1
|
Gholkar AA, Gimeno TV, Edgemon JE, Sim MS, Torres JZ. MI-181 Modulates Cilia Length and Restores Cilia Length in Cells with Defective Shortened Cilia. ACS Chem Biol 2024. [PMID: 39106364 DOI: 10.1021/acschembio.4c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Primary cilia are membrane-covered microtubule-based structures that protrude from the cell surface and are critical for cell signaling and homeostasis during human development and adulthood. Dysregulation of cilia formation, length, and function can lead to a spectrum of human diseases and syndromes known as ciliopathies. Although some genetic and chemical screens have been performed to define important factors that modulate cilia biogenesis and length control, there are currently no clinical treatments that restore cilia length in patients. We report that the microtubule-targeting agent MI-181(mitotic inhibitor-181) is a potent modulator of cilia length and biogenesis. Treatment of retinal pigment epithelial-1 cells with MI-181 induced an increase in the average size of cilia and in the percent ciliated cells under nonstarved conditions. Importantly, MI-181 was effective at rescuing cilia length and ciliation defects in cells that had been treated with the intraflagellar transport inhibitor Ciliobrevin D or the O-GlcNAc transferase inhibitor OSMI-1. Most importantly, MI-181 induced an increase in cilia length and restored ciliation in cells with compromised shortened cilia at low nanomolar concentrations and did not show an inhibitory response at high concentrations. Therefore, MI-181 represents a lead molecule for developing drugs targeting ciliopathies characterized by shortened cilia.
Collapse
Affiliation(s)
- Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Thomas V Gimeno
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Jalie E Edgemon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Myung Shin Sim
- Department of Medicine Statistics Core, University of California, Los Angeles, California 90095, United States
- Department of Medicine's Division of General Internal Medicine and Health Services Research, University of California, Los Angeles, California 90095, United States
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| |
Collapse
|
2
|
Möckl L, Moerner WE. Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. J Am Chem Soc 2020; 142:17828-17844. [PMID: 33034452 PMCID: PMC7582613 DOI: 10.1021/jacs.0c08178] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/31/2022]
Abstract
Single-molecule super-resolution microscopy has developed from a specialized technique into one of the most versatile and powerful imaging methods of the nanoscale over the past two decades. In this perspective, we provide a brief overview of the historical development of the field, the fundamental concepts, the methodology required to obtain maximum quantitative information, and the current state of the art. Then, we will discuss emerging perspectives and areas where innovation and further improvement are needed. Despite the tremendous progress, the full potential of single-molecule super-resolution microscopy is yet to be realized, which will be enabled by the research ahead of us.
Collapse
Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
3
|
Yang TT, Tran MNT, Chong WM, Huang CE, Liao JC. Single-particle tracking localization microscopy reveals nonaxonemal dynamics of intraflagellar transport proteins at the base of mammalian primary cilia. Mol Biol Cell 2019; 30:828-837. [PMID: 30759057 PMCID: PMC6589787 DOI: 10.1091/mbc.e18-10-0654] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Primary cilia play a vital role in cellular sensing and signaling. An essential component of ciliogenesis is intraflagellar transport (IFT), which is involved in IFT protein recruitment, axonemal engagement of IFT protein complexes, and so on. The mechanistic understanding of these processes at the ciliary base was largely missing, because it is challenging to observe the motion of IFT proteins in this crowded region using conventional microscopy. Here, we report short-trajectory tracking of IFT proteins at the base of mammalian primary cilia by optimizing single-particle tracking photoactivated localization microscopy for IFT88-mEOS4b in live human retinal pigment epithelial cells. Intriguingly, we found that mobile IFT proteins “switched gears” multiple times from the distal appendages (DAPs) to the ciliary compartment (CC), moving slowly in the DAPs, relatively fast in the proximal transition zone (TZ), slowly again in the distal TZ, and then much faster in the CC. They could travel through the space between the DAPs and the axoneme without following DAP structures. We further revealed that BBS2 and IFT88 were highly populated at the distal TZ, a potential assembly site. Together, our live-cell single-particle tracking revealed region-dependent slowdown of IFT proteins at the ciliary base, shedding light on staged control of ciliary homeostasis.
