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Carden S, Vitiello E, Rosa E Silva I, Holder J, Quarantotti V, Kishore K, Roamio Franklin VN, D'Santos C, Ochi T, van Breugel M, Gergely F. Proteomic profiling of centrosomes across multiple mammalian cell and tissue types by an affinity capture method. Dev Cell 2023; 58:2393-2410.e9. [PMID: 37852252 DOI: 10.1016/j.devcel.2023.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
Centrosomes are the major microtubule-organizing centers in animals and play fundamental roles in many cellular processes. Understanding how their composition varies across diverse cell types and how it is altered in disease are major unresolved questions, yet currently available centrosome isolation protocols are cumbersome and time-consuming, and they lack scalability. Here, we report the development of centrosome affinity capture (CAPture)-mass spectrometry (MS), a powerful one-step purification method to obtain high-resolution centrosome proteomes from mammalian cells. Utilizing a synthetic peptide derived from CCDC61 protein, CAPture specifically isolates intact centrosomes. Importantly, as a bead-based affinity method, it enables rapid sample processing and multiplexing unlike conventional approaches. Our study demonstrates the power of CAPture-MS to elucidate cell-type-dependent heterogeneity in centrosome composition, dissect hierarchical interactions, and identify previously unknown centrosome components. Overall, CAPture-MS represents a transformative tool to unveil temporal, regulatory, cell-type- and tissue-specific changes in centrosome proteomes in health and disease.
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Affiliation(s)
- Sarah Carden
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Elisa Vitiello
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - James Holder
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Valentina Quarantotti
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | - Clive D'Santos
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Takashi Ochi
- MRC Laboratory of Molecular Biology, Cambridge, UK; The Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
| | - Mark van Breugel
- MRC Laboratory of Molecular Biology, Cambridge, UK; School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK.
| | - Fanni Gergely
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Department of Biochemistry, University of Oxford, Oxford, UK.
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2
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Khan H, Ochi T. Plant PAXX has an XLF-like function and stimulates DNA end joining by the Ku-DNA ligase IV/XRCC4 complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:58-68. [PMID: 37340932 DOI: 10.1111/tpj.16359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/22/2023]
Abstract
Non-homologous end joining (NHEJ) plays a major role in repairing DNA double-strand breaks and is key to genome stability and editing. The minimal core NHEJ proteins, namely Ku70, Ku80, DNA ligase IV and XRCC4, are conserved, but other factors vary in different eukaryote groups. In plants, the only known NHEJ proteins are the core factors, while the molecular mechanism of plant NHEJ remains unclear. Here, we report a previously unidentified plant ortholog of PAXX, the crystal structure of which showed a similar fold to human 'PAXX'. However, plant PAXX has similar molecular functions to human XLF, by directly interacting with Ku70/80 and XRCC4. This suggests that plant PAXX combines the roles of mammalian PAXX and XLF and that these functions merged into a single protein during evolution. This is consistent with a redundant function of PAXX and XLF in mammals.
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Affiliation(s)
- Hira Khan
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Takashi Ochi
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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Li L, Li J, Ou Y, Wu J, Li H, Wang X, Tang L, Dai X, Yang C, Wei Z, Yin Z, Shu Y. Ccdc57 is required for straightening the body axis by regulating ciliary motility in the brain ventricle of zebrafish. J Genet Genomics 2023; 50:253-263. [PMID: 36669737 DOI: 10.1016/j.jgg.2022.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/22/2022] [Accepted: 12/31/2022] [Indexed: 01/19/2023]
Abstract
Recently, cilia defects have been proposed to contribute to scoliosis. Here, we demonstrate that coiled-coil domain-containing 57 (Ccdc57) plays an essential role in straightening the body axis of zebrafish by regulating ciliary beating in the brain ventricle (BV). Zygotic ccdc57 (Zccdc57) mutant zebrafish developes scoliosis without significant changes in their bone density and calcification, and the maternal-zygotic ccdc57 (MZccdc57) mutant embryos display curved bodies since the long-pec stage. The expression of ccdc57 is enriched in ciliated tissues and immunofluorescence analysis reveals colocalization of Ccdc57-HA with acetylated α-tubulin, implicating it in having a role in ciliary function. Further examination reveals that it is the coordinated cilia beating of multiple cilia bundles (MCB) in the MZccdc57 mutant embryos that is affected at 48 hours post fertilization, when the compromised cerebrospinal fluid flow and curved body axis have already occurred. Either ccdc57 mRNA injection or epinephrine treatment reverses the spinal curvature in MZccdc57 mutant larvae from ventrally curly to straight or even dorsally curly and significantly upregulates urotensin signaling. This study reveals the role of ccdc57 in maintaining coordinated cilia beating of MCB in the BV.
