1
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Bakker M, Svensson O, So̷rensen HV, Skepö M. Exploring the Functional Landscape of the p53 Regulatory Domain: The Stabilizing Role of Post-Translational Modifications. J Chem Theory Comput 2024; 20:5842-5853. [PMID: 38973087 PMCID: PMC11270737 DOI: 10.1021/acs.jctc.4c00570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
This study focuses on the intrinsically disordered regulatory domain of p53 and the impact of post-translational modifications. Through fully atomistic explicit water molecular dynamics simulations, we show the wealth of information and detailed understanding that can be obtained by varying the number of phosphorylated amino acids and implementing a restriction in the conformational entropy of the N-termini of that intrinsically disordered region. The take-home message for the reader is to achieve a detailed understanding of the impact of phosphorylation with respect to (1) the conformational dynamics and flexibility, (2) structural effects, (3) protein interactivity, and (4) energy landscapes and conformational ensembles. Although our model system is the regulatory domain p53 of the tumor suppressor protein p53, this study contributes to understanding the general effects of intrinsically disordered phosphorylated proteins and the impact of phosphorylated groups, more specifically, how minor changes in the primary sequence can affect the properties mentioned above.
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Affiliation(s)
- Michael
J. Bakker
- Faculty
of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Oskar Svensson
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- NanoLund, Lund University, Box 118, 221 00 Lund, Sweden
| | - Henrik V. So̷rensen
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- MAX
IV Laboratory, Fotongatan
2, 224 84 Lund, Sweden
| | - Marie Skepö
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- NanoLund, Lund University, Box 118, 221 00 Lund, Sweden
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2
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Benedetti R, Di Crosta M, D’Orazi G, Cirone M. Post-Translational Modifications (PTMs) of mutp53 and Epigenetic Changes Induced by mutp53. BIOLOGY 2024; 13:508. [PMID: 39056701 PMCID: PMC11273943 DOI: 10.3390/biology13070508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
Wild-type (wt) p53 and mutant forms (mutp53) play a key but opposite role in carcinogenesis. wtP53 acts as an oncosuppressor, preventing oncogenic transformation, while mutp53, which loses this property, may instead favor this process. This suggests that a better understanding of the mechanisms activating wtp53 while inhibiting mutp53 may help to design more effective anti-cancer treatments. In this review, we examine possible PTMs with which both wt- and mutp53 can be decorated and discuss how their manipulation could represent a possible strategy to control the stability and function of these proteins, focusing in particular on mutp53. The impact of ubiquitination, phosphorylation, acetylation, and methylation of p53, in the context of several solid and hematologic cancers, will be discussed. Finally, we will describe some of the recent studies reporting that wt- and mutp53 may influence the expression and activity of enzymes responsible for epigenetic changes such as acetylation, methylation, and microRNA regulation and the possible consequences of such changes.
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Affiliation(s)
- Rossella Benedetti
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Michele Di Crosta
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Gabriella D’Orazi
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. D’Annunzio”, 66013 Chieti, Italy
| | - Mara Cirone
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
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3
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Naryzhny S. Puzzle of Proteoform Variety-Where Is a Key? Proteomes 2024; 12:15. [PMID: 38804277 PMCID: PMC11130821 DOI: 10.3390/proteomes12020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.
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Affiliation(s)
- Stanislav Naryzhny
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad Region, Gatchina 188300, Russia
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4
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Ronzhina NL, Zorina ES, Zavialova MG, Legina OK, Naryzhny SN. Variability of haptoglobin beta-chain proteoforms. BIOMEDITSINSKAIA KHIMIIA 2024; 70:114-124. [PMID: 38711411 DOI: 10.18097/pbmc20247002114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Existing knowledge on changes of the haptoglobin (Hp) molecule suggests that it may exist in multiple proteoforms, which obviously exhibit different functions. Using two-dimensional electrophoresis (2DE) in combination with mass spectrometry and immunodetection, we have analyzed blood plasma samples from both healthy donors and patients with primary grade IV glioblastoma (GBM), and obtained a detailed composite 2DE distribution map of β-chain proteoforms, as well as the full-length form of Hp (zonulin). Although the total level of plasma Hp exceeded normal values in cancer patients (especially patients with GBM), the presence of particuar proteoforms, detected by their position on the 2DE map, was very individual. Variability was found in both zonulin and the Hp β-chain. The presence of an alkaline form of zonulin in plasma can be considered a conditional, but insufficient, GBM biomarker. In other words, we found that at the level of minor proteoforms of Hp, even in normal conditions, there was a high individual variability. On the one hand, this raises questions about the reasons for such variability, if it is present not only in Hp, but also in other proteins. On the other hand, this may explain the discrepancy between the number of experimentally detected proteoforms and the theoretically possible ones not only in Hp, but also in other proteins.
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Affiliation(s)
- N L Ronzhina
- B.P. Konstantinov Petersburg Institute of Nuclear Physics, National Research Center "Kurchatov Institute", Gatchina, Leningrad Region, Russia
| | - E S Zorina
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - O K Legina
- B.P. Konstantinov Petersburg Institute of Nuclear Physics, National Research Center "Kurchatov Institute", Gatchina, Leningrad Region, Russia
| | - S N Naryzhny
- B.P. Konstantinov Petersburg Institute of Nuclear Physics, National Research Center "Kurchatov Institute", Gatchina, Leningrad Region, Russia
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5
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Fan J, Chen B, Luo Q, Li J, Huang Y, Zhu M, Chen Z, Li J, Wang J, Liu L, Wei Q, Cao D. Potential molecular biomarkers for the diagnosis and prognosis of bladder cancer. Biomed Pharmacother 2024; 173:116312. [PMID: 38417288 DOI: 10.1016/j.biopha.2024.116312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 03/01/2024] Open
Abstract
Bladder cancer (BC) is a common malignant tumor of urinary system, which can be divided into muscle-invasive BC (MIBC) and nonmuscle-invasive BC (NMIBC). The number of BC patients has been gradually increasing currently. At present, bladder tumours are diagnosed and followed-up using a combination of cystoscopic examination, cytology and histology. However, the detection of early grade tumors, which is much easier to treat effectively than advanced stage disease, is still insufficient. It frequently recurs and can progress when not expeditiously diagnosed and monitored following initial therapy for NMIBC. Treatment strategies are totally different for different stage diseases. Therefore, it is of great practical significance to study new biomarkers for diagnosis and prognosis. In this review, we summarize the current state of biomarker development in BC diagnosis and prognosis prediction. We retrospectively analyse eight diagnostic biomarkers and eight prognostic biomarkers, in which CK, P53, PPARγ, PTEN and ncRNA are emphasized for discussion. Eight molecular subtype systems are also identified. Clinical translation of biomarkers for diagnosis, prognosis, monitoring and treatment will hopefully improve outcomes for patients. These potential biomarkers provide an opportunity to diagnose tumors earlier and with greater accuracy, and help identify those patients most at risk of disease recurrence.
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Affiliation(s)
- Junping Fan
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Bo Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Qiuping Luo
- Out-patient Department, West China Hospital, Sichuan University, Chengdu, China
| | - Jinze Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Yin Huang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Mengli Zhu
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, China
| | - Zeyu Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Jin Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Jia Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Liangren Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China.
| | - Dehong Cao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China.
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6
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Song B, Yang P, Zhang S. Cell fate regulation governed by p53: Friends or reversible foes in cancer therapy. Cancer Commun (Lond) 2024; 44:297-360. [PMID: 38311377 PMCID: PMC10958678 DOI: 10.1002/cac2.12520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
Cancer is a leading cause of death worldwide. Targeted therapies aimed at key oncogenic driver mutations in combination with chemotherapy and radiotherapy as well as immunotherapy have benefited cancer patients considerably. Tumor protein p53 (TP53), a crucial tumor suppressor gene encoding p53, regulates numerous downstream genes and cellular phenotypes in response to various stressors. The affected genes are involved in diverse processes, including cell cycle arrest, DNA repair, cellular senescence, metabolic homeostasis, apoptosis, and autophagy. However, accumulating recent studies have continued to reveal novel and unexpected functions of p53 in governing the fate of tumors, for example, functions in ferroptosis, immunity, the tumor microenvironment and microbiome metabolism. Among the possibilities, the evolutionary plasticity of p53 is the most controversial, partially due to the dizzying array of biological functions that have been attributed to different regulatory mechanisms of p53 signaling. Nearly 40 years after its discovery, this key tumor suppressor remains somewhat enigmatic. The intricate and diverse functions of p53 in regulating cell fate during cancer treatment are only the tip of the iceberg with respect to its equally complicated structural biology, which has been painstakingly revealed. Additionally, TP53 mutation is one of the most significant genetic alterations in cancer, contributing to rapid cancer cell growth and tumor progression. Here, we summarized recent advances that implicate altered p53 in modulating the response to various cancer therapies, including chemotherapy, radiotherapy, and immunotherapy. Furthermore, we also discussed potential strategies for targeting p53 as a therapeutic option for cancer.
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Affiliation(s)
- Bin Song
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengduSichuanP. R. China
| | - Ping Yang
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengduSichuanP. R. China
| | - Shuyu Zhang
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengduSichuanP. R. China
- The Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengduSichuanP. R. China
- Laboratory of Radiation MedicineNHC Key Laboratory of Nuclear Technology Medical TransformationWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduSichuanP. R. China
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7
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Flores BM, Uppalapati CK, Pascual AS, Vong A, Baatz MA, Harrison AM, Leyva KJ, Hull EE. Biological Effects of HDAC Inhibitors Vary with Zinc Binding Group: Differential Effects on Zinc Bioavailability, ROS Production, and R175H p53 Mutant Protein Reactivation. Biomolecules 2023; 13:1588. [PMID: 38002270 PMCID: PMC10669723 DOI: 10.3390/biom13111588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The coordination of zinc by histone deacetylase inhibitors (HDACi), altering the bioavailability of zinc to histone deacetylases (HDACs), is key to HDAC enzyme inhibition. However, the ability of zinc binding groups (ZBGs) to alter intracellular free Zn+2 levels, which may have far-reaching effects, has not been explored. Using two HDACis with different ZBGs, we documented shifts in intracellular free Zn+2 concentrations that correlate with subsequent ROS production. Next, we assayed refolding and reactivation of the R175H mutant p53 protein in vitro to provide greater biological context as the activity of this mutant depends on cellular zinc concentration. The data presented demonstrates the differential activity of HDACi in promoting R175H response element (RE) binding. After cells are treated with HDACi, there are differences in R175H mutant p53 refolding and reactivation, which may be related to treatments. Collectively, we show that HDACis with distinct ZBGs differentially impact the intracellular free Zn+2 concentration, ROS levels, and activity of R175H; therefore, HDACis may have significant activity independent of their ability to alter acetylation levels. Our results suggest a framework for reevaluating the role of zinc in the variable or off-target effects of HDACi, suggesting that the ZBGs of HDAC inhibitors may provide bioavailable zinc without the toxicity associated with zinc metallochaperones such as ZMC1.