Collapse
Affiliation(s)
- T Tony Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Minh Nguyet Thi Tran
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Weng Man Chong
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Chia-En Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Jung-Chi Liao
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan.,Genome and Systems Biology Program, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
4
|
Yoon J, Comerci CJ, Weiss LE, Milenkovic L, Stearns T, Moerner WE. Revealing Nanoscale Morphology of the Primary Cilium Using Super-Resolution Fluorescence Microscopy. Biophys J 2018; 116:319-329. [PMID: 30598282 PMCID: PMC6349968 DOI: 10.1016/j.bpj.2018.11.3136] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/20/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
Super-resolution (SR) microscopy has been used to observe structural details beyond the diffraction limit of ∼250 nm in a variety of biological and materials systems. By combining this imaging technique with both computer-vision algorithms and topological methods, we reveal and quantify the nanoscale morphology of the primary cilium, a tiny tubular cellular structure (∼2-6 μm long and 200-300 nm in diameter). The cilium in mammalian cells protrudes out of the plasma membrane and is important in many signaling processes related to cellular differentiation and disease. After tagging individual ciliary transmembrane proteins, specifically Smoothened, with single fluorescent labels in fixed cells, we use three-dimensional (3D) single-molecule SR microscopy to determine their positions with a precision of 10-25 nm. We gain a dense, pointillistic reconstruction of the surfaces of many cilia, revealing large heterogeneity in membrane shape. A Poisson surface reconstruction algorithm generates a fine surface mesh, allowing us to characterize the presence of deformations by quantifying the surface curvature. Upon impairment of intracellular cargo transport machinery by genetic knockout or small-molecule treatment of cells, our quantitative curvature analysis shows significant morphological differences not visible by conventional fluorescence microscopy techniques. Furthermore, using a complementary SR technique, two-color, two-dimensional stimulated emission depletion microscopy, we find that the cytoskeleton in the cilium, the axoneme, also exhibits abnormal morphology in the mutant cells, similar to our 3D results on the Smoothened-measured ciliary surface. Our work combines 3D SR microscopy and computational tools to quantitatively characterize morphological changes of the primary cilium under different treatments and uses stimulated emission depletion to discover correlated changes in the underlying structure. This approach can be useful for studying other biological or nanoscale structures of interest.
Collapse
Affiliation(s)
- Joshua Yoon
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California
| | - Colin J Comerci
- Biophysics Program, Stanford University, Stanford, California
| | - Lucien E Weiss
- Department of Chemistry, Stanford University, Stanford, California
| | | | - Tim Stearns
- Department of Biology, Stanford University, Stanford, California
| | - W E Moerner
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California.
| |
Collapse
|
5
|
Weng RR, Yang TT, Huang CE, Chang CW, Wang WJ, Liao JC. Super-Resolution Imaging Reveals TCTN2 Depletion-Induced IFT88 Lumen Leakage and Ciliary Weakening. Biophys J 2018; 115:263-275. [PMID: 29866362 DOI: 10.1016/j.bpj.2018.04.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/07/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022] Open
Abstract
The primary cilium is an essential organelle mediating key signaling activities, such as sonic hedgehog signaling. The molecular composition of the ciliary compartment is distinct from that of the cytosol, with the transition zone (TZ) gated the ciliary base. The TZ is a packed and organized protein complex containing multiple ciliopathy-associated protein species. Tectonic 2 (TCTN2) is one of the TZ proteins in the vicinity of the ciliary membrane, and its mutation is associated with Meckel syndrome. Despite its importance in ciliopathies, the role of TCTN2 in ciliary structure and molecules remains unclear. Here, we created a CRISPR/Cas9 TCTN2 knockout human retinal pigment epithelial cell line and conducted quantitative analysis of geometric localization using both wide-field and super-resolution microscopy techniques. We found that TCTN2 depletion resulted in partial TZ damage, loss of ciliary membrane proteins, leakage of intraflagellar transport protein IFT88 toward the basal body lumen, and cilium shortening and curving. The basal body lumen occupancy of IFT88 was also observed in si-RPGRIP1L cells and cytochalasin-D-treated wild-type cells, suggesting varying lumen accessibility for intraflagellar transport proteins under different perturbed conditions. Our findings support two possible models for the lumen leakage of IFT88, i.e., a tip leakage model and a misregulation model. Together, our quantitative image analysis augmented by super-resolution microscopy facilitates the observation of structural destruction and molecular redistribution in TCTN2-/- cilia, shedding light on mechanistic understanding of TZ-protein-associated ciliopathies.
