1
|
Fricke LC, Lindsey ARI. Identification of Parthenogenesis-Inducing Effector Proteins in Wolbachia. Genome Biol Evol 2024; 16:evae036. [PMID: 38530785 PMCID: PMC11019157 DOI: 10.1093/gbe/evae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 03/28/2024] Open
Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis induction" phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 yr ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine-rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model Saccharomyces cerevisiae. We suggest that these proteins are parthenogenesis-inducing factors and our results indicate that this would be made possible by a novel mechanism of bacterial-host interaction.
Collapse
Affiliation(s)
- Laura C Fricke
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Amelia R I Lindsey
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
2
|
Zhang X, Xue J, Jiang S, Zheng H, Wang C. Forkhead-associated phosphopeptide binding domain 1 (FHAD1) deficiency impaired murine sperm motility. PeerJ 2024; 12:e17142. [PMID: 38563001 PMCID: PMC10984166 DOI: 10.7717/peerj.17142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Background Genetic knockout-based studies conducted in mice provide a powerful means of assessing the significance of a gene for fertility. Forkhead-associated phosphopeptide binding domain 1 (FHAD1) contains a conserved FHA domain, that is present in many proteins with phospho-threonine reader activity. How FHAD1 functions in male fertility, however, remains uncertain. Methods Fhad1-/- mice were generated by CRISPR/Cas9-mediated knockout, after which qPCR was used to evaluate changes in gene expression, with subsequent analyses of spermatogenesis and fertility. The testis phenotypes were also examined using immunofluorescence and histological staining, while sperm concentrations and motility were quantified via computer-aided sperm analysis. Cellular apoptosis was assessed using a TUNEL staining assay. Results The Fhad1-/-mice did not exhibit any abnormal changes in fertility or testicular morphology compared to wild-type littermates. Histological analyses confirmed that the testicular morphology of both Fhad1-/-and Fhad1+/+ mice was normal, with both exhibiting intact seminiferous tubules. Relative to Fhad1+/+ mice, however, Fhad1-/-did exhibit reductions in the total and progressive motility of epididymal sperm. Analyses of meiotic division in Fhad1-/-mice also revealed higher levels of apoptotic death during the first wave of spermatogenesis. Discussion The findings suggest that FHAD1 is involved in both meiosis and the modulation of sperm motility.
Collapse
Affiliation(s)
- Xi Zhang
- Department of Reproductive Health and Infertility Clinic, The Affiliated Huai’an No. 1 People’s Hospital of Nanjing Medical University, Huai’an, Jiangsu, China
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiangyang Xue
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children’s Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Shan Jiang
- College of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Haoyu Zheng
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Gynaecology, The Affiliated Huai’an No. 1 People’s Hospital of Nanjing Medical University, Huai’an, Jiangsu, China
| | - Chang Wang
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
- College of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| |
Collapse
|
3
|
He H, Liang L, Jiang S, Liu Y, Huang J, Sun X, Li Y, Jiang Y, Cong L. GINS2 regulates temozolomide chemosensitivity via the EGR1/ECT2 axis in gliomas. Cell Death Dis 2024; 15:205. [PMID: 38467631 PMCID: PMC10928080 DOI: 10.1038/s41419-024-06586-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Temozolomide (TMZ), a DNA alkylating agent, has become the primary treatment for glioma, the most common malignancy of the central nervous system. Although TMZ-containing regimens produce significant clinical response rates, some patients inevitably suffer from inferior treatment outcomes or disease relapse, likely because of poor chemosensitivity of glioma cells due to a robust DNA damage response (DDR). GINS2, a subunit of DNA helicase, contributes to maintaining genomic stability and is highly expressed in various cancers, promoting their development. Here, we report that GINS2 was upregulated in TMZ-treated glioma cells and co-localized with γH2AX, indicating its participation in TMZ-induced DDR. Furthermore, GINS2 regulated the malignant phenotype and TMZ sensitivity of glioma cells, mostly by promoting DNA damage repair by affecting the mRNA stability of early growth response factor 1 (EGR1), which in turn regulates the transcription of epithelial cell-transforming sequence 2 (ECT2). We constructed a GINS2-EGR1-ECT2 prognostic model, which accurately predicted patient survival. Further, we screened Palbociclib/BIX-02189 which dampens GINS2 expression and synergistically inhibits glioma cell proliferation with TMZ. These findings delineate a novel mechanism by which GINS2 regulates the TMZ sensitivity of glioma cells and propose a promising combination therapy to treat glioma.
Collapse
Affiliation(s)
- Hua He
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China
| | - Lu Liang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China
| | - Shiyao Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China
| | - Yueying Liu
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China
| | - Jingjing Huang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China
| | - Xiaoyan Sun
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China
| | - Yi Li
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China
| | - Yiqun Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China.
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China.
| | - Li Cong
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, China.
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, China.
| |
Collapse
|
4
|
Wu SY, Lai HT, Sanjib Banerjee N, Ma Z, Santana JF, Wei S, Liu X, Zhang M, Zhan J, Chen H, Posner B, Chen Y, Price DH, Chow LT, Zhou J, Chiang CM. IDR-targeting compounds suppress HPV genome replication via disruption of phospho-BRD4 association with DNA damage response factors. Mol Cell 2024; 84:202-220.e15. [PMID: 38103559 PMCID: PMC10843765 DOI: 10.1016/j.molcel.2023.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
Compounds binding to the bromodomains of bromodomain and extra-terminal (BET) family proteins, particularly BRD4, are promising anticancer agents. Nevertheless, side effects and drug resistance pose significant obstacles in BET-based therapeutics development. Using high-throughput screening of a 200,000-compound library, we identified small molecules targeting a phosphorylated intrinsically disordered region (IDR) of BRD4 that inhibit phospho-BRD4 (pBRD4)-dependent human papillomavirus (HPV) genome replication in HPV-containing keratinocytes. Proteomic profiling identified two DNA damage response factors-53BP1 and BARD1-crucial for differentiation-associated HPV genome amplification. pBRD4-mediated recruitment of 53BP1 and BARD1 to the HPV origin of replication occurs in a spatiotemporal and BRD4 long (BRD4-L) and short (BRD4-S) isoform-specific manner. This recruitment is disrupted by phospho-IDR-targeting compounds with little perturbation of the global transcriptome and BRD4 chromatin landscape. The discovery of these protein-protein interaction inhibitors (PPIi) not only demonstrates the feasibility of developing PPIi against phospho-IDRs but also uncovers antiviral agents targeting an epigenetic regulator essential for virus-host interaction and cancer development.
Collapse
Affiliation(s)
- Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hsien-Tsung Lai
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - N Sanjib Banerjee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Shuguang Wei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xisheng Liu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Meirong Zhang
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Jian Zhan
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yadong Chen
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - David H Price
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Louise T Chow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
5
|
Crowl S, Coleman MB, Chaphiv A, Naegle KM. A systematic analysis of the effects of splicing on the diversity of post-translational modifications in protein isoforms. bioRxiv 2024:2024.01.10.575062. [PMID: 38260432 PMCID: PMC10802621 DOI: 10.1101/2024.01.10.575062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Post-translational modifications (PTMs) and splicing are known to be important regulatory processes for controlling protein function and activity. However, there have been limitations in analyzing the interplay of alternative splicing and PTMs, both from the standpoint of PTM presence and in the possible diversification of the regulatory windows of PTMs, which define the connection to regulatory enzymes and possible binding partners. Limitations stem from the deep differences in genomic and proteomic databases, where PTMs are predominantly identified by mass spectrometry and subsequently assigned to the canonical isoform of the protein in databases. In this work, we bridge the protein- and genome-centric world views to map PTMs to genomic locations for subsequent projection of PTMs onto alternative isoforms. We then perform a systematic analysis of the diversification of PTMs within all defined protein isoforms, focusing on the PTM-specific profiles that may differ across the various major modifications found in humans, including exploration of how often alternative splicing leads to diversification of the regulatory sequences directly flanking a PTM. We found the interplay between splicing and PTMs is PTM-specific across a range of behaviors, such as PTM inclusion rates across isoforms and tissues. Additionally we found that ≈ 2% of prospective PTM sites exhibited altered regulatory sequences surrounding the modification site, suggesting that regulatory or binding interactions might be diversified in these proteoforms. In addition to exploring isoforms as defined by Ensembl, we applied this PTM-to-isoform mapping approach to explore the impacts of disease-related splicing in prostate cancer, identifying possible new hypotheses as to the variable mechanisms of ESRP1 expression in different cancers.
Collapse
Affiliation(s)
- Sam Crowl
- University of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA, 22903
| | - Maeve Bella Coleman
- University of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA, 22903
| | - Andrew Chaphiv
- University of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA, 22903
| | - Kristen M Naegle
- University of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA, 22903
| |
Collapse
|
6
|
Knittel G, Reinhardt HC. XPO1-Mediated mRNA Export of Genome Maintenance Regulators Drives Chemotherapy Resistance in Aggressive Lymphoma. Cancer Res 2024; 84:3-5. [PMID: 37902414 DOI: 10.1158/0008-5472.can-23-2966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 10/31/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid malignancy and displays vast genetic and transcriptomic heterogeneity. Current treatment guidelines recommend first-line chemoimmunotherapy consisting of an anthracycline backbone, which produces cure rates of approximately 65%. However, the remaining patients will face relapsed or refractory disease, which, even in the era of chimeric antigen receptor T cells, is difficult to treat. In this issue of Cancer Research, Marullo and colleagues investigate the biological underpinnings of the tumor-suppressive activity of the newly approved XPO1 inhibitor selinexor in the treatment of lymphoma. In a translational effort covering genomic and biochemical approaches, combined with in vivo validation experiments and a phase I clinical trial, they demonstrate that upon DNA damage, XPO1 selectively exports transcripts encoding proteins involved in genome maintenance via the RNA-binding proteins THOC4 and eIF4E. Pharmacologic interception of this export process enhances chemosensitivity in various lymphoma models, and combined selinexor plus chemoimmunotherapy displays a favorable toxicity profile and early evidence of efficacy in patients. See related article by Marullo et al., p. 101.
