1
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Bhachoo JS, Garvin AJ. SUMO and the DNA damage response. Biochem Soc Trans 2024; 52:773-792. [PMID: 38629643 PMCID: PMC11088926 DOI: 10.1042/bst20230862] [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: 12/08/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
The preservation of genome integrity requires specialised DNA damage repair (DDR) signalling pathways to respond to each type of DNA damage. A key feature of DDR is the integration of numerous post-translational modification signals with DNA repair factors. These modifications influence DDR factor recruitment to damaged DNA, activity, protein-protein interactions, and ultimately eviction to enable access for subsequent repair factors or termination of DDR signalling. SUMO1-3 (small ubiquitin-like modifier 1-3) conjugation has gained much recent attention. The SUMO-modified proteome is enriched with DNA repair factors. Here we provide a snapshot of our current understanding of how SUMO signalling impacts the major DNA repair pathways in mammalian cells. We highlight repeating themes of SUMO signalling used throughout DNA repair pathways including the assembly of protein complexes, competition with ubiquitin to promote DDR factor stability and ubiquitin-dependent degradation or extraction of SUMOylated DDR factors. As SUMO 'addiction' in cancer cells is protective to genomic integrity, targeting components of the SUMO machinery to potentiate DNA damaging therapy or exacerbate existing DNA repair defects is a promising area of study.
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Affiliation(s)
- Jai S. Bhachoo
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
| | - Alexander J. Garvin
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
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2
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Han J, Mu Y, Huang J. Preserving genome integrity: The vital role of SUMO-targeted ubiquitin ligases. CELL INSIGHT 2023; 2:100128. [PMID: 38047137 PMCID: PMC10692494 DOI: 10.1016/j.cellin.2023.100128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 12/05/2023]
Abstract
Various post-translational modifications (PTMs) collaboratively fine-tune protein activities. SUMO-targeted ubiquitin E3 ligases (STUbLs) emerge as specialized enzymes that recognize SUMO-modified substrates through SUMO-interaction motifs and subsequently ubiquitinate them via the RING domain, thereby bridging the SUMO and ubiquitin signaling pathways. STUbLs participate in a wide array of molecular processes, including cell cycle regulation, DNA repair, replication, and mitosis, operating under both normal conditions and in response to challenges such as genotoxic stress. Their ability to catalyze various types of ubiquitin chains results in diverse proteolytic and non-proteolytic outcomes for target substrates. Importantly, STUbLs are strategically positioned in close proximity to SUMO proteases and deubiquitinases (DUBs), ensuring precise and dynamic control over their target proteins. In this review, we provide insights into the unique properties and indispensable roles of STUbLs, with a particular emphasis on their significance in preserving genome integrity in humans.
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Affiliation(s)
- Jinhua Han
- Institute of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yanhua Mu
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Jun Huang
- Institute of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
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3
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Claessens LA, Verlaan-de Vries M, de Graaf IJ, Vertegaal ACO. SENP6 regulates localization and nuclear condensation of DNA damage response proteins by group deSUMOylation. Nat Commun 2023; 14:5893. [PMID: 37735495 PMCID: PMC10514054 DOI: 10.1038/s41467-023-41623-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
The SUMO protease SENP6 maintains genomic stability, but mechanistic understanding of this process remains limited. We find that SENP6 deconjugates SUMO2/3 polymers on a group of DNA damage response proteins, including BRCA1-BARD1, 53BP1, BLM and ERCC1-XPF. SENP6 maintains these proteins in a hypo-SUMOylated state under unstressed conditions and counteracts their polySUMOylation after hydroxyurea-induced stress. Co-depletion of RNF4 leads to a further increase in SUMOylation of BRCA1, BARD1 and BLM, suggesting that SENP6 antagonizes targeting of these proteins by RNF4. Functionally, depletion of SENP6 results in uncoordinated recruitment and persistence of SUMO2/3 at UVA laser and ionizing radiation induced DNA damage sites. Additionally, SUMO2/3 and DNA damage response proteins accumulate in nuclear bodies, in a PML-independent manner driven by multivalent SUMO-SIM interactions. These data illustrate coordinated regulation of SUMOylated DNA damage response proteins by SENP6, governing their timely localization at DNA damage sites and nuclear condensation state.
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Affiliation(s)
- Laura A Claessens
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Ilona J de Graaf
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands.
