CoChat
Sign Up
Cited by 74Microtubule and mitosis dynamicsAdvanced Fluorescence Microscopy TechniquesNeuroscience and Neuropharmacology Research

Quantitative mapping of dense microtubule arrays in mammalian neurons

Open access
Katrukha, Eugene A, Jurriens, Daphne, Salas Pastene, Desiree M, Kapitein, Lukas C·2021·eLife
DOI 10.7554/elife.67925PMC PMC8416025

Published version of a preprint

Open this paper in CoChat — free account

Abstract

The neuronal microtubule cytoskeleton underlies the polarization and proper functioning of neurons, amongst others by providing tracks for motor proteins that drive intracellular transport. Different subsets of neuronal microtubules, varying in composition, stability, and motor preference, are known to exist, but the high density of microtubules has so far precluded mapping their relative abundance and three-dimensional organization. Here, we use different super-resolution techniques (STED, Expansion Microscopy) to explore the nanoscale organization of the neuronal microtubule network in rat hippocampal neurons. This revealed that in dendrites acetylated microtubules are enriched in the core of the dendritic shaft, while tyrosinated microtubules are enriched near the plasma membrane, thus forming a shell around the acetylated microtubules. Moreover, using a novel analysis pipeline we quantified the absolute number of acetylated and tyrosinated microtubules within dendrites and found that they account for 65–75% and ~20–30% of all microtubules, respectively, leaving only few microtubules that do not fall in either category. Because these different microtubule subtypes facilitate different motor proteins, these novel insights help to understand the spatial regulation of intracellular transport.

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.7554/elife.67925

Cites

3 of 3 references verified0 citation errors · 0 not checkable

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.

A few free checks a day · papers already verified open instantly · results are public

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?

  • Two models have been proposed to explain microtubule stability in axons: one suggests centrally located microtubules are generally more stable while peripheral ones are more dynamic, and the other suggests intra-microtubule heterogeneity with alternating domains of differing stability.

    “Two models have been proposed to explain microtubule stability in axons: one suggests that centrally located microtubules are generally more stable while peripheral ones are more dynamic53–55, and the other model suggests intra-microtubule heterogeneity, in which individual microtubules contain alternating domains with differing stability56,57.”

    From Ghost Neuron preparation unlocks high-resolution structural mapping of intracellular architecture in axons (2026) · cites this paper as [54]

    The Discussion (page unavailable) reports stable microtubules enriched in the core of dendritic shafts and dynamic microtubules in a surrounding shell. It also notes that different parts of one microtubule can have different modifications, but does not describe alternating domains of stability. The claim applies these patterns to axons, whereas this paper's spatial-mapping result concerns dendrites. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • A recent paper using super-resolution microscopy indicates that there could be even more MTs in dendrites than our estimate.

    “A recent paper using super-resolution microscopy indicates that there could be even more MTs in dendrites than our estimate (23).”

    From Active transport by cytoplasmic dynein sustains dendritic MAP2 localization in developing neurons (2026) · cites this paper as [23]

  • Katrukha et al. reported using super-resolution light microscopy that in dendrites 72 ± 6% of microtubules are acetylated and 26 ± 8% are tyrosinated.

    “Katrukha et al. reported using super-resolution light microscopy that in dendrites 72 ± 6% of microtubules are acetylated and 26 ± 8% are tyrosinated (23).”

