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Čajánek L, Smite S, Ivashchenko O, Huranova M. Cilia at the crossroad: convergence of regulatory mechanisms to govern cilia dynamics during cell signaling and the cell cycle. Cell Biosci 2025; 15:81. [PMID: 40483459 PMCID: PMC12144771 DOI: 10.1186/s13578-025-01403-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2025] [Accepted: 04/28/2025] [Indexed: 06/11/2025] Open
Abstract
Cilia are versatile, microtubule-based organelles that facilitate cellular signaling, motility, and environmental sensing in eukaryotic cells. These dynamic structures act as hubs for key developmental signaling pathways, while their assembly and disassembly are intricately regulated along cell cycle transitions. Recent findings show that factors regulating ciliogenesis and cilia dynamics often integrate their roles across other cellular processes, including cell cycle regulation, cytoskeletal organization, and intracellular trafficking, ensuring multilevel crosstalk of mechanisms controlling organogenesis. Disruptions in these shared regulators lead to broad defects associated with both ciliopathies and cancer. This review explores the crosstalk of regulatory mechanisms governing cilia assembly, disassembly, and maintenance during ciliary signaling and the cell cycle, along with the broader implications for development, tissue homeostasis, and disease.
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Affiliation(s)
- Lukáš Čajánek
- Laboratory of Cilia and Centrosome Biology, Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, Brno, 62500, Czech Republic.
- Section of Animal Physiology and Immunology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
| | - Sindija Smite
- Laboratory of Cilia Genetics and Pathology, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 00, Czech Republic
| | - Olha Ivashchenko
- Laboratory of Cilia Genetics and Pathology, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 00, Czech Republic
| | - Martina Huranova
- Laboratory of Cilia Genetics and Pathology, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 00, Czech Republic.
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2
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Hong SR, Chuang YC, Yang WT, Song CS, Yeh HW, Wu BH, Lin IH, Chou PC, Chen SC, Sharma L, Lu JC, Li RY, Chang YC, Liao KJ, Cheng HC, Wang WJ, Wang LHC, Lin YC. Glutamylation of centrosomes ensures their function by recruiting microtubule nucleation factors. EMBO J 2025; 44:2976-2996. [PMID: 40229407 DOI: 10.1038/s44318-025-00435-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 03/26/2025] [Accepted: 03/28/2025] [Indexed: 04/16/2025] Open
Abstract
Centrosomes are tubulin-based organelles that undergo glutamylation, a post-translational modification that conjugates glutamic acid residues to tubulins. Although centrosomal glutamylation has been known for several decades, how this modification regulates centrosome structure and function remains unclear. To address this long-standing issue, we developed a method to spatiotemporally reduce centrosomal glutamylation by recruiting an engineered deglutamylase to centrosomes. We found that centrosome structure remains largely unaffected by centrosomal hypoglutamylation. Intriguingly, glutamylation physically recruits, via electrostatic forces, the NEDD1/CEP192/γ-tubulin complex to centrosomes, ensuring microtubule nucleation and proper trafficking of centriolar satellites. The consequent defect in centriolar satellite trafficking leads to reduced levels of the ciliogenesis factor Talpid3, suppressing ciliogenesis. Centrosome glutamylation also promotes proper mitotic spindle formation and mitosis. In summary, our study provides a new approach to spatiotemporally manipulate glutamylation at centrosomes, and offers novel insights into how centrosomes are organized and regulated by glutamylation.
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Affiliation(s)
- Shi-Rong Hong
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Yi-Chien Chuang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Wen-Ting Yang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Chiou-Shian Song
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Hung-Wei Yeh
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Bing-Huan Wu
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - I-Hsuan Lin
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 300093, Taiwan
| | - Po-Chun Chou
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 300093, Taiwan
| | - Shiau-Chi Chen
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Lohitaksh Sharma
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Jui-Chen Lu
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Rou-Ying Li
- Department of Medical Science, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Ya-Chu Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Kuan-Ju Liao
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Hui-Chun Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Won-Jing Wang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 300093, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan.
- Department of Medical Science, National Tsing Hua University, Hsinchu, 300044, Taiwan.
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3
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Pao YS, Liao KJ, Shiau YC, Chao MH, Li MC, Lin LM, Chang HH, Yeh HW, Chen YJ, Chiu YT, Pan MYC, Chang YH, Shen SY, Lin SY, Cheng HC, Lin YC, Sun YJ, Kuo CC, Hsieh HP, Wang LHC. KIF2C promotes paclitaxel resistance by depolymerizing polyglutamylated microtubules. Dev Cell 2025:S1534-5807(25)00151-0. [PMID: 40157365 DOI: 10.1016/j.devcel.2025.03.004] [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: 03/11/2024] [Revised: 11/27/2024] [Accepted: 03/04/2025] [Indexed: 04/01/2025]
Abstract
The long-term effectiveness of paclitaxel is limited by chemoresistance. In this study, we elucidate the molecular mechanism by which kinesin family member 2C (KIF2C), a well-known microtubule depolymerase, contributes to the development of chemoresistance in triple-negative breast cancer (TNBC). We observed elevated levels of KIF2C, tubulin tyrosination, and polyglutamylation in human and mouse breast cancer cells resistant to paclitaxel. Additionally, these chemoresistant cells possessed cross-resistance to diverse microtubule-targeting agents (MTAs). We demonstrated that KIF2C preferentially depolymerizes polyglutamylated tubulin, even in the presence of paclitaxel. To counter this, we developed 7S9, a chemical inhibitor of KIF2C, that prohibits the dissociation of KIF2C from microtubules. The combination of 7S9 and paclitaxel significantly reduced tumorigenesis in chemoresistant TNBC model in mice. Moreover, 7S9 diminished cancer cell chemoresistance to several clinically available MTAs. Our findings elucidate the molecular mechanism of KIF2C-mediated chemoresistance and highlight KIF2C as a promising target for combating cross-resistance in TNBC.
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Affiliation(s)
- Yuan-Shao Pao
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Kuan-Ju Liao
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Ya-Chia Shiau
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Ming-Hong Chao
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Mu-Chun Li
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan; Biomedical Translation Research Center, Academia Sinica, Taipei City 115202, Taiwan
| | - Li-Mei Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan
| | - Hsin-Huei Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan
| | - Hung-Wei Yeh
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei City 115202, Taiwan
| | - Yu-Ting Chiu
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Max Yu-Chen Pan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Yu-Hsuan Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Shih-Yu Shen
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Shu-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan
| | - Hui-Chun Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City 300044, Taiwan; Department of Medical Sciences, National Tsing Hua University, Hsinchu City 300044, Taiwan
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan.
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan.
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu City 300044, Taiwan; Biomedical Translation Research Center, Academia Sinica, Taipei City 115202, Taiwan.
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu City 300044, Taiwan; Department of Medical Sciences, National Tsing Hua University, Hsinchu City 300044, Taiwan; School of Medicine, National Tsing Hua University, Hsinchu City 300044, Taiwan.
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4
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Badarudeen B, Chiang HJ, Collado L, Wang L, Sanchez I, Dynlacht BD. The tubulin poly-glutamylase complex, TPGC, is required for phosphatidyl inositol homeostasis and cilium assembly and maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.03.641315. [PMID: 40093036 PMCID: PMC11908161 DOI: 10.1101/2025.03.03.641315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
The tubulin poly-glutamylase complex (TPGC) is comprised of TTLL1 and at least five associated proteins that promote the addition of glutamate residues to tubulin tails of microtubules. Despite its discovery two decades ago, the enzyme has been refractory to characterization owing to its complex multimeric nature and the inability to detect poly-glutamylase activity after assembling the six-subunit complex. We now show that TPGC is the key enzyme driving centriolar and ciliary poly-glutamylation. We identified two novel TPGC subunits, TBC1D19 and KIAA1841, and showed that both components play an essential role in the assembly of the eight-subunit holo-enzyme. Remarkably, we were able to reconstitute the activity of TPGC with all eight subunits. TBC1D19 and KIAA1841 were essential for assembly and activity, and loss of TBC1D19 strongly compromised multiple tubulin modifications, including axonemal poly-glutamylation. TBC1D19 loss abolished transport of Arl13b and other ciliary membrane proteins, abrogating primary cilium assembly. Structural modeling revealed an essential role for TBC1D19 and KIAA1841 in complex assembly, microtubule binding, and preferential poly-glutamylation of α-tubulin. We found that TBC1D19 loss abrogated the ciliary localization of phosphatidyl inositol phosphatase, INPP5E, triggering cilium instability. Ciliogenesis in TBC1D19 null cells could be restored through inhibition of a specific phosphatidyl inositol phosphate (PIP) kinase, PIP5K1c, suggesting that TBC1D19 is required to instigate and maintain PIP homeostasis during ciliogenesis. Collectively, our data show that TPGC is a multi-functional enzyme essential for cilium assembly and maintenance.
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He K, Sun X, Chen C, Luc S, Robichaud JH, Zhang Y, Huang Y, Ji B, Ku PI, Subramanian R, Ling K, Hu J. Non-canonical CDK6 activity promotes cilia disassembly by suppressing axoneme polyglutamylation. J Cell Biol 2025; 224:e202405170. [PMID: 39636239 PMCID: PMC11619382 DOI: 10.1083/jcb.202405170] [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: 05/29/2024] [Revised: 10/02/2024] [Accepted: 11/01/2024] [Indexed: 12/07/2024] Open
Abstract
Tubulin polyglutamylation is a posttranslational modification that occurs primarily along the axoneme of cilia. Defective axoneme polyglutamylation impairs cilia function and has been correlated with ciliopathies, including Joubert Syndrome (JBTS). However, the precise mechanisms regulating proper axoneme polyglutamylation remain vague. Here, we show that cyclin-dependent kinase 6 (CDK6), but not its paralog CDK4, localizes to the cilia base and suppresses axoneme polyglutamylation by phosphorylating RAB11 family interacting protein 5 (FIP5) at site S641, a critical regulator of cilia import of glutamylases. S641 phosphorylation disrupts the ciliary recruitment of FIP5 and its association with RAB11, thereby reducing the ciliary import of glutamylases. Encouragingly, the FDA-approved CDK4/6 inhibitor Abemaciclib can effectively restore cilia function in JBTS cells with defective glutamylation. In summary, our study elucidates the regulatory mechanisms governing axoneme polyglutamylation and suggests that developing CDK6-specific inhibitors could be a promising therapeutic strategy to enhance cilia function in ciliopathy patients.
