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Han P, Zhang R, Li R, Li F, Huang L. Identification of an SCF Ubiquitin Ligase Complex that Contributes to Resistance Against Valsa Canker in Apple. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:520-529. [PMID: 38470518 DOI: 10.1094/mpmi-12-23-0206-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
E3 ubiquitin ligases play a critical role in plant disease resistance. Among them, the Skp1-Cullin-F-box protein (SCF) ubiquitin ligase complex is the largest family and regulates the ubiquitination of a wide range of proteins. Apple Valsa canker (AVC) is a fungal disease of apple trees caused by the fungus Valsa mali, which can lead to significant economic losses. However, the function of the SCF complex in apple resistance to this disease is still largely unknown. In this study, we identified an SCF ubiquitin ligase complex that can enhance resistance to Valsa canker in apple. Disease evaluation experiments demonstrated that MdSkp1 increased apple resistance to AVC. Furthermore, MdSkp1 interacted with an F-box protein, MdSKIP14, and interacted with a cullin-1 protein, MdCUL1, to form an SCF ubiquitin ligase complex. Additionally, we revealed both MdSKIP14 and MdCUL1 as positive regulators of AVC resistance. In conclusion, our results identified an SCF complex capable of contributing to apple resistance against AVC, providing a theoretical basis for apple disease resistance and the sustainable development of the industry. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Pengliang Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruotong Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fudong Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lili Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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2
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An J, Zhang X. Crbn-based molecular Glues: Breakthroughs and perspectives. Bioorg Med Chem 2024; 104:117683. [PMID: 38552596 DOI: 10.1016/j.bmc.2024.117683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
CRBN is a substrate receptor for the Cullin Ring E3 ubiquitin ligase 4 (CRL4) complex. It has been observed that CRBN can be exploited by small molecules to facilitate the recruitment and ubiquitination of non-natural CRL4 substrates, resulting in the degradation of neosubstrate through the ubiquitin-proteasome system. This phenomenon, known as molecular glue-induced protein degradation, has emerged as an innovative therapeutic approach in contrast to traditional small-molecule drugs. One key advantage of molecular glues, in comparison to conventional small-molecule drugs adhering to Lipinski's Rule of Five, is their ability to operate without the necessity for specific binding pockets on target proteins. This unique characteristic empowers molecular glues to interact with conventionally intractable protein targets, such as transcription factors and scaffold proteins. The ability to induce the degradation of these previously elusive targets by hijacking the ubiquitin-proteasome system presents a promising avenue for the treatment of recalcitrant diseases. Nevertheless, the rational design of molecular glues remains a formidable challenge due to the limited understanding of their mechanisms and actions. This review offers an overview of recent advances and breakthroughs in the field of CRBN-based molecular glues, while also exploring the prospects for a systematic approach to designing these compounds.
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Affiliation(s)
- Juzeng An
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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3
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Li Z, Chen J, Huang H, Zhan Q, Wang F, Chen Z, Lu X, Sun G. Post-translational modifications in diabetic cardiomyopathy. J Cell Mol Med 2024; 28:e18158. [PMID: 38494853 PMCID: PMC10945092 DOI: 10.1111/jcmm.18158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024] Open
Abstract
The increasing attention towards diabetic cardiomyopathy as a distinctive complication of diabetes mellitus has highlighted the need for standardized diagnostic criteria and targeted treatment approaches in clinical practice. Ongoing research is gradually unravelling the pathogenesis of diabetic cardiomyopathy, with a particular emphasis on investigating various post-translational modifications. These modifications dynamically regulate protein function in response to changes in the internal and external environment, and their disturbance of homeostasis holds significant relevance for the development of chronic ailments. This review provides a comprehensive overview of the common post-translational modifications involved in the initiation and progression of diabetic cardiomyopathy, including O-GlcNAcylation, phosphorylation, methylation, acetylation and ubiquitination. Additionally, the review discusses drug development strategies for targeting key post-translational modification targets, such as agonists, inhibitors and PROTAC (proteolysis targeting chimaera) technology that targets E3 ubiquitin ligases.
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Affiliation(s)
- Zhi Li
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Jie Chen
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Hailong Huang
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Qianru Zhan
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Fengzhi Wang
- Department of Neurology, People's Hospital of Liaoning ProvincePeople's Hospital of China Medical UniversityShenyangChina
| | - Zihan Chen
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Xinwei Lu
- Department of CardiologySiping Central People's HospitalSipingChina
| | - Guozhe Sun
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
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4
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Lei Y, Yu H, Ding S, Liu H, Liu C, Fu R. Molecular mechanism of ATF6 in unfolded protein response and its role in disease. Heliyon 2024; 10:e25937. [PMID: 38434326 PMCID: PMC10907738 DOI: 10.1016/j.heliyon.2024.e25937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/04/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024] Open
Abstract
Activating transcription factor 6 (ATF6), an important signaling molecule in unfolded protein response (UPR), plays a role in the pathogenesis of several diseases, including diseases such as congenital retinal disease, liver fibrosis and ankylosing spondylitis. After endoplasmic reticulum stress (ERS), ATF6 is activated after separation from binding immunoglobulin protein (GRP78/BiP) in the endoplasmic reticulum (ER) and transported to the Golgi apparatus to be hydrolyzed by site 1 and site 2 proteases into ATF6 fragments, which localize to the nucleus and regulate the transcription and expression of ERS-related genes. In these diseases, ERS leads to the activation of UPR, which ultimately lead to the occurrence and development of diseases by regulating the physiological state of cells through the ATF6 signaling pathway. Here, we discuss the evidence for the pathogenic importance of ATF6 signaling in different diseases and discuss preclinical results.
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Affiliation(s)
| | | | - Shaoxue Ding
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Hui Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Chunyan Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
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5
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Iyer-Bierhoff A, Wieczorek M, Peter SM, Ward D, Bens M, Vettorazzi S, Guehrs KH, Tuckermann JP, Heinzel T. Acetylation-induced proteasomal degradation of the activated glucocorticoid receptor limits hormonal signaling. iScience 2024; 27:108943. [PMID: 38333702 PMCID: PMC10850750 DOI: 10.1016/j.isci.2024.108943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Glucocorticoid (GC) signaling is essential for mounting a stress response, however, chronic stress or prolonged GC therapy downregulates the GC receptor (GR), leading to GC resistance. Regulatory mechanisms that refine this equilibrium are not well understood. Here, we identify seven lysine acetylation sites in the amino terminal domain of GR, with lysine 154 (Lys154) in the AF-1 region being the dominant acetyl-acceptor. GR-Lys154 acetylation is mediated by p300/CBP in the nucleus in an agonist-dependent manner and correlates with transcriptional activity. Deacetylation by NAD+-dependent SIRT1 facilitates dynamic regulation of this mark. Notably, agonist-binding to both wild-type GR and an acetylation-deficient mutant elicits similar short-term target gene expression. In contrast, upon extended treatment, the polyubiquitination of the acetylation-deficient GR mutant is impaired resulting in higher protein stability, increased chromatin association and prolonged transactivation. Taken together, reversible acetylation fine-tunes duration of the GC response by regulating proteasomal degradation of activated GR.
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Affiliation(s)
- Aishwarya Iyer-Bierhoff
- Institute of Biochemistry and Biophysics, Centre for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Martin Wieczorek
- Institute of Biochemistry and Biophysics, Centre for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Sina Marielle Peter
- Institute of Biochemistry and Biophysics, Centre for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Dima Ward
- Institute of Biochemistry and Biophysics, Centre for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Martin Bens
- Core Facility Next Generation Sequencing, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Sabine Vettorazzi
- Institute of Comparative Molecular Endocrinology (CME), Ulm University, Helmholtzstrasse 8/1, 89081 Ulm, Germany
| | - Karl-Heinz Guehrs
- Core Facility Proteomics, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Jan P. Tuckermann
- Institute of Comparative Molecular Endocrinology (CME), Ulm University, Helmholtzstrasse 8/1, 89081 Ulm, Germany
| | - Thorsten Heinzel
- Institute of Biochemistry and Biophysics, Centre for Molecular Biomedicine (CMB), Friedrich Schiller University, Hans-Knoell-Strasse 2, 07745 Jena, Germany
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6
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Sepulveda GP, Gushchanskaia ES, Mora-Martin A, Esse R, Nikorich I, Ceballos A, Kwan J, Blum BC, Dholiya P, Emili A, Perissi V, Cardamone MD, Grishok A. DOT1L stimulates MYC/Mondo transcription factor activity by promoting its degradation cycle on chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579191. [PMID: 38370658 PMCID: PMC10871221 DOI: 10.1101/2024.02.06.579191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The proto-oncogene c-MYC is a key representative of the MYC transcription factor network regulating growth and metabolism. MML-1 (Myc- and Mondo-like) is its homolog in C. elegans. The functional and molecular cooperation between c-MYC and H3 lysine 79 methyltransferase DOT1L was demonstrated in several human cancer types, and we have earlier discovered the connection between C. elegans MML-1 and DOT-1.1. Here, we demonstrate the critical role of DOT1L/DOT-1.1 in regulating c-MYC/MML-1 target genes genome-wide by ensuring the removal of "spent" transcription factors from chromatin by the nuclear proteasome. Moreover, we uncover a previously unrecognized proteolytic activity of DOT1L, which may facilitate c-MYC turnover. This new mechanism of c-MYC regulation by DOT1L may lead to the development of new approaches for cancer treatment.
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Affiliation(s)
- Gian P. Sepulveda
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ekaterina S. Gushchanskaia
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Tessera Therapeutics, Somerville, MA, 02143, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Ruben Esse
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Cell and Gene Therapy Catapult, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Iana Nikorich
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ainhoa Ceballos
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Present address: Research Unit, Diagnostica Longwood S.L. 50011 Zaragoza, Spain
| | - Julian Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Benjamin C. Blum
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Prakruti Dholiya
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrew Emili
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
- Division of Computational Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: OHSU Knight Cancer Institute, School of Medicine, Portland, OR, 97239, USA
| | - Valentina Perissi
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Maria D. Cardamone
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Korro Bio Inc., Cambridge, MA, 02139, USA
| | - Alla Grishok
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Genome Science Institute, Boston University, Boston, MA, 02118, USA
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7
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Lumahan LEV, Arif M, Whitener AE, Yi P. Regulating Androgen Receptor Function in Prostate Cancer: Exploring the Diversity of Post-Translational Modifications. Cells 2024; 13:191. [PMID: 38275816 PMCID: PMC10814774 DOI: 10.3390/cells13020191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Androgen receptor (AR) transcriptional activity significantly influences prostate cancer (PCa) progression. In addition to ligand stimulation, AR transcriptional activity is also influenced by a variety of post-translational modifications (PTMs). A number of oncogenes and tumor suppressors have been observed leveraging PTMs to influence AR activity. Subjectively targeting these post-translational modifiers based on their impact on PCa cell proliferation is a rapidly developing area of research. This review elucidates the modifiers, contextualizes the effects of these PTMs on AR activity, and connects these cellular interactions to the progression of PCa.
