Localization ofKif1cmRNA to cell protrusions dictates binding partner specificity of the encoded protein

Abstract

Subcellular localization of messenger RNA (mRNA) is a widespread phenomenon that can impact the regulation and function of the encoded protein. In nonneuronal cells, specific mRNAs localize to cell protrusions, and proper mRNA localization is required for cell migration. However, the mechanisms by which mRNA localization regulates protein function in this setting remain unclear. Here, we examined the functional consequences of localization of the mRNA encoding KIF1C. KIF1C is a kinesin motor protein required for cell migration and mRNA trafficking, including trafficking of its own mRNA. We show thatKif1cmRNA localization does not regulate KIF1C's protein abundance, distribution, or ability to traffic other mRNAs. Conversely,Kif1cmRNA localization to protrusions is required for directed cell migration. We used mass spectrometry to identify binding partners of endogenous KIF1C, which revealed dramatic dysregulation of the number and identity of KIF1C interactors in response toKif1cmRNA mislocalization. These results therefore uncovered a mechanistic connection between mRNA localization to cell protrusions and the specificity of protein–protein interactions. We anticipate that this mechanism is not limited toKif1cand is likely to be a general principle that impacts the functions of proteins encoded by protrusion-enriched mRNAs in nonneuronal cells.

Unraveling Axonal Transcriptional Landscapes: Insights from iPSC-Derived Cortical Neurons and Implications for Motor Neuron Degeneration

“…Instead, most downregulated RNAs in KIF1C-KO axons were related to neurotransmission, the synaptic zone, and misfolded protein clearance. Since the previously mentioned investigations regarding KIF1C have been performed in other cell types (Wang et al ., 2017; Pichon et al ., 2021; Nagel et al ., 2022; Norris & Mendell, 2023), it is possible that KIF1C -dependent transport in CNs uses different motors, independent of APC. However, by which mechanism transport in CNs is conducted needs to be subject of future investigations.…”

“…KIF1C is implicated in many functions, including maintenance of Golgi morphology, cell migration, formation of podosomes in vascular smooth muscle cells and macrophages, and MHC presentation on the cell (Kopp et al ., 2006; del Rio et al ., 2012; Simpson et al ., 2012; Theisen et al ., 2012; Bhuwania et al ., 2014; Efimova et al ., 2014; Lee et al ., 2015). Interestingly, KIF1C has also been implicated in long range directional transport of APC-dependent mRNAs and RNA-dependent transport of the exon junction complex (EJC) into neurites, suggesting KIF1C can bind RNA in a direct or indirect manner (Pichon et al ., 2021; Nagel et al ., 2022; Norris & Mendell, 2023). However, which impact loss of KIF1C has on the axonal transcriptome remains elusive.…”

KIF1C, an RNA transporting kinesin-3, undergoes liquid-liquid phase separation through its C-terminal disordered domain

“…As a kinesin, what does LLPS activity mean for KIF1C's function? Recently, several groups reported that KIF1C associates with and transports mRNAs [43][44][45][46] . These findings are particularly interesting in light of KIF1C's ability to undergo LLPS, as many phase-separating proteins are known to be RNAbinding proteins (RBPs) 27,75 .…”

“…9). First, endogenous KIF1C protein is localized diffusely throughout the cell and only a few small droplets are observed in the cell periphery 45,49 . Second, mRNAs whose localization at the cell periphery is dependent on KIF1C can be transported in the form of single copies and then coalesce into larger clusters once they reach their destination in cell protrusions 43,85 .…”

“…How motor proteins bind to and transport specific mRNAs and other RNA species remains an important question in the field. Recent work has shown that KIF1C, a ubiquitously expressed member of the kinesin-3 family, functions in mRNA transport in numerous cell types [43][44][45][46] . KIF1C had previously been implicated in the transport of Golgi-derived vesicles, integrins, and secretory vesicles [47][48][49] , and thus appears to be a kinesin protein capable of transporting both membrane-bound organelles and membraneless complexes.…”