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Abbaali I, Truong D, Day SD, Mushayeed F, Ganesh B, Haro-Ramirez N, Isles J, Nag H, Pham C, Shah P, Tomar I, Manel-Romero C, Morrissette NS. The tubulin database: Linking mutations, modifications, ligands and local interactions. PLoS One 2023; 18:e0295279. [PMID: 38064432 PMCID: PMC10707541 DOI: 10.1371/journal.pone.0295279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Microtubules are polymeric filaments, constructed of α-β tubulin heterodimers that underlie critical subcellular structures in eukaryotic organisms. Four homologous proteins (γ-, δ-, ε- and ζ-tubulin) additionally contribute to specialized microtubule functions. Although there is an immense volume of publicly available data pertaining to tubulins, it is difficult to assimilate all potentially relevant information across diverse organisms, isotypes, and categories of data. We previously assembled an extensive web-based catalogue of published missense mutations to tubulins with >1,500 entries that each document a specific substitution to a discrete tubulin, the species where the mutation was described and the associated phenotype with hyperlinks to the amino acid sequence and citation(s) for research. This report describes a significant update and expansion of our online resource (TubulinDB.bio.uci.edu) to nearly 18,000 entries. It now encompasses a cross-referenced catalog of post-translational modifications (PTMs) to tubulin drawn from public datasets, primary literature, and predictive algorithms. In addition, tubulin protein structures were used to define local interactions with bound ligands (GTP, GDP and diverse microtubule-targeting agents) and amino acids at the intradimer interface, within the microtubule lattice and with associated proteins. To effectively cross-reference these datasets, we established a universal tubulin numbering system to map entries into a common framework that accommodates specific insertions and deletions to tubulins. Indexing and cross-referencing permitted us to discern previously unappreciated patterns. We describe previously unlinked observations of loss of PTM sites in the context of cancer cells and tubulinopathies. Similarly, we expanded the set of clinical substitutions that may compromise MAP or microtubule-motor interactions by collecting tubulin missense mutations that alter amino acids at the interface with dynein and doublecortin. By expanding the database as a curated resource, we hope to relate model organism data to clinical findings of pathogenic tubulin variants. Ultimately, we aim to aid researchers in hypothesis generation and design of studies to dissect tubulin function.
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Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Shania Deon Day
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Faliha Mushayeed
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Bhargavi Ganesh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Nancy Haro-Ramirez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Juliet Isles
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Hindol Nag
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Catherine Pham
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Priya Shah
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Ishaan Tomar
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Carolina Manel-Romero
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Naomi S. Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
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2
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Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW. Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 2023; 14:5980. [PMID: 37749104 PMCID: PMC10519996 DOI: 10.1038/s41467-023-41615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT. Both GTP- and GDP-tubulin heterodimers adopt similar curved conformations with subtle flexibility differences. In head-to-tail oligomers of tubulin heterodimers, the inter-dimer interface of GDP-tubulin exhibits greater flexibility, particularly in tangential bending. Cryo-EM of the intermediate assembly states reveals two types of tubulin lateral contacts, "Tube-bond" and "MT-bond". Further, molecular dynamics (MD) simulations show that GTP triggers lateral contact formation in MT assembly in multiple sequential steps, gradually straightening the curved tubulin heterodimers. Therefore, we propose a flexible model of GTP-initiated MT assembly, including the formation of longitudinal and lateral contacts, to explain the nucleation and assembly of MT.
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Affiliation(s)
- Ju Zhou
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
- University of California Berkeley, Berkeley, CA, USA
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Yinlong Song
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.
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3
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Amărandi RM, Al-Matarneh MC, Popovici L, Ciobanu CI, Neamțu A, Mangalagiu II, Danac R. Exploring Pyrrolo-Fused Heterocycles as Promising Anticancer Agents: An Integrated Synthetic, Biological, and Computational Approach. Pharmaceuticals (Basel) 2023; 16:865. [PMID: 37375812 DOI: 10.3390/ph16060865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/17/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Five new series of pyrrolo-fused heterocycles were designed through a scaffold hybridization strategy as analogs of the well-known microtubule inhibitor phenstatin. Compounds were synthesized using the 1,3-dipolar cycloaddition of cycloimmonium N-ylides to ethyl propiolate as a key step. Selected compounds were then evaluated for anticancer activity and ability to inhibit tubulin polymerization in vitro. Notably, pyrrolo[1,2-a]quinoline 10a was active on most tested cell lines, performing better than control phenstatin in several cases, most notably on renal cancer cell line A498 (GI50 27 nM), while inhibiting tubulin polymerization in vitro. In addition, this compound was predicted to have a promising ADMET profile. The molecular details of the interaction between compound 10a and tubulin were investigated through in silico docking experiments, followed by molecular dynamics simulations and configurational entropy calculations. Of note, we found that some of the initially predicted interactions from docking experiments were not stable during molecular dynamics simulations, but that configurational entropy loss was similar in all three cases. Our results suggest that for compound 10a, docking experiments alone are not sufficient for the adequate description of interaction details in terms of target binding, which makes subsequent scaffold optimization more difficult and ultimately hinders drug design. Taken together, these results could help shape novel potent antiproliferative compounds with pyrrolo-fused heterocyclic cores, especially from an in silico methodological perspective.
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Affiliation(s)
- Roxana-Maria Amărandi
- TRANSCEND Research Center, Regional Institute of Oncology Iasi, 2-4 General Henri Mathias Berthelot Street, 700483 Iasi, Romania
| | - Maria-Cristina Al-Matarneh
- "Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Lăcrămioara Popovici
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Catalina Ionica Ciobanu
- Institute of Interdisciplinary Research-CERNESIM Centre, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Andrei Neamțu
- TRANSCEND Research Center, Regional Institute of Oncology Iasi, 2-4 General Henri Mathias Berthelot Street, 700483 Iasi, Romania
| | - Ionel I Mangalagiu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Ramona Danac
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
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Pallotto LM, Dilks CM, Park YJ, Smit RB, Lu B, Gopalakrishnan C, Gilleard JS, Andersen EC, Mains PE. Interactions of C. elegans β-tubulins with the microtubule inhibitor and anthelmintic drug albendazole. Genetics 2022; 221:6613138. [PMID: 35731216 DOI: 10.1093/genetics/iyac093] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Parasitic nematodes are major human and agricultural pests, and benzimidazoles are amongst the most important broad spectrum anthelmintic drug class used for their control. Benzimidazole resistance is now widespread in many species of parasitic nematodes in livestock globally and an emerging concern for the sustainable control of human soil transmitted helminths. β-tubulin is the major benzimidazole target, although other genes may influence resistance. Among the six C. elegans β-tubulin genes, loss of ben-1 causes resistance without other apparent defects. Here, we explored the genetics of C. elegans β-tubulin genes in relation to the response to the benzimidazole derivative albendazole. The most highly expressed β-tubulin isotypes, encoded by tbb-1 and tbb-2, were known to be redundant with each other for viability, and their products are predicted not to bind benzimidazoles. We found that tbb-2 mutants, and to a lesser extent tbb-1 mutants, were hypersensitive to albendazole. The double mutant tbb-2 ben-1 is uncoordinated and short, resembling the wild type exposed to albendazole, but the tbb-1 ben-1 double mutant did not show the same phenotypes. These results suggest that tbb-2 is a modifier of ABZ sensitivity. To better understand how BEN-1 mutates to cause benzimidazole resistance, we isolated mutants resistant to albendazole and found that 15 of 16 mutations occurred in the ben-1 coding region. Mutations ranged from likely nulls to hypomorphs, and several corresponded to residues that cause resistance in other organisms. Null alleles of ben-1 are albendazole-resistant and BEN-1 shows high sequence identity with tubulins from other organisms, suggesting that many amino acid changes could cause resistance. However, our results suggest that missense mutations conferring resistance are not evenly distributed across all possible conserved sites. Independent of their roles in benzimidazole resistance, tbb-1 and tbb-2 may have specialized functions as null mutants of tbb-1 or tbb-2 were cold or heat sensitive, respectively.
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Affiliation(s)
- Linda M Pallotto
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Clayton M Dilks
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Ye-Jean Park
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ryan B Smit
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Brian Lu
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | | | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, Faculty of Veterinary Medicine, University of Calgary, Alberta, T2N 4N1 Canada
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Paul E Mains
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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5
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Minagawa M, Shirato M, Toya M, Sato M. Dual Impact of a Benzimidazole Resistant β-Tubulin on Microtubule Behavior in Fission Yeast. Cells 2021; 10:1042. [PMID: 33925026 PMCID: PMC8145593 DOI: 10.3390/cells10051042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
The cytoskeleton microtubule consists of polymerized αβ-tubulin dimers and plays essential roles in many cellular events. Reagents that inhibit microtubule behaviors have been developed as antifungal, antiparasitic, and anticancer drugs. Benzimidazole compounds, including thiabendazole (TBZ), carbendazim (MBC), and nocodazole, are prevailing microtubule poisons that target β-tubulin and inhibit microtubule polymerization. The molecular basis, however, as to how the drug acts on β-tubulin remains controversial. Here, we characterize the S. pombe β-tubulin mutant nda3-TB101, which was previously isolated as a mutant resistance to benzimidazole. The mutation site tyrosine at position 50 is located in the interface of two lateral β-tubulin proteins and at the gate of a putative binging pocket for benzimidazole. Our observation revealed two properties of the mutant tubulin. First, the dynamics of cellular microtubules comprising the mutant β-tubulin were stabilized in the absence of benzimidazole. Second, the mutant protein reduced the affinity to benzimidazole in vitro. We therefore conclude that the mutant β-tubulin Nda3-TB101 exerts a dual effect on microtubule behaviors: the mutant β-tubulin stabilizes microtubules and is insensitive to benzimidazole drugs. This notion fine-tunes the current elusive molecular model regarding binding of benzimidazole to β-tubulin.
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Affiliation(s)
- Mamika Minagawa
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
| | - Minamo Shirato
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
| | - Mika Toya
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
- Faculty of Science and Engineering, Global Center for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masamitsu Sato
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan
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6
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Lee HMT, Sayegh NY, Gayek AS, Jao SLJ, Chalfie M, Zheng C. Epistatic, synthetic, and balancing interactions among tubulin missense mutations affecting neurite growth in Caenorhabditis elegans. Mol Biol Cell 2020; 32:331-347. [PMID: 33378215 PMCID: PMC8098816 DOI: 10.1091/mbc.e20-07-0492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mutations in tubulins affect microtubule (MT) dynamics and functions during neuronal differentiation and their genetic interaction provides insights into the regulation of MT functions. We previously used Caenorhabditis elegans touch receptor neurons to analyze the cellular impact of tubulin mutations and reported the phenotypes of 67 tubulin missense mutations, categorized into three classes: loss-of-function (lf), antimorphic (anti), and neomorphic (neo) alleles. In this study, we isolated 54 additional tubulin alleles through suppressor screens in sensitized backgrounds that caused excessive neurite growth. These alleles included 32 missense mutations not analyzed before, bringing the total number of mutations in our collection to 99. Phenotypic characterization of these newly isolated mutations identified three new types of alleles: partial lf and weak neo alleles of mec-7/β-tubulin that had subtle effects and strong anti alleles of mec-12/α-tubulin. We also discovered complex genetic interactions among the tubulin mutations, including the suppression of neo mutations by intragenic lf and anti alleles, additive and synthetic effects between mec-7 neo alleles, and unexpected epistasis, in which weaker neo alleles masked the effects of stronger neo alleles in inducing ectopic neurite growth. We also observed balancing between neo and anti alleles, whose respective MT-hyperstablizing and -destabilizing effects neutralized each other.