Collapse
Affiliation(s)
- Rueyhung Roc Weng
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - T Tony Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Chia-En Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Chih-Wei Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Won-Jing Wang
- Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei, Taiwan
| | - Jung-Chi Liao
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
6
|
Asgharzadeh P, Özdemir B, Reski R, Röhrle O, Birkhold AI. Computational 3D imaging to quantify structural components and assembly of protein networks. Acta Biomater 2018; 69:206-217. [PMID: 29378323 DOI: 10.1016/j.actbio.2018.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/21/2017] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
Abstract
Traditionally, protein structures have been described by the secondary structure architecture and fold arrangement. However, the relatively novel method of 3D confocal microscopy of fluorescent-protein-tagged networks in living cells allows resolving the detailed spatial organization of these networks. This provides new possibilities to predict network functionality, as structure and function seem to be linked at various scales. Here, we propose a quantitative approach using 3D confocal microscopy image data to describe protein networks based on their nano-structural characteristics. This analysis is constructed in four steps: (i) Segmentation of the microscopic raw data into a volume model and extraction of a spatial graph representing the protein network. (ii) Quantifying protein network gross morphology using the volume model. (iii) Quantifying protein network components using the spatial graph. (iv) Linking these two scales to obtain insights into network assembly. Here, we quantitatively describe the filamentous temperature sensitive Z protein network of the moss Physcomitrella patens and elucidate relations between network size and assembly details. Future applications will link network structure and functionality by tracking dynamic structural changes over time and comparing different states or types of networks, possibly allowing more precise identification of (mal) functions or the design of protein-engineered biomaterials for applications in regenerative medicine. STATEMENT OF SIGNIFICANCE Protein networks are highly complex and dynamic structures that play various roles in biological environments. Analyzing the detailed spatial structure of these networks may lead to new insight into biological functions and malfunctions. Here, we propose a tool set that extracts structural information at two scales of the protein network and allows therefore to address questions such as "how is the network built?" or "how networks grow?".
Collapse
|
7
|
Luo W, Ruba A, Takao D, Zweifel LP, Lim RYH, Verhey KJ, Yang W. Axonemal Lumen Dominates Cytosolic Protein Diffusion inside the Primary Cilium. Sci Rep 2017; 7:15793. [PMID: 29150645 PMCID: PMC5693955 DOI: 10.1038/s41598-017-16103-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 11/03/2017] [Indexed: 12/02/2022] Open
Abstract
Transport of membrane and cytosolic proteins in primary cilia is thought to depend on intraflagellar transport (IFT) and diffusion. However, the relative contribution and spatial routes of each transport mechanism are largely unknown. Although challenging to decipher, the details of these routes are essential for our understanding of protein transport in primary cilia, a critically affected process in many genetic diseases. By using a high-speed virtual 3D super-resolution microscopy, we have mapped the 3D spatial locations of transport routes for various cytosolic proteins in the 250-nm-wide shaft of live primary cilia with a spatiotemporal resolution of 2 ms and <16 nm. Our data reveal two spatially distinguishable transport routes for cytosolic proteins: an IFT-dependent path along the axoneme, and a passive-diffusion route in the axonemal lumen that escaped previous studies. While all cytosolic proteins tested primarily utilize the IFT path in the anterograde direction, differences are observed in the retrograde direction where IFT20 only utilizes IFT, and approximately half of KIF17 and one third of α–tubulin utilizes diffusion besides IFT.