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Affiliation(s)
- Brianna M. Flores
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
- Arizona College of Osteopathic Medicine, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA
| | - Chandana K. Uppalapati
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (C.K.U.); (K.J.L.)
| | - Agnes S. Pascual
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Alan Vong
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Margaux A. Baatz
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Alisha M. Harrison
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Kathryn J. Leyva
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (C.K.U.); (K.J.L.)
| | - Elizabeth E. Hull
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
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8
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Xie X, Yu T, Li X, Zhang N, Foster LJ, Peng C, Huang W, He G. Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials. Signal Transduct Target Ther 2023; 8:335. [PMID: 37669923 PMCID: PMC10480221 DOI: 10.1038/s41392-023-01589-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/22/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.
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Affiliation(s)
- Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Tingting Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Gu He
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
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9
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Kim HM, Zheng X, Lee E. Experimental Insights into the Interplay between Histone Modifiers and p53 in Regulating Gene Expression. Int J Mol Sci 2023; 24:11032. [PMID: 37446210 PMCID: PMC10342072 DOI: 10.3390/ijms241311032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Chromatin structure plays a fundamental role in regulating gene expression, with histone modifiers shaping the structure of chromatin by adding or removing chemical changes to histone proteins. The p53 transcription factor controls gene expression, binds target genes, and regulates their activity. While p53 has been extensively studied in cancer research, specifically in relation to fundamental cellular processes, including gene transcription, apoptosis, and cell cycle progression, its association with histone modifiers has received limited attention. This review explores the interplay between histone modifiers and p53 in regulating gene expression. We discuss how histone modifications can influence how p53 binds to target genes and how this interplay can be disrupted in cancer cells. This review provides insights into the complex mechanisms underlying gene regulation and their implications for potential cancer therapy.
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Affiliation(s)
- Hyun-Min Kim
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan 215316, China
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10
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Łasut-Szyszka B, Rusin M. The Wheel of p53 Helps to Drive the Immune System. Int J Mol Sci 2023; 24:ijms24087645. [PMID: 37108808 PMCID: PMC10143509 DOI: 10.3390/ijms24087645] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The p53 tumor suppressor protein is best known as an inhibitor of the cell cycle and an inducer of apoptosis. Unexpectedly, these functions of p53 are not required for its tumor suppressive activity in animal models. High-throughput transcriptomic investigations as well as individual studies have demonstrated that p53 stimulates expression of many genes involved in immunity. Probably to interfere with its immunostimulatory role, many viruses code for proteins that inactivate p53. Judging by the activities of immunity-related p53-regulated genes it can be concluded that p53 is involved in detection of danger signals, inflammasome formation and activation, antigen presentation, activation of natural killer cells and other effectors of immunity, stimulation of interferon production, direct inhibition of virus replication, secretion of extracellular signaling molecules, production of antibacterial proteins, negative feedback loops in immunity-related signaling pathways, and immunologic tolerance. Many of these p53 functions have barely been studied and require further, more detailed investigations. Some of them appear to be cell-type specific. The results of transcriptomic studies have generated many new hypotheses on the mechanisms utilized by p53 to impact on the immune system. In the future, these mechanisms may be harnessed to fight cancer and infectious diseases.
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Affiliation(s)
- Barbara Łasut-Szyszka
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-101 Gliwice, Poland
| | - Marek Rusin
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-101 Gliwice, Poland
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11
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Wang H, Guo M, Wei H, Chen Y. Targeting p53 pathways: mechanisms, structures, and advances in therapy. Signal Transduct Target Ther 2023; 8:92. [PMID: 36859359 PMCID: PMC9977964 DOI: 10.1038/s41392-023-01347-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/19/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
The TP53 tumor suppressor is the most frequently altered gene in human cancers, and has been a major focus of oncology research. The p53 protein is a transcription factor that can activate the expression of multiple target genes and plays critical roles in regulating cell cycle, apoptosis, and genomic stability, and is widely regarded as the "guardian of the genome". Accumulating evidence has shown that p53 also regulates cell metabolism, ferroptosis, tumor microenvironment, autophagy and so on, all of which contribute to tumor suppression. Mutations in TP53 not only impair its tumor suppressor function, but also confer oncogenic properties to p53 mutants. Since p53 is mutated and inactivated in most malignant tumors, it has been a very attractive target for developing new anti-cancer drugs. However, until recently, p53 was considered an "undruggable" target and little progress has been made with p53-targeted therapies. Here, we provide a systematic review of the diverse molecular mechanisms of the p53 signaling pathway and how TP53 mutations impact tumor progression. We also discuss key structural features of the p53 protein and its inactivation by oncogenic mutations. In addition, we review the efforts that have been made in p53-targeted therapies, and discuss the challenges that have been encountered in clinical development.
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Affiliation(s)
- Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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12
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Nam KM, Martinez-Corral R, Gunawardena J. The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems. Interface Focus 2022; 12:20220013. [PMID: 35860006 PMCID: PMC9184966 DOI: 10.1098/rsfs.2022.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/25/2022] [Indexed: 12/25/2022] Open
Abstract
The linear framework uses finite, directed graphs with labelled edges to model biomolecular systems. Graph vertices represent biochemical species or molecular states, edges represent reactions or transitions and labels represent rates. The graph yields a linear dynamics for molecular concentrations or state probabilities, with the graph Laplacian as the operator, and the labels encode the nonlinear interactions between system and environment. The labels can be specified by vertices of other graphs or by conservation laws or, when the environment consists of thermodynamic reservoirs, they may be constants. In the latter case, the graphs correspond to infinitesimal generators of Markov processes. The key advantage of the framework has been that steady states are determined as rational algebraic functions of the labels by the Matrix-Tree theorems of graph theory. When the system is at thermodynamic equilibrium, this prescription recovers equilibrium statistical mechanics but it continues to hold for non-equilibrium steady states. The framework goes beyond other graph-based approaches in treating the graph as a mathematical object, for which general theorems can be formulated that accommodate biomolecular complexity. It has been particularly effective at analysing enzyme-catalysed modification systems and input-output responses.
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Affiliation(s)
- Kee-Myoung Nam
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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13
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Su Y, Li J, Ji W, Wang G, Fang L, Zhang Q, Ang L, Zhao M, Sen Y, Chen L, Zheng J, Su C, Qin L. Triple-serotype chimeric oncolytic adenovirus exerts multiple synergistic mechanisms against solid tumors. J Immunother Cancer 2022; 10:jitc-2022-004691. [PMID: 35609942 PMCID: PMC9131115 DOI: 10.1136/jitc-2022-004691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 12/23/2022] Open
Abstract
Background Oncolytic virotherapy has become an important branch of cancer immunotherapy. This study investigated the efficacy of an oncolytic adenovirus (OAV), OncoViron, with synergistic mechanisms in the treatment of multiple solid tumors. Methods An OAV, OncoViron, was constructed and investigated by cytological experiments and implanted tumor models of multiple solid tumor cell lines to certify its anticancer efficacy, the synergistic effects of viral oncolysis and transgene anticancer activity of OncoViron, as well as oncolytic virotherapy combined with immunotherapy, were also verified. Results The selective replication of OncoViron mediated high expression of anticancer factors, specifically targeted a variety of solid tumors and significantly inhibited cancer cell proliferation. On a variety of implanted solid tumor models in immunodeficient mice, immunocompetent mice, and humanized mice, OncoViron showed great anticancer effects on its own and in combination with programmed death 1 (PD-1) antibody and chimeric antigen receptor (CAR) T cells. Pathological examination, single-cell sequencing, and spatial transcriptome analysis of animal implanted tumor specimens confirmed that OncoViron significantly altered the gene expression profile of infected cancer cells, not only recruiting a large number of lymphocytes, natural killer cells, and mononuclear macrophages into tumor microenvironment (TME) and activated immune cells, especially T cells but also inducing M1 polarization of macrophages and promoting the release of more immune cytokines, thereby remodeling the TME for coordinating PD-1 antibody or CAR T therapy. Conclusions The chimeric OncoViron is a novel broad-spectrum anticancer product with multiple mechanisms of synergistic and potentiated immunotherapy, creating a good opportunity for combined immunotherapy against solid tumors.
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Affiliation(s)
- Yinghan Su
- Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.,National Center for Liver Cancer (NCLC), Navy Military Medical University, Shanghai 201805, China
| | - Jiang Li
- National Center for Liver Cancer (NCLC), Navy Military Medical University, Shanghai 201805, China.,Department of Molecular Oncology, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai 200438, China
| | - Weidan Ji
- National Center for Liver Cancer (NCLC), Navy Military Medical University, Shanghai 201805, China.,Department of Molecular Oncology, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai 200438, China
| | - Gang Wang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy & Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu, China
| | - Lin Fang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy & Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu, China
| | - Qin Zhang
- Department of Molecular Oncology, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai 200438, China
| | - Lin Ang
- Department of Pathology, Second People's Hospital of Hefei, Hefei 230011, Anhui, China
| | - Min Zhao
- Department of Pathology, Second People's Hospital of Hefei, Hefei 230011, Anhui, China
| | - Yuan Sen
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy & Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu, China
| | - Lei Chen
- National Center for Liver Cancer (NCLC), Navy Military Medical University, Shanghai 201805, China.,Department of Molecular Oncology, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai 200438, China
| | - Junnian Zheng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy & Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu, China
| | - Changqing Su
- National Center for Liver Cancer (NCLC), Navy Military Medical University, Shanghai 201805, China .,Department of Molecular Oncology, Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai 200438, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy & Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu, China
| | - Lunxiu Qin
- Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200040, China
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14
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Rizzotto D, Englmaier L, Villunger A. At a Crossroads to Cancer: How p53-Induced Cell Fate Decisions Secure Genome Integrity. Int J Mol Sci 2021; 22:ijms221910883. [PMID: 34639222 PMCID: PMC8509445 DOI: 10.3390/ijms221910883] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022] Open
Abstract
P53 is known as the most critical tumor suppressor and is often referred to as the guardian of our genome. More than 40 years after its discovery, we are still struggling to understand all molecular details on how this transcription factor prevents oncogenesis or how to leverage current knowledge about its function to improve cancer treatment. Multiple cues, including DNA-damage or mitotic errors, can lead to the stabilization and nuclear translocation of p53, initiating the expression of multiple target genes. These transcriptional programs may be cell-type- and stimulus-specific, as is their outcome that ultimately imposes a barrier to cellular transformation. Cell cycle arrest and cell death are two well-studied consequences of p53 activation, but, while being considered critical, they do not fully explain the consequences of p53 loss-of-function phenotypes in cancer. Here, we discuss how mitotic errors alert the p53 network and give an overview of multiple ways that p53 can trigger cell death. We argue that a comparative analysis of different types of p53 responses, elicited by different triggers in a time-resolved manner in well-defined model systems, is critical to understand the cell-type-specific cell fate induced by p53 upon its activation in order to resolve the remaining mystery of its tumor-suppressive function.