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4
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Salas-Lloret D, Jansen NS, Nagamalleswari E, van der Meulen C, Gracheva E, de Ru AH, Otte HAM, van Veelen PA, Pichler A, Goedhart J, Vertegaal AC, González-Prieto R. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. SCIENCE ADVANCES 2023; 9:eadh2073. [PMID: 37531430 PMCID: PMC10396300 DOI: 10.1126/sciadv.adh2073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
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Affiliation(s)
- Daniel Salas-Lloret
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nicolette S. Jansen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Coen van der Meulen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ekaterina Gracheva
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - H. Anne Marie Otte
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Andrea Pichler
- Max Plank Institute for Immunobiology and Epigenetics, Freiburg, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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5
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Chang YC, Lin K, Baxley RM, Durrett W, Wang L, Stojkova O, Billmann M, Ward H, Myers CL, Bielinsky AK. RNF4 and USP7 cooperate in ubiquitin-regulated steps of DNA replication. Open Biol 2023; 13:230068. [PMID: 37607592 PMCID: PMC10444366 DOI: 10.1098/rsob.230068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
DNA replication requires precise regulation achieved through post-translational modifications, including ubiquitination and SUMOylation. These modifications are linked by the SUMO-targeted E3 ubiquitin ligases (STUbLs). Ring finger protein 4 (RNF4), one of only two mammalian STUbLs, participates in double-strand break repair and resolving DNA-protein cross-links. However, its role in DNA replication has been poorly understood. Using CRISPR/Cas9 genetic screens, we discovered an unexpected dependency of RNF4 mutants on ubiquitin specific peptidase 7 (USP7) for survival in TP53-null retinal pigment epithelial cells. TP53-/-/RNF4-/-/USP7-/- triple knockout (TKO) cells displayed defects in DNA replication that cause genomic instability. These defects were exacerbated by the proteasome inhibitor bortezomib, which limited the nuclear ubiquitin pool. A shortage of free ubiquitin suppressed the ataxia telangiectasia and Rad3-related (ATR)-mediated checkpoint response, leading to increased cell death. In conclusion, RNF4 and USP7 work cooperatively to sustain a functional level of nuclear ubiquitin to maintain the integrity of the genome.
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Affiliation(s)
- Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kevin Lin
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wesley Durrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Olivera Stojkova
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Henry Ward
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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6
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Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres. Int J Mol Sci 2023; 24:ijms24055027. [PMID: 36902458 PMCID: PMC10003056 DOI: 10.3390/ijms24055027] [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: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
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7
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Zhang FL, Yang SY, Liao L, Zhang TM, Zhang YL, Hu SY, Deng L, Huang MY, Andriani L, Ma XY, Shao ZM, Li DQ. Dynamic SUMOylation of MORC2 orchestrates chromatin remodelling and DNA repair in response to DNA damage and drives chemoresistance in breast cancer. Theranostics 2023; 13:973-990. [PMID: 36793866 PMCID: PMC9925317 DOI: 10.7150/thno.79688] [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: 10/09/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Rationale: SUMOylation regulates a plethora of biological processes, and its inhibitors are currently under investigation in clinical trials as anticancer agents. Thus, identifying new targets with site-specific SUMOylation and defining their biological functions will not only provide new mechanistic insights into the SUMOylation signaling but also open an avenue for developing new strategy for cancer therapy. MORC family CW-type zinc finger 2 (MORC2) is a newly identified chromatin-remodeling enzyme with an emerging role in the DNA damage response (DDR), but its regulatory mechanism remains enigmatic. Methods: In vivo and in vitro SUMOylation assays were used to determine the SUMOylation levels of MORC2. Overexpression and knockdown of SUMO-associated enzymes were used to detect their effects on MORC2 SUMOylation. The effect of dynamic MORC2 SUMOylation on the sensitivity of breast cancer cells to chemotherapeutic drugs was examined through in vitro and in vivo functional assays. Immunoprecipitation, GST pull-down, MNase, and chromatin segregation assays were used to explore the underlying mechanisms. Results: Here, we report that MORC2 is modified by small ubiquitin-like modifier 1 (SUMO1) and SUMO2/3 at lysine 767 (K767) in a SUMO-interacting motif dependent manner. MORC2 SUMOylation is induced by SUMO E3 ligase tripartite motif containing 28 (TRIM28) and reversed by deSUMOylase sentrin-specific protease 1 (SENP1). Intriguingly, SUMOylation of MORC2 is decreased at the early stage of DNA damage induced by chemotherapeutic drugs that attenuate the interaction of MORC2 with TRIM28. MORC2 deSUMOylation induces transient chromatin relaxation to enable efficient DNA repair. At the relatively late stage of DNA damage, MORC2 SUMOylation is restored, and SUMOylated MORC2 interacts with protein kinase CSK21 (casein kinase II subunit alpha), which in turn phosphorylates DNA-PKcs (DNA-dependent protein kinase catalytic subunit), thus promoting DNA repair. Notably, expression of a SUMOylation-deficient mutant MORC2 or administration of SUMO inhibitor enhances the sensitivity of breast cancer cells to DNA-damaging chemotherapeutic drugs. Conclusions: Collectively, these findings uncover a novel regulatory mechanism of MORC2 by SUMOylation and reveal the intricate dynamics of MORC2 SUMOylation important for proper DDR. We also propose a promising strategy to sensitize MORC2-driven breast tumors to chemotherapeutic drugs by inhibition of the SUMO pathway.
