1
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Seo D, Yue Y, Yamazaki S, Verhey KJ, Gammon DB. Poxvirus A51R Proteins Negatively Regulate Microtubule-Dependent Transport by Kinesin-1. Int J Mol Sci 2024; 25:7825. [PMID: 39063067 PMCID: PMC11277487 DOI: 10.3390/ijms25147825] [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: 06/05/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Microtubule (MT)-dependent transport is a critical means of intracellular movement of cellular cargo by kinesin and dynein motors. MT-dependent transport is tightly regulated by cellular MT-associated proteins (MAPs) that directly bind to MTs and either promote or impede motor protein function. Viruses have been widely shown to usurp MT-dependent transport to facilitate their virion movement to sites of replication and/or for exit from the cell. However, it is unclear if viruses also negatively regulate MT-dependent transport. Using single-molecule motility and cellular transport assays, we show that the vaccinia virus (VV)-encoded MAP, A51R, inhibits kinesin-1-dependent transport along MTs in vitro and in cells. This inhibition is selective as the function of kinesin-3 is largely unaffected by VV A51R. Interestingly, we show that A51R promotes the perinuclear accumulation of cellular cargo transported by kinesin-1 such as lysosomes and mitochondria during infection. Moreover, A51R also regulates the release of specialized VV virions that exit the cell using kinesin-1-dependent movement. Using a fluorescently tagged rigor mutant of kinesin-1, we show that these motors accumulate on A51R-stabilized MTs, suggesting these stabilized MTs may form a "kinesin-1 sink" to regulate MT-dependent transport in the cell. Collectively, our findings uncover a new mechanism by which viruses regulate host cytoskeletal processes.
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Affiliation(s)
- Dahee Seo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Shin Yamazaki
- Department of Neuroscience and Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Don B. Gammon
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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2
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Chippalkatti R, Parisi B, Kouzi F, Laurini C, Ben Fredj N, Abankwa DK. RAS isoform specific activities are disrupted by disease associated mutations during cell differentiation. Eur J Cell Biol 2024; 103:151425. [PMID: 38795504 DOI: 10.1016/j.ejcb.2024.151425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/02/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
The RAS-MAPK-pathway is aberrantly regulated in cancer and developmental diseases called RASopathies. While typically the impact of Ras on the proliferation of various cancer cell lines is assessed, it is poorly established how Ras affects cellular differentiation. Here we implement the C2C12 myoblast cell line to systematically study the effect of Ras mutants and Ras-pathway drugs on differentiation. We first provide evidence that a minor pool of Pax7+ progenitors replenishes a major pool of transit amplifying cells that are ready to differentiate. Our data indicate that Ras isoforms have distinct roles in the differentiating culture, where K-Ras depletion increases and H-Ras depletion decreases terminal differentiation. This assay could therefore provide significant new insights into Ras biology and Ras-driven diseases. In line with this, we found that all oncogenic Ras mutants block terminal differentiation of transit amplifying cells. By contrast, RASopathy associated K-Ras variants were less able to block differentiation. Profiling of eight targeted Ras-pathway drugs on seven oncogenic Ras mutants revealed their allele-specific activities and distinct abilities to restore normal differentiation as compared to triggering cell death. In particular, the MEK-inhibitor trametinib could broadly restore differentiation, while the mTOR-inhibitor rapamycin broadly suppressed differentiation. We expect that this quantitative assessment of the impact of Ras-pathway mutants and drugs on cellular differentiation has great potential to complement cancer cell proliferation data.
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Affiliation(s)
- Rohan Chippalkatti
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Bianca Parisi
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Farah Kouzi
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Christina Laurini
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Nesrine Ben Fredj
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Daniel Kwaku Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg.
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3
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Fasawe AS, Adams JM, Engelke MF. KIF3A tail domain phosphorylation is not required for ciliogenesis in mouse embryonic fibroblasts. iScience 2024; 27:109149. [PMID: 38405607 PMCID: PMC10884758 DOI: 10.1016/j.isci.2024.109149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/21/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
Primary cilia are essential signaling organelles that protrude from most cells in the body. Heterodimeric kinesin-2 (KIF3A/KIF3B/KAP3) powers several intracellular transport processes, including intraflagellar transport (IFT), essential for ciliogenesis. A long-standing question is how a motor protein is differentially regulated for specific cargos. Since phosphorylation of the KIF3A tail domain was suggested to regulate the activity of kinesin-2 for ciliogenesis, similarly as for the cytosolic cargo N-Cadherin, we set out to map the phosphosites involved in this regulation. Using well-characterized Kif3a-/-; Kif3b-/- mouse embryonic fibroblasts, we performed ciliogenesis rescue assays with a library of phosphomimetic mutants comprising all predicted phosphosites in the KIF3A tail domain. In contrast to previous reports, we found that KIF3A tail domain phosphorylation is dispensable for ciliogenesis in mammals. Thus, mammalian kinesin-2 is differently regulated for IFT than currently thought, consistent with the idea of differential regulation for ciliary and cytosolic cargo.