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Affiliation(s)
- Ho Ming Terence Lee
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | | | - A Sophia Gayek
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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Zhu Y, Zhang Y, He Z, Duan Y, Li Y, Wang J, Zhou M. Detrimental Effects of Multiple Mutations in Position 240 of Fusarium graminearum β 2-Tubulin. PHYTOPATHOLOGY 2020; 110:1522-1529. [PMID: 32352861 DOI: 10.1094/phyto-11-19-0409-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fusarium graminearum causes Fusarium head blight (FHB), a destructive disease of cereal crops worldwide. Carbendazim (methylbenzimidazol-2-ylcarbamate [MBC]) is widely used for controlling FHB. A previous study showed that the F240L mutation in the β2-tubulin of F. graminearum (Fgβ2-tubulin) confers hypersensitivity to MBC. Whether the substitution of phenylalanine by other amino acids in position 240 of the Fgβ2-tubulin gene also confers hypersensitivity to MBC is unknown. Moreover, the biological fitness of these mutants is poorly understood. In this study, we substituted position 240 of Fgβ2-tubulin with other amino acids. We found that the F240A, F240E, F240I, and F240Y mutations in Fgβ2-tubulin could also confer F. graminearum hypersensitivity to MBC, although the effective concentration resulting in 50% inhibition (EC50) differed among the mutations. The F240G mutation, in contrast, decreased the sensitivity to MBC. In addition, a molecular docking assay indicated that the binding affinity between Fgβ2-tubulin and MBC were increased by the F240A, F240E, F240I, and F240Y mutations but decreased by the F240G mutation. All mutants had normal conidial morphology, but the growth rates and pathogenicity of the F240A, F240E, F240G, F240I, and F240Y mutants were significantly decreased. Moreover, the F240A and F240G mutants produced twisted hyphae. In addition, microtubules were sparse and rarely observed in β2F240A-EGFP, β2F240E-EGFP, and β2F240G-EGFP. These results indicate that position 240 (phenylalanine) is not only vital to the function of Fgβ2-tubulin but also plays an important role in regulating the sensitivity of F. graminearum to MBC. Any mutation in this site would be detrimental to survival.
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Affiliation(s)
- Yuanye Zhu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; and State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing, 210095, China
| | - Yuanshuai Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; and State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing, 210095, China
| | - Zongzhe He
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; and State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing, 210095, China
| | - Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; and State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing, 210095, China
| | - Yanjun Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; and State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; and State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; and State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing, 210095, China
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8
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Rosenzweig N, Hanson LE, Mambetova S, Jiang QW, Guza C, Stewart J, Somohano P. Fungicide Sensitivity Monitoring of Alternaria spp. Causing Leaf Spot of Sugarbeet ( Beta vulgaris) in the Upper Great Lakes. PLANT DISEASE 2019; 103:2263-2270. [PMID: 31322489 DOI: 10.1094/pdis-12-18-2282-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alternaria leaf spot (ALS), caused by Alternaria spp., can occur wherever sugarbeet is grown. Infection by Alternaria spp. and disease management has historically been considered a minor issue in sugarbeet production in the United States. An increase of both incidence and severity in 2016 of ALS high enough to cause yield loss has been observed in Michigan. With a renewed need to consider potential management of this disease, the sensitivity was determined for populations of Alternaria spp. to three classes of fungicides currently labeled for management of leaf spot on sugarbeet, including demethylase inhibitor (DMI), quinone outside inhibitor (QoI), and organo-tin fungicides. Leaves with symptoms of ALS were sampled from sugarbeet fields in east-central Michigan and southwestern Ontario, Canada. Monoconidial isolates were obtained to determine sensitivity to each fungicide class above. A spiral gradient dilution method was used to estimate the fungicide effective concentration (in milligrams per liter) that caused a 50% inhibition of fungal growth in vitro for all isolates. Significant temporal shifts were detected in the frequencies of sensitivity phenotypes to DMI and QoI but not organo-tin fungicides from 2016 through 2017. Individual isolates of Alternaria spp. were recovered with cross-resistance to DMI and multiple resistance to DMI, QoI, and triphenyltin hydroxide fungicides. To our knowledge, this is the first report of a fungus other than Cercospora beticola with resistance to organo-tin fungicides. Fungicide sensitivity monitoring indicates that an effective integrated disease management approach combining fungicide efficacy trials and monitoring pathogen biology is essential for developing effective resistance management recommendations.
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Affiliation(s)
- N Rosenzweig
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - L E Hanson
- U.S. Department of Agriculture Agricultural Research Service, East Lansing, MI 48824
| | - S Mambetova
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Q W Jiang
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - C Guza
- Michigan Sugar Company, Bay City, MI 48706
| | - J Stewart
- Michigan Sugar Company, Bay City, MI 48706
| | - P Somohano
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
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9
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The tubulin mutation database: A resource for the cytoskeleton community. Cytoskeleton (Hoboken) 2019; 76:186-191. [DOI: 10.1002/cm.21514] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/21/2018] [Accepted: 01/17/2019] [Indexed: 11/07/2022]
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10
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Chen D, Wu C, Hao C, Huang P, Liu H, Bian Z, Xu JR. Sexual specific functions of Tub1 beta-tubulins require stage-specific RNA processing and expression in Fusarium graminearum. Environ Microbiol 2018; 20:4009-4021. [PMID: 30307105 DOI: 10.1111/1462-2920.14441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 11/27/2022]
Abstract
The wheat head blight fungus Fusarium graminearum has two highly similar beta-tubulin genes with overlapping functions during vegetative growth but only TUB1 is important for sexual reproduction. To better understand their functional divergence during ascosporogenesis, in this study we characterized the sequence elements important for stage-specific functions of TUB1. Deletion of TUB1 blocked the late but not initial stages of perithecium formation. Perithecia formed by tub1 mutant had limited ascogenous hyphae and failed to develop asci. Silencing of TUB1 by MSUD also resulted in defects in ascospore formation. Interestingly, the 3'-UTR of TUB1 was dispensable for growth but essential for its function during sexual reproduction. RIP mutations that specifically affected Tub1 functions during sexual reproduction also were identified in two ascospore progeny. Furthermore, site-directed mutagenesis showed that whereas the non-editable mutations at three A-to-I RNA editing sites had no effects, the N347D (not T362D or I368V) edited mutation affected ascospore development. In addition, the F167Y, but not E198K or F200Y, mutation in TUB1 conferred tolerance to carbendazim and caused a minor defect in sexual reproduction. Taken together, our data indicate TUB1 plays an essential role in ascosporogenesis and sexual-specific functions of TUB1 require stage-specific RNA processing and Tub1 expression.
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Affiliation(s)
- Daipeng Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Chunlan Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chaofeng Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Panpan Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhuyun Bian
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
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11
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Zhu Y, Liang X, Li Y, Duan Y, Zheng Z, Wang J, Zhou M. F240 of β 2-Tubulin Explains why Fusarium graminearum is Less Sensitive to Carbendazim than Botrytis cinerea. PHYTOPATHOLOGY 2018; 108:352-361. [PMID: 29063820 DOI: 10.1094/phyto-09-17-0295-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
β-Tubulin is the target of benzimidazole fungicides, the most widely used of which is carbendazim (methyl benzimidazol-2-ylcarbamate [MBC]). MBC sensitivity is determined by the differential affinity of MBC for β-tubulins. However, the mechanism of less sensitivity of Fusarium graminearum to MBC compared with other fungi, including Botrytis cinerea, Colletotrichum gloeosporioides, and Sclerotinia sclerotiorum, remains exclusive. Alignment of β-tubulin amino acid sequences showed that position 240 of β-tubulins is leucine (L) in most pathogenic fungi but is phenylalanine (F) in the Fgβ2-tubulin of the F. graminearum wild type. The effective concentration resulting in 50% inhibition (EC50) value of MBC against the Fgβ2F240L mutant of F. graminearum is 0.047 μg/ml, which was 10-fold lower than that of wild-type strain 2021. Moreover, The EC50 value of MBC against the BcβL"240"F (actually position 232) mutant of Botrytis cinerea was 0.44 μg/ml, which was ninefold higher than that of B. cinerea wild-type strain Bt4-1. In response to MBC treatment (0.15 μg/ml), microtubules were clearly visible in Fgβ2-enhanced green fluorescent protein (EGFP) but not in Fgβ2F240L-EGFP. Moreover, a molecular docking assay indicated that F240L mutation created a pi-pi interaction between Fgβ2-tubulin and MBC and increased the binding affinity of Fgβ2-tubulin to MBC. Our results suggest that F240 is responsible for the naturally less MBC sensitivity in F. graminearum compared with B. cinerea, C. gloeosporioides, and S. sclerotiorum by decreasing the binding affinity between Fgβ2-tubulin and MBC.
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Affiliation(s)
- Yuanye Zhu
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Pesticide, Jiangsu Province, Nanjing, 210095, China
| | - Xiaoyu Liang
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Pesticide, Jiangsu Province, Nanjing, 210095, China
| | - Yanjun Li
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Pesticide, Jiangsu Province, Nanjing, 210095, China
| | - Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Pesticide, Jiangsu Province, Nanjing, 210095, China
| | - Zhitian Zheng
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Pesticide, Jiangsu Province, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Pesticide, Jiangsu Province, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Pesticide, Jiangsu Province, Nanjing, 210095, China
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12
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Howes SC, Geyer EA, LaFrance B, Zhang R, Kellogg EH, Westermann S, Rice LM, Nogales E. Structural and functional differences between porcine brain and budding yeast microtubules. Cell Cycle 2018; 17:278-287. [PMID: 29278985 PMCID: PMC5914886 DOI: 10.1080/15384101.2017.1415680] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The cytoskeleton of eukaryotic cells relies on microtubules to perform many essential functions. We have previously shown that, in spite of the overall conservation in sequence and structure of tubulin subunits across species, there are differences between mammalian and budding yeast microtubules with likely functional consequences for the cell. Here we expand our structural and function comparison of yeast and porcine microtubules to show different distribution of protofilament number in microtubules assembled in vitro from these two species. The different geometry at lateral contacts between protofilaments is likely due to a more polar interface in yeast. We also find that yeast tubulin forms longer and less curved oligomers in solution, suggesting stronger tubulin:tubulin interactions along the protofilament. Finally, we observed species-specific plus-end tracking activity for EB proteins: yeast Bim1 tracked yeast but not mammalian MTs, and human EB1 tracked mammalian but not yeast MTs. These findings further demonstrate that subtle sequence differences in tubulin sequence can have significant structural and functional consequences in microtubule structure and behavior.