Collapse
Affiliation(s)
- Gero Knittel
- University Hospital Essen, Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Hans Christian Reinhardt
- University Hospital Essen, Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
7
|
Tabatabai A, Arora A, Höfmann S, Jauch M, von Tresckow B, Hansen J, Flümann R, Jachimowicz RD, Klein S, Reinhardt HC, Knittel G. Mouse models of diffuse large B cell lymphoma. Front Immunol 2023; 14:1313371. [PMID: 38124747 PMCID: PMC10731046 DOI: 10.3389/fimmu.2023.1313371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is a genetically highly heterogeneous disease. Yet, to date, the vast majority of patients receive standardized frontline chemo-immune-therapy consisting of an anthracycline backbone. Using these regimens, approximately 65% of patients can be cured, whereas the remaining 35% of patients will face relapsed or refractory disease, which, even in the era of CAR-T cells, is difficult to treat. To systematically tackle this high medical need, it is important to design, generate and deploy suitable in vivo model systems that capture disease biology, heterogeneity and drug response. Recently published, large comprehensive genomic characterization studies, which defined molecular sub-groups of DLBCL, provide an ideal framework for the generation of autochthonous mouse models, as well as an ideal benchmark for cell line-derived or patient-derived mouse models of DLBCL. Here we discuss the current state of the art in the field of mouse modelling of human DLBCL, with a particular focus on disease biology and genetically defined molecular vulnerabilities, as well as potential targeting strategies.
Collapse
Affiliation(s)
- Areya Tabatabai
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Aastha Arora
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Svenja Höfmann
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Maximilian Jauch
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Bastian von Tresckow
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Julia Hansen
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology Aachen Bonn, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ruth Flümann
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology Aachen Bonn, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ron D. Jachimowicz
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology Aachen Bonn, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Sebastian Klein
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Gero Knittel
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
8
|
Fricke LC, Lindsey ARI. Identification of parthenogenesis-inducing effector proteins in Wolbachia. bioRxiv 2023:2023.12.01.569668. [PMID: 38076953 PMCID: PMC10705499 DOI: 10.1101/2023.12.01.569668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis-induction" phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 years ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex-determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model, Saccharomyces cerevisiae. We suggest these proteins are parthenogenesis-inducing factors and our results indicate this would be made possible by a novel mechanism of bacterial-host interaction.
Collapse
Affiliation(s)
- Laura C Fricke
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Amelia RI Lindsey
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, 55108
| |
Collapse
|
9
|
Huang W, Qiu F, Zheng L, Shi M, Shen M, Zhao X, Xiang S. Structural insights into Rad18 targeting by the SLF1 BRCT domains. J Biol Chem 2023; 299:105288. [PMID: 37748650 PMCID: PMC10598736 DOI: 10.1016/j.jbc.2023.105288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023] Open
Abstract
Rad18 interacts with the SMC5/6 localization factor 1 (SLF1) to recruit the SMC5/6 complex to DNA damage sites for repair. The mechanism of the specific Rad18 recognition by SLF1 is unclear. Here, we present the crystal structure of the tandem BRCT repeat (tBRCT) in SLF1 (SLF1tBRCT) bound with the interacting Rad18 peptide. Our structure and biochemical studies demonstrate that SLF1tBRCT interacts with two phosphoserines and adjacent residues in Rad18 for high-affinity and specificity Rad18 recognition. We found that SLF1tBRCT utilizes mechanisms common among tBRCTs as well as unique ones for Rad18 binding, the latter include interactions with an α-helical structure in Rad18 that has not been observed in other tBRCT-bound ligand proteins. Our work provides structural insights into Rad18 targeting by SLF1 and expands the understanding of BRCT-mediated complex assembly.
Collapse
Affiliation(s)
- Wei Huang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, P. R. China
| | - Fangjie Qiu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, P. R. China
| | - Lin Zheng
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, P. R. China
| | - Meng Shi
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, P. R. China
| | - Miaomiao Shen
- National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, P. R. China
| | - Xiaolan Zhao
- Department of Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Song Xiang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, P. R. China.
| |
Collapse
|
10
|
Martin HL, Turner AL, Higgins J, Tang AA, Tiede C, Taylor T, Siripanthong S, Adams TL, Manfield IW, Bell SM, Morrison EE, Bond J, Trinh CH, Hurst CD, Knowles MA, Bayliss RW, Tomlinson DC. Affimer-mediated locking of p21-activated kinase 5 in an intermediate activation state results in kinase inhibition. Cell Rep 2023; 42:113184. [PMID: 37776520 DOI: 10.1016/j.celrep.2023.113184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/17/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023] Open
Abstract
Kinases are important therapeutic targets, and their inhibitors are classified according to their mechanism of action, which range from blocking ATP binding to covalent inhibition. Here, a mechanism of inhibition is highlighted by capturing p21-activated kinase 5 (PAK5) in an intermediate state of activation using an Affimer reagent that binds in the P+1 pocket. PAK5 was identified from a non-hypothesis-driven high-content imaging RNAi screen in urothelial cancer cells. Silencing of PAK5 resulted in reduced cell number, G1/S arrest, and enlargement of cells, suggesting it to be important in urothelial cancer cell line survival and proliferation. Affimer reagents were isolated to identify mechanisms of inhibition. The Affimer PAK5-Af17 recapitulated the phenotype seen with siRNA. Co-crystallization revealed that PAK5-Af17 bound in the P+1 pocket of PAK5, locking the kinase into a partial activation state. This mechanism of inhibition indicates that another class of kinase inhibitors is possible.
Collapse
Affiliation(s)
- Heather L Martin
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Amy L Turner
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Julie Higgins
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Anna A Tang
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas Taylor
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sitthinon Siripanthong
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas L Adams
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Iain W Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sandra M Bell
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Ewan E Morrison
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Jacquelyn Bond
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Richard W Bayliss
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
11
|
Guo J, Sun Y, Liu G. The mechanism of copper transporters in ovarian cancer cells and the prospect of cuproptosis. J Inorg Biochem 2023; 247:112324. [PMID: 37481825 DOI: 10.1016/j.jinorgbio.2023.112324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Copper transporters can not only carry copper (Cu) to maintain the homeostasis of Cu in cells but also transport platinum-based chemotherapy drugs. The effect of copper transporters on chemosensitivity has been demonstrated in a variety of malignancies. In addition, recent studies have reported that copper transporters can act as vectors to induce cuproptosis. Therefore, copper transporters can act on cells through different mechanisms to achieve different purposes. This review mainly describes the current research progress of the intracellular transport mechanism of copper transporters and cuproptosis, and prospects for the application of them in the treatment of ovarian cancer (OC).
Collapse
Affiliation(s)
- Jiahuan Guo
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin 300052, China; Key Laboratory of Cancer Prevention and Therapy of Tianjin, Department of Gynecologic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yue Sun
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Guoyan Liu
- Key Laboratory of Cancer Prevention and Therapy of Tianjin, Department of Gynecologic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.
| |
Collapse
|
12
|
Lewis M, Ono K, Qin Z, Johnsen RC, Baillie DL, Ono S. The α-arrestin SUP-13/ARRD-15 promotes isoform turnover of actin-interacting protein 1 in Caenorhabditis elegans striated muscle. PNAS Nexus 2023; 2:pgad330. [PMID: 37869480 PMCID: PMC10590129 DOI: 10.1093/pnasnexus/pgad330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023]
Abstract
Precise arrangement of actin, myosin, and other regulatory components in a sarcomeric pattern is critical for producing contractile forces in striated muscles. Actin-interacting protein 1 (AIP1), also known as WD-repeat protein 1 (WDR1), is one of essential factors that regulate sarcomeric assembly of actin filaments. In the nematode Caenorhabditis elegans, mutation in unc-78, encoding one of the two AIP1 isoforms, causes severe disorganization of sarcomeric actin filaments and near paralysis, but mutation in sup-13 suppresses the unc-78-mutant phenotypes to restore nearly normal sarcomeric actin organization and worm motility. Here, we identified that sup-13 is a nonsense allele of arrd-15 encoding an α-arrestin. The sup-13/arrd-15 mutation suppressed the phenotypes of unc-78 null mutant but required aipl-1 that encodes a second AIP1 isoform. aipl-1 was normally expressed highly in embryos and downregulated in mature muscle. However, in the sup-13/arrd-15 mutant, the AIPL-1 protein was maintained at high levels in adult muscle to compensate for the absence of the UNC-78 protein. The sup-13/arrd-15 mutation caused accumulation of ubiquitinated AIPL-1 protein, suggesting that a normal function of sup-13/arrd-15 is to enhance degradation of ubiquitinated AIPL-1, thereby promoting transition of AIP1 isoforms from AIPL-1 to UNC-78 in developing muscle. These results suggest that α-arrestin is a novel factor to promote isoform turnover by enhancing protein degradation.
