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Helmold BR, Ahrens A, Fitzgerald Z, Ozdinler PH. Spastin and alsin protein interactome analyses begin to reveal key canonical pathways and suggest novel druggable targets. Neural Regen Res 2025; 20:725-739. [PMID: 38886938 PMCID: PMC11433914 DOI: 10.4103/nrr.nrr-d-23-02068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 06/20/2024] Open
Abstract
Developing effective and long-term treatment strategies for rare and complex neurodegenerative diseases is challenging. One of the major roadblocks is the extensive heterogeneity among patients. This hinders understanding the underlying disease-causing mechanisms and building solutions that have implications for a broad spectrum of patients. One potential solution is to develop personalized medicine approaches based on strategies that target the most prevalent cellular events that are perturbed in patients. Especially in patients with a known genetic mutation, it may be possible to understand how these mutations contribute to problems that lead to neurodegeneration. Protein-protein interaction analyses offer great advantages for revealing how proteins interact, which cellular events are primarily involved in these interactions, and how they become affected when key genes are mutated in patients. This line of investigation also suggests novel druggable targets for patients with different mutations. Here, we focus on alsin and spastin, two proteins that are identified as "causative" for amyotrophic lateral sclerosis and hereditary spastic paraplegia, respectively, when mutated. Our review analyzes the protein interactome for alsin and spastin, the canonical pathways that are primarily important for each protein domain, as well as compounds that are either Food and Drug Administration-approved or are in active clinical trials concerning the affected cellular pathways. This line of research begins to pave the way for personalized medicine approaches that are desperately needed for rare neurodegenerative diseases that are complex and heterogeneous.
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Affiliation(s)
- Benjamin R. Helmold
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Angela Ahrens
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zachary Fitzgerald
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - P. Hande Ozdinler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Feinberg School of Medicine, Les Turner ALS Center at Northwestern University, Chicago, IL, USA
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2
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Jiang F, Yu M, Liang Y, Ding K, Wang Y. Discovery of Novel Diaryl-Substituted Fused Heterocycles Targeting Katanin and Tubulin with Potent Antitumor and Antimultidrug Resistance Efficacy. J Med Chem 2024; 67:12118-12142. [PMID: 38996194 DOI: 10.1021/acs.jmedchem.4c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Disrupting microtubule dynamics has emerged as a promising strategy for cancer treatment. However, drug resistance remains a challenge hindering the development of microtubule-targeting agents. In this work, a novel class of diaryl substituted fused heterocycles were designed, synthesized, and evaluated, which were demonstrated as effective dual katanin and tubulin regulators with antitumor activity. Following three rounds of stepwise optimization, compound 21b, featuring a 3H-imidazo[4,5-b]pyridine core, displayed excellent targeting capabilities on katanin and tubulin, along with notable antiproliferative and antimetastatic effects. Mechanistic studies revealed that 21b disrupts the microtubule network in tumor cells, leading to G2/M cell cycle arrest and apoptosis induction. Importantly, 21b exhibited significant inhibition of tumor growth in MDA-MB-231 and A549/T xenograft tumor models without evident toxicity and side effects. In conclusion, compound 21b presents a novel mechanism for disrupting microtubule dynamics, warranting further investigation as a dual-targeted antitumor agent with potential antimultidrug resistance properties.
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Affiliation(s)
- Fuhao Jiang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Min Yu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yuru Liang
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kuiling Ding
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yang Wang
- School of Pharmacy, Fudan University, Shanghai 201203, China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
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3
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Lian YL, Lin YC. The emerging tools for precisely manipulating microtubules. Curr Opin Cell Biol 2024; 88:102360. [PMID: 38640790 DOI: 10.1016/j.ceb.2024.102360] [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: 11/28/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/21/2024]
Abstract
Cells generate a highly diverse microtubule network to carry out different activities. This network is comprised of distinct tubulin isotypes, tubulins with different post-translational modifications, and many microtubule-based structures. Defects in this complex system cause numerous human disorders. However, how different microtubule subtypes in this network regulate cellular architectures and activities remains largely unexplored. Emerging tools such as photosensitive pharmaceuticals, chemogenetics, and optogenetics enable the spatiotemporal manipulation of structures, dynamics, post-translational modifications, and cross-linking with actin filaments in target microtubule subtypes. This review summarizes the design rationale and applications of these new approaches and aims to provide a roadmap for researchers navigating the intricacies of microtubule dynamics and their post-translational modifications in cellular contexts, thereby opening new avenues for therapeutic interventions.
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Affiliation(s)
- Yen-Ling Lian
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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4
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Xie S, Yang Y, Jin Z, Liu X, Zhang S, Su N, Liu J, Li C, Zhang D, Gao L, Yang Z. Mouse KL2 is a unique MTSE involved in chromosome-based spindle organization and regulated by multiple kinases during female meiosis. J Biomed Res 2024; 38:1-15. [PMID: 38808565 PMCID: PMC11461529 DOI: 10.7555/jbr.37.20230290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/30/2024] Open
Abstract
Microtubule-severing enzymes (MTSEs) play important roles in mitosis and meiosis of the primitive organisms. However, no studies have assessed their roles in mammalian meiosis of females, whose abnormality accounts for over 80% of the cases of gamete-originated human reproductive disease. In the current study, we reported that katanin-like 2 (KL2) was the only MTSE concentrating at chromosomes. Furthermore, the knockdown of KL2 significantly reduced chromosome-based increase in the microtubule (MT) polymer, increased aberrant kinetochore-MT (K-MT) attachment, delayed meiosis, and severely affected normal fertility. Importantly, we demonstrated that the inhibition of aurora B, a key kinase for correcting aberrant K-MT attachment, eliminated KL2 from chromosomes completely. KL2 also interacted with phosphorylated eukaryotic elongation factor-2 kinase; they competed for chromosome binding. We also observed that the phosphorylated KL2 was localized at spindle poles, and that KL2 phosphorylation was regulated by extracellular signal-regulated kinase 1/2. In summary, our study reveals a novel function of MTSEs in mammalian female meiosis and demonstrates that multiple kinases coordinate to regulate the levels of KL2 at chromosomes.
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Affiliation(s)
- Shiya Xie
- State Key Lab of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Central Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
- Department of Gynaecology and Obstetrics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Yanjie Yang
- State Key Lab of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Central Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
- Department of Gynaecology and Obstetrics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Zhen Jin
- Center for Reproductive Medicine, Department of Gynecology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
- Center for Reproductive Medicine, Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Xiaocong Liu
- Laboratory Department of Shihezi People's Hospital, Shihezi, Xinjiang 832099, China
| | - Shuping Zhang
- State Key Lab of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ning Su
- State Key Lab of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jiaqi Liu
- State Key Lab of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Congrong Li
- State Key Lab of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Dong Zhang
- State Key Lab of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Gynaecology and Obstetrics, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Leilei Gao
- Center for Reproductive Medicine, Department of Gynecology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Zhixia Yang
- Central Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
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5
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Beaumale E, Van Hove L, Pintard L, Joly N. Microtubule-binding domains in Katanin p80 subunit are essential for severing activity in C. elegans. J Cell Biol 2024; 223:e202308023. [PMID: 38329452 PMCID: PMC10853069 DOI: 10.1083/jcb.202308023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/22/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
Microtubule-severing enzymes (MSEs), such as Katanin, Spastin, and Fidgetin play essential roles in cell division and neurogenesis. They damage the microtubule (MT) lattice, which can either destroy or amplify the MT cytoskeleton, depending on the cellular context. However, little is known about how they interact with their substrates. We have identified the microtubule-binding domains (MTBD) required for Katanin function in C. elegans. Katanin is a heterohexamer of dimers containing a catalytic subunit p60 and a regulatory subunit p80, both of which are essential for female meiotic spindle assembly. Here, we report that p80-like(MEI-2) dictates Katanin binding to MTs via two MTBDs composed of basic patches. Substituting these patches reduces Katanin binding to MTs, compromising its function in female meiotic-spindle assembly. Structural alignments of p80-like(MEI-2) with p80s from different species revealed that the MTBDs are evolutionarily conserved, even if the specific amino acids involved vary. Our findings highlight the critical importance of the regulatory subunit (p80) in providing MT binding to the Katanin complex.
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Affiliation(s)
- Eva Beaumale
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Lucie Van Hove
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Lionel Pintard
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Nicolas Joly
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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6
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Smart K, Sharp DJ. The fidgetin family: Shaking things up among the microtubule-severing enzymes. Cytoskeleton (Hoboken) 2024; 81:151-166. [PMID: 37823563 DOI: 10.1002/cm.21799] [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: 07/14/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
The microtubule cytoskeleton is required for several crucial cellular processes, including chromosome segregation, cell polarity and orientation, and intracellular transport. These functions rely on microtubule stability and dynamics, which are regulated by microtubule-binding proteins (MTBPs). One such type of regulator is the microtubule-severing enzymes (MSEs), which are ATPases Associated with Diverse Cellular Activities (AAA+ ATPases). The most recently identified family are the fidgetins, which contain three members: fidgetin, fidgetin-like 1 (FL1), and fidgetin-like 2 (FL2). Of the three known MSE families, the fidgetins have the most diverse range of functions in the cell, spanning mitosis/meiosis, development, cell migration, DNA repair, and neuronal function. Furthermore, they offer intriguing novel therapeutic targets for cancer, cardiovascular disease, and wound healing. In the two decades since their first report, there has been great progress in our understanding of the fidgetins; however, there is still much left unknown about this unusual family. This review aims to consolidate the present body of knowledge of the fidgetin family of MSEs and to inspire deeper exploration into the fidgetins and the MSEs as a whole.
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Affiliation(s)
- Karishma Smart
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David J Sharp
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
- Microcures, Inc., Bronx, New York, USA
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7
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Danziger M, Xu F, Noble H, Yang P, Roque DM. Tubulin Complexity in Cancer and Metastasis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1452:21-35. [PMID: 38805123 DOI: 10.1007/978-3-031-58311-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Tubulin plays a fundamental role in cellular function and as the subject for microtubule-active agents in the treatment of ovarian cancer. Microtubule-binding proteins (e.g., tau, MAP1/2/4, EB1, CLIP, TOG, survivin, stathmin) and posttranslational modifications (e.g., tyrosination, deglutamylation, acetylation, glycation, phosphorylation, polyamination) further diversify tubulin functionality and may permit additional opportunities to understand microtubule behavior in disease and to develop microtubule-modifying approaches to combat ovarian cancer. Tubulin-based structures that project from suspended ovarian cancer cells known as microtentacles may contribute to metastatic potential of ovarian cancer cells and could represent an exciting novel therapeutic target.
