Increased microtubule lattice spacing correlates with selective binding of kinesin-1 in cells
Open accessPreprint — published as 10.1083/jcb.202206143 · Paper page
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Microtubules bound by StableMARK have an expanded lattice in cells, as indicated by fluorescence-guided cryo-focused ion beam transmission electron microscopy data.
“Second, MTs bound by StableMARK have an expanded lattice in cells, as indicated by fluorescence-guided cryo-focused ion beam transmission electron microscopy data (de Jager et al., 2022 Preprint).”
From A live-cell marker to visualize the dynamics of stable microtubules throughout the cell cycle (2023) · cites this paper as de Jager et al., 2022 Preprint
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
No references could be resolved yet.
Research works printed but not linked: 62
- Akhmanova, A., and L.C. Kapitein. 2022. Mechanisms of microtubule orga- nization in differentiated animal cells. Nat. Rev. Mol. Cell Biol. 23: 541-558. https://doi.org/10.1038/s41580-022-00473-y · DOI · Paper page
- Alushin, G.M., G.C. Lander, E.H. Kellogg, R. Zhang, D. Baker, and E. Nogales. 2014. High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell. 157:1117-1129. https://doi.org/10.1016/j.cell.2014.03.053 · DOI · Paper page
- Arnold, J., J. Mahamid, V. Lucic, A. de Marco, J.J. Fernandez, T. Laugks, T. Mayer, A.A. Hyman, W. Baumeister, and J.M. Plitzko. 2016. Site-specific cryo-focused ion beam sample preparation guided by 3D correlative microscopy. Biophys. J. 110:860-869. https://doi.org/10.1016/j.bpj.2015 .10.053 · DOI · Paper page
- Bär, J., Y. Popp, M. Bucher, and M. Mikhaylova. 2022. Direct and indirect effects of tubulin post-translational modifications on microtubule sta- bility: Insights and regulations. Biochim. Biophys. Acta Mol. Cell Res. 1869: 119241. https://doi.org/10.1016/j.bbamcr.2022.119241 · DOI
- Barbuti, A.M., and Z.-S. Chen. 2015. Paclitaxel through the ages of anticancer therapy: Exploring its role in chemoresistance and radiation therapy. Cancers. 7:2360-2371. https://doi.org/10.3390/cancers7040897 · DOI
- Bechstedt, S., and G.J. Brouhard. 2012. Doublecortin recognizes the 13- protofilament microtubule cooperatively and tracks microtubule ends. Dev. Cell. 23:181-192. https://doi.org/10.1016/j.devcel.2012.05 .006 · DOI
- Burute, M., and L.C. Kapitein. 2019. Cellular logistics: Unraveling the inter- play between microtubule organization and intracellular transport. Annu. Rev. Cell Dev. Biol. 35:29-54. https://doi.org/10.1146/annurev -cellbio-100818-125149 · DOI
- Castaño-Díez, D., M. Kudryashev, and H. Stahlberg. 2017. Dynamo Catalogue: Geometrical tools and data management for particle picking in sub- tomogram averaging of cryo-electron tomograms. J. Struct. Biol. 197: 135-144. https://doi.org/10.1016/j.jsb.2016.06.005 · DOI
- Cook, A.D., S.W. Manka, S. Wang, C.A. Moores, and J. Atherton. 2020. A microtubule RELION-based pipeline for cryo-EM image processing. J. Struct. Biol. 209:107402. https://doi.org/10.1016/j.jsb.2019.10.004 · DOI · Paper page
- Cross, R.A. 2019. Microtubule lattice plasticity. Curr. Opin. Cell Biol. 56:88-93. https://doi.org/10.1016/j.ceb.2018.10.004 · DOI · Paper page
- Estévez-Gallego, J., F. Josa-Prado, S. Ku, R.M. Buey, F.A. Balaguer, A.E. Prota, D. Lucena-Agell, C. Kamma-Lorger, T. Yagi, H. Iwamoto, et al. 2020. Structural model for differential cap maturation at growing microtubule ends. Elife. 9:e50155. https://doi.org/10.7554/eLife .50155 · DOI · Paper page