Collapse
Affiliation(s)
- Mario Lewis
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kanako Ono
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhaozhao Qin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Robert C Johnsen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - David L Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Shoichiro Ono
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
13
|
Jacobsen NL, Bloch M, Millard PS, Ruidiaz SF, Elsborg JD, Boomsma W, Hendus‐Altenburger R, Hartmann‐Petersen R, Kragelund BB. Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro. Protein Sci 2023; 32:e4733. [PMID: 37463013 PMCID: PMC10443397 DOI: 10.1002/pro.4733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) are often multifunctional and frequently posttranslationally modified. Deleted in split hand/split foot 1 (Dss1-Sem1 in budding yeast) is a highly multifunctional IDP associated with a range of protein complexes. However, it remains unknown if the different functions relate to different modified states. In this work, we show that Schizosaccharomyces pombe Dss1 is a substrate for casein kinase 2 in vitro, and we identify three phosphorylated threonines in its linker region separating two known disordered ubiquitin-binding motifs. Phosphorylations of the threonines had no effect on ubiquitin-binding but caused a slight destabilization of the C-terminal α-helix and mediated a direct interaction with the forkhead-associated (FHA) domain of the RING-FHA E3-ubiquitin ligase defective in mitosis 1 (Dma1). The phosphorylation sites are not conserved and are absent in human Dss1. Sequence analyses revealed that the Txx(E/D) motif, which is important for phosphorylation and Dma1 binding, is not linked to certain branches of the evolutionary tree. Instead, we find that the motif appears randomly, supporting the mechanism of ex nihilo evolution of novel motifs. In support of this, other threonine-based motifs, although frequent, are nonconserved in the linker, pointing to additional functions connected to this region. We suggest that Dss1 acts as an adaptor protein that docks to Dma1 via the phosphorylated FHA-binding motifs, while the C-terminal α-helix is free to bind mitotic septins, thereby stabilizing the complex. The presence of Txx(D/E) motifs in the disordered regions of certain septin subunits may be of further relevance to the formation and stabilization of these complexes.
Collapse
Affiliation(s)
- Nina L. Jacobsen
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Magnus Bloch
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Peter S. Millard
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Sarah F. Ruidiaz
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
| | - Jonas D. Elsborg
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagen ØDenmark
| | | | - Rasmus Hartmann‐Petersen
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| |
Collapse
|
14
|
Jiang Z, Lin Z, Gan Q, Wu P, Zhang X, Xiao Y, She Q, Ni J, Shen Y, Huang Q. The FHA domain protein ArnA functions as a global DNA damage response repressor in the hyperthermophilic archaeon Saccharolobus islandicus. mBio 2023; 14:e0094223. [PMID: 37389462 PMCID: PMC10470591 DOI: 10.1128/mbio.00942-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
Forkhead-associated (FHA) domain proteins specifically recognize phosphorylated threonine via the FHA domain and are involved in signal transduction in various processes especially DNA damage response (DDR) and cell cycle regulation in eukaryotes. Although FHA domain proteins are found in prokaryotes, archaea, and bacteria, their functions are far less clear as compared to the eukaryotic counterparts, and it has not been studied whether archaeal FHA proteins play a role in DDR. Here, we have characterized an FHA protein from the hyperthermophilic Crenarchaeon Saccharolobus islandicus (SisArnA) by genetic, biochemical, and transcriptomic approaches. We find that ΔSisarnA exhibits higher resistance to DNA damage agent 4-nitroquinoline 1-oxide (NQO). The transcription of ups genes, encoding the proteins for pili-mediated cell aggregation and cell survival after DDR, is elevated in ΔSisarnA. The interactions of SisArnA with two predicted partners, SisvWA1 (SisArnB) and SisvWA2 (designated as SisArnE), were enhanced by phosphorylation in vitro. ΔSisarnB displays higher resistance to NQO than the wild type. In addition, the interaction between SisArnA and SisArnB, which is reduced in the NQO-treated cells, is indispensable for DNA binding in vitro. These indicate that SisArnA and SisArnB work together to inhibit the expression of ups genes in vivo. Interestingly, ΔSisarnE is more sensitive to NQO than the wild type, and the interaction between SisArnA and SisArnE is strengthened after NQO treatment, suggesting a positive role of SisArnE in DDR. Finally, transcriptomic analysis reveals that SisArnA represses a number of genes, implying that archaea apply the FHA/phospho-peptide recognition module for extensive transcriptional regulation. IMPORTANCE Cellular adaption to diverse environmental stresses requires a signal sensor and transducer for cell survival. Protein phosphorylation and its recognition by forkhead-associated (FHA) domain proteins are widely used for signal transduction in eukaryotes. Although FHA proteins exist in archaea and bacteria, investigation of their functions, especially those in DNA damage response (DDR), is limited. Therefore, the evolution and functional conservation of FHA proteins in the three domains of life is still a mystery. Here, we find that an FHA protein from the hyperthermophilic Crenarchaeon Saccharolobus islandicus (SisArnA) represses the transcription of pili genes together with its phosphorylated partner SisArnB. SisArnA derepression facilitates DNA exchange and repair in the presence of DNA damage. The fact that more genes including a dozen of those involved in DDR are found to be regulated by SisArnA implies that the FHA/phosphorylation module may serve as an important signal transduction pathway for transcriptional regulation in archaeal DDR.
Collapse
Affiliation(s)
- Zhichao Jiang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Zijia Lin
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qi Gan
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Pengju Wu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xuemei Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yuanxi Xiao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Jinfeng Ni
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qihong Huang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| |
Collapse
|
15
|
Imakura T, Sato S, Koyama K, Ogawa H, Niimura T, Murakami K, Yamashita Y, Haji K, Naito N, Kagawa K, Kawano H, Zamami Y, Ishizawa K, Nishioka Y. A polo-like kinase inhibitor identified by computational repositioning attenuates pulmonary fibrosis. Respir Res 2023; 24:148. [PMID: 37269004 DOI: 10.1186/s12931-023-02446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/08/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a fatal fibrotic lung disease with few effective therapeutic options. Recently, drug repositioning, which involves identifying novel therapeutic potentials for existing drugs, has been popularized as a new approach for the development of novel therapeutic reagents. However, this approach has not yet been fully utilized in the field of pulmonary fibrosis. METHODS The present study identified novel therapeutic options for pulmonary fibrosis using a systematic computational approach for drug repositioning based on integration of public gene expression signatures of drug and diseases (in silico screening approach). RESULTS Among the top compounds predicted to be therapeutic for IPF by the in silico approach, we selected BI2536, a polo-like kinase (PLK) 1/2 inhibitor, as a candidate for treating pulmonary fibrosis using an in silico analysis. However, BI2536 accelerated mortality and weight loss rate in an experimental mouse model of pulmonary fibrosis. Because immunofluorescence staining revealed that PLK1 expression was dominant in myofibroblasts while PLK2 expression was dominant in lung epithelial cells, we next focused on the anti-fibrotic effect of the selective PLK1 inhibitor GSK461364. Consequently, GSK461364 attenuated pulmonary fibrosis with acceptable mortality and weight loss in mice. CONCLUSIONS These findings suggest that targeting PLK1 may be a novel therapeutic approach for pulmonary fibrosis by inhibiting lung fibroblast proliferation without affecting lung epithelial cells. In addition, while in silico screening is useful, it is essential to fully determine the biological activities of candidates by wet-lab validation studies.
Collapse
Affiliation(s)
- Takeshi Imakura
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Seidai Sato
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Kazuya Koyama
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Hirohisa Ogawa
- Department of Pathology and Laboratory Medicine, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Takahiro Niimura
- Department of Clinical Pharmacology and Therapeutics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Kojin Murakami
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Yuya Yamashita
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Keiko Haji
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Nobuhito Naito
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Kozo Kagawa
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Hiroshi Kawano
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Yoshito Zamami
- Department of Clinical Pharmacology and Therapeutics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
- Department of Pharmacy, Okayama University Hospital, Okayama, Japan
| | - Keisuke Ishizawa
- Department of Clinical Pharmacology and Therapeutics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yasuhiko Nishioka
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan.
| |
Collapse
|
16
|
Premnath N, Madanat YF. Novel Investigational Agents and Pathways That May Influence the Future Management of Acute Myeloid Leukemia. Cancers (Basel) 2023; 15:2958. [PMID: 37296920 PMCID: PMC10252053 DOI: 10.3390/cancers15112958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
Acute Myeloid leukemia (AML) is a clinically heterogeneous disease with a 5-year overall survival of 32% between 2012 to 2018. The above number severely dwindles with age and adverse risk of disease, presenting opportunities for new drug development and is an area of dire unmet need. Basic science and clinical investigators across the world have been working on many new and old molecule formulations and combination strategies to improve outcomes in this disease. In this review, we discuss select promising novel agents in various stages of clinical development for patients with AML.
Collapse
Affiliation(s)
- Naveen Premnath
- Division of Hematology and Medical Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA;
| | - Yazan F. Madanat
- Division of Hematology and Medical Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA;
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75235, USA
| |
Collapse
|
17
|
Stehn JR, Floyd SR, Wilker EW, Reinhardt HC, Clarke SM, Huang Q, Polakiewicz RD, Sonenberg N, Kong YW, Yaffe MB. MAPKAP Kinase-2 phosphorylation of PABPC1 controls its interaction with 14-3-3 proteins after DNA damage: A combined kinase and protein array approach. Front Mol Biosci 2023; 10:1148933. [PMID: 37091863 PMCID: PMC10117672 DOI: 10.3389/fmolb.2023.1148933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
14-3-3 proteins play critical roles in controlling multiple aspects of the cellular response to stress and DNA damage including regulation of metabolism, cell cycle progression, cell migration, and apoptotic cell death by binding to protein substrates of basophilic protein kinases following their phosphorylation on specific serine/threonine residues. Although over 200 mammalian proteins that bind to 14-3-3 have been identified, largely through proteomic studies, in many cases the relevant protein kinase responsible for conferring 14-3-3-binding to these proteins is not known. To facilitate the identification of kinase-specific 14-3-3 clients, we developed a biochemical approach using high-density protein filter arrays and identified the translational regulatory molecule PABPC1 as a substrate for Chk1 and MAPKAP Kinase-2 (MK2) in vitro, and for MK2 in vivo, whose phosphorylation results in 14-3-3-binding. We identify Ser-470 on PABPC1 within the linker region connecting the RRM domains to the PABC domain as the critical 14-3-3-binding site, and demonstrate that loss of PABPC1 binding to 14-3-3 results in increased cell proliferation and decreased cell death in response to UV-induced DNA damage.