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Affiliation(s)
- Ayoola S. Fasawe
- School of Biological Sciences, Cell Physiology, Illinois State University, Normal, IL 61790, USA
| | - Jessica M. Adams
- School of Biological Sciences, Cell Physiology, Illinois State University, Normal, IL 61790, USA
| | - Martin F. Engelke
- School of Biological Sciences, Cell Physiology, Illinois State University, Normal, IL 61790, USA
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4
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Budaitis BG, Badieyan S, Yue Y, Blasius TL, Reinemann DN, Lang MJ, Cianfrocco MA, Verhey KJ. A kinesin-1 variant reveals motor-induced microtubule damage in cells. Curr Biol 2022; 32:2416-2429.e6. [PMID: 35504282 PMCID: PMC9993403 DOI: 10.1016/j.cub.2022.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/16/2022]
Abstract
Kinesins drive the transport of cellular cargoes as they walk along microtubule tracks; however, recent work has suggested that the physical act of kinesins walking along microtubules can stress the microtubule lattice. Here, we describe a kinesin-1 KIF5C mutant with an increased ability to generate damage sites in the microtubule lattice as compared with the wild-type motor. The expression of the mutant motor in cultured cells resulted in microtubule breakage and fragmentation, suggesting that kinesin-1 variants with increased damage activity would have been selected against during evolution. The increased ability to damage microtubules is not due to the enhanced motility properties of the mutant motor, as the expression of the kinesin-3 motor KIF1A, which has similar single-motor motility properties, also caused increased microtubule pausing, bending, and buckling but not breakage. In cells, motor-induced microtubule breakage could not be prevented by increased α-tubulin K40 acetylation, a post-translational modification known to increase microtubule flexibility. In vitro, lattice damage induced by wild-type KIF5C was repaired by soluble tubulin and resulted in increased rescues and overall microtubule growth, whereas lattice damage induced by the KIF5C mutant resulted in larger repair sites that made the microtubule vulnerable to breakage and fragmentation when under mechanical stress. These results demonstrate that kinesin-1 motility causes defects in and damage to the microtubule lattice in cells. While cells have the capacity to repair lattice damage, conditions that exceed this capacity result in microtubule breakage and fragmentation and may contribute to human disease.
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Affiliation(s)
- Breane G Budaitis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Somayesadat Badieyan
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - T Lynne Blasius
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana N Reinemann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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Perach M, Zafrir Z, Tuller T, Lewinson O. Identification of conserved slow codons that are important for protein expression and function. RNA Biol 2021; 18:2296-2307. [PMID: 33691590 PMCID: PMC8632084 DOI: 10.1080/15476286.2021.1901185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022] Open
Abstract
ABSTRASTDue to the redundancy of the genetic code most amino acids are encoded by several 'synonymous' codons. These codons are used unevenly, and each organism demonstrates its own unique codon usage bias, where the 'preferred' codons are associated with tRNAs that are found in high concentrations. Therefore, for decades, the prevailing view had been that preferred and non-preferred codons are linked to high or slow translation rates, respectively.However, this simplified view is contrasted by the frequent failures of codon-optimization efforts and by evidence of non-preferred (i.e. 'slow') codons having specific roles important for efficient production of functional proteins. One such specific role of slower codons is the regulation of co-translational protein folding, a complex biophysical process that is very challenging to model or to measure.Here, we combined a genome-wide approach with experiments to investigate the role of slow codons in protein production and co-translational folding. We analysed homologous gene groups from divergent bacteria and identified positions of inter-species conservation of bias towards slow codons. We then generated mutants where the conserved slow codons are substituted with 'fast' ones, and experimentally studied the effects of these codon substitutions. Using cellular and biochemical approaches we find that at certain locations, slow-to-fast codon substitutions reduce protein expression, increase protein aggregation, and impair protein function.This report provides an approach for identifying functionally relevant regions with slower codons and demonstrates that such codons are important for protein expression and function.