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Affiliation(s)
- Dario Rizzotto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (D.R.); (L.E.)
| | - Lukas Englmaier
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (D.R.); (L.E.)
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria
| | - Andreas Villunger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (D.R.); (L.E.)
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Correspondence:
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15
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Margiola S, Gerecht K, Müller MM. Semisynthetic 'designer' p53 sheds light on a phosphorylation-acetylation relay. Chem Sci 2021; 12:8563-8570. [PMID: 34221338 PMCID: PMC8221199 DOI: 10.1039/d1sc00396h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022] Open
Abstract
The tumor suppressor protein p53 is a master regulator of cell fate. The activity of p53 is controlled by a plethora of posttranslational modifications (PTMs). However, despite extensive research, the mechanisms of this regulation are still poorly understood due to a paucity of biochemical studies with p53 carrying defined PTMs. Here, we report a protein semi-synthesis approach to access site-specifically modified p53. We synthesized a set of chemically homogeneous full-length p53 carrying one (Ser20ph and Ser15ph) or two (Ser15,20ph) naturally occurring, damage-associated phosphoryl marks. Refolding and biochemical characterization of semisynthetic p53 variants confirmed their structural and functional integrity. Furthermore, we show that phosphorylation within the N-terminal domain directly enhances p300-dependent acetylation approximately twofold, consistent with the role of these marks in p53 activation. Given that the p53 N-terminus is a hotspot for PTMs, we believe that our approach will contribute greatly to a mechanistic understanding of how p53 is controlled by PTMs.
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Affiliation(s)
- Sofia Margiola
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
| | - Karola Gerecht
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
| | - Manuel M Müller
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
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16
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Timofeev O, Stiewe T. Rely on Each Other: DNA Binding Cooperativity Shapes p53 Functions in Tumor Suppression and Cancer Therapy. Cancers (Basel) 2021; 13:2422. [PMID: 34067731 PMCID: PMC8155944 DOI: 10.3390/cancers13102422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/24/2022] Open
Abstract
p53 is a tumor suppressor that is mutated in half of all cancers. The high clinical relevance has made p53 a model transcription factor for delineating general mechanisms of transcriptional regulation. p53 forms tetramers that bind DNA in a highly cooperative manner. The DNA binding cooperativity of p53 has been studied by structural and molecular biologists as well as clinical oncologists. These experiments have revealed the structural basis for cooperative DNA binding and its impact on sequence specificity and target gene spectrum. Cooperativity was found to be critical for the control of p53-mediated cell fate decisions and tumor suppression. Importantly, an estimated number of 34,000 cancer patients per year world-wide have mutations of the amino acids mediating cooperativity, and knock-in mouse models have confirmed such mutations to be tumorigenic. While p53 cancer mutations are classically subdivided into "contact" and "structural" mutations, "cooperativity" mutations form a mechanistically distinct third class that affect the quaternary structure but leave DNA contacting residues and the three-dimensional folding of the DNA-binding domain intact. In this review we discuss the concept of DNA binding cooperativity and highlight the unique nature of cooperativity mutations and their clinical implications for cancer therapy.
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Affiliation(s)
- Oleg Timofeev
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Philipps-University, 35037 Marburg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Philipps-University, 35037 Marburg, Germany
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17
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Parnandi N, Rendo V, Cui G, Botuyan MV, Remisova M, Nguyen H, Drané P, Beroukhim R, Altmeyer M, Mer G, Chowdhury D. TIRR inhibits the 53BP1-p53 complex to alter cell-fate programs. Mol Cell 2021; 81:2583-2595.e6. [PMID: 33961797 DOI: 10.1016/j.molcel.2021.03.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/19/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022]
Abstract
53BP1 influences genome stability via two independent mechanisms: (1) regulating DNA double-strand break (DSB) repair and (2) enhancing p53 activity. We discovered a protein, Tudor-interacting repair regulator (TIRR), that associates with the 53BP1 Tudor domain and prevents its recruitment to DSBs. Here, we elucidate how TIRR affects 53BP1 function beyond its recruitment to DSBs and biochemically links the two distinct roles of 53BP1. Loss of TIRR causes an aberrant increase in the gene transactivation function of p53, affecting several p53-mediated cell-fate programs. TIRR inhibits the complex formation between the Tudor domain of 53BP1 and a dimethylated form of p53 (K382me2) that is poised for transcriptional activation of its target genes. TIRR mRNA expression levels negatively correlate with the expression of key p53 target genes in breast and prostate cancers. Further, TIRR loss is selectively not tolerated in p53-proficient tumors. Therefore, we establish that TIRR is an important inhibitor of the 53BP1-p53 complex.
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Affiliation(s)
- Nishita Parnandi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Veronica Rendo
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Cancer Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Michaela Remisova
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Huy Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Cancer Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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18
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The Δ133p53 Isoforms, Tuners of the p53 Pathway. Cancers (Basel) 2020; 12:cancers12113422. [PMID: 33218139 PMCID: PMC7698932 DOI: 10.3390/cancers12113422] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary TP53, the most frequently mutated gene in human cancers, has a key role in the maintenance of the genetic stability and, thus, in preventing tumor development. The p53-dependent responses were long thought to be solely driven by canonical p53α. However, it is now known that TP53 physiologically expresses at least 12 p53 isoforms including Δ133p53α, Δ133p53β and Δ133p53γ. The Δ133p53 isoforms are potent modulators of the p53 pathway that regulate critical functions in cancer, physiological and premature aging, neurodegenerative diseases, immunity and inflammation, and tissue repair. This review aims to summarize the current knowledge on the Δ133p53 isoforms and how they contribute to multiple physiological and pathological mechanisms. Critically, further characterization of p53 isoforms may identify novel regulatory modes of p53 pathway functions that contribute to disease progression and facilitate the development of new therapeutic strategies. Abstract The TP53 gene is a critical tumor suppressor and key determinant of cell fate which regulates numerous cellular functions including DNA repair, cell cycle arrest, cellular senescence, apoptosis, autophagy and metabolism. In the last 15 years, the p53 pathway has grown in complexity through the discovery that TP53 differentially expresses twelve p53 protein isoforms in human cells with both overlapping and unique biologic activities. Here, we summarize the current knowledge on the Δ133p53 isoforms (Δ133p53α, Δ133p53β and Δ133p53γ), which are evolutionary derived and found only in human and higher order primates. All three isoforms lack both of the transactivation domains and the beginning of the DNA-binding domain. Despite the absence of these canonical domains, the Δ133p53 isoforms maintain critical functions in cancer, physiological and premature aging, neurodegenerative diseases, immunity and inflammation, and tissue repair. The ability of the Δ133p53 isoforms to modulate the p53 pathway functions underscores the need to include these p53 isoforms in our understanding of how the p53 pathway contributes to multiple physiological and pathological mechanisms. Critically, further characterization of p53 isoforms may identify novel regulatory modes of p53 pathway functions that contribute to disease progression and facilitate the development of new therapeutic strategies.
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19
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Timofeev O, Koch L, Niederau C, Tscherne A, Schneikert J, Klimovich M, Elmshäuser S, Zeitlinger M, Mernberger M, Nist A, Osterburg C, Dötsch V, Hrabé de Angelis M, Stiewe T. Phosphorylation Control of p53 DNA-Binding Cooperativity Balances Tumorigenesis and Aging. Cancer Res 2020; 80:5231-5244. [PMID: 32873634 DOI: 10.1158/0008-5472.can-20-2002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/30/2020] [Accepted: 08/26/2020] [Indexed: 11/16/2022]
Abstract
Posttranslational modifications are essential for regulating the transcription factor p53, which binds DNA in a highly cooperative manner to control expression of a plethora of tumor-suppressive programs. Here we show at the biochemical, cellular, and organismal level that the cooperative nature of DNA binding is reduced by phosphorylation of highly conserved serine residues (human S183/S185, mouse S180) in the DNA-binding domain. To explore the role of this inhibitory phosphorylation in vivo, new phosphorylation-deficient p53-S180A knock-in mice were generated. Chromatin immunoprecipitation sequencing and RNA sequencing studies of S180A knock-in cells demonstrated enhanced DNA binding and increased target gene expression. In vivo, this translated into a tissue-specific vulnerability of the bone marrow that caused depletion of hematopoietic stem cells and impaired proper regeneration of hematopoiesis after DNA damage. Median lifespan was significantly reduced by 20% from 709 days in wild type to only 568 days in S180A littermates. Importantly, lifespan was reduced by a loss of general fitness and increased susceptibility to age-related diseases, not by increased cancer incidence as often seen in other p53-mutant mouse models. For example, S180A knock-in mice showed markedly reduced spontaneous tumorigenesis and increased resistance to Myc-driven lymphoma and Eml4-Alk-driven lung cancer. Preventing phosphorylation of S183/S185 in human cells boosted p53 activity and allowed tumor cells to be killed more efficiently. Together, our data identify p53 DNA-binding domain phosphorylation as a druggable mechanism that balances tumorigenesis and aging. SIGNIFICANCE: These findings demonstrate that p53 tumor suppressor activity is reduced by DNA-binding domain phosphorylation to prevent aging and identify this phosphorylation as a potential target for cancer therapy.See related commentary by Horikawa, p. 5164.