Collapse
Affiliation(s)
- Wangxi Luo
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Andrew Ruba
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ludovit P Zweifel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA.
| |
Collapse
|
8
|
Primary Cilium Formation and Ciliary Protein Trafficking Is Regulated by the Atypical MAP Kinase MAPK15 in Caenorhabditis elegans and Human Cells. Genetics 2017; 207:1423-1440. [PMID: 29021280 DOI: 10.1534/genetics.117.300383] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/05/2017] [Indexed: 11/18/2022] Open
Abstract
Motile and immotile (or primary) cilia are microtubule-based structures that mediate multiple cellular functions, including the transduction of environmental cues, developmental signaling, cellular motility, and modulation of fluid flow. Although their core architectures are similar, motile and primary cilia exhibit marked structural differences that underlie distinct functional properties. However, the extent to which ciliogenesis mechanisms are shared between these different cilia types is not fully described. Here, we report that the atypical MAP kinase MAPK15 (ERK7/8), implicated in the formation of vertebrate motile cilia, also regulates the formation of primary cilia in Caenorhabditis elegans sensory neurons and human cells. We find that MAPK15 localizes to a basal body subdomain with the ciliopathy protein BBS7 and to cell-cell junctions. MAPK15 also regulates the localization of ciliary proteins involved in cilium structure, transport, and signaling. Our results describe a primary cilia-related role for this poorly studied member of the MAPK family in vivo, and indicate a broad requirement for MAPK15 in the formation of multiple ciliary classes across species.
Collapse
|
9
|
Siller SS, Burke MC, Li FQ, Takemaru KI. Chibby functions to preserve normal ciliary morphology through the regulation of intraflagellar transport in airway ciliated cells. Cell Cycle 2016; 14:3163-72. [PMID: 26266958 DOI: 10.1080/15384101.2015.1080396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Airway cilia provide the coordinated motive force for mucociliary transport, which prevents the accumulation of mucus, debris, pollutants, and bacteria in our respiratory tracts. As airway cilia are constantly exposed to the environment and, hence, are an integral component of the pathogenesis of several congenital and chronic pulmonary disorders, it is necessary to understand the molecular mechanisms that control ciliated cell differentiation and ciliogenesis. We have previously reported that loss of the basal body protein Chibby (Cby) results in chronic upper airway infection in mice due to a significant reduction in the number of airway cilia. In the present work, we demonstrate that Cby is required for normal ciliary structure and proper distribution of proteins involved in the bidirectional intraflagellar transport (IFT) system, which consists of 2 distinct sub-complexes, IFT-A and IFT-B, and is essential for ciliary biogenesis and maintenance. In fully differentiated ciliated cells, abnormal paddle-like cilia with dilated ciliary tips are observed in Cby-/- airways and primary cultures of mouse tracheal epithelial cells (MTECs). In addition, IFT88, an IFT-B sub-complex protein, robustly accumulates within the dilated tips of both multicilia in Cby-/- MTECs and primary cilia in Cby-/- mouse embryonic fibroblasts (MEFs). Furthermore, we show that only IFT-B components, including IFT20 and IFT57, but not IFT-A and Bardet-Biedl syndrome (BBS) proteins, amass with IFT88 in these distended tips in Cby-/- ciliated cells. Taken together, our findings suggest that Cby plays a role in the proper distribution of IFT particles to preserve normal ciliary morphology in airway ciliated cells.