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Affiliation(s)
- Michal Perach
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Lewinson
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
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6
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Liang CQ, Wang L, Luo YY, Li QQ, Li YM. Capturing protein droplets: label-free visualization and detection of protein liquid-liquid phase separation with an aggregation-induced emission fluorogen. Chem Commun (Camb) 2021; 57:3805-3808. [PMID: 33876127 DOI: 10.1039/d1cc00947h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We developed a new method for protein droplet visualization by means of a droplet probe (DroProbe) based on an aggregation-induced emission (AIE) fluorogen. A simple method for viscosity comparison of the protein condensed phase based on the lifetime of the DroProbe was also developed.
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Affiliation(s)
- Chu-Qiao Liang
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University Beijing, 100084, P. R. China.
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7
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Budaitis BG, Jariwala S, Rao L, Yue Y, Sept D, Verhey KJ, Gennerich A. Pathogenic mutations in the kinesin-3 motor KIF1A diminish force generation and movement through allosteric mechanisms. J Cell Biol 2021; 220:211720. [PMID: 33496723 PMCID: PMC7844421 DOI: 10.1083/jcb.202004227] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/27/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
The kinesin-3 motor KIF1A functions in neurons, where its fast and superprocessive motility facilitates long-distance transport, but little is known about its force-generating properties. Using optical tweezers, we demonstrate that KIF1A stalls at an opposing load of ~3 pN but more frequently detaches at lower forces. KIF1A rapidly reattaches to the microtubule to resume motion due to its class-specific K-loop, resulting in a unique clustering of force generation events. To test the importance of neck linker docking in KIF1A force generation, we introduced mutations linked to human neurodevelopmental disorders. Molecular dynamics simulations predict that V8M and Y89D mutations impair neck linker docking. Indeed, both mutations dramatically reduce the force generation of KIF1A but not the motor’s ability to rapidly reattach to the microtubule. Although both mutations relieve autoinhibition of the full-length motor, the mutant motors display decreased velocities, run lengths, and landing rates and delayed cargo transport in cells. These results advance our understanding of how mutations in KIF1A can manifest in disease.
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Affiliation(s)
- Breane G Budaitis
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Lu Rao
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Kristen J Verhey
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
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8
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Das S, Singer RH, Yoon YJ. The travels of mRNAs in neurons: do they know where they are going? Curr Opin Neurobiol 2019; 57:110-116. [PMID: 30784978 PMCID: PMC6650148 DOI: 10.1016/j.conb.2019.01.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/14/2019] [Indexed: 11/19/2022]
Abstract
Neurons are highly polarized cells that can extend processes far from the cell body. As such, transport of messenger RNAs serves as a set of blueprints for the synthesis of specific proteins at distal sites. RNA localization to dendrites and axons confers the ability to regulate translation with extraordinary precision in space and time. Although the rationale for RNA localization is quite compelling, it is unclear how a neuron orchestrates such a complex task of distributing over a thousand different mRNAs to their respective subcellular compartments. Recent single-molecule imaging studies have led to insights into the kinetics of individual mRNAs. We can now peer into the transport dynamics of mRNAs in both dendrites and axons.
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Affiliation(s)
- Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Janelia Research Campus, Ashburn, VA, USA.
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Janelia Research Campus, Ashburn, VA, USA.
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9
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Jost APT, Waters JC. Designing a rigorous microscopy experiment: Validating methods and avoiding bias. J Cell Biol 2019; 218:1452-1466. [PMID: 30894402 PMCID: PMC6504886 DOI: 10.1083/jcb.201812109] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 01/06/2023] Open
Abstract
Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.
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10
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Engelke MF, Waas B, Kearns SE, Suber A, Boss A, Allen BL, Verhey KJ. Acute Inhibition of Heterotrimeric Kinesin-2 Function Reveals Mechanisms of Intraflagellar Transport in Mammalian Cilia. Curr Biol 2019; 29:1137-1148.e4. [PMID: 30905605 PMCID: PMC6445692 DOI: 10.1016/j.cub.2019.02.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/02/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
Abstract
The trafficking of components within cilia, called intraflagellar transport (IFT), is powered by kinesin-2 and dynein-2 motors. Loss of function in any subunit of the heterotrimeric KIF3A/KIF3B/KAP kinesin-2 motor prevents ciliogenesis in mammalian cells and has hindered an understanding of how kinesin-2 motors function in cilium assembly and IFT. We used a chemical-genetic approach to generate an inhibitable KIF3A/KIF3B/KAP kinesin-2 motor (i3A/i3B) that is capable of rescuing wild-type (WT) motor function for cilium assembly and Hedgehog signaling in Kif3a/Kif3b double-knockout cells. We demonstrate that KIF3A/KIF3B function is required not just for cilium assembly but also for cilium maintenance, as inhibition of i3A/i3B blocks IFT within 2 min and leads to a complete loss of primary cilia within 8 h. In contrast, inhibition of dynein-2 has no effect on cilium maintenance within the same time frame. The kinetics of cilia loss indicate that two processes contribute to ciliary disassembly in response to cessation of anterograde IFT: a slow shortening that is steady over time and a rapid deciliation that occurs with stochastic onset. We also demonstrate that the kinesin-2 family members KIF3A/KIF3C and KIF17 cannot rescue ciliogenesis in Kif3a/Kif3b double-knockout cells or delay the loss of assembled cilia upon i3A/i3B inhibition. These results demonstrate that KIF3A/KIF3B/KAP is the sole and essential motor for cilium assembly and maintenance in mammalian cells. These findings highlight differences in how kinesin-2 motors were adapted for cilium assembly and IFT function across species.