    From Active transport by cytoplasmic dynein sustains dendritic MAP2 localization in developing neurons (2026) · cites this paper as [23]

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

Flagged first, then by citations

Research works printed but not linked: 41

  1. Ahmad FJ Pienkowski TP Baas PW 1993 Regional differences in Microtubule dynamics in the axon The Journal of Neuroscience 13 856 866 10.1523/JNEUROSCI.13-02-00856.1993 8426241 PMC6576629 · DOI
  2. Akhmanova A Steinmetz MO 2015 Control of microtubule organization and dynamics: two ends in the limelight Nature Reviews Molecular Cell Biology 16 711 726 10.1038/nrm4084 26562752 · DOI · Paper page
  3. Atherton J Houdusse A Moores C 2013 MAPping out distribution routes for kinesin couriers Biology of the Cell 275 n/a 487 10.1111/boc.201300012 23796124 · DOI
  4. Baas PW Deitch JS Black MM Banker GA 1988 Polarity orientation of microtubules in hippocampal neurons: uniformity in the axon and nonuniformity in the dendrite PNAS 85 8335 8339 10.1073/pnas.85.21.8335 3054884 PMC282424 · DOI · Paper page
  5. Baas PW Black MM Banker GA 1989 Changes in microtubule polarity orientation during the development of hippocampal neurons in culture Journal of Cell Biology 109 3085 3094 10.1083/jcb.109.6.3085 PMC2115969 2592416 · DOI
  6. Baas PW Black MM 1990 Individual microtubules in the axon consist of domains that differ in both composition and stability Journal of Cell Biology 111 495 509 10.1083/jcb.111.2.495 PMC2116207 2199458 · DOI · Paper page
  7. Bentley M Banker G 2016 The cellular mechanisms that maintain neuronal polarity Nature Reviews Neuroscience 17 611 622 10.1038/nrn.2016.100 27511065 · DOI
  8. Burute M Kapitein LC 2019 Cellular Logistics: Unraveling the Interplay Between Microtubule Organization and Intracellular Transport Annual Review of Cell and Developmental Biology 35 29 54 10.1146/annurev-cellbio-100818-125149 31394046 · DOI
  9. Cai D McEwen DP Martens JR Meyhofer E Verhey KJ 2009 Single Molecule Imaging Reveals Differences in Microtubule Track Selection Between Kinesin Motors PLOS Biology 7 e1000216 10.1371/journal.pbio.1000216 19823565 PMC2749942 · DOI · Paper page
  10. Descloux A Grußmayer KS Radenovic A 2019 Parameter-free image resolution estimation based on decorrelation analysis Nature Methods 16 918 924 10.1038/s41592-019-0515-7 31451766 · DOI
  11. Dunn S Morrison EE Liverpool TB Molina-París C Cross RA Alonso MC Peckham M 2008 Differential trafficking of Kif5c on tyrosinated and detyrosinated microtubules in live cells Journal of Cell Science 121 1085 1095 10.1242/jcs.026492 18334549 · DOI · Paper page
  12. Esteves da Silva M Adrian M Schätzle P Lipka J Watanabe T Cho S Futai K Wierenga CJ Kapitein LC Hoogenraad CC 2015 Positioning of AMPA Receptor-Containing endosomes regulates synapse architecture Cell Reports 13 933 943 10.1016/j.celrep.2015.09.062 26565907 · DOI
  13. Gao M Maraspini R Beutel O Zehtabian A Eickholt B Honigmann A Ewers H 2018 Expansion stimulated emission depletion microscopy (ExSTED) ACS Nano 12 4178 4185 10.1021/acsnano.8b00776 29672025 · DOI
  14. Guardia CM Farías GG Jia R Pu J Bonifacino JS 2016 BORC functions upstream of kinesins 1 and 3 to coordinate regional movement of lysosomes along different microtubule tracks Cell Reports 17 1950 1961 10.1016/j.celrep.2016.10.062 27851960 PMC5136296 · DOI · Paper page
