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Lees A, Sessler T, McDade S. Dying to Survive-The p53 Paradox. Cancers (Basel) 2021; 13:3257. [PMID: 34209840 PMCID: PMC8268032 DOI: 10.3390/cancers13133257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
The p53 tumour suppressor is best known for its canonical role as "guardian of the genome", activating cell cycle arrest and DNA repair in response to DNA damage which, if irreparable or sustained, triggers activation of cell death. However, despite an enormous amount of work identifying the breadth of the gene regulatory networks activated directly and indirectly in response to p53 activation, how p53 activation results in different cell fates in response to different stress signals in homeostasis and in response to p53 activating anti-cancer treatments remains relatively poorly understood. This is likely due to the complex interaction between cell death mechanisms in which p53 has been activated, their neighbouring stressed or unstressed cells and the local stromal and immune microenvironment in which they reside. In this review, we evaluate our understanding of the burgeoning number of cell death pathways affected by p53 activation and how these may paradoxically suppress cell death to ensure tissue integrity and organismal survival. We also discuss how these functions may be advantageous to tumours that maintain wild-type p53, the understanding of which may provide novel opportunity to enhance treatment efficacy.
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Affiliation(s)
- Andrea Lees
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK;
| | | | - Simon McDade
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK;
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52
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On the specificity of protein-protein interactions in the context of disorder. Biochem J 2021; 478:2035-2050. [PMID: 34101805 PMCID: PMC8203207 DOI: 10.1042/bcj20200828] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023]
Abstract
With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.
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53
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p53/p73 Protein Network in Colorectal Cancer and Other Human Malignancies. Cancers (Basel) 2021; 13:cancers13122885. [PMID: 34207603 PMCID: PMC8227208 DOI: 10.3390/cancers13122885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The p53 family of proteins comprises p53, p63, and p73, which share high structural and functional similarity. The two distinct promoters of each locus, the alternative splicing, and the alternative translation initiation sites enable the generation of numerous isoforms with different protein-interacting domains and distinct activities. The co-expressed p53/p73 isoforms have significant but distinct roles in carcinogenesis. Their activity is frequently impaired in human tumors including colorectal carcinoma due to dysregulated expression and a dominant-negative effect accomplished by some isoforms and p53 mutants. The interactions between isoforms are particularly important to understand the onset of tumor formation, progression, and therapeutic response. The understanding of the p53/p73 network can contribute to the development of new targeted therapies. Abstract The p53 tumor suppressor protein is crucial for cell growth control and the maintenance of genomic stability. Later discovered, p63 and p73 share structural and functional similarity with p53. To understand the p53 pathways more profoundly, all family members should be considered. Each family member possesses two promoters and alternative translation initiation sites, and they undergo alternative splicing, generating multiple isoforms. The resulting isoforms have important roles in carcinogenesis, while their expression is dysregulated in several human tumors including colorectal carcinoma, which makes them potential targets in cancer treatment. Their activities arise, at least in part, from the ability to form tetramers that bind to specific DNA sequences and activate the transcription of target genes. In this review, we summarize the current understanding of the biological activities and regulation of the p53/p73 isoforms, highlighting their role in colorectal tumorigenesis. The analysis of the expression patterns of the p53/p73 isoforms in human cancers provides an important step in the improvement of cancer therapy. Furthermore, the interactions among the p53 family members which could modulate normal functions of the canonical p53 in tumor tissue are described. Lastly, we emphasize the importance of clinical studies to assess the significance of combining the deregulation of different members of the p53 family to define the outcome of the disease.
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54
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Sanborn AL, Yeh BT, Feigerle JT, Hao CV, Townshend RJ, Lieberman Aiden E, Dror RO, Kornberg RD. Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. eLife 2021; 10:68068. [PMID: 33904398 PMCID: PMC8137143 DOI: 10.7554/elife.68068] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/25/2021] [Indexed: 01/07/2023] Open
Abstract
Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity (‘fuzzy’ binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology. Cells adapt and respond to changes by regulating the activity of their genes. To turn genes on or off, they use a family of proteins called transcription factors. Transcription factors influence specific but overlapping groups of genes, so that each gene is controlled by several transcription factors that act together like a dimmer switch to regulate gene activity. The presence of transcription factors attracts proteins such as the Mediator complex, which activates genes by gathering the protein machines that read the genes. The more transcription factors are found near a specific gene, the more strongly they attract Mediator and the more active the gene is. A specific region on the transcription factor called the activation domain is necessary for this process. The biochemical sequences of these domains vary greatly between species, yet activation domains from, for example, yeast and human proteins are often interchangeable. To understand why this is the case, Sanborn et al. analyzed the genome of baker’s yeast and identified 150 activation domains, each very different in sequence. Three-quarters of them bound to a subunit of the Mediator complex called Med15. Sanborn et al. then developed a machine learning algorithm to predict activation domains in both yeast and humans. This algorithm also showed that negatively charged and greasy regions on the activation domains were essential to be activated by the Mediator complex. Further analyses revealed that activation domains used different poses to bind multiple sites on Med15, a behavior known as ‘fuzzy’ binding. This creates a high overall affinity even though the binding strength at each individual site is low, enabling the protein complexes to remain dynamic. These weak interactions together permit fine control over the activity of several genes, allowing cells to respond quickly and precisely to many changes. The computer algorithm used here provides a new way to identify activation domains across species and could improve our understanding of how living things grow, adapt and evolve. It could also give new insights into mechanisms of disease, particularly cancer, where transcription factors are often faulty.
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Affiliation(s)
- Adrian L Sanborn
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States.,Department of Computer Science, Stanford University, Stanford, United States
| | - Benjamin T Yeh
- Department of Computer Science, Stanford University, Stanford, United States
| | - Jordan T Feigerle
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Cynthia V Hao
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | | | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, United States.,Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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55
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p53 mediates target gene association with nuclear speckles for amplified RNA expression. Mol Cell 2021; 81:1666-1681.e6. [PMID: 33823140 DOI: 10.1016/j.molcel.2021.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/05/2021] [Accepted: 03/03/2021] [Indexed: 01/01/2023]
Abstract
Nuclear speckles are prominent nuclear bodies that contain proteins and RNA involved in gene expression. Although links between nuclear speckles and gene activation are emerging, the mechanisms regulating association of genes with speckles are unclear. We find that speckle association of p53 target genes is driven by the p53 transcription factor. Focusing on p21, a key p53 target, we demonstrate that speckle association boosts expression by elevating nascent RNA amounts. p53-regulated speckle association did not depend on p53 transactivation functions but required an intact proline-rich domain and direct DNA binding, providing mechanisms within p53 for regulating gene-speckle association. Beyond p21, a substantial subset of p53 targets have p53-regulated speckle association. Strikingly, speckle-associating p53 targets are more robustly activated and occupy a distinct niche of p53 biology compared with non-speckle-associating p53 targets. Together, our findings illuminate regulated speckle association as a mechanism used by a transcription factor to boost gene expression.
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56
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Zhu G, Pan C, Bei JX, Li B, Liang C, Xu Y, Fu X. Mutant p53 in Cancer Progression and Targeted Therapies. Front Oncol 2020; 10:595187. [PMID: 33240819 PMCID: PMC7677253 DOI: 10.3389/fonc.2020.595187] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/12/2020] [Indexed: 12/17/2022] Open
Abstract
TP53 is the most frequently mutated tumor suppressor gene in human cancer. The majority of mutations of p53 are missense mutations, leading to the expression of the full length p53 mutant proteins. Mutant p53 (Mutp53) proteins not only lose wild-type p53-dependent tumor suppressive functions, but also frequently acquire oncogenic gain-of-functions (GOF) that promote tumorigenesis. In this review, we summarize the recent advances in our understanding of the oncogenic GOF of mutp53 and the potential therapies targeting mutp53 in human cancers. In particular, we discuss the promising drugs that are currently under clinical trials as well as the emerging therapeutic strategies, including CRISPR/Cas9 based genome edition of mutant TP53 allele, small peptide mediated restoration of wild-type p53 function, and immunotherapies that directly eliminate mutp53 expressing tumor cells.