Collapse
Affiliation(s)
- Justine R. Stehn
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Scott R. Floyd
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Erik W. Wilker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - H. Christian Reinhardt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Scott M. Clarke
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Qiuying Huang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Nahum Sonenberg
- Rosalind and Morris Goodman Cancer Centre, Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Yi Wen Kong
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States
- *Correspondence: Yi Wen Kong, ; Michael B. Yaffe,
| | - Michael B. Yaffe
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Divisions of Surgical Oncology, Trauma, and Surgical Critical Care, Beth Israel Deaconess Medical Center, Department of Surgery, Harvard Medical School, Boston, MA, United States
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yi Wen Kong, ; Michael B. Yaffe,
| |
Collapse
|
18
|
Yang D, Xiao P, Qiu B, Yu HF, Teng CB. Copper chaperone antioxidant 1: multiple roles and a potential therapeutic target. J Mol Med (Berl) 2023; 101:527-542. [PMID: 37017692 DOI: 10.1007/s00109-023-02311-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/06/2023]
Abstract
Copper (Cu) was recently demonstrated to play a critical role in cellular physiological and biochemical processes, including energy production and maintenance, antioxidation and enzymatic activity, and signal transduction. Antioxidant 1 (ATOX1), a chaperone of Cu previously named human ATX1 homologue (HAH1), has been found to play an indispensable role in maintaining cellular Cu homeostasis, antioxidative stress, and transcriptional regulation. In the past decade, it has also been found to be involved in a variety of diseases, including numerous neurodegenerative diseases, cancers, and metabolic diseases. Recently, increasing evidence has revealed that ATOX1 is involved in the regulation of cell migration, proliferation, autophagy, DNA damage repair (DDR), and death, as well as in organism development and reproduction. This review summarizes recent advances in the research on the diverse physiological and cytological functions of ATOX1 and the underlying mechanisms of its action in human health and diseases. The potential of ATOX1 as a therapeutic target is also discussed. This review aims to pose unanswered questions related to ATOX1 biology and explore the potential use of ATOX1 as a therapeutic target.
Collapse
Affiliation(s)
- Dian Yang
- Animal Development Biology Laboratory, College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Pengyu Xiao
- Animal Development Biology Laboratory, College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Botao Qiu
- Animal Development Biology Laboratory, College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Hai-Fan Yu
- Animal Development Biology Laboratory, College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China.
| | - Chun-Bo Teng
- Animal Development Biology Laboratory, College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China.
| |
Collapse
|
19
|
Yuan Q, Chu Y, Li X, Shi Y, Chen Y, Zhao J, Lu J, Liu K, Guo Y. CAFrgDB: a database for cancer-associated fibroblasts related genes and their functions in cancer. Cancer Gene Ther 2023:10.1038/s41417-023-00603-4. [PMID: 36922546 DOI: 10.1038/s41417-023-00603-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/03/2023] [Accepted: 02/23/2023] [Indexed: 03/17/2023]
Abstract
As one of the most essential components of the tumor microenvironment (TME), cancer-associated fibroblasts (CAFs) interact extensively with cancer cells and other stromal cells to remodel TME and participate in the pathogenesis of cancer, which earmarked themselves as new promising targets for cancer therapy. Numerous studies have highlighted the heterogeneity and versatility of CAFs in most cancer types. Thus, the identification and appropriate use of CAF-related genes (CAFGenes) in the context of specific cancer types will provide critical insights into disease mechanisms and CAF-related therapeutic targets. In this study, we collected and curated 5421 CAFGenes identified from small- or large-scale experiments, encompassing 4982 responsors that directly or indirectly participate in cancer malignant behaviors managed by CAFs, 1069 secretions that are secreted by CAFs and 281 regulators that contribute in modulating CAFs in human and mouse, which covered 24 cancer types. For these human CAFGenes, we performed gene expression and prognostic marker-based analyses across 24 cancer types using TCGA data. Furthermore, we provided annotations for CAF-associated proteins by integrating the knowledge of protein-protein interaction(s), drug-target relations and basic annotations, from 9 public databases. CAFrgDB (CAF related Gene DataBase) is free for academic research at http://caf.zbiolab.cn and we anticipate CAFrgDB can be a useful resource for further study of CAFs.
Collapse
Affiliation(s)
- Qiang Yuan
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yi Chu
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoyu Li
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yunshu Shi
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yingying Chen
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jimin Zhao
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jing Lu
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Kangdong Liu
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China. .,China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450001, China.
| | - Yaping Guo
- Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
20
|
Huynh O, Ruis K, Montales K, Michael WM. NBS1 binds directly to TOPBP1 via disparate interactions between the NBS1 BRCT1 domain and the TOPBP1 BRCT1 and BRCT2 domains. DNA Repair (Amst) 2023; 123:103461. [PMID: 36738687 PMCID: PMC9992324 DOI: 10.1016/j.dnarep.2023.103461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The TOPBP1 and NBS1 proteins are key components of DNA repair and DNA-based signaling systems. TOPBP1 is a multi-BRCT domain containing protein that plays important roles in checkpoint signaling, DNA replication, and DNA repair. Likewise, NBS1, which is a component of the MRE11-RAD50-NBS1 (MRN) complex, functions in both checkpoint signaling and DNA repair. NBS1 also contains BRCT domains, and previous works have shown that TOPBP1 and NBS1 interact with one another. In this work we examine the interaction between TOPBP1 and NBS1 in detail. We report that NBS1 uses its BRCT1 domain to interact with TOPBP1's BRCT1 domain and, separately, with TOPBP1's BRCT2 domain. Thus, NBS1 can make two distinct contacts with TOPBP1. We report that recombinant TOPBP1 and NBS1 proteins bind one another in a purified system, showing that the interaction is direct and does not require post-translational modifications. Surprisingly, we also report that intact BRCT domains are not required for these interactions, as truncated versions of the domains are sufficient to confer binding. For TOPBP1, we find that small 24-29 amino acid sequences within BRCT1 or BRCT2 allow binding to NBS1, in a transferrable manner. These data expand our knowledge of how the crucial DNA damage response proteins TOPBP1 and NBS1 interact with one another and set the stage for functional analysis of the two disparate binding sites for NBS1 on TOPBP1.
Collapse
Affiliation(s)
- Oanh Huynh
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kenna Ruis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Katrina Montales
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - W Matthew Michael
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
21
|
Wang TT, Wu LL, Wu J, Zhang LS, Shen WJ, Zhao YH, Liu JN, Fu B, Wang X, Li QG, Bai XY, Wang LQ, Chen XM. 14-3-3ζ inhibits maladaptive repair in renal tubules by regulating YAP and reduces renal interstitial fibrosis. Acta Pharmacol Sin 2023; 44:381-392. [PMID: 35840657 PMCID: PMC9889378 DOI: 10.1038/s41401-022-00946-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Acute kidney injury (AKI) refers to a group of common clinical syndromes characterized by acute renal dysfunction, which may lead to chronic kidney disease (CKD), and this process is called the AKI-CKD transition. The transcriptional coactivator YAP can promote the AKI-CKD transition by regulating the expression of profibrotic factors, and 14-3-3 protein zeta (14-3-3ζ), an important regulatory protein of YAP, may prevent the AKI-CKD transition. We established an AKI-CKD model in mice by unilateral renal ischemia-reperfusion injury and overexpressed 14-3-3ζ in mice using a fluid dynamics-based gene transfection technique. We also overexpressed and knocked down 14-3-3ζ in vitro. In AKI-CKD model mice, 14-3-3ζ expression was significantly increased at the AKI stage. During the development of chronic disease, the expression of 14-3-3ζ tended to decrease, whereas active YAP was consistently overexpressed. In vitro, we found that 14-3-3ζ can combine with YAP, promote the phosphorylation of YAP, inhibit YAP nuclear translocation, and reduce the expression of fibrosis-related proteins. In an in vivo intervention experiment, we found that the overexpression of 14-3-3ζ slowed the process of renal fibrosis in a mouse model of AKI-CKD. These findings suggest that 14-3-3ζ can affect the expression of fibrosis-related proteins by regulating YAP, inhibit the maladaptive repair of renal tubular epithelial cells, and prevent the AKI-CKD transition.
