The Human Cytoplasmic Dynein Interactome Reveals Novel Activators of Motility

Abstract

In human cells, cytoplasmic dynein-1 is essential for long-distance transport of many cargos, including organelles, RNAs, proteins, and viruses, towards microtubule minus ends. To understand how a single motor achieves cargo specificity, we identified the human dynein interactome or "transportome" by attaching a promiscuous biotin ligase ("BioID") to seven components of the dynein machinery, including a subunit of the essential cofactor dynactin. This method reported spatial information about the large cytosolic dynein/dynactin complex in living cells. To achieve maximal motile activity and to bind its cargos, human dynein/dynactin requires "activators", of which only five have been described. We developed methods to identify new activators in our BioID data, and discovered that ninein and ninein-like are a new family of dynein activators.Analysis of the protein interactomes for six activators, including ninein and ninein-like, suggests that each dynein activator has multiple cargos.

Murine MPDZ ‐linked hydrocephalus is caused by hyperpermeability of the choroid plexus

“…Since DVL is required for the formation of Wnt‐induced planar polarity of ependymal cells (Ohata et al , ), it is conceivable that CCDC88C ‐linked hydrocephalus was caused by the loss of the alignment of the cilia of the ependymal cells on the lumen of the ventricles and the resulting slowdown of CSF flow. Furthermore, DAPLE binds to (Redwine et al , ) and functions as an activating adaptor of dynein (Reck‐Peterson et al , ), a molecular motor that is required for cilium motility (Gibbons & Rowe, ). To date, the premise that CCDC88C mutations cause hydrocephalus by impeding ciliary function has not been tested.…”

A conserved choreography of mRNAs at centrosomes reveals a localization mechanism involving active polysome transport

“…Interestingly, all eight localized mRNAs encode proteins that either bind MTs directly (ASPM, NUMA1, HMMR, CCDC88C, CEP350) or contribute to MT anchoring (NIN, PCNT, BICD2). Similarly, many of these proteins directly or indirectly bind dynein (BICD2, NIN, CCDC88C, PCNT, NUMA1, HMMR; Redwine et al, 2017). These properties could thus be part of the transport mechanism.…”

Mass spectrometry‐based protein–protein interaction networks for the study of human diseases

“…BirA catalyzes the transformation of biotin to a more reactive form, and the resultant biotin cloud reacts with primary amines of proteins in its vicinity, resulting in their covalent biotinylation (Roux et al, 2018). Subcellular compartments that have been targeted by BioID include the nuclear envelope (Kim et al, 2016b), centrosome (Antonicka et al, 2020), nucleus (preprint: Go et al, 2019), cytoplasm (Redwine et al, 2017), Golgi apparatus (Liu et al, 2018), ER (Hoffman et al, 2019), endosome, lysosome, mitochondrial matrix (Antonicka et al, 2020), cell-cell junctions (Fredriksson et al, 2015), and flagella (Kelly et al, 2020), with labeling efficiency limited in the ER (Roux et al, 2018;preprint: Go et al, 2019). Due to slow reaction kinetics, BioID requires labeling for 18-24 h to produce sufficient material for identification by MS, which can lead to off-target labeling and high background, and somewhat Genetic variants, which may occur rarely across individuals with a specific disease, can be used as the basis of PPI networks.…”