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Affiliation(s)
- Lance Edward V. Lumahan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77204, USA
| | - Mazia Arif
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77205, USA
| | - Amy E. Whitener
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77205, USA
| | - Ping Yi
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77205, USA
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8
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Sharma M, Sidhu AK, Samota MK, Gupta M, Koli P, Choudhary M. Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants. Proteomes 2023; 11:38. [PMID: 38133152 PMCID: PMC10747722 DOI: 10.3390/proteomes11040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Abiotic stresses profoundly alter plant growth and development, resulting in yield losses. Plants have evolved adaptive mechanisms to combat these challenges, triggering intricate molecular responses to maintain tissue hydration and temperature stability during stress. A pivotal player in this defense is histone modification, governing gene expression in response to diverse environmental cues. Post-translational modifications (PTMs) of histone tails, including acetylation, phosphorylation, methylation, ubiquitination, and sumoylation, regulate transcription, DNA processes, and stress-related traits. This review comprehensively explores the world of PTMs of histones in plants and their vital role in imparting various abiotic stress tolerance in plants. Techniques, like chromatin immune precipitation (ChIP), ChIP-qPCR, mass spectrometry, and Cleavage Under Targets and Tag mentation, have unveiled the dynamic histone modification landscape within plant cells. The significance of PTMs in enhancing the plants' ability to cope with abiotic stresses has also been discussed. Recent advances in PTM research shed light on the molecular basis of stress tolerance in plants. Understanding the intricate proteome complexity due to various proteoforms/protein variants is a challenging task, but emerging single-cell resolution techniques may help to address such challenges. The review provides the future prospects aimed at harnessing the full potential of PTMs for improved plant responses under changing climate change.
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Affiliation(s)
- Madhvi Sharma
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Amanpreet K. Sidhu
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Mahesh Kumar Samota
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Regional Station, Abohar 152116, India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
| | - Pushpendra Koli
- Plant Animal Relationship Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi 284003, India;
- Post-Harvest Biosecurity, Murdoch University, Perth, WA 6150, Australia
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
- School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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9
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Yao L, Jiang Z, Wang Y, Hu Y, Hao G, Zhong W, Wan S, Xin X. High air humidity dampens salicylic acid pathway and NPR1 function to promote plant disease. EMBO J 2023; 42:e113499. [PMID: 37728254 PMCID: PMC10620762 DOI: 10.15252/embj.2023113499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
The occurrence of plant disease is determined by interactions among host, pathogen, and environment. Air humidity shapes various aspects of plant physiology and high humidity has long been known to promote numerous phyllosphere diseases. However, the molecular basis of how high humidity interferes with plant immunity to favor disease has remained elusive. Here we show that high humidity is associated with an "immuno-compromised" status in Arabidopsis plants. Furthermore, accumulation and signaling of salicylic acid (SA), an important defense hormone, are significantly inhibited under high humidity. NPR1, an SA receptor and central transcriptional co-activator of SA-responsive genes, is less ubiquitinated and displays a lower promoter binding affinity under high humidity. The cellular ubiquitination machinery, particularly the Cullin 3-based E3 ubiquitin ligase mediating NPR1 protein ubiquitination, is downregulated under high humidity. Importantly, under low humidity the Cullin 3a/b mutant plants phenocopy the low SA gene expression and disease susceptibility that is normally observed under high humidity. Our study uncovers a mechanism by which high humidity dampens a major plant defense pathway and provides new insights into the long-observed air humidity influence on diseases.
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Affiliation(s)
- Lingya Yao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Zeyu Jiang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yiping Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yezhou Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Guodong Hao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Weili Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Shiwei Wan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Xiu‐Fang Xin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
- Chinese Academy of Sciences (CAS) and CAS John Innes Centre of Excellence for Plant and Microbial SciencesShanghaiChina
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10
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Bonnet DMV, Tirot L, Grob S, Jullien PE. Methylome Response to Proteasome Inhibition by Pseudomonas syringae Virulence Factor Syringolin A. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:693-704. [PMID: 37414416 DOI: 10.1094/mpmi-06-23-0080-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
DNA methylation is an important epigenetic mark required for proper gene expression and silencing of transposable elements. DNA methylation patterns can be modified by environmental factors such as pathogen infection, in which modification of DNA methylation can be associated with plant resistance. To counter the plant defense pathways, pathogens produce effector molecules, several of which act as proteasome inhibitors. Here, we investigated the effect of proteasome inhibition by the bacterial virulence factor syringolin A (SylA) on genome-wide DNA methylation. We show that SylA treatment results in an increase of DNA methylation at centromeric and pericentromeric regions of Arabidopsis chromosomes. We identify several CHH differentially methylated regions (DMRs) that are enriched in the proximity of transcriptional start sites. SylA treatment does not result in significant changes in small RNA composition. However, significant changes in genome transcriptional activity can be observed, including a strong upregulation of resistance genes that are located on chromosomal arms. We hypothesize that DNA methylation changes could be linked to the upregulation of some atypical members of the de novo DNA methylation pathway, namely AGO3, AGO9, and DRM1. Our data suggests that modification of genome-wide DNA methylation resulting from an inhibition of the proteasome by bacterial effectors could be part of an epi-genomic arms race against pathogens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Louis Tirot
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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11
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Rieu P, Arnoux-Courseaux M, Tichtinsky G, Parcy F. Thinking outside the F-box: how UFO controls angiosperm development. THE NEW PHYTOLOGIST 2023; 240:945-959. [PMID: 37664990 DOI: 10.1111/nph.19234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023]
Abstract
The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Moïra Arnoux-Courseaux
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
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12
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Lee Z, Kim S, Choi SJ, Joung E, Kwon M, Park HJ, Shim JS. Regulation of Flowering Time by Environmental Factors in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3680. [PMID: 37960036 PMCID: PMC10649094 DOI: 10.3390/plants12213680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
The timing of floral transition is determined by both endogenous molecular pathways and external environmental conditions. Among these environmental conditions, photoperiod acts as a cue to regulate the timing of flowering in response to seasonal changes. Additionally, it has become clear that various environmental factors also control the timing of floral transition. Environmental factor acts as either a positive or negative signal to modulate the timing of flowering, thereby establishing the optimal flowering time to maximize the reproductive success of plants. This review aims to summarize the effects of environmental factors such as photoperiod, light intensity, temperature changes, vernalization, drought, and salinity on the regulation of flowering time in plants, as well as to further explain the molecular mechanisms that link environmental factors to the internal flowering time regulation pathway.
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Affiliation(s)
- Zion Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea; (Z.L.); (S.K.); (S.J.C.); (E.J.)
| | - Sohyun Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea; (Z.L.); (S.K.); (S.J.C.); (E.J.)
| | - Su Jeong Choi
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea; (Z.L.); (S.K.); (S.J.C.); (E.J.)
| | - Eui Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea; (Z.L.); (S.K.); (S.J.C.); (E.J.)
| | - Moonhyuk Kwon
- Division of Life Science, ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Hee Jin Park
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea; (Z.L.); (S.K.); (S.J.C.); (E.J.)
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju 61186, Republic of Korea
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13
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Pispa J, Mikkonen E, Arpalahti L, Jin C, Martínez-Fernández C, Cerón J, Holmberg CI. AKIR-1 regulates proteasome subcellular function in Caenorhabditis elegans. iScience 2023; 26:107886. [PMID: 37767001 PMCID: PMC10520889 DOI: 10.1016/j.isci.2023.107886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Polyubiquitinated proteins are primarily degraded by the ubiquitin-proteasome system (UPS). Proteasomes are present both in the cytoplasm and nucleus. Here, we investigated mechanisms coordinating proteasome subcellular localization and activity in a multicellular organism. We identified the nuclear protein-encoding gene akir-1 as a proteasome regulator in a genome-wide Caenorhabditis elegans RNAi screen. We demonstrate that depletion of akir-1 causes nuclear accumulation of endogenous polyubiquitinated proteins in intestinal cells, concomitant with slower in vivo proteasomal degradation in this subcellular compartment. Remarkably, akir-1 is essential for nuclear localization of proteasomes both in oocytes and intestinal cells but affects differentially the subcellular distribution of polyubiquitinated proteins. We further reveal that importin ima-3 genetically interacts with akir-1 and influences nuclear localization of a polyubiquitin-binding reporter. Our study shows that the conserved AKIR-1 is an important regulator of the subcellular function of proteasomes in a multicellular organism, suggesting a role for AKIR-1 in proteostasis maintenance.
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Affiliation(s)
- Johanna Pispa
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Elisa Mikkonen
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Leena Arpalahti
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Congyu Jin
- Department of Anatomy, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Carmen Martínez-Fernández
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Julián Cerón
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carina I. Holmberg
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
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14
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Dheekollu J, Wiedmer A, Soldan SS, Castro- Muñoz LJ, Chen C, Tang HY, Speicher DW, Lieberman PM. Regulation of EBNA1 protein stability and DNA replication activity by PLOD1 lysine hydroxylase. PLoS Pathog 2023; 19:e1010478. [PMID: 37262099 PMCID: PMC10263308 DOI: 10.1371/journal.ppat.1010478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/13/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023] Open
Abstract
Epstein-Barr virus (EBV) is a ubiquitous human γ-herpesvirus that is causally associated with various malignancies and autoimmune disease. Epstein-Barr Nuclear Antigen 1 (EBNA1) is the viral-encoded DNA binding protein required for viral episome maintenance and DNA replication during latent infection in proliferating cells. EBNA1 is known to be a highly stable protein, but the mechanisms regulating protein stability and how this may be linked to EBNA1 function is not fully understood. Proteomic analysis of EBNA1 revealed interaction with Procollagen Lysine-2 Oxoglutarate 5 Dioxygenase (PLOD) family of proteins. Depletion of PLOD1 by shRNA or inhibition with small molecule inhibitors 2,-2' dipyridyl resulted in the loss of EBNA1 protein levels, along with a selective growth inhibition of EBV-positive lymphoid cells. PLOD1 depletion also caused a loss of EBV episomes from latently infected cells and inhibited oriP-dependent DNA replication. Mass spectrometry identified EBNA1 peptides with lysine hydroxylation at K460 or K461. Mutation of K460, but not K461 abrogates EBNA1-driven DNA replication of oriP, but did not significantly affect EBNA1 DNA binding. Mutations in both K460 and K461 perturbed interactions with PLOD1, as well as decreased EBNA1 protein stability. These findings suggest that PLOD1 is a novel interaction partner of EBNA1 that regulates EBNA1 protein stability and function in viral plasmid replication, episome maintenance and host cell survival.