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Affiliation(s)
- Kai He
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Xiaobo Sun
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - San Luc
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jielu Hao Robichaud
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Yingyi Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Yan Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Biyun Ji
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pei-I Ku
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Robert M. and Billie Kelley Pirnie Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA
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6
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Liu X, Ge X. Classical cell cycle kinase limits tubulin polyglutamylation and cilium stability. J Cell Biol 2025; 224:e202412034. [PMID: 39812708 PMCID: PMC11734621 DOI: 10.1083/jcb.202412034] [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] [Indexed: 01/30/2025] Open
Abstract
Tubulin polyglutamylation is essential for maintaining cilium stability and function, and defective tubulin polyglutamylation is associated with ciliopathies. However, the regulatory mechanism underlying proper axonemal polyglutamylation remains unclear. He et al. (https://doi.org/10.1083/jcb.202405170) discovered that Cdk7/Cdk6/FIP5 phosphorylation cascade controls the ciliary import of tubulin glutamylases, thereby modulating axoneme polyglutamylation and ciliary signaling.
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Affiliation(s)
- Xiaoliang Liu
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, USA
| | - Xuecai Ge
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, USA
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7
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Jun JH, Cha H, Ko JY, Kim HS, Yoo KH, Park JH. Loss of Kat2b impairs intraflagellar transport and the Hedgehog signaling pathway in primary cilia. Sci Rep 2025; 15:2127. [PMID: 39820844 PMCID: PMC11739504 DOI: 10.1038/s41598-025-86292-5] [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] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 01/09/2025] [Indexed: 01/19/2025] Open
Abstract
Primary cilia are sensory organelles that regulate various signaling pathways. When microtubules are compared to a highway, motor proteins carry and transport cargo proteins, which are tuned by post-translational modifications, such as acetylation. However, the role of acetylation in primary cilia regulation remains unclear. In this study, histone K (lysine) acetyltransferase 2 B (Kat2b) was identified as a novel regulator of primary cilia. Kat2b, which mainly regulates transcription as a p300/CBP associated factor, is localized to the cytosol, centrosome, and cilium basal body. In addition, basal Kat2b expression gradually increased during ciliogenesis. Kat2b regulates the rate of cilia assembly, particularly in the early stages, and loss of Kat2b reduces the recruitment of intraflagellar transport (IFT) components to the ciliary axoneme and impairs Hedgehog (Hh) signaling activation. In addition, Kat2b-knockout mice showed mild abnormalities and ciliary IFT defects in the kidneys. These results establish a link between acetylation regulated by Kat2b and its relevance to ciliary assembly and function.
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Affiliation(s)
- Jae Hee Jun
- Department of Biological Science, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Hwayeon Cha
- Department of Biological Science, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Je Yeong Ko
- Department of Biological Science, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Ho-Shik Kim
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Science, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
| | - Jong Hoon Park
- Department of Biological Science, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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Sun Y, Chen Z, Jin M, Xie H, Zhao C. Ciliary length regulation by intraflagellar transport in zebrafish. eLife 2024; 13:RP93168. [PMID: 39671305 PMCID: PMC11643619 DOI: 10.7554/elife.93168] [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] [Indexed: 12/15/2024] Open
Abstract
How cells regulate the size of their organelles remains a fundamental question in cell biology. Cilia, with their simple structure and surface localization, provide an ideal model for investigating organelle size control. However, most studies on cilia length regulation are primarily performed on several single-celled organisms. In contrast, the mechanism of length regulation in cilia across diverse cell types within multicellular organisms remains a mystery. Similar to humans, zebrafish contain diverse types of cilia with variable lengths. Taking advantage of the transparency of zebrafish embryos, we conducted a comprehensive investigation into intraflagellar transport (IFT), an essential process for ciliogenesis. By generating a transgenic line carrying Ift88-GFP transgene, we observed IFT in multiple types of cilia with varying lengths. Remarkably, cilia exhibited variable IFT speeds in different cell types, with longer cilia exhibiting faster IFT speeds. This increased IFT speed in longer cilia is likely not due to changes in common factors that regulate IFT, such as motor selection, BBSome proteins, or tubulin modification. Interestingly, longer cilia in the ear cristae tend to form larger IFT compared to shorter spinal cord cilia. Reducing the size of IFT particles by knocking down Ift88 slowed IFT speed and resulted in the formation of shorter cilia. Our study proposes an intriguing model of cilia length regulation via controlling IFT speed through the modulation of the size of the IFT complex. This discovery may provide further insights into our understanding of how organelle size is regulated in higher vertebrates.
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Affiliation(s)
- Yi Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of ChinaQingdaoChina
- Fang Zongxi Center for Marine Evo Devo, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of ChinaQingdaoChina
| | - Zhe Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of ChinaQingdaoChina
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua UniversityBeijingChina
| | - Minjun Jin
- Institute of Evolution & Marine Biodiversity, Ocean University of ChinaQingdaoChina
- Fang Zongxi Center for Marine Evo Devo, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of ChinaQingdaoChina
| | - Haibo Xie
- Institute of Evolution & Marine Biodiversity, Ocean University of ChinaQingdaoChina
- Fang Zongxi Center for Marine Evo Devo, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of ChinaQingdaoChina
| | - Chengtian Zhao
- Institute of Evolution & Marine Biodiversity, Ocean University of ChinaQingdaoChina
- Fang Zongxi Center for Marine Evo Devo, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of ChinaQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology CenterQingdaoChina
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Chen S, Zeng N, Liu GY, Wang H, Lin T, Tai Y, Chen C, Fang Y, Chuang Y, Kao C, Cheng H, Wu B, Sun P, Bayansan O, Chiu Y, Shih C, Chung W, Yang J, Wang LH, Chiang P, Chen C, Wagner OI, Wang Y, Lin Y. Precise Control of Intracellular Trafficking and Receptor-Mediated Endocytosis in Living Cells and Behaving Animals. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405568. [PMID: 39401410 PMCID: PMC11615828 DOI: 10.1002/advs.202405568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 09/15/2024] [Indexed: 12/06/2024]
Abstract
Intracellular trafficking, an extremely complex network, dynamically orchestrates nearly all cellular activities. A versatile method that enables the manipulation of target transport pathways with high spatiotemporal accuracy in vitro and in vivo is required to study how this network coordinates its functions. Here, a new method called RIVET (Rapid Immobilization of target Vesicles on Engaged Tracks) is presented. Utilizing inducible dimerization between target vesicles and selective cytoskeletons, RIVET can spatiotemporally halt numerous intracellular trafficking pathways within seconds in a reversible manner. Its highly specific perturbations allow for the real-time dissection of the dynamic relationships among different trafficking pathways. Moreover, RIVET is capable of inhibiting receptor-mediated endocytosis. This versatile system can be applied from the cellular level to whole organisms. RIVET opens up new avenues for studying intracellular trafficking under various physiological and pathological conditions and offers potential strategies for treating trafficking-related disorders.
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Affiliation(s)
- Shiau‐Chi Chen
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Neng‐Jie Zeng
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Grace Y. Liu
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Hsien‐Chu Wang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Tzu‐Ying Lin
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Yi‐Ling Tai
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Chiao‐Yun Chen
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Yin Fang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Yi‐Chien Chuang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Ching‐Lin Kao
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Hsuan Cheng
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Bing‐Huang Wu
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Pin‐Chiao Sun
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Odvogmed Bayansan
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Yu‐Ting Chiu
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Chi‐Hsuan Shih
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Wen‐Hong Chung
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Jia‐Bin Yang
- Institute of Molecular and Cellular BiologyNational Taiwan UniversityTaipei106319Taiwan
| | - Lily Hui‐Ching Wang
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu300044Taiwan
- School of MedicineNational Tsing Hua UniversityHsinChu300044Taiwan
- Department of Medical ScienceNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Po‐Han Chiang
- Institute of Biomedical EngineeringNational Yang Ming Chiao Tung UniversityHsinchu300093Taiwan
| | - Chun‐Hao Chen
- Institute of Molecular and Cellular BiologyNational Taiwan UniversityTaipei106319Taiwan
| | - Oliver I. Wagner
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Yi‐Ching Wang
- Department of PharmacologyCollege of MedicineNational Cheng Kung UniversityTainan701401Taiwan
| | - Yu‐Chun Lin
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu300044Taiwan
- Department of Medical ScienceNational Tsing Hua UniversityHsinchu300044Taiwan
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10
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Mercey O, Gadadhar S, Magiera MM, Lebrun L, Kostic C, Moulin A, Arsenijevic Y, Janke C, Guichard P, Hamel V. Glutamylation imbalance impairs the molecular architecture of the photoreceptor cilium. EMBO J 2024; 43:6679-6704. [PMID: 39528655 PMCID: PMC11649768 DOI: 10.1038/s44318-024-00284-1] [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: 07/29/2024] [Revised: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024] Open
Abstract
Microtubules, composed of conserved α/β-tubulin dimers, undergo complex post-translational modifications (PTMs) that fine-tune their properties and interactions with other proteins. Cilia exhibit several tubulin PTMs, such as polyglutamylation, polyglycylation, detyrosination, and acetylation, with functions that are not fully understood. Mutations in AGBL5, which encodes the deglutamylating enzyme CCP5, have been linked to retinitis pigmentosa, suggesting that altered polyglutamylation may cause photoreceptor cell degeneration, though the underlying mechanisms are unclear. Using super-resolution ultrastructure expansion microscopy (U-ExM) in mouse and human photoreceptor cells, we observed that most tubulin PTMs accumulate at the connecting cilium that links outer and inner photoreceptor segments. Mouse models with increased glutamylation (Ccp5-/- and Ccp1-/-) or loss of tubulin acetylation (Atat1-/-) showed that aberrant glutamylation, but not acetylation loss, disrupts outer segment architecture. This disruption includes exacerbation of the connecting cilium, loss of the bulge region, and destabilization of the distal axoneme. Additionally, we found significant impairment in tubulin glycylation, as well as reduced levels of intraflagellar transport proteins and of retinitis pigmentosa-associated protein RPGR. Our findings indicate that proper glutamylation levels are crucial for maintaining the molecular architecture of the photoreceptor cilium.
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Affiliation(s)
- Olivier Mercey
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Sudarshan Gadadhar
- Institut Curie, PSL Research University, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore, India
| | - Maria M Magiera
- Institut Curie, PSL Research University, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Laura Lebrun
- Institut Curie, PSL Research University, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Corinne Kostic
- Group for Retinal Disorder Research, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Alexandre Moulin
- Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Yvan Arsenijevic
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Carsten Janke
- Institut Curie, PSL Research University, CNRS UMR3348, Orsay, France.
- Université Paris-Saclay, CNRS UMR3348, Orsay, France.