- Ettinger, A., J. van Haren, S.A. Ribeiro, and T. Wittmann. 2016. Doublecortin is excluded from growing microtubule ends and recognizes the GDP- microtubule lattice. Curr. Biol. 26:1549-1555. https://doi.org/10.1016/j .cub.2016.04.020 · DOI · Paper page
- Fermie, J., L. de Jager, H.E. Foster, T. Veenendaal, C. de Heus, S. van Dijk, C. Ten Brink, V. Oorschot, L. Yang, W. Li, et al. 2022. Bimodal endocytic probe for three-dimensional correlative light and electron microscopy. Cell Rep. Methods. 2:100220. https://doi.org/10.1016/j.crmeth.2022 .100220 · DOI
- Ferro, L.S., Q. Fang, L. Eshun-Wilson, J. Fernandes, A. Jack, D.P. Farrell, M. Golcuk, T. Huijben, K. Costa, M. Gur, et al. 2022. Structural and functional insight into regulation of kinesin-1 by microtubule- associated protein MAP7. Science. 375:326-331. https://doi.org/10.1126/ science.abf6154 · DOI · Paper page
- Gadadhar, S., S. Bodakuntla, K. Natarajan, and C. Janke. 2017. The tubulin code at a glance. J. Cell Sci. 130:1347-1353. https://doi.org/10.1242/jcs .199471 · DOI
- Guedes-Dias, P., J.J. Nirschl, N. Abreu, M.K. Tokito, C. Janke, M.M. Magiera, and E.L.F. Holzbaur. 2019. Kinesin-3 responds to local microtubule dynamics to target synaptic cargo delivery to the presynapse. Curr. Biol. 29:268-282.e8. https://doi.org/10.1016/j.cub.2018.11.065 · DOI · Paper page
- Gwosch, K.C., J.K. Pape, F. Balzarotti, P. Hoess, J. Ellenberg, J. Ries, and S.W. Hell. 2020. MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells. Nat. Methods. 17:217-224. https://doi.org/10.1038/ s41592-019-0688-0 · DOI
- Hagen, W.J.H., W. Wan, and J.A.G. Briggs. 2017. Implementation of a cryo- electron tomography tilt-scheme optimized for high resolution sub- tomogram averaging. J. Struct. Biol. 197:191-198. https://doi.org/10.1016/ j.jsb.2016.06.007 · DOI
- Hammond, J.W., C.-F. Huang, S. Kaech, C. Jacobson, G. Banker, and K.J. Verhey. 2010. Posttranslational modifications of tubulin and the po- larized transport of kinesin-1 in neurons. Mol. Biol. Cell. 21:572-583. https://doi.org/10.1091/mbc.e09-01-0044 · DOI · Paper page
- Hyman, A.A., D. Chrétien, I. Arnal, and R.H. Wade. 1995. Structural changes accompanying GTP hydrolysis in microtubules: Information from a slowly hydrolyzable analogue guanylyl-(alpha,beta)-methylene-di- phosphonate. J. Cell Biol. 128:117-125. https://doi.org/10.1083/jcb.128.1 .117 · DOI · Paper page
- Iwanski, M.K., and L.C. Kapitein. 2023. Cellular cartography: Towards an atlas of the neuronal microtubule cytoskeleton. Front. Cell Dev. Biol. 11: 1052245. https://doi.org/10.3389/fcell.2023.1052245 · DOI · Paper page
- Janke, C., and M.M. Magiera. 2020. The tubulin code and its role in con- trolling microtubule properties and functions. Nat. Rev. Mol. Cell Biol. 21: 307-326. https://doi.org/10.1038/s41580-020-0214-3 · DOI · Paper page
- Jansen, K.I., M.K. Iwanski, M. Burute, and L.C. Kapitein. 2023. A live-cell marker to visualize the dynamics of stable microtubules throughout the cell cycle. J. Cell Biol. 222:e202106105. https://doi.org/10.1083/jcb .202106105 · DOI · Paper page
- Kellogg, E.H., N.M.A. Hejab, S. Howes, P. Northcote, J.H. Miller, J.F. Díaz, K.H. Downing, and E. Nogales. 2017. Insights into the distinct mechanisms of action of taxane and non-taxane microtubule stabilizers from cryo-EM structures. J. Mol. Biol. 429:633-646. https://doi.org/10.1016/j.jmb.2017 .01.001 · DOI · Paper page
- Kellogg, E.H., N.M.A. Hejab, S. Poepsel, K.H. Downing, F. DiMaio, and E. Nogales. 2018. Near-atomic model of microtubule-tau interactions. Science. 360:1242-1246. https://doi.org/10.1126/science.aat1780 · DOI · Paper page
