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Smith KP, Chakravarthy S, Rahi A, Chakraborty M, Vosberg KM, Tonelli M, Plach MG, Grigorescu AA, Curtis JE, Varma D. SAXS/MC studies of the mixed-folded protein Cdt1 reveal monomeric, folded over conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573975. [PMID: 38260441 PMCID: PMC10802334 DOI: 10.1101/2024.01.03.573975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cdt1 is a protein critical for DNA replication licensing and is well-established to be a binding partner of the minichromosome maintenance (MCM) complex. Cdt1 has also been demonstrated to have an emerging, "moonlighting" role at the kinetochore via direct binding to microtubules and to the Ndc80 complex. However, it is not known how the structure and conformations of Cdt1 could allow for these multiple, completely unique sets of protein complexes. And while there exist multiple robust methods to study entirely folded or entirely unfolded proteins, structure-function studies of combined, mixed folded/disordered proteins remain challenging. It this work, we employ multiple orthogonal biophysical and computational techniques to provide a detailed structural characterization of human Cdt1 92-546. DSF and DSCD show both folded winged helix (WH) domains of Cdt1 are relatively unstable. CD and NMR show the N-terminal and the linker regions are intrinsically disordered. Using DLS and SEC-MALS, we show that Cdt1 is polydisperse, monomeric at high concentrations, and without any apparent inter-molecular self-association. SEC-SAXS of the monomer in solution enabled computational modeling of the protein in silico. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble. Using experimental SAXS data, we filtered for conformations which did and did not fit our data. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with our SAXS data. The best fit models have the N-terminal and linker regions extended into solution and the two folded domains close to each other in apparent "folded over" conformations. The best fit Cdt1 conformations are consistent with a function as a scaffold protein which may be sterically blocked without the presence of binding partners. Our studies also provide a template for combining experimental and computational biophysical techniques to study mixed-folded proteins.
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Affiliation(s)
- Kyle P Smith
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Present Address, Xylia Therapeutics, Waltham, MA, 02451, USA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Amit Rahi
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Manas Chakraborty
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kristen M Vosberg
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Arabela A Grigorescu
- Keck Biophysics Facility, Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60201, USA
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD, 20899, United States
| | - Dileep Varma
- Department of Cell & Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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Rahi A, Chakraborty M, Agarwal S, Vosberg KM, Agarwal S, Wang AY, McKenney RJ, Varma D. The Ndc80-Cdt1-Ska1 complex is a central processive kinetochore-microtubule coupling unit. J Cell Biol 2023; 222:e202208018. [PMID: 37265445 PMCID: PMC10238862 DOI: 10.1083/jcb.202208018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/17/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
It is known that microtubule-binding proteins including the Ska1 complex and the DNA replication licensing factor, Cdt1, enable the kinetochore-localized Ndc80 complex to form robust kinetochore-microtubule attachments. However, it is not clear how the Ndc80 complex is stably coupled to dynamic spindle microtubule plus-ends. Here, we have developed a conditional auxin-inducible degron approach to reveal a function for Cdt1 in chromosome segregation and kinetochore-microtubule interactions that is separable from its role in DNA replication licensing. Further, we demonstrate that a direct interaction between Cdt1 and Ska1 is required for recruiting Cdt1 to kinetochores and spindle microtubules. Cdt1 phosphorylation by Cdk1 kinase is critical for Ska1 binding, kinetochore-microtubule attachments, and mitotic progression. Furthermore, we show that Cdt1 synergizes with Ndc80 and Ska1 for microtubule binding, including forming a diffusive, tripartite Ndc80-Cdt1-Ska1 complex that can processively track dynamic microtubule plus-ends in vitro. Taken together, our data identify the Ndc80-Cdt1-Ska1 complex as a central molecular unit that can promote processive bidirectional tip-tracking of microtubules by kinetochores.
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Affiliation(s)
- Amit Rahi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Manas Chakraborty
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Kristen M. Vosberg
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Annie Y. Wang
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Richard J. McKenney
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California Davis, Davis, CA, USA
| | - Dileep Varma
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Sun MC, Fang K, Li ZX, Chu Y, Xu AP, Zhao ZY, Leng ZY, Zhang YW, Zhang ZH, Zhang L, Chen T, Xu MD. ETV5 overexpression promotes progression of esophageal squamous cell carcinoma by upregulating SKA1 and TRPV2. Int J Med Sci 2022; 19:1072-1081. [PMID: 35813298 PMCID: PMC9254378 DOI: 10.7150/ijms.71892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/30/2022] [Indexed: 01/23/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is notorious for the rapid progression especially early tumor metastasis due to the unclear mechanism. Recently, ETV5 attracts much attention for its potential role as an oncogenic transcription factor involved in multiple cancers. However, no one reported the mechanism behind the association between ETV5 expression and esophageal squamous cell carcinoma progression. In this study, we found that ETV5 was upregulated in ESCC both from online database and our ESCC tissues and ETV5 was associated with tumor staging and prognosis. Knockdown of ETV5 or its downstream genes SKA1 and TRPV2 significantly suppress ESCC cells migration and invasion, respectively. Additionally, in vivo study showed knockdown of ETV5 inhibited tumor metastasis. Further experiments unveiled ETV5 could transcriptionally upregulate the expression of SKA1 and TRPV2 and further activate MMPs in ESCC progression. In conclusion, ETV5 was associated with ESCC tumor staging and ESCC prognosis clinically. ETV5 promoted metastasis of ESCC by activating MMPs through augmenting the transcription of SKA1 and TRPV2. ETV5 was likely to be a novel oncogene and therapeutic target in ESCC.
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Affiliation(s)
- Ming-Chuang Sun
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Kang Fang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Zhao-Xing Li
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Yuan Chu
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Ai-Ping Xu
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Zi-Ying Zhao
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Zhu-Yun Leng
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Yun-Wei Zhang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Ze-Hua Zhang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Li Zhang
- Department of Pathology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Tao Chen
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Mei-Dong Xu
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
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