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Affiliation(s)
- Jayaraju Dheekollu
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Andreas Wiedmer
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Samantha S. Soldan
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | | | - Christopher Chen
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - David W. Speicher
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
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15
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Marchena-Cruz E, Camino LP, Bhandari J, Silva S, Marqueta-Gracia JJ, Amdeen SA, Guillén-Mendoza C, García-Rubio ML, Calderón-Montaño JM, Xue X, Luna R, Aguilera A. DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops. Cell Rep 2023; 42:112148. [PMID: 36827184 PMCID: PMC10066596 DOI: 10.1016/j.celrep.2023.112148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is an R-loop resolvase, whereas the MeCP2 methyl-CpG-binding protein uncovers a link between DNA methylation and R loops. Thus, our results suggest that a plethora of gene dysfunctions can alter cell physiology via affecting R-loop homeostasis by different mechanisms.
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Affiliation(s)
- Esther Marchena-Cruz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Lola P Camino
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Jay Bhandari
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Sónia Silva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - José Javier Marqueta-Gracia
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Shahad A Amdeen
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Cristina Guillén-Mendoza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - José M Calderón-Montaño
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Xiaoyu Xue
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
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16
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Klaus L, de Almeida BP, Vlasova A, Nemčko F, Schleiffer A, Bergauer K, Hofbauer L, Rath M, Stark A. Systematic identification and characterization of repressive domains in Drosophila transcription factors. EMBO J 2023; 42:e112100. [PMID: 36545802 PMCID: PMC9890238 DOI: 10.15252/embj.2022112100] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA-binding transcription factors that mediate activation and repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied: the identities and properties of their repressive domains (RDs) are typically unknown and the specific co-repressors (CoRs) they recruit have not been determined. Here, we develop a high-throughput, next-generation sequencing-based screening method, repressive-domain (RD)-seq, to systematically identify RDs in complex DNA-fragment libraries. Screening more than 200,000 fragments covering the coding sequences of all transcription-related proteins in Drosophila melanogaster, we identify 195 RDs in known repressors and in proteins not previously associated with repression. Many RDs contain recurrent short peptide motifs, which are conserved between fly and human and are required for RD function, as demonstrated by motif mutagenesis. Moreover, we show that RDs that contain one of five distinct repressive motifs interact with and depend on different CoRs, such as Groucho, CtBP, Sin3A, or Smrter. These findings advance our understanding of repressors, their sequences, and the functional impact of sequence-altering mutations and should provide a valuable resource for further studies.
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Affiliation(s)
- Loni Klaus
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Bernardo P de Almeida
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Filip Nemčko
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Katharina Bergauer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Lorena Hofbauer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Martina Rath
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Medical University of ViennaVienna BioCenter (VBC)ViennaAustria
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17
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Rieu P, Turchi L, Thévenon E, Zarkadas E, Nanao M, Chahtane H, Tichtinsky G, Lucas J, Blanc-Mathieu R, Zubieta C, Schoehn G, Parcy F. The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements. NATURE PLANTS 2023; 9:315-329. [PMID: 36732360 DOI: 10.1038/s41477-022-01336-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
In angiosperms, flower development requires the combined action of the transcription factor LEAFY (LFY) and the ubiquitin ligase adaptor F-box protein, UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show in transient assays and stable transgenic plants that the connection to ubiquitination pathways suggested by the UFO F-box domain is mostly dispensable. On the basis of biochemical and genome-wide studies, we establish that UFO instead acts by forming an active transcriptional complex with LFY at newly discovered regulatory elements. Structural characterization of the LFY-UFO-DNA complex by cryo-electron microscopy further demonstrates that UFO performs this function by directly interacting with both LFY and DNA. Finally, we propose that this complex might have a deep evolutionary origin, largely predating flowering plants. This work reveals a unique mechanism of an F-box protein directly modulating the DNA binding specificity of a master transcription factor.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
- Translational Innovation in Medicine and Complexity, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Emmanuel Thévenon
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Eleftherios Zarkadas
- IBS, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
- EMBL, ISBG, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Max Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
- Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Institut de Recherche Pierre Fabre, Soual, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Guy Schoehn
- IBS, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France.
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18
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Lalnunthangi A, Dakpa G, Tiwari S. Multifunctional role of the ubiquitin proteasome pathway in phagocytosis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 194:179-217. [PMID: 36631192 DOI: 10.1016/bs.pmbts.2022.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Phagocytosis is a specialized form of endocytosis where large cells and particles (>0.5μm) are engulfed by the phagocytic cells, and ultimately digested in the phagolysosomes. This process not only eliminates unwanted particles and pathogens from the extracellular sources, but also eliminates apoptotic cells within the body, and is critical for maintenance of tissue homeostasis. It is believed that both endocytosis and phagocytosis share common pathways after particle internalization, but specialized features and differences between these two routes of internalization are also likely. The recruitment and removal of each protein/particle during the maturation of endocytic/phagocytic vesicles has to be tightly regulated to ensure their timely action. Ubiquitin proteasome pathway (UPP), degrades unwanted proteins by post-translational modification of proteins with chains of conserved protein Ubiquitin (Ub), with subsequent recognition of Ub chains by the 26S proteasomes and substrate degradation by this protease. This pathway utilizes different Ub linkages to modify proteins to regulate protein-protein interaction, localization, and activity. Due to its vast number of targets, it is involved in many cellular pathways, including phagocytosis. This chapters describes the basic steps and signaling in phagocytosis and different roles that UPP plays at multiple steps in regulating phagocytosis directly, or through its interaction with other phagosomal proteins. How aberrations in UPP function affect phagocytosis and their association with human diseases, and how pathogens exploit this pathway for their own benefit is also discussed.
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Affiliation(s)
| | | | - Swati Tiwari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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19
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Shang K, Zhang L, Yu Y, Xiao H, Gao Y, Yang L, Huang J, Song H, Han H. Disulfide-containing polymer delivery of C527 and a Platinum(IV) prodrug selectively inhibited protein ubiquitination and tumor growth on cisplatin resistant and patient-derived liver cancer models. Mater Today Bio 2023; 18:100548. [PMID: 36713799 PMCID: PMC9874064 DOI: 10.1016/j.mtbio.2023.100548] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
USP1 (Ubiquitin-specific protease 1) is closely related to the prognosis of patients with liver cancer and plays an important role in DNA damage repair. C527 is a selective USP1 inhibitor (USP1i), which can regulate the protein ubiquitination to effectively inhibit the proliferation of cancer cells. However, its clinical application is hindered due to the poor water solubility and lack of tumor targeting. Moreover, the efficacy of single use of USP1i is still limited. Herein, a glutathione (GSH) sensitive amphiphilic polymer (poly (2-HD-co-HPMDA)-mPEG, PHHM) with disulfide bonds in the main chain was designed to encapsulate the USP1i as well as platinum (IV) prodrug (Pt (IV)-C12), resulting in the formation of composite nanoparticles, i.e., NP-Pt-USP1i. NP-Pt-USP1i can inhibit the DNA damage repair by targeting USP1 by the encapsulated USP1i, which ultimately increases the sensitivity of tumor cells to cisplatin and enhances the anti-cancer efficacy of cisplatin. Finally, an intraperitoneal tumor mice model and a patient-derived xenograft (PDX) of liver cancer mice model were established to prove that NP-Pt-USP1i could effectively inhibit the tumor growth. This work further validated the possibility of therapeutically target USP1 by USP1i in combination with DNA damaging alkylating agents, which could become a promising cancer treatment modality in the future.
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Affiliation(s)
- Kun Shang
- Institute of Medical Technology, Peking University Health Science Center, Beijing, 100191, China
| | - Lingpu Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yingjie Yu
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Science, Beijing, 100190, China,Corresponding author.
| | - Yajuan Gao
- Department of Radiology, Peking University Third Hospital, Beijing, 100191, China,NMPA key Laboratory for Evaluation of Medical Imaging Equipment and Technique, Beijing, 100191, China
| | - Liu Yang
- Department of Radiology, Peking University Third Hospital, Beijing, 100191, China,Beijing Key Laboratory of Magnetic Resonance Imaging Devices and Technology, Peking University Third Hospital, Beijing, 100191, China
| | - Jia Huang
- Department of Hepatobiliary Surgery, China-Japan Friendship Hospital, Beijing, 100029, China,Corresponding author.
| | - Haiqin Song
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 20023, China,Corresponding author.
| | - Hongbin Han
- Department of Radiology, Peking University Third Hospital, Beijing, 100191, China,Peking University Shenzhen Graduate School, Shenzhen, 518055, China,Corresponding author. Department of Radiology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China.
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20
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Kołat D, Zhao LY, Kciuk M, Płuciennik E, Kałuzińska-Kołat Ż. AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization. Cells 2022; 11:cells11244124. [PMID: 36552887 PMCID: PMC9776946 DOI: 10.3390/cells11244124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/26/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Formerly hailed as "undruggable" proteins, transcription factors (TFs) are now under investigation for targeted therapy. In cancer, this may alter, inter alia, immune evasion or replicative immortality, which are implicated in genome organization, a process that accompanies multi-step tumorigenesis and which frequently develops in a non-random manner. Still, targeting-related research on some TFs is scarce, e.g., among AP-2 proteins, which are known for their altered functionality in cancer and prognostic importance. Using public repositories, bioinformatics tools, and RNA-seq data, the present study examined the ligandability of all AP-2 members, selecting the best one, which was investigated in terms of mutations, targets, co-activators, correlated genes, and impact on genome organization. AP-2 proteins were found to have the conserved "TF_AP-2" domain, but manifested different binding characteristics and evolution. Among them, AP-2δ has not only the highest number of post-translational modifications and extended strands but also contains a specific histidine-rich region and cleft that can receive a ligand. Uterine, colon, lung, and stomach tumors are most susceptible to AP-2δ mutations, which also co-depend with cancer hallmark genes and drug targets. Considering AP-2δ targets, some of them were located proximally in the spatial genome or served as co-factors of the genes regulated by AP-2δ. Correlation and functional analyses suggested that AP-2δ affects various processes, including genome organization, via its targets; this has been eventually verified in lung adenocarcinoma using expression and immunohistochemistry data of chromosomal conformation-related genes. In conclusion, AP-2δ affects chromosomal conformation and is the most appropriate target for cancer therapy focused on the AP-2 family.
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Affiliation(s)
- Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, 90-136 Lodz, Poland
- Correspondence:
| | - Lin-Yong Zhao
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu 610041, China
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, 90-752 Lodz, Poland
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21
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Disruption of male fertility-critical Dcaf17 dysregulates mouse testis transcriptome. Sci Rep 2022; 12:21456. [PMID: 36509865 PMCID: PMC9744869 DOI: 10.1038/s41598-022-25826-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
During mammalian spermatogenesis, the ubiquitin proteasome system maintains protein homoeostasis (proteastasis) and spermatogenic cellular functions. DCAF17 is a substrate receptor in the ubiquitin CRL4 E3 Ligase complex, absence of which causes oligoasthenoteratozoospermia in mice resulting in male infertility. To determine the molecular phenomenon underlying the infertility phenotype caused by disrupting Dcaf17, we performed RNA-sequencing-based gene expression profiling of 3-weeks and 8-weeks old Dcaf17 wild type and Dcaf17 disrupted mutant mice testes. At three weeks, 44% and 56% differentially expressed genes (DEGs) were up- and down-regulated, respectively, with 32% and 68% DEGs were up- and down-regulated, respectively at 8 weeks. DEGs include protein coding genes and lncRNAs distributed across all autosomes and the X chromosome. Gene ontology analysis revealed major biological processes including proteolysis, regulation of transcription and chromatin remodelling are affected due to Dcaf17 disruption. We found that Dcaf17 disruption up-regulated several somatic genes, while germline-associated genes were down-regulated. Up to 10% of upregulated, and 12% of downregulated, genes were implicated in male reproductive phenotypes. Moreover, a large proportion of the up-regulated genes were highly expressed in spermatogonia and spermatocytes, while the majority of downregulated genes were predominantly expressed in round spermatids. Collectively, these data show that the Dcaf17 disruption affects directly or indirectly testicular proteastasis and transcriptional signature in mouse.