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Affiliation(s)
- Lu Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Juan Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Yuan Ou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Jiaxin Wu
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Huilin Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xin Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Liying Tang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xiangyan Dai
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Zehong Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Yuqin Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.
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Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes. Commun Biol 2022; 5:312. [PMID: 35383272 PMCID: PMC8983713 DOI: 10.1038/s42003-022-03269-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Obtaining the high-resolution structures of proteins and their complexes is a crucial aspect of understanding the mechanisms of life. Experimental structure determination methods are time-consuming, expensive and cannot keep pace with the growing number of protein sequences available through genomic DNA sequencing. Thus, the ability to accurately predict the structure of proteins from their sequence is a holy grail of structural and computational biology that would remove a bottleneck in our efforts to understand as well as rationally engineer living systems. Recent advances in protein structure prediction, in particular the breakthrough with the AI-based tool AlphaFold2 (AF2), hold promise for achieving this goal, but the practical utility of AF2 remains to be explored. Focusing on proteins with essential roles in centrosome and centriole biogenesis, we demonstrate the quality and usability of the AF2 prediction models and we show that they can provide important insights into the modular organization of two key players in this process, CEP192 and CEP44. Furthermore, we used the AF2 algorithm to elucidate and then experimentally validate previously unknown prime features in the structure of TTBK2 bound to CEP164, as well as the Chibby1-FAM92A complex for which no structural information was available to date. These findings have important implications in understanding the regulation and function of these complexes. Finally, we also discuss some practical limitations of AF2 and anticipate the implications for future research approaches in the centriole/centrosome field. Using experimental data, the authors assess the quality and discuss the limitations of AlphaFold2 predictions of protein structures and protein-protein interactions essential for centrosome and centriole biogenesis.
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Nommick A, Boutin C, Rosnet O, Schirmer C, Bazellières E, Thomé V, Loiseau E, Viallat A, Kodjabachian L. Lrrcc1 and Ccdc61 are conserved effectors of multiciliated cell function. J Cell Sci 2022; 135:274401. [DOI: 10.1242/jcs.258960] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Ciliated epithelia perform essential functions across animal evolution, ranging from locomotion of marine organisms to mucociliary clearance of airways in mammals. These epithelia are composed of multiciliated cells (MCCs) harbouring myriads of motile cilia, which rest on modified centrioles called basal bodies (BBs), and beat coordinately to generate directed fluid flows. Thus, BB biogenesis and organization is central to MCC function. In basal eukaryotes, the coiled-coil domain proteins Lrrcc1 and Ccdc61 were shown to be required for proper BB construction and function. Here, we used the Xenopus embryonic ciliated epidermis to characterize Lrrcc1 and Ccdc61 in vertebrate MCCs. We found that they both encode BB components, localized proximally at the junction with striated rootlets. Knocking down either gene caused defects in BB docking, spacing, and polarization. Moreover, their depletion impaired the apical cytoskeleton, and altered ciliary beating. Consequently, cilia-powered fluid flow was greatly reduced in morphant tadpoles, which displayed enhanced mortality when exposed to pathogenic bacteria. This work illustrates how integration across organizational scales make elementary BB components essential for the emergence of the physiological function of ciliated epithelia.
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Affiliation(s)
- Aude Nommick
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Camille Boutin
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Olivier Rosnet
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Claire Schirmer
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Elsa Bazellières
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Etienne Loiseau
- Aix Marseille Univ, CNRS, CINaM, Turing Center for Living Systems, Marseille, France
| | - Annie Viallat
- Aix Marseille Univ, CNRS, CINaM, Turing Center for Living Systems, Marseille, France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
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Kinetic and structural roles for the surface in guiding SAS-6 self-assembly to direct centriole architecture. Nat Commun 2021; 12:6180. [PMID: 34702818 PMCID: PMC8548535 DOI: 10.1038/s41467-021-26329-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 09/24/2021] [Indexed: 11/24/2022] Open
Abstract
Discovering mechanisms governing organelle assembly is a fundamental pursuit in biology. The centriole is an evolutionarily conserved organelle with a signature 9-fold symmetrical chiral arrangement of microtubules imparted onto the cilium it templates. The first structure in nascent centrioles is a cartwheel, which comprises stacked 9-fold symmetrical SAS-6 ring polymers emerging orthogonal to a surface surrounding each resident centriole. The mechanisms through which SAS-6 polymerization ensures centriole organelle architecture remain elusive. We deploy photothermally-actuated off-resonance tapping high-speed atomic force microscopy to decipher surface SAS-6 self-assembly mechanisms. We show that the surface shifts the reaction equilibrium by ~104 compared to solution. Moreover, coarse-grained molecular dynamics and atomic force microscopy reveal that the surface converts the inherent helical propensity of SAS-6 polymers into 9-fold rings with residual asymmetry, which may guide ring stacking and impart chiral features to centrioles and cilia. Overall, our work reveals fundamental design principles governing centriole assembly. The centriole exhibits an evolutionarily conserved 9-fold radial symmetry that stems from a cartwheel containing vertically stacked ring polymers that harbor 9 homodimers of the protein SAS-6. Here the authors show how dual properties inherent to surface-guided SAS-6 self-assembly possess spatial information that dictates correct scaffolding of centriole architecture.