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Affiliation(s)
- Michael Danziger
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Fuhua Xu
- Division of Gynecologic Oncology, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Helen Noble
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Peixin Yang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dana M Roque
- Division of Gynecologic Oncology, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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8
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Gibson C, Jönsson H, Spelman TA. Mean-field theory approach to three-dimensional nematic phase transitions in microtubules. Phys Rev E 2023; 108:064414. [PMID: 38243538 DOI: 10.1103/physreve.108.064414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/16/2023] [Indexed: 01/21/2024]
Abstract
Microtubules are dynamic intracellular fibers that have been observed experimentally to undergo spontaneous self-alignment. We formulate a three-dimensional (3D) mean-field theory model to analyze the nematic phase transition of microtubules growing and interacting within a 3D space, then make a comparison with computational simulations. We identify a control parameter G_{eff} and predict a unique critical value G_{eff}=1.56 for which a phase transition can occur. Furthermore, we show both analytically and using simulations that this predicted critical value does not depend on the presence of zippering. The mean-field theory developed here provides an analytical estimate of microtubule patterning characteristics without running time-consuming simulations and is a step towards bridging scales from microtubule behavior to multicellular simulations.
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Affiliation(s)
- Cameron Gibson
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, United Kingdom
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843, USA
| | - Henrik Jönsson
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, United Kingdom
- Centre for Environmental and Climate Science, Lund University, SE-223 62 Lund, Sweden
| | - Tamsin A Spelman
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, United Kingdom
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9
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Ma C, Wang J, Tu Q, Bo W, Hu Z, Zhuo R, Wu R, Dong Z, Qiang L, Liu Y, Liu M. Fidgetin interacting with microtubule end binding protein EB3 affects axonal regrowth in spinal cord injury. Neural Regen Res 2023; 18:2727-2732. [PMID: 37449637 DOI: 10.4103/1673-5374.373716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Fidgetin, a microtubule-severing enzyme, regulates neurite outgrowth, axonal regeneration, and cell migration by trimming off the labile domain of microtubule polymers. Because maintenance of the microtubule labile domain is essential for axon initiation, elongation, and navigation, it is of interest to determine whether augmenting the microtubule labile domain via depletion of fidgetin serves as a therapeutic approach to promote axonal regrowth in spinal cord injury. In this study, we constructed rat models of spinal cord injury and sciatic nerve injury. Compared with spinal cord injury, we found that expression level of tyrosinated microtubules in the labile portion of microtubules continuously increased, whereas fidgetin decreased after peripheral nerve injury. Depletion of fidgetin enhanced axon regeneration after spinal cord injury, whereas expression level of end binding protein 3 (EB3) markedly increased. Next, we performed RNA interference to knockdown EB3 or fidgetin. We found that deletion of EB3 did not change fidgetin expression. Conversely, deletion of fidgetin markedly increased expression of tyrosinated microtubules and EB3. Deletion of fidgetin increased the amount of EB3 at the end of neurites and thereby increased the level of tyrosinated microtubules. Finally, we deleted EB3 and overexpressed fidgetin. We found that fidgetin trimmed tyrosinated tubulins by interacting with EB3. When fidgetin was deleted, the labile portion of microtubules was elongated, and as a result the length of axons and number of axon branches were increased. These findings suggest that fidgetin can be used as a novel therapeutic target to promote axonal regeneration after spinal cord injury. Furthermore, they reveal an innovative mechanism by which fidgetin preferentially severs labile microtubules.
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Affiliation(s)
- Chao Ma
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University; Medical School of Nantong University, Nantong, Jiangsu Province, China
| | - Junpei Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Qifeng Tu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Weijuan Bo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Zunlu Hu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Run Zhuo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Ronghua Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Zhangji Dong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Liang Qiang
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Yan Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Mei Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
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10
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de Keijzer J, van Spoordonk R, van der Meer-Verweij JE, Janson M, Ketelaar T. Kinesin-4 optimizes microtubule orientations for responsive tip growth guidance in moss. J Cell Biol 2023; 222:e202202018. [PMID: 37389658 PMCID: PMC10316633 DOI: 10.1083/jcb.202202018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/18/2023] [Accepted: 06/06/2023] [Indexed: 07/01/2023] Open
Abstract
Tip-growing cells of, amongst others, plants and fungi secrete wall materials in a highly polarized fashion for fast and efficient colonization of the environment. A polarized microtubule cytoskeleton, in which most microtubule ends are directed toward the growing apex, has been implicated in directing growth. Its organizing principles, in particular regarding maintenance of network unipolarity, have remained elusive. We show that a kinesin-4 protein, hitherto best known for a role in cytokinesis, suppresses encounters between antiparallel microtubules. Without this activity, microtubules hyper-aligned along the growth axis and increasingly grew away from the apex. Cells themselves displayed an overly straight growth path and a delayed gravitropic response. This result revealed conflicting systemic needs for a stable growth direction and an ability to change course in response to extracellular cues. Thus, the use of selective inhibition of microtubule growth at antiparallel overlaps constitutes a new organizing principle within a unipolar microtubule array.
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Affiliation(s)
- Jeroen de Keijzer
- Laboratory of Cell Biology, Wageningen University, Wageningen, Netherlands
| | | | | | - Marcel Janson
- Laboratory of Cell Biology, Wageningen University, Wageningen, Netherlands
| | - Tijs Ketelaar
- Laboratory of Cell Biology, Wageningen University, Wageningen, Netherlands
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11
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Kusch S, Singh M, Thieron H, Spanu PD, Panstruga R. Site-specific analysis reveals candidate cross-kingdom small RNAs, tRNA and rRNA fragments, and signs of fungal RNA phasing in the barley-powdery mildew interaction. MOLECULAR PLANT PATHOLOGY 2023; 24:570-587. [PMID: 36917011 DOI: 10.1111/mpp.13324] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 05/18/2023]
Abstract
The establishment of host-microbe interactions requires molecular communication between both partners, which may involve the mutual transfer of noncoding small RNAs. Previous evidence suggests that this is also true for powdery mildew disease in barley, which is caused by the fungal pathogen Blumeria hordei. However, previous studies lacked spatial resolution regarding the accumulation of small RNAs upon host infection by B. hordei. Here, we analysed site-specific small RNA repertoires in the context of the barley-B. hordei interaction. To this end, we dissected infected leaves into separate fractions representing different sites that are key to the pathogenic process: epiphytic fungal mycelium, infected plant epidermis, isolated haustoria, a vesicle-enriched fraction from infected epidermis, and extracellular vesicles. Unexpectedly, we discovered enrichment of specific 31-33-base 5'-terminal fragments of barley 5.8S ribosomal RNA in extracellular vesicles and infected epidermis, as well as particular B. hordei transfer RNA fragments in haustoria. We describe canonical small RNAs from both the plant host and the fungal pathogen that may confer cross-kingdom RNA interference activity. Interestingly, we found first evidence of phased small interfering RNAs in B. hordei, a feature usually attributed to plants, which may be associated with the posttranscriptional control of fungal coding genes, pseudogenes, and transposable elements. Our data suggest a key and possibly site-specific role for cross-kingdom RNA interference and noncoding RNA fragments in the host-pathogen communication between B. hordei and its host barley.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Mansi Singh
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Pietro D Spanu
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
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12
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Lindsay KA, Abdelhamid N, Kahawatte S, Dima RI, Sackett DL, Finegan TM, Ross JL. A Tale of 12 Tails: Katanin Severing Activity Affected by Carboxy-Terminal Tail Sequences. Biomolecules 2023; 13:biom13040620. [PMID: 37189368 DOI: 10.3390/biom13040620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
In cells, microtubule location, length, and dynamics are regulated by a host of microtubule-associated proteins and enzymes that read where to bind and act based on the microtubule “tubulin code,” which is predominantly encoded in the tubulin carboxy-terminal tail (CTT). Katanin is a highly conserved AAA ATPase enzyme that binds to the tubulin CTTs to remove dimers and sever microtubules. We have previously demonstrated that short CTT peptides are able to inhibit katanin severing. Here, we examine the effects of CTT sequences on this inhibition activity. Specifically, we examine CTT sequences found in nature, alpha1A (TUBA1A), detyrosinated alpha1A, Δ2 alpha1A, beta5 (TUBB/TUBB5), beta2a (TUBB2A), beta3 (TUBB3), and beta4b (TUBB4b). We find that these natural CTTs have distinct abilities to inhibit, most noticeably beta3 CTT cannot inhibit katanin. Two non-native CTT tail constructs are also unable to inhibit, despite having 94% sequence identity with alpha1 or beta5 sequences. Surprisingly, we demonstrate that poly-E and poly-D peptides are capable of inhibiting katanin significantly. An analysis of the hydrophobicity of the CTT constructs indicates that more hydrophobic polypeptides are less inhibitory than more polar polypeptides. These experiments not only demonstrate inhibition, but also likely interaction and targeting of katanin to these various CTTs when they are part of a polymerized microtubule filament.
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13
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Ikeda R, Sakagami T, Hamada M, Sakamoto T, Hatabu T, Saito N, Ando M. De novo transcriptome analysis of the centrohelid Raphidocystis contractilis to identify genes involved in microtubule-based motility. J Eukaryot Microbiol 2023; 70:e12955. [PMID: 36409155 DOI: 10.1111/jeu.12955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/17/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
The centrohelid heliozoan Raphidocystis contractilis has many radiating axopodia, each containing axopodial microtubules. The axopodia show rapid contraction at nearly a video rate (30 frames per second) in response to mechanical stimuli. The axopodial contraction is accompanied by cytoskeletal microtubule depolymerization, but the molecular mechanism of this phenomenon has not been elucidated. In this study, we performed de novo transcriptome sequencing of R. contractilis to identify genes involved in microtubule dynamics such as the rapid axopodial contraction. The transcriptome sequencing generated 7.15-Gbp clean reads in total, which were assembled as 31,771 unigenes. Using the obtained gene sets, we identified several microtubule-severing proteins which might be involved in the rapid axopodial contraction, and kinesin-like genes that occur in gene duplication. On the other hand, some genes for microtubule motor proteins involved in the formation and motility of flagella were not found in R. contractilis, suggesting that the gene repertoire of R. contractilis reflected the morphological features of nonflagellated protists. Our transcriptome analysis provides basic information for the analysis of the molecular mechanism underlying microtubule dynamics in R. contractilis.