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22
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Niu X, Lu H, Fan Y, Wang W, Yuan Y, Hawkins M, Zhang J, Ye Z, Miao M, Liu Y, Xiao F. Manipulation of the transcription factor SlNAC1 for improved tolerance to abiotic stress in tomato. PLANT, CELL & ENVIRONMENT 2022; 45:3537-3550. [PMID: 36128662 DOI: 10.1111/pce.14437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/15/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The tomato transcription factor SlNAC1 plays an important role in abiotic stress response and is fine-tuned at both transcriptional and posttranslational levels. The SlNAC1 gene is strongly induced by multiple abiotic stresses and the SlNAC1 protein is subjected to ubiquitin proteasome-mediated degradation. We found here that SlNAC1 possesses two distinct transactivation domains (TADs), TAD1 and TAD2. Significantly, the instability of SlNAC1 was attributed to the acidic amino acid-rich TAD1, in which the instability and transcriptional potential of TAD1 functionally overlapped; whereas the glutamine-rich TAD2 was stable and accounted for the abiotic stress signalling mediated by SlNAC1. Towards the goal of enhanced tolerance to abiotic stress in tomatoes, we manipulated SlNAC1 at both gene and protein levels: we generated a stable and functional SlNAC1 mutant SlNAC1∆191-270 by removing TAD1 and further engineered it to be stress-controllable by fusing the corresponding cDNA with the abiotic stress-inducible promoter ProStNAC1 . Transgenic tomato plants expressing the ProStNAC1 ::SlNAC1∆191-270 transgene did not display any undesired traits and exhibited enhanced tolerance to cold, drought and salt stresses. Taken together, our manipulation of the stress-related transcription factor via conditional expression of its derived stable and functional mutant provides a successful example for developing crops dynamically adapted to abiotic stress.
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Affiliation(s)
- Xiangli Niu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Han Lu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Youhong Fan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Wenjie Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Yulin Yuan
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Madigan Hawkins
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Min Miao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Yongsheng Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- State Key Laboratory of Tea Plant Biology and Utilization, School of Horticulture, Anhui Agricultural University, Hefei, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
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23
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Asimaki E, Petriukov K, Renz C, Meister C, Ulrich HD. Fast friends - Ubiquitin-like modifiers as engineered fusion partners. Semin Cell Dev Biol 2022; 132:132-145. [PMID: 34840080 PMCID: PMC9703124 DOI: 10.1016/j.semcdb.2021.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022]
Abstract
Ubiquitin and its relatives are major players in many biological pathways, and a variety of experimental tools based on biological chemistry or protein engineering is available for their manipulation. One popular approach is the use of linear fusions between the modifier and a protein of interest. Such artificial constructs can facilitate the understanding of the role of ubiquitin in biological processes and can be exploited to control protein stability, interactions and degradation. Here we summarize the basic design considerations and discuss the advantages as well as limitations associated with their use. Finally, we will refer to several published case studies highlighting the principles of how they provide insight into pathways ranging from membrane protein trafficking to the control of epigenetic modifications.
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24
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Maneix L, Iakova P, Moree SE, Hsu JI, Mistry RM, Stossi F, Lulla P, Sun Z, Sahin E, Yellapragada SV, Catic A. Proteasome Inhibitors Silence Oncogenes in Multiple Myeloma through Localized Histone Deacetylase 3 (HDAC3) Stabilization and Chromatin Condensation. CANCER RESEARCH COMMUNICATIONS 2022; 2:1693-1710. [PMID: 36846090 PMCID: PMC9949381 DOI: 10.1158/2767-9764.crc-22-0255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Proteasome inhibitors have become the standard of care for multiple myeloma (MM). Blocking protein degradation particularly perturbs the homeostasis of short-lived polypeptides such as transcription factors and epigenetic regulators. To determine how proteasome inhibitors directly impact gene regulation, we performed an integrative genomics study in MM cells. We discovered that proteasome inhibitors reduce the turnover of DNA-associated proteins and repress genes necessary for proliferation through epigenetic silencing. Specifically, proteasome inhibition results in the localized accumulation of histone deacetylase 3 (HDAC3) at defined genomic sites, which reduces H3K27 acetylation and increases chromatin condensation. The loss of active chromatin at super-enhancers critical for MM, including the super-enhancer controlling the proto-oncogene c-MYC, reduces metabolic activity and cancer cell growth. Epigenetic silencing is attenuated by HDAC3 depletion, suggesting a tumor-suppressive element of this deacetylase in the context of proteasome inhibition. In the absence of treatment, HDAC3 is continuously removed from DNA by the ubiquitin ligase SIAH2. Overexpression of SIAH2 increases H3K27 acetylation at c-MYC-controlled genes, increases metabolic output, and accelerates cancer cell proliferation. Our studies indicate a novel therapeutic function of proteasome inhibitors in MM by reshaping the epigenetic landscape in an HDAC3-dependent manner. As a result, blocking the proteasome effectively antagonizes c-MYC and the genes controlled by this proto-oncogene.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Polina Iakova
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Shannon E. Moree
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Joanne I. Hsu
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ragini M. Mistry
- Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - Premal Lulla
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Zheng Sun
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
| | - Sarvari V. Yellapragada
- Department of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
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25
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Pitts S, Liu H, Ibrahim A, Garg A, Felgueira CM, Begum A, Fan W, Teh S, Low JY, Ford B, Schneider DA, Hay R, Laiho M. Identification of an E3 ligase that targets the catalytic subunit of RNA Polymerase I upon transcription stress. J Biol Chem 2022; 298:102690. [PMID: 36372232 PMCID: PMC9727647 DOI: 10.1016/j.jbc.2022.102690] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
RNA Polymerase I (Pol I) synthesizes rRNA, which is the first and rate-limiting step in ribosome biogenesis. Factors governing the stability of the polymerase complex are not known. Previous studies characterizing Pol I inhibitor BMH-21 revealed a transcriptional stress-dependent pathway for degradation of the largest subunit of Pol I, RPA194. To identify the E3 ligase(s) involved, we conducted a cell-based RNAi screen for ubiquitin pathway genes. We establish Skp-Cullin-F-box protein complex F-box protein FBXL14 as an E3 ligase for RPA194. We show that FBXL14 binds to RPA194 and mediates RPA194 ubiquitination and degradation in cancer cells treated with BMH-21. Mutation analysis in yeast identified lysines 1150, 1153, and 1156 on Rpa190 relevant for the protein degradation. These results reveal the regulated turnover of Pol I, showing that the stability of the catalytic subunit is controlled by the F-box protein FBXL14 in response to transcription stress.
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Affiliation(s)
- Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adel Ibrahim
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Amit Garg
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Catarina Mendes Felgueira
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Asma Begum
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Selina Teh
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jin-Yih Low
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brittany Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ronald Hay
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland,For correspondence: Marikki Laiho
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26
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The Proteostasis Network: A Global Therapeutic Target for Neuroprotection after Spinal Cord Injury. Cells 2022; 11:cells11213339. [PMID: 36359735 PMCID: PMC9658791 DOI: 10.3390/cells11213339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 01/18/2023] Open
Abstract
Proteostasis (protein homeostasis) is critical for cellular as well as organismal survival. It is strictly regulated by multiple conserved pathways including the ubiquitin-proteasome system, autophagy, the heat shock response, the integrated stress response, and the unfolded protein response. These overlapping proteostasis maintenance modules respond to various forms of cellular stress as well as organismal injury. While proteostasis restoration and ultimately organism survival is the main evolutionary driver of such a regulation, unresolved disruption of proteostasis may engage pro-apoptotic mediators of those pathways to eliminate defective cells. In this review, we discuss proteostasis contributions to the pathogenesis of traumatic spinal cord injury (SCI). Most published reports focused on the role of proteostasis networks in acute/sub-acute tissue damage post-SCI. Those reports reveal a complex picture with cell type- and/or proteostasis mediator-specific effects on loss of neurons and/or glia that often translate into the corresponding modulation of functional recovery. Effects of proteostasis networks on such phenomena as neuro-repair, post-injury plasticity, as well as systemic manifestations of SCI including dysregulation of the immune system, metabolism or cardiovascular function are currently understudied. However, as potential interventions that target the proteostasis networks are expected to impact many cell types across multiple organ systems that are compromised after SCI, such therapies could produce beneficial effects across the wide spectrum of highly variable human SCI.
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27
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Hunter JE, Campbell AE, Hannaway NL, Kerridge S, Luli S, Butterworth JA, Sellier H, Mukherjee R, Dhillon N, Sudhindar PD, Shukla R, Brownridge PJ, Bell HL, Coxhead J, Taylor L, Leary P, Hasoon MS, Collins I, Garrett MD, Eyers CE, Perkins ND. Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway. Biochem J 2022; 479:2063-2086. [PMID: 36240066 PMCID: PMC9704646 DOI: 10.1042/bcj20220102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 12/19/2022]
Abstract
Previously, we discovered that deletion of c-Rel in the Eµ-Myc mouse model of lymphoma results in earlier onset of disease, a finding that contrasted with the expected function of this NF-κB subunit in B-cell malignancies. Here we report that Eµ-Myc/cRel-/- cells have an unexpected and major defect in the CHK1 pathway. Total and phospho proteomic analysis revealed that Eµ-Myc/cRel-/- lymphomas highly resemble wild-type (WT) Eµ-Myc lymphomas treated with an acute dose of the CHK1 inhibitor (CHK1i) CCT244747. Further analysis demonstrated that this is a consequence of Eµ-Myc/cRel-/- lymphomas having lost expression of CHK1 protein itself, an effect that also results in resistance to CCT244747 treatment in vivo. Similar down-regulation of CHK1 protein levels was also seen in CHK1i resistant U2OS osteosarcoma and Huh7 hepatocellular carcinoma cells. Further investigation revealed that the deubiquitinase USP1 regulates CHK1 proteolytic degradation and that its down-regulation in our model systems is responsible, at least in part, for these effects. We demonstrate that treating WT Eµ-Myc lymphoma cells with the USP1 inhibitor ML323 was highly effective at reducing tumour burden in vivo. Targeting USP1 activity may thus be an alternative therapeutic strategy in MYC-driven tumours.