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Affiliation(s)
- Gaoyang Zhu
- Postdoctoral Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Chaoyun Pan
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jin-Xin Bei
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Bo Li
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chen Liang
- Shenzhen International Institute for Biomedical Research, Shenzhen, China
| | - Yang Xu
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Xuemei Fu
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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57
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Dudás EF, Pálfy G, Menyhárd DK, Sebák F, Ecsédi P, Nyitray L, Bodor A. Tumor-Suppressor p53TAD 1-60 Forms a Fuzzy Complex with Metastasis-Associated S100A4: Structural Insights and Dynamics by an NMR/MD Approach. Chembiochem 2020; 21:3087-3095. [PMID: 32511842 PMCID: PMC7689910 DOI: 10.1002/cbic.202000348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Indexed: 01/05/2023]
Abstract
Conformationally flexible protein complexes represent a major challenge for structural and dynamical studies. We present herein a method based on a hybrid NMR/MD approach to characterize the complex formed between the disordered p53TAD1-60 and the metastasis-associated S100A4. Disorder-to-order transitions of both TAD1 and TAD2 subdomains upon interaction is detected. Still, p53TAD1-60 remains highly flexible in the bound form, with residues L26, M40, and W53 being anchored to identical hydrophobic pockets of the S100A4 monomer chains. In the resulting "fuzzy" complex, the clamp-like binding of p53TAD1-60 relies on specific hydrophobic anchors and on the existence of extended flexible segments. Our results demonstrate that structural and dynamical NMR parameters (cumulative Δδ, SSP, temperature coefficients, relaxation time, hetNOE) combined with MD simulations can be used to build a structural model even if, due to high flexibility, the classical solution structure calculation is not possible.
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Affiliation(s)
- Erika F. Dudás
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
- MTA-ELTE Protein Modelling Research GroupPázmány Péter sétány. 1/aBudapest1117Hungary
| | - Fanni Sebák
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
- Doctoral School of Pharmaceutical SciencesSemmelweis UniversityÜllői út 26Budapest1085Hungary
| | - Péter Ecsédi
- Department of BiochemistryEötvös Loránd UniversityPázmány Péter sétány 1/cBudapest1117Hungary
| | - László Nyitray
- Department of BiochemistryEötvös Loránd UniversityPázmány Péter sétány 1/cBudapest1117Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
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58
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Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Sci Rep 2020; 10:16176. [PMID: 32999415 PMCID: PMC7528078 DOI: 10.1038/s41598-020-73234-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
The tumor suppressor protein p53 is critical for cell fate decisions, including apoptosis, senescence, and cell cycle arrest. p53 is a tetrameric transcription factor that binds DNA response elements to regulate transcription of target genes. p53 response elements consist of two decameric half-sites, and data suggest one p53 dimer in the tetramer binds to each half-site. Despite a broad literature describing p53 binding DNA, unanswered questions remain, due partly to the need for more quantitative and structural studies with full length protein. Here we describe a single molecule fluorescence system to visualize full length p53 tetramers binding DNA in real time. The data revealed a dynamic interaction in which tetrameric p53/DNA complexes assembled and disassembled without a dimer/DNA intermediate. On a wild type DNA containing two half sites, p53/DNA complexes existed in two kinetically distinct populations. p53 tetramers bound response elements containing only one half site to form a single population of complexes with reduced kinetic stability. Altering the spacing and helical phasing between two half sites affected both the population distribution of p53/DNA complexes and their kinetic stability. Our real time single molecule measurements of full length p53 tetramers binding DNA reveal the parameters that define the stability of p53/DNA complexes, and provide insight into the pathways by which those complexes assemble.
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59
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The Undervalued Avenue to Reinstate Tumor Suppressor Functionality of the p53 Protein Family for Improved Cancer Therapy-Drug Repurposing. Cancers (Basel) 2020; 12:cancers12092717. [PMID: 32971841 PMCID: PMC7563196 DOI: 10.3390/cancers12092717] [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: 08/21/2020] [Revised: 09/13/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
p53 and p73 are critical tumor suppressors that are often inactivated in human cancers through various mechanisms. Owing to their high structural homology, the proteins have many joined functions and recognize the same set of genes involved in apoptosis and cell cycle regulation. p53 is known as the 'guardian of the genome' and together with p73 forms a barrier against cancer development and progression. The TP53 is mutated in more than 50% of all human cancers and the germline mutations in TP53 predispose to the early onset of multiple tumors in Li-Fraumeni syndrome (LFS), the inherited cancer predisposition. In cancers where TP53 gene is intact, p53 is degraded. Despite the ongoing efforts, the treatment of cancers remains challenging. This is due to late diagnoses, the toxicity of the current standard of care and marginal benefit of newly approved therapies. Presently, the endeavors focus on reactivating p53 exclusively, neglecting the potential of the restoration of p73 protein for cancer eradication. Taken that several small molecules reactivating p53 failed in clinical trials, there is a need to develop new treatments targeting p53 proteins in cancer. This review outlines the most advanced strategies to reactivate p53 and p73 and describes drug repurposing approaches for the efficient reinstatement of the p53 proteins for cancer therapy.
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60
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Kraus RJ, Cordes BLA, Sathiamoorthi S, Patel P, Yuan X, Iempridee T, Yu X, Lee DL, Lambert PF, Mertz JE. Reactivation of Epstein-Barr Virus by HIF-1α Requires p53. J Virol 2020; 94:e00722-20. [PMID: 32641480 PMCID: PMC7459560 DOI: 10.1128/jvi.00722-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
We previously reported that the cellular transcription factor hypoxia-inducible factor 1α (HIF-1α) binds a hypoxia response element (HRE) located within the promoter of Epstein-Barr virus's (EBV's) latent-lytic switch BZLF1 gene, Zp, inducing viral reactivation. In this study, EBV-infected cell lines derived from gastric cancers and Burkitt lymphomas were incubated with HIF-1α-stabilizing drugs: the iron chelator deferoxamine (Desferal [DFO]), a neddylation inhibitor (pevonedistat [MLN-4924]), and a prolyl hydroxylase inhibitor (roxadustat [FG-4592]). DFO and MLN-4924, but not FG-4592, induced accumulation of both lytic EBV proteins and phosphorylated p53 in cell lines that contain a wild-type p53 gene. FG-4592 also failed to activate transcription from Zp in a reporter assay despite inducing accumulation of HIF-1α and transcription from another HRE-containing promoter. Unexpectedly, DFO failed to induce EBV reactivation in cell lines that express mutant or no p53 or when p53 expression was knocked down with short hairpin RNAs (shRNAs). Likewise, HIF-1α failed to activate transcription from Zp when p53 was knocked out by CRISPR-Cas9. Importantly, DFO induced binding of p53 as well as HIF-1α to Zp in chromatin immunoprecipitation (ChIP) assays, but only when the HRE was present. Nutlin-3, a drug known to induce accumulation of phosphorylated p53, synergized with DFO and MLN-4924 in inducing EBV reactivation. Conversely, KU-55933, a drug that inhibits ataxia telangiectasia mutated, thereby preventing p53 phosphorylation, inhibited DFO-induced EBV reactivation. Lastly, activation of Zp transcription by DFO and MLN-4924 mapped to its HRE. Thus, we conclude that induction of BZLF1 gene expression by HIF-1α requires phosphorylated, wild-type p53 as a coactivator, with HIF-1α binding recruiting p53 to Zp.IMPORTANCE EBV, a human herpesvirus, is latently present in most nasopharyngeal carcinomas, Burkitt lymphomas, and some gastric cancers. To develop a lytic-induction therapy for treating patients with EBV-associated cancers, we need a way to efficiently reactivate EBV into lytic replication. EBV's BZLF1 gene product, Zta, usually controls this reactivation switch. We previously showed that HIF-1α binds the BZLF1 gene promoter, inducing Zta synthesis, and HIF-1α-stabilizing drugs can induce EBV reactivation. In this study, we determined which EBV-positive cell lines are reactivated by classes of HIF-1α-stabilizing drugs. We found, unexpectedly, that HIF-1α-stabilizing drugs only induce reactivation when they also induce accumulation of phosphorylated, wild-type p53. Fortunately, p53 phosphorylation can also be provided by drugs such as nutlin-3, leading to synergistic reactivation of EBV. These findings indicate that some HIF-1α-stabilizing drugs may be helpful as part of a lytic-induction therapy for treating patients with EBV-positive malignancies that contain wild-type p53.