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Affiliation(s)
- Risa Ikeda
- Laboratory of Cell Physiology, Department of Science Education, Faculty of Education, Okayama University, Okayama, Japan.,Laboratory of Animal Physiology and Pharmacology, Department of Animal Science, Faculty of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Tosuke Sakagami
- Laboratory of Cell Physiology, Department of Science Education, Faculty of Education, Okayama University, Okayama, Japan.,Laboratory of Animal Physiology and Pharmacology, Department of Animal Science, Faculty of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Mayuko Hamada
- Ushimado Marine Institute, Faculty of Science and Technology, Okayama University, Okayama, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Faculty of Science and Technology, Okayama University, Okayama, Japan
| | - Toshimitsu Hatabu
- Laboratory of Animal Physiology and Pharmacology, Department of Animal Science, Faculty of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Noboru Saito
- Laboratory of Animal Physiology and Pharmacology, Department of Animal Science, Faculty of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Motonori Ando
- Laboratory of Cell Physiology, Department of Science Education, Faculty of Education, Okayama University, Okayama, Japan.,Laboratory of Animal Physiology and Pharmacology, Department of Animal Science, Faculty of Environmental and Life Science, Okayama University, Okayama, Japan
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14
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Microtubule-severing protein Fidgetin-like 1 promotes spindle organization during meiosis of mouse oocytes. ZYGOTE 2022; 30:872-881. [PMID: 36148793 DOI: 10.1017/s0967199422000417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Microtubule-severing proteins (MTSPs) play important roles in mitosis and interphase. However, to the best of our knowledge, no previous studies have evaluated the role of MTSPs in female meiosis in mammals. It was found that FIGNL1, a member of MTSPs, was predominantly expressed in mouse oocytes and distributed at the spindle poles during meiosis in the present study. FIGNL1 was co-localized and interacted with γ-tubulin, an important component of the microtubule tissue centre (MTOC). Fignl1 knockdown by specific small interfering RNA caused spindle defects characterized by an abnormal length:width ratio and decreased microtubule density, which consequently led to aberrant chromosome arrangement, oocyte maturation and fertilization obstacles. In conclusion, the present results suggested that FIGNL1 may be an essential factor in oocyte maturation by influencing the meiosis process via the formation of spindles.
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15
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Messina G, Prozzillo Y, Monache FD, Santopietro MV, Dimitri P. Evolutionary conserved relocation of chromatin remodeling complexes to the mitotic apparatus. BMC Biol 2022; 20:172. [PMID: 35922843 PMCID: PMC9351137 DOI: 10.1186/s12915-022-01365-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 01/02/2023] Open
Abstract
Background ATP-dependent chromatin remodeling complexes are multi-protein machines highly conserved across eukaryotic genomes. They control sliding and displacing of the nucleosomes, modulating histone-DNA interactions and making nucleosomal DNA more accessible to specific binding proteins during replication, transcription, and DNA repair, which are processes involved in cell division. The SRCAP and p400/Tip60 chromatin remodeling complexes in humans and the related Drosophila Tip60 complex belong to the evolutionary conserved INO80 family, whose main function is promoting the exchange of canonical histone H2A with the histone variant H2A in different eukaryotic species. Some subunits of these complexes were additionally shown to relocate to the mitotic apparatus and proposed to play direct roles in cell division in human cells. However, whether this phenomenon reflects a more general function of remodeling complex components and its evolutionary conservation remains unexplored. Results We have combined cell biology, reverse genetics, and biochemical approaches to study the subcellular distribution of a number of subunits belonging to the SRCAP and p400/Tip60 complexes and assess their involvement during cell division progression in HeLa cells. Interestingly, beyond their canonical chromatin localization, the subunits under investigation accumulate at different sites of the mitotic apparatus (centrosomes, spindle, and midbody), with their depletion yielding an array of aberrant outcomes of mitosis and cytokinesis, thus causing genomic instability. Importantly, this behavior was conserved by the Drosophila melanogaster orthologs tested, despite the evolutionary divergence between fly and humans has been estimated at approximately 780 million years ago. Conclusions Overall, our results support the existence of evolutionarily conserved diverse roles of chromatin remodeling complexes, whereby subunits of the SRCAP and p400/Tip60 complexes relocate from the interphase chromatin to the mitotic apparatus, playing moonlighting functions required for proper execution of cell division. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01365-5.
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Affiliation(s)
- Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy. .,Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Rome, Italy.
| | - Yuri Prozzillo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Francesca Delle Monache
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | | | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.
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16
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Peyrégne S, Kelso J, Peter BM, Pääbo S. The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals. eLife 2022; 11:e75464. [PMID: 35816093 PMCID: PMC9273211 DOI: 10.7554/elife.75464] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/14/2022] [Indexed: 12/13/2022] Open
Abstract
Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
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17
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Costa AC, Sousa MM. The Role of Spastin in Axon Biology. Front Cell Dev Biol 2022; 10:934522. [PMID: 35865632 PMCID: PMC9294387 DOI: 10.3389/fcell.2022.934522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/07/2022] [Indexed: 12/05/2022] Open
Abstract
Neurons are highly polarized cells with elaborate shapes that allow them to perform their function. In neurons, microtubule organization—length, density, and dynamics—are essential for the establishment of polarity, growth, and transport. A mounting body of evidence shows that modulation of the microtubule cytoskeleton by microtubule-associated proteins fine tunes key aspects of neuronal cell biology. In this respect, microtubule severing enzymes—spastin, katanin and fidgetin—a group of microtubule-associated proteins that bind to and generate internal breaks in the microtubule lattice, are emerging as key modulators of the microtubule cytoskeleton in different model systems. In this review, we provide an integrative view on the latest research demonstrating the key role of spastin in neurons, specifically in the context of axonal cell biology. We focus on the function of spastin in the regulation of microtubule organization, and axonal transport, that underlie its importance in the intricate control of axon growth, branching and regeneration.
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Affiliation(s)
- Ana Catarina Costa
- Nerve Regeneration Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação Em Saúde (i3S), University of Porto, Porto, Portugal
- Graduate Program in Molecular and Cell Biology, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- *Correspondence: Ana Catarina Costa, ; Monica Mendes Sousa,
| | - Monica Mendes Sousa
- Nerve Regeneration Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação Em Saúde (i3S), University of Porto, Porto, Portugal
- *Correspondence: Ana Catarina Costa, ; Monica Mendes Sousa,
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18
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Wu Z, Guo M, Yang J, Xiao Y, Liu W. Katanin subunits p60 and p80, potential biomarkers for papillary thyroid carcinoma to distinguish nodular goiter: STROBE. Medicine (Baltimore) 2022; 101:e29402. [PMID: 35713446 PMCID: PMC9276123 DOI: 10.1097/md.0000000000029402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
Katanin subunits p60 and p80 are involved in microtubule-mediated cytoskeletal organization during cell division. Their aberrant expression has been found in prostate, breast, and non-small cell lung (NSCLC) cancers. It has recently been reported that compared with adjacent papillary thyroid carcinoma (PTC) tissues, both are highly expressed in tumor tissues. Here, we investigated whether katanin subunits p60 and p80 can be used as potential biomarkers for PTC to distinguish nodular goiter (NG).Immunohistochemistry was performed to investigate the expression of katanin subunits p60 and p80 in the tissues of 97 cases of PTC and NG. This cohort included 87 cases with PTC (74 classical or conventional (CPTC) and 13 follicular (FVPTC) variants) and 10 cases with NG.We found that katanin subunits p60 and p80 were expressed in PTC, but not in NG. The cutoff values of katanin p60 and p80 for PTC were 22.43% and 0.83%, respectively. The katanin subunit p60 was significantly associated with lymph node metastasis. Katanin subunit p80 was more highly expressed in CPTC than in FVPTC. The expression of the katanin subunit p60 was positively correlated with the expression of katanin p80 in PTC. Importantly, we found that overexpression of katanin p60 increased the expression of katanin p80 in a human papillary thyroid carcinoma KTC-1 cell line, which further supports the existence of katanin p60 and p80 feedback loops.Our results indicate that katanin subunits p60 and p80 may be used as potential PTC biomarkers to distinguish NG and may be novel therapeutic targets for PTC.
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Affiliation(s)
- Zhangming Wu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Miao Guo
- Department of Clinical Laboratory, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Jing Yang
- Department of Pathology, College of Basic Medical Sciences of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Yanjie Xiao
- Department of Epidemiology, Public Health College of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Wei Liu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, Liaoning, China
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19
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Miao R, Siao W, Zhang N, Lei Z, Lin D, Bhalerao RP, Lu C, Xu W. Katanin-Dependent Microtubule Ordering in Association with ABA Is Important for Root Hydrotropism. Int J Mol Sci 2022; 23:ijms23073846. [PMID: 35409205 PMCID: PMC8999029 DOI: 10.3390/ijms23073846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
Root hydrotropism refers to root directional growth toward soil moisture. Cortical microtubule arrays are essential for determining the growth axis of the elongating cells in plants. However, the role of microtubule reorganization in root hydrotropism remains elusive. Here, we demonstrate that the well-ordered microtubule arrays and the microtubule-severing protein KATANIN (KTN) play important roles in regulating root hydrotropism in Arabidopsis. We found that the root hydrotropic bending of the ktn1 mutant was severely attenuated but not root gravitropism. After hydrostimulation, cortical microtubule arrays in cells of the elongation zone of wild-type (WT) Col-0 roots were reoriented from transverse into an oblique array along the axis of cell elongation, whereas the microtubule arrays in the ktn1 mutant remained in disorder. Moreover, we revealed that abscisic acid (ABA) signaling enhanced the root hydrotropism of WT and partially rescued the oryzalin (a microtubule destabilizer) alterative root hydrotropism of WT but not ktn1 mutants. These results suggest that katanin-dependent microtubule ordering is required for root hydrotropism, which might work downstream of ABA signaling pathways for plant roots to search for water.