Collapse
Affiliation(s)
- Tian-Tian Wang
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Ling-Ling Wu
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Jie Wu
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Li-Sheng Zhang
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wan-Jun Shen
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Ying-Hua Zhao
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Jiao-Na Liu
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Bo Fu
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Xu Wang
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Qing-Gang Li
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Xue-Yuan Bai
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China
| | - Li-Qiang Wang
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Xiang-Mei Chen
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, 100853, China.
| |
Collapse
|
22
|
Yang T, Zhu C, Shi Y, Shen Y, Gao Y, Zhang B, Jin R, Liu D, Ouyang Y, Liu X, Wang W, Yang P, Xu Q, Cai J, Chen D. RDIVpSGP motif of ASPP2 binds to 14-3-3 and enhances ASPP2/k18/14-3-3 ternary complex formulation to promote BRAF/MEK/ERK signal inhibited cell proliferation in hepatocellular carcinoma. Cancer Gene Ther 2022; 29:1616-27. [PMID: 35504951 DOI: 10.1038/s41417-022-00474-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/27/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023]
Abstract
The Apoptosis Stimulating Protein of p53 2 (ASPP2) is a heterozygous insufficient tumor suppressor; however, its molecular mechanism(s) in tumor suppression is not completely understood. ASPP2 plays an essential role in cell growth, as shown by liver hepatocellular carcinoma (LIHC) RNA-seq assay using the Cancer Genome Atlas (TCGA) and High-Throughput-PCR assay using ASPP2 knockdown cells. These observations were further confirmed by in vivo and in vitro experiments. Mechanistically, N-terminus ASPP2 interacted with Keratin 18 (k18) in vivo and in vitro. Interestingly, the RDIVpSGP motif of ASPP2 associates with 14-3-3 and promotes ASPP2/k18/14-3-3 ternary-complex formation which promotes MEK/ERK signal activation by impairing 14-3-3 and BRAF association. Additionally, ASPP2-rAd injection promotes paclitaxel-suppressed tumor growth by suppressing cell proliferation in the BALB/c nude mice model. ASPP2 and k18 were preferentially downregulated in Hepatocellular Carcinoma (HCC), which predicted poor prognosis in HCC patients. Overall, these findings suggested that ASPP2 promoted BRAF/MEK/ERK signal activation by promoting the formation of an ASPP2/k18/14-3-3 ternary complex via the RDIVpSGP motif at the N terminus. Moreover, this study provides novel insights into the molecular mechanism of tumor suppression in HCC patients.
Collapse
|
23
|
Iwahori S, Umaña AC, Kalejta RF, Murata T. Serine 13 of the human cytomegalovirus viral cyclin-dependent kinase UL97 is required for regulatory protein 14-3-3 binding and UL97 stability. J Biol Chem 2022; 298:102513. [PMID: 36150501 PMCID: PMC9587022 DOI: 10.1016/j.jbc.2022.102513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/14/2022] Open
Abstract
The human cytomegalovirus (HCMV) UL97 protein is a conserved herpesvirus protein kinase (CHPK) and a viral cyclin-dependent kinase (v-CDK). However, mechanisms regulating its activity in the context of infection are unknown. Here, we identified several cellular regulatory 14-3-3 proteins as UL97-interacting partners that promote UL97 stability. Humans are known to encode seven isoforms of 14-3-3 proteins (β, ε, η, γ, σ, θ, and ζ) that bind phosphoserines or phosphothreonines to impact protein structure, stability, activity, and localization. Our proteomic analysis of UL97 identified 49 interacting partners, including 14-3-3 isoforms β, η, and γ. Furthermore, coimmunoprecipitation with Western blotting assays demonstrated that UL97 interaction with 14-3-3 isoforms β, ε, η, γ, and θ occurs in a kinase activity-dependent manner. Using mutational analysis, we determined the serine residue at amino acid 13 of UL97 is crucial for 14-3-3 interaction. We demonstrate UL97 S13A (serine to alanine substitution at residue 13) retains kinase activity but the mutant protein accumulated at lower levels than WT UL97. Finally, we show both laboratory (AD169) and clinical (TB40/E) strains of HCMV encoding UL97 S13A replicated with WT kinetics in fibroblasts but showed decreased UL97 accumulation. Taken together, we conclude that 14-3-3 proteins interact with and stabilize UL97 during HCMV infection.
Collapse
Affiliation(s)
- Satoko Iwahori
- Department of Virology and Parasitology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan; Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Angie C Umaña
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert F Kalejta
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA.
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.
| |
Collapse
|
24
|
Longarini EJ, Matic I. The fast-growing business of Serine ADP-ribosylation. DNA Repair (Amst) 2022; 118:103382. [DOI: 10.1016/j.dnarep.2022.103382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022]
|
25
|
Ovejero S, Soulet C, Kumanski S, Moriel-Carretero M. Coordination between phospholipid pools and DNA damage sensing. Biol Cell 2022; 114:211-219. [PMID: 35524759 DOI: 10.1111/boc.202200007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/27/2022]
Abstract
Both phospholipid synthesis and the detection of DNA damage are coupled to cell cycle progression, yet whether these two aspects crosstalk to each other remains unassessed. We postulate here that shortage of phospholipids, which negatively affects proliferation, may reduce the need for checkpoint activation in response to DNA damage. By exploring the DDR activation in response to seven different genotoxins, in three distinct cell types, and manipulating phospholipid synthesis both pharmacologically and genetically, we point at the DNA damage response kinase ATR as responsible for the coordination between phospholipid levels and DNA damage sensing. Further, our analysis reveals the functional significance of this crosstalk to keep genome homeostasis. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Sara Ovejero
- Institut de Génétique Humaine (IGH), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France.,Department of Biological Hematology, CHU Montpellier, Montpellier, 34295, France
| | - Caroline Soulet
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France
| | - Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France
| |
Collapse
|
26
|
Hu J, Li G. Recent Progress in Fluorescent Chemosensors for Protein Kinases. Chem Asian J 2022; 17:e202200182. [PMID: 35486328 DOI: 10.1002/asia.202200182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Indexed: 11/10/2022]
Abstract
Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.
Collapse
Affiliation(s)
- Jun Hu
- Fujian Agriculture and Forestry University, College of Life Sciences, No.15 Shangxiadian Road, Cangshan District, 350002, Fuzhou, CHINA
| | - Gao Li
- Minjiang University, College of Material and Chemical Engineering, CHINA
| |
Collapse
|
27
|
Ruis K, Huynh O, Montales K, Barr NA, Michael WM. Delineation of a minimal topoisomerase II binding protein 1 (TOPBP1) for regulated activation of ATR at DNA double-strand breaks. J Biol Chem 2022; 298:101992. [PMID: 35490781 PMCID: PMC9257406 DOI: 10.1016/j.jbc.2022.101992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022] Open
Abstract
Topoisomerase II Binding Protein 1 (TOPBP1) is an important activator of the DNA damage response kinase Ataxia Telangiectasia and Rad3-related (ATR), although the mechanism by which this activation occurs is not yet known. TOPBP1 contains nine copies of the BRCA1 C-terminal repeat (BRCT) motif, which allows protein–protein and protein–DNA interactions. TOPBP1 also contains an ATR activation domain (AAD), which physically interacts with ATR and its partner ATR-interacting protein (ATRIP) in a manner that stimulates ATR kinase activity. It is unclear which of TOPBP1’s nine BRCT domains participate in the reaction, as well as the individual roles played by these relevant BRCT domains. To address this knowledge gap, here, we delineated a minimal TOPBP1 that can activate ATR at DNA double-strand breaks in a regulated manner. We named this minimal TOPBP1 “Junior” and we show that Junior is composed of just three regions: BRCT0-2, the AAD, and BRCT7&8. We further defined the individual functions of these three regions by showing that BRCT0-2 is required for recruitment to DNA double-strand breaks and is dispensable thereafter, and that BRCT7&8 is dispensable for recruitment but essential to allow the AAD to multimerize and activate ATR. The delineation of TOPBP1 Junior creates a leaner, simplified, and better understood TOPBP1 and provides insight into the mechanism of ATR activation.
Collapse
Affiliation(s)
- Kenna Ruis
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089
| | - Oanh Huynh
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089
| | - Katrina Montales
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089
| | - Nina A Barr
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089
| | - W Matthew Michael
- Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089.
| |
Collapse
|
28
|
Kliche J, Ivarsson Y. Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. Biochem J 2022; 479:1-22. [PMID: 34989786 PMCID: PMC8786283 DOI: 10.1042/bcj20200714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
Collapse
Affiliation(s)
- Johanna Kliche
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| |
Collapse
|
29
|
Alam P, Tyagi R, Farah MA, Rehman MT, Hussain A, AlAjmi MF, Siddiqui NA, Al-Anazi KM, Amin S, Mujeeb M, Mir SR. Cytotoxicity and molecular docking analysis of racemolactone I, a new sesquiterpene lactone isolated from Inula racemosa. Pharm Biol 2021; 59:941-952. [PMID: 35294328 PMCID: PMC8274518 DOI: 10.1080/13880209.2021.1946090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/15/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
CONTEXT Traditionally, Inula racemosa Hook. f. (Asteraceae) has been reported to be effective in cancer treatment which motivated the authors to explore the plant for novel anticancer compounds. OBJECTIVE To isolate and characterize new cytotoxic phytoconstituents from I. racemosa roots. MATERIALS AND METHODS The column chromatography of I. racemosa ethyl acetate extract furnished a novel sesquiterpene lactone whose structure was established by NMR (1D/2D), ES-MS and its cytotoxic properties were assessed on HeLa, MDAMB-231, and A549 cell lines using MTT and LDH (lactate dehydrogenase) assays. Further, morphological changes were analyzed by flow cytometry, mitochondrial membrane potential, AO-EtBr dual staining, and comet assay. Molecular docking and simulation were performed using Glide and Desmond softwares, respectively, to validate the mechanism of action. RESULTS The isolated compound was identified as racemolactone I (compound 1). Amongst the cell lines tested, considerable changes were observed in HeLa cells. Compound 1 (IC50 = 0.9 µg/mL) significantly decreased cell viability (82%) concomitantly with high LDH release (76%) at 15 µg/mL. Diverse morphological alterations along with significant increase (9.23%) in apoptotic cells and decrease in viable cells were observed. AO-EtBr dual staining also confirmed the presence of 20% apoptotic cells. A gradual decrease in mitochondrial membrane potential was observed. HeLa cells showed significantly increased comet tail length (48.4 µm), indicating broken DNA strands. In silico studies exhibited that compound 1 binds to the active site of Polo-like kinase-1 and forms a stable complex. CONCLUSIONS Racemolactone I was identified as potential anticancer agent, which can further be confirmed by in vivo investigations.