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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11
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Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024; 20:1493-1504. [PMID: 38658656 PMCID: PMC11529724 DOI: 10.1038/s41589-024-01599-0] [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: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
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Affiliation(s)
- Kishore K Mahalingan
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry & Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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12
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He K, Jiang H, Li W, Toutounchi S, Huang Y, Wu J, Ma X, Baehr W, Pignolo RJ, Ling K, Zhou X, Wang H, Hu J. Primary cilia mediate skeletogenic BMP and Hedgehog signaling in heterotopic ossification. Sci Transl Med 2024; 16:eabn3486. [PMID: 39047114 DOI: 10.1126/scitranslmed.abn3486] [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: 11/22/2021] [Revised: 04/04/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
Heterotopic ossification (HO), defined as the formation of extraskeletal bone in muscle and soft tissues, is a diverse pathological process caused by either genetic mutations or inciting trauma. Fibrodysplasia ossificans progressiva (FOP) is a genetic form of HO caused by mutations in the bone morphogenetic protein (BMP) type I receptor gene activin A receptor type 1 (ACVR1). These mutations make ACVR1 hypersensitive to BMP and responsive to activin A. Hedgehog (Hh) signaling also contributes to HO development. However, the exact pathophysiology of how skeletogenic cells contribute to endochondral ossification in FOP remains unknown. Here, we showed that the wild-type or FOP-mutant ACVR1 localized in the cilia of stem cells from human exfoliated deciduous teeth with key FOP signaling components, including activin A receptor type 2A/2B, SMAD family member 1/5, and FK506-binding protein 12kD. Cilia suppression by deletion of intraflagellar transport 88 or ADP ribosylation factor like GTPase 3 effectively inhibited pathological BMP and Hh signaling, subdued aberrant chondro-osteogenic differentiation in primary mouse or human FOP cells, and diminished in vivo extraskeletal ossification in Acvr1Q207D, Sox2-Cre; Acvr1R206H/+ FOP mice and in burn tenotomy-treated wild-type mice. Our results provide a rationale for early and localized suppression of cilia in affected tissues after injury as a therapeutic strategy against either genetic or acquired HO.
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Affiliation(s)
- Kai He
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905 USA
| | - Heng Jiang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905 USA
| | - Weijun Li
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905 USA
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905 USA
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Saman Toutounchi
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905 USA
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905 USA
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Yan Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905 USA
| | - Jianfeng Wu
- Department of Orthopedics, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Xiaoyu Ma
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905 USA
| | - Wolfgang Baehr
- Department of Ophthalmology, University of Utah, Salt Lake City, UT 84132, USA
| | - Robert J Pignolo
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905 USA
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905 USA
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905 USA
| | - Xuhui Zhou
- Translational Research Center of Orthopedics, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Haitao Wang
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905 USA
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905 USA
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905 USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Robert M. and Billie Kelley Pirnie Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN 55905, USA
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13
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Chen J, Zehr EA, Gruschus JM, Szyk A, Liu Y, Tanner ME, Tjandra N, Roll-Mecak A. Tubulin code eraser CCP5 binds branch glutamates by substrate deformation. Nature 2024; 631:905-912. [PMID: 39020174 DOI: 10.1038/s41586-024-07699-0] [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: 01/20/2024] [Accepted: 06/11/2024] [Indexed: 07/19/2024]
Abstract
Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes1. Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification2. It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family1. Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function3-9, and mutations in CCPs lead to human disease10-13. Here we report cryo-electron microscopy structures of the glutamylation eraser CCP5 in complex with the microtubule, and X-ray structures in complex with transition-state analogues. Combined with NMR analysis, these analyses show that CCP5 deforms the tubulin main chain into a unique turn that enables lock-and-key recognition of the branch glutamate in a cationic pocket that is unique to CCP family proteins. CCP5 binding of the sequences flanking the branch point primarily through peptide backbone atoms enables processing of diverse tubulin isotypes and non-tubulin substrates. Unexpectedly, CCP5 exhibits inefficient processing of an abundant β-tubulin isotype in the brain. This work provides an atomistic view into glutamate branch recognition and resolution, and sheds light on homeostasis of the tubulin glutamylation syntax.
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Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - James M Gruschus
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Agnieszka Szyk
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Yanjie Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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14
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Viar GA, Pigino G. Tubulin posttranslational modifications through the lens of new technologies. Curr Opin Cell Biol 2024; 88:102362. [PMID: 38701611 DOI: 10.1016/j.ceb.2024.102362] [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: 01/16/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024]
Abstract
The Tubulin Code revolutionizes our understanding of microtubule dynamics and functions, proposing a nuanced system governed by tubulin isotypes, posttranslational modifications (PTMs) and microtubule-associated proteins (MAPs). Tubulin isotypes, diverse across species, contribute structural complexity, and are thought to influence microtubule functions. PTMs encode dynamic information on microtubules, which are read by several microtubule interacting proteins and impact on cellular processes. Here we discuss recent technological and methodological advances, such as in genome engineering, live cell imaging, expansion microscopy, and cryo-electron microscopy that reveal new elements and levels of complexity of the tubulin code, including new modifying enzymes and nanopatterns of PTMs on individual microtubules. The Tubulin Code's exploration holds transformative potential, guiding therapeutic strategies and illuminating connections to diseases like cancer and neurodegenerative disorders, underscoring its relevance in decoding fundamental cellular language.
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Affiliation(s)
| | - Gaia Pigino
- Human Technopole, via Rita Levi Montalcini 1, Milan, Italy.
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15
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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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16
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Sabharwal V, Boyanapalli SPP, Shee A, Nonet ML, Nandi A, Chaudhuri D, Koushika SP. F-box protein FBXB-65 regulates anterograde transport of the kinesin-3 motor UNC-104 through a PTM near its cargo-binding PH domain. J Cell Sci 2024; 137:jcs261553. [PMID: 38477340 PMCID: PMC11058344 DOI: 10.1242/jcs.261553] [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: 08/15/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024] Open
Abstract
Axonal transport in neurons is essential for cargo movement between the cell body and synapses. Caenorhabditis elegans UNC-104 and its homolog KIF1A are kinesin-3 motors that anterogradely transport precursors of synaptic vesicles (pre-SVs) and are degraded at synapses. However, in C. elegans, touch neuron-specific knockdown of the E1 ubiquitin-activating enzyme, uba-1, leads to UNC-104 accumulation at neuronal ends and synapses. Here, we performed an RNAi screen and identified that depletion of fbxb-65, which encodes an F-box protein, leads to UNC-104 accumulation at neuronal distal ends, and alters UNC-104 net anterograde movement and levels of UNC-104 on cargo without changing synaptic UNC-104 levels. Split fluorescence reconstitution showed that UNC-104 and FBXB-65 interact throughout the neuron. Our theoretical model suggests that UNC-104 might exhibit cooperative cargo binding that is regulated by FBXB-65. FBXB-65 regulates an unidentified post-translational modification (PTM) of UNC-104 in a region beside the cargo-binding PH domain. Both fbxb-65 and UNC-104, independently of FBXB-65, regulate axonal pre-SV distribution, transport of pre-SVs at branch points and organismal lifespan. FBXB-65 regulates a PTM of UNC-104 and the number of motors on the cargo surface, which can fine-tune cargo transport to the synapse.
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Affiliation(s)
- Vidur Sabharwal
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Amir Shee
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
- Northwestern Institute on Complex Systems and ESAM, Northwestern University, Evanston, IL 60208, USA
| | - Michael L. Nonet
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Amitabha Nandi
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Sandhya P. Koushika
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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17
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Jentzsch J, Wunderlich H, Thein M, Bechthold J, Brehm L, Krauss SW, Weiss M, Ersfeld K. Microtubule polyglutamylation is an essential regulator of cytoskeletal integrity in Trypanosoma brucei. J Cell Sci 2024; 137:jcs261740. [PMID: 38205672 DOI: 10.1242/jcs.261740] [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: 10/19/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Tubulin polyglutamylation, catalysed by members of the tubulin tyrosine ligase-like (TTLL) protein family, is an evolutionarily highly conserved mechanism involved in the regulation of microtubule dynamics and function in eukaryotes. In the protozoan parasite Trypanosoma brucei, the microtubule cytoskeleton is essential for cell motility and maintaining cell shape. In a previous study, we showed that T. brucei TTLL6A and TTLL12B are required to regulate microtubule dynamics at the posterior cell pole. Here, using gene deletion, we show that the polyglutamylase TTLL1 is essential for the integrity of the highly organised microtubule structure at the cell pole, with a phenotype distinct from that observed in TTLL6A- and TTLL12B-depleted cells. Reduced polyglutamylation in TTLL1-deficient cells also leads to increased levels in tubulin tyrosination, providing new evidence for an interplay between the tubulin tyrosination and detyrosination cycle and polyglutamylation. We also show that TTLL1 acts differentially on specific microtubule doublets of the flagellar axoneme, although the absence of TTLL1 appears to have no measurable effect on cell motility.
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Affiliation(s)
- Jana Jentzsch
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Hannes Wunderlich
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Marinus Thein
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Julia Bechthold
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Lucas Brehm
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Sebastian W Krauss
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Klaus Ersfeld
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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18
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Turan FB, Ercan ME, Firat-Karalar EN. A Chemically Inducible Organelle Rerouting Assay to Probe Primary Cilium Assembly, Maintenance, and Disassembly in Cultured Cells. Methods Mol Biol 2024; 2725:55-78. [PMID: 37856017 DOI: 10.1007/978-1-0716-3507-0_3] [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] [Indexed: 10/20/2023]
Abstract
The primary cilium is a conserved, microtubule-based organelle that protrudes from the surface of most vertebrate cells as well as sensory cells of many organisms. It transduces extracellular chemical and mechanical cues to regulate diverse cellular processes during development and physiology. Loss-of-function studies via RNA interference and CRISPR/Cas9-mediated gene knockouts have been the main tool for elucidating the functions of proteins, protein complexes, and organelles implicated in cilium biology. However, these methods are limited in studying acute spatiotemporal functions of proteins as well as the connection between their cellular positioning and functions. A powerful approach based on inducible recruitment of plus or minus end-directed molecular motors to the protein of interest enables fast and precise control of protein activity in time and in space. In this chapter, we present a chemically inducible heterodimerization method for functional perturbation of centriolar satellites, an emerging membrane-less organelle involved in cilium biogenesis and function. The method we present is based on rerouting of centriolar satellites to the cell center or the periphery in mammalian epithelial cells. We also describe how this method can be applied to study the temporal functions of centriolar satellites during primary cilium assembly, maintenance, and disassembly.
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Affiliation(s)
- F Basak Turan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - M Erdem Ercan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.
- Koc University School of Medicine, Istanbul, Turkey.
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19
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Shim MS, Dixon A, Nettesheim A, Perkumas KM, Stamer WD, Sun Y, Liton PB. Shear stress induces autophagy in Schlemm's canal cells via primary cilia-mediated SMAD2/3 signaling pathway. AUTOPHAGY REPORTS 2023; 2:2236519. [PMID: 37637387 PMCID: PMC10448710 DOI: 10.1080/27694127.2023.2236519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 08/29/2023]
Abstract
The Schlemm's canal (SC) is a circular, lymphatic-like vessel located at the limbus of the eye that participates in the regulation of aqueous humor drainage to control intraocular pressure (IOP). Circumferential flow of aqueous humor within the SC lumen generates shear stress, which regulates SC cell behaviour. Using biochemical analysis and real-time live cell imaging techniques, we have investigated the activation of autophagy in SC cells by shear stress. We report, for the first time, the primary cilium (PC)-dependent activation of autophagy in SC cells in response to shear stress. Moreover, we identified PC-dependent shear stress-induced autophagy to be positively regulated by phosphorylation of SMAD2 in its linker and C-terminal regions. Additionally, SMAD2/3 signaling was found to transcriptionally activate LC3B, ATG5 and ATG7 in SC cells. Intriguingly, concomitant to SMAD2-dependent activation of autophagy, we also report here the activation of mTOR pathway, a classical autophagy inhibitor, in SC cells by shear stress. mTOR activation was found to also be dependent on the PC. Moreover, pharmacological inhibition of class I PI3K increased phosphorylation of SMAD2 at the linker and activated autophagy. Together, our data indicates an interplay between PI3K and SMAD2/3 signaling pathways in the regulation of PC-dependent shear stress-induced autophagy in SC cells.