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Affiliation(s)
- Martin F Engelke
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
| | - Bridget Waas
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Sarah E Kearns
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayana Suber
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Allison Boss
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Benjamin L Allen
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
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11
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Arpağ G, Norris SR, Mousavi SI, Soppina V, Verhey KJ, Hancock WO, Tüzel E. Motor Dynamics Underlying Cargo Transport by Pairs of Kinesin-1 and Kinesin-3 Motors. Biophys J 2019; 116:1115-1126. [PMID: 30824116 PMCID: PMC6428962 DOI: 10.1016/j.bpj.2019.01.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 05/25/2018] [Accepted: 01/03/2019] [Indexed: 01/01/2023] Open
Abstract
Intracellular cargo transport by kinesin family motor proteins is crucial for many cellular processes, particularly vesicle transport in axons and dendrites. In a number of cases, the transport of specific cargo is carried out by two classes of kinesins that move at different speeds and thus compete during transport. Despite advances in single-molecule characterization and modeling approaches, many questions remain regarding the effect of intermotor tension on motor attachment/reattachment rates during cooperative multimotor transport. To understand the motor dynamics underlying multimotor transport, we analyzed the complexes of kinesin-1 and kinesin-3 motors attached through protein scaffolds moving on immobilized microtubules in vitro. To interpret the observed behavior, simulations were carried out using a model that incorporated motor stepping, attachment/detachment rates, and intermotor force generation. In single-molecule experiments, isolated kinesin-3 motors moved twofold faster and had threefold higher landing rates than kinesin-1. When the positively charged loop 12 of kinesin-3 was swapped with that of kinesin-1, the landing rates reversed, indicating that this "K-loop" is a key determinant of the motor reattachment rate. In contrast, swapping loop 12 had negligible effects on motor velocities. Two-motor complexes containing one kinesin-1 and one kinesin-3 moved at different speeds depending on the identity of their loop 12, indicating the importance of the motor reattachment rate on the cotransport speed. Simulations of these loop-swapped motors using experimentally derived motor parameters were able to reproduce the experimental results and identify best fit parameters for the motor reattachment rates for this geometry. Simulation results also supported previous work, suggesting that kinesin-3 microtubule detachment is very sensitive to load. Overall, the simulations demonstrate that the transport behavior of cargo carried by pairs of kinesin-1 and -3 motors are determined by three properties that differ between these two families: the unloaded velocity, the load dependence of detachment, and the motor reattachment rate.
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Affiliation(s)
- Göker Arpağ
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Stephen R Norris
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - S Iman Mousavi
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts
| | | | - Kristen J Verhey
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, State College, Pennsylvania.
| | - Erkan Tüzel
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts.
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12
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13
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Banaz N, Mäkelä J, Uphoff S. Choosing the right label for single-molecule tracking in live bacteria: side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2019; 52:064002. [PMID: 30799881 PMCID: PMC6372142 DOI: 10.1088/1361-6463/aaf255] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/07/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
Visualizing and quantifying molecular motion and interactions inside living cells provides crucial insight into the mechanisms underlying cell function. This has been achieved by super-resolution localization microscopy and single-molecule tracking in conjunction with photoactivatable fluorescent proteins (PA-FPs). An alternative labelling approach relies on genetically-encoded protein tags with cell-permeable fluorescent ligands which are brighter and less prone to photobleaching than fluorescent proteins but require a laborious labelling process. Either labelling method is associated with significant advantages and disadvantages that should be taken into consideration depending on the microscopy experiment planned. Here, we describe an optimised procedure for labelling Halo-tagged proteins in live Escherichia coli cells. We provide a side-by-side comparison of Halo tag with different fluorescent ligands against the popular photoactivatable fluorescent protein PAmCherry. Using test proteins with different intracellular dynamics, we evaluated fluorescence intensity, background, photostability, and results from single-molecule localization and tracking experiments. Capitalising on the brightness and extended spectral range of fluorescent Halo ligands, we also demonstrate high-speed and dual-colour single-molecule tracking.