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Affiliation(s)
- Oleg Timofeev
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany.
| | - Lukas Koch
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Constantin Niederau
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Alina Tscherne
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Jean Schneikert
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Maria Klimovich
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Sabrina Elmshäuser
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Marie Zeitlinger
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Marco Mernberger
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Philipps-University Marburg, Marburg, Germany
| | | | | | - Martin Hrabé de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany. .,Genomics Core Facility, Philipps-University Marburg, Marburg, Germany
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20
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Sabapathy K, Lane DP. Understanding p53 functions through p53 antibodies. J Mol Cell Biol 2020; 11:317-329. [PMID: 30907951 PMCID: PMC6487784 DOI: 10.1093/jmcb/mjz010] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/20/2019] [Accepted: 02/11/2019] [Indexed: 01/19/2023] Open
Abstract
TP53 is the most frequently mutated gene across all cancer types. Our understanding of its functions has evolved since its discovery four decades ago. Initially thought to be an oncogene, it was later realized to be a critical tumour suppressor. A significant amount of our knowledge about p53 functions have come from the use of antibodies against its various forms. The early anti-p53 antibodies contributed to the recognition of p53 accumulation as a common feature of cancer cells and to our understanding of p53 DNA-binding and transcription activities. They led to the concept that conformational changes can facilitate p53’s activity as a growth inhibitory protein. The ensuing p53 conformational-specific antibodies further underlined p53’s conformational flexibility, collectively forming the basis for current efforts to generate therapeutic molecules capable of altering the conformation of mutant p53. A subsequent barrage of antibodies against post-translational modifications on p53 has clarified p53’s roles further, especially with respect to the mechanistic details and context-dependence of its activity. More recently, the generation of p53 mutation-specific antibodies have highlighted the possibility to go beyond the general framework of our comprehension of mutant p53—and promises to provide insights into the specific properties of individual p53 mutants. This review summarizes our current knowledge of p53 functions derived through the major classes of anti-p53 antibodies, which could be a paradigm for understanding other molecular events in health and disease.
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Affiliation(s)
- Kanaga Sabapathy
- Laboratory of Molecular Carcinogenesis, Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, Singapore.,Department of Biochemistry, National University of Singapore (NUS), 8 Medical Drive, Singapore, Singapore.,Institute of Molecular and Cellular Biology, 61 Biopolis Drive, Singapore, Singapore
| | - David P Lane
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
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21
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Knockdown of TFAM in Tumor Cells Retarded Autophagic Flux through Regulating p53 Acetylation and PISD Expression. Cancers (Basel) 2020; 12:cancers12020493. [PMID: 32093281 PMCID: PMC7072172 DOI: 10.3390/cancers12020493] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial transcription factor A (TFAM) is required for mitochondrial DNA replication and transcription, which are essential for mitochondrial biogenesis. Previous studies reported that depleting mitochondrial functions by genetic deletion of TFAM impaired autophagic activities. However, the underlying mechanisms remain largely unknown. In the current study, we identified that knockdown of TFAM repressed the synthesis of autophagy bio-marker LC3-II in tumor cells and decreased the expression of phosphatidyl-serine decarboxylase (PISD). Besides, downregulation of PISD with siRNA reduced the level of LC3-II, indicating that depletion of TFAM retarded autophagy via inhibiting PISD expression. Furthermore, it was found that the tumor repressor p53 could stimulate the transcription and expression of PISD by binding the PISD enhancer. Additionally, the protein stability and transcriptional activity of p53 in TFAM knockdown tumor cells was attenuated, and this was associated with decreased acetylation, especially the acetylation of lysine 382 of p53. Finally, we identified that TFAM knockdown increased the NAD+/NADH ratio in tumor cells. This led to the upregulation of Sirtuin1 (SIRT1), a NAD-dependent protein deacetylase, to deacetylate p53 and attenuated its transcriptional activation on PISD. In summary, our study discovered a new mechanism regarding disturbed autophagy in tumor cells with mitochondrial dysfunction due to the depletion of TFAM.
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22
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Abstract
Mutated or dysregulated transcription factors represent a unique class of drug targets that mediate aberrant gene expression, including blockade of differentiation and cell death gene expression programmes, hallmark properties of cancers. Transcription factor activity is altered in numerous cancer types via various direct mechanisms including chromosomal translocations, gene amplification or deletion, point mutations and alteration of expression, as well as indirectly through non-coding DNA mutations that affect transcription factor binding. Multiple approaches to target transcription factor activity have been demonstrated, preclinically and, in some cases, clinically, including inhibition of transcription factor-cofactor protein-protein interactions, inhibition of transcription factor-DNA binding and modulation of levels of transcription factor activity by altering levels of ubiquitylation and subsequent proteasome degradation or by inhibition of regulators of transcription factor expression. In addition, several new approaches to targeting transcription factors have recently emerged including modulation of auto-inhibition, proteolysis targeting chimaeras (PROTACs), use of cysteine reactive inhibitors, targeting intrinsically disordered regions of transcription factors and combinations of transcription factor inhibitors with kinase inhibitors to block the development of resistance. These innovations in drug development hold great promise to yield agents with unique properties that are likely to impact future cancer treatment.
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Affiliation(s)
- John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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23
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Karakostis K, Fåhraeus R. Shaping the regulation of the p53 mRNA tumour suppressor: the co-evolution of genetic signatures. BMC Cancer 2019; 19:915. [PMID: 31519161 PMCID: PMC6743176 DOI: 10.1186/s12885-019-6118-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Structured RNA regulatory motifs exist from the prebiotic stages of the RNA world to the more complex eukaryotic systems. In cases where a functional RNA structure is within the coding sequence a selective pressure drives a parallel co-evolution of the RNA structure and the encoded peptide domain. The p53-MDM2 axis, describing the interactions between the p53 tumor suppressor and the MDM2 E3 ubiquitin ligase, serves as particularly useful model revealing how secondary RNA structures have co-evolved along with corresponding interacting protein motifs, thus having an impact on protein - RNA and protein - protein interactions; and how such structures developed signal-dependent regulation in mammalian systems. The p53(BOX-I) RNA sequence binds the C-terminus of MDM2 and controls p53 synthesis while the encoded peptide domain binds MDM2 and controls p53 degradation. The BOX-I peptide domain is also located within p53 transcription activation domain. The folding of the p53 mRNA structure has evolved from temperature-regulated in pre-vertebrates to an ATM kinase signal-dependent pathway in mammalian cells. The protein - protein interaction evolved in vertebrates and became regulated by the same signaling pathway. At the same time the protein - RNA and protein - protein interactions evolved, the p53 trans-activation domain progressed to become integrated into a range of cellular pathways. We discuss how a single synonymous mutation in the BOX-1, the p53(L22 L), observed in a chronic lymphocyte leukaemia patient, prevents the activation of p53 following DNA damage. The concepts analysed and discussed in this review may serve as a conceptual mechanistic paradigm of the co-evolution and function of molecules having roles in cellular regulation, or the aetiology of genetic diseases and how synonymous mutations can affect the encoded protein.
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Affiliation(s)
| | - Robin Fåhraeus
- Université Paris 7, INSERM UMR 1131, 27 Rue Juliette Dodu, 75010 Paris, France
- Department of Medical Biosciences, Umea University, SE-90185 Umea, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
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24
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Naryzhny SN, Legina OK. [Structural-functional diversity of p53 proteoforms]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 65:263-276. [PMID: 31436168 DOI: 10.18097/pbmc20196504263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Protein p53 is one of the most studied proteins. This attention is primarily due to its key role in the cellular mechanisms associated with carcinogenesis. Protein p53 is a transcription factor involved in a wide variety of processes: cell cycle regulation and apoptosis, signaling inside the cell, DNA repair, coordination of metabolic processes, regulation of cell interactions, etc. This multifunctionality is apparently determined by the fact that p53 is a vivid example of how the same protein can be represented by numerous proteoforms bearing completely different functional loads. By alternative splicing, using different promoters and translation initiation sites, the TP53 gene gives rise to at least 12 isoforms, which can additionally undergo numerous (>200) post-translational modifications. Proteoforms generated due to numerous point mutations in the TP53 gene are adding more complexity to this picture. The proteoforms produced are involved in various processes, such as the regulation of p53 transcriptional activity in response to various factors. This review is devoted to the description of the currently known p53 proteoforms, as well as their possible functionality.
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Affiliation(s)
- S N Naryzhny
- Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad region, Gatchina, Russia
| | - O K Legina
- Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad region, Gatchina, Russia
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25
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Garg S, Afzal S, Elwakeel A, Sharma D, Radhakrishnan N, Dhanjal JK, Sundar D, Kaul SC, Wadhwa R. Marine Carotenoid Fucoxanthin Possesses Anti-Metastasis Activity: Molecular Evidence. Mar Drugs 2019; 17:md17060338. [PMID: 31195739 PMCID: PMC6627158 DOI: 10.3390/md17060338] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/12/2022] Open
Abstract
Fucoxanthin is commonly found in marine organisms; however, to date, it has been one of the scarcely explored natural compounds. We investigated its activities in human cancer cell culture-based viability, migration, and molecular assays, and found that it possesses strong anticancer and anti-metastatic activities that work irrespective of the p53 status of cancer cells. In our experiments, fucoxanthin caused the transcriptional suppression of mortalin. Cell phenotype-driven molecular analyses on control and treated cells demonstrated that fucoxanthin caused a decrease in hallmark proteins associated with cell proliferation, survival, and the metastatic spread of cancer cells at doses that were relatively safe to the normal cells. The data suggested that the cancer therapy regimen may benefit from the recruitment of fucoxanthin; hence, it warrants further attention for basic mechanistic studies as well as drug development.
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Affiliation(s)
- Sukant Garg
- DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8565, Japan.
| | - Sajal Afzal
- DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8565, Japan.
- School of Integrative & Global Majors, University of Tsukuba, Tsukuba 305-8577, Japan.
| | - Ahmed Elwakeel
- DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8565, Japan.
- School of Integrative & Global Majors, University of Tsukuba, Tsukuba 305-8577, Japan.
| | - Damini Sharma
- DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8565, Japan.
- School of Integrative & Global Majors, University of Tsukuba, Tsukuba 305-8577, Japan.
| | - Navaneethan Radhakrishnan
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi 110-016, India.
| | - Jaspreet Kaur Dhanjal
- DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8565, Japan.
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi 110-016, India.
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi 110-016, India.
| | - Sunil C Kaul
- DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8565, Japan.
| | - Renu Wadhwa
- DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8565, Japan.
- School of Integrative & Global Majors, University of Tsukuba, Tsukuba 305-8577, Japan.