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MESH Headings
- Cell Line, Tumor
- Cyclopentanes/pharmacology
- Deferoxamine/pharmacology
- Enzyme Inhibitors/pharmacology
- Epithelial Cells/drug effects
- Epithelial Cells/metabolism
- Epithelial Cells/virology
- Gene Expression Regulation
- Glycine/analogs & derivatives
- Glycine/pharmacology
- Herpesvirus 4, Human/drug effects
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/growth & development
- Herpesvirus 4, Human/metabolism
- Host-Pathogen Interactions/drug effects
- Host-Pathogen Interactions/genetics
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/agonists
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Imidazoles/pharmacology
- Iron Chelating Agents/pharmacology
- Isoquinolines/pharmacology
- Lymphocytes/drug effects
- Lymphocytes/metabolism
- Lymphocytes/virology
- Morpholines/pharmacology
- Piperazines/pharmacology
- Prolyl-Hydroxylase Inhibitors/pharmacology
- Promoter Regions, Genetic
- Protein Binding/drug effects
- Pyrimidines/pharmacology
- Pyrones/pharmacology
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Response Elements
- Signal Transduction
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Tumor Suppressor Protein p53/antagonists & inhibitors
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Virus Activation/drug effects
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Affiliation(s)
- Richard J Kraus
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Blue-Leaf A Cordes
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Saraniya Sathiamoorthi
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Parita Patel
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Xueying Yuan
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Tawin Iempridee
- National Nanotechnology Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Xianming Yu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Denis L Lee
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Janet E Mertz
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
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61
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Yoo DY, Barros SA, Brown GC, Rabot C, Bar-Sagi D, Arora PS. Macropinocytosis as a Key Determinant of Peptidomimetic Uptake in Cancer Cells. J Am Chem Soc 2020; 142:14461-14471. [PMID: 32786217 DOI: 10.1021/jacs.0c02109] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptides and peptidomimetics represent the middle space between small molecules and large proteins-they retain the relatively small size and synthetic accessibility of small molecules while providing high binding specificity for biomolecular partners typically observed with proteins. During the course of our efforts to target intracellular protein-protein interactions in cancer, we observed that the cellular uptake of peptides is critically determined by the cell line-specifically, we noted that peptides show better uptake in cancer cells with enhanced macropinocytic indices. Here, we describe the results of our analysis of cellular penetration by different classes of conformationally stabilized peptides. We tested the uptake of linear peptides, peptide macrocycles, stabilized helices, β-hairpin peptides, and cross-linked helix dimers in 11 different cell lines. Efficient uptake of these conformationally defined constructs directly correlated with the macropinocytic activity of each cell line: high uptake of compounds was observed in cells with mutations in certain signaling pathways. Significantly, the study shows that constrained peptides follow the same uptake mechanism as proteins in macropinocytic cells, but unlike proteins, peptide mimics can be readily designed to resist denaturation and proteolytic degradation. Our findings expand the current understanding of cellular uptake in cancer cells by designed peptidomimetics and suggest that cancer cells with certain mutations are suitable mediums for the study of biological pathways with peptide leads.
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Affiliation(s)
- Daniel Y Yoo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Stephanie A Barros
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Gordon C Brown
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Christian Rabot
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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62
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Ecsédi P, Gógl G, Hóf H, Kiss B, Harmat V, Nyitray L. Structure Determination of the Transactivation Domain of p53 in Complex with S100A4 Using Annexin A2 as a Crystallization Chaperone. Structure 2020; 28:943-953.e4. [PMID: 32442400 DOI: 10.1016/j.str.2020.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/05/2020] [Accepted: 05/01/2020] [Indexed: 11/29/2022]
Abstract
To fully understand the environmental factors that influence crystallization is an enormous task, therefore crystallographers are still forced to work "blindly" trying as many crystallizing conditions and mutations to improve crystal packing as possible. Numerous times these random attempts simply fail even when using state-of-the-art techniques. As an alternative, crystallization chaperones, having good crystal-forming properties, can be invoked. Today, the almost exclusively used such protein is the maltose-binding protein (MBP) and crystallographers need other widely applicable options. Here, we introduce annexin A2 (ANXA2), which has just as good, if not better, crystal-forming ability than the wild-type MBP. Using ANXA2 as heterologous fusion partner, we were able to solve the atomic resolution structure of a challenging crystallization target, the transactivation domain (TAD) of p53 in complex with the metastasis-associated protein S100A4. p53 TAD forms an asymmetric fuzzy complex with the symmetric S1004 and could interfere with its function.
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Affiliation(s)
- Péter Ecsédi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Gergő Gógl
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest 1117, Hungary; Institute of Genetics and of Molecular and Cellular Biology, IGBMC, Strasbourg 67400, France
| | - Henrietta Hóf
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Bence Kiss
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Veronika Harmat
- ELTE Eötvös Loránd University, Institute of Chemistry, MTA-ELTE Protein Modeling Research Group, Budapest 1117, Hungary
| | - László Nyitray
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest 1117, Hungary.
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63
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Kumar D, Mishra PM, Gadhave K, Giri R. Conformational dynamics of p53 N-terminal TAD2 region under different solvent conditions. Arch Biochem Biophys 2020; 689:108459. [DOI: 10.1016/j.abb.2020.108459] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/28/2020] [Accepted: 06/03/2020] [Indexed: 01/31/2023]
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64
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Bargonetti J, Prives C. Gain-of-function mutant p53: history and speculation. J Mol Cell Biol 2020; 11:605-609. [PMID: 31283823 PMCID: PMC6735697 DOI: 10.1093/jmcb/mjz067] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- Jill Bargonetti
- Department of Biological Sciences Hunter College and The Graduate Center, City University of New York, New York, NY 10021, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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65
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Zhao T, Sun D, Zhao M, Lai Y, Liu Y, Zhang Z. N 6-methyladenosine mediates arsenite-induced human keratinocyte transformation by suppressing p53 activation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113908. [PMID: 31931413 PMCID: PMC7082205 DOI: 10.1016/j.envpol.2019.113908] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/11/2019] [Accepted: 12/31/2019] [Indexed: 05/31/2023]
Abstract
N6-methyladenosine (m6A), the most abundant and reversible RNA modification, plays critical a role in tumorigenesis. However, whether m6A can regulate p53, a leading antitumor protein remains poorly understood. In this study, we explored the regulatory role of m6A on p53 activation using an arsenite-transformed keratinocyte model, the HaCaT-T cell line. We created the cell line by exposing human keratinocyte HaCaT cells to 1 μM arsenite for 5 months. We found that the cells exhibited an increased m6A level along with an aberrant expression of the methyltransferases, demethylase, and readers of m6A. Moreover, the cells exhibited decreased p53 activity and reduced p53 phosphorylation, acetylation, and transactivation with a high nucleus export rate of p53. Knockdown of the m6A methyltransferase, METTL3 significantly decreased m6A level, restoring p53 activation and inhibiting cellular transformation phenotypes in the arsenite-transformed cells. Further, using both a bioinformatics analysis and experimental approaches, we demonstrated that m6A downregulated the expression of the positive p53 regulator, PRDM2, through the YTHDF2-promoted decay of PRDM2 mRNAs. We showed that m6A upregulated the expression of the negative p53 regulator, YY1 and MDM2 through YTHDF1-stimulated translation of YY1 and MDM2 mRNA. Taken together, our study revealed the novel role of m6A in mediating arsenite-induced human keratinocyte transformation by suppressing p53 activation. This study further sheds light on the mechanisms of arsenic carcinogenesis via RNA epigenetics.
