Increased microtubule lattice spacing correlates with selective binding of kinesin-1 in cells

Abstract

Within the cell cargo is transported via motor proteins walking along microtubules. The affinity of motor proteins for microtubules is controlled by various layers of regulation like tubulin isoforms, post- translational modifications and microtubule associated proteins. Recently, the conformation of the microtubule lattice has also emerged as a potential regulatory factor, but to what extent it acts as an additional layer of regulation has remained unclear. In this study, we used cryo-correlative light and electron microscopy to study microtubule lattices inside cells. We find that, while most microtubules have a compacted lattice (∼41 Å), a significant proportion of the microtubule cores have expanded lattice spacings and that these lattice spacings could be modulated by the microtubule stabilizing drug Taxol. Furthermore, kinesin-1 predominantly binds microtubules with a more expanded lattice spacing (∼41.6 Å). The different lattice spacings present in the cell can thus act as an additional factor that modulates the binding of motor proteins to specific microtubule subsets.

Cellular cartography: Towards an atlas of the neuronal microtubule cytoskeleton

“…Interestingly, the rigor was observed to transiently associate with many microtubules in the cell, but had a high unbinding-rate from dynamic microtubules such that it only accumulated on stable microtubules. This marker was also shown to preferentially associate with (stable) microtubules with an expanded lattice in U2OS cells ( de Jager et al, 2022 ) and in vitro ( Jansen et al, 2023 ). This makes it interesting to consider how this compares with the track selectivity of wild-type (motile) kinesin-1.…”

“…In contrast, kinesin-1 has been shown to expand the microtubule lattice, at least in vitro , with ∼10% lattice occupancy ( Peet et al, 2018 ; Shima et al, 2018 ). Furthermore, a kinesin-1 rigor (with a mutation that prevents it from hydrolyzing ATP, rendering it non-motile) has been shown to localize preferentially to microtubules with an expanded lattice in cells ( de Jager et al, 2022 ). Thus, there is some flexibility in the structure of tubulin and this could serve as a means for proteins to bind cooperatively and communicate allosterically via the microtubule lattice ( Brouhard and Rice, 2018 ).…”

“…Kinesin-1/KIF5A,B,C Stable (expanded) Prefers acetylated microtubules in COS-7 cells and rat hippocampal neurons (Cai et al, 2009;Farías et al, 2015;Tas et al, 2017;Jansen et al, 2023); can expand the microtubule lattice (Peet et al, 2018); a kinesin-1 rigor localizes specifically to microtubules with an expanded lattice in U2OS cells (de Jager et al, 2022) Kinesin-4/KIF21B Stable Moves cargo with a retrograde bias in PEX assays in rat hippocampal neurons unless plus-end-out microtubules are stabilized (Masucci et al, 2021) Dynein Dynamic Cofactor p150 Glued binds preferentially to tyrosinated microtubules in fibroblasts and in vitro (Peris et al, 2006;McKenney et al, 2016) Kinesin-3/KIF1A Dynamic Rigor KIF1A is ~2-fold enriched on tyrosinated microtubules compared to acetylated microtubules in soma of neurons and COS-7 cells (Tas et al, 2017) Kinesin-13/MCAK/KIFA Dynamic Prefers tyrosinated microtubules in mouse embryonic fibroblasts and in vitro (Peris et al, 2009) MAP7 Stable Potently recruits and activates kinesin-1 in vitro and in HeLa cells (Monroy et al, 2018;Hooikaas et al, 2019;Ferro et al, 2022) MAP7D1 Stable MAP7D1 localizes to some sort of subset in HeLa cells; recruits and activates kinesin-1 (Hooikaas et al, 2019) MAP7D2 Stable Localizes to the axon initial segment and helps kinesin-1 traffic into the axon of rat hippocampal neurons (Pan et al, 2019) MAP7D3 Stable Recruits and activates kinesin-1 in vitro and in HeLa cells (Hooikaas et al, 2019) MAP6 Stable Stabilizes microtubules against cold and nocodazole-induced depolymerization in mouse (embryonic) fibroblasts, HeLa cells, and neurons (Bosc et al, 2003;Delphin et al, 2012;Cuveillier et al, 2020); resists tubulin compaction leading to coiled microtubules in vitro (Cuveillier et al, 2020) MAP4 Stable? Does not compact microtubule lattice in vitro (Siahaan et al, 2022); can bind microtubule at the same time as kinesin-1 (Shigematsu et al, 2018) MAP9 Dynamic?…”

Optogenetic control of kinesins -1, -2, -3 and dynein reveals their specific roles in vesicular transport

“…Optogenetically inhibiting multiple kinesins at the same time showed a more prominent directional switch with the majority of cargoes shifting to dynein-driven motility (Figure S6), indicating that multiple types of kinesins work together to transport cargoes (44). Interestingly, microtubuleassociated proteins (MAPs) like tau and MAP7 preferentially target kinesin-1 (43,45), which is sensitive to tubulin lattice spacing (46). Kinesin-1 and -3 prefer microtubules marked with different set of post-translational modifications (47,48).…”

Tau oligomerization on microtubules in health and disease

“…This dual mode of cooperativity therefore allows tau to stake out territory on the microtubule and maintain the underlying compacted lattice state. Importantly, heterogeneity of tubulin nucleotide state, defects in the lattice, and microtubule lattice spacing has been reported in vivo, posing the hypothesis that MAP binding may be one way to control the compaction state, and therefore downstream effector interactions with the lattice (Atherton et al, 2018;Dimitrov et al, 2008;Gazzola et al, 2023;Jager et al, 2022;Triclin et al, 2021).…”