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Affiliation(s)
- Stuart C Howes
- a Biophysics Graduate Group , UC Berkeley , CA 94720 , USA and Department of Molecular Cell Biology , Leiden University Medical Center , 2333 ZC Leiden , Netherlands
| | - Elisabeth A Geyer
- b UT Southwestern Medical Center , Departments of Biophysics and Biochemistry , Dallas , TX 75390 , USA
| | - Benjamin LaFrance
- c Molecular and Cell Biology Graduate Program , UC Berkeley , CA 94720 , USA
| | - Rui Zhang
- d Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , CA 94720 , USA.,e Howard Hughes Medical Institute , UC Berkeley , CA 94720-3220 , USA.,f Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , MO 63110 , USA
| | - Elizabeth H Kellogg
- d Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , CA 94720 , USA.,e Howard Hughes Medical Institute , UC Berkeley , CA 94720-3220 , USA
| | - Stefan Westermann
- g Research Institute of Molecular Pathology , Dr. Bohr-Gasse 7, 1030 Vienna , Austria
| | - Luke M Rice
- b UT Southwestern Medical Center , Departments of Biophysics and Biochemistry , Dallas , TX 75390 , USA
| | - Eva Nogales
- d Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , CA 94720 , USA.,e Howard Hughes Medical Institute , UC Berkeley , CA 94720-3220 , USA.,h Molecular and Cell Biology Department and QB3 Institute , UC Berkeley , CA 94720 , USA
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13
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Affiliation(s)
- Graham Bell
- Biology Department, McGill University, Montreal, Quebec H3A 1B1, Canada
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14
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Zheng C, Diaz-Cuadros M, Nguyen KCQ, Hall DH, Chalfie M. Distinct effects of tubulin isotype mutations on neurite growth in Caenorhabditis elegans. Mol Biol Cell 2017; 28:2786-2801. [PMID: 28835377 PMCID: PMC5638583 DOI: 10.1091/mbc.e17-06-0424] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/20/2022] Open
Abstract
Different tubulin isotypes perform different functions in the regulation of microtubule (MT) structure and neurite growth, and missense mutations of tubulin genes have three types of distinct effects on MT stability and neurite growth. One α-tubulin isotype appears to induce relative instability due to the lack of potential posttranslational modification sites. Tubulins, the building block of microtubules (MTs), play a critical role in both supporting and regulating neurite growth. Eukaryotic genomes contain multiple tubulin isotypes, and their missense mutations cause a range of neurodevelopmental defects. Using the Caenorhabditis elegans touch receptor neurons, we analyzed the effects of 67 tubulin missense mutations on neurite growth. Three types of mutations emerged: 1) loss-of-function mutations, which cause mild defects in neurite growth; 2) antimorphic mutations, which map to the GTP binding site and intradimer and interdimer interfaces, significantly reduce MT stability, and cause severe neurite growth defects; and 3) neomorphic mutations, which map to the exterior surface, increase MT stability, and cause ectopic neurite growth. Structure-function analysis reveals a causal relationship between tubulin structure and MT stability. This stability affects neuronal morphogenesis. As part of this analysis, we engineered several disease-associated human tubulin mutations into C. elegans genes and examined their impact on neuronal development at the cellular level. We also discovered an α-tubulin (TBA-7) that appears to destabilize MTs. Loss of TBA-7 led to the formation of hyperstable MTs and the generation of ectopic neurites; the lack of potential sites for polyamination and polyglutamination on TBA-7 may be responsible for this destabilization.
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Affiliation(s)
- Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | - Ken C Q Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027
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15
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Howes SC, Geyer EA, LaFrance B, Zhang R, Kellogg EH, Westermann S, Rice LM, Nogales E. Structural differences between yeast and mammalian microtubules revealed by cryo-EM. J Cell Biol 2017; 216:2669-2677. [PMID: 28652389 PMCID: PMC5584162 DOI: 10.1083/jcb.201612195] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/31/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023] Open
Abstract
Yeast MTs do not appear to undergo the lattice compaction seen in mammalian MTs upon GTP hydrolysis. Binding of the +TIP Bim1, both between and within αβ-tubulin dimers, causes compaction of yeast MTs and their rapid disassembly. 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.
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Affiliation(s)
- Stuart C Howes
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA
| | - Elisabeth A Geyer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Benjamin LaFrance
- Molecular and Cell Biology Graduate Program, University of California, Berkeley, Berkeley, CA
| | - Rui Zhang
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Elizabeth H Kellogg
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Stefan Westermann
- Department of Molecular Genetics, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Luke M Rice
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eva Nogales
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA .,Department of Molecular Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
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16
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Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS. Genetics 2016; 205:185-199. [PMID: 28049706 DOI: 10.1534/genetics.116.194852] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4) by Set1 complex/COMPASS is a hallmark of eukaryotic chromatin, but it remains poorly understood how this post-translational modification contributes to the regulation of biological processes like the cell cycle. Here, we report a H3K4 methylation-dependent pathway in Saccharomyces cerevisiae that governs toxicity toward benomyl, a microtubule destabilizing drug. Benomyl-sensitive growth of wild-type cells required mono- and dimethylation of H3K4 and Pho23, a PHD-containing subunit of the Rpd3L complex. Δset1 and Δpho23 deletions suppressed defects associated with ipl1-2 aurora kinase mutant, an integral component of the spindle assembly checkpoint during mitosis. Benomyl resistance of Δset1 strains was accompanied by deregulation of all four tubulin genes and the phenotype was suppressed by tub2-423 and Δtub3 mutations, establishing a genetic link between H3K4 methylation and microtubule function. Most interestingly, sine wave fitting and clustering of transcript abundance time series in synchronized cells revealed a requirement for Set1 for proper cell-cycle-dependent gene expression and Δset1 cells displayed delayed entry into S phase. Disruption of G1/S regulation in Δmbp1 and Δswi4 transcription factor mutants duplicated both benomyl resistance and suppression of ipl1-2 as was observed with Δset1 Taken together our results support a role for H3K4 methylation in the coordination of cell-cycle progression and proper assembly of the mitotic spindle during mitosis.
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17
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Geyer EA, Burns A, Lalonde BA, Ye X, Piedra FA, Huffaker TC, Rice LM. A mutation uncouples the tubulin conformational and GTPase cycles, revealing allosteric control of microtubule dynamics. eLife 2015; 4:e10113. [PMID: 26439009 PMCID: PMC4728127 DOI: 10.7554/elife.10113] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/06/2015] [Indexed: 11/18/2022] Open
Abstract
Microtubule dynamic instability depends on the GTPase activity of the polymerizing αβ-tubulin subunits, which cycle through at least three distinct conformations as they move into and out of microtubules. How this conformational cycle contributes to microtubule growing, shrinking, and switching remains unknown. Here, we report that a buried mutation in αβ-tubulin yields microtubules with dramatically reduced shrinking rate and catastrophe frequency. The mutation causes these effects by suppressing a conformational change that normally occurs in response to GTP hydrolysis in the lattice, without detectably changing the conformation of unpolymerized αβ-tubulin. Thus, the mutation weakens the coupling between the conformational and GTPase cycles of αβ-tubulin. By showing that the mutation predominantly affects post-GTPase conformational and dynamic properties of microtubules, our data reveal that the strength of the allosteric response to GDP in the lattice dictates the frequency of catastrophe and the severity of rapid shrinking. DOI:http://dx.doi.org/10.7554/eLife.10113.001 Protein filaments called microtubules help move cargo around inside cells. Chromosomes, which contain the cell’s genetic blueprints, are the microtubule’s most precious cargo. Before a cell divides, microtubules grow from the ends of the dividing cell towards the middle, where they attach to the chromosomes that are lined up along the centerline. Then the microtubules shrink and drag the chromosomes back to the opposite ends of the cell. This allows each of the new cells to get one copy of each chromosome. When the microtubules are growing, a molecule called guanosine triphosphate (or GTP) is attached to the proteins at the end of the filament. This acts like a cap and protects the microtubule from shrinking. Later a chemical reaction converts GTP into GDP (short for guanosine diphosphate). Without the protective GTP cap, the microtubule quickly shrinks. At the same time, the proteins that make up the microtubule also change shape. In the microtubule, the proteins adopt a straight shape when GTP is attached. The proteins favor a different shape in the microtubule when GDP is attached. However, it is unclear if or how these shape changes contribute to how a microtubule grows or shrinks. Geyer et al. now show how this shape shifting can influence microtubule shrinking, by first identifying a mutation in yeast microtubule proteins that cause the proteins to remain straight even when GDP is attached. Next, powerful microscopes were used to make time-lapse videos of the mutated microtubules. This allowed Geyer et al. to observe how the mutated microtubules behaved and compare this to the behavior of normal microtubules. The experiments revealed that the mutated microtubules were less likely to begin shrinking than typical microtubules. The mutated microtubules also shrunk more slowly. These findings indicate that the shape changes control the speed of shrinking and frequency of entering the shrinking phase. These new details about the control of microtubule growth and shrinkage may help scientists studying how cell division happens in both healthy and cancerous cells. DOI:http://dx.doi.org/10.7554/eLife.10113.002
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Affiliation(s)
- Elisabeth A Geyer
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Alexander Burns
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Beth A Lalonde
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Xuecheng Ye
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Felipe-Andres Piedra
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Tim C Huffaker
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Luke M Rice
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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18
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Rosenzweig N, Hanson LE, Clark G, Franc GD, Stump WL, Jiang QW, Stewart J, Kirk WW. Use of PCR-RFLP Analysis to Monitor Fungicide Resistance in Cercospora beticola Populations from Sugarbeet (Beta vulgaris) in Michigan, United States. PLANT DISEASE 2015; 99:355-362. [PMID: 30699698 DOI: 10.1094/pdis-03-14-0241-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic resistance to Quinone outside inhibitor (QoI) and benzimidazole fungicides may be responsible for a recent decline in efficacy of chemical control management strategies for Cercospora leaf spot (CLS) caused by Cercospora beticola in Michigan sugarbeet (Beta vulgaris) fields. The target genes and fungicide resistance mutations are known for these two fungicides. Based on this, two standard polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assays were developed to detect the G143A and E198A point mutations in the fungal mitochondrial cytochrome b and the β-tubulin genes, respectively. These mutations confer a high level of resistance to either QoI or benzimidazole fungicides. The presence of the G143A and E198A mutations was monitored within C. beticola populations recovered from Michigan sugarbeet production fields collected in 2012. Both the QoI-resistant cytochrome b allele and the benzimidazole-resistant β-tubulin allele were detected directly from leaf tissue following a PCR-RFLP assay. Using either detection assay, the G143A and E198A mutations were detected in over 90% of the 118 field samples originating from Michigan sugarbeet production under fungicide management programs for CLS control. Monitoring of the G143A and E198A mutations in fields located in 9 counties and 58 townships indicated that the mutations were widespread in Michigan sugarbeet production areas. The PCR-based assays used and developed in this study were effective in detecting the presence of the G143A and E198A mutations in C. beticola field populations from Michigan.