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Affiliation(s)
- Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Manyu Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA, 33199
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA, 33199
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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66
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67
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Loh SN. Follow the Mutations: Toward Class-Specific, Small-Molecule Reactivation of p53. Biomolecules 2020; 10:biom10020303. [PMID: 32075132 PMCID: PMC7072143 DOI: 10.3390/biom10020303] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
The mutational landscape of p53 in cancer is unusual among tumor suppressors because most of the alterations are of the missense type and localize to a single domain: the ~220 amino acid DNA-binding domain. Nearly all of these mutations produce the common effect of reducing p53’s ability to interact with DNA and activate transcription. Despite this seemingly simple phenotype, no mutant p53-targeted drugs are available to treat cancer patients. One of the main reasons for this is that the mutations exert their effects via multiple mechanisms—loss of DNA contacts, reduction in zinc-binding affinity, and lowering of thermodynamic stability—each of which involves a distinct type of physical impairment. This review discusses how this knowledge is informing current efforts to develop small molecules that repair these defects and restore function to mutant p53. Categorizing the spectrum of p53 mutations into discrete classes based on their inactivation mechanisms is the initial step toward personalized cancer therapy based on p53 allele status.
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Affiliation(s)
- Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
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68
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Fujiyama H, Tsuji T, Hironaka K, Yoshida K, Sugimoto N, Fujita M. GRWD1 directly interacts with p53 and negatively regulates p53 transcriptional activity. J Biochem 2020; 167:15-24. [PMID: 31545368 DOI: 10.1093/jb/mvz075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022] Open
Abstract
Glutamate-rich WD40 repeat containing 1 (GRWD1) functions as a histone chaperone to promote loading of the MCM replication helicase at replication origins. GRWD1 is overexpressed in several cancer cell lines, and GRWD1 overexpression confers tumorigenic potential in human cells. However, less is known concerning its oncogenic activity. Our previous analysis showed that GRWD1 negatively regulates the tumour suppressor p53 via the RPL11-MDM2-p53 and RPL23-MDM2-p53 axes. Here, we demonstrate that GRWD1 directly interacts with p53 via the p53 DNA-binding domain. Upon DNA damage, GRWD1 downregulation resulted in increased p21 expression. Conversely, GRWD1 co-expression suppressed several p53-regulated promoters. GRWD1 interacted with the p21 and MDM2 promoters, and these interactions required p53. By using the Human Cancer Genome Atlas database, we found that GRWD1 expression levels are inversely correlated with the expression levels of some p53-target genes. Interestingly, high GRWD1 expression in combination with low expression levels of some p53-target genes was significantly correlated with poor prognosis in skin melanoma patients with wild-type p53. Taken together, our findings suggest a novel oncogenic function of GRWD1 as a transcriptional regulator of p53 and that GRWD1 might be an attractive therapeutic target and prognostic marker in cancer therapy.
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Affiliation(s)
- Hiroki Fujiyama
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Takahiro Tsuji
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kensuke Hironaka
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
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69
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The Emerging Landscape of p53 Isoforms in Physiology, Cancer and Degenerative Diseases. Int J Mol Sci 2019; 20:ijms20246257. [PMID: 31835844 PMCID: PMC6941119 DOI: 10.3390/ijms20246257] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
p53, first described four decades ago, is now established as a master regulator of cellular stress response, the “guardian of the genome”. p53 contributes to biological robustness by behaving in a cellular-context dependent manner, influenced by several factors (e.g., cell type, active signalling pathways, the type, extent and intensity of cellular damage, cell cycle stage, nutrient availability, immune function). The p53 isoforms regulate gene transcription and protein expression in response to the stimuli so that the cell response is precisely tuned to the cell signals and cell context. Twelve isoforms of p53 have been described in humans. In this review, we explore the interactions between p53 isoforms and other proteins contributing to their established cellular functions, which can be both tumour-suppressive and oncogenic in nature. Evidence of p53 isoform in human cancers is largely based on RT-qPCR expression studies, usually investigating a particular type of isoform. Beyond p53 isoform functions in cancer, it is implicated in neurodegeneration, embryological development, progeroid phenotype, inflammatory pathology, infections and tissue regeneration, which are described in this review.
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70
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Deng Q, Hu H, Yu X, Liu S, Wang L, Chen W, Zhang C, Zeng Z, Cao Y, Xu-Monette ZY, Li L, Zhang M, Rosenfeld S, Bao S, Hsi E, Young KH, Lu Z, Li Y. Tissue-specific microRNA expression alters cancer susceptibility conferred by a TP53 noncoding variant. Nat Commun 2019; 10:5061. [PMID: 31699989 PMCID: PMC6838078 DOI: 10.1038/s41467-019-13002-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/16/2019] [Indexed: 12/15/2022] Open
Abstract
A noncoding polymorphism (rs78378222) in TP53, carried by scores of millions of people, was previously associated with moderate risk of brain tumors and other neoplasms. We find a positive association between this variant and soft tissue sarcoma. In sharp contrast, it is protective against breast cancer. We generated a mouse line carrying this variant and found that it accelerates spontaneous tumorigenesis and glioma development, but strikingly, delays mammary tumorigenesis. The variant creates a miR-382-5p targeting site and compromises a miR-325-3p site. Their differential expression results in p53 downregulation in the brain, but p53 upregulation in the mammary gland of polymorphic mice compared to that of wild-type littermates. Thus, this variant is at odds with Li-Fraumeni Syndrome mutants in breast cancer predisposition yet consistent in glioma predisposition. Our findings elucidate an underlying mechanism of cancer susceptibility that is conferred by genetic variation and yet altered by microRNA expression.
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Affiliation(s)
- Qipan Deng
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hui Hu
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Medical Laboratory, Central Hospital of Wuhan, Wuhan, China
| | - Xinfang Yu
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shuanglin Liu
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lei Wang
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Weiqun Chen
- Department of Medical Laboratory, Central Hospital of Wuhan, Wuhan, China
| | - Chi Zhang
- Department of Medical Laboratory, Central Hospital of Wuhan, Wuhan, China
| | - Zhaoyang Zeng
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Key Laboratory of Carcinogenesis and Invasion, Ministry of Education, Xiangya Hospital; Cancer Research Institute, Xiangya School of Medicine, Central South University; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Invasion, Ministry of Education, Xiangya Hospital; Cancer Research Institute, Xiangya School of Medicine, Central South University; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Zijun Y Xu-Monette
- Department of Pathology, Division of Hematopathology, Duke University Medical Center, Durham, NC, USA
| | - Ling Li
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University; Lymphoma Diagnosis and Treatment Center of Henan Province, Zhengzhou, China
| | - Mingzhi Zhang
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University; Lymphoma Diagnosis and Treatment Center of Henan Province, Zhengzhou, China
| | - Steven Rosenfeld
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shideng Bao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Eric Hsi
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ken H Young
- Department of Pathology, Division of Hematopathology, Duke University Medical Center, Durham, NC, USA
| | - Zhongxin Lu
- Department of Medical Laboratory, Central Hospital of Wuhan, Wuhan, China.
| | - Yong Li
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA.
