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Shi T, Hu Z, Tian L, Yang Y. Advances in lung adenocarcinoma: A novel perspective on prognoses and immune responses of CENPO as an oncogenic superenhancer. Transl Oncol 2023; 34:101691. [PMID: 37207381 DOI: 10.1016/j.tranon.2023.101691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/13/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most prevalent form of lung cancer globally, and its treatment remains a significant challenge. Therefore, it is crucial to comprehend the microenvironment to improve therapy and prognosis urgently. In this study, we utilized bioinformatic methods to analyze the transcription expression profile of patient samples with complete clinical information from the TCGA-LUAD datasets. To validate our findings, we also analyzed the Gene Expression Omnibus (GEO) datasets. The super-enhancer (SE) was visualized using the peaks of the H3K27ac and H3K4me1 ChIP-seq signal, which were identified by the Integrative Genomics Viewer (IGV). To further investigate the role of Centromere protein O (CENPO) in LUAD, we conducted various assays including Western blot, qRT-PCR, flow cytometry, wound healing and transwell assays to assess the cell functions of CENPO in vitro. The overexpression of CENPO is linked to a poor prognosis in patients with LUAD. Strong signal peaks of H3K27ac and H3K4me1 were also observed near the predicted SE regions of CENPO. CENPO was found to be positively associated with the expression levels of immune checkpoints and drug IC50 value (Roscovitine and TGX221), but negatively associated with the fraction levels of several immature cells and drug IC50 value (CCT018159, GSK1904529A, Lenaildomide, and PD-173074). Additionally, CENPO-associated prognostic signature (CPS) was identified as an independent risk factor. The high-risk group for LUAD is identified based on CPS enrichment, which involved not only endocytosis that transfers mitochondria to promote cell survival in response to chemotherapy but also cell cycle promotion that leads to drug resistance. The removal of CENPO significantly suppressed metastasis and induced arrest and apoptosis of LUAD cells. The involvement of CENPO in the immunosuppression of LUAD provides a prognostic signature for LUAD patients.
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Affiliation(s)
- Tongdong Shi
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital of Chongqing Medical University, No.288 Tianwen Avenue, Nan'an District, Chongqing 401336, People's Republic of China
| | - Zaoxiu Hu
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University, No.519 Kunzhou Road, Xishan District, Kunming, Yunnan 650118, People's Republic of China
| | - Li Tian
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital of Chongqing Medical University, No.288 Tianwen Avenue, Nan'an District, Chongqing 401336, People's Republic of China
| | - Yanlong Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, People's Republic of China.
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Shahi A, Kahle J, Hopkins C, Diakonova M. The SH2 domain and kinase activity of JAK2 target JAK2 to centrosome and regulate cell growth and centrosome amplification. PLoS One 2022; 17:e0261098. [PMID: 35089929 PMCID: PMC8797172 DOI: 10.1371/journal.pone.0261098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
JAK2 is cytokine-activated non-receptor tyrosine kinase. Although JAK2 is mainly localized at the plasma membrane, it is also present on the centrosome. In this study, we demonstrated that JAK2 localization to the centrosome depends on the SH2 domain and intact kinase activity. We created JAK2 mutants deficient in centrosomal localization ΔSH2, K882E and (ΔSH2, K882E). We showed that JAK2 WT clone strongly enhances cell proliferation as compared to control cells while JAK2 clones ΔSH2, K882E and (ΔSH2, K882E) proliferate slower than JAK2 WT cells. These mutant clones also progress much slower through the cell cycle as compared to JAK2 WT clone and the enhanced proliferation of JAK2 WT cells is accompanied by increased S -> G2 progression. Both the SH2 domain and the kinase activity of JAK2 play a role in prolactin-dependent activation of JAK2 substrate STAT5. We showed that JAK2 is an important regulator of centrosome function as the SH2 domain of JAK2 regulates centrosome amplification. The cells overexpressing ΔSH2 and (ΔSH2, K-E) JAK2 have almost three-fold the amplified centrosomes of WT cells. In contrast, the kinase activity of JAK2 is dispensable for centrosome amplification. Our observations provide novel insight into the role of SH2 domain and kinase activity of JAK2 in centrosome localization of JAK2 and in the regulation of cell growth and centrosome biogenesis.
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Affiliation(s)
- Aashirwad Shahi
- Department of Biological Sciences, University of Toledo, Toledo, OH, United States of America
| | - Jacob Kahle
- Department of Biological Sciences, University of Toledo, Toledo, OH, United States of America
| | - Chandler Hopkins
- Department of Biological Sciences, University of Toledo, Toledo, OH, United States of America
| | - Maria Diakonova
- Department of Biological Sciences, University of Toledo, Toledo, OH, United States of America
- * E-mail:
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3
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Gao Y, Ping L, Duong D, Zhang C, Dammer EB, Li Y, Chen P, Chang L, Gao H, Wu J, Xu P. Mass-Spectrometry-Based Near-Complete Draft of the Saccharomyces cerevisiae Proteome. J Proteome Res 2021; 20:1328-1340. [PMID: 33443437 DOI: 10.1021/acs.jproteome.0c00721] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proteomics approaches designed to catalogue all open reading frames (ORFs) under a defined set of growth conditions of an organism have flourished in recent years. However, no proteome has been sequenced completely so far. Here, we generate the largest yeast proteome data set, including 5610 identified proteins, using a strategy based on optimized sample preparation and high-resolution mass spectrometry. Among the 5610 identified proteins, 94.1% are core proteins, which achieves near-complete coverage of the yeast ORFs. Comprehensive analysis of missing proteins showed that proteins are missed mainly due to physical properties. A review of protein abundance shows that our proteome encompasses a uniquely broad dynamic range. Additionally, these values highly correlate with mRNA abundance, implying a high level of accuracy, sensitivity, and precision. We present examples of how the data could be used, including reannotating gene localization, providing expression evidence of pseudogenes. Our near-complete yeast proteome data set will be a useful and important resource for further systematic studies.