Collapse
Affiliation(s)
- Perwez Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Rama Tyagi
- Phyto-Pharmaceutical Research Lab, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Fahad AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Nasir Ali Siddiqui
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | | | - Saima Amin
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Mohd. Mujeeb
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Showkat R. Mir
- Phyto-Pharmaceutical Research Lab, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| |
Collapse
|
30
|
Lin T, Sun L, Lee JE, Kim SY, Jin DI. DNA damage repair is suppressed in porcine aged oocytes. J Anim Sci Technol 2021; 63:984-997. [PMID: 34796342 PMCID: PMC8564305 DOI: 10.5187/jast.2021.e90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 12/24/2022]
Abstract
This study sought to evaluate DNA damage and repair in porcine postovulatory aged
oocytes. The DNA damage response, which was assessed by H2A.X expression,
increased in porcine aged oocytes over time. However, the aged oocytes exhibited
a significant decrease in the expression of RAD51, which reflects the DNA damage
repair capacity. Further experiments suggested that the DNA repair ability was
suppressed by the downregulation of genes involved in the homologous
recombination (HR) and nonhomologous end-joining (NHEJ) pathways. The expression
levels of the cell cycle checkpoint genes, CHEK1 and
CHEK2, were upregulated in porcine aged oocytes in response
to induced DNA damage. Immunofluorescence results revealed that the expression
level of H3K79me2 was significantly lower in porcine aged oocytes than in
control oocytes. In addition, embryo quality was significantly reduced in aged
oocytes, as assessed by measuring the cell proliferation capacity. Our results
provide evidence that DNA damage is increased and the DNA repair ability is
suppressed in porcine aged oocytes. These findings increase our understanding of
the events that occur during postovulatory oocyte aging.
Collapse
Affiliation(s)
- Tao Lin
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China.,Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Ling Sun
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China.,Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Jae Eun Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - So Yeon Kim
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Dong Il Jin
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| |
Collapse
|
31
|
Sanchez A, Lee D, Kim DI, Miller KM. Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Front Genet 2021; 12:747734. [PMID: 34659365 PMCID: PMC8514019 DOI: 10.3389/fgene.2021.747734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/31/2021] [Indexed: 01/25/2023] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.
Collapse
Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Dae In Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| |
Collapse
|
32
|
Morgan D, Berggren KL, Spiess CD, Smith HM, Tejwani A, Weir SJ, Lominska CE, Thomas SM, Gan GN. Mitogen-activated protein kinase-activated protein kinase-2 (MK2) and its role in cell survival, inflammatory signaling, and migration in promoting cancer. Mol Carcinog 2021; 61:173-199. [PMID: 34559922 DOI: 10.1002/mc.23348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/19/2022]
Abstract
Cancer and the immune system share an intimate relationship. Chronic inflammation increases the risk of cancer occurrence and can also drive inflammatory mediators into the tumor microenvironment enhancing tumor growth and survival. The p38 MAPK pathway is activated both acutely and chronically by stress, inflammatory chemokines, chronic inflammatory conditions, and cancer. These properties have led to extensive efforts to find effective drugs targeting p38, which have been unsuccessful. The immediate downstream serine/threonine kinase and substrate of p38 MAPK, mitogen-activated-protein-kinase-activated-protein-kinase-2 (MK2) protects cells against stressors by regulating the DNA damage response, transcription, protein and messenger RNA stability, and motility. The phosphorylation of downstream substrates by MK2 increases inflammatory cytokine production, drives an immune response, and contributes to wound healing. By binding directly to p38 MAPK, MK2 is responsible for the export of p38 MAPK from the nucleus which gives MK2 properties that make it unique among the large number of p38 MAPK substrates. Many of the substrates of both p38 MAPK and MK2 are separated between the cytosol and nucleus and interfering with MK2 and altering this intracellular translocation has implications for the actions of both p38 MAPK and MK2. The inhibition of MK2 has shown promise in combination with both chemotherapy and radiotherapy as a method for controlling cancer growth and metastasis in a variety of cancers. Whereas the current data are encouraging the field requires the development of selective and well tolerated drugs to target MK2 and a better understanding of its effects for effective clinical use.
Collapse
Affiliation(s)
- Deri Morgan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Kiersten L Berggren
- Department of Internal Medicine, Division of Medical Oncology, Section of Radiation Oncology, UNM School of Medicine, The University of New Mexico, Albuquerque, New Mexico, USA
| | - Colby D Spiess
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Hannah M Smith
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Ajay Tejwani
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Scott J Weir
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Christopher E Lominska
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Sufi M Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.,Department of Otolaryngology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Gregory N Gan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, Kansas, USA.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
33
|
Lu ZC, Jiang F, Wu YD. Phosphate binding sites prediction in phosphorylation-dependent protein-protein interactions. Bioinformatics 2021; 37:4712-4718. [PMID: 34270697 DOI: 10.1093/bioinformatics/btab525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Phosphate binding plays an important role in modulating protein-protein interactions, which are ubiquitous in various biological processes. Accurate prediction of phosphate binding sites is an important but challenging task. Small size and diversity of phosphate binding sites lead to a substantial challenge for developing accurate prediction methods. RESULTS Here we present the phosphate binding site predictor (PBSP), a novel and accurate approach to identifying phosphate binding sites from protein structures. PBSP combines an energy-based ligand-binding sites identification method with reverse focused docking using a phosphate probe. We show that PBSP outperforms not only general ligand binding sites predictors but also other existing phospholigand-specific binding sites predictors. It achieves ∼95% success rate for top 10 predicted sites with an average Matthews correlation coefficient (MCC) value of 0.84 for successful predictions. PBSP can accurately predict phosphate binding modes, with average position error of 1.4 Å and 2.4 Å in bound and unbound datasets, respectively. Lastly, visual inspection of the predictions is conducted. Reasons for failed predictions are further analyzed and possible ways to improve the performance are provided. These results demonstrate a novel and accurate approach to phosphate binding sites identification in protein structures. AVAILABILITY The software and benchmark datasets are freely available at http://web.pkusz.edu.cn/wu/PBSP/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zheng-Chang Lu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,NanoAI Biotech Co., Ltd, Shenzhen, 518118, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,Shenzhen Bay Laboratory, Shenzhen, 518055, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| |
Collapse
|
34
|
Benoit I, Brownell S, Douville RN. Predicted Cellular Interactors of the Endogenous Retrovirus-K Integrase Enzyme. Microorganisms 2021; 9:1509. [PMID: 34361946 DOI: 10.3390/microorganisms9071509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
Integrase (IN) enzymes are found in all retroviruses and are crucial in the retroviral integration process. Many studies have revealed how exogenous IN enzymes, such as the human immunodeficiency virus (HIV) IN, contribute to altered cellular function. However, the same consideration has not been given to viral IN originating from symbionts within our own DNA. Endogenous retrovirus-K (ERVK) is pathologically associated with neurological and inflammatory diseases along with several cancers. The ERVK IN interactome is unknown, and the question of how conserved the ERVK IN protein-protein interaction motifs are as compared to other retroviral integrases is addressed in this paper. The ERVK IN protein sequence was analyzed using the Eukaryotic Linear Motif (ELM) database, and the results are compared to ELMs of other betaretroviral INs and similar eukaryotic INs. A list of putative ERVK IN cellular protein interactors was curated from the ELM list and submitted for STRING analysis to generate an ERVK IN interactome. KEGG analysis was used to identify key pathways potentially influenced by ERVK IN. It was determined that the ERVK IN potentially interacts with cellular proteins involved in the DNA damage response (DDR), cell cycle, immunity, inflammation, cell signaling, selective autophagy, and intracellular trafficking. The most prominent pathway identified was viral carcinogenesis, in addition to select cancers, neurological diseases, and diabetic complications. This potentiates the role of ERVK IN in these pathologies via protein-protein interactions facilitating alterations in key disease pathways.
Collapse
|
35
|
Sekurova ON, Sun YQ, Zehl M, Rückert C, Stich A, Busche T, Kalinowski J, Zotchev SB. Coupling of the engineered DNA "mutator" to a biosensor as a new paradigm for activation of silent biosynthetic gene clusters in Streptomyces. Nucleic Acids Res 2021; 49:8396-8405. [PMID: 34197612 PMCID: PMC8373060 DOI: 10.1093/nar/gkab583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/31/2021] [Accepted: 06/23/2021] [Indexed: 11/14/2022] Open
Abstract
DNA replication fidelity in Streptomyces bacteria, prolific producers of many medically important secondary metabolites, is understudied, while in Escherichia coli it is controlled by DnaQ, the ϵ subunit of DNA polymerase III (DNA PolIII). Manipulation of dnaQ paralogues in Streptomyces lividans TK24, did not lead to increased spontaneous mutagenesis in this bacterium suggesting that S. lividans DNA PolIII uses an alternative exonuclease activity for proofreading. In Mycobacterium tuberculosis, such activity is attributed to the DnaE protein representing α subunit of DNA PolIII. Eight DnaE mutants designed based on the literature data were overexpressed in S. lividans, and recombinant strains overexpressing two of these mutants displayed markedly increased frequency of spontaneous mutagenesis (up to 1000-fold higher compared to the control). One of these ‘mutators’ was combined in S. lividans with a biosensor specific for antibiotic coelimycin, which biosynthetic gene cluster is present but not expressed in this strain. Colonies giving a positive biosensor signal appeared at a frequency of ca 10–5, and all of them were found to produce coelimycin congeners. This result confirmed that our approach can be applied for chemical- and radiation-free mutagenesis in Streptomyces leading to activation of orphan biosynthetic gene clusters and discovery of novel bioactive secondary metabolites.