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Affiliation(s)
- N Rosenzweig
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 612, Wilson Road, 35 Plant Biology Building, East Lansing, MI 48824, USA
| | - L E Hanson
- Department of Plant, Soil and Microbial Science, and United States Department of Agriculture Agricultural Research Service, 1066 Bogue Street, Room 494, East Lansing, MI 48824, USA
| | - G Clark
- Michigan Sugar Company, Euclid Road, Bay City, MI 48706, USA
| | - G D Franc
- Department of Plant Sciences, University of Wyoming, Laramie, WY 82071
| | - W L Stump
- Department of Plant Sciences, University of Wyoming, Laramie, WY 82071
| | - Q W Jiang
- Department of Plant, Soil and Microbial Sciences, Michigan State University
| | | | - W W Kirk
- Department of Plant, Soil and Microbial Sciences, Michigan State University
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19
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Lucas JA, Hawkins NJ, Fraaije BA. The evolution of fungicide resistance. ADVANCES IN APPLIED MICROBIOLOGY 2014; 90:29-92. [PMID: 25596029 DOI: 10.1016/bs.aambs.2014.09.001] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fungicides are widely used in developed agricultural systems to control disease and safeguard crop yield and quality. Over time, however, resistance to many of the most effective fungicides has emerged and spread in pathogen populations, compromising disease control. This review describes the development of resistance using case histories based on four important diseases of temperate cereal crops: eyespot (Oculimacula yallundae and Oculimacula acuformis), Septoria tritici blotch (Zymoseptoria tritici), powdery mildew (Blumeria graminis), and Fusarium ear blight (a complex of Fusarium and Microdochium spp). The sequential emergence of variant genotypes of these pathogens with reduced sensitivity to the most active single-site fungicides, methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, and succinate dehydrogenase inhibitors illustrates an ongoing evolutionary process in response to the introduction and use of different chemical classes. Analysis of the molecular mechanisms and genetic basis of resistance has provided more rapid and precise methods for detecting and monitoring the incidence of resistance in field populations, but when or where resistance will occur remains difficult to predict. The extent to which the predictability of resistance evolution can be improved by laboratory mutagenesis studies and fitness measurements, comparison between pathogens, and reconstruction of evolutionary pathways is discussed. Risk models based on fungal life cycles, fungicide properties, and exposure to the fungicide are now being refined to take account of additional traits associated with the rate of pathogen evolution. Experimental data on the selection of specific mutations or resistant genotypes in pathogen populations in response to fungicide treatments can be used in models evaluating the most effective strategies for reducing or preventing resistance. Resistance management based on robust scientific evidence is vital to prolong the effective life of fungicides and safeguard their future use in crop protection.
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Affiliation(s)
- John A Lucas
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Nichola J Hawkins
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Bart A Fraaije
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
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20
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Laflamme G, Tremblay-Boudreault T, Roy MA, Andersen P, Bonneil É, Atchia K, Thibault P, D'Amours D, Kwok BH. Structural maintenance of chromosome (SMC) proteins link microtubule stability to genome integrity. J Biol Chem 2014; 289:27418-31. [PMID: 25135640 DOI: 10.1074/jbc.m114.569608] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Structural maintenance of chromosome (SMC) proteins are key organizers of chromosome architecture and are essential for genome integrity. They act by binding to chromatin and connecting distinct parts of chromosomes together. Interestingly, their potential role in providing connections between chromatin and the mitotic spindle has not been explored. Here, we show that yeast SMC proteins bind directly to microtubules and can provide a functional link between microtubules and DNA. We mapped the microtubule-binding region of Smc5 and generated a mutant with impaired microtubule binding activity. This mutant is viable in yeast but exhibited a cold-specific conditional lethality associated with mitotic arrest, aberrant spindle structures, and chromosome segregation defects. In an in vitro reconstitution assay, this Smc5 mutant also showed a compromised ability to protect microtubules from cold-induced depolymerization. Collectively, these findings demonstrate that SMC proteins can bind to and stabilize microtubules and that SMC-microtubule interactions are essential to establish a robust system to maintain genome integrity.
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Affiliation(s)
- Guillaume Laflamme
- From the Chemical Biology of Cell Division Laboratory, the Laboratory of Cell Cycle Regulation and Chromosome Structure, and
| | | | - Marc-André Roy
- the Laboratory of Cell Cycle Regulation and Chromosome Structure, and
| | | | - Éric Bonneil
- the Laboratory of Proteomics and Bioanalytical Mass Spectrometry, Institute for Research in Immunology and Cancer, and
| | - Kaleem Atchia
- From the Chemical Biology of Cell Division Laboratory
| | - Pierre Thibault
- the Laboratory of Proteomics and Bioanalytical Mass Spectrometry, Institute for Research in Immunology and Cancer, and the Departments of Chemistry
| | - Damien D'Amours
- the Laboratory of Cell Cycle Regulation and Chromosome Structure, and Pathology and Cellular Biology, and
| | - Benjamin H Kwok
- From the Chemical Biology of Cell Division Laboratory, Medicine, Université de Montréal, Station Centre-Ville, Montréal, Québec H3C 3J7, Canada
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21
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Abstract
Microtubules play essential roles in a wide variety of cellular processes including cell division, motility, and vesicular transport. Microtubule function depends on the polymerization dynamics of tubulin and specific interactions between tubulin and diverse microtubule-associated proteins. To date, investigation of the structural and functional properties of tubulin and tubulin mutants has been limited by the inability to obtain functional protein from overexpression systems, and by the heterogeneous mixture of tubulin isotypes typically isolated from higher eukaryotes. The budding yeast, Saccharomyces cerevisiae, has emerged as a leading system for tubulin structure-function analysis. Yeast cells encode a single beta-tubulin gene and can be engineered to express just one of two alpha isotypes. Moreover, yeast allows site-directed modification of tubulin genes at the endogenous loci expressed under the native promoter and regulatory elements. These advantageous features provide a homogeneous and controlled environment for analysis of the functional consequences of specific mutations. Here, we present the techniques to generate site-specific tubulin mutations in diploid and haploid cells, assess the ability of the mutated protein to support cell viability, measure overall microtubule stability, and define changes in the specific parameters of microtubule dynamic instability. We also outline strategies to determine whether mutations disrupt interactions with microtubule-associated proteins. Microtubule-based functions in yeast are well defined, which allows the observed changes in microtubule properties to be related to the role of microtubules in specific cellular processes.
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Affiliation(s)
- Anna Luchniak
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Yusuke Fukuda
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - Mohan L. Gupta
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
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22
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Maurer S, Fourniol F, Bohner G, Moores C, Surrey T. EBs recognize a nucleotide-dependent structural cap at growing microtubule ends. Cell 2012; 149:371-82. [PMID: 22500803 PMCID: PMC3368265 DOI: 10.1016/j.cell.2012.02.049] [Citation(s) in RCA: 281] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/19/2011] [Accepted: 02/10/2012] [Indexed: 11/24/2022]
Abstract
Growing microtubule ends serve as transient binding platforms for essential proteins that regulate microtubule dynamics and their interactions with cellular substructures. End-binding proteins (EBs) autonomously recognize an extended region at growing microtubule ends with unknown structural characteristics and then recruit other factors to the dynamic end structure. Using cryo-electron microscopy, subnanometer single-particle reconstruction, and fluorescence imaging, we present a pseudoatomic model of how the calponin homology (CH) domain of the fission yeast EB Mal3 binds to the end regions of growing microtubules. The Mal3 CH domain bridges protofilaments except at the microtubule seam. By binding close to the exchangeable GTP-binding site, the CH domain is ideally positioned to sense the microtubule's nucleotide state. The same microtubule-end region is also a stabilizing structural cap protecting the microtubule from depolymerization. This insight supports a common structural link between two important biological phenomena, microtubule dynamic instability and end tracking.
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Affiliation(s)
- Sebastian P. Maurer
- Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Franck J. Fourniol
- Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Gergő Bohner
- Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Carolyn A. Moores
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Thomas Surrey
- Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Johnson V, Ayaz P, Huddleston P, Rice LM. Design, overexpression, and purification of polymerization-blocked yeast αβ-tubulin mutants. Biochemistry 2011; 50:8636-44. [PMID: 21888381 DOI: 10.1021/bi2005174] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microtubule dynamics play essential roles in intracellular organization and cell division. They result from structural and biochemical properties of αβ-tubulin heterodimers and how these polymerizing subunits interact with themselves and with regulatory proteins. A broad understanding of the underlying mechanisms has been established, but fundamental questions remain unresolved. The lack of routine access to recombinant αβ-tubulin represents an obstacle to deeper insight into αβ-tubulin structure, biochemistry, and recognition. Indeed, the widespread reliance on animal brain αβ-tubulin means that very few in vitro studies have taken advantage of powerful and ordinarily routine techniques like site-directed mutagenesis. Here we report new methods for purifying wild-type or mutant yeast αβ-tubulin from inducibly overexpressing strains of Saccharomyces cerevisiae. Inducible overexpression is an improvement over existing approaches that rely on constitutive expression: it provides higher yields while also allowing otherwise lethal mutants to be purified. We also designed and purified polymerization-blocked αβ-tubulin mutants. These "blocked" forms of αβ-tubulin give a dominant lethal phenotype when expressed in cells; they cannot form microtubules in vitro and when present in mixtures inhibit the polymerization of wild-type αβ-tubulin. The effects of blocking mutations are very specific, because purified mutants exhibit normal hydrodynamic properties, bind GTP, and interact with a tubulin-binding domain. The ability to overexpress and purify wild-type αβ-tubulin, or mutants like the ones we report here, creates new opportunities for structural studies of αβ-tubulin and its complexes with regulatory proteins, and for biochemical and functional studies of microtubule dynamics and its regulation.
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Affiliation(s)
- Vinu Johnson
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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Caudron F, Denarier E, Thibout-Quintana JC, Brocard J, Andrieux A, Fourest-Lieuvin A. Mutation of Ser172 in yeast β tubulin induces defects in microtubule dynamics and cell division. PLoS One 2010; 5:e13553. [PMID: 21042413 PMCID: PMC2958848 DOI: 10.1371/journal.pone.0013553] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 09/25/2010] [Indexed: 02/07/2023] Open
Abstract
Ser172 of β tubulin is an important residue that is mutated in a human brain disease and phosphorylated by the cyclin-dependent kinase Cdk1 in mammalian cells. To examine the role of this residue, we used the yeast S. cerevisiae as a model and produced two different mutations (S172A and S172E) of the conserved Ser172 in the yeast β tubulin Tub2p. The two mutants showed impaired cell growth on benomyl-containing medium and at cold temperatures, altered microtubule (MT) dynamics, and altered nucleus positioning and segregation. When cytoplasmic MT effectors Dyn1p or Kar9p were deleted in S172A and S172E mutants, cells were viable but presented increased ploidy. Furthermore, the two β tubulin mutations exhibited synthetic lethal interactions with Bik1p, Bim1p or Kar3p, which are effectors of cytoplasmic and spindle MTs. In the absence of Mad2p-dependent spindle checkpoint, both mutations are deleterious. These findings show the importance of Ser172 for the correct function of both cytoplasmic and spindle MTs and for normal cell division.