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Affiliation(s)
- Yuan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Lingyan Ping
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Duc Duong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,Center for Neurodegenerative Diseases, Emory Proteomics Service Center, and Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Chengpu Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Eric B Dammer
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,Center for Neurodegenerative Diseases, Emory Proteomics Service Center, and Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Peiru Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Huiying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Junzhu Wu
- School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P. R. China.,Anhui Medical University, Hefei 230032, P. R. China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
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4
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Ghaleb A, Padellan M, Marchenko N. Mutant p53 drives the loss of heterozygosity by the upregulation of Nek2 in breast cancer cells. Breast Cancer Res 2020; 22:133. [PMID: 33267874 PMCID: PMC7709447 DOI: 10.1186/s13058-020-01370-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Mutations in one allele of the TP53 gene in early stages are frequently followed by the loss of the remaining wild-type p53 (wtp53) allele (p53LOH) during tumor progression. Despite the strong notion of p53LOH as a critical step in tumor progression, its oncogenic outcomes that facilitate the selective pressure for p53LOH occurrence were not elucidated. METHODS Using MMTV;ErbB2 mouse model of breast cancer carrying heterozygous R172H p53 mutation, we identified a novel gain-of-function (GOF) activity of mutant p53 (mutp53): the exacerbated loss of wtp53 allele in response to γ-irradiation. RESULTS As consequences of p53LOH in mutp53 heterozygous cells, we observed profound stabilization of mutp53 protein, the loss of p21 expression, the abrogation of G2/M checkpoint, chromosomal instability, centrosome amplification, and transcriptional upregulation of mitotic kinase Nek2 (a member of Never in Mitosis (NIMA) Kinases family) involved in the regulation of centrosome function. To avoid the mitotic catastrophe in the absence of G2/M checkpoint, cells with centrosome amplification adapt Nek2-mediated centrosomes clustering as pro-survival mutp53 GOF mechanism enabling unrestricted proliferation and clonal expansion of cells with p53LOH. Thus, the clonal dominance of mutp53 cells with p53LOH may represent the mechanism of irradiation-induced p53LOH. We show that pharmacological and genetic ablation of Nek2 decreases centrosome clustering and viability of specifically mutp53 cells with p53LOH. CONCLUSION In a heterogeneous tumor population, Nek2 inhibition may alter the selective pressure for p53LOH by contraction of the mutp53 population with p53LOH, thus, preventing the outgrowth of genetically unstable, more aggressive cells.
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Affiliation(s)
- Amr Ghaleb
- Department of Pathology, Stony Brook University, Stony Brook, NY, 11794-8691, USA.
| | - Malik Padellan
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - Natalia Marchenko
- Department of Pathology, Stony Brook University, Stony Brook, NY, 11794-8691, USA
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Liu X, Liu X, Wang H, Dou Z, Ruan K, Hill DL, Li L, Shi Y, Yao X. Phase separation drives decision making in cell division. J Biol Chem 2020; 295:13419-13431. [PMID: 32699013 DOI: 10.1074/jbc.rev120.011746] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of biomolecules drives the formation of subcellular compartments with distinct physicochemical properties. These compartments, free of lipid bilayers and therefore called membraneless organelles, include nucleoli, centrosomes, heterochromatin, and centromeres. These have emerged as a new paradigm to account for subcellular organization and cell fate decisions. Here we summarize recent studies linking LLPS to mitotic spindle, heterochromatin, and centromere assembly and their plasticity controls in the context of the cell division cycle, highlighting a functional role for phase behavior and material properties of proteins assembled onto heterochromatin, centromeres, and central spindles via LLPS. The techniques and tools for visualizing and harnessing membraneless organelle dynamics and plasticity in mitosis are also discussed, as is the potential for these discoveries to promote new research directions for investigating chromosome dynamics, plasticity, and interchromosome interactions in the decision-making process during mitosis.
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Affiliation(s)
- Xing Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China School of Life Science, Hefei, China; Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Center for Physical Sciences at Nanoscale, Hefei, China; Keck Center for Cellular Dynamics and Organoids Plasticity, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Xu Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China School of Life Science, Hefei, China; Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Center for Physical Sciences at Nanoscale, Hefei, China; Keck Center for Cellular Dynamics and Organoids Plasticity, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Haowei Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China School of Life Science, Hefei, China; Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Center for Physical Sciences at Nanoscale, Hefei, China
| | - Zhen Dou
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China School of Life Science, Hefei, China; Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Center for Physical Sciences at Nanoscale, Hefei, China
| | - Ke Ruan
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China School of Life Science, Hefei, China; Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Center for Physical Sciences at Nanoscale, Hefei, China
| | - Donald L Hill
- Comprehensive Cancer Center, University of Alabama, Birmingham, Alabama, USA
| | - Lin Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yunyu Shi
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China School of Life Science, Hefei, China; Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Center for Physical Sciences at Nanoscale, Hefei, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China School of Life Science, Hefei, China; Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Center for Physical Sciences at Nanoscale, Hefei, China; Keck Center for Cellular Dynamics and Organoids Plasticity, Morehouse School of Medicine, Atlanta, Georgia, USA; Comprehensive Cancer Center, University of Alabama, Birmingham, Alabama, USA; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China.