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Affiliation(s)
- Rui Miao
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Resource and Environment, Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China; (R.M.); (W.S.); (N.Z.); (Z.L.)
| | - Wei Siao
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Resource and Environment, Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China; (R.M.); (W.S.); (N.Z.); (Z.L.)
| | - Na Zhang
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Resource and Environment, Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China; (R.M.); (W.S.); (N.Z.); (Z.L.)
| | - Zuliang Lei
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Resource and Environment, Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China; (R.M.); (W.S.); (N.Z.); (Z.L.)
| | - Deshu Lin
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China;
| | - Rishikesh P. Bhalerao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umea, Sweden
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China;
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Resource and Environment, Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China; (R.M.); (W.S.); (N.Z.); (Z.L.)
- Correspondence:
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20
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Omolaoye TS, Hachim MY, du Plessis SS. Using publicly available transcriptomic data to identify mechanistic and diagnostic biomarkers in azoospermia and overall male infertility. Sci Rep 2022; 12:2584. [PMID: 35173218 PMCID: PMC8850557 DOI: 10.1038/s41598-022-06476-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
Azoospermia, which is the absence of spermatozoa in an ejaculate occurring due to defects in sperm production, or the obstruction of the reproductive tract, affects about 1% of all men and is prevalent in up to 10–15% of infertile males. Conventional semen analysis remains the gold standard for diagnosing and treating male infertility; however, advances in molecular biology and bioinformatics now highlight the insufficiency thereof. Hence, the need to widen the scope of investigating the aetiology of male infertility stands pertinent. The current study aimed to identify common differentially expressed genes (DEGs) that might serve as potential biomarkers for non-obstructive azoospermia (NOA) and overall male infertility. DEGs across different datasets of transcriptomic profiling of testis from human patients with different causes of infertility/ impaired spermatogenesis and/or azoospermia were explored using the gene expression omnibus (GEO) database. Following the search using the GEOquery, 30 datasets were available, with 5 meeting the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEO2R tool. The annotated genes of the probes in each dataset were intersected with DEGs from all other datasets. Enriched Ontology Clustering for the identified genes was performed using Metascape to explore the possible connection or interaction between the genes. Twenty-five DEGs were shared between most of the datasets, which might indicate their role in the pathogenesis of male infertility. Of the 25 DEGs, eight genes (THEG, SPATA20, ROPN1L, GSTF1, TSSK1B, CABS1, ADAD1, RIMBP3) are either involved in the overall spermatogenic processes or at specific phases of spermatogenesis. We hypothesize that alteration in the expression of these genes leads to impaired spermatogenesis and, ultimately, male infertility. Thus, these genes can be used as potential biomarkers for the early detection of NOA.
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Affiliation(s)
- Temidayo S Omolaoye
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Mahmood Yaseen Hachim
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.
| | - Stefan S du Plessis
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.,Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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21
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Li CR, Wang RL, Xie SY, Li YR, Gao LL, Yang ZX, Zhang D. Fidgetin knockdown and knockout influences female reproduction distinctly in mice. J Biomed Res 2022; 36:269-279. [PMID: 35965436 PMCID: PMC9376731 DOI: 10.7555/jbr.36.20220086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Microtubule-severing proteins (MTSPs), are a family of proteins which use adenosine triphosphate to sever microtubules. MTSPs have been shown to play an important role in multiple microtubule-involved cellular processes. One member of this family, fidgetin (FIGN), is also involved in male fertility; however, no studies have explored its roles in female fertility. In this study, we found mouse fidgetin is rich within oocyte zona pellucida (ZP) and is the only MTSP member to do so. Fidgetin also appears to interact with all three ZP proteins. These findings prompted us to propose that fidgetin might prevent polyspermy. Results from in vitro maturation oocytes analysis showed that fidgetin knockdown did cause polyspermy. We then deleted all three fidgetin isoforms with CRISPR/Cas9 technologies; however, female mice remained healthy and with normal fertility. Of all mouse MTSPs, only the mRNA level of fidgetin-like 1 (FIGNL1) significantly increased. Therefore, we assert that fidgetin-like 1 compensates fidgetin's roles in fidgetin knockout female mice.
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Affiliation(s)
- Cong-Rong Li
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ruo-Lei Wang
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Shi-Ya Xie
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yan-Ru Li
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Lei-Lei Gao
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhi-Xia Yang
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Dong Zhang and Zhi-Xia Yang, State Key Lab of Reproductive Medicine, Nanjing Medical University, 101 Longmian Ave, Nanjing, Jiangsu 211166, China. Tel/Fax: +86-25-86869504, E-mails:
and
| | - Dong Zhang
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Animal Core Facility, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Dong Zhang and Zhi-Xia Yang, State Key Lab of Reproductive Medicine, Nanjing Medical University, 101 Longmian Ave, Nanjing, Jiangsu 211166, China. Tel/Fax: +86-25-86869504, E-mails:
and
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22
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Transitions from Centrosomal to Non-centrosomal Microtubule Organization During Cellular Polarization. THE CENTROSOME AND ITS FUNCTIONS AND DYSFUNCTIONS 2022; 235:75-79. [DOI: 10.1007/978-3-031-20848-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Hiasa R, Kakimoto KI, Takegawa K, Higuchi Y. Involvement of AAA ATPase AipA in endocytosis of the arginine permease AoCan1 depending on AoAbp1 in Aspergillus oryzae. Fungal Biol 2021; 126:149-161. [DOI: 10.1016/j.funbio.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022]
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24
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Guerra VI, Haynes G, Byrne M, Hart MW. Selection on genes associated with the evolution of divergent life histories: Gamete recognition or something else? Evol Dev 2021; 23:423-438. [PMID: 34549504 DOI: 10.1111/ede.12392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/17/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022]
Abstract
Gamete compatibility, and fertilization success, is mediated by gamete-recognition genes (GRGs) that are expected to show genetic evidence of a response to sexual selection associated with mating system traits. Changes in the strength of sexual selection can arise from the resolution of sperm competition among males, sexual conflicts of interest between males and females, or other mechanisms of sexual selection. To assess these expectations, we compared patterns of episodic diversifying selection among genes expressed in the gonads of Cryptasterina pentagona and C. hystera, which recently speciated and have evolved different mating systems (gonochoric or hermaphroditic), modes of fertilization (outcrossing or selfing), and dispersal (planktonic larvae or internal brooding). Cryptasterina spp. inhabit the upper intertidal of the coast of Queensland and coral islands of the Great Barrier Reef. We found some evidence for positive selection on a GRG in the outcrossing C. pentagona, and we found evidence of loss of gene function in a GRG of the self-fertilizing C. hystera. The modification or loss of gene functionality may be evidence of relaxed selection on some aspects of gamete interaction in C. hystera. In addition to these genes involved in gamete interactions, we also found genes under selection linked to abiotic stress, chromosomal regulation, polyspermy, and egg-laying. We interpret those results as possible evidence that Cryptasterina spp. with different mating systems may have been adapting in divergent ways to oxidative stress or other factors associated with reproduction in the physiologically challenging environment of the high intertidal. RESEARCH HIGHLIGHTS: Recent speciation between two sea stars was unlikely the result of selection on gamete-recognition genes annotated in this study. Instead, our results point to selection on genes linked to the intertidal environment and reproduction.
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Affiliation(s)
- Vanessa I Guerra
- Department of Biological Sciences and Crawford Laboratory of Evolutionary Studies, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Gwilym Haynes
- Department of Biological Sciences and Crawford Laboratory of Evolutionary Studies, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maria Byrne
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Michael W Hart
- Department of Biological Sciences and Crawford Laboratory of Evolutionary Studies, Simon Fraser University, Burnaby, British Columbia, Canada
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25
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Wang H, Sun J, Yang F, Weng Y, Chen P, Du S, Wei A, Li Y. CsKTN1 for a katanin p60 subunit is associated with the regulation of fruit elongation in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2429-2441. [PMID: 34043036 DOI: 10.1007/s00122-021-03833-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
We identified a short fruit3 (sf3) mutant in cucumber. Map-based cloning revealed that CsKTN1 gene encodes a katanin p60 subunit, which is associated with the regulation of fruit elongation. Fruit length is an important horticultural trait for both fruit yield and quality of cucumber (Cucumis sativus L.). Knowledge on the molecular regulation of fruit elongation in cucumber is very limited. In this study, we identified and characterized a cucumber short fruit3 (sf3) mutant. Histological examination indicated that the shorter fruit in the mutant was due to reduced cell numbers. Genetic analysis revealed that the phenotype of the sf3 mutant was controlled by a single gene with semi-dominant inheritance. By map-based cloning and Arabidopsis genetic transformation, we showed that Sf3 was a homolog of KTN1 (CsKTN1) encoding a katanin p60 subunit. A non-synonymous mutation in the fifth exon of CsKTN1 resulted in an amino acid substitution from Serine in the wild type to Phenylalanine in the sf3 mutant. CsKTN1 expressed in all tissues of both the wild type and the sf3 mutant. However, there was no significant difference in CsKTN1 expression levels between the wild type and the sf3 mutant. The hormone quantitation and RNA-seq analysis suggested that auxin and gibberellin contents are decreased in sf3 by changing the expression levels of genes related with auxin and gibberellin metabolism and signaling. This work helps understand the function of the katanin and the molecular mechanisms of fruit growth regulation in cucumber.
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Affiliation(s)
- Hui Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jing Sun
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fan Yang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiqun Weng
- Horticulture Department, USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shengli Du
- Tianjin Vegetable Research Center, Tianjin, 300192, China
- National Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300192, China
| | - Aimin Wei
- Tianjin Vegetable Research Center, Tianjin, 300192, China.