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Affiliation(s)
- Nehir Banaz
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jarno Mäkelä
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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14
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Jaykumar AB, Caceres PS, Ortiz PA. Single-molecule labeling for studying trafficking of renal transporters. Am J Physiol Renal Physiol 2018; 315:F1243-F1249. [PMID: 30043625 DOI: 10.1152/ajprenal.00082.2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The ability to detect and track single molecules presents the advantage of visualizing the complex behavior of transmembrane proteins with a time and space resolution that would otherwise be lost with traditional labeling and biochemical techniques. Development of new imaging probes has provided a robust method to study their trafficking and surface dynamics. This mini-review focuses on the current technology available for single-molecule labeling of transmembrane proteins, their advantages, and limitations. We also discuss the application of these techniques to the study of renal transporter trafficking in light of recent research.
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Affiliation(s)
- Ankita Bachhawat Jaykumar
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital , Detroit, Michigan.,Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan
| | - Paulo S Caceres
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital , Detroit, Michigan
| | - Pablo A Ortiz
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital , Detroit, Michigan.,Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan
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15
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Tymanskyj SR, Yang BH, Verhey KJ, Ma L. MAP7 regulates axon morphogenesis by recruiting kinesin-1 to microtubules and modulating organelle transport. eLife 2018; 7:36374. [PMID: 30132755 PMCID: PMC6133550 DOI: 10.7554/elife.36374] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
Neuronal cell morphogenesis depends on proper regulation of microtubule-based transport, but the underlying mechanisms are not well understood. Here, we report our study of MAP7, a unique microtubule-associated protein that interacts with both microtubules and the motor protein kinesin-1. Structure-function analysis in rat embryonic sensory neurons shows that the kinesin-1 interacting domain in MAP7 is required for axon and branch growth but not for branch formation. Also, two unique microtubule binding sites are found in MAP7 that have distinct dissociation kinetics and are both required for branch formation. Furthermore, MAP7 recruits kinesin-1 dynamically to microtubules, leading to alterations in organelle transport behaviors, particularly pause/speed switching. As MAP7 is localized to branch sites, our results suggest a novel mechanism mediated by the dual interactions of MAP7 with microtubules and kinesin-1 in the precise control of microtubule-based transport during axon morphogenesis.
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Affiliation(s)
- Stephen R Tymanskyj
- Jefferson Synaptic Biology Center, Vickie and Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, United States.,Department of Neuroscience, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, United States
| | - Benjamin H Yang
- Jefferson Synaptic Biology Center, Vickie and Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, United States.,Department of Neuroscience, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, United States
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Le Ma
- Jefferson Synaptic Biology Center, Vickie and Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, United States.,Department of Neuroscience, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, United States
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16
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Norris SR, Jung S, Singh P, Strothman CE, Erwin AL, Ohi MD, Zanic M, Ohi R. Microtubule minus-end aster organization is driven by processive HSET-tubulin clusters. Nat Commun 2018; 9:2659. [PMID: 29985404 PMCID: PMC6037785 DOI: 10.1038/s41467-018-04991-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/20/2018] [Indexed: 12/20/2022] Open
Abstract
Higher-order structures of the microtubule (MT) cytoskeleton are comprised of two architectures: bundles and asters. Although both architectures are critical for cellular function, the molecular pathways that drive aster formation are poorly understood. Here, we study aster formation by human minus-end-directed kinesin-14 (HSET/KIFC1). We show that HSET is incapable of forming asters from preformed, nongrowing MTs, but rapidly forms MT asters in the presence of soluble (non-MT) tubulin. HSET binds soluble (non-MT) tubulin via its N-terminal tail domain to form heterogeneous HSET-tubulin clusters containing multiple motors. Cluster formation induces motor processivity and rescues the formation of asters from nongrowing MTs. We then show that excess soluble (non-MT) tubulin stimulates aster formation in HeLa cells overexpressing HSET during mitosis. We propose a model where HSET can toggle between MT bundle and aster formation in a manner governed by the availability of soluble (non-MT) tubulin.
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Affiliation(s)
- Stephen R Norris
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Seungyeon Jung
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Prashant Singh
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Claire E Strothman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Amanda L Erwin
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109-2216, USA
- The Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI, 48109-2216, USA
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109-2216, USA
- The Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI, 48109-2216, USA
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109-2216, USA.