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26
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Casanovas A, Gallardo Ó, Carrascal M, Abian J. TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells. Bioinformatics 2019; 35:1404-1413. [PMID: 30219844 DOI: 10.1093/bioinformatics/bty805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/20/2018] [Accepted: 09/12/2018] [Indexed: 01/07/2023] Open
Abstract
MOTIVATION Protein function is regulated by post-translational modifications (PTMs) that may act individually or interact with others in a phenomenon termed PTM cross-talk. Multiple databases have been dedicated to PTMs, including recent initiatives oriented towards the in silico prediction of PTM interactions. The study of PTM cross-talk ultimately requires experimental evidence about whether certain PTMs coexist in a single protein molecule. However, available resources do not assist researchers in the experimental detection of co-modified peptides. RESULTS Herein, we present TCellXTalk, a comprehensive database of phosphorylation, ubiquitination and acetylation sites in human T cells that supports the experimental detection of co-modified peptides using targeted or directed mass spectrometry. We demonstrate the efficacy of TCellXTalk and the strategy presented here in a proof of concept experiment that enabled the identification and quantification of 15 co-modified (phosphorylated and ubiquitinated) peptides from CD3 proteins of the T-cell receptor complex. To our knowledge, these are the first co-modified peptide sequences described in this widely studied cell type. Furthermore, quantitative data showed distinct dynamics for co-modified peptides upon T cell activation, demonstrating differential regulation of co-occurring PTMs in this biological context. Overall, TCellXTalk facilitates the experimental detection of co-modified peptides in human T cells and puts forward a novel and generic strategy for the study of PTM cross-talk. AVAILABILITY AND IMPLEMENTATION TCellXTalk is available at https://www.tcellxtalk.org. Source Code is available at https://bitbucket.org/lp-csic-uab/tcellxtalk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Albert Casanovas
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Barcelona, Spain.,Autonomous University of Barcelona, E-08193 Bellaterra, Spain
| | - Óscar Gallardo
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Barcelona, Spain
| | - Montserrat Carrascal
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Barcelona, Spain
| | - Joaquin Abian
- Proteomics Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Barcelona, Spain.,Autonomous University of Barcelona, E-08193 Bellaterra, Spain
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27
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Hafner A, Bulyk ML, Jambhekar A, Lahav G. The multiple mechanisms that regulate p53 activity and cell fate. Nat Rev Mol Cell Biol 2019; 20:199-210. [DOI: 10.1038/s41580-019-0110-x] [Citation(s) in RCA: 452] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Wang Z, Yang K, Zheng Q, Zhang C, Tang H, Babicheva A, Jiang Q, Li M, Chen Y, Carr SG, Wu K, Zhang Q, Balistrieri A, Wang C, Song S, Ayon RJ, Desai AA, Black SM, Garcia JGN, Makino A, Yuan JXJ, Lu W, Wang J. Divergent changes of p53 in pulmonary arterial endothelial and smooth muscle cells involved in the development of pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol 2018; 316:L216-L228. [PMID: 30358436 DOI: 10.1152/ajplung.00538.2017] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The tumor-suppressive role of p53, a transcription factor that regulates the expression of many genes, has been linked to cell cycle arrest, apoptosis, and senescence. The noncanonical function or the pathogenic role of p53 has more recently been implicated in pulmonary vascular disease. We previously reported that rapid nuclear accumulation of hypoxia-inducible factor (HIF)-1α in pulmonary arterial smooth muscle cells (PASMCs) upregulates transient receptor potential channels and enhances Ca2+ entry to increase cytosolic Ca2+ concentration ([Ca2+]cyt). Also, we observed differences in HIF-1α/2α expression in PASMCs and pulmonary arterial endothelial cells (PAECs). Here we report that p53 is increased in PAECs, but decreased in PASMCs, isolated from mice with hypoxia-induced pulmonary hypertension (PH) and rats with monocrotaline (MCT)-induced PH (MCT-PH). The increased p53 in PAECs from rats with MCT-PH is associated with an increased ratio of Bax/Bcl-2, while the decreased p53 in PASMCs is associated with an increased HIF-1α. Furthermore, p53 is downregulated in PASMCs isolated from patients with idiopathic pulmonary arterial hypertension compared with PASMCs from normal subjects. Overexpression of p53 in normal PASMCs inhibits store-operated Ca2+ entry (SOCE) induced by passive depletion of intracellularly stored Ca2+ in the sarcoplasmic reticulum, while downregulation of p53 enhances SOCE. These data indicate that differentially regulated expression of p53 and HIF-1α/2α in PASMCs and PAECs and the cross talk between p53 and HIF-1α/2α in PASMCs and PAECs may play an important role in the development of PH via, at least in part, induction of PAEC apoptosis and PASMC proliferation.
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Affiliation(s)
- Ziyi Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China.,Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Kai Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Qiuyu Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Chenting Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Haiyang Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China.,Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Aleksandra Babicheva
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Qian Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Meichan Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Yuqin Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Shane G Carr
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Kang Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China.,Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Qian Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China.,Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona.,Department of Physiology, The University of Arizona College of Medicine , Tucson, Arizona
| | - Angela Balistrieri
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Christina Wang
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Shanshan Song
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Ramon J Ayon
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Ankit A Desai
- Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona
| | - Stephen M Black
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona.,Department of Physiology, The University of Arizona College of Medicine , Tucson, Arizona
| | - Joe G N Garcia
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona.,Department of Physiology, The University of Arizona College of Medicine , Tucson, Arizona
| | - Ayako Makino
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona.,Department of Physiology, The University of Arizona College of Medicine , Tucson, Arizona
| | - Jason X-J Yuan
- Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona.,Department of Physiology, The University of Arizona College of Medicine , Tucson, Arizona
| | - Wenju Lu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Jian Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou , China.,Division of Translational and Regenerative Medicine , Tucson, Arizona.,Department of Medicine, The University of Arizona College of Medicine , Tucson, Arizona.,Division of Pulmonary and Critical Care Medicine, The People's Hospital of Inner Mongolia, Huhhot, Inner Mongolia, China
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29
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Compton PD, Kelleher NL, Gunawardena J. Estimating the Distribution of Protein Post-Translational Modification States by Mass Spectrometry. J Proteome Res 2018; 17:2727-2734. [PMID: 29945451 DOI: 10.1021/acs.jproteome.8b00150] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Post-translational modifications (PTMs) of proteins play a central role in cellular information encoding, but the complexity of PTM state has been challenging to unravel. A single molecule can exhibit a "modform" or combinatorial pattern of co-occurring PTMs across multiple sites, and a molecular population can exhibit a distribution of amounts of different modforms. How can this "modform distribution" be estimated by mass spectrometry (MS)? Bottom-up MS, based on cleavage into peptides, destroys correlations between PTMs on different peptides, but it is conceivable that multiple proteases with appropriate patterns of cleavage could reconstruct the modform distribution. We introduce a mathematical language for describing MS measurements and show, on the contrary, that no matter how many distinct proteases are available, the shortfall in information required for reconstruction worsens exponentially with increasing numbers of sites. Whereas top-down MS on intact proteins can do better, current technology cannot prevent the exponential worsening. However, our analysis also shows that all forms of MS yield linear equations for modform amounts. This permits different MS protocols to be integrated and the modform distribution to be constrained within a high-dimensional "modform region", which may offer a feasible proxy for analyzing information encoding.
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Affiliation(s)
- Philip D Compton
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Neil L Kelleher
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States.,Department of Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Jeremy Gunawardena
- Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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30
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Xiao M, An Y, Wang F, Yao C, Zhang C, Xin J, Duan Y, Zhao X, Fang N, Ji S. A chimeric protein PTEN-L-p53 enters U251 cells to repress proliferation and invasion. Exp Cell Res 2018; 369:234-242. [PMID: 29802838 DOI: 10.1016/j.yexcr.2018.05.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/13/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022]
Abstract
PTEN, a well-known tumor suppressor, dephosphorylates PIP3 and inhibits AKT activity. A translational variant of PTEN has been identified and termed PTEN-Long (PTEN-L). The additional 173 amino acids (PTEN-L leader) at the N-terminal constitute a potential signal peptide. Differing from canonical PTEN, PTEN-L is secreted into the extracellular fluid and re-enters recipient cells, playing the similar roles as PTEN in vivo and in vitro. This character confers the PTEN-L a therapeutic ability via directly protein delivering instead of traditional DNA and RNA vector options. In the present study, we employed PTEN-L leader to assemble a fusion protein, PTEN-L-p53, inosculated with the transcriptional regulator TP53, which is another powerful tumor suppressor. We overexpressed PTEN-L-p53 in HEK293T cells and detected it in both the cytoplasm and nucleus. Subsequently, we found that PTEN-L-p53 was secreted outside of the cells and detected in the culture media by immunoblotting. Furthermore, we demonstrated that PTEN-L-p53 freely entered the cells and suppressed the viability of U251cells (p53R273H, a cell line with p53 R273H-mutation). PTEN-L-p53 is composed of endogenous protein/peptide bearing low immunogenicity, and only the junction region between PTEN-L leader and p53 can act as a new immune epitope. Accordingly, this fusion protein can potentially be used as a therapeutic option for TP53-abnormality cancers.
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Affiliation(s)
- Man Xiao
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China
| | - Yang An
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China
| | - Fengling Wang
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China
| | - Chao Yao
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China
| | - Chu Zhang
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China
| | - Junfang Xin
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China
| | - Yongjian Duan
- Department of Oncology, The First Affiliated Hospital of Henan University, Kaifeng, Henan Province, China
| | | | - Na Fang
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China.
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, Medical School, Henan University, Kaifeng, Henan Province, China; Department of Oncology, The First Affiliated Hospital of Henan University, Kaifeng, Henan Province, China.
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31
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Probing the interaction of the p53 C-terminal domain to the histone demethylase LSD1. Arch Biochem Biophys 2017; 632:202-208. [PMID: 28784588 DOI: 10.1016/j.abb.2017.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/18/2022]
Abstract
The p53 transcription factor plays a central role in the regulation of the expression of several genes, and itself is post-translationally regulated through its different domains. Of particular relevance for p53 function is its intrinsically disordered C-terminal domain (CTD), representing a hotspot for post-translational modifications and a docking site for transcriptional regulators. For example, the histone H3 lysine demethylase 1 (LSD1) interacts with p53 via the p53-CTD for mutual regulation. To biochemically and functionally characterize this complex, we evaluated the in vitro interactions of LSD1 with several p53-CTD peptides differing in length and modifications. Binding was demonstrated through thermal shift, enzymatic and fluorescence polarization assays, but no enzymatic activity could be detected on methylated p53-CTD peptides in vitro. These experiments were performed using the wild-type enzyme and LSD1 variants that are mutated on three active-site residues. We found that LSD1 demethylase activity is inhibited by p53-CTD. We also noted that the association between the two proteins is mediated by mostly non-specific electrostatic interactions involving conserved active-site residues of LSD1 and a highly charged segment of the p53-CTD. We conclude that p53-CTD inhibits LSD1 activity and that the direct association between the two proteins can contribute to their functional cross-talk.