- Kluyver, T., B. Ragan-Kelley, F. Pérez, B.E. Granger, M. Bussonnier, J. Fred- eric, K. Kelley, J.B. Hamrick, J. Grout, and S. Corlay. 2016. Jupyter Notebooks-a publishing format for reproducible computational work- flows. In Positioning and Power in Academic Publishing: Players, Agents and Agendas. F. Loizides and B. Scmidt, editors. IOS Press, Amsterdam, The Netherlands. 87-90. https://doi.org/10.3233/978-1 -61499-649-1-87 · DOI
- Kremer, J.R., D.N. Mastronarde, and J.R. McIntosh. 1996. Computer visuali- zation of three-dimensional image data using IMOD. J. Struct. Biol. 116: 71-76. https://doi.org/10.1006/jsbi.1996.0013 · DOI
- LaFrance, B.J., J. Roostalu, G. Henkin, B.J. Greber, R. Zhang, D. Normanno, C.O. McCollum, T. Surrey, and E. Nogales. 2022. Structural transitions in the GTP cap visualized by cryo-electron microscopy of catalytically inactive microtubules. Proc. Natl. Acad. Sci. USA. 119:e2114994119. https://doi.org/10.1073/pnas.2114994119 · DOI · Paper page
- Mandelkow, E., J. Thomas, and C. Cohen. 1977. Microtubule structure at low resolution by x-ray diffraction. Proc. Natl. Acad. Sci. USA. 74:3370-3374. https://doi.org/10.1073/pnas.74.8.3370 · DOI
- Manka, S.W., and C.A. Moores. 2018a. Microtubule structure by cryo-EM: Snapshots of dynamic instability. Essays Biochem. 62:737-751. https://doi .org/10.1042/EBC20180031 · DOI · Paper page
- Manka, S.W., and C.A. Moores. 2018b. The role of tubulin-tubulin lattice contacts in the mechanism of microtubule dynamic instability. Nat. Struct. Mol. Biol. 25:607-615. https://doi.org/10.1038/s41594-018-0087-8 · DOI · Paper page
- Mastronarde, D.N. 2003. SerialEM: A program for automated tilt series acqui- sition on tecnai microscopes using prediction of specimen position. Mi- crosc. Microanal. 9:1182-1183. https://doi.org/10.1017/S1431927603445911 · DOI
- Orr, G.A., P. Verdier-Pinard, H. McDaid, and S.B. Horwitz. 2003. Mechanisms of Taxol resistance related to microtubules. Oncogene. 22:7280-7295. https://doi.org/10.1038/sj.onc.1206934 · DOI · Paper page
- de Jager et al. Journal of Cell Biology 11 of 12 Stable microtubules have expanded lattices https://doi.org/10.1083/jcb.202206143 · DOI · Paper page
- Peet, D.R., N.J. Burroughs, and R.A. Cross. 2018. Kinesin expands and sta- bilizes the GDP-microtubule lattice. Nat. Nanotechnol. 13:386-391. https://doi.org/10.1038/s41565-018-0084-4 · DOI · Paper page
- Rai, A., T. Liu, S. Glauser, E.A. Katrukha, J. Estévez-Gallego, R. Rodríguez- García, W.S. Fang, J.F. Díaz, M.O. Steinmetz, K.H. Altmann, et al. 2020. Taxanes convert regions of perturbed microtubule growth into rescue sites. Nat. Mater. 19:355-365. https://doi.org/10.1038/s41563-019-0546-6 · DOI
- Rice, S., A.W. Lin, D. Safer, C.L. Hart, N. Naber, B.O. Carragher, S.M. Cain, E. Pechatnikova, E.M. Wilson-Kubalek, M. Whittaker, et al. 1999. A structural change in the kinesin motor protein that drives motility. Nature. 402:778-784. https://doi.org/10.1038/45483 · DOI · Paper page
- Rigort, A., F.J.B. Bäuerlein, E. Villa, M. Eibauer, T. Laugks, W. Baumeister, and J.M. Plitzko. 2012. Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc. Natl. Acad. Sci. USA. 109: 4449-4454. https://doi.org/10.1073/pnas.1201333109 · DOI
- Roll-Mecak, A. 2020. The tubulin code in microtubule dynamics and infor- mation encoding. Dev. Cell. 54:7-20. https://doi.org/10.1016/j.devcel .2020.06.008 · DOI
- Schindelin, J., I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, et al. 2012. Fiji: An open-source platform for biological-image analysis. Nat. Methods. 9: 676-682. https://doi.org/10.1038/nmeth.2019 · DOI · Paper page