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6
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Li Y, Dammer EB, Gao Y, Lan Q, Villamil MA, Duong DM, Zhang C, Ping L, Lauinger L, Flick K, Xu Z, Wei W, Xing X, Chang L, Jin J, Hong X, Zhu Y, Wu J, Deng Z, He F, Kaiser P, Xu P. Proteomics Links Ubiquitin Chain Topology Change to Transcription Factor Activation. Mol Cell 2019; 76:126-137.e7. [PMID: 31444107 DOI: 10.1016/j.molcel.2019.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/28/2019] [Accepted: 06/28/2019] [Indexed: 12/31/2022]
Abstract
A surprising complexity of ubiquitin signaling has emerged with identification of different ubiquitin chain topologies. However, mechanisms of how the diverse ubiquitin codes control biological processes remain poorly understood. Here, we use quantitative whole-proteome mass spectrometry to identify yeast proteins that are regulated by lysine 11 (K11)-linked ubiquitin chains. The entire Met4 pathway, which links cell proliferation with sulfur amino acid metabolism, was significantly affected by K11 chains and selected for mechanistic studies. Previously, we demonstrated that a K48-linked ubiquitin chain represses the transcription factor Met4. Here, we show that efficient Met4 activation requires a K11-linked topology. Mechanistically, our results propose that the K48 chain binds to a topology-selective tandem ubiquitin binding region in Met4 and competes with binding of the basal transcription machinery to the same region. The change to K11-enriched chain architecture releases this competition and permits binding of the basal transcription complex to activate transcription.
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Affiliation(s)
- Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Eric B Dammer
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China; Center for Neurodegenerative Diseases, Emory Proteomics Service Center, and Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Yuan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Qiuyan Lan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P.R. China
| | - Mark A Villamil
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Duc M Duong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China; Center for Neurodegenerative Diseases, Emory Proteomics Service Center, and Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Chengpu Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Lingyan Ping
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P.R. China
| | - Linda Lauinger
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Karin Flick
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Zhongwei Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Wei Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Xiaohua Xing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Jianping Jin
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, P.R. China
| | - Xuechuan Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P.R. China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China
| | - Junzhu Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P.R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P.R. China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China.
| | - Peter Kaiser
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697-1700, USA.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, P.R. China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P.R. China; Guizhou University School of Medicine, Guiyang 550025, P.R. China.
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7
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Yao X, Smolka AJ. Gastric Parietal Cell Physiology and Helicobacter pylori-Induced Disease. Gastroenterology 2019; 156:2158-2173. [PMID: 30831083 PMCID: PMC6715393 DOI: 10.1053/j.gastro.2019.02.036] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/13/2022]
Abstract
Acidification of the gastric lumen poses a barrier to transit of potentially pathogenic bacteria and enables activation of pepsin to complement nutrient proteolysis initiated by salivary proteases. Histamine-induced activation of the PKA signaling pathway in gastric corpus parietal cells causes insertion of proton pumps into their apical plasma membranes. Parietal cell secretion and homeostasis are regulated by signaling pathways that control cytoskeletal changes required for apical membrane remodeling and organelle and proton pump activities. Helicobacter pylori colonization of human gastric mucosa affects gastric epithelial cell plasticity and homeostasis, promoting epithelial progression to neoplasia. By intervening in proton pump expression, H pylori regulates the abundance and diversity of microbiota that populate the intestinal lumen. We review stimulation-secretion coupling and renewal mechanisms in parietal cells and the mechanisms by which H pylori toxins and effectors alter cell secretory pathways (constitutive and regulated) and organelles to establish and maintain their inter- and intracellular niches. Studies of bacterial toxins and their effector proteins have provided insights into parietal cell physiology and the mechanisms by which pathogens gain control of cell activities, increasing our understanding of gastrointestinal physiology, microbial infectious disease, and immunology.
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Affiliation(s)
- Xuebiao Yao
- MOE Key Laboratory of Cellular Dynamics, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Hefei, China; Keck Center for Cellular Dynamics and Organoids Plasticity, Morehouse School of Medicine, Atlanta, Georgia.
| | - Adam J. Smolka
- Gastroenterology and Hepatology Division, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
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Venghateri JB, Jindal B, Panda D. The centrosome: a prospective entrant in cancer therapy. Expert Opin Ther Targets 2015; 19:957-72. [PMID: 25787715 DOI: 10.1517/14728222.2015.1018823] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION The centrosome plays an essential role in the cell cycle. The centrosome and its associated proteins assist in nucleating and organizing microtubules. A structural or a functional aberration in the centrosome is known to cause abnormal cell proliferation leading to tumors. Therefore, the centrosome is considered as a promising anti-cancer target. AREAS COVERED This review begins with a brief introduction to the centrosome and its role in the cell cycle. We elaborate on the centrosome-associated proteins that regulate microtubule dynamics. In addition, we discuss the centrosomal protein kinase targets such as cyclin-dependent, polo-like and aurora kinases. Inhibitors targeting these kinases are undergoing clinical trials for cancer chemotherapy. Further, we shed light on new approaches to target the centrosomal proteins for cancer therapy. EXPERT OPINION Insights into the functioning of the centrosomal proteins will be extremely beneficial in validating the centrosome as a target in cancer therapy. New strategies either as a single entity or in combination with current chemotherapeutic agents should be researched or exploited to reveal the promises that the centrosome holds for future cancer therapy.
