mock community sample was measured on a Qubit 3.0 fluorometer and Qubit dsDNA HS assay kit (Thermo Fisher Scientific), and the quality of the DNA was measured by gel electrophoresis on an Agilent 2200 Tapestation using Genomic Screentapes (Agilent Technologies)

Online protocol
Sources of DNA
DNA extraction
PacBio UMI data generation and processing
Generation of rRNA operon reference sequences for mock microbial community
Resources availability
PB UMI
CAAGCAGAAGACGGCATACGAGAT AATGATACGGCGACCACCGAGATC
Total time
Clustered Consensus Sequences
Findings
ENA Accession
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call