- Schorb, M., and J.A. Briggs. 2014. Correlated cryo-fluorescence and cryo- electron microscopy with high spatial precision and improved sensi- tivity. Ultramicroscopy. 143:24-32. https://doi.org/10.1016/j.ultramic .2013.10.015 · DOI · Paper page
- Shaner, N.C., G.G. Lambert, A. Chammas, Y. Ni, P.J. Cranfill, M.A. Baird, B.R. Sell, J.R. Allen, R.N. Day, M. Israelsson, et al. 2013. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat. Methods. 10:407-409. https://doi.org/10.1038/nmeth.2413 · DOI
- Shen, Y., and K.M. Ori-McKenney. 2023. Macromolecular crowding tailors the microtubule cytoskeleton through tubulin modifications and microtubule-associated proteins. bioRxiv. https://doi.org/10.1101/2023 .06.14.544846 (Preprint posted June 14, 2023). · DOI
- Shima, T., M. Morikawa, J. Kaneshiro, T. Kambara, S. Kamimura, T. Yagi, H. Iwamoto, S. Uemura, H. Shigematsu, M. Shirouzu, et al. 2018. Kinesin- binding-triggered conformation switching of microtubules contributes to polarized transport. J. Cell Biol. 217:4164-4183. https://doi.org/10 .1083/jcb.201711178 · DOI · Paper page
- Shin, G.J. 2023. Towards a mechanistic understanding of axon transport and endocytic changes underlying paclitaxel-induced peripheral neuropathy. Exp. Neurol. 359:114258. https://doi.org/10.1016/j.expneurol.2022.114258 · DOI
- Siahaan, V., R. Tan, T. Humhalova, L. Libusova, S.E. Lacey, T. Tan, M. Dacy, K.M. Ori-McKenney, R.J. McKenney, M. Braun, and Z. Lansky. 2022. Microtubule lattice spacing governs cohesive envelope formation of tau family proteins. Nat. Chem. Biol. 18:1224-1235. https://doi.org/10.1038/ s41589-022-01096-2 · DOI · Paper page
- Tirnauer, J.S., and B.E. Bierer. 2000. EB1 proteins regulate microtubule dy- namics, cell polarity, and chromosome stability. J. Cell Biol. 149:761-766. https://doi.org/10.1083/jcb.149.4.761 · DOI
- Unser, M., B.L. Trus, and A.C. Steven. 1987. A new resolution criterion based on spectral signal-to-noise ratios. Ultramicroscopy. 23:39-51. https://doi .org/10.1016/0304-3991(87)90225-7 · DOI
- Vale, R.D., C.M. Coppin, F. Malik, F.J. Kull, and R.A. Milligan. 1994. Tubulin GTP hydrolysis influences the structure, mechanical properties, and kinesin-driven transport of microtubules. J. Biol. Chem. 269:23769-23775. https://doi.org/10.1016/S0021-9258(17)31582-X · DOI · Paper page
- Verhey, K.J., and J. Gaertig. 2007. The tubulin code. Cell Cycle. 6:2152-2160. https://doi.org/10.4161/cc.6.17.4633 · DOI · Paper page
- Virtanen, P., R. Gommers, T.E. Oliphant, M. Haberland, T. Reddy, D. Cour- napeau, E. Burovski, P. Peterson, W. Weckesser, J. Bright, et al. 2020. SciPy 1.0: Fundamental algorithms for scientific computing in Python. Nat. Methods. 17:261-272. https://doi.org/10.1038/s41592-019-0686-2 · DOI · Paper page
- Wagner, F.R., R. Watanabe, R. Schampers, D. Singh, H. Persoon, M. Schaffer, P. Fruhstorfer, J. Plitzko, and E. Villa. 2020. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomog- raphy. Nat. Protoc. 15:2041-2070. https://doi.org/10.1038/s41596-020 -0320-x · DOI
- Watanabe, R., R. Buschauer, J. Bohning, M. Audagnotto, K. Lasker, T.W. Lu, D. Boassa, S. Taylor, and E. Villa. 2020. The in situ structure of Parkinson's disease-linked LRRK2. Cell. 182:1508-1518.e16. https://doi.org/10.1016/j .cell.2020.08.004 · DOI
- Wolff, G., R.W.A.L. Limpens, S. Zheng, E.J. Snijder, D.A. Agard, A.J. Koster, and M. Bárcena. 2019. Mind the gap: Micro-expansion joints drastically decrease the bending of FIB-milled cryo-lamellae. J. Struct. Biol. 208: 107389. https://doi.org/10.1016/j.jsb.2019.09.006 · DOI · Paper page