Collapse
Affiliation(s)
- Olga N Sekurova
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Yi-Qian Sun
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Austria
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Anna Stich
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Sergey B Zotchev
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| |
Collapse
|
36
|
Hoggard T, Hollatz AJ, Cherney RE, Seman MR, Fox CA. The Fkh1 Forkhead associated domain promotes ORC binding to a subset of DNA replication origins in budding yeast. Nucleic Acids Res 2021; 49:10207-10220. [PMID: 34095951 PMCID: PMC8501964 DOI: 10.1093/nar/gkab450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
The pioneer event in eukaryotic DNA replication is binding of chromosomal DNA by the origin recognitioncomplex (ORC). The ORC-DNA complex directs the formation of origins, the specific chromosomal regions where DNA synthesis initiates. In all eukaryotes, incompletely understood features of chromatin promote ORC-DNA binding. Here, we uncover a role for the Fkh1 (Forkhead homolog) protein and its forkhead associated (FHA) domain in promoting ORC-origin binding and origin activity at a subset of origins in Saccharomyces cerevisiae. Several of the FHA-dependent origins examined required a distinct Fkh1 binding site located 5′ of and proximal to their ORC sites (5′-FKH-T site). Genetic and molecular experiments provided evidence that the Fkh1-FHA domain promoted origin activity directly through Fkh1 binding to this 5′ FKH-T site. Nucleotide substitutions within two relevant origins that enhanced their ORC-DNA affinity bypassed the requirement for their 5′ FKH-T sites and for the Fkh1-FHA domain. Significantly, assessment of ORC-origin binding by ChIPSeq provided evidence that this mechanism was relevant at ∼25% of yeast origins. Thus, the FHA domain of the conserved cell-cycle transcription factor Fkh1 enhanced origin selection in yeast at the level of ORC-origin binding.
Collapse
Affiliation(s)
- Timothy Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Allison J Hollatz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Rachel E Cherney
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Melissa R Seman
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Catherine A Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| |
Collapse
|
37
|
Abstract
Chromosome segregation in eukaryotes is driven by the kinetochore, a macromolecular complex that connects centromeric DNA to microtubules of the spindle apparatus. Kinetochores in well-studied model eukaryotes consist of a core set of proteins that are broadly conserved among distant eukaryotic phyla. By contrast, unicellular flagellates of the class Kinetoplastida have a unique set of 36 kinetochore components. The evolutionary origin and history of these kinetochores remain unknown. Here, we report evidence of homology between axial element components of the synaptonemal complex and three kinetoplastid kinetochore proteins KKT16-18. The synaptonemal complex is a zipper-like structure that assembles between homologous chromosomes during meiosis to promote recombination. By using sensitive homology detection protocols, we identify divergent orthologues of KKT16-18 in most eukaryotic supergroups, including experimentally established chromosomal axis components, such as Red1 and Rec10 in budding and fission yeast, ASY3-4 in plants and SYCP2-3 in vertebrates. Furthermore, we found 12 recurrent duplications within this ancient eukaryotic SYCP2–3 gene family, providing opportunities for new functional complexes to arise, including KKT16-18 in the kinetoplastid parasite Trypanosoma brucei. We propose the kinetoplastid kinetochore system evolved by repurposing meiotic components of the chromosome synapsis and homologous recombination machinery that were already present in early eukaryotes.
Collapse
Affiliation(s)
- Eelco C Tromer
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Thomas A Wemyss
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Patryk Ludzia
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
| |
Collapse
|
38
|
Abstract
Human Nbs1, a component of the MRN complex involved in DNA double strand break repair, contains a concatenated N-terminal FHA-BRCT1/2 sequence that supports interaction with multiple phosphopeptide binding partners. MDC1 binding localizes Nbs1 to the damage site, while binding of CDK-phosphorylated CtIP activates additional ATM-dependent CtIP phosphorylation, modulating substrate-dependent resection. We have investigated the phosphopeptide binding characteristics of Nbs1 BRCT1/2 based on a molecular modeling approach that revealed structural homology with the tandem TopBP1 BRCT7/8 domains. Relevance of the model was substantiated by the ability of TopBP1-binding FANCJ phosphopeptide to interact with hsNbsBRCT1/2, albeit with lower affinity. The modeled BRCT1/2 is characterized by low pSer/pThr selectivity, preference for a cationic residue at the + 2 position, and an inter-domain binding cleft selective for hydrophobic residues at the + 3/ + 4 positions. These features provide insight into the basis for interaction of SDT motifs with the BRCT1/2 domains and allowed identification of CtIP pSer347- and pThr847-containing phosphopeptides as high and lower affinity ligands, respectively. Among other binding partners considered, rodent XRCC1 contains an SDT sequence in the second linker consistent with high-affinity Nbs1 binding, while human XRCC1 lacks this motif, but contains other phosphorylated sequences that exhibit low-affinity binding.
Collapse
Affiliation(s)
- Kyungmin Kim
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Thomas W Kirby
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA.
| |
Collapse
|
39
|
Liang CT, Roscow OMA, Zhang W. Recent developments in engineering protein-protein interactions using phage display. Protein Eng Des Sel 2021; 34:6297171. [PMID: 34117768 DOI: 10.1093/protein/gzab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Targeted inhibition of misregulated protein-protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. However, many constraints remain, including shallow binding surfaces and dynamic conformation changes upon interaction. A particularly challenging aspect is the undesirable off-target effects caused by inherent structural similarity among the protein families. To tackle this problem, phage display has been used to engineer PPIs for high-specificity binders with improved binding affinity and greatly reduced undesirable interactions with closely related proteins. Although general steps of phage display are standardized, library design is highly variable depending on experimental contexts. Here in this review, we examined recent advances in the structure-based combinatorial library design and the advantages and limitations of different approaches. The strategies described here can be explored for other protein-protein interactions and aid in designing new libraries or improving on previous libraries.
Collapse
Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Olivia M A Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, Ontario M5G1M1, Canada
| |
Collapse
|
40
|
Nishad S, Chauhan PK, Sowdhamini R, Ghosh A. Chronic exposure of humans to high level natural background radiation leads to robust expression of protective stress response proteins. Sci Rep 2021; 11:1777. [PMID: 33469066 DOI: 10.1038/s41598-020-80405-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding exposures to low doses of ionizing radiation are relevant since most environmental, diagnostic radiology and occupational exposures lie in this region. However, the molecular mechanisms that drive cellular responses at these doses, and the subsequent health outcomes, remain unclear. A local monazite-rich high level natural radiation area (HLNRA) in the state of Kerala on the south-west coast of Indian subcontinent show radiation doses extending from ≤ 1 to ≥ 45 mGy/y and thus, serve as a model resource to understand low dose mechanisms directly on healthy humans. We performed quantitative discovery proteomics based on multiplexed isobaric tags (iTRAQ) coupled with LC–MS/MS on human peripheral blood mononuclear cells from HLNRA individuals. Several proteins involved in diverse biological processes such as DNA repair, RNA processing, chromatin modifications and cytoskeletal organization showed distinct expression in HLNRA individuals, suggestive of both recovery and adaptation to low dose radiation. In protein–protein interaction (PPI) networks, YWHAZ (14-3-3ζ) emerged as the top-most hub protein that may direct phosphorylation driven pro-survival cellular processes against radiation stress. PPI networks also identified an integral role for the cytoskeletal protein ACTB, signaling protein PRKACA; and the molecular chaperone HSPA8. The data will allow better integration of radiation biology and epidemiology for risk assessment [Data are available via ProteomeXchange with identifier PXD022380].
Collapse
|
41
|
Montales K, Kim A, Ruis K, Michael WM. Structure-function analysis of TOPBP1's role in ATR signaling using the DSB-mediated ATR activation in Xenopus egg extracts (DMAX) system. Sci Rep 2021; 11:467. [PMID: 33432091 DOI: 10.1038/s41598-020-80626-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/23/2020] [Indexed: 11/20/2022] Open
Abstract
The protein kinase ATR is activated at sites of DNA double-strand breaks where it plays important roles in promoting DNA end resection and regulating cell cycle progression. TOPBP1 is a multi BRCT repeat containing protein that activates ATR at DSBs. Here we have developed an experimental tool, the DMAX system, to study the biochemical mechanism for TOPBP1-mediated ATR signalling. DMAX combines simple, linear dsDNA molecules with Xenopus egg extracts and results in a physiologically relevant, DSB-induced activation of ATR. We find that DNAs of 5000 nucleotides, at femtomolar concentration, potently activate ATR in this system. By combining immunodepletion and add-back of TOPBP1 point mutants we use DMAX to determine which of TOPBP1’s nine BRCT domains are required for recruitment of TOPBP1 to DSBs and which domains are needed for ATR-mediated phosphorylation of CHK1. We find that BRCT1 and BRCT7 are important for recruitment and that BRCT5 functions downstream of recruitment to promote ATR-mediated phosphorylation of CHK1. We also show that BRCT7 plays a second role, independent of recruitment, in promoting ATR signalling. These findings supply a new research tool for, and new insights into, ATR biology.