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Affiliation(s)
- Jill E. Hunter
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Amy E. Campbell
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Nicola L. Hannaway
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Scott Kerridge
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Saimir Luli
- Newcastle University Clinical and Translational Research Institute, Preclinical In Vivo Imaging (PIVI), Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Jacqueline A. Butterworth
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Helene Sellier
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Reshmi Mukherjee
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Nikita Dhillon
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Praveen D. Sudhindar
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Ruchi Shukla
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Philip J. Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Hayden L. Bell
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Jonathan Coxhead
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Leigh Taylor
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Peter Leary
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Megan S.R. Hasoon
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Ian Collins
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton SM2 5NG, U.K
| | - Michelle D. Garrett
- School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Neil D. Perkins
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
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28
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Feng R, Mayuranathan T, Huang P, Doerfler PA, Li Y, Yao Y, Zhang J, Palmer LE, Mayberry K, Christakopoulos GE, Xu P, Li C, Cheng Y, Blobel GA, Simon MC, Weiss MJ. Activation of γ-globin expression by hypoxia-inducible factor 1α. Nature 2022; 610:783-790. [PMID: 36224385 PMCID: PMC9773321 DOI: 10.1038/s41586-022-05312-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 09/02/2022] [Indexed: 12/24/2022]
Abstract
Around birth, globin expression in human red blood cells (RBCs) shifts from γ-globin to β-globin, which results in fetal haemoglobin (HbF, α2γ2) being gradually replaced by adult haemoglobin (HbA, α2β2)1. This process has motivated the development of innovative approaches to treat sickle cell disease and β-thalassaemia by increasing HbF levels in postnatal RBCs2. Here we provide therapeutically relevant insights into globin gene switching obtained through a CRISPR-Cas9 screen for ubiquitin-proteasome components that regulate HbF expression. In RBC precursors, depletion of the von Hippel-Lindau (VHL) E3 ubiquitin ligase stabilized its ubiquitination target, hypoxia-inducible factor 1α (HIF1α)3,4, to induce γ-globin gene transcription. Mechanistically, HIF1α-HIF1β heterodimers bound cognate DNA elements in BGLT3, a long noncoding RNA gene located 2.7 kb downstream of the tandem γ-globin genes HBG1 and HBG2. This was followed by the recruitment of transcriptional activators, chromatin opening and increased long-range interactions between the γ-globin genes and their upstream enhancer. Similar induction of HbF occurred with hypoxia or with inhibition of prolyl hydroxylase domain enzymes that target HIF1α for ubiquitination by the VHL E3 ubiquitin ligase. Our findings link globin gene regulation with canonical hypoxia adaptation, provide a mechanism for HbF induction during stress erythropoiesis and suggest a new therapeutic approach for β-haemoglobinopathies.
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Affiliation(s)
- Ruopeng Feng
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Phillip A Doerfler
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Yao
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Zhang
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Lance E Palmer
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kalin Mayberry
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Peng Xu
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yong Cheng
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA.
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29
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Fernando LM, Quesada-Candela C, Murray M, Ugoaru C, Yanowitz JL, Allen AK. Proteasomal subunit depletions differentially affect germline integrity in C. elegans. Front Cell Dev Biol 2022; 10:901320. [PMID: 36060813 PMCID: PMC9428126 DOI: 10.3389/fcell.2022.901320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
The 26S proteasome is a multi-subunit protein complex that is canonically known for its ability to degrade proteins in cells and maintain protein homeostasis. Non-canonical or non-proteolytic roles of proteasomal subunits exist but remain less well studied. We provide characterization of germline-specific functions of different 19S proteasome regulatory particle (RP) subunits in C. elegans using RNAi specifically from the L4 stage and through generation of endogenously tagged 19S RP lid subunit strains. We show functions for the 19S RP in regulation of proliferation and maintenance of integrity of mitotic zone nuclei, in polymerization of the synaptonemal complex (SC) onto meiotic chromosomes and in the timing of SC subunit redistribution to the short arm of the bivalent, and in turnover of XND-1 proteins at late pachytene. Furthermore, we report that certain 19S RP subunits are required for proper germ line localization of WEE-1.3, a major meiotic kinase. Additionally, endogenous fluorescent labeling revealed that the two isoforms of the essential 19S RP proteasome subunit RPN-6.1 are expressed in a tissue-specific manner in the hermaphrodite. Also, we demonstrate that the 19S RP subunits RPN-6.1 and RPN-7 are crucial for the nuclear localization of the lid subunits RPN-8 and RPN-9 in oocytes, further supporting the ability to utilize the C. elegans germ line as a model to study proteasome assembly real-time. Collectively, our data support the premise that certain 19S RP proteasome subunits are playing tissue-specific roles, especially in the germ line. We propose C. elegans as a versatile multicellular model to study the diverse proteolytic and non-proteolytic roles that proteasome subunits play in vivo.
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Affiliation(s)
| | - Cristina Quesada-Candela
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Makaelah Murray
- Department of Biology, Howard University, Washington, DC, United States
| | - Caroline Ugoaru
- Department of Biology, Howard University, Washington, DC, United States
| | - Judith L. Yanowitz
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Departments of Developmental Biology, Microbiology, and Molecular Genetics, The Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
| | - Anna K. Allen
- Department of Biology, Howard University, Washington, DC, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
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30
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Rodriguez K, Do A, Senay-Aras B, Perales M, Alber M, Chen W, Reddy GV. Concentration-dependent transcriptional switching through a collective action of cis-elements. SCIENCE ADVANCES 2022; 8:eabo6157. [PMID: 35947668 PMCID: PMC9365274 DOI: 10.1126/sciadv.abo6157] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Gene expression specificity of homeobox transcription factors has remained paradoxical. WUSCHEL activates and represses CLAVATA3 transcription at lower and higher concentrations, respectively. We use computational modeling and experimental analysis to investigate the properties of the cis-regulatory module. We find that intrinsically each cis-element can only activate CLAVATA3 at a higher WUSCHEL concentration. However, together, they repress CLAVATA3 at higher WUSCHEL and activate only at lower WUSCHEL, showing that the concentration-dependent interactions among cis-elements regulate both activation and repression. Biochemical experiments show that two adjacent functional cis-elements bind WUSCHEL with higher affinity and dimerize at relatively lower levels. Moreover, increasing the distance between cis-elements prolongs WUSCHEL monomer binding window, resulting in higher CLAVATA3 activation. Our work showing a constellation of optimally spaced cis-elements of defined affinities determining activation and repression thresholds in regulating CLAVATA3 transcription provides a previously unknown mechanism of cofactor-independent regulation of transcription factor binding in mediating gene expression specificity.
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Affiliation(s)
- Kevin Rodriguez
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Albert Do
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Betul Senay-Aras
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Mariano Perales
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Weitao Chen
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - G. Venugopala Reddy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
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31
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Yao H, Xie W, Dai Y, Liu Y, Gu W, Li J, Wu L, Xie J, Rui W, Ren B, Xue L, Cheng Y, Lin S, Li C, Tang H, Wang Y, Lou M, Zhang X, Hu R, Shang H, Huang J, Wu ZB. TRIM65 determines the fate of a novel subtype of pituitary neuroendocrine tumors via ubiquitination and degradation of TPIT. Neuro Oncol 2022; 24:1286-1297. [PMID: 35218667 PMCID: PMC9340636 DOI: 10.1093/neuonc/noac053] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Pituitary neuroendocrine tumors (PitNETs) are common intracranial tumors that are classified into seven histological subtypes, including lactotroph, somatotroph, corticotroph, thyrotroph, gonadotroph, null cell, and plurihormonal PitNETs. However, the molecular characteristics of these types of PitNETs are not completely clear. METHODS A total of 180 consecutive cases of PitNETs were collected to perform RNA sequencing. All subtypes of PitNETs were distinguished by unsupervised clustering analysis. We investigated the regulation of TPIT by TRIM65 and its effects on ACTH production and secretion in ACTH-secreting pituitary cell lines, as well as in murine models using biochemical analyses, confocal microscopy, and luciferase reporter assays. RESULTS A novel subtype of PitNETs derived from TPIT lineage cells was identified as with normal TPIT transcription but with lowered protein expression. Furthermore, for the first time, TRIM65 was identified as the E3 ubiquitin ligase of TPIT. Depending on the RING domain, TRIM65 ubiquitinated and degraded the TPIT protein at multiple Lys sites. In addition, TRIM65-mediated ubiquitination of TPIT inhibited POMC transcription and ACTH production to determine the fate of the novel subtype of PitNETs in vitro and in vivo. CONCLUSION Our studies provided a novel classification of PitNETs and revealed that the TRIM65-TPIT complex controlled the fate of the novel subtype of PitNETs, which provides a potential therapy target for Cushing's disease.
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Affiliation(s)
- Hong Yao
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wanqun Xie
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanting Liu
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiting Gu
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfeng Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Xie
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiwei Rui
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bohan Ren
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Li Xue
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yijun Cheng
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaojian Lin
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changsheng Li
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Tang
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meiqing Lou
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobiao Zhang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ronggui Hu
- State Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai,China
| | - Hanbing Shang
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyan Huang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhe Bao Wu
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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32
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Gu Q, Wang Y, Zhao X, Yuan B, Zhang M, Tan Z, Zhang X, Chen Y, Wu H, Luo Y, Keller NP, Gao X, Ma Z. Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress. Nucleic Acids Res 2022; 50:6190-6210. [PMID: 35687128 PMCID: PMC9226496 DOI: 10.1093/nar/gkac498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Abstract
Poaceae plants can locally accumulate iron to suppress pathogen infection. It remains unknown how pathogens overcome host-derived iron stress during their successful infections. Here, we report that Fusarium graminearum (Fg), a destructive fungal pathogen of cereal crops, is challenged by host-derived high-iron stress. Fg infection induces host alkalinization, and the pH-dependent transcription factor FgPacC undergoes a proteolytic cleavage into the functional isoform named FgPacC30 under alkaline host environment. Subsequently FgPacC30 binds to a GCCAR(R = A/G)G element at the promoters of the genes involved in iron uptake and inhibits their expression, leading to adaption of Fg to high-iron stress. Mechanistically, FgPacC30 binds to FgGcn5 protein, a catalytic subunit of Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, leading to deregulation of histone acetylation at H3K18 and H2BK11, and repression of iron uptake genes. Moreover, we identified a protein kinase FgHal4, which is highly induced by extracellular high-iron stress and protects FgPacC30 against 26S proteasome-dependent degradation by promoting FgPacC30 phosphorylation at Ser2. Collectively, this study uncovers a novel inhibitory mechanism of the SAGA complex by a transcription factor that enables a fungal pathogen to adapt to dynamic microenvironments during infection.