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Affiliation(s)
- Myoung Sup Shim
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - Angela Dixon
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - April Nettesheim
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - Kristin M. Perkumas
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - W. Daniel Stamer
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - Yang Sun
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Paloma B. Liton
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
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20
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Chen J, Roll-Mecak A. Glutamylation is a negative regulator of microtubule growth. Mol Biol Cell 2023; 34:ar70. [PMID: 37074962 PMCID: PMC10295482 DOI: 10.1091/mbc.e23-01-0030] [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: 01/30/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/20/2023] Open
Abstract
Microtubules are noncovalent polymers built from αβ-tubulin dimers. The disordered C-terminal tubulin tails are functionalized with multiple glutamate chains of variable lengths added and removed by tubulin tyrosine ligases (TTLLs) and carboxypeptidases (CCPs). Glutamylation is abundant on stable microtubule arrays such as in axonemes and axons, and its dysregulation leads to human pathologies. Despite this, the effects of glutamylation on intrinsic microtubule dynamics are unclear. Here we generate tubulin with short and long glutamate chains and show that glutamylation slows the rate of microtubule growth and increases catastrophes as a function of glutamylation levels. This implies that the higher stability of glutamylated microtubules in cells is due to effectors. Interestingly, EB1 is minimally affected by glutamylation and thus can report on the growth rates of both unmodified and glutamylated microtubules. Finally, we show that glutamate removal by CCP1 and 5 is synergistic and occurs preferentially on soluble tubulin, unlike TTLL enzymes that prefer microtubules. This substrate preference establishes an asymmetry whereby once the microtubule depolymerizes, the released tubulin is reset to a less-modified state, while polymerized tubulin accumulates the glutamylation mark. Our work shows that a modification on the disordered tubulin tails can directly affect microtubule dynamics and furthers our understanding of the mechanistic underpinnings of the tubulin code.
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Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, and
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, and
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
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21
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Wang Y, Zhang Y, Guo X, Zheng Y, Zhang X, Feng S, Wu HY. CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis. BMC Biol 2023; 21:124. [PMID: 37226238 DOI: 10.1186/s12915-023-01622-1] [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] [Received: 10/25/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The axonemal microtubules of primary cilium undergo a conserved protein posttranslational modification (PTM) - polyglutamylation. This reversible procedure is processed by tubulin tyrosine ligase-like polyglutamylases to form secondary polyglutamate side chains, which are metabolized by the 6-member cytosolic carboxypeptidase (CCP) family. Although polyglutamylation modifying enzymes have been linked to ciliary architecture and motility, it was unknown whether they also play a role in ciliogenesis. RESULTS In this study, we found that CCP5 expression is transiently downregulated upon the initiation of ciliogenesis, but recovered after cilia are formed. Overexpression of CCP5 inhibited ciliogenesis, suggesting that a transient downregulation of CCP5 expression is required for ciliation initiation. Interestingly, the inhibitory effect of CCP5 on ciliogenesis does not rely on its enzyme activity. Among other 3 CCP members tested, only CCP6 can similarly suppress ciliogenesis. Using CoIP-MS analysis, we identified a protein that potentially interacts with CCP - CP110, a known negative regulator of ciliogenesis, whose degradation at the distal end of mother centriole permits cilia assembly. We found that both CCP5 and CCP6 can modulate CP110 level. Particularly, CCP5 interacts with CP110 through its N-terminus. Loss of CCP5 or CCP6 led to the disappearance of CP110 at the mother centriole and abnormally increased ciliation in cycling RPE-1 cells. Co-depletion of CCP5 and CCP6 synergized this abnormal ciliation, suggesting their partially overlapped function in suppressing cilia formation in cycling cells. In contrast, co-depletion of the two enzymes did not further increase the length of cilia, although CCP5 and CCP6 differentially regulate polyglutamate side-chain length of ciliary axoneme and both contribute to limiting cilia length, suggesting that they may share a common pathway in cilia length control. Through inducing the overexpression of CCP5 or CCP6 at different stages of ciliogenesis, we further demonstrated that CCP5 or CCP6 inhibited cilia formation before ciliogenesis, while shortened the length of cilia after cilia formation. CONCLUSION These findings reveal the dual role of CCP5 and CCP6. In addition to regulating cilia length, they also retain CP110 level to suppress cilia formation in cycling cells, pointing to a novel regulatory mechanism for ciliogenesis mediated by demodifying enzymes of a conserved ciliary PTM, polyglutamylation.
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Affiliation(s)
- Yujuan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Building 24, Room 417-8, Tianjin, 300072, China
| | - Yuan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Building 24, Room 417-8, Tianjin, 300072, China
| | - Xinyu Guo
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Building 24, Room 417-8, Tianjin, 300072, China
| | - Yiqiang Zheng
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Building 24, Room 417-8, Tianjin, 300072, China
| | - Xinjie Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Building 24, Room 417-8, Tianjin, 300072, China
| | - Shanshan Feng
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, 51063, China
| | - Hui-Yuan Wu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Building 24, Room 417-8, Tianjin, 300072, China.
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22
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Sénicourt B, Cloutier G, Basora N, Fallah S, Laniel A, Lavoie C, Beaulieu JF. Primary Cilium Identifies a Quiescent Cell Population in the Human Intestinal Crypt. Cells 2023; 12:1059. [PMID: 37048132 PMCID: PMC10093653 DOI: 10.3390/cells12071059] [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: 10/27/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Primary cilia are sensory antennae located at the cell surface which mediate a variety of extracellular signals involved in development, tissue homeostasis, stem cells and cancer. Primary cilia are found in an extensive array of vertebrae cells but can only be generated when cells become quiescent. The small intestinal epithelium is a rapidly self-renewing tissue organized into a functional unit called the crypt-villus axis, containing progenitor and differentiated cells, respectively. Terminally differentiated villus cells are notoriously devoid of primary cilia. We sought to determine if intestinal crypts contain a quiescent cell population that could be identified by the presence of primary cilia. Here we show that primary cilia are detected in a subset of cells located deep in the crypts slightly above a Paneth cell population. Using a normal epithelial proliferative crypt cell model, we show that primary cilia assembly and activity correlate with a quiescent state. These results provide further evidence for the existence of a quiescent cell population in the human small intestine and suggest the potential for new modes of regulation in stem cell dynamics.
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Affiliation(s)
- Blanche Sénicourt
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Shebrooke, Sherbrooke, QC J1H5N4, Canada
| | - Gabriel Cloutier
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Shebrooke, Sherbrooke, QC J1H5N4, Canada
| | - Nuria Basora
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Shebrooke, Sherbrooke, QC J1H5N4, Canada
| | - Sepideh Fallah
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Shebrooke, Sherbrooke, QC J1H5N4, Canada
| | - Andréanne Laniel
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
| | - Christine Lavoie
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
| | - Jean-François Beaulieu
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Shebrooke, Sherbrooke, QC J1H5N4, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
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23
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Cheng H, Kao Y, Chen T, Sharma L, Yang W, Chuang Y, Huang S, Lin H, Huang Y, Kao C, Yang L, Bearon R, Cheng H, Hsia K, Lin Y. Actin filaments form a size-dependent diffusion barrier around centrosomes. EMBO Rep 2022; 24:e54935. [PMID: 36314725 PMCID: PMC9827556 DOI: 10.15252/embr.202254935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023] Open
Abstract
The centrosome, a non-membranous organelle, constrains various soluble molecules locally to execute its functions. As the centrosome is surrounded by various dense components, we hypothesized that it may be bordered by a putative diffusion barrier. After quantitatively measuring the trapping kinetics of soluble proteins of varying size at centrosomes by a chemically inducible diffusion trapping assay, we find that centrosomes are highly accessible to soluble molecules with a Stokes radius of less than 5.8 nm, whereas larger molecules rarely reach centrosomes, indicating the existence of a size-dependent diffusion barrier at centrosomes. The permeability of this barrier is tightly regulated by branched actin filaments outside of centrosomes and it decreases during anaphase when branched actin temporally increases. The actin-based diffusion barrier gates microtubule nucleation by interfering with γ-tubulin ring complex recruitment. We propose that actin filaments spatiotemporally constrain protein complexes at centrosomes in a size-dependent manner.
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Affiliation(s)
- Hsuan Cheng
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Yu‐Lin Kao
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Ting Chen
- Institute of Bioinformatics and Structural BiologyNational Tsing Hua UniversityHsinchuTaiwan
| | - Lohitaksh Sharma
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Wen‐Ting Yang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Yi‐Chien Chuang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Shih‐Han Huang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Hong‐Rui Lin
- Institute of Bioinformatics and Structural BiologyNational Tsing Hua UniversityHsinchuTaiwan
| | - Yao‐Shen Huang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Chi‐Ling Kao
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Lee‐Wei Yang
- Institute of Bioinformatics and Structural BiologyNational Tsing Hua UniversityHsinchuTaiwan,Physics DivisionNational Center for Theoretical SciencesTaipeiTaiwan
| | - Rachel Bearon
- Department of Mathematical ScienceUniversity of LiverpoolLiverpoolUK
| | - Hui‐Chun Cheng
- Institute of Bioinformatics and Structural BiologyNational Tsing Hua UniversityHsinchuTaiwan
| | | | - Yu‐Chun Lin
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan,Department of Medical ScienceNational Tsing Hua UniversityHsinchuTaiwan
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24
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Liu GY, Chen S, Lee G, Shaiv K, Chen P, Cheng H, Hong S, Yang W, Huang S, Chang Y, Wang H, Kao C, Sun P, Chao M, Lee Y, Tang M, Lin Y. Precise control of microtubule disassembly in living cells. EMBO J 2022; 41:e110472. [PMID: 35686621 PMCID: PMC9340485 DOI: 10.15252/embj.2021110472] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/15/2022] [Accepted: 05/05/2022] [Indexed: 12/28/2022] Open
Abstract
Microtubules tightly regulate various cellular activities. Our understanding of microtubules is largely based on experiments using microtubule-targeting agents, which, however, are insufficient to dissect the dynamic mechanisms of specific microtubule populations, due to their slow effects on the entire pool of microtubules. To overcome this technological limitation, we have used chemo and optogenetics to disassemble specific microtubule subtypes, including tyrosinated microtubules, primary cilia, mitotic spindles, and intercellular bridges, by rapidly recruiting engineered microtubule-cleaving enzymes onto target microtubules in a reversible manner. Using this approach, we show that acute microtubule disassembly swiftly halts vesicular trafficking and lysosomal dynamics. It also immediately triggers Golgi and ER reorganization and slows the fusion/fission of mitochondria without affecting mitochondrial membrane potential. In addition, cell rigidity is increased after microtubule disruption owing to increased contractile stress fibers. Microtubule disruption furthermore prevents cell division, but does not cause cell death during interphase. Overall, the reported tools facilitate detailed analysis of how microtubules precisely regulate cellular architecture and functions.