- The Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI, 48109-2216, USA.
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17
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Yue Y, Blasius TL, Zhang S, Jariwala S, Walker B, Grant BJ, Cochran JC, Verhey KJ. Altered chemomechanical coupling causes impaired motility of the kinesin-4 motors KIF27 and KIF7. J Cell Biol 2018; 217:1319-1334. [PMID: 29351996 PMCID: PMC5881503 DOI: 10.1083/jcb.201708179] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/28/2017] [Accepted: 01/02/2018] [Indexed: 01/08/2023] Open
Abstract
Despite their shared ability to regulate microtubule polymerization dynamics, kinesin-4 motors display dramatically different motility properties ranging from fast processive motility to no movement. Yue et al. demonstrate that for KIF7 and KIF27, altered chemomechanical coupling results in immotile behavior and slow processive movement, respectively. Kinesin-4 motors play important roles in cell division, microtubule organization, and signaling. Understanding how motors perform their functions requires an understanding of their mechanochemical and motility properties. We demonstrate that KIF27 can influence microtubule dynamics, suggesting a conserved function in microtubule organization across the kinesin-4 family. However, kinesin-4 motors display dramatically different motility characteristics: KIF4 and KIF21 motors are fast and processive, KIF7 and its Drosophila melanogaster homologue Costal2 (Cos2) are immotile, and KIF27 is slow and processive. Neither KIF7 nor KIF27 can cooperate for fast processive transport when working in teams. The mechanistic basis of immotile KIF7 behavior arises from an inability to release adenosine diphosphate in response to microtubule binding, whereas slow processive KIF27 behavior arises from a slow adenosine triphosphatase rate and a high affinity for both adenosine triphosphate and microtubules. We suggest that evolutionarily selected sequence differences enable immotile KIF7 and Cos2 motors to function not as transporters but as microtubule-based tethers of signaling complexes.
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Affiliation(s)
- Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - T Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Stephanie Zhang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Benjamin Walker
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | - Barry J Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Jared C Cochran
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
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18
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Ruhnow F, Kloβ L, Diez S. Challenges in Estimating the Motility Parameters of Single Processive Motor Proteins. Biophys J 2018; 113:2433-2443. [PMID: 29211997 DOI: 10.1016/j.bpj.2017.09.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/16/2017] [Accepted: 09/21/2017] [Indexed: 11/26/2022] Open
Abstract
Cytoskeletal motor proteins are essential to the function of a wide range of intracellular mechano-systems. The biophysical characterization of their movement along their filamentous tracks is therefore of large importance. Toward this end, single-molecule, in vitro stepping-motility assays are commonly used to determine motor velocity and run length. However, comparing results from such experiments has proved difficult due to influences from variations in the experimental conditions and the data analysis methods. Here, we investigate the movement of fluorescently labeled, processive, dimeric motor proteins and propose a unified algorithm to correct the measurements for finite filament length as well as photobleaching. Particular emphasis is put on estimating the statistical errors associated with the proposed evaluation method, as knowledge of these values is crucial when comparing measurements from different experiments. Testing our approach with simulated and experimental data from GFP-labeled kinesin-1 motors stepping along immobilized microtubules, we show 1) that velocity distributions should be fitted by a t location-scale probability density function rather than by a normal distribution; 2) that the impossibility to measure events shorter than the image acquisition time needs to be taken into account; 3) that the interaction time and run length of the motors can be estimated independent of the filament length distribution; and 4) that the dimeric nature of the motors needs to be considered when correcting for photobleaching. Moreover, our analysis reveals that controlling the temperature during the experiments with a precision below 1 K is of importance. We believe our method will not only improve the evaluation of experimental data, but also allow for better statistical comparisons between different populations of motor proteins (e.g., with distinct mutations or linked to different cargos) and filaments (e.g., in distinct nucleotide states or with different posttranslational modifications). Therefore, we include a detailed workflow for image processing and analysis (including MATLAB code), serving as a tutorial for the estimation of motility parameters in stepping-motility assays.