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Affiliation(s)
- Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Yujie Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Xiaozhen Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Bingqin Yuan
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Mengxuan Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Zheng Tan
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Xinyue Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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33
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Xie K, Tan K, Naylor MJ. Transcription Factors as Novel Therapeutic Targets and Drivers of Prostate Cancer Progression. Front Oncol 2022; 12:854151. [PMID: 35547880 PMCID: PMC9082354 DOI: 10.3389/fonc.2022.854151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/23/2022] [Indexed: 11/24/2022] Open
Abstract
Prostate cancer is the second most diagnosed cancer among men worldwide. Androgen deprivation therapy, the most common targeted therapeutic option, is circumvented as prostate cancer progresses from androgen dependent to castrate-resistant disease. Whilst the nuclear receptor transcription factor, androgen receptor, drives the growth of prostate tumor during initial stage of the disease, androgen resistance is associated with poorly differentiated prostate cancer. In the recent years, increased research has highlighted the aberrant transcriptional activities of a small number of transcription factors. Along with androgen receptors, dysregulation of these transcription factors contributes to both the poorly differentiated phenotypes of prostate cancer cells and the initiation and progression of prostate carcinoma. As master regulators of cell fate decisions, these transcription factors may provide opportunity for the development of novel therapeutic targets for the management of prostate cancer. Whilst some transcriptional regulators have previously been notoriously difficult to directly target, technological advances offer potential for the indirect therapeutic targeting of these transcription factors and the capacity to reprogram cancer cell phenotype. This mini review will discuss how recent advances in our understanding of transcriptional regulators and material science pave the way to utilize these regulatory molecules as therapeutic targets in prostate cancer.
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Affiliation(s)
- Kangzhe Xie
- Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine & Health, University of Sydney, Sydney, NSW, Australia
| | - Keely Tan
- Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine & Health, University of Sydney, Sydney, NSW, Australia
| | - Matthew J Naylor
- Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine & Health, University of Sydney, Sydney, NSW, Australia
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34
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Martyn JE, Gomez-Valero L, Buchrieser C. The evolution and role of eukaryotic-like domains in environmental intracellular bacteria: the battle with a eukaryotic cell. FEMS Microbiol Rev 2022; 46:6529235. [DOI: 10.1093/femsre/fuac012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Intracellular pathogens that are able to thrive in different environments, such as Legionella spp. which preferentially live in protozoa in aquatic environments or environmental Chlamydiae which replicate either within protozoa or a range of animals, possess a plethora of cellular biology tools to influence their eukaryotic host. The host manipulation tools that evolved in the interaction with protozoa, confer these bacteria the capacity to also infect phylogenetically distinct eukaryotic cells, such as macrophages and thus they can also be human pathogens. To manipulate the host cell, bacteria use protein secretion systems and molecular effectors. Although these molecular effectors are encoded in bacteria, they are expressed and function in a eukaryotic context often mimicking or inhibiting eukaryotic proteins. Indeed, many of these effectors have eukaryotic-like domains. In this review we propose that the main pathways environmental intracellular bacteria need to subvert in order to establish the host eukaryotic cell as a replication niche are chromatin remodelling, ubiquitination signalling, and modulation of protein-protein interactions via tandem repeat domains. We then provide mechanistic insight into how these proteins might have evolved as molecular weapons. Finally, we highlight that in environmental intracellular bacteria the number of eukaryotic-like domains and proteins is considerably higher than in intracellular bacteria specialised to an isolated niche, such as obligate intracellular human pathogens. As mimics of eukaryotic proteins are critical components of host pathogen interactions, this distribution of eukaryotic-like domains suggests that the environment has selected them.
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Affiliation(s)
- Jessica E Martyn
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
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35
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Moree SE, Maneix L, Iakova P, Stossi F, Sahin E, Catic A. Imaging-Based Screening of Deubiquitinating Proteases Identifies Otubain-1 as a Stabilizer of c-MYC. Cancers (Basel) 2022; 14:806. [PMID: 35159073 PMCID: PMC8833929 DOI: 10.3390/cancers14030806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
The ubiquitin-proteasome pathway precisely controls the turnover of transcription factors in the nucleus, playing an important role in maintaining appropriate quantities of these regulatory proteins. The transcription factor c-MYC is essential for normal development and is a critical cancer driver. Despite being highly expressed in several tissues and malignancies, the c-MYC protein is also continuously targeted by the ubiquitin-proteasome pathway, which can either facilitate or inhibit c-MYC degradation. Deubiquitinating proteases can remove ubiquitin chains from target proteins and rescue them from proteasomal digestion. This study sought to determine novel elements of the ubiquitin-proteasome pathway that regulate c-MYC levels. We performed an overexpression screen with 41 human proteases to identify which deubiquitinases stabilize c-MYC. We discovered that the highly expressed Otubain-1 (OTUB1) protease increases c-MYC protein levels. Confirming its role in enhancing c-MYC activity, we found that elevated OTUB1 correlates with inferior clinical outcomes in the c-MYC-dependent cancer multiple myeloma, and overexpression of OTUB1 accelerates the growth of myeloma cells. In summary, our study identifies OTUB1 as a novel amplifier of the proto-oncogene c-MYC.
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Affiliation(s)
- Shannon E. Moree
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (S.E.M.); (L.M.); (P.I.); (F.S.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laure Maneix
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (S.E.M.); (L.M.); (P.I.); (F.S.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Polina Iakova
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (S.E.M.); (L.M.); (P.I.); (F.S.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (S.E.M.); (L.M.); (P.I.); (F.S.)
- Gulf Coast Consortia, Center for Advanced Microscopy and Image Informatics, Houston, TX 77030, USA
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Andre Catic
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (S.E.M.); (L.M.); (P.I.); (F.S.)
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA;
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
- Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
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36
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Liu Y, Ding R, Xu Z, Xue Y, Zhang D, Zhang Y, Li W, Li X. Roles and Mechanisms of the Protein Quality Control System in Alzheimer's Disease. Int J Mol Sci 2021; 23:345. [PMID: 35008771 PMCID: PMC8745298 DOI: 10.3390/ijms23010345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the deposition of senile plaques (SPs) and the formation of neurofibrillary tangles (NTFs), as well as neuronal dysfunctions in the brain, but in fact, patients have shown a sustained disease progression for at least 10 to 15 years before these pathologic biomarkers can be detected. Consequently, as the most common chronic neurological disease in the elderly, the challenge of AD treatment is that it is short of effective biomarkers for early diagnosis. The protein quality control system is a collection of cellular pathways that can recognize damaged proteins and thereby modulate their turnover. Abundant evidence indicates that the accumulation of abnormal proteins in AD is closely related to the dysfunction of the protein quality control system. In particular, it is the synthesis, degradation, and removal of essential biological components that have already changed in the early stage of AD, which further encourages us to pay more attention to the protein quality control system. The review mainly focuses on the endoplasmic reticulum system (ERS), autophagy-lysosome system (ALS) and the ubiquitin-proteasome system (UPS), and deeply discusses the relationship between the protein quality control system and the abnormal proteins of AD, which can not only help us to understand how and why the complex regulatory system becomes malfunctional during AD progression, but also provide more novel therapeutic strategies to prevent the development of AD.
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Affiliation(s)
| | | | | | | | | | | | | | - Xing Li
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (Y.L.); (R.D.); (Z.X.); (Y.X.); (D.Z.); (Y.Z.); (W.L.)
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37
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Zou J, Cai Z, Liang Z, Liang Y, Zhang G, Yang J, Zhang Y, Lin H, Tan M. Different fusion tags affect the activity of ubiquitin overexpression on spastin protein stability. Eur J Histochem 2021; 65. [PMID: 34873900 PMCID: PMC8678624 DOI: 10.4081/ejh.2021.3352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/23/2021] [Indexed: 11/23/2022] Open
Abstract
Spastin is one of the proteins which lead to hereditary spastic paraplegia (HSP), whose dysfunction towards microtubule severing and membrane transporting is critically important. The present study is to elucidate the mechanisms of the protein stability regulation of spastin. The ubiquitin encoding plasmids were transfected into COS-7 cells with different fusion tags including Green Fluorescent Protein (GFP), mCherry and Flag. The expression level of spastin was detected, microtubule severing activity and neurite outgrowth were quantified. The data showed that ubiquitin overexpression significantly induced the decreased expression of spastin, suppressed the activity of microtubule severing in COS-7 cells and inhibited the promoting effect on neurite outgrowth in cultured hippocampal neurons. Furthermore, when modulating the overexpression experiments of ubiquitin, it was found that relatively small tag like Flag, but not large tags such as GFP or mCherry fused with ubiquitin, retained the activity on spastin stability. The present study investigated the effects of small/large tags addition to ubiquitin and the novel mechanisms of post-transcriptional modifications of spastin on regulating neurite outgrowth, in the attempt to experimentally elucidate the mechanisms that control the level or stability of spastin in hereditary spastic paraplegia.
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Affiliation(s)
- Jianyu Zou
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Zhenbin Cai
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Zhi Liang
- Department of Orthopaedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen.
| | - Yaozhong Liang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Guowei Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Jie Yang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Yunlong Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Hongsheng Lin
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Minghui Tan
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
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Xu J, Li B, Song W, Cao L, Zhu C, Lin S. Tumor suppressor functions of miRNA-375 in nasopharyngeal carcinoma through inhibition of ubiquitin-specific protease 1 expression. Int J Biochem Cell Biol 2021; 141:106092. [PMID: 34626803 DOI: 10.1016/j.biocel.2021.106092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/26/2021] [Accepted: 09/30/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) development involves many genetic alterations. This study profiled differentially expressed microRNAs (DE-miRNAs) and selected miR-375 for further study. METHODS DE-miRNAs were screened using online databases and subjected to various analyzes. miR-375 mimics with negative control (NC) cDNA, and a ubiquitin-specific protease 1 (USP1) as well as a NC group were transfected into NPC cells for analysis by quantitative PCR, western blotting, wound healing, Transwell, flow cytometry, cell counting kit-8 (CCK-8), and luciferase gene reporter assays. RESULTS Among these DE-miRNAs, miR-375 was downregulated and miR-21 was upregulated in NPC cells. Bioinformatical analysis identified USP1 as a potential target gene of miR-375. Increased USP1 expression was associated with poor survival of head and neck cancer patients. The luciferase assay confirmed miR-375 binding to the USP1 3'-untranslated region (UTR), while the transfection experiment confirmed miR-375 expression reduced USP1 expression. USP1 overexpression reversed the anti-tumor activity of miR-375 in NPC cells as determined by tumor cell migration, invasion, apoptosis, and viability assays. In addition, USP1 overexpression activated phosphoinositide 3-kinase (PI3K) signaling, whereas a selective PI3K inhibitor (S2739) could reverse the effects of USP1 on NPC cells in vitro. CONCLUSIONS miR-375 and miR-21 are both related to NPC and miR-375 can target USP1. Further experiments revealed that up-regulated miR-375 expression led to USP1 down-regulation, and miR-375 overexpression suppressed PI3K/Akt signaling and inhibited NPC cell migration and invasion, but promoted NPC cell apoptosis.