  15. Hirokawa N Niwa S Tanaka Y 2010 Molecular motors in neurons: transport mechanisms and roles in brain function, development, and disease Neuron 68 610 638 10.1016/j.neuron.2010.09.039 21092854 · DOI · Paper page
  16. Hu X Viesselmann C Nam S Merriam E Dent EW 2008 Activity-dependent dynamic microtubule invasion of dendritic spines Journal of Neuroscience 28 13094 13105 10.1523/JNEUROSCI.3074-08.2008 19052200 PMC6671621 · DOI
  17. Janke C Magiera MM 2020 The tubulin code and its role in controlling microtubule properties and functions Nature Reviews Molecular Cell Biology 21 307 326 10.1038/s41580-020-0214-3 32107477 · DOI · Paper page
  18. Jaworski J Kapitein LC Gouveia SM Dortland BR Wulf PS Grigoriev I Camera P Spangler SA Di Stefano P Demmers J Krugers H Defilippi P Akhmanova A Hoogenraad CC 2009 Dynamic microtubules regulate dendritic spine morphology and synaptic plasticity Neuron 61 85 100 10.1016/j.neuron.2008.11.013 19146815 · DOI · Paper page
  19. Jurriens D van Batenburg V Katrukha EA Kapitein LC 2021 Mapping the neuronal cytoskeleton using expansion microscopy Methods in Cell Biology 161 105 124 10.1016/bs.mcb.2020.04.018 33478685 · DOI
  20. Kapitein LC Yau KW Hoogenraad CC 2010 Microtubule dynamics in dendritic spines Methods in Cell Biology 97 111 132 10.1016/S0091-679X(10)97007-6 20719268 · DOI
  21. Kapitein LC Hoogenraad CC 2011 Which way to go? cytoskeletal organization and polarized transport in neurons Molecular and Cellular Neuroscience 46 9 20 10.1016/j.mcn.2010.08.015 20817096 · DOI
  22. Kapitein LC Hoogenraad CC 2015 Building the neuronal microtubule cytoskeleton Neuron 87 492 506 10.1016/j.neuron.2015.05.046 26247859 · DOI
  23. Katrukha EA 2021 Quantitative mapping of dense microtubule arrays in mammalian neurons Figshare 3 10.6084/m9.figshare.c.5306546.v3 PMC8416025 34313224 · DOI
  24. Kubota Y Karube F Nomura M Gulledge AT Mochizuki A Schertel A Kawaguchi Y 2011 Conserved properties of dendritic trees in four cortical interneuron subtypes Scientific Reports 1 89 10.1038/srep00089 22355608 PMC3216575 · DOI
  25. Lipka J Kapitein LC Jaworski J Hoogenraad CC 2016 Microtubule-binding protein doublecortin-like kinase 1 (DCLK1) guides kinesin-3-mediated cargo transport to dendrites The EMBO Journal 35 302 318 10.15252/embj.201592929 26758546 PMC4741305 · DOI
  26. McVicker DP Awe AM Richters KE Wilson RL Cowdrey DA Hu X Chapman ER Dent EW 2016 Transport of a kinesin-cargo pair along microtubules into dendritic spines undergoing synaptic plasticity Nature Communications 7 12741 10.1038/ncomms12741 27658622 PMC5411814 · DOI · Paper page
  27. Nekooki-Machida Y Hagiwara H 2020 Role of tubulin acetylation in cellular functions and diseases Medical Molecular Morphology 53 191 197 10.1007/s00795-020-00260-8 32632910 · DOI
  28. Park JH Roll-Mecak A 2018 The tubulin code in neuronal polarity Current Opinion in Neurobiology 51 95 102 10.1016/j.conb.2018.03.001 29554585 PMC7214607 · DOI
  29. Paturle-Lafanechère L Eddé B Denoulet P Van Dorsselaer A Mazarguil H Le Caer JP Wehland J Job D 1991 Characterization of a major brain tubulin variant which cannot be tyrosinated Biochemistry 30 10523 10528 10.1021/bi00107a022 1931974 · DOI
  30. Preibisch S Saalfeld S Tomancak P 2009 Globally optimal stitching of tiled 3D microscopic image acquisitions Bioinformatics 25 1463 1465 10.1093/bioinformatics/btp184 19346324 PMC2682522 · DOI · Paper page