Collapse
Affiliation(s)
- Saul S Siller
- a Medical Scientist Training Program; Stony Brook University; Stony Brook , NY USA.,b Graduate Program in Molecular and Cellular Pharmacology; Stony Brook University; Stony Brook , NY USA.,c Department of Pharmacological Sciences ; Stony Brook University; Stony Brook , NY USA
| | - Michael C Burke
- a Medical Scientist Training Program; Stony Brook University; Stony Brook , NY USA.,d Graduate Program in Genetics; Stony Brook University; Stony Brook , NY USA
| | - Feng-Qian Li
- b Graduate Program in Molecular and Cellular Pharmacology; Stony Brook University; Stony Brook , NY USA.,c Department of Pharmacological Sciences ; Stony Brook University; Stony Brook , NY USA
| | - Ken-Ichi Takemaru
- a Medical Scientist Training Program; Stony Brook University; Stony Brook , NY USA.,b Graduate Program in Molecular and Cellular Pharmacology; Stony Brook University; Stony Brook , NY USA.,c Department of Pharmacological Sciences ; Stony Brook University; Stony Brook , NY USA.,d Graduate Program in Genetics; Stony Brook University; Stony Brook , NY USA
| |
Collapse
|
10
|
Huang F, Sirinakis G, Allgeyer ES, Schroeder LK, Duim WC, Kromann EB, Phan T, Rivera-Molina FE, Myers JR, Irnov I, Lessard M, Zhang Y, Handel MA, Jacobs-Wagner C, Lusk CP, Rothman JE, Toomre D, Booth MJ, Bewersdorf J. Ultra-High Resolution 3D Imaging of Whole Cells. Cell 2016; 166:1028-1040. [PMID: 27397506 PMCID: PMC5005454 DOI: 10.1016/j.cell.2016.06.016] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/02/2016] [Accepted: 06/03/2016] [Indexed: 12/23/2022]
Abstract
Fluorescence nanoscopy, or super-resolution microscopy, has become an important tool in cell biological research. However, because of its usually inferior resolution in the depth direction (50-80 nm) and rapidly deteriorating resolution in thick samples, its practical biological application has been effectively limited to two dimensions and thin samples. Here, we present the development of whole-cell 4Pi single-molecule switching nanoscopy (W-4PiSMSN), an optical nanoscope that allows imaging of three-dimensional (3D) structures at 10- to 20-nm resolution throughout entire mammalian cells. We demonstrate the wide applicability of W-4PiSMSN across diverse research fields by imaging complex molecular architectures ranging from bacteriophages to nuclear pores, cilia, and synaptonemal complexes in large 3D cellular volumes.
Collapse
Affiliation(s)
- Fang Huang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - George Sirinakis
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Edward S Allgeyer
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Lena K Schroeder
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Whitney C Duim
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Harvey Mudd College, Claremont, CA 91711, USA
| | - Emil B Kromann
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, CT 06520, USA
| | - Thomy Phan
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Felix E Rivera-Molina
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Jordan R Myers
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Mark Lessard
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Yongdeng Zhang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | | | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - C Patrick Lusk
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - James E Rothman
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Derek Toomre
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Martin J Booth
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK; Centre for Neural Circuits and Behaviour, University of Oxford, Oxford OX1 3SR, UK
| | - Joerg Bewersdorf
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, CT 06520, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA.
| |
Collapse
|
11
|
Abstract
Super resolution imaging is becoming an increasingly important tool in the arsenal of methods available to cell biologists. In recognition of its potential, the Nobel Prize for chemistry was awarded to three investigators involved in the development of super resolution imaging methods in 2014. The availability of commercial instruments for super resolution imaging has further spurred the development of new methods and reagents designed to take advantage of super resolution techniques. Super resolution offers the advantages traditionally associated with light microscopy, including the use of gentle fixation and specimen preparation methods, the ability to visualize multiple elements within a single specimen, and the potential to visualize dynamic changes in living specimens over time. However, imaging of living cells over time is difficult and super resolution imaging is computationally demanding. In this review, we discuss the advantages/disadvantages of different super resolution systems for imaging fixed live specimens, with particular regard to cytoskeleton structures.
Collapse
Affiliation(s)
- Eric A Shelden
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Zachary T Colburn
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jonathan C R Jones
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| |
Collapse
|
12
|
Abstract
The characteristic lengths of molecular arrangement in primary cilia are below the diffraction limit of light, challenging structural and functional studies of ciliary proteins. Superresolution microscopy can reach up to a 20 nm resolution, significantly improving the ability to map molecules in primary cilia. Here we describe detailed experimental procedure of STED microscopy imaging and dSTORM imaging, two of the most powerful superresolution imaging techniques. Specifically, we emphasize the use of these two methods on imaging proteins in primary cilia.