- National Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300192, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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26
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Buijs RR, Hummel JJA, Burute M, Pan X, Cao Y, Stucchi R, Altelaar M, Akhmanova A, Kapitein LC, Hoogenraad CC. WDR47 protects neuronal microtubule minus ends from katanin-mediated severing. Cell Rep 2021; 36:109371. [PMID: 34260930 DOI: 10.1016/j.celrep.2021.109371] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/17/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Axons and dendrites are long extensions of neurons that contain arrays of noncentrosomal microtubules. Calmodulin-regulated spectrin-associated proteins (CAMSAPs) bind to and stabilize free microtubule minus ends and are critical for proper neuronal development and function. Previous studies have shown that the microtubule-severing ATPase katanin interacts with CAMSAPs and limits the length of CAMSAP-decorated microtubule stretches. However, how CAMSAP and microtubule minus end dynamics are regulated in neurons is poorly understood. Here, we show that the neuron-enriched protein WDR47 interacts with CAMSAPs and is critical for axon and dendrite development. We find that WDR47 accumulates at CAMSAP2-decorated microtubules, is essential for maintaining CAMSAP2 stretches, and protects minus ends from katanin-mediated severing. We propose a model where WDR47 protects CAMSAP2 at microtubule minus ends from katanin activity to ensure proper stabilization of the neuronal microtubule network.
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Affiliation(s)
- Robin R Buijs
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands
| | - Jessica J A Hummel
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands
| | - Mithila Burute
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands
| | - Xingxiu Pan
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands
| | - Yujie Cao
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands
| | - Riccardo Stucchi
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 Utrecht, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 Utrecht, the Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 Utrecht, the Netherlands; Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA.
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27
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Rai SK, Savastano A, Singh P, Mukhopadhyay S, Zweckstetter M. Liquid-liquid phase separation of tau: From molecular biophysics to physiology and disease. Protein Sci 2021; 30:1294-1314. [PMID: 33930220 PMCID: PMC8197432 DOI: 10.1002/pro.4093] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
Biomolecular condensation via liquid-liquid phase separation (LLPS) of intrinsically disordered proteins/regions (IDPs/IDRs), with and without nucleic acids, has drawn widespread interest due to the rapidly unfolding role of phase-separated condensates in a diverse range of cellular functions and human diseases. Biomolecular condensates form via transient and multivalent intermolecular forces that sequester proteins and nucleic acids into liquid-like membrane-less compartments. However, aberrant phase transitions into gel-like or solid-like aggregates might play an important role in neurodegenerative and other diseases. Tau, a microtubule-associated neuronal IDP, is involved in microtubule stabilization, regulates axonal outgrowth and transport in neurons. A growing body of evidence indicates that tau can accomplish some of its cellular activities via LLPS. However, liquid-to-solid transition resulting in the abnormal aggregation of tau is associated with neurodegenerative diseases. The physical chemistry of tau is crucial for governing its propensity for biomolecular condensation which is governed by various intermolecular and intramolecular interactions leading to simple one-component and complex multi-component condensates. In this review, we aim at capturing the current scientific state in unveiling the intriguing molecular mechanism of phase separation of tau. We particularly focus on the amalgamation of existing and emerging biophysical tools that offer unique spatiotemporal resolutions on a wide range of length- and time-scales. We also discuss the link between quantitative biophysical measurements and novel biological insights into biomolecular condensation of tau. We believe that this account will provide a broad and multidisciplinary view of phase separation of tau and its association with physiology and disease.
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Affiliation(s)
- Sandeep K. Rai
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical SciencesIndian Institute of Science Education and Research (IISER)MohaliIndia
| | - Adriana Savastano
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Priyanka Singh
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical SciencesIndian Institute of Science Education and Research (IISER)MohaliIndia
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical SciencesIndian Institute of Science Education and Research (IISER)MohaliIndia
| | - Markus Zweckstetter
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
- Department for NMR‐based Structural BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
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28
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Spastin interacts with CRMP5 to promote spindle organization in mouse oocytes by severing microtubules. ZYGOTE 2021; 30:80-91. [PMID: 34034836 DOI: 10.1017/s0967199421000344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microtubule-severing protein (MTSP) is critical for the survival of both mitotic and postmitotic cells. However, the study of MTSP during meiosis of mammalian oocytes has not been reported. We found that spastin, a member of the MTSP family, was highly expressed in oocytes and aggregated in spindle microtubules. After knocking down spastin by specific siRNA, the spindle microtubule density of meiotic oocytes decreased significantly. When the oocytes were cultured in vitro, the oocytes lacking spastin showed an obvious maturation disorder. Considering the microtubule-severing activity of spastin, we speculate that spastin on spindles may increase the number of microtubule broken ends by severing the microtubules, therefore playing a nucleating role, promoting spindle assembly and ensuring normal meiosis. In addition, we found the colocalization and interaction of collapsin response mediator protein 5 (CRMP5) and spastin in oocytes. CRMP5 can provide structural support and promote microtubule aggregation, creating transportation routes, and can interact with spastin in the microtubule activity of nerve cells (30). Knocking down CRMP5 may lead to spindle abnormalities and developmental disorders in oocytes. Overexpression of spastin may reverse the abnormal phenotype caused by the deletion of CRMP5. In summary, our data support a model in which the interaction between spastin and CRMP5 promotes the assembly of spindle microtubules in oocytes by controlling microtubule dynamics, therefore ensuring normal meiosis.
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29
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Baker L, Tar M, Kramer AH, Villegas GA, Charafeddine RA, Vafaeva O, Nacharaju P, Friedman J, Davies KP, Sharp DJ. Fidgetin-like 2 negatively regulates axonal growth and can be targeted to promote functional nerve regeneration. JCI Insight 2021; 6:138484. [PMID: 33872220 PMCID: PMC8262307 DOI: 10.1172/jci.insight.138484] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/01/2021] [Indexed: 02/05/2023] Open
Abstract
The microtubule (MT) cytoskeleton plays a critical role in axon growth and guidance. Here, we identify the MT-severing enzyme fidgetin-like 2 (FL2) as a negative regulator of axon regeneration and a therapeutic target for promoting nerve regeneration after injury. Genetic knockout of FL2 in cultured adult dorsal root ganglion neurons resulted in longer axons and attenuated growth cone retraction in response to inhibitory molecules. Given the axonal growth-promoting effects of FL2 depletion in vitro, we tested whether FL2 could be targeted to promote regeneration in a rodent model of cavernous nerve (CN) injury. The CNs are parasympathetic nerves that regulate blood flow to the penis, which are commonly damaged during radical prostatectomy (RP), resulting in erectile dysfunction (ED). Application of FL2-siRNA after CN injury significantly enhanced functional nerve recovery. Remarkably, following bilateral nerve transection, visible and functional nerve regeneration was observed in 7 out of 8 animals treated with FL2-siRNA, while no control-treated animals exhibited regeneration. These studies identify FL2 as a promising therapeutic target for enhancing regeneration after peripheral nerve injury and for mitigating neurogenic ED after RP - a condition for which, at present, only poor treatment options exist.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - David J. Sharp
- Department of Physiology and Biophysics
- Dominick P. Purpura Department of Neuroscience, and
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, USA
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30
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Cupido T, Jones NH, Grasso MJ, Pisa R, Kapoor TM. A chemical genetics approach to examine the functions of AAA proteins. Nat Struct Mol Biol 2021; 28:388-397. [PMID: 33782614 DOI: 10.1038/s41594-021-00575-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022]
Abstract
The structural conservation across the AAA (ATPases associated with diverse cellular activities) protein family makes designing selective chemical inhibitors challenging. Here, we identify a triazolopyridine-based fragment that binds the AAA domain of human katanin, a microtubule-severing protein. We have developed a model for compound binding and designed ASPIR-1 (allele-specific, proximity-induced reactivity-based inhibitor-1), a cell-permeable compound that selectively inhibits katanin with an engineered cysteine mutation. Only in cells expressing mutant katanin does ASPIR-1 treatment increase the accumulation of CAMSAP2 at microtubule minus ends, confirming specific on-target cellular activity. Importantly, ASPIR-1 also selectively inhibits engineered cysteine mutants of human VPS4B and FIGL1-AAA proteins, involved in organelle dynamics and genome stability, respectively. Structural studies confirm our model for compound binding at the AAA ATPase site and the proximity-induced reactivity-based inhibition. Together, our findings suggest a chemical genetics approach to decipher AAA protein functions across essential cellular processes and to test hypotheses for developing therapeutics.
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Affiliation(s)
- Tommaso Cupido
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Natalie H Jones
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Michael J Grasso
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Rudolf Pisa
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
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31
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Habicht J, Mooneyham A, Hoshino A, Shetty M, Zhang X, Emmings E, Yang Q, Coombes C, Gardner MK, Bazzaro M. UNC-45A breaks the microtubule lattice independently of its effects on non-muscle myosin II. J Cell Sci 2021; 134:jcs.248815. [PMID: 33262310 DOI: 10.1242/jcs.248815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022] Open
Abstract
In invertebrates, UNC-45 regulates myosin stability and functions. Vertebrates have two distinct isoforms of the protein: UNC-45B, expressed in muscle cells only, and UNC-45A, expressed in all cells and implicated in regulating both non-muscle myosin II (NMII)- and microtubule (MT)-associated functions. Here, we show that, in vitro and in human and rat cells, UNC-45A binds to the MT lattice, leading to MT bending, breakage and depolymerization. Furthermore, we show that UNC-45A destabilizes MTs independent of its C-terminal NMII-binding domain and even in the presence of the NMII inhibitor blebbistatin. These findings identified UNC-45A as a novel type of MT-severing protein with a dual non-mutually exclusive role in regulating NMII activity and MT stability. Because many human diseases, from cancer to neurodegenerative diseases, are caused by or associated with deregulation of MT stability, our findings have profound implications in the biology of MTs, as well as the biology of human diseases and possible therapeutic implications for their treatment.This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
- Juri Habicht
- Bradenburg Medical School - Theodor Fontane, Neuruppin 16816, Germany.,Masonic Cancer Center and Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ashley Mooneyham
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Asumi Hoshino
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mihir Shetty
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiaonan Zhang
- Bradenburg Medical School - Theodor Fontane, Neuruppin 16816, Germany.,Masonic Cancer Center and Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Edith Emmings
- Bradenburg Medical School - Theodor Fontane, Neuruppin 16816, Germany
| | - Qing Yang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Courtney Coombes
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Martina Bazzaro
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
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32
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Wang J, Dey A, Kramer AH, Miao Y, Liu J, Baker L, Friedman JM, Nacharaju P, Chuck RS, Zhang C, Sharp DJ. A Novel Therapeutic Approach to Corneal Alkaline Burn Model by Targeting Fidgetin-Like 2, a Microtubule Regulator. Transl Vis Sci Technol 2021; 10:17. [PMID: 33510956 PMCID: PMC7804583 DOI: 10.1167/tvst.10.1.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/11/2020] [Indexed: 12/26/2022] Open
Abstract
Purpose The purpose of this study was to determine the efficacy of nanoparticle-encapsulated Fidgetin-like 2 (FL2) siRNA (FL2-NPsi), a novel therapeutic agent targeting the FL2 gene, for the treatment of corneal alkaline chemical injury. Methods Eighty 12-week-old, male Sprague-Dawley rats were divided evenly into 8 treatment groups: prednisolone, empty nanoparticles, control-NPsi (1 µM, 10 µM, and 20 µM) and FL2-NPsi (1 µM, 10 µM, and 20 µM). An alkaline burn was induced onto the cornea of each rat, which was then treated for 14 days according to group assignment. Clinical, histopathologic, and immunohistochemical analyses were conducted to assess for wound healing. FL2-NPsi-mediated knockdown of FL2 was confirmed by in vitro quantitative polymerase chain reaction (qPCR). Toxicity assays were performed to assess for apoptosis (terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labeling [TUNEL] assay) and nerve damage (whole mount immunochemical staining). Statistical analyses were performed using Student's t-test and ANOVA. Results Compared with controls, FL2-NPsi-treated groups demonstrated enhanced corneal wound healing, with the 10 and 20 µM FL2-NPsi-treated groups demonstrating maximum rates of corneal re-epithelialization as assessed by ImageJ software, enhanced corneal transparency, and improved stromal organization on histology. Immunohistochemical analysis of vascular endothelial cells, macrophages, and neutrophils did not show significant differences between treatment groups. FL2-NPsi was not found to be toxic to nerves or induce apoptosis (p = 0.917). Conclusions Dose-response studies found both 10 and 20 µM FL2-NPsi to be efficacious in this rat model. FL2-NPsi may offer a novel treatment for corneal alkaline chemical injuries. Translational Relevance Basic cell biology findings about the microtubule cytoskeleton were used to design a therapeutic to enhance corneal cell migration, highlighting the promise of targeting microtubules to regulate corneal wound healing.