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Affiliation(s)
- Felix Ruhnow
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Linda Kloβ
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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19
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Impact of fluorescent protein fusions on the bacterial flagellar motor. Sci Rep 2017; 7:12583. [PMID: 28974721 PMCID: PMC5626733 DOI: 10.1038/s41598-017-11241-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/22/2017] [Indexed: 01/16/2023] Open
Abstract
Fluorescent fusion proteins open a direct and unique window onto protein function. However, they also introduce the risk of perturbation of the function of the native protein. Successful applications of fluorescent fusions therefore rely on a careful assessment and minimization of the side effects, but such insight is still lacking for many applications. This is particularly relevant in the study of the internal dynamics of motor proteins, where both the chemical and mechanical reaction coordinates can be affected. Fluorescent proteins fused to the stator of the Bacterial Flagellar Motor (BFM) have previously been used to unveil the motor subunit dynamics. Here we report the effects on single motors of three fluorescent proteins fused to the stators, all of which altered BFM behavior. The torque generated by individual stators was reduced while their stoichiometry remained unaffected. MotB fusions decreased the switching frequency and induced a novel bias-dependent asymmetry in the speed in the two directions. These effects could be mitigated by inserting a linker at the fusion point. These findings provide a quantitative account of the effects of fluorescent fusions to the stator on BFM dynamics and their alleviation- new insights that advance the use of fluorescent fusions to probe the dynamics of protein complexes.
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20
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Sánchez-Rico C, Voith von Voithenberg L, Warner L, Lamb DC, Sattler M. Effects of Fluorophore Attachment on Protein Conformation and Dynamics Studied by spFRET and NMR Spectroscopy. Chemistry 2017; 23:14267-14277. [PMID: 28799205 DOI: 10.1002/chem.201702423] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Indexed: 12/28/2022]
Abstract
Fluorescence-based techniques are widely used to study biomolecular conformations, intra- and intermolecular interactions, and conformational dynamics of macromolecules. Especially for fluorescence-based single-molecule experiments, the choice of the fluorophore and labeling position are highly important. In this work, we studied the biophysical and structural effects that are associated with the conjugation of fluorophores to cysteines in the splicing factor U2AF65 by using single pair Förster resonance energy transfer (FRET) and nuclear magnetic resonance (NMR) spectroscopy. It is shown that certain acceptor fluorophores are advantageous depending on the experiments performed. The effects of dye attachment on the protein conformation were characterized using heteronuclear NMR experiments. The presence of hydrophobic and aromatic moieties in the fluorophores can significantly affect the conformation of the conjugated protein, presumably by transient interactions with the protein surface. Guidelines are provided for carefully choosing fluorophores, considering their photophysical properties and chemical features for the design of FRET experiments, and for minimizing artifacts.
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Affiliation(s)
- Carolina Sánchez-Rico
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Lena Voith von Voithenberg
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Lisa Warner
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
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21
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Neumann S, Chassefeyre R, Campbell GE, Encalada SE. KymoAnalyzer: a software tool for the quantitative analysis of intracellular transport in neurons. Traffic 2016; 18:71-88. [PMID: 27770501 DOI: 10.1111/tra.12456] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 12/17/2022]
Abstract
In axons, proper localization of proteins, vesicles, organelles, and other cargoes is accomplished by the highly regulated coordination of kinesins and dyneins, molecular motors that bind to cargoes and translocate them along microtubule (MT) tracks. Impairment of axonal transport is implicated in the pathogenesis of multiple neurodegenerative disorders including Alzheimer's and Huntington's diseases. To understand how MT-based cargo motility is regulated and to delineate its role in neurodegeneration, it is critical to analyze the detailed dynamics of moving cargoes inside axons. Here, we present KymoAnalyzer, a software tool that facilitates the robust analysis of axonal transport from time-lapse live-imaging sequences. KymoAnalyzer is an open-source software that automatically classifies particle trajectories and systematically calculates velocities, run lengths, pauses, and a wealth of other parameters that are characteristic of motor-based transport. We anticipate that laboratories will easily use this package to unveil previously uncovered intracellular transport details of individually-moving cargoes inside neurons.