Collapse
|
42
|
Fraga de Andrade I, Mehta C, Bresnick EH. Post-transcriptional control of cellular differentiation by the RNA exosome complex. Nucleic Acids Res 2020; 48:11913-11928. [PMID: 33119769 PMCID: PMC7708067 DOI: 10.1093/nar/gkaa883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.
Collapse
Affiliation(s)
- Isabela Fraga de Andrade
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| |
Collapse
|
43
|
Ruan H, Kiselar J, Zhang W, Li S, Xiong R, Liu Y, Yang S, Lai L. Integrative structural modeling of a multidomain polo-like kinase. Phys Chem Chem Phys 2020; 22:27581-27589. [PMID: 33236741 DOI: 10.1039/d0cp05030j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polo-like kinase 1 (PLK1) is a key regulator and coordinator for mitotic signaling that contains two major functional units of a kinase domain (KD) and a polo-box domain (PBD). While individual domain structures of the KD and the PBD are known, how they interact and assemble into a functional complex remains an open question. The structural model from the KD-PBD-Map205PBM heterotrimeric crystal structure of zebrafish PLK1 represents a major step in understanding the KD and the PBD interactions. However, how these two domains interact when connected by a linker in the full length PLK1 needs further investigation. By integrating different sources of structural data from small-angle X-ray scattering, hydroxyl radical protein footprinting, and computational sampling, here we report an overall architecture for PLK1 multidomain assembly between the KD and the PBD. Our model revealed that the KD uses its C-lobe to interact with the PBD via the site near the phosphopeptide binding site in its auto-inhibitory state in solution. Disruption of this auto-inhibition via site-directed mutagenesis at the KD-PBD interface increases its kinase activity, supporting the functional role of KD-PBD interactions predicted for regulating the PLK1 kinase function. Our results indicate that the full length human PLK1 takes dynamic structures with a variety of domain-domain interfaces in solution.
Collapse
Affiliation(s)
- Hao Ruan
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Afdal P, Ismail HA, Ashraf M, Hafez N, Nasry N, Hafez N, Youssef N, Samy N, Saeed R, AbdelMassih AF. Peroxisome proliferator-activated receptor agonists and reversal of vascular degeneration through DNA repair, a step toward drug-induced regenerative medicine. Cardiovasc Endocrinol Metab 2020; 9:128-131. [PMID: 33225227 PMCID: PMC7673771 DOI: 10.1097/xce.0000000000000217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/28/2020] [Indexed: 11/27/2022]
Abstract
Endothelial dysfunction with subsequent degeneration and vasoocclusive remodeling is the hallmark of many cardiovascular disorders including pulmonary vascular disease (PVD). To date, the available treatments slows disease progression but does not prevent deterioration. Reversing such pathologies would spare many patients risky surgeries and long waiting lists for a possible organ donor. Peroxisome proliferator-activated receptor agonists were first introduced as sole insulin sensitizers, however, there is increasing body of evidence that they have different actions on DNA which might help reverse vascular degeneration. This effect appears to be mainly achieved through enhancement of DNA damage responses (DDR). The aforementioned effect could offer new insights about repurposing drugs for achieving organ or tissue regeneration, an understudied field named drug-induced regenerative medicine.
Collapse
Affiliation(s)
- Peter Afdal
- Students and Internship Research Program (Research Accessibility Team)
| | | | - Mirette Ashraf
- Students and Internship Research Program (Research Accessibility Team)
| | - Nada Hafez
- Students and Internship Research Program (Research Accessibility Team)
| | - Nardine Nasry
- Students and Internship Research Program (Research Accessibility Team)
| | - Nouran Hafez
- Students and Internship Research Program (Research Accessibility Team)
| | - Nourhan Youssef
- Students and Internship Research Program (Research Accessibility Team)
| | - Nourhan Samy
- Students and Internship Research Program (Research Accessibility Team)
| | - Rana Saeed
- Students and Internship Research Program (Research Accessibility Team)
| | | |
Collapse
|
45
|
Sandy Z, da Costa IC, Schmidt CK. More than Meets the ISG15: Emerging Roles in the DNA Damage Response and Beyond. Biomolecules 2020; 10:E1557. [PMID: 33203188 DOI: 10.3390/biom10111557] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Maintenance of genome stability is a crucial priority for any organism. To meet this priority, robust signalling networks exist to facilitate error-free DNA replication and repair. These signalling cascades are subject to various regulatory post-translational modifications that range from simple additions of chemical moieties to the conjugation of ubiquitin-like proteins (UBLs). Interferon Stimulated Gene 15 (ISG15) is one such UBL. While classically thought of as a component of antiviral immunity, ISG15 has recently emerged as a regulator of genome stability, with key roles in the DNA damage response (DDR) to modulate p53 signalling and error-free DNA replication. Additional proteomic analyses and cancer-focused studies hint at wider-reaching, uncharacterised functions for ISG15 in genome stability. We review these recent discoveries and highlight future perspectives to increase our understanding of this multifaceted UBL in health and disease.
Collapse
|
46
|
Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications. Curr Med Chem 2020; 27:6306-6355. [DOI: 10.2174/0929867326666190620101637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 12/15/2022]
Abstract
Background:
Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs).
Objective:
This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field.
Method:
Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed.
Results and Conclusion:
PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| |
Collapse
|
47
|
Sluchanko NN. Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins. Biochem J 2020; 477:1219-25. [PMID: 32271882 DOI: 10.1042/BCJ20200084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 12/24/2022]
Abstract
Many major protein-protein interaction networks are maintained by 'hub' proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that 'read' the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273-1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.
Collapse
|
48
|
Bröckelmann PJ, de Jong MRW, Jachimowicz RD. Targeting DNA Repair, Cell Cycle, and Tumor Microenvironment in B Cell Lymphoma. Cells 2020; 9:cells9102287. [PMID: 33066395 PMCID: PMC7602196 DOI: 10.3390/cells9102287] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 01/07/2023] Open
Abstract
The DNA double-strand break (DSB) is the most cytotoxic lesion and compromises genome stability. In an attempt to efficiently repair DSBs, cells activate ATM kinase, which orchestrates the DNA damage response (DDR) by activating cell cycle checkpoints and initiating DSB repair pathways. In physiological B cell development, however, programmed DSBs are generated as intermediates for effective immune responses and the maintenance of genomic integrity. Disturbances of these pathways are at the heart of B cell lymphomagenesis. Here, we review the role of DNA repair and cell cycle control on B cell development and lymphomagenesis. In addition, we highlight the intricate relationship between the DDR and the tumor microenvironment (TME). Lastly, we provide a clinical perspective by highlighting treatment possibilities of defective DDR signaling and the TME in mantle cell lymphoma, which serves as a blueprint for B cell lymphomas.
Collapse
Affiliation(s)
- Paul J. Bröckelmann
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany;
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), University of Cologne, 50937 Cologne, Germany
| | - Mathilde R. W. de Jong
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Ron D. Jachimowicz
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany;
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), University of Cologne, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence: ; Tel.: +49-(0)221-37970-580
| |
Collapse
|
49
|
Kim A, Montales K, Ruis K, Senebandith H, Gasparyan H, Cowan Q, Michael WM. Biochemical analysis of TOPBP1 oligomerization. DNA Repair (Amst) 2020; 96:102973. [PMID: 32987353 DOI: 10.1016/j.dnarep.2020.102973] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/20/2020] [Accepted: 09/09/2020] [Indexed: 11/24/2022]
Abstract
TOPBP1 is an important scaffold protein that helps orchestrate the cellular response to DNA damage. Although it has been previously appreciated that TOPBP1 can form oligomers, how this occurs and the functional consequences for oligomerization were not yet known. Here, we use protein binding assays and other biochemical techniques to study how TOPBP1 self associates. TOPBP1 contains 9 copies of the BRCT domain, and we report that a subset of these BRCT domains interact with one another to drive oligomerization. An intact BRCT 2 domain is required for TOPBP1 oligomerization and we find that the BRCT1&2 region of TOPBP1 interacts with itself and with the BRCT4&5 pair. RAD9 and RHINO are two heterologous binding partners for TOPBP1's BRCT 1&2 domains, and we show that binding of these partners does not come at the expense of TOPBP1 oligomerization. Furthermore, we show that a TOPBP1 oligomer can simultaneously interact with both RAD9 and RHINO. Lastly, we find that the oligomeric state necessary for TOPBP1 to activate the ATR protein kinase is likely to be a tetramer.
Collapse
|
50
|
Huang Y, Yang M, Huang W. 14-3-3 σ: A potential biomolecule for cancer therapy. Clin Chim Acta 2020; 511:50-8. [PMID: 32950519 DOI: 10.1016/j.cca.2020.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 12/22/2022]
Abstract
As more studies have focused on the function of 14-3-3 proteins, their role in tumor progression has gradually improved. In the 14-3-3 protein family, 14-3-3σ is the protein that is most associated with tumor occurrence and development. In some malignancies, 14-3-3σ acts as a tumor suppressor via p53 and tumor suppressor genes. In most tumors, 14-3-3σ overexpression increases resistance to chemotherapy and radiotherapy and mediates the G2-M checkpoint after DNA damage. Although 14-3-3σ overexpression has been closely associated with poorer prognosis in pancreatic, gastric and colorectal cancer, its role in gallbladder and nasopharyngeal cancer remains less clear. As such, the function of 14-3-3σ in specific cancer types needs to be further clarified. It has been hypothesized that a role may be related to its molecular chaperone function combined with various protein ligands. In this review, we examine the role of 14-3-3σ in tumor development and drug resistance. We discuss the potential of targeting 14-3-3σ regulators in cancer therapy and treatment.
Collapse
|