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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71
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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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72
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Raj N, Bam R. Reciprocal Crosstalk Between YAP1/Hippo Pathway and the p53 Family Proteins: Mechanisms and Outcomes in Cancer. Front Cell Dev Biol 2019; 7:159. [PMID: 31448276 PMCID: PMC6695833 DOI: 10.3389/fcell.2019.00159] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022] Open
Abstract
The YAP1/Hippo and p53 pathways are critical protectors of genome integrity in response to DNA damage. Together, these pathways secure cellular adaptation and maintain overall tissue integrity through transcriptional re-programing downstream of various environmental and biological cues generated during normal tissue growth, cell proliferation, and apoptosis. Genetic perturbations in YAP1/Hippo and p53 pathways are known to contribute to the cells’ ability to turn rogue and initiate tumorigenesis. The Hippo and p53 pathways cooperate on many levels and are closely coordinated through multiple molecular components of their signaling pathways. Several functional and physical interactions have been reported to occur between YAP1/Hippo pathway components and the three p53 family members, p53, p63, and p73. Primarily, functional status of p53 family proteins dictates the subcellular localization, protein stability and transcriptional activity of the core component of the Hippo pathway, Yes-associated protein 1 (YAP1). In this review, we dissect the critical points of crosstalk between the YAP1/Hippo pathway components, with a focus on YAP1, and the p53 tumor suppressor protein family. For each p53 family member, we discuss the biological implications of their interaction with Hippo pathway components in determining cell fate under the conditions of tissue homeostasis and cancer pathogenesis.
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Affiliation(s)
- Nitin Raj
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, United States
| | - Rakesh Bam
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, United States
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73
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Chen JQ, Chen HY, Dai WJ, Lv QJ, Chen CYC. Artificial Intelligence Approach to Find Lead Compounds for Treating Tumors. J Phys Chem Lett 2019; 10:4382-4400. [PMID: 31304749 DOI: 10.1021/acs.jpclett.9b01426] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
It has been demonstrated that MMP13 enzyme is related to most cancer cell tumors. The world's largest traditional Chinese medicine database was applied to screen for structure-based drug design and ligand-based drug design. To predict drug activity, machine learning models (Random Forest (RF), AdaBoost Regressor (ABR), Gradient Boosting Regressor (GBR)), and Deep Learning models were utilized to validate the Docking results, and we obtained an R2 of 0.922 on the training set and 0.804 on the test set in the RF algorithm. For the Deep Learning algorithm, R2 of the training set is 0.90, and R2 of the test set is 0.810. However, these TCM compounds fly away during the molecular dynamics (MD) simulation. We seek another method: peptide design. All peptide database were screened by the Docking process. Modification peptides were optimized the interaction modes, and the affinities were assessed with ZDOCK protocol and Refine Docked protein protocol. The 300 ns MD simulation evaluated the stability of receptor-peptide complexes. The double-site effect appeared on S2, a designed peptide based on a known inhibitor, when complexed with BCL2. S3, a designed peptide referred from endogenous inhibitor P16, competed against cyclin when binding with CDK6. The MDM2 inhibitors S5 and S6 were derived from the P53 structure and stable binding with MDM2. A flexible region of peptides S5 and S6 may enhance the binding ability by changing its own conformation, which was unforeseen. These peptides (S2, S3, S5, and S6) are potentially interesting to treat cancer; however, these findings need to be affirmed by biological testing, which will be conducted in the near future.
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Affiliation(s)
- Jian-Qiang Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
| | - Hsin-Yi Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
| | - Wen-Jie Dai
- School of Pharmacy , Sun Yat-sen University , Shenzhen 510275 , China
| | - Qiu-Jie Lv
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
| | - Calvin Yu-Chian Chen
- School of Intelligent Systems Engineering, Artificial Intelligence Medical Center , Sun Yat-sen University , Shenzhen 510275 , China
- Department of Medical Research , China Medical University Hospital , Taichung 40447 , Taiwan
- Department of Bioinformatics and Medical Engineering , Asia University , Taichung 41354 , Taiwan
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74
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Hartlmüller C, Spreitzer E, Göbl C, Falsone F, Madl T. NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:305-317. [PMID: 31297688 PMCID: PMC6692294 DOI: 10.1007/s10858-019-00248-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/11/2019] [Indexed: 05/12/2023]
Abstract
In order to understand the conformational behavior of intrinsically disordered proteins (IDPs) and their biological interaction networks, the detection of residual structure and long-range interactions is required. However, the large number of degrees of conformational freedom of disordered proteins require the integration of extensive sets of experimental data, which are difficult to obtain. Here, we provide a straightforward approach for the detection of residual structure and long-range interactions in IDPs under near-native conditions using solvent paramagnetic relaxation enhancement (sPRE). Our data indicate that for the general case of an unfolded chain, with a local flexibility described by the overwhelming majority of available combinations, sPREs of non-exchangeable protons can be accurately predicted through an ensemble-based fragment approach. We show for the disordered protein α-synuclein and disordered regions of the proteins FOXO4 and p53 that deviation from random coil behavior can be interpreted in terms of intrinsic propensity to populate local structure in interaction sites of these proteins and to adopt transient long-range structure. The presented modification-free approach promises to be applicable to study conformational dynamics of IDPs and other dynamic biomolecules in an integrative approach.
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Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 87548, Garching, Germany
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Christoph Göbl
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Fabio Falsone
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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75
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Lee MS, Lee SO, Lee MK, Yi GS, Lee CK, Ryu KS, Chi SW. Solution structure of MUL1-RING domain and its interaction with p53 transactivation domain. Biochem Biophys Res Commun 2019; 516:533-539. [PMID: 31235254 DOI: 10.1016/j.bbrc.2019.06.101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
Mitochondrial E3 ubiquitin ligase 1 (MUL1) is a multifunctional mitochondrial protein involved in various biological processes such as mitochondrial dynamics, cell growth, apoptosis, and mitophagy. MUL1 mediates the ubiquitylation of mitochondrial p53 for proteasomal degradation. Although the interaction of MUL1-RING domain with its substrate, p53, is a unique mechanism in RING-mediated ubiquitylation, the molecular basis of this process remains unknown. In this study, we determined the solution structure of the MUL1-RING domain and characterized its interaction with the p53 transactivation domain (p53-TAD) by nuclear magnetic resonance (NMR) spectroscopy. The overall structure of the MUL1-RING domain is similar to those of RING domains of other E3 ubiquitinases. The MUL1-RING domain adopts a ββαβ fold with three anti-parallel β-strands and one α-helix, containing a canonical cross-brace motif for the ligation of two zinc ions. Through NMR chemical shift perturbation experiments, we determined the p53-TAD-binding site in the MUL1-RING domain and showed that the MUL1-RING domain interacts mainly with the p53-TAD2 subdomain composed of residues 39-57. Taken together, our results provide a molecular basis for the novel recognition mechanism of the p53-TAD substrate by the MUL1-RING domain.