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Affiliation(s)
| | - Eric Denarier
- Grenoble Institut des Neurosciences, Institut National de la Santé et de la Recherche Médicale Unité 836, Université Joseph Fourier – Grenoble 1, Grenoble, France
- Groupe Physiopathologie du Cytosquelette, Institut de Recherches en Technologies et Sciences pour le Vivant, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | | | - Jacques Brocard
- Grenoble Institut des Neurosciences, Institut National de la Santé et de la Recherche Médicale Unité 836, Université Joseph Fourier – Grenoble 1, Grenoble, France
| | - Annie Andrieux
- Grenoble Institut des Neurosciences, Institut National de la Santé et de la Recherche Médicale Unité 836, Université Joseph Fourier – Grenoble 1, Grenoble, France
- Groupe Physiopathologie du Cytosquelette, Institut de Recherches en Technologies et Sciences pour le Vivant, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Anne Fourest-Lieuvin
- Grenoble Institut des Neurosciences, Institut National de la Santé et de la Recherche Médicale Unité 836, Université Joseph Fourier – Grenoble 1, Grenoble, France
- Groupe Physiopathologie du Cytosquelette, Institut de Recherches en Technologies et Sciences pour le Vivant, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
- * E-mail:
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25
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α-Tubulin mutations alter oryzalin affinity and microtubule assembly properties to confer dinitroaniline resistance. EUKARYOTIC CELL 2010; 9:1825-34. [PMID: 20870876 DOI: 10.1128/ec.00140-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Plant and protozoan microtubules are selectively sensitive to dinitroanilines, which do not disrupt vertebrate or fungal microtubules. Tetrahymena thermophila is an abundant source of dinitroaniline-sensitive tubulin, and we have modified the single T. thermophila α-tubulin gene to create strains that solely express mutant α-tubulin in functional dimers. Previous research identified multiple α-tubulin mutations that confer dinitroaniline resistance in the human parasite Toxoplasma gondii, and when two of these mutations (L136F and I252L) were introduced into T. thermophila, they conferred resistance in these free-living ciliates. Purified tubulin heterodimers composed of L136F or I252L α-tubulin display decreased affinity for the dinitroaniline oryzalin relative to wild-type T. thermophila tubulin. Moreover, the L136F substitution dramatically reduces the critical concentration for microtubule assembly relative to the properties of wild-type T. thermophila tubulin. Our data provide additional support for the proposed dinitroaniline binding site on α-tubulin and validate the use of T. thermophila for expression of genetically homogeneous populations of mutant tubulins for biochemical characterization.
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26
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Chee MK, Haase SB. B-cyclin/CDKs regulate mitotic spindle assembly by phosphorylating kinesins-5 in budding yeast. PLoS Genet 2010; 6:e1000935. [PMID: 20463882 PMCID: PMC2865516 DOI: 10.1371/journal.pgen.1000935] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 04/02/2010] [Indexed: 12/02/2022] Open
Abstract
Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis, the full complement of relevant CDK targets has not been identified. It has previously been shown in a variety of model systems that B-type cyclin/CDK complexes, kinesin-5 motors, and the SCFCdc4 ubiquitin ligase are required for the separation of spindle poles and assembly of a bipolar spindle. It has been suggested that, in budding yeast, B-type cyclin/CDK (Clb/Cdc28) complexes promote spindle pole separation by inhibiting the degradation of the kinesins-5 Kip1 and Cin8 by the anaphase-promoting complex (APCCdh1). We have determined, however, that the Kip1 and Cin8 proteins are present at wild-type levels in the absence of Clb/Cdc28 kinase activity. Here, we show that Kip1 and Cin8 are in vitro targets of Clb2/Cdc28 and that the mutation of conserved CDK phosphorylation sites on Kip1 inhibits spindle pole separation without affecting the protein's in vivo localization or abundance. Mass spectrometry analysis confirms that two CDK sites in the tail domain of Kip1 are phosphorylated in vivo. In addition, we have determined that Sic1, a Clb/Cdc28-specific inhibitor, is the SCFCdc4 target that inhibits spindle pole separation in cells lacking functional Cdc4. Based on these findings, we propose that Clb/Cdc28 drives spindle pole separation by direct phosphorylation of kinesin-5 motors. The assembly of a bipolar mitotic spindle is essential for the accurate segregation of sister chromatids during mitosis and, hence, for successful cell division. Spindle assembly depends on the successful duplication of the spindle poles, followed by their separation to opposing ends of the cell. Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle, the relevant CDK targets have not been identified. Motor proteins of the kinesin-5 family generate movement on the microtubules that make up the spindle and are believed to power spindle pole separation. By employing the budding yeast Saccharomyces cerevisiae as a model, we have found evidence that cyclin/CDKs control spindle assembly by phosphorylating the kinesins-5 Kip1 and Cin8. When phosphorylation at a conserved CDK site in the motor domain of Kip1 is blocked, spindle pole separation is greatly diminished but neither protein abundance nor localization is affected. We have also obtained direct evidence by mass spectrometry that Kip1 and Cin8 are phosphorylated in vivo at consensus CDK sites in their tail domains. Our findings suggest that B-cyclin/CDKs regulate spindle assembly by regulating kinesin-5 motor activity.
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Affiliation(s)
- Mark K. Chee
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Steven B. Haase
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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27
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Tischfield MA, Baris HN, Wu C, Rudolph G, Van Maldergem L, He W, Chan WM, Andrews C, Demer JL, Robertson RL, Mackey DA, Ruddle JB, Bird TD, Gottlob I, Pieh C, Traboulsi EI, Pomeroy SL, Hunter DG, Soul JS, Newlin A, Sabol LJ, Doherty EJ, de Uzcátegui CE, de Uzcátegui N, Collins MLZ, Sener EC, Wabbels B, Hellebrand H, Meitinger T, de Berardinis T, Magli A, Schiavi C, Pastore-Trossello M, Koc F, Wong AM, Levin AV, Geraghty MT, Descartes M, Flaherty M, Jamieson RV, Møller HU, Meuthen I, Callen DF, Kerwin J, Lindsay S, Meindl A, Gupta ML, Pellman D, Engle EC. Human TUBB3 mutations perturb microtubule dynamics, kinesin interactions, and axon guidance. Cell 2010; 140:74-87. [PMID: 20074521 PMCID: PMC3164117 DOI: 10.1016/j.cell.2009.12.011] [Citation(s) in RCA: 413] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 09/11/2009] [Accepted: 11/02/2009] [Indexed: 01/14/2023]
Abstract
We report that eight heterozygous missense mutations in TUBB3, encoding the neuron-specific beta-tubulin isotype III, result in a spectrum of human nervous system disorders that we now call the TUBB3 syndromes. Each mutation causes the ocular motility disorder CFEOM3, whereas some also result in intellectual and behavioral impairments, facial paralysis, and/or later-onset axonal sensorimotor polyneuropathy. Neuroimaging reveals a spectrum of abnormalities including hypoplasia of oculomotor nerves and dysgenesis of the corpus callosum, anterior commissure, and corticospinal tracts. A knock-in disease mouse model reveals axon guidance defects without evidence of cortical cell migration abnormalities. We show that the disease-associated mutations can impair tubulin heterodimer formation in vitro, although folded mutant heterodimers can still polymerize into microtubules. Modeling each mutation in yeast tubulin demonstrates that all alter dynamic instability whereas a subset disrupts the interaction of microtubules with kinesin motors. These findings demonstrate that normal TUBB3 is required for axon guidance and maintenance in mammals.
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Affiliation(s)
- Max A. Tischfield
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- FM Kirby Neurobiology Center, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Genomics, Children’s Hospital Boston, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Hagit N. Baris
- Program in Genomics, Children’s Hospital Boston, Boston, MA 02115 USA
- Department of Medicine (Genetics), Children’s Hospital Boston, Boston, MA 02115 USA
| | - Chen Wu
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- FM Kirby Neurobiology Center, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Guenther Rudolph
- University Eye Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Lionel Van Maldergem
- Centre de génétique humaine Université de Liège, Domaine universitaire du Sart-Tilman, B-4000 Liège, Belgium
| | - Wei He
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- FM Kirby Neurobiology Center, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Genomics, Children’s Hospital Boston, Boston, MA 02115 USA
| | - Wai-Man Chan
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- FM Kirby Neurobiology Center, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Genomics, Children’s Hospital Boston, Boston, MA 02115 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Caroline Andrews
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- FM Kirby Neurobiology Center, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Genomics, Children’s Hospital Boston, Boston, MA 02115 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Joseph L. Demer
- Department of Ophthalmology and Jules Stein Eye Institute, David Geffen Medical School at University of California Los Angeles
- Department of Neurology, David Geffen Medical School at University of California Los Angeles
- Neuroscience Interdepartmental Program, David Geffen Medical School at University of California Los Angeles
- Bioengineering Interdepartmental Program, David Geffen Medical School at University of California Los Angeles
| | | | - David A. Mackey
- Centre for Eye Research Australia, Department of Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, 3002, Australia
- Department of Ophthalmology, Royal Hobart Hospital, University of Tasmania, Hobart Tasmania, 7000, Australia
| | - Jonathan B. Ruddle
- Centre for Eye Research Australia, Department of Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, 3002, Australia
| | - Thomas D. Bird
- Department of Neurology and the Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- GRECC, VA Puget Sound Health Care System, Seattle, WA
| | - Irene Gottlob
- Ophthalmology Group, University of Leicester, Leicester, LE2 7LX, UK
| | - Christina Pieh
- University Eye Hospital, University of Freiburg, Killianstr. 6, 79106 Freiburg, Germany
| | - Elias I. Traboulsi
- Cole Eye Institute, Cleveland Clinic i32, 9500 Euclid Avenue Cleveland, OH 44195
| | - Scott L. Pomeroy
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- FM Kirby Neurobiology Center, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - David G. Hunter
- Department of Ophthalmology, Children’s Hospital Boston, Boston, MA 02115 USA
| | - Janet S. Soul
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Newlin
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL 60201
| | - Louise J. Sabol
- Department of Ophthalmology, Geisinger Medical Institute, Danville, Pennsylvania
| | - Edward J. Doherty
- Atlantic Health Science Centre, Saint John Regional Hospital, Saint John New Brunswick, Canada
| | - Clara E. de Uzcátegui
- Instituto de Oftalmologia, Av. Cajigal 48. Piso 3 Consultorio 8. San Bernardino, Caracas 1010 Venezuela
| | - Nicolas de Uzcátegui
- Department of Ophthalmology, Upstate Medical University SUNY. Eye Consultants Of Syracuse, 1101 Erie Blvd. East Ste 100. Syracuse NY 13210
| | | | - Emin C. Sener
- Department of Ophthalmology, Hacettepe University Hospitals, Ankara 06100, Turkey
| | - Bettina Wabbels
- Department of Ophthalmology, University of Bonn, Abbestr. 2, D-53127, Bonn, Germany
| | - Heide Hellebrand
- Department of Obstetrics and Gynaecology, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr 22, 81675 Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr 22, 81675 Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Teresa de Berardinis
- Department of Ophthalmologic Sciences, Faculty of Medicine and Surgery, University “Federico II”, Naples, Italy
| | - Adriano Magli
- Department of Ophthalmologic Sciences, Faculty of Medicine and Surgery, University “Federico II”, Naples, Italy
| | | | - Marco Pastore-Trossello
- Department of Neuro-Radiology, S.Orsola-Malpighi Hospital via Albertoni, 15, 40138, Bologna, Italy
| | - Feray Koc
- Department of Ophthalmology and Strabismus, and Neuroophthalmology, Acıbadem University Kocaeli Hospital, Kocaeli 41100 Turkey
| | - Agnes M. Wong
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario Canada