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32
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Piao S, Pei HZ, Huang B, Baek SH. Ovarian tumor domain-containing protein 1 deubiquitinates and stabilizes p53. Cell Signal 2017; 33:22-29. [DOI: 10.1016/j.cellsig.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/22/2022]
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33
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Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, LeDuc RD, Parker WR, Thomas PM, Kelleher NL, Brodbelt JS. High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer. J Proteome Res 2017; 16:2072-2079. [PMID: 28412815 DOI: 10.1021/acs.jproteome.7b00043] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale. However, utilization of UVPD for high-throughput top-down analysis to date has been limited by bioinformatics. Here we detected 153 proteins and 489 proteoforms using UVPD and 271 proteins and 982 proteoforms using higher energy collisional dissociation (HCD) in a comparative analysis of HeLa whole-cell lysate by qualitative top-down proteomics. Of the total detected proteoforms, 286 overlapped between the UVPD and HCD data sets, with 68% of proteoforms having C scores greater than 40 for UVPD and 63% for HCD. The average sequence coverage (28 ± 20% for UVPD versus 17 ± 8% for HCD, p < 0.0001) was found to be higher for UVPD than HCD and with a trend toward improvement in q value for the UVPD data set. This study demonstrates the complementarity of UVPD and HCD for more extensive protein profiling and proteoform characterization.
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Affiliation(s)
- Timothy P Cleland
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Alexandra J VanNispen
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - W Ryan Parker
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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34
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Hung G, Flint SJ. Normal human cell proteins that interact with the adenovirus type 5 E1B 55kDa protein. Virology 2017; 504:12-24. [PMID: 28135605 PMCID: PMC5337154 DOI: 10.1016/j.virol.2017.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 12/31/2022]
Abstract
Several of the functions of the human adenovirus type 5 E1B 55kDa protein are fulfilled via the virus-specific E3 ubiquitin ligase it forms with the viral E4 Orf6 protein and several cellular proteins. Important substrates of this enzyme have not been identified, and other functions, including repression of transcription of interferon-sensitive genes, do not require the ligase. We therefore used immunoaffinity purification and liquid chromatography-mass spectrometry of lysates of normal human cells infected in parallel with HAdV-C5 and E1B 55kDa protein-null mutant viruses to identify specifically E1B 55kDa-associated proteins. The resulting set of >90 E1B-associated proteins contained the great majority identified previously, and was enriched for those associated with the ubiquitin-proteasome system, RNA metabolism and the cell cycle. We also report very severe inhibition of viral genome replication when cells were exposed to both specific or non-specific siRNAs and interferon prior to infection.
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Affiliation(s)
- George Hung
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - S J Flint
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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35
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Newman M, Sfaxi R, Saha A, Monchaud D, Teulade-Fichou MP, Vagner S. The G-Quadruplex-Specific RNA Helicase DHX36 Regulates p53 Pre-mRNA 3'-End Processing Following UV-Induced DNA Damage. J Mol Biol 2016; 429:3121-3131. [PMID: 27940037 DOI: 10.1016/j.jmb.2016.11.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/26/2016] [Accepted: 11/30/2016] [Indexed: 12/17/2022]
Abstract
Pre-mRNA 3'-end processing, the process through which almost all eukaryotic mRNAs acquire a poly(A) tail is generally inhibited during the cellular DNA damage response leading to a profound impact on the level of protein expression since unprocessed transcripts at the 3'-end will be degraded or unable to be transported to the cytoplasm. However, a compensatory mechanism involving the binding of the hnRNP H/F family of RNA binding proteins to an RNA G-quadruplex (G4) structure located in the vicinity of a polyadenylation site has previously been described to allow the transcript encoding the p53 tumour suppressor protein to be properly processed during DNA damage and to provide the cells with a way to react to DNA damage. Here we report that the DEAH (Asp-Glu-Ala-His) box RNA helicase DHX36/RHAU/G4R1, which specifically binds to and resolves parallel-stranded G4, is necessary to maintain p53 pre-mRNA 3'-end processing following UV-induced DNA damage. DHX36 binds to the p53 RNA G4, while mutation of the G4 impairs the ability of DHX36 to maintain pre-mRNA 3'-end processing. Stabilization of the p53 RNA G4 with two different G4 ligands (PNADOTASQ and PhenDC3), which is expected from previous studies to prevent DHX36 from binding and unwinding G4s, also impairs p53 pre-mRNA 3'-end processing following UV. Our work identifies DHX36 as a new actor in the compensatory mechanisms that are in place to ensure that the mRNAs encoding p53 are still processed following UV.
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Affiliation(s)
- Michelle Newman
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France
| | - Rym Sfaxi
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France
| | - Abhijit Saha
- Institut Curie, PSL Research University, CNRS UMR9187-INSERM U1196, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, UMR9187-INSERM U1196, F-91405 Orsay, France
| | - David Monchaud
- Institute of Molecular Chemistry, University of Dijon, ICMUB CNRS UMR6302, F-21078 Dijon, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187-INSERM U1196, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, UMR9187-INSERM U1196, F-91405 Orsay, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France.
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Laptenko O, Tong DR, Manfredi J, Prives C. The Tail That Wags the Dog: How the Disordered C-Terminal Domain Controls the Transcriptional Activities of the p53 Tumor-Suppressor Protein. Trends Biochem Sci 2016; 41:1022-1034. [PMID: 27669647 DOI: 10.1016/j.tibs.2016.08.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 01/22/2023]
Abstract
The p53 tumor suppressor is a transcription factor (TF) that exerts antitumor functions through its ability to regulate the expression of multiple genes. Within the p53 protein resides a relatively short unstructured C-terminal domain (CTD) that remarkably participates in virtually every aspect of p53 performance as a TF. Because these aspects are often interdependent and it is not always possible to dissect them experimentally, there has been a great deal of controversy about the CTD. In this review we evaluate the significance and key features of this interesting region of p53 and its impact on the many aspects of p53 function in light of previous and more recent findings.
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Affiliation(s)
- Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - David R Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - James Manfredi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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37
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Beckerman R, Yoh K, Mattia-Sansobrino M, Zupnick A, Laptenko O, Karni-Schmidt O, Ahn J, Byeon IJ, Keezer S, Prives C. Lysines in the tetramerization domain of p53 selectively modulate G1 arrest. Cell Cycle 2016; 15:1425-38. [PMID: 27210019 DOI: 10.1080/15384101.2016.1170270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Functional in a tetrameric state, the protein product of the p53 tumor suppressor gene confers its tumor-suppressive activity by transactivating genes which promote cell-cycle arrest, senescence, or programmed cell death. How p53 distinguishes between these divergent outcomes is still a matter of considerable interest. Here we discuss the impact of 2 mutations in the tetramerization domain that confer unique properties onto p53. By changing lysines 351 and 357 to arginine, thereby blocking all post-translational modifications of these residues, DNA binding and transcriptional regulation by p53 remain virtually unchanged. On the other hand, by changing these lysines to glutamine (2KQ-p53), thereby neutralizing their positive charge and potentially mimicking acetylation, p53 is impaired in the induction of cell cycle arrest and yet can still effectively induce cell death. Surprisingly, when 2KQ-p53 is expressed at high levels in H1299 cells, it can bind to and transactivate numerous p53 target genes including p21, but not others such as miR-34a and cyclin G1 to the same extent as wild-type p53. Our findings show that strong induction of p21 is not sufficient to block H1299 cells in G1, and imply that modification of one or both of the lysines within the tetramerization domain may serve as a mechanism to shunt p53 from inducing cell cycle arrest.
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Affiliation(s)
| | - Kathryn Yoh
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | | | | | - Oleg Laptenko
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Orit Karni-Schmidt
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Jinwoo Ahn
- b Department of Structural Biology , University of Pittsburgh , Pittsburgh , PA , USA
| | - In-Ja Byeon
- b Department of Structural Biology , University of Pittsburgh , Pittsburgh , PA , USA
| | - Susan Keezer
- c Cell Signaling Technology, Inc. , Danvers , MA , USA
| | - Carol Prives
- a Department of Biological Sciences , Columbia University , New York , NY , USA
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38
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Stępiński D. Nucleolus-derived mediators in oncogenic stress response and activation of p53-dependent pathways. Histochem Cell Biol 2016; 146:119-39. [PMID: 27142852 DOI: 10.1007/s00418-016-1443-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2016] [Indexed: 12/12/2022]
Abstract
Rapid growth and division of cells, including tumor ones, is correlated with intensive protein biosynthesis. The output of nucleoli, organelles where translational machineries are formed, depends on a rate of particular stages of ribosome production and on accessibility of elements crucial for their effective functioning, including substrates, enzymes as well as energy resources. Different factors that induce cellular stress also often lead to nucleolar dysfunction which results in ribosome biogenesis impairment. Such nucleolar disorders, called nucleolar or ribosomal stress, usually affect cellular functioning which in fact is a result of p53-dependent pathway activation, elicited as a response to stress. These pathways direct cells to new destinations such as cell cycle arrest, damage repair, differentiation, autophagy, programmed cell death or aging. In the case of impaired nucleolar functioning, nucleolar and ribosomal proteins mediate activation of the p53 pathways. They are also triggered as a response to oncogenic factor overexpression to protect tissues and organs against extensive proliferation of abnormal cells. Intentional impairment of any step of ribosome biosynthesis which would direct the cells to these destinations could be a strategy used in anticancer therapy. This review presents current knowledge on a nucleolus, mainly in relation to cancer biology, which is an important and extremely sensitive element of the mechanism participating in cellular stress reaction mediating activation of the p53 pathways in order to counteract stress effects, especially cancer development.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
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Abstract
p53 has been studied intensively as a major tumour suppressor that detects oncogenic events in cancer cells and eliminates them through senescence (a permanent non-proliferative state) or apoptosis. Consistent with this role, p53 activity is compromised in a high proportion of all cancer types, either through mutation of the TP53 gene (encoding p53) or changes in the status of p53 modulators. p53 has additional roles, which may overlap with its tumour-suppressive capacity, in processes including the DNA damage response, metabolism, aging, stem cell differentiation and fertility. Moreover, many mutant p53 proteins, termed 'gain-of-function' (GOF), acquire new activities that help drive cancer aggression. p53 is regulated mainly through protein turnover and operates within a negative-feedback loop with its transcriptional target, MDM2 (murine double minute 2), an E3 ubiquitin ligase which mediates the ubiquitylation and proteasomal degradation of p53. Induction of p53 is achieved largely through uncoupling the p53-MDM2 interaction, leading to elevated p53 levels. Various stress stimuli acting on p53 (such as hyperproliferation and DNA damage) use different, but overlapping, mechanisms to achieve this. Additionally, p53 activity is regulated through critical context-specific or fine-tuning events, mediated primarily through post-translational mechanisms, particularly multi-site phosphorylation and acetylation. In the present review, I broadly examine these events, highlighting their regulatory contributions, their ability to integrate signals from cellular events towards providing most appropriate response to stress conditions and their importance for tumour suppression. These are fascinating aspects of molecular oncology that hold the key to understanding the molecular pathology of cancer and the routes by which it may be tackled therapeutically.