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Affiliation(s)
- Grace Y Liu
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Shiau‐Chi Chen
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Gang‐Hui Lee
- Department of Physiology, College of MedicineNational Cheng Kung UniversityTainanTaiwan
- International Center for Wound Repair and RegenerationNational Cheng Kung UniversityTainanTaiwan
| | - Kritika Shaiv
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Pin‐Yu Chen
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Hsuan Cheng
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Shi‐Rong Hong
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Wen‐Ting Yang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Shih‐Han Huang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Ya‐Chu Chang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Hsien‐Chu Wang
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Ching‐Lin Kao
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Pin‐Chiao Sun
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Ming‐Hong Chao
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Yian‐Ying Lee
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
| | - Ming‐Jer Tang
- Department of Physiology, College of MedicineNational Cheng Kung UniversityTainanTaiwan
- International Center for Wound Repair and RegenerationNational Cheng Kung UniversityTainanTaiwan
| | - Yu‐Chun Lin
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchuTaiwan
- Department of Medical ScienceNational Tsing Hua UniversityHsinchuTaiwan
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25
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Van De Weghe JC, Gomez A, Doherty D. The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. Annu Rev Genomics Hum Genet 2022; 23:301-329. [PMID: 35655331 DOI: 10.1146/annurev-genom-121321-093528] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Joubert syndrome (JS), Meckel syndrome (MKS), and nephronophthisis (NPH) ciliopathy spectrum could be the poster child for advances and challenges in Mendelian human genetics over the past half century. Progress in understanding these conditions illustrates many core concepts of human genetics. The JS phenotype alone is caused by pathogenic variants in more than 40 genes; remarkably, all of the associated proteins function in and around the primary cilium. Primary cilia are near-ubiquitous, microtubule-based organelles that play crucial roles in development and homeostasis. Protruding from the cell, these cellular antennae sense diverse signals and mediate Hedgehog and other critical signaling pathways. Ciliary dysfunction causes many human conditions termed ciliopathies, which range from multiple congenital malformations to adult-onset single-organ failure. Research on the genetics of the JS-MKS-NPH spectrum has spurred extensive functional work exploring the broadly important role of primary cilia in health and disease. This functional work promises to illuminate the mechanisms underlying JS-MKS-NPH in humans, identify therapeutic targets across genetic causes, and generate future precision treatments. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA;
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
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26
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Liu C, Chen Y, Xie Y, Xiang M. Tubulin Post-translational Modifications: Potential Therapeutic Approaches to Heart Failure. Front Cell Dev Biol 2022; 10:872058. [PMID: 35493101 PMCID: PMC9039000 DOI: 10.3389/fcell.2022.872058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
In recent decades, advancing insights into the mechanisms of cardiac dysfunction have focused on the involvement of microtubule network. A variety of tubulin post-translational modifications have been discovered to fine-tune the microtubules’ properties and functions. Given the limits of therapies based on conserved structures of the skeleton, targeting tubulin modifications appears to be a potentially promising therapeutic strategy. Here we review the current understanding of tubulin post-translational modifications in regulating microtubule functions in the cardiac system. We also discussed how altered modifications may lead to a range of cardiac dysfunctions, many of which are linked to heart failure.
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Affiliation(s)
- Chang Liu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuwen Chen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yao Xie
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meixiang Xiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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27
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Rocha C, Prinos P. Post-transcriptional and Post-translational Modifications of Primary Cilia: How to Fine Tune Your Neuronal Antenna. Front Cell Neurosci 2022; 16:809917. [PMID: 35295905 PMCID: PMC8918543 DOI: 10.3389/fncel.2022.809917] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022] Open
Abstract
Primary cilia direct cellular signaling events during brain development and neuronal differentiation. The primary cilium is a dynamic organelle formed in a multistep process termed ciliogenesis that is tightly coordinated with the cell cycle. Genetic alterations, such as ciliary gene mutations, and epigenetic alterations, such as post-translational modifications and RNA processing of cilia related factors, give rise to human neuronal disorders and brain tumors such as glioblastoma and medulloblastoma. This review discusses the important role of genetics/epigenetics, as well as RNA processing and post-translational modifications in primary cilia function during brain development and cancer formation. We summarize mouse and human studies of ciliogenesis and primary cilia activity in the brain, and detail how cilia maintain neuronal progenitor populations and coordinate neuronal differentiation during development, as well as how cilia control different signaling pathways such as WNT, Sonic Hedgehog (SHH) and PDGF that are critical for neurogenesis. Moreover, we describe how post-translational modifications alter cilia formation and activity during development and carcinogenesis, and the impact of missplicing of ciliary genes leading to ciliopathies and cell cycle alterations. Finally, cilia genetic and epigenetic studies bring to light cellular and molecular mechanisms that underlie neurodevelopmental disorders and brain tumors.
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Affiliation(s)
- Cecilia Rocha
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
- *Correspondence: Cecilia Rocha,
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Panagiotis Prinos,
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28
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Wang L, Paudyal SC, Kang Y, Owa M, Liang FX, Spektor A, Knaut H, Sánchez I, Dynlacht BD. Regulators of tubulin polyglutamylation control nuclear shape and cilium disassembly by balancing microtubule and actin assembly. Cell Res 2022; 32:190-209. [PMID: 34782749 PMCID: PMC8807603 DOI: 10.1038/s41422-021-00584-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/05/2021] [Indexed: 02/03/2023] Open
Abstract
Cytoskeletal networks play an important role in regulating nuclear morphology and ciliogenesis. However, the role of microtubule (MT) post-translational modifications in nuclear shape regulation and cilium disassembly has not been explored. Here we identified a novel regulator of the tubulin polyglutamylase complex (TPGC), C11ORF49/CSTPP1, that regulates cytoskeletal organization, nuclear shape, and cilium disassembly. Mechanistically, loss of C11ORF49/CSTPP1 impacts the assembly and stability of the TPGC, which modulates long-chain polyglutamylation levels on microtubules (MTs) and thereby balances the binding of MT-associated proteins and actin nucleators. As a result, loss of TPGC leads to aberrant, enhanced assembly of MTs that penetrate the nucleus, which in turn leads to defects in nuclear shape, and disorganization of cytoplasmic actin that disrupts the YAP/TAZ pathway and cilium disassembly. Further, we showed that C11ORF49/CSTPP1-TPGC plays mechanistically distinct roles in the regulation of nuclear shape and cilium disassembly. Remarkably, disruption of C11ORF49/CSTPP1-TPGC also leads to developmental defects in vivo. Our findings point to an unanticipated nexus that links tubulin polyglutamylation with nuclear shape and ciliogenesis.
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Affiliation(s)
- Lei Wang
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA.
| | - Sharad C Paudyal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuchen Kang
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Mikito Owa
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, NYU Langone Health, New York, NY, USA
| | - Alexander Spektor
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Irma Sánchez
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Brian D Dynlacht
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA.
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29
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Stilling S, Kalliakoudas T, Benninghoven-Frey H, Inoue T, Falkenburger BH. PIP2 determines length and stability of primary cilia by balancing membrane turnovers. Commun Biol 2022; 5:93. [PMID: 35079141 PMCID: PMC8789910 DOI: 10.1038/s42003-022-03028-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 12/23/2021] [Indexed: 11/09/2022] Open
Abstract
AbstractPrimary cilia are sensory organelles on many postmitotic cells. The ciliary membrane is continuous with the plasma membrane but differs in its phospholipid composition with phosphatidylinositol 4,5-bisposphate (PIP2) being much reduced toward the ciliary tip. In order to determine the functional significance of this difference, we used chemically induced protein dimerization to rapidly synthesize or degrade PIP2 selectively in the ciliary membrane. We observed ciliary fission when PIP2 was synthesized and a growing ciliary length when PIP2 was degraded. Ciliary fission required local actin polymerisation in the cilium, the Rho kinase Rac, aurora kinase A (AurkA) and histone deacetylase 6 (HDAC6). This pathway was previously described for ciliary disassembly before cell cycle re-entry. Activating ciliary receptors in the presence of dominant negative dynamin also increased ciliary PIP2, and the associated vesicle budding required ciliary PIP2. Finally, ciliary shortening resulting from constitutively increased ciliary PIP2 was mediated by the same actin – AurkA – HDAC6 pathway. Taken together, changes in ciliary PIP2 are a unifying point for ciliary membrane stability and turnover. Different stimuli increase ciliary PIP2 to secrete vesicles and reduce ciliary length by a common pathway. The paucity of PIP2 in the distal cilium therefore ensures ciliary stability.
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30
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Gómez AE, Christman AK, Van De Weghe JC, Finn M, Doherty D. Systematic analysis of cilia characteristics and Hedgehog signaling in five immortal cell lines. PLoS One 2022; 17:e0266433. [PMID: 36580465 PMCID: PMC9799305 DOI: 10.1371/journal.pone.0266433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/08/2022] [Indexed: 12/30/2022] Open
Abstract
Dysfunction of the primary cilium, a microtubule-based signaling organelle, leads to genetic conditions called ciliopathies. Hedgehog (Hh) signaling is mediated by the primary cilium in vertebrates and is therefore implicated in ciliopathies; however, it is not clear which immortal cell lines are the most appropriate for modeling pathway response in human disease; therefore, we systematically evaluated Hh in five commercially available, immortal mammalian cell lines: ARPE-19, HEK293T, hTERT RPE-1, NIH/3T3, and SH-SY5Y. Under proper conditions, all of the cell lines ciliated adequately for our subsequent experiments, except for SH-SY5Y which were excluded from further analysis. hTERT RPE-1 and NIH/3T3 cells relocalized Hh pathway components Smoothened (SMO) and GPR161 and upregulated Hh target genes in response to pathway stimulation. In contrast, pathway stimulation did not induce target gene expression in ARPE-19 and HEK293T cells, despite SMO and GPR161 relocalization. These data indicate that human hTERT RPE-1 cells and murine NIH/3T3 cells, but not ARPE-19 and HEK293T cells, are suitable for modeling the role of Hh signaling in ciliopathies.