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Affiliation(s)
- Min-Sung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea; Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Sang-Ok Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea; College of Pharmacy, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea
| | - Gwan-Su Yi
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Chong-Kil Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kyoung-Seok Ryu
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea; Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea.
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea; Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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76
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Watanabe S, Tsuchiya K, Nishimura R, Shirasaki T, Katsukura N, Hibiya S, Okamoto R, Nakamura T, Watanabe M. TP53 Mutation by CRISPR System Enhances the Malignant Potential of Colon Cancer. Mol Cancer Res 2019; 17:1459-1467. [DOI: 10.1158/1541-7786.mcr-18-1195] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/07/2019] [Accepted: 04/11/2019] [Indexed: 12/30/2022]
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77
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Catizone AN, Good CR, Alexander KA, Berger SL, Sammons MA. Comparison of genotoxic versus nongenotoxic stabilization of p53 provides insight into parallel stress-responsive transcriptional networks. Cell Cycle 2019; 18:809-823. [PMID: 30966857 PMCID: PMC6527265 DOI: 10.1080/15384101.2019.1593643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/31/2019] [Accepted: 02/15/2019] [Indexed: 12/19/2022] Open
Abstract
The tumor suppressor protein p53 is activated in response to diverse intrinsic and extrinsic cellular stresses and controls a broad cell-protective gene network. Whether p53:DNA binding and subsequent transcriptional activation differs downstream of these diverse intrinsic and extrinsic activators is controversial. Using primary human fibroblasts, we assessed the genome-wide profile of p53 binding, chromatin structure, and transcriptional dynamics after either genotoxic or nongenotoxic activation of p53. Activation of p53 by treatment with either etoposide or the small-molecule MDM2 inhibitor nutlin 3A yields strikingly similar genome-wide binding of p53 and concomitant changes to local chromatin modifications and structure. DNA damage, but not p53 activation per se, leads to increased expression of genes in an inflammatory cytokine pathway. The NF-κB pathway inhibitor Bay 11-7082 abrogates etoposide-mediated activation of the inflammation gene signature but does not affect expression of canonical p53 target genes. Our data demonstrate that differential activation of p53 within the same cell type leads to highly similar genome-wide binding, chromatin dynamics, and gene expression dynamics and that DNA damage-mediated signaling through NF-κB likely controls the observed pro-inflammatory cytokine gene expression pattern.
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Affiliation(s)
- Allison N. Catizone
- Department of Biological Sciences, The State University of New York at Albany, Albany, NY, USA
| | - Charly Ryan Good
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine A. Alexander
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L. Berger
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Morgan A. Sammons
- Department of Biological Sciences, The State University of New York at Albany, Albany, NY, USA
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78
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Levine AJ. Targeting Therapies for the p53 Protein in Cancer Treatments. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2019. [DOI: 10.1146/annurev-cancerbio-030518-055455] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Half of all human cancers contain TP53 mutations, and in many other cancers, the function of the p53 protein is compromised. The diversity of these mutations and phenotypes presents a challenge to the development of drugs that target p53 mutant cancer cells. This review describes the rationale for many different approaches in the development of p53 targeted therapies: ( a) viruses and gene therapies, ( b) increased levels and activity of wild-type p53 proteins in cancer cells, ( c) p53 protein gain-of-function inhibitors, ( d) p53 protein loss-of-function structural correctors, ( e) mutant p53 protein synthetic lethal drugs interfering with the p53 pathway, and ( f) cellular immune responses to mutant p53 protein antigens. As these types of therapies are developed, tested, and evaluated, the best of them will have a significant impact upon cancer treatments and possibly prevention.
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79
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Alavi MV. Targeted OMA1 therapies for cancer. Int J Cancer 2019; 145:2330-2341. [PMID: 30714136 DOI: 10.1002/ijc.32177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/20/2019] [Accepted: 01/23/2019] [Indexed: 12/12/2022]
Abstract
The mitochondrial inner membrane proteins OMA1 and OPA1 belong to the BAX/BAK1-dependent apoptotic signaling pathway, which can be regulated by tumor protein p53 and the prohibitins PHB and PHB2 in the context of neoplastic disease. For the most part these proteins have been studied separate from each other. Here, I argue that the OMA1 mechanism of action represents the missing link between p53 and cytochrome c release. The mitochondrial fusion protein OPA1 is cleaved by OMA1 in a stress-dependent manner generating S-OPA1. Excessive S-OPA1 can facilitate outer membrane permeabilization upon BAX/BAK1 activation through its membrane shaping properties. p53 helps outer membrane permeabilization in a 2-step process. First, cytosolic p53 activates BAX/BAK1 at the mitochondrial surface. Then, in a second step, p53 binds to prohibitin thereby releasing the restraint on OMA1. This activates OMA1, which cleaves OPA1 and promotes cytochrome c release. Clearly, OMA1 and OPA1 are not root causes for cancer. Yet many cancer cells rely on this pathway for survival, which can explain why loss of p53 function promotes tumor growth and confers resistance to chemotherapies.
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80
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Li X, Liu M, Ji JY. Understanding Obesity as a Risk Factor for Uterine Tumors Using Drosophila. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1167:129-155. [PMID: 31520353 DOI: 10.1007/978-3-030-23629-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple large-scale epidemiological studies have identified obesity as an important risk factor for a variety of human cancers, particularly cancers of the uterus, gallbladder, kidney, liver, colon, and ovary, but there is much uncertainty regarding how obesity increases the cancer risks. Given that obesity has been consistently identified as a major risk factor for uterine tumors, the most common malignancies of the female reproductive system, we use uterine tumors as a pathological context to survey the relevant literature and propose a novel hypothesis: chronic downregulation of the cyclin-dependent kinase 8 (CDK8) module, composed of CDK8 (or its paralog CDK19), Cyclin C, MED12 (or MED12L), and MED13 (or MED13L), by elevated insulin or insulin-like growth factor signaling in obese women may increase the chances to dysregulate the activities of transcription factors regulated by the CDK8 module, thereby increasing the risk of uterine tumors. Although we focus on endometrial cancer and uterine leiomyomas (or fibroids), two major forms of uterine tumors, our model may offer additional insights into how obesity increases the risk of other types of cancers and diseases. To illustrate the power of model organisms for studying human diseases, here we place more emphasis on the findings obtained from Drosophila melanogaster.
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Affiliation(s)
- Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA.
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81
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Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A 2018; 115:E11302-E11310. [PMID: 30420502 DOI: 10.1073/pnas.1814051115] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Atomic resolution characterization of the full-length p53 tetramer has been hampered by its size and the presence of extensive intrinsically disordered regions at both the N and C termini. As a consequence, the structural characteristics and dynamics of the disordered regions are poorly understood within the context of the intact p53 tetramer. Here we apply trans-intein splicing to generate segmentally 15N-labeled full-length p53 constructs in which only the resonances of the N-terminal transactivation domain (NTAD) are visible in NMR spectra, allowing us to observe this region of p53 with unprecedented detail within the tetramer. The N-terminal region is dynamically disordered in the full-length p53 tetramer, fluctuating between states in which it is free and fully exposed to solvent and states in which it makes transient contacts with the DNA-binding domain (DBD). Chemical-shift changes and paramagnetic spin-labeling experiments reveal that the amphipathic AD1 and AD2 motifs of the NTAD interact with the DNA-binding surface of the DBD through primarily electrostatic interactions. Importantly, this interaction inhibits binding of nonspecific DNA to the DBD while having no effect on binding to a specific p53 recognition element. We conclude that the NTAD:DBD interaction functions to enhance selectivity toward target genes by inhibiting binding to nonspecific sites in genomic DNA. This work provides some of the highest-resolution data on the disordered N terminus of the nearly 180-kDa full-length p53 tetramer and demonstrates a regulatory mechanism by which the N terminus of p53 transiently interacts with the DBD to enhance target site discrimination.