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Affiliation(s)
- Jiayuan Xu
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Bangliang Li
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Wei Song
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Longhe Cao
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Chuansai Zhu
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Sen Lin
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
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Anyona SB, Raballah E, Cheng Q, Hurwitz I, Ndege C, Munde E, Otieno W, Seidenberg PD, Schneider KA, Lambert CG, McMahon BH, Ouma C, Perkins DJ. Differential Gene Expression in Host Ubiquitination Processes in Childhood Malarial Anemia. Front Genet 2021; 12:764759. [PMID: 34880904 PMCID: PMC8646022 DOI: 10.3389/fgene.2021.764759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Malaria remains one of the leading global causes of childhood morbidity and mortality. In holoendemic Plasmodium falciparum transmission regions, such as western Kenya, severe malarial anemia [SMA, hemoglobin (Hb) < 6.0 g/dl] is the primary form of severe disease. Ubiquitination is essential for regulating intracellular processes involved in innate and adaptive immunity. Although dysregulation in ubiquitin molecular processes is central to the pathogenesis of multiple human diseases, the expression patterns of ubiquitination genes in SMA remain unexplored. Methods: To examine the role of the ubiquitination processes in pathogenesis of SMA, differential gene expression profiles were determined in Kenyan children (n = 44, aged <48 mos) with either mild malarial anemia (MlMA; Hb ≥9.0 g/dl; n = 23) or SMA (Hb <6.0 g/dl; n = 21) using the Qiagen Human Ubiquitination Pathway RT2 Profiler PCR Array containing a set of 84 human ubiquitination genes. Results: In children with SMA, 10 genes were down-regulated (BRCC3, FBXO3, MARCH5, RFWD2, SMURF2, UBA6, UBE2A, UBE2D1, UBE2L3, UBR1), and five genes were up-regulated (MDM2, PARK2, STUB1, UBE2E3, UBE2M). Enrichment analyses revealed Ubiquitin-Proteasomal Proteolysis as the top disrupted process, along with altered sub-networks involved in proteasomal, protein, and ubiquitin-dependent catabolic processes. Conclusion: Collectively, these novel results show that protein coding genes of the ubiquitination processes are involved in the pathogenesis of SMA.
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Affiliation(s)
- Samuel B. Anyona
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, Kenya,University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, Kenya,*Correspondence: Samuel B. Anyona,
| | - Evans Raballah
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, Kenya,Department of Medical Laboratory Sciences, School of Public Health Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Qiuying Cheng
- Center for Global Health, University of New Mexico, Albuquerque, NM, United States
| | - Ivy Hurwitz
- Center for Global Health, University of New Mexico, Albuquerque, NM, United States
| | - Caroline Ndege
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, Kenya
| | - Elly Munde
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, Kenya,Department of Clinical Medicine, School of Health Science, Kirinyaga University, Kerugoya, Kenya
| | - Walter Otieno
- Department of Pediatrics and Child Health, School of Medicine, Maseno University, Maseno, Kenya
| | - Philip D. Seidenberg
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM, United States
| | - Kristan A. Schneider
- Department Applied Computer and Bio-Sciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | | | - Benjamin H. McMahon
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Collins Ouma
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, Kenya,Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | - Douglas J. Perkins
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, Kenya,Center for Global Health, University of New Mexico, Albuquerque, NM, United States
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40
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Cáceres-Gutiérrez RE, Andonegui MA, Oliva-Rico DA, González-Barrios R, Luna F, Arriaga-Canon C, López-Saavedra A, Prada D, Castro C, Parmentier L, Díaz-Chávez J, Alfaro-Mora Y, Navarro-Delgado EI, Fabian-Morales E, Tran B, Shetty J, Zhao Y, Alcaraz N, De la Rosa C, Reyes JL, Hédouin S, Hubé F, Francastel C, Herrera LA. Proteasome inhibition alters mitotic progression through the upregulation of centromeric α-Satellite RNAs. FEBS J 2021; 289:1858-1875. [PMID: 34739170 PMCID: PMC9299679 DOI: 10.1111/febs.16261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 09/19/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022]
Abstract
Cell cycle progression requires control of the abundance of several proteins and RNAs over space and time to properly transit from one phase to the next and to ensure faithful genomic inheritance in daughter cells. The proteasome, the main protein degradation system of the cell, facilitates the establishment of a proteome specific to each phase of the cell cycle. Its activity also strongly influences transcription. Here, we detected the upregulation of repetitive RNAs upon proteasome inhibition in human cancer cells using RNA‐seq. The effect of proteasome inhibition on centromeres was remarkable, especially on α‐Satellite RNAs. We showed that α‐Satellite RNAs fluctuate along the cell cycle and interact with members of the cohesin ring, suggesting that these transcripts may take part in the regulation of mitotic progression. Next, we forced exogenous overexpression and used gapmer oligonucleotide targeting to demonstrate that α‐Sat RNAs have regulatory roles in mitosis. Finally, we explored the transcriptional regulation of α‐Satellite DNA. Through in silico analyses, we detected the presence of CCAAT transcription factor‐binding motifs within α‐Satellite centromeric arrays. Using high‐resolution three‐dimensional immuno‐FISH and ChIP‐qPCR, we showed an association between the α‐Satellite upregulation and the recruitment of the transcription factor NFY‐A to the centromere upon MG132‐induced proteasome inhibition. Together, our results show that the proteasome controls α‐Satellite RNAs associated with the regulation of mitosis.
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Affiliation(s)
- Rodrigo E Cáceres-Gutiérrez
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Marco A Andonegui
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Diego A Oliva-Rico
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Rodrigo González-Barrios
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Fernando Luna
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Cristian Arriaga-Canon
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Alejandro López-Saavedra
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Diddier Prada
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico.,Departamento de Informática Biomédica, Faculty of Medicine, UNAM, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Clementina Castro
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Laurent Parmentier
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - José Díaz-Chávez
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Yair Alfaro-Mora
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Erick I Navarro-Delgado
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Eunice Fabian-Morales
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico
| | - Bao Tran
- NCI CCR Sequencing Facility, Frederick National Laboratory for Cancer Research, MD, USA
| | - Jyoti Shetty
- NCI CCR Sequencing Facility, Frederick National Laboratory for Cancer Research, MD, USA
| | - Yongmei Zhao
- NCI CCR Sequencing Facility, Frederick National Laboratory for Cancer Research, MD, USA
| | - Nicolas Alcaraz
- The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,National Institute of Genomic Medicine, Mexico City, Mexico
| | - Carlos De la Rosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José L Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sabrine Hédouin
- Epigenetics and Cell Fate, CNRS UMR7216, Université de Paris, Paris, France
| | - Florent Hubé
- Epigenetics and Cell Fate, CNRS UMR7216, Université de Paris, Paris, France
| | - Claire Francastel
- Epigenetics and Cell Fate, CNRS UMR7216, Université de Paris, Paris, France
| | - Luis A Herrera
- Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Unidad de Investigación Biomédica en Cáncer, Mexico City, Mexico.,Dirección General, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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41
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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42
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Yusenko MV, Biyanee A, Andersson MK, Radetzki S, von Kries JP, Stenman G, Klempnauer KH. Proteasome inhibitors suppress MYB oncogenic activity in a p300-dependent manner. Cancer Lett 2021; 520:132-142. [PMID: 34256093 DOI: 10.1016/j.canlet.2021.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 01/18/2023]
Abstract
Studies of the role of MYB in human malignancies have highlighted MYB as a potential drug target for acute myeloid leukemia (AML) and adenoid cystic carcinoma (ACC). Although transcription factors are often considered un-druggable, recent work has demonstrated successful targeting of MYB by low molecular weight compounds. This has fueled the notion that inhibition of MYB has potential as a therapeutic approach against MYB-driven malignancies. Here, we have used a MYB reporter cell line to screen a library of FDA-approved drugs for novel MYB inhibitors. We demonstrate that proteasome inhibitors have significant MYB-inhibitory activity, prompting us to characterize the proteasome inhibitor oprozomib in more detail. Oprozomib was shown to interfere with the ability of the co-activator p300 to stimulate MYB activity and to exert anti-proliferative effects on human AML and ACC cells. Overall, our work demonstrated suppression of oncogenic MYB activity as a novel result of proteasome inhibition.
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Affiliation(s)
- Maria V Yusenko
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Abhiruchi Biyanee
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Mattias K Andersson
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Silke Radetzki
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Jens P von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
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43
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Ecker J, Thatikonda V, Sigismondo G, Selt F, Valinciute G, Oehme I, Müller C, Buhl JL, Ridinger J, Usta D, Qin N, van Tilburg CM, Herold-Mende C, Remke M, Sahm F, Westermann F, Kool M, Wechsler-Reya RJ, Chavez L, Krijgsveld J, Jäger N, Pfister SM, Witt O, Milde T. Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma. Neuro Oncol 2021; 23:226-239. [PMID: 32822486 DOI: 10.1093/neuonc/noaa191] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The sensitivity of myelocytomatosis oncogene (MYC) amplified medulloblastoma to class I histone deacetylase (HDAC) inhibition has been shown previously; however, understanding the underlying molecular mechanism is crucial for selection of effective HDAC inhibitors for clinical use. The aim of this study was to investigate the direct molecular interaction of MYC and class I HDAC2, and the impact of class I HDAC inhibition on MYC function. METHODS Co-immunoprecipitation and mass spectrometry were used to determine the co-localization of MYC and HDAC2. Chromatin immunoprecipitation (ChIP) sequencing and gene expression profiling were used to analyze the co-localization of MYC and HDAC2 on DNA and the impact on transcriptional activity in primary tumors and a MYC amplified cell line treated with the class I HDAC inhibitor entinostat. The effect on MYC was investigated by quantitative real-time PCR, western blot, and immunofluorescence. RESULTS HDAC2 is a cofactor of MYC in MYC amplified medulloblastoma. The MYC-HDAC2 complex is bound to genes defining the MYC-dependent transcriptional profile. Class I HDAC inhibition leads to stabilization and reduced DNA binding of MYC protein, inducing a downregulation of MYC activated genes (MAGs) and upregulation of MYC repressed genes (MRGs). MAGs and MRGs are characterized by opposing biological functions and by distinct enhancer-box distribution. CONCLUSIONS Our data elucidate the molecular interaction of MYC and HDAC2 and support a model in which inhibition of class I HDACs directly targets MYC's transactivating and transrepressing functions.
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Affiliation(s)
- Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Venu Thatikonda
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - Gintvile Valinciute
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Carina Müller
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Juliane L Buhl
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Johannes Ridinger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Diren Usta
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Nan Qin
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | | | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany.,Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Natalie Jäger
- Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
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Im JH, Ko JH, Kim WC, Crain B, Keathley D, Han KH. Mitogen-activated protein kinase 6 negatively regulates secondary wall biosynthesis by modulating MYB46 protein stability in Arabidopsis thaliana. PLoS Genet 2021; 17:e1009510. [PMID: 33826618 PMCID: PMC8055014 DOI: 10.1371/journal.pgen.1009510] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/19/2021] [Accepted: 03/25/2021] [Indexed: 11/18/2022] Open
Abstract
The R2R3-MYB transcription factor MYB46 functions as a master switch for secondary cell wall biosynthesis, ensuring the exquisite expression of the secondary wall biosynthetic genes in the tissues where secondary walls are critical for growth and development. At the same time, suppression of its function is needed when/where formation of secondary walls is not desirable. Little is known about how this opposing control of secondary cell wall formation is achieved. We used both transient and transgenic expression of MYB46 and mitogen-activated protein kinase 6 (MPK6) to investigate the molecular mechanism of the post-translational regulation of MYB46. We show that MYB46 is phosphorylated by MPK6, leading to site specific phosphorylation-dependent degradation of MYB46 by the ubiquitin-mediated proteasome pathway. In addition, the MPK6-mediated MYB46 phosphorylation was found to regulate in planta secondary wall forming function of MYB46. Furthermore, we provide experimental evidences that MYB83, a paralog of MYB46, is not regulated by MPK6. The coupling of MPK signaling to MYB46 function provides insights into the tissue- and/or condition-specific activity of MYB46 for secondary wall biosynthesis.