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Affiliation(s)
- Jubina B Venghateri
- Indian Institute of Technology Bombay, IITB-Monash Research Academy , Powai, Mumbai 400076 , India
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Liu X, Song Z, Huo Y, Zhang J, Zhu T, Wang J, Zhao X, Aikhionbare F, Zhang J, Duan H, Wu J, Dou Z, Shi Y, Yao X. Chromatin protein HP1 interacts with the mitotic regulator borealin protein and specifies the centromere localization of the chromosomal passenger complex. J Biol Chem 2015; 289:20638-49. [PMID: 24917673 DOI: 10.1074/jbc.m114.572842] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Accurate mitosis requires the chromosomal passenger protein complex (CPC) containing Aurora B kinase, borealin, INCENP, and survivin, which orchestrates chromosome dynamics. However, the chromatin factors that specify the CPC to the centromere remain elusive. Here we show that borealin interacts directly with heterochromatin protein 1 (HP1) and that this interaction is mediated by an evolutionarily conserved PXVXL motif in the C-terminal borealin with the chromo shadow domain of HP1. This borealin-HP1 interaction recruits the CPC to the centromere and governs an activation of Aurora B kinase judged by phosphorylation of Ser-7 in CENP-A, a substrate of Aurora B. Consistently, modulation of the motif PXVXL leads to defects in CPC centromere targeting and aberrant Aurora B activity. On the other hand, the localization of the CPC in the midzone is independent of the borealin-HP1 interaction, demonstrating the spatial requirement of HP1 in CPC localization to the centromere. These findings reveal a previously unrecognized but direct link between HP1 and CPC localization in the centromere and illustrate the critical role of borealin-HP1 interaction in orchestrating an accurate cell division.
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10
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Huang Z, Ma L, Wang Y, Pan Z, Ren J, Liu Z, Xue Y. MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. Nucleic Acids Res 2014; 43:D328-34. [PMID: 25392421 PMCID: PMC4383938 DOI: 10.1093/nar/gku1125] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We reported an updated database of MiCroKiTS 4.0 (http://microkit.biocuckoo.org) for proteins temporally and spatially localized in distinct subcellular positions including midbody, centrosome, kinetochore, telomere and mitotic spindle during cell division/mitosis. The database was updated from our previously developed database of MiCroKit 3.0, which contained 1489 proteins mostly forming super-complexes at midbody, centrosome and kinetochore from seven eukaryotes. Since the telomere and spindle apparatus are critical for cell division, the proteins localized at the two positions were also integrated. From the scientific literature, we curated 1872 experimentally identified proteins which at least locate in one of the five positions from eight species. Then the ortholog detection was performed to identify potential MiCroKiTS proteins from 144 eukaryotic organisms, which contains 66, 45 and 33 species of animals, fungi and plants, respectively. In total, 87 983 unique proteins with corresponding localization information were integrated into the database. The primary references of experimentally identified localizations were provided and the fluorescence microscope figures for the localizations of human proteins were shown. The orthologous relations between predicted and experimental localizations were also present. Taken together, we anticipate the database can serve as a useful resource for further analyzing the molecular mechanisms during cell division.
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Affiliation(s)
- Zhengnan Huang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lili Ma
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yongbo Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhicheng Pan
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jian Ren
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zexian Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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11
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Zheng Y, Guo J, Li X, Xie Y, Hou M, Fu X, Dai S, Diao R, Miao Y, Ren J. An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the proteins in the functional supercomplexes. Front Microbiol 2014; 5:573. [PMID: 25400627 PMCID: PMC4212687 DOI: 10.3389/fmicb.2014.00573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/11/2014] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic cells may divide via the critical cellular process of cell division/mitosis, resulting in two daughter cells with the same genetic information. A large number of dedicated proteins are involved in this process and spatiotemporally assembled into three distinct super-complex structures/organelles, including the centrosome/spindle pole body, kinetochore/centromere and cleavage furrow/midbody/bud neck, so as to precisely modulate the cell division/mitosis events of chromosome alignment, chromosome segregation and cytokinesis in an orderly fashion. In recent years, many efforts have been made to identify the protein components and architecture of these subcellular organelles, aiming to uncover the organelle assembly pathways, determine the molecular mechanisms underlying the organelle functions, and thereby provide new therapeutic strategies for a variety of diseases. However, the organelles are highly dynamic structures, making it difficult to identify the entire components. Here, we review the current knowledge of the identified protein components governing the organization and functioning of organelles, especially in human and yeast cells, and discuss the multi-localized protein components mediating the communication between organelles during cell division.
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Affiliation(s)
- Yueyuan Zheng
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Junjie Guo
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Xu Li
- Orthopaedic Department of Anhui Medical University Affiliated Provincial Hospital Hefei, China
| | - Yubin Xie
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Mingming Hou
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Xuyang Fu
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Shengkun Dai
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Rucheng Diao
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Yanyan Miao
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
| | - Jian Ren
- Cancer Center, School of Life Sciences, School of Advanced Computing, Cooperative Innovation Center for High Performance Computing, Sun Yat-sen University Guangzhou, China
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12
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JAK2 tyrosine kinase phosphorylates and is negatively regulated by centrosomal protein Ninein. Mol Cell Biol 2014; 35:111-31. [PMID: 25332239 DOI: 10.1128/mcb.01138-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
JAK2 is a cytoplasmic tyrosine kinase critical for cytokine signaling. In this study, we have identified a novel centrosome-associated complex containing ninein and JAK2. We have found that active JAK2 localizes around the mother centrioles, where it partly colocalizes with ninein, a protein involved in microtubule (MT) nucleation and anchoring. We demonstrated that JAK2 is an important regulator of centrosome function. Depletion of JAK2 or use of JAK2-null cells causes defects in MT anchoring and increased numbers of cells with mitotic defects; however, MT nucleation is unaffected. We showed that JAK2 directly phosphorylates the N terminus of ninein while the C terminus of ninein inhibits JAK2 kinase activity in vitro. Overexpressed wild-type (WT) or C-terminal (amino acids 1179 to 1931) ninein inhibits JAK2. This ninein-dependent inhibition of JAK2 significantly decreases prolactin- and interferon gamma (IFN-γ)-induced tyrosyl phosphorylation of STAT1 and STAT5. Downregulation of ninein enhances JAK2 activation. These results indicate that JAK2 is a novel member of centrosome-associated complex and that this localization regulates both centrosomal function and JAK2 kinase activity, thus controlling cytokine-activated molecular pathways.