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82
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Steels A, Verhelle A, Zwaenepoel O, Gettemans J. Intracellular displacement of p53 using transactivation domain (p53 TAD) specific nanobodies. MAbs 2018; 10:1045-1059. [PMID: 30111239 DOI: 10.1080/19420862.2018.1502025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The tumor suppressor p53 is of crucial importance in the prevention of cellular transformation. In the presence of cellular stress signals, the negative feedback loop between p53 and Mdm2, its main negative regulator, is disrupted, which results in the activation and stabilization of p53. Via a complex interplay between both transcription-dependent and - independent functions of p53, the cell will go through transient cell cycle arrest, cellular senescence or apoptosis. However, it remains difficult to completely fathom the mechanisms behind p53 regulation and its responses, considering the presence of multiple layers involved in fine-tuning them. In order to take the next step forward, novel research tools are urgently needed. We have developed single-domain antibodies, also known as nanobodies, that specifically bind with the N-terminal transactivation domain of wild type p53, but that leave the function of p53 as a transcriptional transactivator intact. When the nanobodies are equipped with a mitochondrial-outer-membrane (MOM)-tag, we can capture p53 at the mitochondria. This nanobody-induced mitochondrial delocalization of p53 is, in specific cases, associated with a decrease in cell viability and with morphological changes in the mitochondria. These findings underpin the potential of nanobodies as bona fide research tools to explore protein function and to unravel their biochemical pathways.
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Affiliation(s)
- Anneleen Steels
- a Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
| | - Adriaan Verhelle
- a Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
| | - Olivier Zwaenepoel
- a Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
| | - Jan Gettemans
- a Department of Biochemistry, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
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83
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Kannappan R, Mattapally S, Wagle PA, Zhang J. Transactivation domain of p53 regulates DNA repair and integrity in human iPS cells. Am J Physiol Heart Circ Physiol 2018; 315:H512-H521. [PMID: 29775409 PMCID: PMC6172637 DOI: 10.1152/ajpheart.00160.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/23/2018] [Accepted: 05/03/2018] [Indexed: 12/12/2022]
Abstract
The role of p53 transactivation domain (p53-TAD), a multifunctional and dynamic domain, on DNA repair and retaining DNA integrity in human induced pluripotent stem cells (hiPSCs) has never been studied. p53-TAD was knocked out in iPSCs using CRISPR/Cas9 and was confirmed by DNA sequencing. p53-TAD knockout (KO) cells were characterized by accelerated proliferation, decreased population doubling time, and unaltered Bcl-2, Bcl-2-binding component 3, insulin-like growth factor 1 receptor, and Bax and altered Mdm2, p21, and p53-induced death domain transcript expression. In p53-TAD KO cells, the p53-regulated DNA repair proteins xeroderma pigmentosum group A, DNA polymerase H, and DNA-binding protein 2 expression were found to be reduced compared with p53 wild-type cells. Exposure to a low dose of doxorubicin (Doxo) induced similar DNA damage and DNA damage response (DDR) as measured by RAD50 and MRE11 expression, checkpoint kinase 2 activation, and γH2A.X recruitment at DNA strand breaks in both cell groups, indicating that silence of p53-TAD does not affect the DDR mechanism upstream of p53. After removal of Doxo, p53 wild-type hiPSCs underwent DNA repair, corrected their damaged DNA, and restored DNA integrity. Conversely, p53-TAD KO hiPSCs did not undergo complete DNA repair and failed to restore DNA integrity. More importantly, continuous culture of p53-TAD KO hiPSCs underwent G2/M cell cycle arrest and expressed the cellular senescent marker p16INK4a. Our data clearly show that silence of the TAD of p53 did not affect DDR but affected the DNA repair process, implying the crucial role of p53-TAD in maintaining DNA integrity. Therefore, activating p53-TAD domain using small molecules may promote DNA repair and integrity of cells and prevent cellular senescence.
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Affiliation(s)
- Ramaswamy Kannappan
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Saidulu Mattapally
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Pooja A Wagle
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Jianyi Zhang
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
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84
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Jazvinšćak Jembrek M, Slade N, Hof PR, Šimić G. The interactions of p53 with tau and Aß as potential therapeutic targets for Alzheimer’s disease. Prog Neurobiol 2018; 168:104-127. [DOI: 10.1016/j.pneurobio.2018.05.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/04/2018] [Accepted: 05/01/2018] [Indexed: 12/24/2022]
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85
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Ouyang Y, Zhao L, Zhang Z. Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00067k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The conformations of p53 TAD2 in complexes and sampled in simulations with five force fields.
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Affiliation(s)
- Yanhua Ouyang
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
| | - Likun Zhao
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
| | - Zhuqing Zhang
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
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86
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Sullivan KD, Galbraith MD, Andrysik Z, Espinosa JM. Mechanisms of transcriptional regulation by p53. Cell Death Differ 2017; 25:133-143. [PMID: 29125602 PMCID: PMC5729533 DOI: 10.1038/cdd.2017.174] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 12/19/2022] Open
Abstract
p53 is a transcription factor that suppresses tumor growth through regulation of dozens of target genes with diverse biological functions. The activity of this master transcription factor is inactivated in nearly all tumors, either by mutations in the TP53 locus or by oncogenic events that decrease the activity of the wild-type protein, such as overexpression of the p53 repressor MDM2. However, despite decades of intensive research, our collective understanding of the p53 signaling cascade remains incomplete. In this review, we focus on recent advances in our understanding of mechanisms of p53-dependent transcriptional control as they relate to five key areas: (1) the functionally distinct N-terminal transactivation domains, (2) the diverse regulatory roles of its C-terminal domain, (3) evidence that p53 is solely a direct transcriptional activator, not a direct repressor, (4) the ability of p53 to recognize many of its enhancers across diverse chromatin environments, and (5) mechanisms that modify the p53-dependent transcriptional program in a context-dependent manner.
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Affiliation(s)
- Kelly D Sullivan
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zdenek Andrysik
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80203, USA
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87
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Mello SS, Valente LJ, Raj N, Seoane JA, Flowers BM, McClendon J, Bieging-Rolett KT, Lee J, Ivanochko D, Kozak MM, Chang DT, Longacre TA, Koong AC, Arrowsmith CH, Kim SK, Vogel H, Wood LD, Hruban RH, Curtis C, Attardi LD. A p53 Super-tumor Suppressor Reveals a Tumor Suppressive p53-Ptpn14-Yap Axis in Pancreatic Cancer. Cancer Cell 2017; 32:460-473.e6. [PMID: 29017057 PMCID: PMC5659188 DOI: 10.1016/j.ccell.2017.09.007] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/19/2017] [Accepted: 09/08/2017] [Indexed: 12/25/2022]
Abstract
The p53 transcription factor is a critical barrier to pancreatic cancer progression. To unravel mechanisms of p53-mediated tumor suppression, which have remained elusive, we analyzed pancreatic cancer development in mice expressing p53 transcriptional activation domain (TAD) mutants. Surprisingly, the p5353,54 TAD2 mutant behaves as a "super-tumor suppressor," with an enhanced capacity to both suppress pancreatic cancer and transactivate select p53 target genes, including Ptpn14. Ptpn14 encodes a negative regulator of the Yap oncoprotein and is necessary and sufficient for pancreatic cancer suppression, like p53. We show that p53 deficiency promotes Yap signaling and that PTPN14 and TP53 mutations are mutually exclusive in human cancers. These studies uncover a p53-Ptpn14-Yap pathway that is integral to p53-mediated tumor suppression.