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Affiliation(s)
- Jessie Wang
- Department of Ophthalmology & Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- MicroCures, Inc., Bronx, NY, USA
| | | | | | - Yuan Miao
- Department of Ophthalmology & Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Juan Liu
- Department of Ophthalmology & Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Joel M. Friedman
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Parimala Nacharaju
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Roy S. Chuck
- Department of Ophthalmology & Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cheng Zhang
- Department of Ophthalmology & Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David J. Sharp
- Department of Ophthalmology & Visual Sciences, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- MicroCures, Inc., Bronx, NY, USA
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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33
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Schabla NM, Mondal K, Swanson PC. DCAF1 (VprBP): emerging physiological roles for a unique dual-service E3 ubiquitin ligase substrate receptor. J Mol Cell Biol 2020; 11:725-735. [PMID: 30590706 PMCID: PMC6821201 DOI: 10.1093/jmcb/mjy085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022] Open
Abstract
Cullin-RING ligases (CRLs) comprise a large group of modular eukaryotic E3 ubiquitin ligases. Within this family, the CRL4 ligase (consisting of the Cullin4 [CUL4] scaffold protein, the Rbx1 RING finger domain protein, the DNA damage-binding protein 1 [DDB1], and one of many DDB1-associated substrate receptor proteins) has been intensively studied in recent years due to its involvement in regulating various cellular processes, its role in cancer development and progression, and its subversion by viral accessory proteins. Initially discovered as a target for hijacking by the human immunodeficiency virus accessory protein r, the normal targets and function of the CRL4 substrate receptor protein DDB1–Cul4-associated factor 1 (DCAF1; also known as VprBP) had remained elusive, but newer studies have begun to shed light on these questions. Here, we review recent progress in understanding the diverse physiological roles of this DCAF1 in supporting various general and cell type-specific cellular processes in its context with the CRL4 E3 ligase, as well as another HECT-type E3 ligase with which DCAF1 also associates, called EDD/UBR5. We also discuss emerging questions and areas of future study to uncover the dynamic roles of DCAF1 in normal physiology.
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Affiliation(s)
- N Max Schabla
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, USA
| | - Koushik Mondal
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, USA
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, USA
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34
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Katanin P60: a potential biomarker for lymph node metastasis and prognosis for non-small cell lung cancer. World J Surg Oncol 2020; 18:157. [PMID: 32631334 PMCID: PMC7339556 DOI: 10.1186/s12957-020-01939-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/29/2020] [Indexed: 12/24/2022] Open
Abstract
Background This study aimed to assess the correlation of katanin P60 expression with clinical characteristics and survival profiles of surgical non-small cell lung cancer (NSCLC) patients. Methods Two hundred and sixty-five primary NSCLC patients treated by surgical resection were retrospectively viewed. The expression of katanin P60 in the tumor specimen was detected by the immunohistochemical (IHC) staining assay. Preoperative clinical data were collected from patients’ medical records, and survival data were extracted from follow-up records. Results There were 127 (47.9%) and 138 (52.1%) patients with katanin P60-low expression and -high expression, respectively; in addition, patients presenting katanin P60-high+, -high++, and -high+++ expression were 62 (23.4%), 63 (23.8%), and 13 (4.9%), respectively. Katanin P60 expression was correlated with lymph node (LYN) metastasis and advanced TNM stage but not pathological grade, tumor size, carcinoembryonic antigen (CEA) level or other non-tumor features in NSCLC patients. Regarding survival profiles, disease-free survival (DFS) and overall survival (OS) were both the lowest in katanin P60-high+++ expression patients, followed with katanin P60-high++ patients, katanin P60-high+ patients, and the highest in katanin P60-low expression patients. Further analysis illustrated that katanin P60-high expression was an independent predictive factor for unfavorable DFS and OS in NSCLC patients. Conclusions Katanin P60 presents potential as a biomarker for lymph node metastasis and prognosis in NSCLC patients.
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35
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Joly N, Beaumale E, Van Hove L, Martino L, Pintard L. Phosphorylation of the microtubule-severing AAA+ enzyme Katanin regulates C. elegans embryo development. J Cell Biol 2020; 219:e201912037. [PMID: 32412594 PMCID: PMC7265321 DOI: 10.1083/jcb.201912037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/25/2020] [Accepted: 03/03/2020] [Indexed: 12/15/2022] Open
Abstract
The evolutionarily conserved microtubule (MT)-severing AAA-ATPase enzyme Katanin is emerging as a critical regulator of MT dynamics. In Caenorhabditis elegans, Katanin MT-severing activity is essential for meiotic spindle assembly but is toxic for the mitotic spindle. Here we analyzed Katanin dynamics in C. elegans and deciphered the role of Katanin phosphorylation in the regulation of its activity and stability. Katanin is abundant in oocytes, and its levels drop after meiosis, but unexpectedly, a significant fraction is present throughout embryogenesis, where it is dynamically recruited to the centrosomes and chromosomes during mitosis. We show that the minibrain kinase MBK-2, which is activated during meiosis, phosphorylates Katanin at multiple serines. We demonstrate unequivocally that Katanin phosphorylation at a single residue is necessary and sufficient to target Katanin for proteasomal degradation after meiosis, whereas phosphorylation at the other sites only inhibits Katanin ATPase activity stimulated by MTs. Our findings suggest that cycles of phosphorylation and dephosphorylation fine-tune Katanin level and activity to deliver the appropriate MT-severing activity during development.
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Affiliation(s)
- Nicolas Joly
- Programme Equipes Labellisées Ligue contre le Cancer – Team “Cell Cycle and Development,” Centre National de la Recherche Scientifique – UMR7592, Institut Jacques Monod/University of Paris, Paris, France
| | | | | | | | - Lionel Pintard
- Programme Equipes Labellisées Ligue contre le Cancer – Team “Cell Cycle and Development,” Centre National de la Recherche Scientifique – UMR7592, Institut Jacques Monod/University of Paris, Paris, France
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36
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Tadepalle N, Robers L, Veronese M, Zentis P, Babatz F, Brodesser S, Gruszczyk AV, Schauss A, Höning S, Rugarli EI. Microtubule-dependent and independent roles of spastin in lipid droplet dispersion and biogenesis. Life Sci Alliance 2020; 3:3/6/e202000715. [PMID: 32321733 PMCID: PMC7184029 DOI: 10.26508/lsa.202000715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
Lipid droplets (LDs) are metabolic organelles that store neutral lipids and dynamically respond to changes in energy availability by accumulating or mobilizing triacylglycerols (TAGs). How the plastic behavior of LDs is regulated is poorly understood. Hereditary spastic paraplegia is a central motor axonopathy predominantly caused by mutations in SPAST, encoding the microtubule-severing protein spastin. The spastin-M1 isoform localizes to nascent LDs in mammalian cells; however, the mechanistic significance of this targeting is not fully explained. Here, we show that tightly controlled levels of spastin-M1 are required to inhibit LD biogenesis and TAG accumulation. Spastin-M1 maintains the morphogenesis of the ER when TAG synthesis is prevented, independent from microtubule binding. Moreover, spastin plays a microtubule-dependent role in mediating the dispersion of LDs from the ER upon glucose starvation. Our results reveal a dual role of spastin to shape ER tubules and to regulate LD movement along microtubules, opening new perspectives for the pathogenesis of hereditary spastic paraplegia.
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Affiliation(s)
- Nimesha Tadepalle
- Institute for Genetics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Lennart Robers
- Institute for Genetics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Matteo Veronese
- Institute for Genetics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Peter Zentis
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Felix Babatz
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Anja V Gruszczyk
- Institute for Genetics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Astrid Schauss
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Stefan Höning
- Institute for Biochemistry I, University of Cologne, Cologne, Germany
| | - Elena I Rugarli
- Institute for Genetics, University of Cologne, Cologne, Germany .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
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37
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Matis M. The Mechanical Role of Microtubules in Tissue Remodeling. Bioessays 2020; 42:e1900244. [PMID: 32249455 DOI: 10.1002/bies.201900244] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Indexed: 12/31/2022]
Abstract
During morphogenesis, tissues undergo extensive remodeling to get their final shape. Such precise sculpting requires the application of forces generated within cells by the cytoskeleton and transmission of these forces through adhesion molecules within and between neighboring cells. Within individual cells, microtubules together with actomyosin filaments and intermediate filaments form the composite cytoskeleton that controls cell mechanics during tissue rearrangements. While studies have established the importance of actin-based mechanical forces that are coupled via intercellular junctions, relatively little is known about the contribution of other cytoskeletal components such as microtubules to cell mechanics during morphogenesis. In this review the focus is on recent findings, highlighting the direct mechanical role of microtubules beyond its well-established role in trafficking and signaling during tissue formation.