| | - Alex V. Levin
- Pediatric Ophthalmology and Ocular Genetics, Wills Eye Institute, Philadelphia, PA
| | | | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Maree Flaherty
- Department of Ophthalmology, The Children’s Hospital at Westmead, Sydney, Australia
| | - Robyn V. Jamieson
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, Australia
- The University of Sydney, Sydney, Australia
| | - H. U. Møller
- Department of Ophthalmology, Viborg Hospital, DK 8000 Viborg Denmark
| | - Ingo Meuthen
- Department of Hematology-Oncology, Kliniken der Stadt Köln, Neufelderstr. 32, 51067 Köln, Germany
| | - David F. Callen
- Breast Cancer Genetics Group, School of Medicine, University of Adelaide, Australia
| | - Janet Kerwin
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Susan Lindsay
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
- MRC-Wellcome Trust Human Developmental Biology Resource (Newcastle), Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Alfons Meindl
- Department of Obstetrics and Gynaecology, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr 22, 81675 Munich, Germany
| | - Mohan L. Gupta
- Division of Hematology/Oncology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - David Pellman
- Division of Hematology/Oncology, Children’s Hospital Boston, Boston, MA 02115 USA
- Division of Hematology/Oncology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Elizabeth C. Engle
- Department of Neurology, Children’s Hospital Boston, Boston, MA 02115 USA
- FM Kirby Neurobiology Center, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Genomics, Children’s Hospital Boston, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Children’s Hospital Boston, Boston, MA 02115 USA
- Department of Medicine (Genetics), Children’s Hospital Boston, Boston, MA 02115 USA
- Department of Ophthalmology, Children’s Hospital Boston, Boston, MA 02115 USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Pieraccini S, Saladino G, Cappelletti G, Cartelli D, Francescato P, Speranza G, Manitto P, Sironi M. In silico design of tubulin-targeted antimitotic peptides. Nat Chem 2009; 1:642-8. [DOI: 10.1038/nchem.401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 09/08/2009] [Indexed: 11/09/2022]
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Secondary mutations correct fitness defects in Toxoplasma gondii with dinitroaniline resistance mutations. Genetics 2008; 180:845-56. [PMID: 18780736 DOI: 10.1534/genetics.108.092494] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dinitroanilines (oryzalin, trifluralin, ethafluralin) disrupt microtubules in protozoa but not in vertebrate cells, causing selective death of intracellular Toxoplasma gondii parasites without affecting host cells. Parasites containing alpha1-tubulin point mutations are dinitroaniline resistant but show increased rates of aberrant replication relative to wild-type parasites. T. gondii parasites bearing the F52Y mutation were previously demonstrated to spontaneously acquire two intragenic mutations that decrease both resistance levels and replication defects. Parasites bearing the G142S mutation are largely dependent on oryzalin for viable growth in culture. We isolated 46 T. gondii lines that have suppressed microtubule defects associated with the G142S or the F52Y mutations by acquiring secondary mutations. These compensatory mutations were alpha1-tubulin pseudorevertants or extragenic suppressors (the majority alter the beta1-tubulin gene). Many secondary mutations were located in tubulin domains that suggest that they function by destabilizing microtubules. Most strikingly, we identified seven novel mutations that localize to an eight-amino-acid insert that stabilizes the alpha1-tubulin M loop, including one (P364R) that acts as a compensatory mutation in both F52Y and G142S lines. These lines have reduced dinitroaniline resistance but most perform better than parental lines in competition assays, indicating that there is a trade-off between resistance and replication fitness.
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30
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He XC, Qin YM, Xu Y, Hu CY, Zhu YX. Molecular cloning, expression profiling, and yeast complementation of 19 beta-tubulin cDNAs from developing cotton ovules. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:2687-95. [PMID: 18596112 PMCID: PMC2486464 DOI: 10.1093/jxb/ern127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Microtubules are a major structural component of the cytoskeleton and participate in cell division, intracellular transport, and cell morphogenesis. In the present study, 795 cotton tubulin expressed sequence tags were analysed and 19 beta-tubulin genes (TUB) cloned from a cotton cDNA library. Among the group, 12 cotton TUBs (GhTUBs) are reported for the first time here. Transcription profiling revealed that nine GhTUBs were highly expressed in elongating fibre cells as compared with fuzzless-lintless mutant ovules. Treating cultured wild-type cotton ovules with exogenous phytohormones showed that individual genes can be induced by different agents. Gibberellin induced expression of GhTUB1 and GhTUB3, ethylene induced expression of GhTUB5, GhTUB9, and GhTUB12, brassinosteroids induced expression of GhTUB1, GhTUB3, GhTUB9, and GhTUB12, and lignoceric acid induced expression of GhTUB1, GhTUB3, and GhTUB12. When GhTUBs were transformed into the Saccharomyces cerevisiae inviable mutant, tub2, which is deficient in beta-tubulin, one ovule-specific and eight of nine fibre-preferential GhTUBs rescued this lethality. This study suggests that the proteins encoded by cotton GhTUBs are involved during cotton fibre development.
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Affiliation(s)
| | - Yong-Mei Qin
- To whom correspondence should be addressed. E-mail:
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31
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Ma C, Li C, Ganesan L, Oak J, Tsai S, Sept D, Morrissette NS. Mutations in alpha-tubulin confer dinitroaniline resistance at a cost to microtubule function. Mol Biol Cell 2007; 18:4711-20. [PMID: 17881728 PMCID: PMC2096588 DOI: 10.1091/mbc.e07-04-0379] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protozoan microtubules are sensitive to disruption by dinitroanilines, compounds that kill intracellular Toxoplasma gondii parasites without affecting microtubules in vertebrate host cells. We previously isolated a number of resistant Toxoplasma lines that harbor mutations to the alpha1-tubulin gene. Some of the mutations are localized in or near the M and N loops, domains that coordinate lateral interactions between protofilaments. Other resistance mutations map to a computationally identified binding site beneath the N loop. Allelic replacement of wild-type alpha1-tubulin with the individual mutations is sufficient to confer dinitroaniline resistance. Some mutations seem to increase microtubule length, suggesting that they increase subunit affinity. All mutations are associated with replication defects that decrease parasite viability. When parasites bearing the N loop mutation Phe52Tyr are grown without dinitroaniline selection, they spontaneously acquired secondary mutations in the M loop (Ala273Val) or in an alpha-tubulin-specific insert that stabilizes the M loop (Asp367Val). Parasites with the double mutations have both reduced resistance and diminished incidence of replication defects, suggesting that the secondary mutations decrease protofilament affinity to increase parasite fitness.
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Affiliation(s)
- Christopher Ma
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
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32
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Abstract
The eukaryotic cytoskeleton appears to have evolved from ancestral precursors related to prokaryotic FtsZ and MreB. FtsZ and MreB show 40-50% sequence identity across different bacterial and archaeal species. Here I suggest that this represents the limit of divergence that is consistent with maintaining their functions for cytokinesis and cell shape. Previous analyses have noted that tubulin and actin are highly conserved across eukaryotic species, but so divergent from their prokaryotic relatives as to be hardly recognizable from sequence comparisons. One suggestion for this extreme divergence of tubulin and actin is that it occurred as they evolved very different functions from FtsZ and MreB. I will present new arguments favoring this suggestion, and speculate on pathways. Moreover, the extreme conservation of tubulin and actin across eukaryotic species is not due to an intrinsic lack of variability, but is attributed to their acquisition of elaborate mechanisms for assembly dynamics and their interactions with multiple motor and binding proteins. A new structure-based sequence alignment identifies amino acids that are conserved from FtsZ to tubulins. The highly conserved amino acids are not those forming the subunit core or protofilament interface, but those involved in binding and hydrolysis of GTP.
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Affiliation(s)
- Harold P Erickson
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710-3709, USA.
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33
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Al-Bassam J, Larsen NA, Hyman AA, Harrison SC. Crystal structure of a TOG domain: conserved features of XMAP215/Dis1-family TOG domains and implications for tubulin binding. Structure 2007; 15:355-62. [PMID: 17355870 DOI: 10.1016/j.str.2007.01.012] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 01/14/2007] [Accepted: 01/31/2007] [Indexed: 11/22/2022]
Abstract
Members of the XMAP215/Dis1 family of microtubule-associated proteins (MAPs) are essential for microtubule growth. MAPs in this family contain several 250 residue repeats, called TOG domains, which are thought to bind tubulin dimers and promote microtubule polymerization. We have determined the crystal structure of a single TOG domain from the Caenorhabditis elegans homolog, Zyg9, to 1.9 A resolution, and from it we describe a structural blueprint for TOG domains. These domains are flat, paddle-like structures, composed of six HEAT-repeat elements stacked side by side. The two wide faces of the paddle contain the HEAT-repeat helices, and the two narrow faces, the intra- and inter-HEAT repeat turns. Solvent-exposed residues in the intrarepeat turns are conserved, both within a particular protein and across the XMAP215/Dis1 family. Mutation of some of these residues in the TOG1 domain from the budding yeast homolog, Stu2p, shows that this face indeed participates in the tubulin contact.
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Affiliation(s)
- Jawdat Al-Bassam
- Jack and Eileen Connors Laboratory of Structural Biology , Harvard Medical School, Boston, MA 02115, USA
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Zou G, Ying SH, Shen ZC, Feng MG. Multi-sited mutations of beta-tubulin are involved in benzimidazole resistance and thermotolerance of fungal biocontrol agent Beauveria bassiana. Environ Microbiol 2007; 8:2096-105. [PMID: 17107551 DOI: 10.1111/j.1462-2920.2006.01086.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fungicide resistance and thermotolerance of biocontrol agents in mitosporic fungi are of merits for enhancing fungal formulations against insect pests in the field. Among 20 wild strains of Beauveria bassiana (a well-known fungal biocontrol agent) tested in this study, 19 were sensitive or highly sensitive to carbendazim (methyl 2-benzimidazole carbamate), a typical benzimidazole fungicide, despite low resistance found in one strain. Sequential mutagenesis of a carbendazim-sensitive wild strain [minimal inhibitory concentration (MIC) = 1.32 microg ml(-1)] under artificial selection pressure generated 11 mutants sharing a common MIC of > 1000 microg ml(-1) without visible variation in colony growth and conidiation capacity. This represents at least 758-fold enhancement of the resistance among the mutants. However, accompanied with the enhanced resistance, all the mutants became less thermotolerable. Stressed at 48 degrees C, conidial LT(50)s of the mutants varied from 1.8 to 9.6 min and were lower than the parental LT(50) (36 min). Moreover, the contents of hydrophobin-like proteins in conidial walls declined significantly among the mutants compared with that of the wild parent. Mutations commonly relating to benzimidazole resistance in fungi were located at Q134, F167 and/or E198 around the taxol-binding site of beta-tubulin by sequencing the beta-tubulin of the mutants. Also, mutations of other 37 amino acid residues in the sequences (each having one to five residues mutated) were found for the first time and they were diverse in spatial structure. All mutations restricted to the half of beta-tubulin close to alpha-tubulin were likely involved in variation in each of the traits concerned but their interactions were complicated.