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Affiliation(s)
- Fang-Lin Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Shao-Ying Yang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li Liao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Tai-Mei Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yin-Ling Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Shu-Yuan Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ling Deng
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Min-Ying Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lisa Andriani
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiao-Yan Ma
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhi-Min Shao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Breast Cancer, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Da-Qiang Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Breast Cancer, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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8
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Ilic D, Magnussen HM, Tirard M. Stress - Regulation of SUMO conjugation and of other Ubiquitin-Like Modifiers. Semin Cell Dev Biol 2022; 132:38-50. [PMID: 34996712 DOI: 10.1016/j.semcdb.2021.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022]
Abstract
Stress is unavoidable and essential to cellular and organismal evolution and failure to adapt or restore homeostasis can lead to severe diseases or even death. At the cellular level, stress drives a plethora of molecular changes, of which variations in the profile of protein post-translational modifications plays a key role in mediating the adaptative response of the genome and proteome to stress. In this context, post-translational modification of proteins by ubiquitin-like modifiers, (Ubl), notably SUMO, is an essential stress response mechanism. In this review, aiming to draw universal concepts of the Ubls stress response, we will decipher how stress alters the expression level, activity, specificity and/or localization of the proteins involved in the conjugation pathways of the various type-I Ubls, and how this result in the modification of particular Ubl targets that will translate an adaptive physiological stress response and allow cells to restore homeostasis.
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Affiliation(s)
- Dragana Ilic
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg; Faculty of Biology, University of Freiburg, D-79104 Freiburg; Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, D-37075 Göttingen
| | - Helge M Magnussen
- MRC Protein Phosphorylation and Ubiquitination Unit, Sir James Black Center, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Marilyn Tirard
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, D-37075 Göttingen.
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9
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea,Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea,Corresponding author. Tel: +82-53-950-6352; Fax: +82-53-955-5522; E-mail:
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10
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707 DOI: 10.5483/bmbrep.2022.55.11.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2023] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
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11
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Singh M, Zhang S, Perez AM, Lee EYC, Lee MYWT, Zhang D. POLDIP3: At the Crossroad of RNA and DNA Metabolism. Genes (Basel) 2022; 13:1921. [PMID: 36360158 PMCID: PMC9690394 DOI: 10.3390/genes13111921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
POLDIP3 was initially identified as a DNA polymerase delta (Pol δ) interacting protein almost twenty years ago. Intriguingly, it also interacts with proteins involved in a variety of RNA related biological processes, such as transcription, pre-mRNA splicing, mRNA export, and translation. Studies in recent years revealed that POLDIP3 also plays critical roles in disassembling genome wide R-loop formation and activating the DNA damage checkpoint in vivo. Here, we review the functions of POLDIP3 in various RNA and DNA related cellular processes. We then propose a unified model to illustrate how POLDIP3 plays such a versatile role at the crossroad of the RNA and DNA metabolism.
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Affiliation(s)
- Manrose Singh
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Alexis M. Perez
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
| | - Ernest Y. C. Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Marietta Y. W. T. Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
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12
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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13
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de Renty C, Pond KW, Yagle MK, Ellis NA. BLM Sumoylation Is Required for Replication Stability and Normal Fork Velocity During DNA Replication. Front Mol Biosci 2022; 9:875102. [PMID: 35847987 PMCID: PMC9284272 DOI: 10.3389/fmolb.2022.875102] [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: 02/13/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
BLM is sumoylated in response to replication stress. We have studied the role of BLM sumoylation in physiologically normal and replication-stressed conditions by expressing in BLM-deficient cells a BLM with SUMO acceptor-site mutations, which we refer to as SUMO-mutant BLM cells. SUMO-mutant BLM cells exhibited multiple defects in both stressed and unstressed DNA replication conditions, including, in hydroxyurea-treated cells, reduced fork restart and increased fork collapse and, in untreated cells, slower fork velocity and increased fork instability as assayed by track-length asymmetry. We further showed by fluorescence recovery after photobleaching that SUMO-mutant BLM protein was less dynamic than normal BLM and comprised a higher immobile fraction at collapsed replication forks. BLM sumoylation has previously been linked to the recruitment of RAD51 to stressed forks in hydroxyurea-treated cells. An important unresolved question is whether the failure to efficiently recruit RAD51 is the explanation for replication stress in untreated SUMO-mutant BLM cells.