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Affiliation(s)
- Arianna Ericka Gómez
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- Molecular Medicine and Mechanisms of Disease PhD Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Angela K. Christman
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Julie Craft Van De Weghe
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Malaney Finn
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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31
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Primary cilia and the reciprocal activation of AKT and SMAD2/3 regulate stretch-induced autophagy in trabecular meshwork cells. Proc Natl Acad Sci U S A 2021; 118:2021942118. [PMID: 33753495 DOI: 10.1073/pnas.2021942118] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Activation of autophagy is one of the responses elicited by high intraocular pressure (IOP) and mechanical stretch in trabecular meshwork (TM) cells. However, the mechanosensor and the molecular mechanisms by which autophagy is induced by mechanical stretch in these or other cell types is largely unknown. Here, we have investigated the mechanosensor and downstream signaling pathway that regulate cyclic mechanical stretch (CMS)-induced autophagy in TM cells. We report that primary cilia act as a mechanosensor for CMS-induced autophagy and identified a cross-regulatory talk between AKT1 and noncanonical SMAD2/3 signaling as critical components of primary cilia-mediated activation of autophagy by mechanical stretch. Furthermore, we demonstrated the physiological significance of our findings in ex vivo perfused eyes. Removal of primary cilia disrupted the homeostatic IOP compensatory response and prevented the increase in LC3-II protein levels in response to elevated pressure challenge, strongly supporting a role of primary cilia-mediated autophagy in regulating IOP homeostasis.
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32
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Boschen KE, Fish EW, Parnell SE. Prenatal alcohol exposure disrupts Sonic hedgehog pathway and primary cilia genes in the mouse neural tube. Reprod Toxicol 2021; 105:136-147. [PMID: 34492310 PMCID: PMC8529623 DOI: 10.1016/j.reprotox.2021.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022]
Abstract
Neurulation-stage alcohol exposure (NAE; embryonic day [E] 8-10) is associated with midline craniofacial and CNS defects that likely arise from disruption of morphogen pathways, such as Sonic hedgehog (Shh). Notably, midline anomalies are also a hallmark of genetic ciliopathies such as Joubert syndrome. We tested whether NAE alters Shh pathway signaling and the number and function of primary cilia, organelles critical for Shh pathway transduction. Female C57BL/6 J mice were administered two doses of alcohol (2.9 g/kg/dose) or vehicle on E9. Embryos were collected 6, 12, or 24 h later, and changes to Shh, cell cycle genes, and primary cilia were measured in the rostroventral neural tube (RVNT). Within the first 24 h post-NAE, reductions in Shh pathway and cell cycle gene expression and the ratio of Gli3 forms in the full-length activator state were observed. RVNT volume and cell layer width were reduced at 12 h. In addition, altered expression of multiple cilia-related genes was observed at 6 h post-NAE. As a further test of cilia gene-ethanol interaction, mice heterozygous for Kif3a exhibited perturbed behavior during adolescence following NAE compared to vehicle-treated mice, and Kif3a heterozygosity exacerbated the hyperactive effects of NAE on exploratory activity. These data demonstrate that NAE downregulates the Shh pathway in a region of the neural tube that gives rise to alcohol-sensitive brain structures and identifies disruption of primary cilia function, or a "transient ciliopathy", as a possible cellular mechanism of prenatal alcohol pathogenesis.
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Affiliation(s)
- Karen E Boschen
- Bowles Center on Alcohol Studies, University of North Carolina, Chapel Hill, NC, USA
| | - Eric W Fish
- Bowles Center on Alcohol Studies, University of North Carolina, Chapel Hill, NC, USA
| | - Scott E Parnell
- Bowles Center on Alcohol Studies, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.
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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease. Proc Natl Acad Sci U S A 2021; 118:2106770118. [PMID: 34548398 PMCID: PMC8488674 DOI: 10.1073/pnas.2106770118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic analysis identified ttc30a as a ciliopathy network component, and targeting it replicated skeletal malformations and renal cysts as seen in patients and the amphibian models. A loss of Ttc30a affected cilia by altering posttranslational tubulin modifications. Our findings identify TTC30A/B as a component of ciliary segmentation essential for cartilage differentiation and renal tubulogenesis. These findings may lead to novel therapeutic targets in treating ciliary skeletopathies and cystic kidney disease. Skeletal ciliopathies (e.g., Jeune syndrome, short rib polydactyly syndrome, and Sensenbrenner syndrome) are frequently associated with nephronophthisis-like cystic kidney disease and other organ manifestations. Despite recent progress in genetic mapping of causative loci, a common molecular mechanism of cartilage defects and cystic kidneys has remained elusive. Targeting two ciliary chondrodysplasia loci (ift80 and ift172) by CRISPR/Cas9 mutagenesis, we established models for skeletal ciliopathies in Xenopus tropicalis. Froglets exhibited severe limb deformities, polydactyly, and cystic kidneys, closely matching the phenotype of affected patients. A data mining–based in silico screen found ttc30a to be related to known skeletal ciliopathy genes. CRISPR/Cas9 targeting replicated limb malformations and renal cysts identical to the models of established disease genes. Loss of Ttc30a impaired embryonic renal excretion and ciliogenesis because of altered posttranslational tubulin acetylation, glycylation, and defective axoneme compartmentalization. Ttc30a/b transcripts are enriched in chondrocytes and osteocytes of single-cell RNA-sequenced embryonic mouse limbs. We identify TTC30A/B as an essential node in the network of ciliary chondrodysplasia and nephronophthisis-like disease proteins and suggest that tubulin modifications and cilia segmentation contribute to skeletal and renal ciliopathy manifestations of ciliopathies in a cell type–specific manner. These findings have implications for potential therapeutic strategies.
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Zhang Y, Hao J, Tarrago MG, Warner GM, Giorgadze N, Wei Q, Huang Y, He K, Chen C, Peclat TR, White TA, Ling K, Tchkonia T, Kirkland JL, Chini EN, Hu J. FBF1 deficiency promotes beiging and healthy expansion of white adipose tissue. Cell Rep 2021; 36:109481. [PMID: 34348145 PMCID: PMC8428195 DOI: 10.1016/j.celrep.2021.109481] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/06/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
Preadipocytes dynamically produce sensory cilia. However, the role of primary cilia in preadipocyte differentiation and adipose homeostasis remains poorly understood. We previously identified transition fiber component FBF1 as an essential player in controlling selective cilia import. Here, we establish Fbf1tm1a/tm1a mice and discover that Fbf1tm1a/tm1a mice develop severe obesity, but surprisingly, are not predisposed to adverse metabolic complications. Obese Fbf1tm1a/tm1a mice possess unexpectedly healthy white fat tissue characterized by spontaneous upregulated beiging, hyperplasia but not hypertrophy, and low inflammation along the lifetime. Mechanistically, FBF1 governs preadipocyte differentiation by constraining the beiging program through an AKAP9-dependent, cilia-regulated PKA signaling, while recruiting the BBS chaperonin to transition fibers to suppress the hedgehog signaling-dependent adipogenic program. Remarkably, obese Fbf1tm1a/tm1a mice further fed a high-fat diet are protected from diabetes and premature death. We reveal a central role for primary cilia in the fate determination of preadipocytes and the generation of metabolically healthy fat tissue.
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Affiliation(s)
- Yingyi Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jielu Hao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Mariana G Tarrago
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Anesthesiology, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Gina M Warner
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Anesthesiology, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Nino Giorgadze
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Qing Wei
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Yan Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Kai He
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Thais R Peclat
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Anesthesiology, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Thomas A White
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tamar Tchkonia
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Eduardo N Chini
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Anesthesiology, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA; Mayo Clinic Robert M. and Billie Kelley Pirnie Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA.
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Abstract
The intraflagellar transport (IFT) system is a remarkable molecular machine used by cells to assemble and maintain the cilium, a long organelle extending from eukaryotic cells that gives rise to motility, sensing and signaling. IFT plays a critical role in building the cilium by shuttling structural components and signaling receptors between the ciliary base and tip. To provide effective transport, IFT-A and IFT-B adaptor protein complexes assemble into highly repetitive polymers, called IFT trains, that are powered by the motors kinesin-2 and IFT-dynein to move bidirectionally along the microtubules. This dynamic system must be precisely regulated to shuttle different cargo proteins between the ciliary tip and base. In this Cell Science at a Glance article and the accompanying poster, we discuss the current structural and mechanistic understanding of IFT trains and how they function as macromolecular machines to assemble the structure of the cilium.
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Affiliation(s)
- Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany.,Human Technopole, Via Cristina Belgioioso 171, 20157 Milan, Italy
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36
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Mathieu H, Patten SA, Aragon-Martin JA, Ocaka L, Simpson M, Child A, Moldovan F. Genetic variant of TTLL11 gene and subsequent ciliary defects are associated with idiopathic scoliosis in a 5-generation UK family. Sci Rep 2021; 11:11026. [PMID: 34040021 PMCID: PMC8155187 DOI: 10.1038/s41598-021-90155-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Idiopathic scoliosis (IS) is a complex 3D deformation of the spine with a strong genetic component, most commonly found in adolescent girls. Adolescent idiopathic scoliosis (AIS) affects around 3% of the general population. In a 5-generation UK family, linkage analysis identified the locus 9q31.2-q34.2 as a candidate region for AIS; however, the causative gene remained unidentified. Here, using exome sequencing we identified a rare insertion c.1569_1570insTT in the tubulin tyrosine ligase like gene, member 11 (TTLL11) within that locus, as the IS causative gene in this British family. Two other TTLL11 mutations were also identified in two additional AIS cases in the same cohort. Analyses of primary cells of individuals carrying the c.1569_1570insTT (NM_194252) mutation reveal a defect at the primary cilia level, which is less present, smaller and less polyglutamylated compared to control. Further, in a zebrafish, the knock down of ttll11, and the mutated ttll11 confirmed its role in spine development and ciliary function in the fish retina. These findings provide evidence that mutations in TTLL11, a ciliary gene, contribute to the pathogenesis of IS.
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Affiliation(s)
- Hélène Mathieu
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, 2.17.026, Montreal, QC, H3T 1C5, Canada
| | - Shunmoogum A Patten
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC, H7V1B7, Canada
| | | | - Louise Ocaka
- Centre for Translational Omics-GOSgene, Department of Genetics and Genomic Medicine, UCL GOSH Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Michael Simpson
- Genetics and Molecular Medicine, King's College London, SE1 1UL, London, UK
| | - Anne Child
- Marfan Trust, NHLI, Imperial College, Guy Scadding Building, London, SW3 6LY, UK.
| | - Florina Moldovan
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, 2.17.026, Montreal, QC, H3T 1C5, Canada.
- Faculty of Dentistry, Université de Montréal, Montreal, QC, H3T 1J4, Canada.