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Affiliation(s)
- Gen Zou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
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35
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Huang B, Huffaker TC. Dynamic microtubules are essential for efficient chromosome capture and biorientation in S. cerevisiae. ACTA ACUST UNITED AC 2006; 175:17-23. [PMID: 17030980 PMCID: PMC2064488 DOI: 10.1083/jcb.200606021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Attachment of chromosomes to the mitotic spindle has been proposed to require dynamic microtubules that randomly search three-dimensional space and become stabilized upon capture by kinetochores. In this study, we test this model by examining chromosome capture in Saccharomyces cerevisiae mutants with attenuated microtubule dynamics. Although viable, these cells are slow to progress through mitosis. Preanaphase cells contain a high proportion of chromosomes that are attached to only one spindle pole and missegregate in the absence of the spindle assembly checkpoint. Measurement of the rates of chromosome capture and biorientation demonstrate that both are severely decreased in the mutants. These results provide direct evidence that dynamic microtubules are critical for efficient chromosome capture and biorientation and support the hypothesis that microtubule search and capture plays a central role in assembly of the mitotic spindle.
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Affiliation(s)
- Baoying Huang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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36
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Redick SD, Stricker J, Briscoe G, Erickson HP. Mutants of FtsZ targeting the protofilament interface: effects on cell division and GTPase activity. J Bacteriol 2005; 187:2727-36. [PMID: 15805519 PMCID: PMC1070378 DOI: 10.1128/jb.187.8.2727-2736.2005] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial cell division protein FtsZ assembles into straight protofilaments, one subunit thick, in which subunits appear to be connected by identical bonds or interfaces. These bonds involve the top surface of one subunit making extensive contact with the bottom surface of the subunit above it. We have investigated this interface by site-directed mutagenesis. We found nine bottom and eight top mutants that were unable to function for cell division. We had expected that some of the mutants might poison cell division substoichiometrically, but this was not found for any mutant. Eight of the bottom mutants exhibited dominant negative effects (reduced colony size) and four completely blocked colony formation, but this required expression of the mutant protein at four to five times the wild-type FtsZ level. Remarkably, the top mutants were even weaker, most showing no effect at the highest expression level. This suggests a directional assembly or treadmilling, where subunit addition is primarily to the bottom end of the protofilament. Selected pairs of top and bottom mutants showed no GTPase activity up to 10 to 20 microM, in contrast to the high GTPase activity of wild-type FtsZ above 1 muM. Overall, these results suggest that in order for a subunit to bind a protofilament at the 1 microM K(d) for elongation, it must have functional interfaces at both the top and bottom. This is inconsistent with the present model of the protofilament, as a simple stack of subunits one on top of the other, and may require a new structural model.
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Affiliation(s)
- Sambra D Redick
- Department of Cell Biology, Duke University, 3709 Duke University Medical Center, Durham, NC 27710, USA
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37
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Sontag CA, Staley JT, Erickson HP. In vitro assembly and GTP hydrolysis by bacterial tubulins BtubA and BtubB. ACTA ACUST UNITED AC 2005; 169:233-8. [PMID: 15851515 PMCID: PMC2171859 DOI: 10.1083/jcb.200410027] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arecent study identified genuine tubulin proteins, BtubA and BtubB, in the bacterial genus Prosthecobacter. We have expressed BtubA and BtubB in Escherichia coli and studied their in vitro assembly. BtubB by itself formed rings with an outer diameter of 35–36 nm in the presence of GTP or GDP. Mixtures of BtubB and BtubA formed long protofilament bundles, 4–7 protofilaments wide (20–30 protofilaments in the three-dimensional bundle). Regardless of the starting stoichiometry, the polymers always contained equal concentrations of BtubA and BtubB, suggesting that BtubA and B alternate along the protofilament. BtubA showed negligible GTP hydrolysis, whereas BtubB hydrolyzed 0.40 mol GTP per min per mol BtubB. This GTPase activity increased to 1.37 per min when mixed 1:1 with BtubA. A critical concentration of 0.4–1.0 μM was indicated by light scattering experiments and extrapolation of GTPase versus concentration, thus suggesting a cooperative assembly mechanism.
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Affiliation(s)
- Christopher A Sontag
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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38
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Clark SW, Rose MD. Alanine scanning of Arp1 delineates a putative binding site for Jnm1/dynamitin and Nip100/p150Glued. Mol Biol Cell 2005; 16:3999-4012. [PMID: 15975903 PMCID: PMC1196314 DOI: 10.1091/mbc.e05-02-0093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Arp1p is the only actin-related protein (ARP) known to form actin-like filaments. Unlike actin, Arp1p functions with microtubules, as part of the dynein regulator, dynactin. Arp1p's dissimilar functions imply interactions with a distinct set of proteins. To distinguish surface features relating to Arp1p's core functions and to identify the footprint of protein interactions essential for dynactin function, we performed the first complete charge-cluster-to-alanine scanning mutagenesis of an ARP and compared the results with a similar study of actin. The Arp1p mutations revealed three nonoverlapping surfaces with distinct genetic properties. One of these surfaces encompassed a region unique to Arp1p that is crucial for Jnm1p (dynamitin/p50) and Nip100p (p150(Glued)) association as well as pointed-end associations. Unlike the actin mutations, none of the ARP1 alleles disrupt filament formation; however, one pointed-end allele delayed the elution of Arp1p on gel filtration, consistent with loss of additional subunits.
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Affiliation(s)
- Sean W Clark
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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39
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Habura A, Wegener L, Travis JL, Bowser SS. Structural and functional implications of an unusual foraminiferal beta-tubulin. Mol Biol Evol 2005; 22:2000-9. [PMID: 15944439 DOI: 10.1093/molbev/msi190] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have obtained sequence data for beta-tubulin genes from eight species of Foraminifera (forams) and alpha-tubulin sequences from four species, sampling major taxonomic groups from a wide range of environments. Analysis of the beta-tubulin sequences demonstrates that foram beta-tubulins possess the highest degree of divergence of any tubulin gene sequenced to date and represent a novel form of the protein. In contrast, foram alpha-tubulin genes resemble the conventional alpha-tubulins seen in other organisms. Partition homogeneity analysis shows that the foraminiferal beta-tubulin gene has followed an evolutionary path that is distinct from that of all other organisms. Our findings indicate that positive selective pressure occurred on the beta-tubulin subunit in ancestral forams prior to their diversification. The specific substitutions observed have implications for microtubule (MT) assembly dynamics. The regions most strongly affected are implicated in lateral contacts between protofilaments and in taxol binding. We predict that these changes strengthen lateral contacts between adjacent dimers in a manner similar to that induced by taxol binding, thus allowing the formation of the tubulin "helical filaments" observed in forams by electron microscopy. Our results also indicate that substantial changes to these portions of the beta-tubulin molecule can be made without sacrificing essential MT functions.
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Affiliation(s)
- Andrea Habura
- Wadsworth Center, New York State Department of Health, Albany, New York, USA.
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40
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Denis V, Cyert MS. Molecular analysis reveals localization of Saccharomyces cerevisiae protein kinase C to sites of polarized growth and Pkc1p targeting to the nucleus and mitotic spindle. EUKARYOTIC CELL 2005; 4:36-45. [PMID: 15643058 PMCID: PMC544167 DOI: 10.1128/ec.4.1.36-45.2005] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The catalytic activity and intracellular localization of protein kinase C (PKC) are both highly regulated in vivo. This family of kinases contains conserved regulatory motifs, i.e., the C1, C2, and HR1 domains, which target PKC isoforms to specific subcellular compartments and restrict their activity spatially. Saccharomyces cerevisiae contains a single PKC isozyme, Pkc1p, which contains all of the regulatory motifs found in mammalian PKCs. Pkc1p localizes to sites of polarized growth, consistent with its main function in maintaining cell integrity. We dissected the molecular basis of Pkc1p localization by expressing each of its domains individually and in combinations as green fluorescent protein fusions. We find that the Rho1p-binding domains, HR1 and C1, are responsible for targeting Pkc1p to the bud tip and cell periphery, respectively. We demonstrate that Pkc1p activity is required for its normal localization to the bud neck, which also depends on the integrity of the septin ring. In addition, we show for the first time that yeast protein kinase C can accumulate in the nucleus, and we identify a nuclear exit signal as well as nuclear localization signals within the Pkc1p sequence. Thus, we propose that Pkc1p shuttles in and out of the nucleus and consequently has access to nuclear substrates. Surprisingly, we find that deletion of the HR1 domain results in Pkc1p localization to the mitotic spindle and that the C2 domain is responsible for this targeting. This novel nuclear and spindle localization of Pkc1p may provide a molecular explanation for previous observations that suggest a role for Pkc1p in regulating microtubule function.
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Affiliation(s)
- Valérie Denis
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA
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41
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Downing KH. Structural basis for the action of drugs that affect microtubule dynamics. ACTA ACUST UNITED AC 2005. [DOI: 10.1517/14728222.4.2.219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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42
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Affiliation(s)
- R G Burns
- Biophysics Section, Blackett Laboratory, Imperial College of Science, Technology and Medicine, London, UK SW7 2BZ
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43
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You L, Gillilan R, Huffaker TC. Model for the yeast cofactor A-beta-tubulin complex based on computational docking and mutagensis. J Mol Biol 2004; 341:1343-54. [PMID: 15321725 DOI: 10.1016/j.jmb.2004.06.081] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Revised: 06/24/2004] [Accepted: 06/29/2004] [Indexed: 11/16/2022]
Abstract
Virtually every biological process involves protein-protein contact but relatively few protein-protein complexes have been solved by X-ray crystallography. As more individual protein structures become available, computational methods are likely to play increasingly important roles in defining these interactions. Tubulin folding and dimer formation are complex processes requiring a variety of protein cofactors. One of these is cofactor A, which interacts with beta-tubulin prior to assembly of the alpha-tubulin-beta-tubulin heterodimer. In the yeast Saccharomyces cerevisiae, beta-tubulin is encoded by TUB2 and cofactor A by RBL2. We have used computational docking and site-directed mutagenesis to generate a model of the Rbl2-Tub2 complex from the solved structures of these two proteins. Residues in the N termini and the loops of the Rbl2 homodimer appear to mediate binding to beta-tubulin. These interact with beta-tubulin residues in the region that contains helices H9 and H10. Rbl2 and alpha-tubulin share overlapping binding sites on the beta-tubulin molecule providing a structural explanation for the mutually exclusive binding of Rbl2 and alpha-tubulin to beta-tubulin.