Collapse
Affiliation(s)
- T Tony Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, No 1, Roosevelt Rd. Sec 4, Taipei, 10617, Taiwan
| | - Weng Man Chong
- Institute of Atomic and Molecular Sciences, Academia Sinica, No 1, Roosevelt Rd. Sec 4, Taipei, 10617, Taiwan
| | - Jung-Chi Liao
- Institute of Atomic and Molecular Sciences, Academia Sinica, No 1, Roosevelt Rd. Sec 4, Taipei, 10617, Taiwan.
| |
Collapse
|
13
|
Superresolution Pattern Recognition Reveals the Architectural Map of the Ciliary Transition Zone. Sci Rep 2015; 5:14096. [PMID: 26365165 PMCID: PMC4568515 DOI: 10.1038/srep14096] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/18/2015] [Indexed: 12/31/2022] Open
Abstract
The transition zone (TZ) of primary cilia serves as a diffusion barrier to regulate ciliogenesis and receptor localization for key signaling events such as sonic hedgehog signaling. Its gating mechanism is poorly understood due to the tiny volume accommodating a large number of ciliopathy-associated molecules. Here we performed stimulated emission depletion (STED) imaging of collective samples and recreated superresolved relative localizations of eight representative species of ciliary proteins using position averages and overlapped with representative electron microscopy (EM) images, defining an architectural foundation at the ciliary base. Upon this framework, transmembrane proteins TMEM67 and TCTN2 were accumulated at the same axial level as MKS1 and RPGRIP1L, suggesting that their regulation roles for tissue-specific ciliogenesis occur at a specific level of the TZ. CEP290 is surprisingly localized at a different axial level bridging the basal body (BB) and other TZ proteins. Upon this molecular architecture, two reservoirs of intraflagellar transport (IFT) particles, correlating with phases of ciliary growth, are present: one colocalized with the transition fibers (TFs) while the other situated beyond the distal edge of the TZ. Together, our results reveal an unprecedented structural framework of the TZ, facilitating our understanding in molecular screening and assembly at the ciliary base.
Collapse
|
14
|
TTBK2: a tau protein kinase beyond tau phosphorylation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:575170. [PMID: 25950000 PMCID: PMC4407412 DOI: 10.1155/2015/575170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 12/12/2022]
Abstract
Tau tubulin kinase 2 (TTBK2) is a kinase known to phosphorylate tau and tubulin. It has recently drawn much attention due to its involvement in multiple important cellular processes. Here, we review the current understanding of TTBK2, including its sequence, structure, binding sites, phosphorylation substrates, and cellular processes involved. TTBK2 possesses a casein kinase 1 (CK1) kinase domain followed by a ~900 amino acid segment, potentially responsible for its localization and substrate recruitment. It is known to bind to CEP164, a centriolar protein, and EB1, a microtubule plus-end tracking protein. In addition to autophosphorylation, known phosphorylation substrates of TTBK2 include tau, tubulin, CEP164, CEP97, and TDP-43, a neurodegeneration-associated protein. Mutations of TTBK2 are associated with spinocerebellar ataxia type 11. In addition, TTBK2 is essential for regulating the growth of axonemal microtubules in ciliogenesis. It also plays roles in resistance of cancer target therapies and in regulating glucose and GABA transport. Reported sites of TTBK2 localization include the centriole/basal body, the midbody, and possibly the mitotic spindles. Together, TTBK2 is a multifunctional kinase involved in important cellular processes and demands augmented efforts in investigating its functions.
Collapse
|
15
|
Henkel B, Drose DR, Ackels T, Oberland S, Spehr M, Neuhaus EM. Co-expression of anoctamins in cilia of olfactory sensory neurons. Chem Senses 2014; 40:73-87. [PMID: 25500808 DOI: 10.1093/chemse/bju061] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Vertebrates can sense and identify a vast array of chemical cues. The molecular machinery involved in chemodetection and transduction is expressed within the cilia of olfactory sensory neurons. Currently, there is only limited information available on the distribution and density of individual signaling components within the ciliary compartment. Using super-resolution microscopy, we show here that cyclic-nucleotide-gated channels and calcium-activated chloride channels of the anoctamin family are localized to discrete microdomains in the ciliary membrane. In addition to ANO2, a second anoctamin, ANO6, also localizes to ciliary microdomains. This observation, together with the fact that ANO6 and ANO2 co-localize, indicates a role for ANO6 in olfactory signaling. We show that both ANO2 and ANO6 can form heteromultimers and that this heteromerization alters the recombinant channels' physiological properties. Thus, we provide evidence for interaction of ANO2 and ANO6 in olfactory cilia, with possible physiological relevance for olfactory signaling.