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Ho EK, Stearns T. Hedgehog signaling and the primary cilium: implications for spatial and temporal constraints on signaling. Development 2021; 148:dev195552. [PMID: 33914866 PMCID: PMC8126410 DOI: 10.1242/dev.195552] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanisms of vertebrate Hedgehog signaling are linked to the biology of the primary cilium, an antenna-like organelle that projects from the surface of most vertebrate cell types. Although the advantages of restricting signal transduction to cilia are often noted, the constraints imposed are less frequently considered, and yet they are central to how Hedgehog signaling operates in developing tissues. In this Review, we synthesize current understanding of Hedgehog signal transduction, ligand secretion and transport, and cilia dynamics to explore the temporal and spatial constraints imposed by the primary cilium on Hedgehog signaling in vivo.
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Affiliation(s)
- Emily K. Ho
- Department of Developmental Biology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
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38
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Akella JS, Barr MM. The tubulin code specializes neuronal cilia for extracellular vesicle release. Dev Neurobiol 2021; 81:231-252. [PMID: 33068333 PMCID: PMC8052387 DOI: 10.1002/dneu.22787] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/07/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022]
Abstract
Cilia are microtubule-based organelles that display diversity in morphology, ultrastructure, protein composition, and function. The ciliary microtubules of C. elegans sensory neurons exemplify this diversity and provide a paradigm to understand mechanisms driving ciliary specialization. Only a subset of ciliated neurons in C. elegans are specialized to make and release bioactive extracellular vesicles (EVs) into the environment. The cilia of extracellular vesicle releasing neurons have distinct axonemal features and specialized intraflagellar transport that are important for releasing EVs. In this review, we discuss the role of the tubulin code in the specialization of microtubules in cilia of EV releasing neurons.
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Affiliation(s)
- Jyothi S Akella
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Maureen M Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
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39
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CCP1, a Tubulin Deglutamylase, Increases Survival of Rodent Spinal Cord Neurons following Glutamate-Induced Excitotoxicity. eNeuro 2021; 8:ENEURO.0431-20.2021. [PMID: 33688040 PMCID: PMC8021396 DOI: 10.1523/eneuro.0431-20.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/25/2021] [Accepted: 02/12/2021] [Indexed: 01/21/2023] Open
Abstract
Microtubules (MTs) are cytoskeletal elements that provide structural support and act as roadways for intracellular transport in cells. MTs are also needed for neurons to extend and maintain long axons and dendrites that establish connectivity to transmit information through the nervous system. Therefore, in neurons, the ability to independently regulate cytoskeletal stability and MT-based transport in different cellular compartments is essential. Posttranslational modification of MTs is one mechanism by which neurons regulate the cytoskeleton. The carboxypeptidase CCP1 negatively regulates posttranslational polyglutamylation of MTs. In mammals, loss of CCP1, and the resulting hyperglutamylation of MTs, causes neurodegeneration. It has also long been known that CCP1 expression is activated by neuronal injury; however, whether CCP1 plays a neuroprotective role after injury is unknown. Using shRNA-mediated knock-down of CCP1 in embryonic rat spinal cord cultures, we demonstrate that CCP1 protects spinal cord neurons from excitotoxic death. Unexpectedly, excitotoxic injury reduced CCP1 expression in our system. We previously demonstrated that the CCP1 homolog in Caenorhabditis elegans is important for maintenance of neuronal cilia. Although cilia enhance neuronal survival in some contexts, it is not yet clear whether CCP1 maintains cilia in mammalian spinal cord neurons. We found that knock-down of CCP1 did not result in loss or shortening of cilia in cultured spinal cord neurons, suggesting that its effect on survival of excitotoxicity is independent of cilia. Our results support the idea that enzyme regulators of MT polyglutamylation might be therapeutically targeted to prevent excitotoxic death after spinal cord injuries.
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40
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Yang WT, Hong SR, He K, Ling K, Shaiv K, Hu J, Lin YC. The Emerging Roles of Axonemal Glutamylation in Regulation of Cilia Architecture and Functions. Front Cell Dev Biol 2021; 9:622302. [PMID: 33748109 PMCID: PMC7970040 DOI: 10.3389/fcell.2021.622302] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
Cilia, which either generate coordinated motion or sense environmental cues and transmit corresponding signals to the cell body, are highly conserved hair-like structures that protrude from the cell surface among diverse species. Disruption of ciliary functions leads to numerous human disorders, collectively referred to as ciliopathies. Cilia are mechanically supported by axonemes, which are composed of microtubule doublets. It has been recognized for several decades that tubulins in axonemes undergo glutamylation, a post-translational polymodification, that conjugates glutamic acid chains onto the C-terminal tail of tubulins. However, the physiological roles of axonemal glutamylation were not uncovered until recently. This review will focus on how cells modulate glutamylation on ciliary axonemes and how axonemal glutamylation regulates cilia architecture and functions, as well as its physiological importance in human health. We will also discuss the conventional and emerging new strategies used to manipulate glutamylation in cilia.
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Affiliation(s)
- Wen-Ting Yang
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
| | - Shi-Rong Hong
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
| | - Kai He
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Kritika Shaiv
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
| | - JingHua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, United States
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
- Department of Medical Science, National Tsing Hua University, HsinChu City, Taiwan
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41
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Latour BL, Van De Weghe JC, Rusterholz TD, Letteboer SJ, Gomez A, Shaheen R, Gesemann M, Karamzade A, Asadollahi M, Barroso-Gil M, Chitre M, Grout ME, van Reeuwijk J, van Beersum SE, Miller CV, Dempsey JC, Morsy H, Bamshad MJ, Nickerson DA, Neuhauss SC, Boldt K, Ueffing M, Keramatipour M, Sayer JA, Alkuraya FS, Bachmann-Gagescu R, Roepman R, Doherty D. Dysfunction of the ciliary ARMC9/TOGARAM1 protein module causes Joubert syndrome. J Clin Invest 2021; 130:4423-4439. [PMID: 32453716 DOI: 10.1172/jci131656] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Joubert syndrome (JBTS) is a recessive neurodevelopmental ciliopathy characterized by a pathognomonic hindbrain malformation. All known JBTS genes encode proteins involved in the structure or function of primary cilia, ubiquitous antenna-like organelles essential for cellular signal transduction. Here, we used the recently identified JBTS-associated protein armadillo repeat motif-containing 9 (ARMC9) in tandem-affinity purification and yeast 2-hybrid screens to identify a ciliary module whose dysfunction underlies JBTS. In addition to the known JBTS-associated proteins CEP104 and CSPP1, we identified coiled-coil domain containing 66 (CCDC66) and TOG array regulator of axonemal microtubules 1 (TOGARAM1) as ARMC9 interaction partners. We found that TOGARAM1 variants cause JBTS and disrupt TOGARAM1 interaction with ARMC9. Using a combination of protein interaction analyses, characterization of patient-derived fibroblasts, and analysis of CRISPR/Cas9-engineered zebrafish and hTERT-RPE1 cells, we demonstrated that dysfunction of ARMC9 or TOGARAM1 resulted in short cilia with decreased axonemal acetylation and polyglutamylation, but relatively intact transition zone function. Aberrant serum-induced ciliary resorption and cold-induced depolymerization in ARMC9 and TOGARAM1 patient cell lines suggest a role for this new JBTS-associated protein module in ciliary stability.
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Affiliation(s)
- Brooke L Latour
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Tamara Ds Rusterholz
- Institute of Medical Genetics, and.,Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Stef Jf Letteboer
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Matthias Gesemann
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Arezou Karamzade
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Asadollahi
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Manali Chitre
- Department of Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Megan E Grout
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Jeroen van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sylvia Ec van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Caitlin V Miller
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Jennifer C Dempsey
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Heba Morsy
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | | | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, USA.,The University of Washington Center for Mendelian Genomics is detailed in Supplemental Acknowledgments.,University of Washington Center for Mendelian Genomics, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Deborah A Nickerson
- The University of Washington Center for Mendelian Genomics is detailed in Supplemental Acknowledgments.,University of Washington Center for Mendelian Genomics, Seattle, Washington, USA
| | - Stephan Cf Neuhauss
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Karsten Boldt
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Marius Ueffing
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Mohammad Keramatipour
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, and.,Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
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42
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Hsu Y, Seo S, Sheffield VC. Photoreceptor cilia, in contrast to primary cilia, grant entry to a partially assembled BBSome. Hum Mol Genet 2021; 30:87-102. [PMID: 33517424 DOI: 10.1093/hmg/ddaa284] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 11/16/2020] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
The BBSome is a protein complex consisting of BBS1, BBS2, BBS4, BBS5, BBS7, BBS8, BBS9 and BBS18 that associates with intraflagellar transport complexes and specializes in ciliary trafficking. In primary cilia, ciliary entry requires the fully assembled BBSome as well as the small GTPase, ARL6 (BBS3). Retinal photoreceptors possess specialized cilia. In light of key structural and functional differences between primary and specialized cilia, we examined the principles of BBSome recruitment to photoreceptor cilia. We performed sucrose gradient fractionation using retinal lysates of Bbs2-/-, Bbs7-/-, Bbs8-/- and Bbs3-/- mice to determine the status of BBSome assembly, then determined localization of BBSome components using immunohistochemistry. Surprisingly, we found that a subcomplex of the BBSome containing at least BBS1, BBS5, BBS8 and BBS9 is recruited to cilia in the absence of BBS2 or BBS7. In contrast, a BBSome subcomplex consisting of BBS1, BBS2, BBS5, BBS7 and BBS9 is found in Bbs8-/- retinas and is denied ciliary entry in photoreceptor cells. In addition, the BBSome remains fully assembled in Bbs3-/- retinas and can be recruited to photoreceptor cilia in the absence of BBS3. We compared phenotypic severity of their retinal degeneration phenotypes. These findings demonstrate that unlike primary cilia, photoreceptor cilia admit a partially assembled BBSome meeting specific requirements. In addition, the recruitment of the BBSome to photoreceptor cilia does not require BBS3. These findings indicate that the ciliary entry of the BBSome is subjected to cell-specific regulation, particularly in cells with highly adapted forms of cilia such as photoreceptors.
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Affiliation(s)
- Ying Hsu
- Department of Pediatrics, Division of Medical Genetics and Genomics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Seongjin Seo
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Val C Sheffield
- Department of Pediatrics, Division of Medical Genetics and Genomics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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Failler M, Giro-Perafita A, Owa M, Srivastava S, Yun C, Kahler DJ, Unutmaz D, Esteva FJ, Sánchez I, Dynlacht BD. Whole-genome screen identifies diverse pathways that negatively regulate ciliogenesis. Mol Biol Cell 2020; 32:169-185. [PMID: 33206585 PMCID: PMC8120696 DOI: 10.1091/mbc.e20-02-0111] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We performed a high-throughput whole-genome RNAi screen to identify novel inhibitors of ciliogenesis in normal and basal breast cancer cells. Our screen uncovered a previously undisclosed, extensive network of genes linking integrin signaling and cellular adhesion to the extracellular matrix (ECM) with inhibition of ciliation in both normal and cancer cells. Surprisingly, a cohort of genes encoding ECM proteins was also identified. We characterized several ciliation inhibitory genes and showed that their silencing was accompanied by altered cytoskeletal organization and induction of ciliation, which restricts cell growth and migration in normal and breast cancer cells. Conversely, supplying an integrin ligand, vitronectin, to the ECM rescued the enhanced ciliation observed on silencing this gene. Aberrant ciliation could also be suppressed through hyperactivation of the YAP/TAZ pathway, indicating a potential mechanistic basis for our findings. Our findings suggest an unanticipated reciprocal relationship between ciliation and cellular adhesion to the ECM and provide a resource that could vastly expand our understanding of controls involving “outside-in” and “inside-out” signaling that restrain cilium assembly.