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13
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Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development. SCIENCE CHINA-LIFE SCIENCES 2014; 57:1162-71. [PMID: 25119674 DOI: 10.1007/s11427-014-4714-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/01/2014] [Indexed: 12/17/2022]
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14
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Abstract
Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time. Microbial communities and their processes are the foundations of ecosystems. The ecological roles of rare microorganisms are largely unknown, but it is thought that they contribute to community stability by acting as a reservoir that can rapidly respond to environmental changes. We investigated the occurrence of typically rare taxa that very occasionally become more prominent in their communities (“conditionally rare”). We quantified conditionally rare taxa in time series from a wide variety of ecosystems and discovered that not only were conditionally rare taxa present in all of the examples, but they also contributed disproportionately to temporal changes in diversity when they were most abundant. This result indicates an important and general role for rare microbial taxa within their communities.
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15
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Kuhn M, Hyman AA, Beyer A. Coiled-coil proteins facilitated the functional expansion of the centrosome. PLoS Comput Biol 2014; 10:e1003657. [PMID: 24901223 PMCID: PMC4046923 DOI: 10.1371/journal.pcbi.1003657] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/15/2014] [Indexed: 12/16/2022] Open
Abstract
Repurposing existing proteins for new cellular functions is recognized as a main mechanism of evolutionary innovation, but its role in organelle evolution is unclear. Here, we explore the mechanisms that led to the evolution of the centrosome, an ancestral eukaryotic organelle that expanded its functional repertoire through the course of evolution. We developed a refined sequence alignment technique that is more sensitive to coiled coil proteins, which are abundant in the centrosome. For proteins with high coiled-coil content, our algorithm identified 17% more reciprocal best hits than BLAST. Analyzing 108 eukaryotic genomes, we traced the evolutionary history of centrosome proteins. In order to assess how these proteins formed the centrosome and adopted new functions, we computationally emulated evolution by iteratively removing the most recently evolved proteins from the centrosomal protein interaction network. Coiled-coil proteins that first appeared in the animal–fungi ancestor act as scaffolds and recruit ancestral eukaryotic proteins such as kinases and phosphatases to the centrosome. This process created a signaling hub that is crucial for multicellular development. Our results demonstrate how ancient proteins can be co-opted to different cellular localizations, thereby becoming involved in novel functions. The centrosome helps cells to divide, and is important for the development of animals. It has its evolutionary origins in the basal body, which was present in the last common ancestor of all eukaryotes. Here, we study how the evolution of novel proteins helped the formation of the centrosome. Coiled-coil proteins are important for the function of the centrosome. But, they have repeating patterns that can confuse existing methods for finding related proteins. We refined these methods by adjusting for the special properties of the coiled-coil regions. This enabled us to find more distant relatives of centrosomal proteins. We then tested how novel proteins affect the protein interaction network of the centrosome. We did this by removing the most novel proteins step by step. At each stage, we observed how the remaining proteins are connected to the centriole, the core of the centrosome. We found that coiled-coil proteins that first occurred in the ancestor of fungi and animals help to recruit older proteins. By being recruited to the centrosome, these older proteins acquired new functions. We thus now have a clearer picture of how the centrosome became such an important part of animal cells.
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Affiliation(s)
- Michael Kuhn
- Biotechnology Center, TU Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- * E-mail: (AAH); (AB)
| | - Andreas Beyer
- Biotechnology Center, TU Dresden, Dresden, Germany
- University of Cologne, Cologne, Germany
- * E-mail: (AAH); (AB)
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16
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Xu Q, Zhang Y, Xiong X, Huang Y, Salisbury JL, Hu J, Ling K. PIPKIγ targets to the centrosome and restrains centriole duplication. J Cell Sci 2014; 127:1293-305. [PMID: 24434581 DOI: 10.1242/jcs.141465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Centriole biogenesis depends on the polo-like kinase (PLK4) and a small group of structural proteins. The spatiotemporal regulation of these proteins at pre-existing centrioles is essential to ensure that centriole duplication occurs once per cell cycle. Here, we report that phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1C, hereafter referred to as PIPKIγ) plays an important role in centriole fidelity. PIPKIγ localized in a ring-like pattern in the intermediate pericentriolar materials around the proximal end of the centriole in G1, S and G2 phases, but not in M phase. This localization was dependent upon an association with centrosomal protein of 152 KDa (CEP152). Without detaining cells in S or M phase, the depletion of PIPKIγ led to centriole amplification in a manner that was dependent upon PLK4 and spindle assembly abnormal protein 6 homolog (SAS6). The expression of exogenous PIPKIγ reduced centriole amplification that occurred as a result of endogenous PIPKIγ depletion, hydroxyurea treatment or PLK4 overexpression, suggesting that PIPKIγ is likely to function at the PLK4 level to restrain centriole duplication. Importantly, we found that PIPKIγ bound to the cryptic polo-box domain of PLK4 and that this binding reduced the kinase activity of PLK4. Together, our findings suggest that PIPKIγ is a novel negative regulator of centriole duplication, which acts by modulating the homeostasis of PLK4 activity.