  31. Roll-Mecak A 2019 How cells exploit tubulin diversity to build functional cellular microtubule mosaics Current Opinion in Cell Biology 56 102 108 10.1016/j.ceb.2018.10.009 30466050 PMC7214606 · DOI
  32. Schätzle P Esteves da Silva M Tas RP Katrukha EA Hu HY Wierenga CJ Kapitein LC Hoogenraad CC 2018 Activity-Dependent actin remodeling at the base of dendritic spines promotes microtubule entry Current Biology 28 2081 2093 10.1016/j.cub.2018.05.004 29910073 · DOI
  33. Schulze E Kirschner M 1987 Dynamic and stable populations of microtubules in cells Journal of Cell Biology 104 277 288 10.1083/jcb.104.2.277 PMC2114424 3543024 · DOI
  34. Sirajuddin M Rice LM Vale RD 2014 Regulation of microtubule motors by tubulin isotypes and post-translational modifications Nature Cell Biology 16 335 344 10.1038/ncb2920 24633327 PMC4117587 · DOI
  35. Steger C 1998 An unbiased detector of curvilinear structures IEEE Transactions on Pattern Analysis and Machine Intelligence 20 113 125 10.1109/34.659930 · DOI
  36. Stiess M Bradke F 2011 Neuronal polarization: the cytoskeleton leads the way Developmental Neurobiology 71 430 444 10.1002/dneu.20849 21557499 · DOI
  37. Tas RP Chazeau A Cloin BMC Lambers MLA Hoogenraad CC Kapitein LC 2017 Differentiation between oppositely oriented microtubules controls polarized neuronal transport Neuron 96 1264 1271 10.1016/j.neuron.2017.11.018 29198755 PMC5746200 · DOI · Paper page
  38. Tempes A Weslawski J Brzozowska A Jaworski J 2020 Role of dynein-dynactin complex, kinesins, motor adaptors, and their phosphorylation in dendritogenesis Journal of Neurochemistry 155 10 28 10.1111/jnc.15010 32196676 · DOI
  39. Tillberg PW Chen F Piatkevich KD Zhao Y Yu CC English BP Gao L Martorell A Suk HJ Yoshida F DeGennaro EM Roossien DH Gong G Seneviratne U Tannenbaum SR Desimone R Cai D Boyden ES 2016 Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies Nature Biotechnology 34 987 992 10.1038/nbt.3625 27376584 PMC5068827 · DOI
  40. Valenstein ML Roll-Mecak A 2016 Graded control of microtubule severing by tubulin glutamylation Cell 164 911 921 10.1016/j.cell.2016.01.019 26875866 PMC6459029 · DOI
  41. van de Willige D Hoogenraad CC Akhmanova A 2016 Microtubule plus-end tracking proteins in neuronal development Cellular and Molecular Life Sciences 73 2053 2077 10.1007/s00018-016-2168-3 26969328 PMC4834103 · DOI

Cited by

Sorted by citations

Authors
Katrukha, E. A., Jurriens, D., Salas Pastene, D. M., & Kapitein, L. C.
Affiliations
  • Utrecht University (NL)
  • Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
Corresponding author
Kapitein, Lukas C
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2021-07-27
Volume
10
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.67925
PMC
PMC8416025
OpenAlex
W3183692149
Cited by
74
References
3
Citations by year
2026: 14 · 2025: 16 · 2024: 13 · 2023: 12 · 2022: 16 · 2021: 3
FWCI
5.74
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
Funders
  • H2020 European Research Council (819219)
  • ZonMw (91217002)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
Keywords
neuronal microtubules, microtubule cytoskeleton, hippocampal neurons, intracellular transport, motor proteins, super-resolution microscopy, STED microscopy, expansion microscopy
MeSH terms
Acetylation, Animals, Female, Hippocampus, Male, Microtubules, Neurons, Protein Processing, Post-Translational, Tubulin, Developmental Biology, Kinesins, Rats

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