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Affiliation(s)
- Liru You
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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44
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Klumpp LM, Brendza KM, Gatial JE, Hoenger A, Saxton WM, Gilbert SP. Microtubule-kinesin interface mutants reveal a site critical for communication. Biochemistry 2004; 43:2792-803. [PMID: 15005614 PMCID: PMC1543712 DOI: 10.1021/bi035830e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Strict coordination of the two motor domains of kinesin is required for driving the processive movement of organelles along microtubules. Glutamate 164 of the kinesin heavy chain was shown to be critical for kinesin function through in vivo genetics in Drosophila melanogaster. The mutant motor E164K exhibited reduced steady-state ATPase activity and higher affinity for both ATP and microtubules. Moreover, an alanine substitution at this position (E164A) caused similar defects. It became stalled on the microtubule and was unable to bind and hydrolyze ATP at the second motor domain. Glu(164), which has been conserved through evolution, is located at the motor-microtubule interface close to key residues on helix alpha12 of beta-tubulin. We explored further the contributions of Glu(164) to motor function using several site-directed mutant proteins: E164K, E164N, E164D, E164Q, and D165A. The results indicate that the microtubule-E164K complex can only bind and hydrolyze one ATP. ATP with increased salt was able to dissociate a population of E164K motors from the microtubule but could not dissociate E164A. We tested the basis of the stabilized microtubule interaction with E164K, E164N, and E164A. The results provide new insights about the motor-microtubule interface and the pathway of communication for processive motility.
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Affiliation(s)
- Lisa M Klumpp
- Department of Biological Sciences, 518 Langley Hall, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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45
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Gupta K, Bishop J, Peck A, Brown J, Wilson L, Panda D. Antimitotic Antifungal Compound Benomyl Inhibits Brain Microtubule Polymerization and Dynamics and Cancer Cell Proliferation at Mitosis, by Binding to a Novel Site in Tubulin. Biochemistry 2004; 43:6645-55. [PMID: 15157098 DOI: 10.1021/bi036112v] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The antifungal agent benomyl [methyl-1-(butylcarbamoyl)-2-benzimidazolecarbamate] is used throughout the world against a wide range of agricultural fungal diseases. In this paper, we investigated the interaction of benomyl with mammalian brain tubulin and microtubules. Using the hydrophobic fluorescent probe 1-anilinonaphthalene-8-sulfonic acid, benomyl was found to bind to brain tubulin with a dissociation constant of 11.9 +/- 1.2 microM. Further, benomyl bound to at a novel site, distinct from the well-characterized colchicine and vinblastine binding sites. Benomyl altered the far-UV circular dichroism spectrum of tubulin and reduced the accessibility of its cysteine residues to modification by 5,5'-dithiobis-2-nitrobenzoic acid, indicating that benomyl binding to tubulin induces a conformational change in the tubulin. Benomyl inhibited the polymerization of brain tubulin into microtubules, with 50% inhibition occurring at a concentration of 70-75 microM. Furthermore, it strongly suppressed the dynamic instability behavior of individual brain microtubules in vitro as determined by video microscopy. It reduced the growing and shortening rates of the microtubules but did not alter the catastrophe or rescue frequencies. The unexpected potency of benomyl against mammalian microtubule polymerization and dynamics prompted us to investigate the effects of benomyl on HeLa cell proliferation and mitosis. Benomyl inhibited proliferation of the cells with an IC(50) of 5 microM, and it blocked mitotic spindle function by perturbing microtubule and chromosome organization. The greater than expected actions of benomyl on mammalian microtubules and mitosis together with its relatively low toxicity suggest that it might be useful as an adjuvant in cancer chemotherapy.
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Affiliation(s)
- Kamlesh Gupta
- School of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Mumbai India 400076
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46
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Lila T, Renau TE, Wilson L, Philips J, Natsoulis G, Cope MJ, Watkins WJ, Buysse J. Molecular basis for fungal selectivity of novel antimitotic compounds. Antimicrob Agents Chemother 2003; 47:2273-82. [PMID: 12821479 PMCID: PMC161869 DOI: 10.1128/aac.47.7.2273-2282.2003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Compounds that selectively disrupt fungal mitosis have proven to be effective in controlling agricultural pests, but no specific mitotic inhibitor is available for the treatment of systemic mycoses in mammalian hosts. In an effort to identify novel mitotic inhibitors, we used a cell-based screening strategy that exploited the hypersensitivity of a yeast alpha-tubulin mutant strain to growth inhibition by antimitotic agents. The compounds identified inhibited yeast nuclear division and included one structural class of compounds shown to be fungus specific. MC-305904 and structural analogs inhibited fungal cell mitosis and inhibited the in vitro polymerization of fungal tubulin but did not block mammalian cell microtubule function or mammalian tubulin polymerization. Extensive analysis of yeast mutations that specifically alter sensitivity to MC-305904 structural analogs suggested that compounds in the series bind to a site on fungal beta-tubulin near amino acid 198. Features of the proposed binding site explain the observed fungal tubulin specificity of the series and are consistent with structure-activity relationships among a library of related compounds.
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Affiliation(s)
- Thomas Lila
- Essential Therapeutics, Mountain View, California 94043, USA.
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47
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McDonald HB, Helfant AH, Mahony EM, Khosla SK, Goetsch L. Mutational analysis reveals a role for the C terminus of the proteasome subunit Rpt4p in spindle pole body duplication in Saccharomyces cerevisiae. Genetics 2002; 162:705-20. [PMID: 12399382 PMCID: PMC1462277 DOI: 10.1093/genetics/162.2.705] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ubiquitin/proteasome pathway plays a key role in regulating cell cycle progression. Previously, we reported that a conditional mutation in the Saccharomyces cerevisiae gene RPT4/PCS1, which encodes one of six ATPases in the proteasome 19S cap complex/regulatory particle (RP), causes failure of spindle pole body (SPB) duplication. To improve our understanding of Rpt4p, we created 58 new mutations, 53 of which convert clustered, charged residues to alanine. Virtually all mutations that affect the N-terminal region, which contains a putative nuclear localization signal and coiled-coil motif, result in a wild-type phenotype. Nine mutations that affect the central ATPase domain and the C-terminal region confer recessive lethality. The two conditional mutations identified, rpt4-145 and rpt4-150, affect the C terminus. After shift to high temperature, these mutations generally cause cells to progress slowly through the first cell cycle and to arrest in the second cycle with large buds, a G2 content of DNA, and monopolar spindles, although this phenotype can vary depending on the medium. Additionally, we describe a genetic interaction between RPT4 and the naturally polymorphic gene SSD1, which in wild-type form modifies the rpt4-145 phenotype such that cells arrest in G2 of the first cycle with complete bipolar spindles.
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Affiliation(s)
- Heather B McDonald
- Department of Biology, Colgate University, Hamilton, New York 13346, USA.
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48
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Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG. Relating molecular flexibility to function: a case study of tubulin. Biophys J 2002; 83:663-80. [PMID: 12124255 PMCID: PMC1302177 DOI: 10.1016/s0006-3495(02)75199-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Microtubules (MT), along with a variety of associated motor proteins, are involved in a range of cellular functions including vesicle movement, chromosome segregation, and cell motility. MTs are assemblies of heterodimeric proteins, alpha beta-tubulins, the structure of which has been determined by electron crystallography of zinc-induced, pacilitaxel-stabilized tubulin sheets. These data provide a basis for examining relationships between structural features and protein function. Here, we study the fluctuation dynamics of the tubulin dimer with the aim of elucidating its functional motions relevant to substrate binding, polymerization/depolymerization and MT assembly. A coarse-grained model, harmonically constrained according to the crystal structure, is used to explore the global dynamics of the dimer. Our results identify six regions of collective motion, comprised of structurally close but discontinuous sequence fragments, observed only in the dimeric form, dimerization being a prerequisite for domain identification. Boundaries between regions of collective motions appear to act as linkages, found primarily within secondary-structure elements that lack sequence conservation, but are located at minima in the fluctuation curve, at positions of hydrophobic residues. Residue fluctuations within these domains identify the most mobile regions as loops involved in recognition of the adjacent regions. The least mobile regions are associated with nucleotide binding sites where lethal mutations occur. The functional coupling of motions between and within regions identifies three global motions: torsional and wobbling movements, en bloc, between the alpha- and beta-tubulin monomers, and stretching longitudinally. Further analysis finds the antitumor drug pacilitaxel (TaxotereR) to reduce flexibility in the M loop of the beta-tubulin monomer; an effect that may contribute to tightening lateral interactions between protofilaments assembled into MTs. Our analysis provides insights into relationships between intramolecular tubulin movements of MT organization and function.
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Affiliation(s)
- Ozlem Keskin
- Computational Technologies Laboratory, Screening Technologies Branch, Developmental Therapeutics Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702 USA.
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49
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Yin H, You L, Pasqualone D, Kopski KM, Huffaker TC. Stu1p is physically associated with beta-tubulin and is required for structural integrity of the mitotic spindle. Mol Biol Cell 2002; 13:1881-92. [PMID: 12058056 PMCID: PMC117611 DOI: 10.1091/mbc.01-09-0458] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Formation of the bipolar mitotic spindle relies on a balance of forces acting on the spindle poles. The primary outward force is generated by the kinesin-related proteins of the BimC family that cross-link antiparallel interpolar microtubules and slide them past each other. Here, we provide evidence that Stu1p is also required for the production of this outward force in the yeast Saccharomyces cerevisiae. In the temperature-sensitive stu1-5 mutant, spindle pole separation is inhibited, and preanaphase spindles collapse, with their previously separated poles being drawn together. The temperature sensitivity of stu1-5 can be suppressed by doubling the dosage of Cin8p, a yeast BimC kinesin-related protein. Stu1p was observed to be a component of the mitotic spindle localizing to the midregion of anaphase spindles. It also binds to microtubules in vitro, and we have examined the nature of this interaction. We show that Stu1p interacts specifically with beta-tubulin and identify the domains required for this interaction on both Stu1p and beta-tubulin. Taken together, these findings suggest that Stu1p binds to interpolar microtubules of the mitotic spindle and plays an essential role in their ability to provide an outward force on the spindle poles.
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Affiliation(s)
- Hongwei Yin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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50
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Eichenmuller B, Everley P, Palange J, Lepley D, Suprenant KA. The human EMAP-like protein-70 (ELP70) is a microtubule destabilizer that localizes to the mitotic apparatus. J Biol Chem 2002; 277:1301-9. [PMID: 11694528 DOI: 10.1074/jbc.m106628200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this report, we show that the echinoderm microtubule (MT)-associated protein (EMAP) and related EMAP-like proteins (ELPs) share a similar domain organization with a highly conserved hydrophobic ELP (HELP) domain and a large tryptophan-aspartic acid (WD) repeat domain. To determine the function of mammalian ELPs, we generated antibodies against a 70-kDa human ELP and showed that ELP70 coassembled with MTs in HeLa cell extracts and colocalized with MTs in the mitotic apparatus. To determine whether ELP70 bound to MTs directly, human ELP70 was expressed and purified to homogeneity from baculovirus-infected Sf9 cells. Purified ELP70 bound to purified MTs with a stoichiometry of 0.40 +/- 0.04 mol of ELP70/mol of tubulin dimer and with an intrinsic dissociation constant of 0.44 +/- 0.13 microm. Using a nucleated assembly assay and video-enhanced differential interference contrast microscopy, we demonstrated that ELP70 reduced seeded nucleation, reduced the growth rate, and promoted MT catastrophes in a concentration-dependent manner. As a result, ELP70-containing MTs were significantly shorter than MTs assembled from tubulin alone. These data indicate that ELP70 is a novel MT destabilizer. A lateral destabilization model is presented to describe ELP70's effects on microtubules.
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Affiliation(s)
- Bernd Eichenmuller
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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