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Affiliation(s)
- Jong Hee Im
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- National Academy of Agricultural Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, College of Life Science and Graduate School of Biotechnology, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- * E-mail: (J-HK); (K-HH)
| | - Won-Chan Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Brent Crain
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Daniel Keathley
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Kyung-Hwan Han
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Department of Forestry, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail: (J-HK); (K-HH)
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45
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Kawabe H, Stegmüller J. The role of E3 ubiquitin ligases in synapse function in the healthy and diseased brain. Mol Cell Neurosci 2021; 112:103602. [DOI: 10.1016/j.mcn.2021.103602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 02/08/2023] Open
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Gupta A, Behl T, Aleya L, Rahman MH, Yadav HN, Pal G, Kaur I, Arora S. Role of UPP pathway in amelioration of diabetes-associated complications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19601-19614. [PMID: 33660172 DOI: 10.1007/s11356-021-12781-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Type 2 diabetes (T2D) is one of the most widely spread metabolic disorder also called as "life style" disease. Due to the alarming number of patients, there is great need to therapies targeting functions which can help in maintaining the homeostasis of glucose levels and improving insulin sensitivity. Detailed analysis was done through various research and review papers which was searched using MEDLINE, BIOSIS, and EMBASE using various keywords. This search retrieved the most appropriate content on these molecules targeting UPP pathway. From this extensive review involving UPP pathway, it was concluded that the role of ubiquitin's is not only limited to neurodegenerative disorders but also plays a critical role in progression of diabetes including obesity, insulin resistance, and various neurogenerative disorders but it also targets proteasomal degradation including mediation of cellular signaling pathways. Thus, drugs targeting UPP not only may show effect against diabetes but also are therapeutically beneficial in the treatment of diabetes-associated complications which may be obtained. Thus, based on the available information and data on UPP functions, it can be concluded that regulation of UPP pathway via downstream regulators mainly E1, E2, and E3 may bring promising results. Drugs targeting these transcriptional factors may emerge as a novel therapy in the treatment of diabetes and diabetes-associated complications.
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Affiliation(s)
- Amit Gupta
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Md Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Seoul, South Korea
- Department of Pharmacy, Southeast University, Banani, Dhaka, 1213, Bangladesh
| | | | - Giridhari Pal
- Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sandeep Arora
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
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47
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Pan Z, Bajsa‐Hirschel J, Vaughn JN, Rimando AM, Baerson SR, Duke SO. In vivo assembly of the sorgoleone biosynthetic pathway and its impact on agroinfiltrated leaves of Nicotiana benthamiana. THE NEW PHYTOLOGIST 2021; 230:683-697. [PMID: 33460457 PMCID: PMC8048663 DOI: 10.1111/nph.17213] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Sorgoleone, a hydrophobic compound exuded from root hair cells of Sorghum spp., accounts for much of the allelopathic activity of the genus. The enzymes involved in the biosynthesis of this compound have been identified and functionally characterized. Here, we report the successful assembly of the biosynthetic pathway and the significant impact of in vivo synthesized sorgoleone on the heterologous host Nicotiana benthamiana. A multigene DNA construct was prepared for the expression of genes required for sorgoleone biosynthesis in planta and deployed in N. benthamiana leaf tissues via Agrobacterium-mediated transient expression. RNA-sequencing was conducted to investigate the effects of sorgoleone, via expression of its biosynthesis pathway, on host gene expression. The production of sorgoleone in agroinfiltrated leaves as detected by gas chromatography/mass spectrometry (GC/MS) resulted in the formation of necrotic lesions, indicating that the compound caused severe phytotoxicity to these tissues. RNA-sequencing profiling revealed significant changes in gene expression in the leaf tissues expressing the pathway during the formation of sorgoleone-induced necrotic lesions. Transcriptome analysis suggested that the compound produced in vivo impaired the photosynthetic system as a result of downregulated gene expression for the photosynthesis apparatus and elevated expression of proteasomal genes which may play a major role in the phytotoxicity of sorgoleone.
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Affiliation(s)
- Zhiqiang Pan
- Natural Products Utilization Research UnitUS Department of Agriculture, Agricultural Research ServiceUniversityMS38677USA
| | - Joanna Bajsa‐Hirschel
- Natural Products Utilization Research UnitUS Department of Agriculture, Agricultural Research ServiceUniversityMS38677USA
| | - Justin N. Vaughn
- Genomics and Bioinformatics Research UnitUSDA, ARSAthensGA30605USA
| | - Agnes M. Rimando
- Natural Products Utilization Research UnitUS Department of Agriculture, Agricultural Research ServiceUniversityMS38677USA
| | - Scott R. Baerson
- Natural Products Utilization Research UnitUS Department of Agriculture, Agricultural Research ServiceUniversityMS38677USA
| | - Stephen O. Duke
- Natural Products Utilization Research UnitUS Department of Agriculture, Agricultural Research ServiceUniversityMS38677USA
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Hickey CM, Breckel C, Zhang M, Theune WC, Hochstrasser M. Protein quality control degron-containing substrates are differentially targeted in the cytoplasm and nucleus by ubiquitin ligases. Genetics 2021; 217:1-19. [PMID: 33683364 PMCID: PMC8045714 DOI: 10.1093/genetics/iyaa031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Intracellular proteolysis by the ubiquitin-proteasome system regulates numerous processes and contributes to protein quality control (PQC) in all eukaryotes. Covalent attachment of ubiquitin to other proteins is specified by the many ubiquitin ligases (E3s) expressed in cells. Here we determine the E3s in Saccharomyces cerevisiae that function in degradation of proteins bearing various PQC degradation signals (degrons). The E3 Ubr1 can function redundantly with several E3s, including nuclear-localized San1, endoplasmic reticulum/nuclear membrane-embedded Doa10, and chromatin-associated Slx5/Slx8. Notably, multiple degrons are targeted by more ubiquitylation pathways if directed to the nucleus. Degrons initially assigned as exclusive substrates of Doa10 were targeted by Doa10, San1, and Ubr1 when directed to the nucleus. By contrast, very short hydrophobic degrons-typical targets of San1-are shown here to be targeted by Ubr1 and/or San1, but not Doa10. Thus, distinct types of PQC substrates are differentially recognized by the ubiquitin system in a compartment-specific manner. In human cells, a representative short hydrophobic degron appended to the C-terminus of GFP-reduced protein levels compared with GFP alone, consistent with a recent study that found numerous natural hydrophobic C-termini of human proteins can act as degrons. We also report results of bioinformatic analyses of potential human C-terminal degrons, which reveal that most peptide substrates of Cullin-RING ligases (CRLs) are of low hydrophobicity, consistent with previous data showing CRLs target degrons with specific sequences. These studies expand our understanding of PQC in yeast and human cells, including the distinct but overlapping PQC E3 substrate specificity of the cytoplasm and nucleus.
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Affiliation(s)
- Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Carolyn Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Mengwen Zhang
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - William C Theune
- Department of Biology and Environmental Science, University of New Haven, West Haven, CT 06516, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
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49
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Piedade WP, Famulski JK. E3 ubiquitin ligase-mediated regulation of vertebrate ocular development; new insights into the function of SIAH enzymes. Biochem Soc Trans 2021; 49:327-340. [PMID: 33616626 PMCID: PMC7924998 DOI: 10.1042/bst20200613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 01/18/2023]
Abstract
Developmental regulation of the vertebrate visual system has been a focus of investigation for generations as understanding this critical time period has direct implications on our understanding of congenital blinding disease. The majority of studies to date have focused on transcriptional regulation mediated by morphogen gradients and signaling pathways. However, recent studies of post translational regulation during ocular development have shed light on the role of the ubiquitin proteasome system (UPS). This rather ubiquitous yet highly diverse system is well known for regulating protein function and localization as well as stability via targeting for degradation by the 26S proteasome. Work from many model organisms has recently identified UPS activity during various milestones of ocular development including retinal morphogenesis, retinal ganglion cell function as well as photoreceptor homeostasis. In particular work from flies and zebrafish has highlighted the role of the E3 ligase enzyme family, Seven in Absentia Homologue (Siah) during these events. In this review, we summarize the current understanding of UPS activity during Drosophila and vertebrate ocular development, with a major focus on recent findings correlating Siah E3 ligase activity with two major developmental stages of vertebrate ocular development, retinal morphogenesis and photoreceptor specification and survival.
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50
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Silveira MA, Tav C, Bérube-Simard FA, Cuppens T, Leclercq M, Fournier É, Côté MC, Droit A, Bilodeau S. Modulating HSF1 levels impacts expression of the estrogen receptor α and antiestrogen response. Life Sci Alliance 2021; 4:4/5/e202000811. [PMID: 33593922 PMCID: PMC7893817 DOI: 10.26508/lsa.202000811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
This work shows that activation of the main cellular stress response pathway is responsible for antiestrogen resistance in breast cancer, a process that is reversible. Master transcription factors control the transcriptional program and are essential to maintain cellular functions. Among them, steroid nuclear receptors, such as the estrogen receptor α (ERα), are central to the etiology of hormone-dependent cancers which are accordingly treated with corresponding endocrine therapies. However, resistance invariably arises. Here, we show that high levels of the stress response master regulator, the heat shock factor 1 (HSF1), are associated with antiestrogen resistance in breast cancer cells. Indeed, overexpression of HSF1 leads to ERα degradation, decreased expression of ERα-activated genes, and antiestrogen resistance. Furthermore, we demonstrate that reducing HSF1 levels reinstates expression of the ERα and restores response to antiestrogens. Last, our results establish a proof of concept that inhibition of HSF1, in combination with antiestrogens, is a valid strategy to tackle resistant breast cancers. Taken together, we are proposing a mechanism where high HSF1 levels interfere with the ERα-dependent transcriptional program leading to endocrine resistance in breast cancer.
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Affiliation(s)
- Maruhen Ad Silveira
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada
| | - Christophe Tav
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada
| | - Félix-Antoine Bérube-Simard
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada
| | - Tania Cuppens
- Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada
| | - Mickaël Leclercq
- Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada
| | - Maxime C Côté
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada
| | - Arnaud Droit
- Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada.,Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada .,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, Canada
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