Collapse
Affiliation(s)
- Bastian Henkel
- Department of Pharmacology and Toxicology, University Hospital Jena, Drackendorfer Strasse 1, 07747 Jena, Germany, Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany, FU Berlin, Fachbereich Biologie, Chemie und Pharmazie , Takustr. 3, 14195 Berlin, Germany and
| | - Daniela R Drose
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Tobias Ackels
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Sonja Oberland
- Department of Pharmacology and Toxicology, University Hospital Jena, Drackendorfer Strasse 1, 07747 Jena, Germany, Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany, FU Berlin, Fachbereich Biologie, Chemie und Pharmazie , Takustr. 3, 14195 Berlin, Germany and
| | - Marc Spehr
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Eva M Neuhaus
- Department of Pharmacology and Toxicology, University Hospital Jena, Drackendorfer Strasse 1, 07747 Jena, Germany, Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,
| |
Collapse
|
16
|
Abstract
Optical imaging is crucial for addressing fundamental problems in all areas of life science. With the use of confocal and two-photon fluorescence microscopy, complex dynamic structures and functions in a plethora of tissue and cell types have been visualized. However, the resolution of 'classical' optical imaging methods is poor due to the diffraction limit and does not allow resolution of the cellular microcosmos. On the other hand, the novel stimulated emission depletion (STED) microscopy technique, because of its targeted on/off-switching of fluorescence, is not hampered by a diffraction-limited resolution barrier. STED microscopy can therefore provide much sharper images, permitting nanoscale visualization by sequential imaging of individual-labelled biomolecules, which should allow previous findings to be reinvestigated and provide novel information. The aim of this review is to highlight promising developments in and applications of STED microscopy and their impact on unresolved issues in biomedical science.
Collapse
Affiliation(s)
- H Blom
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | | |
Collapse
|
17
|
Neupane B, Ligler FS, Wang G. Review of recent developments in stimulated emission depletion microscopy: applications on cell imaging. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:080901. [PMID: 25121478 DOI: 10.1117/1.jbo.19.8.080901] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/21/2014] [Indexed: 06/03/2023]
Abstract
Stimulated emission depletion (STED) microscopy is one type of far-field optical technique demonstrated to provide subdiffraction resolution. STED microscopy utilizes a donut-shaped depletion beam to limit the probe volume to be much smaller than a diffraction-limited spot. Resolutions as small as a few tens of nanometers laterally are reported for cell analysis. The different versions of STED microscopes are described and contrasted in terms of their applicability for biological imaging. Finally, we suggest likely avenues for improving the performance and increasing the utility of STED microscopy.
Collapse
Affiliation(s)
- Bhanu Neupane
- University of North Carolina at Chapel Hill and North Carolina State University, Department of Biomedical Engineering, Raleigh, North Carolina 27599-7115, United States
| | - Frances S Ligler
- University of North Carolina at Chapel Hill and North Carolina State University, Department of Biomedical Engineering, Raleigh, North Carolina 27599-7115, United States
| | - Gufeng Wang
- North Carolina State University, Department of Chemistry, Raleigh, North Carolina 27695-8204, United States
| |
Collapse
|
18
|
SAS-6 assembly templated by the lumen of cartwheel-less centrioles precedes centriole duplication. Dev Cell 2014; 30:238-45. [PMID: 25017693 DOI: 10.1016/j.devcel.2014.05.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/25/2014] [Accepted: 05/10/2014] [Indexed: 11/23/2022]
Abstract
Centrioles are 9-fold symmetric structures duplicating once per cell cycle. Duplication involves self-oligomerization of the centriolar protein SAS-6, but how the 9-fold symmetry is invariantly established remains unclear. Here, we found that SAS-6 assembly can be shaped by preexisting (or mother) centrioles. During S phase, SAS-6 molecules are first recruited to the proximal lumen of the mother centriole, adopting a cartwheel-like organization through interactions with the luminal wall, rather than via their self-oligomerization activity. The removal or release of luminal SAS-6 requires Plk4 and the cartwheel protein STIL. Abolishing either the recruitment or the removal of luminal SAS-6 hinders SAS-6 (or centriole) assembly at the outside wall of mother centrioles. After duplication, the lumen of engaged mother centrioles becomes inaccessible to SAS-6, correlating with a block for reduplication. These results lead to a proposed model that centrioles may duplicate via a template-based process to preserve their geometry and copy number.