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Affiliation(s)
- Qingwen Xu
- Department of Biochemistry and Molecular Biology, and Division of Hypertension and Nephrology, Mayo Clinic, 200 First Street SW, Rochester, MN 55902, USA
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17
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Alves-Cruzeiro JMDC, Nogales-Cadenas R, Pascual-Montano AD. CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. Nucleic Acids Res 2014; 42:D430-6. [PMID: 24270791 PMCID: PMC3964966 DOI: 10.1093/nar/gkt1126] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/22/2013] [Accepted: 10/24/2013] [Indexed: 01/01/2023] Open
Abstract
We present the second generation of centrosomeDB, available online at http://centrosome.cnb.csic.es, with a significant expansion of 1357 human and drosophila centrosomal genes and their corresponding information. The centrosome of animal cells takes part in important biological processes such as the organization of the interphase microtubule cytoskeleton and the assembly of the mitotic spindle. The active research done during the past decades has produced lots of data related to centrosomal proteins. Unfortunately, the accumulated data are dispersed among diverse and heterogeneous sources of information. We believe that the availability of a repository collecting curated evidences of centrosomal proteins would constitute a key resource for the scientific community. This was our first motivation to introduce CentrosomeDB in NAR database issue in 2009, collecting a set of human centrosomal proteins that were reported in the literature and other sources. The intensive use of this resource during these years has encouraged us to present this new expanded version. Using our database, the researcher is offered the possibility to study the evolution, function and structure of the centrosome. We have compiled information from many sources, including Gene Ontology, disease-association, single nucleotide polymorphisms and associated gene expression experiments. Special interest has been paid to protein-protein interaction.
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Affiliation(s)
| | - Rubén Nogales-Cadenas
- Functional Bioinformatics Group, National Center for Biotechnology-CSIC, Madrid 28049, Spain
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18
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Pihan GA. Centrosome dysfunction contributes to chromosome instability, chromoanagenesis, and genome reprograming in cancer. Front Oncol 2013; 3:277. [PMID: 24282781 PMCID: PMC3824400 DOI: 10.3389/fonc.2013.00277] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/28/2013] [Indexed: 12/19/2022] Open
Abstract
The unique ability of centrosomes to nucleate and organize microtubules makes them unrivaled conductors of important interphase processes, such as intracellular payload traffic, cell polarity, cell locomotion, and organization of the immunologic synapse. But it is in mitosis that centrosomes loom large, for they orchestrate, with clockmaker's precision, the assembly and functioning of the mitotic spindle, ensuring the equal partitioning of the replicated genome into daughter cells. Centrosome dysfunction is inextricably linked to aneuploidy and chromosome instability, both hallmarks of cancer cells. Several aspects of centrosome function in normal and cancer cells have been molecularly characterized during the last two decades, greatly enhancing our mechanistic understanding of this tiny organelle. Whether centrosome defects alone can cause cancer, remains unanswered. Until recently, the aggregate of the evidence had suggested that centrosome dysfunction, by deregulating the fidelity of chromosome segregation, promotes and accelerates the characteristic Darwinian evolution of the cancer genome enabled by increased mutational load and/or decreased DNA repair. Very recent experimental work has shown that missegregated chromosomes resulting from centrosome dysfunction may experience extensive DNA damage, suggesting additional dimensions to the role of centrosomes in cancer. Centrosome dysfunction is particularly prevalent in tumors in which the genome has undergone extensive structural rearrangements and chromosome domain reshuffling. Ongoing gene reshuffling reprograms the genome for continuous growth, survival, and evasion of the immune system. Manipulation of molecular networks controlling centrosome function may soon become a viable target for specific therapeutic intervention in cancer, particularly since normal cells, which lack centrosome alterations, may be spared the toxicity of such therapies.
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Affiliation(s)
- German A Pihan
- Department of Pathology and Laboratory Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, MA , USA
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19
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Dos Santos HG, Abia D, Janowski R, Mortuza G, Bertero MG, Boutin M, Guarín N, Méndez-Giraldez R, Nuñez A, Pedrero JG, Redondo P, Sanz M, Speroni S, Teichert F, Bruix M, Carazo JM, Gonzalez C, Reina J, Valpuesta JM, Vernos I, Zabala JC, Montoya G, Coll M, Bastolla U, Serrano L. Structure and non-structure of centrosomal proteins. PLoS One 2013; 8:e62633. [PMID: 23671615 PMCID: PMC3650010 DOI: 10.1371/journal.pone.0062633] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/24/2013] [Indexed: 11/19/2022] Open
Abstract
Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php.