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Affiliation(s)
- Stephano S Mello
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liz J Valente
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nitin Raj
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jose A Seoane
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brittany M Flowers
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacob McClendon
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn T Bieging-Rolett
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonghyeob Lee
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Danton Ivanochko
- Princess Margaret Cancer Centre, Structural Genomics Consortium and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Margaret M Kozak
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel T Chang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Teri A Longacre
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Albert C Koong
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Structural Genomics Consortium and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Seung K Kim
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannes Vogel
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christina Curtis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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88
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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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89
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Chillemi G, Kehrloesser S, Bernassola F, Desideri A, Dötsch V, Levine AJ, Melino G. Structural Evolution and Dynamics of the p53 Proteins. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a028308. [PMID: 27091942 DOI: 10.1101/cshperspect.a028308] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The family of the p53 tumor suppressive transcription factors includes p73 and p63 in addition to p53 itself. Given the high degree of amino-acid-sequence homology and structural organization shared by the p53 family members, they display some common features (i.e., induction of cell death, cell-cycle arrest, senescence, and metabolic regulation in response to cellular stress) as well as several distinct properties. Here, we describe the structural evolution of the family members with recent advances on the molecular dynamic studies of p53 itself. A crucial role of the carboxy-terminal domain in regulating the properties of the DNA-binding domain (DBD) supports an induced-fit mechanism, in which the binding of p53 on individual promoters is preferentially regulated by the KOFF over KON.
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Affiliation(s)
- Giovanni Chillemi
- CINECA, SCAI-SuperComputing Applications and Innovation Department, Rome 00185, Italy
| | - Sebastian Kehrloesser
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Francesca Bernassola
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata," 00133 Rome, Italy
| | | | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Arnold J Levine
- Institute for Advanced Study, Princeton, New Jersey 08540.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903
| | - Gerry Melino
- Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, United Kingdom
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90
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Levine AJ, Puzio-Kuter AM, Chan CS, Hainaut P. The Role of the p53 Protein in Stem-Cell Biology and Epigenetic Regulation. Cold Spring Harb Perspect Med 2016; 6:a026153. [PMID: 27352800 PMCID: PMC5008064 DOI: 10.1101/cshperspect.a026153] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The p53 protein plays a passive and an active role in stem cells. The transcriptional activities of p53 for cell-cycle arrest and DNA repair are largely turned off in stem cells, but there is some indication that long-term stem-cell viability may require other p53-regulated functions. When p53 is activated in stem cells, it stops cell division and promotes the commitment to a differentiation pathway and the formation of progenitor cells. In the absence of any p53 activity, stem-cell replication continues and mistakes in the normal epigenetic pathway occur at a higher probability. In the presence of a functionally active p53 protein, epigenetic stability is enforced and stem-cell replication is regulated by commitment to differentiation. Over a lifetime of an organism, stem-cell clones compete in a tissue niche for Darwinian replicative advantages and in doing so accumulate mutations that permit stem-cell replication. Mutations in the p53 gene give stem cells this advantage, increase the clonal stem-cell population, and lower the age at which cancers can occur. Li-Fraumeni patients that inherit p53 mutations develop tumors in a tissue-type-specific fashion at younger ages. Throughout the life of a Li-Fraumeni patient, the tumor types that arise occur in tissues where stem cells are active and cell division is most rapid. Thus, p53 mutations that are inherited or occur during developmental life act in stem cells of the mesenchymal and epithelial lineages, whereas p53 mutations that occur in progenitor or differentiated (somatic) cells later in life function in tissues of endodermal origins, indicating that p53 may function differently in different developmental lineages.
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Affiliation(s)
- Arnold J Levine
- Institute for Advanced Study, Princeton, New Jersey 08340 Cancer Institute of New Jersey of Rutgers Medical School, New Brunswick, New Jersey 08903
| | - Anna M Puzio-Kuter
- Institute for Advanced Study, Princeton, New Jersey 08340 Cancer Institute of New Jersey of Rutgers Medical School, New Brunswick, New Jersey 08903
| | - Chang S Chan
- Institute for Advanced Study, Princeton, New Jersey 08340 Cancer Institute of New Jersey of Rutgers Medical School, New Brunswick, New Jersey 08903
| | - Pierre Hainaut
- Grenoble Institute for Research on Cancer, Grenoble, France
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YAMAGUCHI K, URAKAMI K, NAGASHIMA T, SHIMODA Y, OHNAMI S, OHNAMI S, OHSHIMA K, MOCHIZUKI T, HATAKEYAMA K, SERIZAWA M, AKIYAMA Y, MARUYAMA K, KATAGIRI H, ISHIDA Y, TAKAHASHI K, NISHIMURA S, TERASHIMA M, KAWAMURA T, KINUGASA Y, YAMAKAWA Y, ONITSUKA T, OHDE Y, SUGINO T, ITO I, MATSUBAYASHI H, HORIUCHI Y, MIZUGUCHI M, YAMAZAKI M, INOUE K, WAKAMATSU K, SUGIYAMA M, UESAKA K, KUSUHARA M. Prevalence of low-penetrant germline TP53 D49H mutation in Japanese cancer patients . Biomed Res 2016; 37:259-64. [DOI: 10.2220/biomedres.37.259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Ken YAMAGUCHI
- Shizuoka Cancer Center Hospital
- Shizuoka Cancer Center Research Institute
| | - Kenichi URAKAMI
- Cancer Diagnostics Research Di-vision, Shizuoka Cancer Center Research Institute
| | - Takeshi NAGASHIMA
- Cancer Diagnostics Research Di-vision, Shizuoka Cancer Center Research Institute
- SRL Inc
| | - Yuji SHIMODA
- Cancer Diagnostics Research Di-vision, Shizuoka Cancer Center Research Institute
- SRL Inc
| | - Shumpei OHNAMI
- Cancer Diagnostics Research Di-vision, Shizuoka Cancer Center Research Institute
| | - Sumiko OHNAMI
- Cancer Diagnostics Research Di-vision, Shizuoka Cancer Center Research Institute
| | - Keiichi OHSHIMA
- Medical Genetics Division, Shizuoka Cancer Center Research Institute
| | - Tohru MOCHIZUKI
- Medical Genetics Division, Shizuoka Cancer Center Research Institute
| | | | - Masakuni SERIZAWA
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute
| | - Yasuto AKIYAMA
- Immunotherapy Division, Shizuoka Cancer Center Research Institute
| | - Kouji MARUYAMA
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute
| | | | - Yuji ISHIDA
- Division of Pediatrics, Shizuoka Cancer Center Hospital
| | | | | | | | | | - Yusuke KINUGASA
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital
| | - Yushi YAMAKAWA
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital
| | - Tetsuro ONITSUKA
- Division of Head and Neck Surgery, Shizuoka Cancer Center Hospital
| | - Yasuhisa OHDE
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital
| | | | - Ichiro ITO
- Division of Pathology, Shizuoka Cancer Center Hospital
| | | | - Yasue HORIUCHI
- Division of Genetic Counseling, Shizuoka Cancer Center Hospital
| | | | | | | | - Kimiko WAKAMATSU
- Office for Patient’s Information Protection, Shizuoka Cancer Center Hospital
| | - Misato SUGIYAMA
- Office for Patient’s Information Protection, Shizuoka Cancer Center Hospital
| | - Katsuhiko UESAKA
- Office for Patient’s Information Protection, Shizuoka Cancer Center Hospital
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital
| | - Masatoshi KUSUHARA
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute
- Regional Resources Division, Shizuoka Cancer Center Research Institute
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