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Affiliation(s)
- Sylvia Neumann
- Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California
| | - Romain Chassefeyre
- Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California
| | - George E Campbell
- Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California
| | - Sandra E Encalada
- Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California
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22
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Teng KW, Ishitsuka Y, Ren P, Youn Y, Deng X, Ge P, Lee SH, Belmont AS, Selvin PR. Labeling proteins inside living cells using external fluorophores for microscopy. eLife 2016; 5. [PMID: 27935478 PMCID: PMC5148600 DOI: 10.7554/elife.20378] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 11/21/2016] [Indexed: 12/31/2022] Open
Abstract
Site-specific fluorescent labeling of proteins inside live mammalian cells has been achieved by employing Streptolysin O, a bacterial toxin which forms temporary pores in the membrane and allows delivery of virtually any fluorescent probes, ranging from labeled IgG’s to small ligands, with high efficiency (>85% of cells). The whole process, including recovery, takes 30 min, and the cell is ready to be imaged immediately. A variety of cell viability tests were performed after treatment with SLO to ensure that the cells have intact membranes, are able to divide, respond normally to signaling molecules, and maintains healthy organelle morphology. When combined with Oxyrase, a cell-friendly photostabilizer, a ~20x improvement in fluorescence photostability is achieved. By adding in glutathione, fluorophores are made to blink, enabling super-resolution fluorescence with 20–30 nm resolution over a long time (~30 min) under continuous illumination. Example applications in conventional and super-resolution imaging of native and transfected cells include p65 signal transduction activation, single molecule tracking of kinesin, and specific labeling of a series of nuclear and cytoplasmic protein complexes. DOI:http://dx.doi.org/10.7554/eLife.20378.001
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Affiliation(s)
- Kai Wen Teng
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Yuji Ishitsuka
- Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pin Ren
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Xiang Deng
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pinghua Ge
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Sang Hak Lee
- Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Andrew S Belmont
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
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23
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Tiwari A, Copeland CA, Han B, Hanson CA, Raghunathan K, Kenworthy AK. Caveolin-1 is an aggresome-inducing protein. Sci Rep 2016; 6:38681. [PMID: 27929047 PMCID: PMC5144149 DOI: 10.1038/srep38681] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 11/14/2016] [Indexed: 02/06/2023] Open
Abstract
Caveolin-1 (Cav1) drives the formation of flask-shaped membrane invaginations known as caveolae that participate in signaling, clathrin-independent endocytosis and mechanotransduction. Overexpression or mutations of Cav1 can lead to its mistrafficking, including its accumulation in a perinuclear compartment previously identified as the Golgi complex. Here, we show that in the case of overexpressed Cav1-GFP, this perinuclear compartment consists of cytoplasmic inclusion bodies generated in response to the accumulation of aggregates of misfolded proteins, known as aggresomes. Aggresomes containing Cav1-GFP are encased within vimentin cages, form in a microtubule-dependent manner, and are enriched in a number of key regulators of protein turnover, including ubiquitin, VCP/p97 and proteasomes. Interestingly, aggresome induction was cell-type dependent and was observed for many but not all Cav1 constructs tested. Furthermore, endogenous Cav1 accumulated in aggresomes formed in response to proteosomal inhibition. Our finding that Cav1 is both an aggresome-inducing and aggresome-localized protein provides new insights into how cells handle and respond to misfolded Cav1. They also raise the possibility that aggresome formation may contribute to some of reported phenotypes associated with overexpressed and/or mutant forms of Cav1.
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Affiliation(s)
- Ajit Tiwari
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Courtney A Copeland
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Bing Han
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Caroline A Hanson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Krishnan Raghunathan
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Epithelial Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
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24
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Sturgill EG, Norris SR, Guo Y, Ohi R. Kinesin-5 inhibitor resistance is driven by kinesin-12. J Cell Biol 2016; 213:213-27. [PMID: 27091450 PMCID: PMC5084272 DOI: 10.1083/jcb.201507036] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 03/10/2016] [Indexed: 12/27/2022] Open
Abstract
The kinesin-5 Eg5 is essential for mitotic progression, and the lethal effects of Eg5 inhibitors make these inhibitors attractive candidates for chemotherapy drugs. Sturgill et al. show that kinesin-12 and a nonmotile Eg5 mutant form an alternative spindle assembly pathway that provides resistance to Eg5 inhibitors. The microtubule (MT) cytoskeleton bipolarizes at the onset of mitosis to form the spindle. In animal cells, the kinesin-5 Eg5 primarily drives this reorganization by actively sliding MTs apart. Its primacy during spindle assembly renders Eg5 essential for mitotic progression, demonstrated by the lethal effects of kinesin-5/Eg5 inhibitors (K5Is) administered in cell culture. However, cultured cells can acquire resistance to K5Is, indicative of alternative spindle assembly mechanisms and/or pharmacological failure. Through characterization of novel K5I-resistant cell lines, we unveil an Eg5 motility-independent spindle assembly pathway that involves both an Eg5 rigor mutant and the kinesin-12 Kif15. This pathway centers on spindle MT bundling instead of Kif15 overexpression, distinguishing it from those previously described. We further show that large populations (∼107 cells) of HeLa cells require Kif15 to survive K5I treatment. Overall, this study provides insight into the functional plasticity of mitotic kinesins during spindle assembly and has important implications for the development of antimitotic regimens that target this process.
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Affiliation(s)
- Emma G Sturgill
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Stephen R Norris
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
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