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Affiliation(s)
| | - David Abia
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - Robert Janowski
- Institut de Biologia Molecular de Barcelona (IBMB), Baldiri Reixac 10–12, Barcelona, Spain
- Institute for Research in Biomedicine (IRB-Barcelona) Baldiri Reixac 10–12, Barcelona, Spain
| | - Gulnahar Mortuza
- Centro Nacional de Investigación Oncológica (CNIO), Madrid, Spain
| | | | - Maïlys Boutin
- Institut de Biologia Molecular de Barcelona (IBMB), Baldiri Reixac 10–12, Barcelona, Spain
- Institute for Research in Biomedicine (IRB-Barcelona) Baldiri Reixac 10–12, Barcelona, Spain
| | - Nayibe Guarín
- Institut de Biologia Molecular de Barcelona (IBMB), Baldiri Reixac 10–12, Barcelona, Spain
- Institute for Research in Biomedicine (IRB-Barcelona) Baldiri Reixac 10–12, Barcelona, Spain
| | | | - Alfonso Nuñez
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - Juan G. Pedrero
- Centro Nacional de Investigación Oncológica (CNIO), Madrid, Spain
| | - Pilar Redondo
- Centro Nacional de Investigación Oncológica (CNIO), Madrid, Spain
| | - María Sanz
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | | | - Florian Teichert
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - Marta Bruix
- Instituto de Química Física Rocasolano (IQFR), CSIC, Madrid, Spain
| | - José M. Carazo
- Centro Nacional de Biotecnología (CNB),-CSIC, Madrid, Spain
| | - Cayetano Gonzalez
- Institute for Research in Biomedicine (IRB-Barcelona) Baldiri Reixac 10–12, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain
| | - José Reina
- Institute for Research in Biomedicine (IRB-Barcelona) Baldiri Reixac 10–12, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain
| | | | | | | | | | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB), Baldiri Reixac 10–12, Barcelona, Spain
- Institute for Research in Biomedicine (IRB-Barcelona) Baldiri Reixac 10–12, Barcelona, Spain
| | - Ugo Bastolla
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), Barcelona, Spain
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Liu Z, Ren J, Cao J, He J, Yao X, Jin C, Xue Y. Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. Brief Bioinform 2013; 14:344-60. [PMID: 22851512 DOI: 10.1093/bib/bbs041] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Substantial evidence has confirmed that Polo-like kinases (Plks) play a crucial role in a variety of cellular processes via phosphorylation-mediated signaling transduction. Identification of Plk phospho-binding proteins and phosphorylation substrates is fundamental for elucidating the molecular mechanisms of Plks. Here, we present an integrative approach for the analysis of Plk-specific phospho-binding and phosphorylation sites (p-sites) in proteins. From the currently available phosphoproteomic data, we predicted tens of thousands of potential Plk phospho-binding and phosphorylation sites in eukaryotes, respectively. Furthermore, statistical analysis suggested that Plk phospho-binding proteins are more closely implicated in mitosis than their phosphorylation substrates. Additional computational analysis together with in vitro and in vivo experimental assays demonstrated that human Mis18B is a novel interacting partner of Plk1, while pT14 and pS48 of Mis18B were identified as phospho-binding sites. Taken together, this systematic analysis provides a global landscape of the complexity and diversity of potential Plk-mediated phosphoregulation, and the prediction results can be helpful for further experimental investigation.
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Affiliation(s)
- Zexian Liu
- Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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21
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Habermann K, Lange BM. New insights into subcomplex assembly and modifications of centrosomal proteins. Cell Div 2012; 7:17. [PMID: 22800182 PMCID: PMC3479078 DOI: 10.1186/1747-1028-7-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/04/2012] [Indexed: 12/19/2022] Open
Abstract
This review provides a brief overview of the recent work on centrosome proteomics, protein complex identification and functional characterization with an emphasis on the literature of the last three years. Proteomics, genetic screens and comparative genomics studies in different model organisms have almost exhaustively identified the molecular components of the centrosome. However, much knowledge is still missing on the protein-protein interactions, protein modifications and molecular changes the centrosome undergoes throughout the cell cycle and development. The dynamic nature of this large multi-protein complex is reflected in the variety of annotated subcellular locations and biological processes of its proposed components. Some centrosomal proteins and complexes have been studied intensively in different organisms and provided detailed insight into centrosome functions. For example, the molecular, structural and functional characterization of the γ-Tubulin ring complex (γ-TuRC) and the the discovery of the Augmin/HAUS complex has advanced our understanding of microtubule (MT) capture, nucleation and organization. Surprising findings revealed new functions and localizations of proteins that were previously regarded as bona fide centriolar or centrosome components, e.g. at the kinetochore or in the nuclear pore complex regulating MT plus end capture or mRNA processing. Many centrosome components undergo posttranslational modifications such as phosphorylation, SUMOylation and ubiquitylation that are critical in modulating centrosome function and biology. A wealth of information has recently become available driven by new developments in technologies such as mass spectrometry, light and electron microscopy providing more detailed molecular and structural definition of the centrosome and particular roles of proteins throughout the cell cycle and development.
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Affiliation(s)
- Karin Habermann
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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22
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Liu Z, Yuan F, Ren J, Cao J, Zhou Y, Yang Q, Xue Y. GPS-ARM: computational analysis of the APC/C recognition motif by predicting D-boxes and KEN-boxes. PLoS One 2012; 7:e34370. [PMID: 22479614 PMCID: PMC3315528 DOI: 10.1371/journal.pone.0034370] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/27/2012] [Indexed: 11/19/2022] Open
Abstract
Anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase incorporated with Cdh1 and/or Cdc20 recognizes and interacts with specific substrates, and faithfully orchestrates the proper cell cycle events by targeting proteins for proteasomal degradation. Experimental identification of APC/C substrates is largely dependent on the discovery of APC/C recognition motifs, e.g., the D-box and KEN-box. Although a number of either stringent or loosely defined motifs proposed, these motif patterns are only of limited use due to their insufficient powers of prediction. We report the development of a novel GPS-ARM software package which is useful for the prediction of D-boxes and KEN-boxes in proteins. Using experimentally identified D-boxes and KEN-boxes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted. By extensive evaluation and comparison, the GPS-ARM performance was found to be much better than the one using simple motifs. With this powerful tool, we predicted 4,841 potential D-boxes in 3,832 proteins and 1,632 potential KEN-boxes in 1,403 proteins from H. sapiens, while further statistical analysis suggested that both the D-box and KEN-box proteins are involved in a broad spectrum of biological processes beyond the cell cycle. In addition, with the co-localization information, we predicted hundreds of mitosis-specific APC/C substrates with high confidence. As the first computational tool for the prediction of APC/C-mediated degradation, GPS-ARM is a useful tool for information to be used in further experimental investigations. The GPS-ARM is freely accessible for academic researchers at: http://arm.biocuckoo.org.