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Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly. Nat Commun 2021; 12:3805. [PMID: 34155202 PMCID: PMC8217511 DOI: 10.1038/s41467-021-23897-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
Centrioles are evolutionarily conserved multi-protein organelles essential for forming cilia and centrosomes. Centriole biogenesis begins with self-assembly of SAS-6 proteins into 9-fold symmetrical ring polymers, which then stack into a cartwheel that scaffolds organelle formation. The importance of this architecture has been difficult to decipher notably because of the lack of precise tools to modulate the underlying assembly reaction. Here, we developed monobodies against Chlamydomonas reinhardtii SAS-6, characterizing three in detail with X-ray crystallography, atomic force microscopy and cryo-electron microscopy. This revealed distinct monobody-target interaction modes, as well as specific consequences on ring assembly and stacking. Of particular interest, monobody MBCRS6-15 induces a conformational change in CrSAS-6, resulting in the formation of a helix instead of a ring. Furthermore, we show that this alteration impairs centriole biogenesis in human cells. Overall, our findings identify monobodies as powerful molecular levers to alter the architecture of multi-protein complexes and tune centriole assembly.
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Asa ADDC, Wanotayan R, Sharma MK, Tsukada K, Shimada M, Matsumoto Y. Functional analysis of XRCC4 mutations in reported microcephaly and growth defect patients in terms of radiosensitivity. JOURNAL OF RADIATION RESEARCH 2021; 62:380-389. [PMID: 33842963 PMCID: PMC8127669 DOI: 10.1093/jrr/rrab016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/01/2021] [Indexed: 05/08/2023]
Abstract
Non-homologous end joining is one of the main pathways for DNA double-strand break (DSB) repair and is also implicated in V(D)J recombination in immune system. Therefore, mutations in non-homologous end-joining (NHEJ) proteins were found to be associated with immunodeficiency in human as well as in model animals. Several human patients with mutations in XRCC4 were reported to exhibit microcephaly and growth defects, but unexpectedly showed normal immune function. Here, to evaluate the functionality of these disease-associated mutations of XRCC4 in terms of radiosensitivity, we generated stable transfectants expressing these mutants in XRCC4-deficient murine M10 cells and measured their radiosensitivity by colony formation assay. V83_S105del, R225X and D254Mfs*68 were expressed at a similar level to wild-type XRCC4, while W43R, R161Q and R275X were expressed at even higher level than wild-type XRCC4. The expression levels of DNA ligase IV in the transfectants with these mutants were comparable to that in the wild-type XRCC4 transfectant. The V83S_S105del transfectant and, to a lesser extent, D254Mfs*68 transfectant, showed substantially increased radiosensitivity compared to the wild-type XRCC4 transfectant. The W43R, R161Q, R225X and R275X transfectants showed a slight but statistically significant increase in radiosensitivity compared to the wild-type XRCC4 transfectant. When expressed as fusion proteins with Green fluorescent protein (GFP), R225X, R275X and D254Mfs*68 localized to the cytoplasm, whereas other mutants localized to the nucleus. These results collectively indicated that the defects of XRCC4 in patients might be mainly due to insufficiency in protein quantity and impaired functionality, underscoring the importance of XRCC4's DSB repair function in normal development.
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Affiliation(s)
- Anie Day D C Asa
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Rujira Wanotayan
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Department of Radiological Technology, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Mukesh Kumar Sharma
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Department of Zoology, SPC Government College, Ajmer-305001, Rajasthan, India
| | - Kaima Tsukada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Mikio Shimada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yoshihisa Matsumoto
- Corresponding author. Yoshihisa Matsumoto, Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550 Japan. E-mail: ; FAX: +81-3-5734-3703
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