Collapse
|
19
|
Nathwani BB, Miller CH, Yang TLT, Solimano JL, Liao JC. Morphological Differences of Primary Cilia Between Human Induced Pluripotent Stem Cells and Their Parental Somatic Cells. Stem Cells Dev 2014; 23:115-23. [DOI: 10.1089/scd.2013.0162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Bhavik B. Nathwani
- Department of Mechanical Engineering, Columbia University, New York, New York
| | - Christine H. Miller
- Department of Biomedical Engineering, Columbia University, New York, New York
| | - Tung-Lin Tony Yang
- Department of Mechanical Engineering, Columbia University, New York, New York
| | | | - Jung-Chi Liao
- Department of Mechanical Engineering, Columbia University, New York, New York
- Department of Biomedical Engineering, Columbia University, New York, New York
| |
Collapse
|
20
|
Truong-Quang BA, Lenne PF. Membrane microdomains: from seeing to understanding. FRONTIERS IN PLANT SCIENCE 2014; 5:18. [PMID: 24600455 PMCID: PMC3927121 DOI: 10.3389/fpls.2014.00018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/15/2014] [Indexed: 05/08/2023]
Abstract
The plasma membrane is a composite material, which forms a semi-permeable barrier and an interface for communication between the intracellular and extracellular environments. While the existence of membrane microdomains with nanoscale organization has been proved by the application of numerous biochemical and physical methods, direct observation of these heterogeneities using optical microscopy has remained challenging for decades, partly due to the optical diffraction limit, which restricts the resolution to ~200 nm. During the past years, new optical methods which circumvent this fundamental limit have emerged. Not only do these techniques allow direct visualization, but also quantitative characterization of nanoscopic structures. We discuss how these emerging optical methods have refined our knowledge of membrane microdomains and how they may shed light on the basic principles of the mesoscopic membrane organization.
Collapse
Affiliation(s)
| | - Pierre-François Lenne
- *Correspondence: Pierre-François Lenne, Developmental Biology Institute of Marseilles, UMR 7288 CNRS, Aix-Marseille Université, 13288 Marseille Cedex 9, France e-mail:
| |
Collapse
|
21
|
Chacko JV, Zanacchi FC, Diaspro A. Probing cytoskeletal structures by coupling optical superresolution and AFM techniques for a correlative approach. Cytoskeleton (Hoboken) 2013; 70:729-40. [PMID: 24027190 PMCID: PMC4265841 DOI: 10.1002/cm.21139] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/28/2013] [Accepted: 09/01/2013] [Indexed: 01/14/2023]
Abstract
In this article, we describe and show the application of some of the most advanced fluorescence superresolution techniques, STED AFM and STORM AFM microscopy towards imaging of cytoskeletal structures, such as microtubule filaments. Mechanical and structural properties can play a relevant role in the investigation of cytoskeletal structures of interest, such as microtubules, that provide support to the cell structure. In fact, the mechanical properties, such as the local stiffness and the elasticity, can be investigated by AFM force spectroscopy with tens of nanometers resolution. Force curves can be analyzed in order to obtain the local elasticity (and the Young's modulus calculation by fitting the force curves from every pixel of interest), and the combination with STED/STORM microscopy integrates the measurement with high specificity and yields superresolution structural information. This hybrid modality of superresolution-AFM working is a clear example of correlative multimodal microscopy.
Collapse
Affiliation(s)
- Jenu Varghese Chacko
- Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy; Dipartimento di Fisica, Università degli Studi di Genova, Genova, Italy
| | | | | |
Collapse
|
22
|
|