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Affiliation(s)
- Maja Matis
- Institute of Cell Biology, Medical Faculty, University of Münster, Münster, 48149, Germany.,'Cells in Motion' Interfaculty Centre, University of Münster, Münster, 48149, Germany
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38
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Varikoti RA, Macke AC, Speck V, Ross JL, Dima RI. Molecular investigations into the unfoldase action of severing enzymes on microtubules. Cytoskeleton (Hoboken) 2020; 77:214-228. [DOI: 10.1002/cm.21606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 12/20/2022]
Affiliation(s)
| | - Amanda C. Macke
- Department of Chemistry University of Cincinnati Cincinnati Ohio USA
| | - Virginia Speck
- Department of Chemistry University of Cincinnati Cincinnati Ohio USA
| | | | - Ruxandra I. Dima
- Department of Chemistry University of Cincinnati Cincinnati Ohio USA
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39
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Shin SC, Im SK, Jang EH, Jin KS, Hur EM, Kim EE. Structural and Molecular Basis for Katanin-Mediated Severing of Glutamylated Microtubules. Cell Rep 2020; 26:1357-1367.e5. [PMID: 30699360 DOI: 10.1016/j.celrep.2019.01.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/09/2018] [Accepted: 01/04/2019] [Indexed: 12/28/2022] Open
Abstract
Katanin was the first microtubule (MT)-severing enzyme discovered, but how katanin executes MT severing remains poorly understood. Here, we report X-ray crystal structures of the apo and ATPγS-bound states of the catalytic AAA domain of human katanin p60 at 3.0 and 2.9 Å resolution, respectively. Comparison of the two structures reveals conformational changes induced by ATP binding and how such changes ensure hexamer stability. Moreover, we uncover structural details of pore loops (PLs) and show that Arg283, a residue unique to katanin among MT-severing enzymes, protrudes from PL1 and lines the entry of the catalytic pore. Functional studies suggest that PL1 and Arg283 play essential roles in the recognition and remodeling of the glutamylated, C-terminal tubulin tail and regulation of axon growth. In addition, domain-swapping experiments in katanin and spastin suggest that the non-homologous N-terminal region, which contains the MT-interacting and trafficking domain and a linker, confers specificity to the severing process.
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Affiliation(s)
- Sang Chul Shin
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Sun-Kyoung Im
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Eun-Hae Jang
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Neuroscience, Korea University of Science and Technology, Daejeon, Republic of Korea; Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, 37673, Republic of Korea
| | - Eun-Mi Hur
- Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea.
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40
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Trushina NI, Mulkidjanian AY, Brandt R. The microtubule skeleton and the evolution of neuronal complexity in vertebrates. Biol Chem 2020; 400:1163-1179. [PMID: 31116700 DOI: 10.1515/hsz-2019-0149] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/21/2022]
Abstract
The evolution of a highly developed nervous system is mirrored by the ability of individual neurons to develop increased morphological complexity. As microtubules (MTs) are crucially involved in neuronal development, we tested the hypothesis that the evolution of complexity is driven by an increasing capacity of the MT system for regulated molecular interactions as it may be implemented by a higher number of molecular players and a greater ability of the individual molecules to interact. We performed bioinformatics analysis on different classes of components of the vertebrate neuronal MT cytoskeleton. We show that the number of orthologs of tubulin structure proteins, MT-binding proteins and tubulin-sequestering proteins expanded during vertebrate evolution. We observed that protein diversity of MT-binding and tubulin-sequestering proteins increased by alternative splicing. In addition, we found that regions of the MT-binding protein tau and MAP6 displayed a clear increase in disorder extent during evolution. The data provide evidence that vertebrate evolution is paralleled by gene expansions, changes in alternative splicing and evolution of coding sequences of components of the MT system. The results suggest that in particular evolutionary changes in tubulin-structure proteins, MT-binding proteins and tubulin-sequestering proteins were prominent drivers for the development of increased neuronal complexity.
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Affiliation(s)
- Nataliya I Trushina
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastraße 7, D-49076 Osnabrück, Germany.,A.N. Belozersky Institute of Physico-Chemical Biology and School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roland Brandt
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Center for Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Institute of Cognitive Science, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
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41
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Dima RI, Stan G. Computational Studies of Mechanical Remodeling of Substrate Proteins by AAA+ Biological Nanomachines. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1356.ch008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ruxandra I. Dima
- Department of Chemistry, University of Cincinnati, P. O. Box 210172, Cincinnati, Ohio 45221, United States
| | - George Stan
- Department of Chemistry, University of Cincinnati, P. O. Box 210172, Cincinnati, Ohio 45221, United States
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42
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AtKATANIN1 Modulates Microtubule Depolymerization and Reorganization in Response to Salt Stress in Arabidopsis. Int J Mol Sci 2019; 21:ijms21010138. [PMID: 31878228 PMCID: PMC6981882 DOI: 10.3390/ijms21010138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/13/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022] Open
Abstract
The microtubule cytoskeleton is a dynamic system that plays vital roles in fundamental cellular processes and in responses to environmental stumili. Salt stress induced depolymerization and reorganization of microtubules are believed to function in the promotion of survival in Arabidopsis. Microtubule-severing enzyme ATKATANIN1 (AtKTN1) is recognized as a MAP that help to maintain organized microtubule structure. To date, whether AtKTN1 is involved in response to salt stress in Arabidopsis remains unknown. Here, our phenotypic analysis showed that the overexpression of AtKTN1 decreased tolerance to salt stress, whereas the knock-out of AtKTN1 increased salt tolerance in the early stage but decreased salt tolerance in the later stage. Microscopic analysis revealed that microtubule organization and dynamics are distorted in both overexpression and mutant cells which, in turn, resulted in an abnormal disassembly and reorganization under salt stress. Moreover, qRT analysis revealed that stress-responsive genes were down-regulated in overexpression and mutant cells compared to WT cells under salt stress. Taken together, our results indicated roles of AtKTN1 in modulating microtubule organization, salt-stress induced microtubule disruption and recovery, and its involvement in stress-related signaling pathways.
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43
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Vajente N, Norante R, Redolfi N, Daga A, Pizzo P, Pendin D. Microtubules Stabilization by Mutant Spastin Affects ER Morphology and Ca 2+ Handling. Front Physiol 2019; 10:1544. [PMID: 31920731 PMCID: PMC6933510 DOI: 10.3389/fphys.2019.01544] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/05/2019] [Indexed: 01/21/2023] Open
Abstract
The endoplasmic reticulum (ER) extends as a network of interconnected tubules and sheet-like structures in eukaryotic cells. ER tubules dynamically change their morphology and position within the cells in response to physiological stimuli and these network rearrangements depend on the microtubule (MT) cytoskeleton. Store-operated calcium entry (SOCE) relies on the repositioning of ER tubules to form specific ER-plasma membrane junctions. Indeed, the tips of polymerizing MTs are supposed to provide the anchor for ER tubules to move toward the plasma membrane, however the precise role of the cytoskeleton during SOCE has not been conclusively clarified. Here we exploit an in vivo approach involving the manipulation of MT dynamics in Drosophila melanogaster by neuronal expression of a dominant-negative variant of the MT-severing protein spastin to induce MT hyper-stabilization. We show that MT stabilization alters ER morphology, favoring an enrichment in ER sheets at the expense of tubules. Stabilizing MTs has a negative impact on the process of SOCE and results in a reduced ER Ca2+ content, affecting the flight ability of the flies. Restoring proper MT organization by administering the MT-destabilizing drug vinblastine, chronically or acutely, rescues ER morphology, SOCE and flight ability, indicating that MT dynamics impairment is responsible for all the phenotypes observed.
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Affiliation(s)
- Nicola Vajente
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Rosa Norante
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Nelly Redolfi
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Andrea Daga
- Laboratory of Molecular Biology, Scientific Institute IRCCS E. Medea, Lecco, Italy
| | - Paola Pizzo
- Department of Biomedical Sciences, University of Padua, Padua, Italy.,Neuroscience Institute-Italian National Research Council (CNR), Padua, Italy
| | - Diana Pendin
- Department of Biomedical Sciences, University of Padua, Padua, Italy.,Neuroscience Institute-Italian National Research Council (CNR), Padua, Italy
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44
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The molecular principles governing the activity and functional diversity of AAA+ proteins. Nat Rev Mol Cell Biol 2019; 21:43-58. [PMID: 31754261 DOI: 10.1038/s41580-019-0183-6] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/26/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are macromolecular machines that convert the chemical energy contained in ATP molecules into powerful mechanical forces to remodel a vast array of cellular substrates, including protein aggregates, macromolecular complexes and polymers. AAA+ proteins have key functionalities encompassing unfolding and disassembly of such substrates in different subcellular localizations and, hence, power a plethora of fundamental cellular processes, including protein quality control, cytoskeleton remodelling and membrane dynamics. Over the past 35 years, many of the key elements required for AAA+ activity have been identified through genetic, biochemical and structural analyses. However, how ATP powers substrate remodelling and whether a shared mechanism underlies the functional diversity of the AAA+ superfamily were uncertain. Advances in cryo-electron microscopy have enabled high-resolution structure determination of AAA+ proteins trapped in the act of processing substrates, revealing a conserved core mechanism of action. It has also become apparent that this common mechanistic principle is structurally adjusted to carry out a diverse array of biological functions. Here, we review how substrate-bound structures of AAA+ proteins have expanded our understanding of ATP-driven protein remodelling.