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40
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Friso G, van Wijk KJ. Posttranslational Protein Modifications in Plant Metabolism. PLANT PHYSIOLOGY 2015; 169:1469-87. [PMID: 26338952 PMCID: PMC4634103 DOI: 10.1104/pp.15.01378] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 05/18/2023]
Abstract
Posttranslational modifications (PTMs) of proteins greatly expand proteome diversity, increase functionality, and allow for rapid responses, all at relatively low costs for the cell. PTMs play key roles in plants through their impact on signaling, gene expression, protein stability and interactions, and enzyme kinetics. Following a brief discussion of the experimental and bioinformatics challenges of PTM identification, localization, and quantification (occupancy), a concise overview is provided of the major PTMs and their (potential) functional consequences in plants, with emphasis on plant metabolism. Classic examples that illustrate the regulation of plant metabolic enzymes and pathways by PTMs and their cross talk are summarized. Recent large-scale proteomics studies mapped many PTMs to a wide range of metabolic functions. Unraveling of the PTM code, i.e. a predictive understanding of the (combinatorial) consequences of PTMs, is needed to convert this growing wealth of data into an understanding of plant metabolic regulation.
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Affiliation(s)
- Giulia Friso
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
| | - Klaas J van Wijk
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
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41
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Tong Q, Mazur SJ, Rincon-Arano H, Rothbart SB, Kuznetsov DM, Cui G, Liu WH, Gete Y, Klein BJ, Jenkins L, Mer G, Kutateladze AG, Strahl BD, Groudine M, Appella E, Kutateladze TG. An acetyl-methyl switch drives a conformational change in p53. Structure 2015; 23:322-31. [PMID: 25651062 DOI: 10.1016/j.str.2014.12.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/03/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
Abstract
Individual posttranslational modifications (PTMs) of p53 mediate diverse p53-dependent responses; however, much less is known about the combinatorial action of adjacent modifications. Here, we describe crosstalk between the early DNA damage response mark p53K382me2 and the surrounding PTMs that modulate binding of p53 cofactors, including 53BP1 and p300. The 1.8 Å resolution crystal structure of the tandem Tudor domain (TTD) of 53BP1 in complex with p53 peptide acetylated at K381 and dimethylated at K382 (p53K381acK382me2) reveals that the dual PTM induces a conformational change in p53. The α-helical fold of p53K381acK382me2 positions the side chains of R379, K381ac, and K382me2 to interact with TTD concurrently, reinforcing a modular design of double PTM mimetics. Biochemical and nuclear magnetic resonance analyses show that other surrounding PTMs, including phosphorylation of serine/threonine residues of p53, affect association with TTD. Our findings suggest a novel PTM-driven conformation switch-like mechanism that may regulate p53 interactions with binding partners.
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Affiliation(s)
- Qiong Tong
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hector Rincon-Arano
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Scott B Rothbart
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Dmitry M Kuznetsov
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Wallace H Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yantenew Gete
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Lisa Jenkins
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mark Groudine
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Radiation Oncology, University Washington School of Medicine, Seattle, WA 98109, USA
| | - Ettore Appella
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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42
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Carr SM, Poppy Roworth A, Chan C, La Thangue NB. Post-translational control of transcription factors: methylation ranks highly. FEBS J 2015; 282:4450-65. [PMID: 26402372 DOI: 10.1111/febs.13524] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/04/2015] [Accepted: 09/21/2015] [Indexed: 01/31/2023]
Abstract
Methylation of lysine and arginine residues on histones has long been known to determine both chromatin structure and gene expression. In recent years, the methylation of non-histone proteins has emerged as a prevalent modification which impacts on diverse processes such as cell cycle control, DNA repair, senescence, differentiation, apoptosis and tumourigenesis. Many of these non-histone targets represent transcription factors, cell signalling molecules and tumour suppressor proteins. Evidence now suggests that the dysregulation of methyltransferases, demethylases and reader proteins is involved in the development of many diseases, including cancer, and several of these proteins represent potential therapeutic targets for small molecule compounds, fuelling a recent surge in chemical inhibitor design. Such molecules will greatly help us to understand the role of methylation in both health and disease.
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Affiliation(s)
- Simon M Carr
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, UK
| | - A Poppy Roworth
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, UK
| | - Cheryl Chan
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, UK
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43
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Lei M, Xie W, Sun E, Sun Y, Tian D, Liu C, Han R, Li N, Liu M, Han R, Liu L. microRNA-21 Regulates Cell Proliferation and Migration and Cross Talk with PTEN and p53 in Bladder Cancer. DNA Cell Biol 2015; 34:626-32. [PMID: 26230405 DOI: 10.1089/dna.2015.2868] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Mingde Lei
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Wanqin Xie
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Erlin Sun
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Yan Sun
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Dawei Tian
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Chunyu Liu
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Rong Han
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Na Li
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Min Liu
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Ruifa Han
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Liwei Liu
- Department of Urology, Tianjin Institute of Urology, Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
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44
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Ho DH, Kim H, Kim J, Sim H, Ahn H, Kim J, Seo H, Chung KC, Park BJ, Son I, Seol W. Leucine-Rich Repeat Kinase 2 (LRRK2) phosphorylates p53 and induces p21(WAF1/CIP1) expression. Mol Brain 2015; 8:54. [PMID: 26384650 PMCID: PMC4575451 DOI: 10.1186/s13041-015-0145-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/04/2015] [Indexed: 11/25/2022] Open
Abstract
Background Leucine-rich repeat kinase 2 (LRRK2) is a gene in which a mutation causes Parkinson’s disease (PD), and p53 is a prototype tumor suppressor. In addition, activation of p53 in patient with PD has been reported by several studies. Because phosphorylation of p53 is critical for regulating its activity and LRRK2 is a kinase, we tested whether p53 is phosphorylated by LRRK2. Results LRRK2 phosphorylates threonine (Thr) at TXR sites in an in vitro kinase assay, and the T304 and T377 were identified as putative phosphorylated residues. An increase of phospho-Thr in the p53 TXR motif was confirmed in the cells overexpressing G2019S, and human induced pluripotent stem (iPS) cells of a G2019S carrier. Interactions between LRRK2 and p53 were confirmed by co-immunoprecipitation of lysates of differentiated SH-SY5Y cells. LRRK2 mediated p53 phosphorylation translocalizes p53 predominantly to nucleus and increases p21WAF1/CIP1 expression in SH-SY5Y cells based on reverse transcription-polymerase chain reaction and Western blot assay results. The luciferase assay using the p21WAF1/CIP1 promoter-reporter also confirmed that LRRK2 kinase activity increases p21 expression. Exogenous expression of G2019S and the phosphomimetic p53 T304/377D mutants increased expression of p21WAF1/CIP1 and cleaved PARP, and cytotoxicity in the same cells. We also observed increase of p21 expression in rat primary neuron cells after transient expression of p53 T304/377D mutants and the mid-brain lysates of the G2019S transgenic mice. Conclusion p53 is a LRRK2 kinase substrate. Phosphorylation of p53 by LRRK2 induces p21WAF1/CIP1 expression and apoptosis in differentiated SH-SY5Y cells and rat primary neurons. Electronic supplementary material The online version of this article (doi:10.1186/s13041-015-0145-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dong Hwan Ho
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, 321 Sanbon-ro, Gunposhi, Gyeonggido, Republic of Korea.,Department of Molecular and Life Sciences, Hanyang University, Ansanshi, Gyeonggido, Republic of Korea
| | - Hyejung Kim
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, 321 Sanbon-ro, Gunposhi, Gyeonggido, Republic of Korea
| | - Jisun Kim
- Department of Molecular and Life Sciences, Hanyang University, Ansanshi, Gyeonggido, Republic of Korea
| | - Hyuna Sim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.,Korea University of Science & Technology (UST), 113 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyunjun Ahn
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.,Korea University of Science & Technology (UST), 113 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Janghwan Kim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.,Korea University of Science & Technology (UST), 113 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyemyung Seo
- Department of Molecular and Life Sciences, Hanyang University, Ansanshi, Gyeonggido, Republic of Korea
| | - Kwang Chul Chung
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Pusan, Republic of Korea
| | - Ilhong Son
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, 321 Sanbon-ro, Gunposhi, Gyeonggido, Republic of Korea. .,Department of Neurology, Sanbon Medical Center, College of Medicine, Wonkwang University, 321 Sanbon-ro, Gunposhi, Gyeonggido, Republic of Korea.
| | - Wongi Seol
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, 321 Sanbon-ro, Gunposhi, Gyeonggido, Republic of Korea.
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45
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Tong Q, Cui G, Botuyan MV, Rothbart SB, Hayashi R, Musselman CA, Singh N, Appella E, Strahl BD, Mer G, Kutateladze TG. Structural plasticity of methyllysine recognition by the tandem tudor domain of 53BP1. Structure 2015; 23:312-21. [PMID: 25579814 DOI: 10.1016/j.str.2014.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022]
Abstract
p53 is dynamically regulated through various posttranslational modifications (PTMs), which differentially modulate its function and stability. The dimethylated marks p53K370me2 and p53K382me2 are associated with p53 activation or stabilization and both are recognized by the tandem Tudor domain (TTD) of 53BP1, a p53 cofactor. Here we detail the molecular mechanisms for the recognition of p53K370me2 and p53K382me2 by 53BP1. The solution structures of TTD in complex with the p53K370me2 and p53K382me2 peptides show a remarkable plasticity of 53BP1 in accommodating these diverse dimethyllysine-containing sequences. We demonstrate that dimeric TTDs are capable of interacting with the two PTMs on a single p53K370me2K382me2 peptide, greatly strengthening the 53BP1-p53 interaction. Analysis of binding affinities of TTD toward methylated p53 and histones reveals strong preference of 53BP1 for p53K382me2, H4K20me2, and H3K36me2 and suggests a possible role of multivalent contacts of 53BP1 in p53 targeting to and accumulation at the sites of DNA damage.