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Affiliation(s)
- Marion Failler
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Ariadna Giro-Perafita
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Mikito Owa
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Shalini Srivastava
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Chi Yun
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - David J Kahler
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Derya Unutmaz
- Jackson Laboratory for Genomic Medicine and University of Connecticut School of Medicine, Farmington, CT 06031
| | - Francisco J Esteva
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Irma Sánchez
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Brian D Dynlacht
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
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Jentzsch J, Sabri A, Speckner K, Lallinger-Kube G, Weiss M, Ersfeld K. Microtubule polyglutamylation is important for regulating cytoskeletal architecture and motility in Trypanosoma brucei. J Cell Sci 2020; 133:jcs248047. [PMID: 32843576 DOI: 10.1242/jcs.248047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/30/2020] [Indexed: 11/20/2022] Open
Abstract
The shape of kinetoplastids, such as Trypanosoma brucei, is precisely defined during the stages of the life cycle and governed by a stable subpellicular microtubule cytoskeleton. During the cell cycle and transitions between life cycle stages, this stability has to transiently give way to a dynamic behaviour to enable cell division and morphological rearrangements. How these opposing requirements of the cytoskeleton are regulated is poorly understood. Two possible levels of regulation are activities of cytoskeleton-associated proteins and microtubule post-translational modifications (PTMs). Here, we investigate the functions of two putative tubulin polyglutamylases in T. brucei, TTLL6A and TTLL12B. Depletion of both proteins leads to a reduction in tubulin polyglutamylation in situ and is associated with disintegration of the posterior cell pole, loss of the microtubule plus-end-binding protein EB1 and alterations of microtubule dynamics. We also observe a reduced polyglutamylation of the flagellar axoneme. Quantitative motility analysis reveals that the PTM imbalance correlates with a transition from directional to diffusive cell movement. These data show that microtubule polyglutamylation has an important role in regulating cytoskeletal architecture and motility in the parasite T. bruceiThis article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jana Jentzsch
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Adal Sabri
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Konstantin Speckner
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Gertrud Lallinger-Kube
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Klaus Ersfeld
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
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The emerging role of tubulin posttranslational modifications in cilia and ciliopathies. BIOPHYSICS REPORTS 2020. [DOI: 10.1007/s41048-020-00111-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes. Nat Struct Mol Biol 2020; 27:802-813. [PMID: 32747782 DOI: 10.1038/s41594-020-0462-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/12/2020] [Indexed: 11/08/2022]
Abstract
Glutamylation, introduced by tubulin tyrosine ligase-like (TTLL) enzymes, is the most abundant modification of brain tubulin. Essential effector proteins read the tubulin glutamylation pattern, and its misregulation causes neurodegeneration. TTLL glutamylases post-translationally add glutamates to internal glutamates in tubulin carboxy-terminal tails (branch initiation, through an isopeptide bond), and additional glutamates can extend these (elongation). TTLLs are thought to specialize in initiation or elongation, but the mechanistic basis for regioselectivity is unknown. We present cocrystal structures of murine TTLL6 bound to tetrahedral intermediate analogs that delineate key active-site residues that make this enzyme an elongase. We show that TTLL4 is exclusively an initiase and, through combined structural and phylogenetic analyses, engineer TTLL6 into a branch-initiating enzyme. TTLL glycylases add glycines post-translationally to internal glutamates, and we find that the same active-site residues discriminate between initiase and elongase glycylases. These active-site specializations of TTLL glutamylases and glycylases ultimately yield the chemical complexity of cellular microtubules.
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47
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Acute inhibition of centriolar satellite function and positioning reveals their functions at the primary cilium. PLoS Biol 2020; 18:e3000679. [PMID: 32555591 PMCID: PMC7326281 DOI: 10.1371/journal.pbio.3000679] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/30/2020] [Accepted: 06/04/2020] [Indexed: 12/12/2022] Open
Abstract
Centriolar satellites are dynamic, membraneless granules composed of over 200 proteins. They store, modify, and traffic centrosome and primary cilium proteins, and help to regulate both the biogenesis and some functions of centrosomes and cilium. In most cell types, satellites cluster around the perinuclear centrosome, but their integrity and cellular distribution are dynamically remodeled in response to different stimuli, such as cell cycle cues. Dissecting the specific and temporal functions and mechanisms of satellites and how these are influenced by their cellular positioning and dynamics has been challenging using genetic approaches, particularly in ciliated and proliferating cells. To address this, we developed a chemical-based trafficking assay to rapidly and efficiently redistribute satellites to either the cell periphery or center, and fuse them into stable clusters in a temporally controlled way. Induced satellite clustering at either the periphery or center resulted in antagonistic changes in the pericentrosomal levels of a subset of proteins, revealing a direct and selective role for their positioning in protein targeting and sequestration. Systematic analysis of the interactome of peripheral satellite clusters revealed enrichment of proteins implicated in cilium biogenesis and mitosis. Importantly, induction of peripheral satellite targeting in ciliated cells revealed a function for satellites not just for efficient cilium assembly but also in the maintenance of steady-state cilia and in cilia disassembly by regulating the structural integrity of the ciliary axoneme. Finally, perturbing satellite distribution and dynamics inhibited their mitotic dissolution, and mitotic progression was perturbed only in cells with centrosomal satellite clustering. Collectively, our results for the first time showed a direct link between satellite functions and their pericentrosomal clustering, suggested new mechanisms underlying satellite functions during cilium assembly, and provided a new tool for probing temporal satellite functions in different contexts What happens when centriolar satellites are not in the right place at the right time? By redistributing satellites to the periphery or center of the cell and assessing the consequences of their mispositioning, this study reveals novel functions for satellites during mitosis, cilium maintenance, and cilium disassembly and suggests new mechanisms.
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48
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The tubulin code and its role in controlling microtubule properties and functions. Nat Rev Mol Cell Biol 2020; 21:307-326. [PMID: 32107477 DOI: 10.1038/s41580-020-0214-3] [Citation(s) in RCA: 499] [Impact Index Per Article: 99.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Microtubules are core components of the eukaryotic cytoskeleton with essential roles in cell division, shaping, motility and intracellular transport. Despite their functional heterogeneity, microtubules have a highly conserved structure made from almost identical molecular building blocks: the tubulin proteins. Alternative tubulin isotypes and a variety of post-translational modifications control the properties and functions of the microtubule cytoskeleton, a concept known as the 'tubulin code'. Here we review the current understanding of the molecular components of the tubulin code and how they impact microtubule properties and functions. We discuss how tubulin isotypes and post-translational modifications control microtubule behaviour at the molecular level and how this translates into physiological functions at the cellular and organism levels. We then go on to show how fine-tuning of microtubule function by some tubulin modifications can affect homeostasis and how perturbation of this fine-tuning can lead to a range of dysfunctions, many of which are linked to human disease.
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49
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Bennett HW, Gustavsson AK, Bayas CA, Petrov PN, Mooney N, Moerner WE, Jackson PK. Novel fibrillar structure in the inversin compartment of primary cilia revealed by 3D single-molecule superresolution microscopy. Mol Biol Cell 2020; 31:619-639. [PMID: 31895004 PMCID: PMC7202064 DOI: 10.1091/mbc.e19-09-0499] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary cilia in many cell types contain a periaxonemal subcompartment called the inversin compartment. Four proteins have been found to assemble within the inversin compartment: INVS, ANKS6, NEK8, and NPHP3. The function of the inversin compartment is unknown, but it appears to be critical for normal development, including left–right asymmetry and renal tissue homeostasis. Here we combine superresolution imaging of human RPE1 cells, a classic model for studying primary cilia in vitro, with a genetic dissection of the protein–protein binding relationships that organize compartment assembly to develop a new structural model. We observe that INVS is the core structural determinant of a compartment composed of novel fibril-like substructures, which we identify here by three-dimensional single-molecule superresolution imaging. We find that NEK8 and ANKS6 depend on INVS for localization to these fibrillar assemblies and that ANKS6-NEK8 density within the compartment is regulated by NEK8. Together, NEK8 and ANKS6 are required downstream of INVS to localize and concentrate NPHP3 within the compartment. In the absence of these upstream components, NPHP3 is redistributed within cilia. These results provide a more detailed structure for the inversin compartment and introduce a new example of a membraneless compartment organized by protein–protein interactions.
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Affiliation(s)
- Henrietta W Bennett
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Anna-Karin Gustavsson
- Department of Chemistry, Stanford University, Stanford, CA 94305.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE 17177, Sweden
| | - Camille A Bayas
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nancie Mooney
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
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50
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Akella JS, Silva M, Morsci NS, Nguyen KC, Rice WJ, Hall DH, Barr MM. Cell type-specific structural plasticity of the ciliary transition zone in C. elegans. Biol Cell 2019; 111:95-107. [PMID: 30681171 DOI: 10.1111/boc.201800042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND INFORMATION The current consensus on cilia development posits that the ciliary transition zone (TZ) is formed via extension of nine centrosomal microtubules. In this model, TZ structure remains unchanged in microtubule number throughout the cilium life cycle. This model does not however explain structural variations of TZ structure seen in nature and could also lend itself to the misinterpretation that deviations from nine-doublet microtubule ultrastructure represent an abnormal phenotype. Thus, a better understanding of events that occur at the TZ in vivo during metazoan development is required. RESULTS To address this issue, we characterized ultrastructure of two types of sensory cilia in developing Caenorhabditis elegans. We discovered that, in cephalic male (CEM) and inner labial quadrant (IL2Q) sensory neurons, ciliary TZs are structurally plastic and remodel from one structure to another during animal development. The number of microtubule doublets forming the TZ can be increased or decreased over time, depending on cilia type. Both cases result in structural TZ intermediates different from TZ in cilia of adult animals. In CEM cilia, axonemal extension and maturation occurs concurrently with TZ structural maturation. CONCLUSIONS AND SIGNIFICANCE Our work extends the current model to include the structural plasticity of metazoan transition zone, which can be structurally delayed, maintained or remodelled in cell type-specific manner.
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Affiliation(s)
- Jyothi S Akella
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08854, USA
| | - Malan Silva
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08854, USA.,Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | | | - Ken C Nguyen
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - William J Rice
- Simons Electron Microscopy Center, New York Structural Biology Center, NY, 10027, USA
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Maureen M Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08854, USA
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