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Affiliation(s)
- Zexian Liu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Fang Yuan
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jian Ren
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jun Cao
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yanhong Zhou
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qing Yang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (QY); (YX)
| | - Yu Xue
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (QY); (YX)
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23
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Nido GS, Méndez R, Pascual-García A, Abia D, Bastolla U. Protein disorder in the centrosome correlates with complexity in cell types number. MOLECULAR BIOSYSTEMS 2011; 8:353-67. [PMID: 22076659 DOI: 10.1039/c1mb05199g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we study the properties and the evolution of proteins that constitute the Centrosome, the complex molecular assembly that regulates the division and differentiation of animal cells. We found that centrosomal proteins are predicted to be significantly enriched in disordered and coiled-coil regions, more phosphorylated and longer than control proteins of the same organism. Interestingly, the ratio of these properties in centrosomal and control proteins tends to increase with the number of cell-types. We reconstructed indels evolution, finding that indels significantly increase disorder in both centrosomal and control proteins, at a rate that is typically larger along branches associated with a large growth in cell-types number, and larger for centrosomal than for control proteins. Substitutions show a similar trend for coiled-coil, but they contribute less to the evolution of disorder. Our results suggest that the increase in cell-types number in animal evolution is correlated with the gain of disordered and coiled-coil regions in centrosomal proteins, establishing a connection between organism and molecular complexity. We argue that the structural plasticity conferred to the Centrosome by disordered regions and phosphorylation plays an important role in its mechanical properties and its regulation in space and time.
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Affiliation(s)
- G S Nido
- Centro de Biología Molecular Severo Ochoa, (CSIC-UAM), Madrid, Spain
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24
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Identification of a predominant co-regulation among kinetochore genes, prospective regulatory elements, and association with genomic instability. PLoS One 2011; 6:e25991. [PMID: 22016797 PMCID: PMC3189923 DOI: 10.1371/journal.pone.0025991] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 09/15/2011] [Indexed: 01/01/2023] Open
Abstract
The NCI-60 cell line panel is the most extensively characterized set of cells in existence, and has been used extensively as a screening tool for drug discovery. Previously, the potential of this panel has not been applied to the fundamental cellular processes of chromosome segregation. In the current study, we used data from multiple microarray platforms accumulated for the NCI-60 to characterize an expression pattern of genes involved in kinetochore assembly. This analysis revealed that 17 genes encoding the constitutive centromere associated network of the kinetochore core (the CCAN complex) plus four additional genes with established importance in kinetochore maintenance (CENPE, CENPF, INCENP, and MIS12) exhibit similar patterns of expression in the NCI-60, suggesting a mechanism for co-regulated transcription of these genes which is maintained despite the multiple genetic and epigenetic rearrangements accumulated in these cells (such as variations in DNA copy number and karyotypic complexity). A complex group of potential regulatory influences are identified for these genes, including the transcription factors CREB1, E2F1, FOXE1, and FOXM1, DNA copy number variation, and microRNAs has-miR-200a, 23a, 23b, 30a, 30c, 27b, 374b, 365. Thus, our results provide a template for experimental studies on the regulation of genes encoding kinetochore proteins, the process that, when aberrant, leads to the aneuploidy that is a hallmark of many cancers. We propose that the comparison of expression profiles in the NCI-60 cell line panel could be a tool for the identification of other gene groups whose products are involved in the assembly of organelle protein complexes.
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25
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Smith KR, Kieserman EK, Wang PI, Basten SG, Giles RH, Marcotte EM, Wallingford JB. A role for central spindle proteins in cilia structure and function. Cytoskeleton (Hoboken) 2011; 68:112-24. [PMID: 21246755 DOI: 10.1002/cm.20498] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 11/28/2010] [Indexed: 12/29/2022]
Abstract
Cytokinesis and ciliogenesis are fundamental cellular processes that require strict coordination of microtubule organization and directed membrane trafficking. These processes have been intensely studied, but there has been little indication that regulatory machinery might be extensively shared between them. Here, we show that several central spindle/midbody proteins (PRC1, MKLP-1, INCENP, centriolin) also localize in specific patterns at the basal body complex in vertebrate ciliated epithelial cells. Moreover, bioinformatic comparisons of midbody and cilia proteomes reveal a highly significant degree of overlap. Finally, we used temperature-sensitive alleles of PRC1/spd-1 and MKLP-1/zen-4 in C. elegans to assess ciliary functions while bypassing these proteins' early role in cell division. These mutants displayed defects in both cilia function and cilia morphology. Together, these data suggest the conserved reuse of a surprisingly large number of proteins in the cytokinetic apparatus and in cilia.
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Affiliation(s)
- Katherine R Smith
- Section of Molecular Cell and Developmental Biology, University of Texas at Austin, Austin, Texas, USA
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26
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Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information. Biochem Biophys Res Commun 2010; 401:382-4. [PMID: 20854791 DOI: 10.1016/j.bbrc.2010.09.061] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 09/14/2010] [Indexed: 01/21/2023]
Abstract
In the process of cell division, a great deal of proteins is assembled into three distinct organelles, namely midbody, centrosome and kinetochore. Knowing the localization of microkit (midbody, centrosome and kinetochore) proteins will facilitate drug target discovery and provide novel insights into understanding their functions. In this study, a support vector machine (SVM) model, MicekiPred, was presented to predict the localization of microkit proteins based on gene ontology (GO) information. A total accuracy of 77.51% was achieved using the jackknife cross-validation. This result shows that the model will be an effective complementary tool for future experimental study. The prediction model and dataset used in this article can be freely downloaded from http://cobi.uestc.edu.cn/people/hlin/tools/MicekiPred/.
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