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Affiliation(s)
- Qiong Tong
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Scott B Rothbart
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ryo Hayashi
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Catherine A Musselman
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Namit Singh
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ettore Appella
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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46
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Impact of the adenoviral E4 Orf3 protein on the activity and posttranslational modification of p53. J Virol 2015; 89:3209-20. [PMID: 25568206 DOI: 10.1128/jvi.03072-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
UNLABELLED Our previous studies have established that the p53 populations that accumulate in normal human cells exposed to etoposide or infected by an E1B 55-kDa protein-null mutant of human adenovirus type 5 carry a large number of posttranslational modifications at numerous residues (C. J. DeHart, J. S. Chahal, S. J. Flint, and D. H. Perlman, Mol Cell Proteomics 13:1-17, 2014, http://dx.doi.org/10.1074/mcp.M113.030254). In the absence of this E1B protein, the p53 transcriptional program is not induced, and it has been reported that the viral E4 Orf3 protein inactivates p53 (C. Soria, F. E. Estermann, K. C. Espantman, and C. C. O'Shea, Nature 466:1076-1081, 2010, http://dx.doi.org/10.1038/nature09307). As the latter protein disrupts nuclear Pml bodies, sites at which p53 is modified, we used mass spectrometry to catalogue the posttranscriptional modifications of the p53 population that accumulates when neither the E1B 55-kDa nor the E4 Orf3 protein is made in infected cells. Eighty-five residues carrying 163 modifications were identified. The overall patterns of posttranslational modification of this population and p53 present in cells infected by an E1B 55-kDa-null mutant were similar. The efficiencies with which the two forms of p53 bound to a consensus DNA recognition sequence could not be distinguished and were lower than that of transcriptionally active p53. The absence of the E4 Orf3 protein increased expression of several p53-responsive genes when the E1B protein was also absent from infected cells. However, expression of these genes did not attain the levels observed when p53 was activated in response to etoposide treatment and remained lower than those measured in mock-infected cells. IMPORTANCE The tumor suppressor p53, a master regulator of cellular responses to stress, is inactivated and destroyed in cells infected by species C human adenoviruses, such as type 5. It is targeted for proteasomal degradation by the action of a virus-specific E3 ubiquitin ligase that contains the viral E1B 55-kDa and E4 Orf6 proteins, while the E4 Orf3 protein has been reported to block its ability to stimulate expression of p53-dependent genes. The comparisons reported here of the posttranslational modifications and activities of p53 populations that accumulate in infected normal human cells in the absence of both mechanisms of inactivation or of only the E3 ligase revealed little impact of the E4 Orf3 protein. These observations indicate that E4 Orf3-dependent disruption of Pml bodies does not have a major effect on the pattern of p53 posttranslational modifications in adenovirus-infected cells. Furthermore, they suggest that one or more additional viral proteins contribute to blocking p53 activation and the consequences that are deleterious for viral reproduction, such as apoptosis or cell cycle arrest.
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Krist B, Florczyk U, Pietraszek-Gremplewicz K, Józkowicz A, Dulak J. The Role of miR-378a in Metabolism, Angiogenesis, and Muscle Biology. Int J Endocrinol 2015; 2015:281756. [PMID: 26839547 PMCID: PMC4709675 DOI: 10.1155/2015/281756] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/30/2015] [Indexed: 02/06/2023] Open
Abstract
MicroRNA-378a (miR-378a, previously known as miR-378) is one of the small noncoding RNA molecules able to regulate gene expression at posttranscriptional level. Its two mature strands, miR-378a-3p and miR-378a-5p, originate from the first intron of the peroxisome proliferator-activated receptor gamma, coactivator 1 beta (ppargc1b) gene encoding PGC-1β. Embedding in the sequence of this transcriptional regulator of oxidative energy metabolism implies involvement of miR-378a in metabolic pathways, mitochondrial energy homeostasis, and related biological processes such as muscle development, differentiation, and regeneration. On the other hand, modulating the expression of proangiogenic factors such as vascular endothelial growth factor, angiopoietin-1, or interleukin-8, influencing inflammatory reaction, and affecting tumor suppressors, such as SuFu and Fus-1, miR-378a is considered as a part of an angiogenic network in tumors. In the latter, miR-378a can evoke broader actions by enhancing cell survival, reducing apoptosis, and promoting cell migration and invasion. This review describes the current knowledge on miR-378a linking oxidative/lipid metabolism, muscle biology, and blood vessel formation.
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Affiliation(s)
- Bart Krist
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Urszula Florczyk
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Katarzyna Pietraszek-Gremplewicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Alicja Józkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Jozef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
- *Jozef Dulak:
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Ji X, Huang Q, Yu L, Nussinov R, Ma B. Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs. Int J Mol Sci 2014; 15:13275-98. [PMID: 25075982 PMCID: PMC4159794 DOI: 10.3390/ijms150813275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 02/06/2023] Open
Abstract
p53 protein has about thirty phosphorylation sites located at the N- and C-termini and in the core domain. The phosphorylation sites are relatively less mutated than other residues in p53. To understand why and how p53 phosphorylation sites are rarely mutated in human cancer, using a bioinformatics approaches, we examined the phosphorylation site and its nearby flanking residues, focusing on the consensus phosphorylation motif pattern, amino-acid correlations within the phosphorylation motifs, the propensity of structural disorder of the phosphorylation motifs, and cancer mutations observed within the phosphorylation motifs. Many p53 phosphorylation sites are targets for several kinases. The phosphorylation sites match 17 consensus sequence motifs out of the 29 classified. In addition to proline, which is common in kinase specificity-determining sites, we found high propensity of acidic residues to be adjacent to phosphorylation sites. Analysis of human cancer mutations in the phosphorylation motifs revealed that motifs with adjacent acidic residues generally have fewer mutations, in contrast to phosphorylation sites near proline residues. p53 phosphorylation motifs are mostly disordered. However, human cancer mutations within phosphorylation motifs tend to decrease the disorder propensity. Our results suggest that combination of acidic residues Asp and Glu with phosphorylation sites provide charge redundancy which may safe guard against loss-of-function mutations, and that the natively disordered nature of p53 phosphorylation motifs may help reduce mutational damage. Our results further suggest that engineering acidic amino acids adjacent to potential phosphorylation sites could be a p53 gene therapy strategy.
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Affiliation(s)
- Xiaona Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Long Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
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Loughery J, Cox M, Smith LM, Meek DW. Critical role for p53-serine 15 phosphorylation in stimulating transactivation at p53-responsive promoters. Nucleic Acids Res 2014; 42:7666-80. [PMID: 24928858 PMCID: PMC4081099 DOI: 10.1093/nar/gku501] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The p53 tumour suppressor is induced by various stress stimuli and coordinates an adaptive gene expression programme leading to growth arrest or cell death. Some stimuli, such as DNA damage, lead to rapid and substantial multisite phosphorylation of p53, nucleated initially through phosphorylation of serine 15. Other stimuli, such as hyper-proliferation, do not stimulate p53-phosphorylation, raising questions regarding the physiological role for phosphorylation. Here, we show that a basal level of Ser15 phosphorylation occurs in both unstimulated cells and cells stimulated pharmacologically to induce p53. p53 in which Ser15 is substituted by alanine (S15A) fails to mediate p53-dependent transcription or growth arrest but can be rescued by substitution with aspartate (S15D: a phospho-mimic). Chromatin immunoprecipitation (ChIP) analyses show that, while wt- and S15A-p53 are detectable on the CDKN1A (p21) promoter (as a representative p53-responsive promoter), S15A-p53 does not stimulate histone acetylation (a measure of chromatin relaxation), nor is its recruitment stimulated, in response to a DNA damage or pharmacological stimulus. These data demonstrate that Ser15 phosphorylation is required for p53 function in the physiological context of p53-responsive promoters and suggest a key and possibly universal role even for low levels of this modification in promoting p53-transcription function.
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Affiliation(s)
- Jayne Loughery
- Division of Cancer Research, Medical Research Institute, The University of Dundee, Ninewells Hospital, James Arrott Drive, Dundee DD1 9SY, United Kingdom
| | - Miranda Cox
- Division of Cancer Research, Medical Research Institute, The University of Dundee, Ninewells Hospital, James Arrott Drive, Dundee DD1 9SY, United Kingdom
| | - Linda M Smith
- Division of Cancer Research, Medical Research Institute, The University of Dundee, Ninewells Hospital, James Arrott Drive, Dundee DD1 9SY, United Kingdom
| | - David W Meek
- Division of Cancer Research, Medical Research Institute, The University of Dundee, Ninewells Hospital, James Arrott Drive, Dundee DD1 9SY, United Kingdom
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Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci 2014; 23:1077-93. [PMID: 24888500 DOI: 10.1002/pro.2494] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/26/2014] [Accepted: 05/27/2014] [Indexed: 12/24/2022]
Abstract
UNLABELLED The structural, functional, and mechanistic characterization of several types of post-translational modifications (PTMs) is well-documented. PTMs, however, may interact or interfere with one another when regulating protein function. Yet, characterization of the structural and functional signatures of their crosstalk has been hindered by the scarcity of data. To this end, we developed a unified sequence-based predictor of 23 types of PTM sites that, we believe, is a useful tool in guiding biological experiments and data interpretation. We then used experimentally determined and predicted PTM sites to investigate two particular cases of potential PTM crosstalk in eukaryotes. First, we identified proteins statistically enriched in multiple types of PTM sites and found that they show preferences toward intrinsically disordered regions as well as functional roles in transcriptional, posttranscriptional, and developmental processes. Second, we observed that target sites modified by more than one type of PTM, referred to as shared PTM sites, show even stronger preferences toward disordered regions than their single-PTM counterparts; we explain this by the need for these regions to accommodate multiple partners. Finally, we investigated the influence of single and shared PTMs on differential regulation of protein-protein interactions. We provide evidence that molecular recognition features (MoRFs) show significant preferences for PTM sites, particularly shared PTM sites, implicating PTMs in the modulation of this specific type of macromolecular recognition. We conclude that intrinsic disorder is a strong structural prerequisite for complex PTM-based regulation, particularly in context-dependent protein-protein interactions related to transcriptional and developmental processes. AVAILABILITY www.modpred.org.
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Affiliation(s)
- Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, 47405
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