Structural Differences Between Yeast and Mammalian Microtubules Revealed by Cryo-EM

Overview

Journal J Cell Biol

Specialty Cell Biology

Date 2017 Jun 28

PMID 28652389

Citations 47

Authors

Stuart C Howes

Elisabeth A Geyer

Benjamin LaFrance

Rui Zhang

Elizabeth H Kellogg

Stefan Westermann

Luke M Rice

Eva Nogales

Affiliations

Soon will be listed here.

Abstract

Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end-tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts. At the concentrations used in cryo-electron microscopy, Bim1 causes the compaction of yeast microtubules and induces their rapid disassembly. Our studies demonstrate structural differences between yeast and mammalian microtubules that likely underlie their differing polymerization dynamics. These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures.

Citing Articles

Exploring tubulin-paclitaxel binding modes through extensive molecular dynamics simulations.

Bozdaganyan M, Fedorov V, Kholina E, Kovalenko I, Gudimchuk N, Orekhov P Sci Rep. 2025; 15(1):8378.

PMID: 40069250 PMC: 11897383. DOI: 10.1038/s41598-025-92805-z.

Structural insights into the interplay between microtubule polymerases, γ-tubulin complexes and their receptors.

Zheng A, Vermeulen B, Wurtz M, Neuner A, Lubbehusen N, Mayer M Nat Commun. 2025; 16(1):402.

PMID: 39757296 PMC: 11701102. DOI: 10.1038/s41467-024-55778-7.

Structure of blood cell-specific tubulin and demonstration of dimer spacing compaction in a single protofilament.

Montecinos F, Eren E, Watts N, Sackett D, Wingfield P J Biol Chem. 2024; 301(2):108132.

PMID: 39725029 PMC: 11791314. DOI: 10.1016/j.jbc.2024.108132.

Functional genetics reveals modulators of antimicrotubule drug sensitivity.

Su K, Radul E, Maier N, Tsang M, Goul C, Moodie B J Cell Biol. 2024; 224(2).

PMID: 39570287 PMC: 11590752. DOI: 10.1083/jcb.202403065.

Structure of the native γ-tubulin ring complex capping spindle microtubules.

Dendooven T, Yatskevich S, Burt A, Chen Z, Bellini D, Rappsilber J Nat Struct Mol Biol. 2024; 31(7):1134-1144.

PMID: 38609662 PMC: 11257966. DOI: 10.1038/s41594-024-01281-y.

References

Schatz P, Solomon F, Botstein D . Isolation and characterization of conditional-lethal mutations in the TUB1 alpha-tubulin gene of the yeast Saccharomyces cerevisiae. Genetics. 1988; 120(3):681-95. PMC: 1203547. DOI: 10.1093/genetics/120.3.681. View

Kollman J, Greenberg C, Li S, Moritz M, Zelter A, Fong K . Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nat Struct Mol Biol. 2015; 22(2):132-7. PMC: 4318760. DOI: 10.1038/nsmb.2953. View

Rohou A, Grigorieff N . CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 2015; 192(2):216-21. PMC: 6760662. DOI: 10.1016/j.jsb.2015.08.008. View

Dougherty C, Himes R, Wilson L, Farrell K . Detection of GTP and Pi in wild-type and mutated yeast microtubules: implications for the role of the GTP/GDP-Pi cap in microtubule dynamics. Biochemistry. 1998; 37(31):10861-5. DOI: 10.1021/bi980677n. View

Gupta Jr M, Bode C, Georg G, Himes R . Understanding tubulin-Taxol interactions: mutations that impart Taxol binding to yeast tubulin. Proc Natl Acad Sci U S A. 2003; 100(11):6394-7. PMC: 164457. DOI: 10.1073/pnas.1131967100. View

Emsley P, Lohkamp B, Scott W, Cowtan K . Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501. PMC: 2852313. DOI: 10.1107/S0907444910007493. View

Geyer E, Burns A, Lalonde B, Ye X, Piedra F, Huffaker T . A mutation uncouples the tubulin conformational and GTPase cycles, revealing allosteric control of microtubule dynamics. Elife. 2015; 4:e10113. PMC: 4728127. DOI: 10.7554/eLife.10113. View

Drummond D, Kain S, Newcombe A, Hoey C, Katsuki M, Cross R . Purification of tubulin from the fission yeast Schizosaccharomyces pombe. Methods Mol Biol. 2011; 777:29-55. DOI: 10.1007/978-1-61779-252-6_3. View

Machin N, Lee J, Barnes G . Microtubule stability in budding yeast: characterization and dosage suppression of a benomyl-dependent tubulin mutant. Mol Biol Cell. 1995; 6(9):1241-59. PMC: 301280. DOI: 10.1091/mbc.6.9.1241. View

10.

Kellogg E, Hejab N, Howes S, Northcote P, Miller J, Fernando Diaz J . Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures. J Mol Biol. 2017; 429(5):633-646. PMC: 5325780. DOI: 10.1016/j.jmb.2017.01.001. View

11.

Hyman A, Chretien D, Arnal I, Wade R . Structural changes accompanying GTP hydrolysis in microtubules: information from a slowly hydrolyzable analogue guanylyl-(alpha,beta)-methylene-diphosphonate. J Cell Biol. 1995; 128(1-2):117-25. PMC: 2120325. DOI: 10.1083/jcb.128.1.117. View

12.

Lyumkis D, Brilot A, Theobald D, Grigorieff N . Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol. 2013; 183(3):377-388. PMC: 3824613. DOI: 10.1016/j.jsb.2013.07.005. View

13.

Heymann J, Belnap D . Bsoft: image processing and molecular modeling for electron microscopy. J Struct Biol. 2006; 157(1):3-18. DOI: 10.1016/j.jsb.2006.06.006. View

14.

Johnson V, Ayaz P, Huddleston P, Rice L . Design, overexpression, and purification of polymerization-blocked yeast αβ-tubulin mutants. Biochemistry. 2011; 50(40):8636-44. DOI: 10.1021/bi2005174. View

15.

Ti S, Pamula M, Howes S, Duellberg C, Cade N, Kleiner R . Mutations in Human Tubulin Proximal to the Kinesin-Binding Site Alter Dynamic Instability at Microtubule Plus- and Minus-Ends. Dev Cell. 2016; 37(1):72-84. PMC: 4832424. DOI: 10.1016/j.devcel.2016.03.003. View

16.

Li X, Mooney P, Zheng S, Booth C, Braunfeld M, Gubbens S . Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods. 2013; 10(6):584-90. PMC: 3684049. DOI: 10.1038/nmeth.2472. View

17.

Zhang R, Nogales E . A new protocol to accurately determine microtubule lattice seam location. J Struct Biol. 2015; 192(2):245-54. PMC: 4634897. DOI: 10.1016/j.jsb.2015.09.015. View

18.

Mitchison T, Kirschner M . Dynamic instability of microtubule growth. Nature. 1984; 312(5991):237-42. DOI: 10.1038/312237a0. View

19.

Valenstein M, Roll-Mecak A . Graded Control of Microtubule Severing by Tubulin Glutamylation. Cell. 2016; 164(5):911-21. PMC: 6459029. DOI: 10.1016/j.cell.2016.01.019. View

20.

Davis A, Sage C, Wilson L, Farrell K . Purification and biochemical characterization of tubulin from the budding yeast Saccharomyces cerevisiae. Biochemistry. 1993; 32(34):8823-35. DOI: 10.1021/bi00085a013. View