- Yue, Y., T. Hotta, T. Higaki, K.J. Verhey, and R. Ohi. 2023. Microtubule de- tyrosination by VASH1/SVBP is regulated by the conformational state of tubulin in the lattice. Curr. Biol. 33:4111-4123.e7. https://doi.org/10.1016/ j.cub.2023.07.062 · DOI · Paper page
- Zhang, R., G.M. Alushin, A. Brown, and E. Nogales. 2015. Mechanistic origin of microtubule dynamic instability and its modulation by EB proteins. Cell. 162:849-859. https://doi.org/10.1016/j.cell.2015.07.012 · DOI · Paper page
- Zhang, R., B. LaFrance, and E. Nogales. 2018. Separating the effects of nu- cleotide and EB binding on microtubule structure. Proc. Natl. Acad. Sci. USA. 115:E6191-E6200. https://doi.org/10.1073/pnas.1802637115 · DOI · Paper page
- Zhang, R., J. Roostalu, T. Surrey, and E. Nogales. 2017. Structural insight into TPX2-stimulated microtubule assembly. Elife. 6:e30959. https://doi .org/10.7554/eLife.30959 · DOI
- Zheng, S.Q., E. Palovcak, J.P. Armache, K.A. Verba, Y. Cheng, and D.A. Agard. 2017. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods. 14:331-332. https:// doi.org/10.1038/nmeth.4193 · DOI
- Zhou, Y., M. Handley, G. Carles, and A.R. Harvey. 2019. Advances in 3D single particle localization microscopy. APL Photon. 4:060901. https://doi.org/ 10.1063/1.5093310 · DOI
- Zivanov, J., J. Otón, Z. Ke, A. von Kügelgen, E. Pyle, K. Qu, D. Morado, D. Castaño-Díez, G. Zanetti, T.A.M. Bharat, et al. 2022. A Bayesian ap- proach to single-particle electron cryo-tomography in RELION-4.0. Elife. 11:e83724. https://doi.org/10.7554/eLife.83724 · DOI
- de Jager et al. Journal of Cell Biology 12 of 12 Stable microtubules have expanded lattices https://doi.org/10.1083/jcb.202206143 · DOI · Paper page
Cited by
Sorted by citations
A live-cell marker to visualize the dynamics of stable microtubules throughout the cell cycle
Jansen, K. I., Iwanski, M. K., Burute, M., & Kapitein, L. C. (2023) · Journal of Cell Biology · doi:10.1083/jcb.202106105 · Cited by 39 · see citing works
Self-citation
- Authors
- de Jager, L., Jansen, K. I., Kapitein, L. C., Förster, F., & Howes, S. C.
- Affiliations
- Utrecht University (NL)
- Corresponding author
- Kapitein, Lukas C.
- Förster, Friedrich
- Howes, Stuart C.
- Venue
- The Journal of Cell Biology
- Publisher
- openRxiv
- Published
- 2022-05-25
- Volume
- 224
- Issue
- 1
- ISSN
- 0021-9525 (ISSN-L)
- PMC
- PMC11471893
- OpenAlex
- W4403284162
- Cited by
- 25
- References
- 0
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 4 · 2023: 6 · 2022: 1
- FWCI
- 4.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- The Journal of Cell Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Universiteit Utrecht
- Radboud Universiteit
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (022.006.001, 184.034.014, OCENW.XL21.XL21.048, 84.034.014)
- Universitair Medisch Centrum Utrecht
- European Research Council (724425, 819219)
- H2020 European Research Council (724425)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
- Health Sciences › Medicine › Oncology › Cancer Treatment and Pharmacology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular Mechanics and Interactions
- Keywords
- microtubule lattice, lattice spacing, microtubule stability, paclitaxel, microtubule-associated proteins, microtubule dynamics, cryo-electron tomography
- MeSH terms
- Animals, Humans, Microtubule-Associated Proteins, Microtubules, Tubulin, Paclitaxel, Cryoelectron Microscopy, Electron Microscope Tomography
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review