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45
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Kırımtay K, Selçuk E, Kelle D, Erman B, Karabay A. p53 regulates katanin-p60 promoter in HCT 116 cells. Gene 2019; 727:144241. [PMID: 31715301 DOI: 10.1016/j.gene.2019.144241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/29/2022]
Abstract
Tumor suppressor protein p53, which functions in the cell cycle, apoptosis and neuronal differentiation via transcriptional regulations of target genes or interactions with several proteins, has been associated with neurite outgrowth through microtubule re-organization. We previously demonstrated in neurons that upon p53 induction, the level of microtubule severing protein Katanin-p60 increases, indicating that p53 might be a transcriptional regulator of the KATNA1 gene encoding Katanin-p60. In this context, we firstly elucidated the activity of KATNA1 regulatory regions and endogenous KATNA1 mRNA levels in the presence or absence of p53 using HCT 116 WT and HCT 116 p53 (-/-) cells. Next, we demonstrated the binding of p53 to the KATNA1 promoter and then investigated the role of p53 on KATNA1 gene expression by ascertaining KATNA1 mRNA and Katanin-p60 protein levels upon p53 overexpression and activation in both cells. Moreover, we showed changes in microtubule network upon increased Katanin-p60 level due to p53 overexpression. Also, the changes in KATNA1 mRNA and Katanin-p60 protein levels upon p53 knockdown were investigated. Our results indicate that p53 is an activator of KATNA1 gene expression and we show that both p53 and Katanin-p60 expression have strict regulations and are maintained at balanced levels as they are vital proteins to orchestrate either survival and apoptosis or differentiation.
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Affiliation(s)
- Koray Kırımtay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Ece Selçuk
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey; Department of Molecular Biology and Genetics, Istanbul Medeniyet University, Istanbul, Turkey
| | - Dolunay Kelle
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Sabancı University, Istanbul, Turkey
| | - Arzu Karabay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.
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46
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Peterman E, Prekeris R. The postmitotic midbody: Regulating polarity, stemness, and proliferation. J Cell Biol 2019; 218:3903-3911. [PMID: 31690620 PMCID: PMC6891101 DOI: 10.1083/jcb.201906148] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/17/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Peterman and Prekeris review abscission and discuss the diverse roles for the postmitotic midbody in regulating polarity, tumorigenesis, and stemness. Abscission, the final stage of cell division, requires well-orchestrated changes in endocytic trafficking, microtubule severing, actin clearance, and the physical sealing of the daughter cell membranes. These processes are highly regulated, and any missteps in localized membrane and cytoskeleton dynamics often lead to a delay or a failure in cell division. The midbody, a microtubule-rich structure that forms during cytokinesis, is a key regulator of abscission and appears to function as a signaling platform coordinating cytoskeleton and endosomal dynamics during the terminal stages of cell division. It was long thought that immediately following abscission and the conclusion of cell division, the midbody is either released or rapidly degraded by one of the daughter cells. Recently, the midbody has gained prominence for exerting postmitotic functions. In this review, we detail the role of the midbody in orchestrating abscission, as well as discuss the relatively new field of postabscission midbody biology, particularly focusing on how it may act to regulate cell polarity and its potential to regulate cell tumorigenicity or stemness.
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Affiliation(s)
- Eric Peterman
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
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47
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The Microtubule Severing Protein Katanin Regulates Proliferation of Neuronal Progenitors in Embryonic and Adult Neurogenesis. Sci Rep 2019; 9:15940. [PMID: 31685876 PMCID: PMC6828949 DOI: 10.1038/s41598-019-52367-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/12/2019] [Indexed: 12/14/2022] Open
Abstract
Microtubule severing regulates cytoskeletal rearrangement underlying various cellular functions. Katanin, a heterodimer, consisting of catalytic (p60) and regulatory (p80) subunits severs dynamic microtubules to modulate several stages of cell division. The role of p60 katanin in the mammalian brain with respect to embryonic and adult neurogenesis is poorly understood. Here, we generated a Katna1 knockout mouse and found that consistent with a critical role of katanin in mitosis, constitutive homozygous Katna1 depletion is lethal. Katanin p60 haploinsufficiency induced an accumulation of neuronal progenitors in the subventricular zone during corticogenesis, and impaired their proliferation in the adult hippocampus dentate gyrus (DG) subgranular zone. This did not compromise DG plasticity or spatial and contextual learning and memory tasks employed in our study, consistent with the interpretation that adult neurogenesis may be associated with selective forms of hippocampal-dependent cognitive processes. Our data identify a critical role for the microtubule-severing protein katanin p60 in regulating neuronal progenitor proliferation in vivo during embryonic development and adult neurogenesis.
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48
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Yoshida S, Yoshida K. Multiple functions of DYRK2 in cancer and tissue development. FEBS Lett 2019; 593:2953-2965. [PMID: 31505048 DOI: 10.1002/1873-3468.13601] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 01/09/2023]
Abstract
Dual-specificity tyrosine-regulated kinases (DYRKs) are evolutionarily conserved from yeast to mammals. Accumulating studies have revealed that DYRKs have important roles in regulation of the cell cycle and survival. DYRK2, a member of the class II DYRK family protein, is a key regulator of p53, and phosphorylates it at Ser46 to induce apoptosis in response to DNA damage. Moreover, recent studies have uncovered that DYRK2 regulates G1/S transition, epithelial-mesenchymal-transition, and stemness in human cancer cells. DYRK2 also appears to have roles in tissue development in lower eukaryotes. Thus, the elucidation of mechanisms for DYRK2 during mammalian tissue development will promote the understanding of cell differentiation, tissue homeostasis, and congenital diseases as well as cancer. In this review, we discuss the roles of DYRK2 in tumor cells. Moreover, we focus on DYRK2-dependent developmental mechanisms in several species including fly (Drosophila), worm (Caenorhabditis elegans), zebrafish (Danio rerio), and mammals.
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Affiliation(s)
- Saishu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kiyotsugu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
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49
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Atkins M, Gasmi L, Bercier V, Revenu C, Del Bene F, Hazan J, Fassier C. FIGNL1 associates with KIF1Bβ and BICD1 to restrict dynein transport velocity during axon navigation. J Cell Biol 2019; 218:3290-3306. [PMID: 31541015 PMCID: PMC6781435 DOI: 10.1083/jcb.201805128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 05/30/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023] Open
Abstract
Atkins et al. identify a new role for Fidgetin-like 1 in motor axon navigation via its regulation of bidirectional axonal transport. They show that Fidgetin-like 1 binds Kif1bβ and the opposed polarity-directed motor dynein/dynactin in a molecular complex and controls circuit wiring by reducing dynein velocity in developing motor axons. Neuronal connectivity relies on molecular motor-based axonal transport of diverse cargoes. Yet the precise players and regulatory mechanisms orchestrating such trafficking events remain largely unknown. We here report the ATPase Fignl1 as a novel regulator of bidirectional transport during axon navigation. Using a yeast two-hybrid screen and coimmunoprecipitation assays, we showed that Fignl1 binds the kinesin Kif1bβ and the dynein/dynactin adaptor Bicaudal D-1 (Bicd1) in a molecular complex including the dynactin subunit dynactin 1. Fignl1 colocalized with Kif1bβ and showed bidirectional mobility in zebrafish axons. Notably, Kif1bβ and Fignl1 loss of function similarly altered zebrafish motor axon pathfinding and increased dynein-based transport velocity of Rab3 vesicles in these navigating axons, pinpointing Fignl1/Kif1bβ as a dynein speed limiter complex. Accordingly, disrupting dynein/dynactin activity or Bicd1/Fignl1 interaction induced motor axon pathfinding defects characteristic of Fignl1 gain or loss of function, respectively. Finally, pharmacological inhibition of dynein activity partially rescued the axon pathfinding defects of Fignl1-depleted larvae. Together, our results identify Fignl1 as a key dynein regulator required for motor circuit wiring.
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Affiliation(s)
- Melody Atkins
- Sorbonne Université, University Pierre and Marie Curie-Université Paris 6, Institut de Biologie Paris Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte Recherche 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Laïla Gasmi
- Sorbonne Université, University Pierre and Marie Curie-Université Paris 6, Institut de Biologie Paris Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte Recherche 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Valérie Bercier
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Céline Revenu
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Filippo Del Bene
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Jamilé Hazan
- Sorbonne Université, University Pierre and Marie Curie-Université Paris 6, Institut de Biologie Paris Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte Recherche 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Coralie Fassier
- Sorbonne Université, University Pierre and Marie Curie-Université Paris 6, Institut de Biologie Paris Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte Recherche 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
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50
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Aggarwal P, Wei L, Cao Y, Liu Q, Guttman JA, Wang Q, Leung KY. Edwardsiella induces microtubule-severing in host epithelial cells. Microbiol Res 2019; 229:126325. [PMID: 31563838 DOI: 10.1016/j.micres.2019.126325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/20/2019] [Accepted: 08/25/2019] [Indexed: 12/28/2022]
Abstract
Edwardsiella bacteria cause economic losses to a variety of commercially important fish globally. Human infections are rare and result in a gastroenteritis-like illness. Because these bacteria are evolutionarily related to other Enterobacteriaceae and the host cytoskeleton is a common target of enterics, we hypothesized that Edwardsiella may cause similar phenotypes. Here we use HeLa and Caco-2 infection models to show that microtubules are severed during the late infections. This microtubule alteration phenotype was not dependant on the type III or type VI secretion system (T3SS and T6SS) of the bacteria as ΔT3SS and ΔT6SS mutants of E. piscicida EIB202 and E. tarda ATCC15947 that lacks both also caused microtubule disassembly. Immunolocalization experiments showed the host katanin catalytic subunits A1 and A like 1 proteins at regions of microtubule severing, suggesting their involvement in the microtubule disassembly events. To identify bacterial components involved in this phenotype, we screened a 2,758 transposon library of E. piscicida EIB202 and found that 4 single mutations in the atpFHAGDC operon disrupted microtubule disassembly in HeLa cells. We then constructed three atp deletion mutants; they all could not disassemble host microtubules. This work provides the first clear evidence of host cytoskeletal alterations during Edwardsiella infections.
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Affiliation(s)
- Priyanka Aggarwal
- Department of Biological Sciences, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Lifan Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuping Cao
- Guangdong Technion, Israel Institute of Technology, Shantou, Guangdong, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Engineering Research Center of Marine Cultured Animal Vaccines, Shanghai, China; Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Julian A Guttman
- Department of Biological Sciences, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada.
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Engineering Research Center of Marine Cultured Animal Vaccines, Shanghai, China; Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Ka Yin Leung
- Guangdong Technion, Israel Institute of Technology, Shantou, Guangdong, China.
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