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Affiliation(s)
- Christelle de Renty
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Kelvin W Pond
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Mary K Yagle
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Nathan A Ellis
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States.,Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, United States
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14
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Ellis N, Zhu J, Yagle MK, Yang WC, Huang J, Kwako A, Seidman MM, Matunis MJ. RNF4 Regulates the BLM Helicase in Recovery From Replication Fork Collapse. Front Genet 2021; 12:753535. [PMID: 34868226 PMCID: PMC8633118 DOI: 10.3389/fgene.2021.753535] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/25/2021] [Indexed: 12/01/2022] Open
Abstract
Sumoylation is an important enhancer of responses to DNA replication stress and the SUMO-targeted ubiquitin E3 ligase RNF4 regulates these responses by ubiquitylation of sumoylated DNA damage response factors. The specific targets and functional consequences of RNF4 regulation in response to replication stress, however, have not been fully characterized. Here we demonstrated that RNF4 is required for the restart of DNA replication following prolonged hydroxyurea (HU)-induced replication stress. Contrary to its role in repair of γ-irradiation-induced DNA double-strand breaks (DSBs), our analysis revealed that RNF4 does not significantly impact recognition or repair of replication stress-associated DSBs. Rather, using DNA fiber assays, we found that the firing of new DNA replication origins, which is required for replication restart following prolonged stress, was inhibited in cells depleted of RNF4. We also provided evidence that RNF4 recognizes and ubiquitylates sumoylated Bloom syndrome DNA helicase BLM and thereby promotes its proteosome-mediated turnover at damaged DNA replication forks. Consistent with it being a functionally important RNF4 substrate, co-depletion of BLM rescued defects in the firing of new replication origins observed in cells depleted of RNF4 alone. We concluded that RNF4 acts to remove sumoylated BLM from collapsed DNA replication forks, which is required to facilitate normal resumption of DNA synthesis after prolonged replication fork stalling and collapse.
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Affiliation(s)
- Nathan Ellis
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Jianmei Zhu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Mary K Yagle
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Wei-Chih Yang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, United States
| | - Alexander Kwako
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, United States
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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15
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Giordano I, Pirone L, Muratore V, Landaluze E, Pérez C, Lang V, Garde-Lapido E, Gonzalez-Lopez M, Barroso-Gomila O, Vertegaal ACO, Aransay AM, Rodriguez JA, Rodriguez MS, Sutherland JD, Barrio R. SALL1 Modulates CBX4 Stability, Nuclear Bodies, and Regulation of Target Genes. Front Cell Dev Biol 2021; 9:715868. [PMID: 34621739 PMCID: PMC8490708 DOI: 10.3389/fcell.2021.715868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Development is orchestrated through a complex interplay of multiple transcription factors. The comprehension of this interplay will help us to understand developmental processes. Here we analyze the relationship between two key transcription factors: CBX4, a member of the Polycomb Repressive Complex 1 (PRC1), and SALL1, a member of the Spalt-like family with important roles in embryogenesis and limb development. Both proteins localize to nuclear bodies and are modified by the small ubiquitin-like modifier (SUMO). Our results show that CBX4 and SALL1 interact in the nucleoplasm and that increased SALL1 expression reduces ubiquitination of CBX4, enhancing its stability. This is accompanied by an increase in the number and size of CBX4-containing Polycomb bodies, and by a greater repression of CBX4 target genes. Thus, our findings uncover a new way of SALL1-mediated regulation of Polycomb bodies through modulation of CBX4 stability, with consequences in the regulation of its target genes, which could have an impact in cell differentiation and development.
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Affiliation(s)
- Immacolata Giordano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Lucia Pirone
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Eukene Landaluze
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Coralia Pérez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Valerie Lang
- Viralgen Vector Core, Parque Científico y Tecnológico de Guipúzcoa, San Sebastián, Spain
| | - Elisa Garde-Lapido
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Monika Gonzalez-Lopez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ana M Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination-CNRS, Paul Sabatier: Université Toulouse III, Toulouse, France
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
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16
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ATM controls the extent of DNA end resection by eliciting sequential posttranslational modifications of CtIP. Proc Natl Acad Sci U S A 2021; 118:2022600118. [PMID: 33723063 DOI: 10.1073/pnas.2022600118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA end resection is a critical step in the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR). However, the mechanisms governing the extent of resection at DSB sites undergoing homology-directed repair remain unclear. Here, we show that, upon DSB induction, the key resection factor CtIP is modified by the ubiquitin-like protein SUMO at lysine 578 in a PIAS4-dependent manner. CtIP SUMOylation occurs on damaged chromatin and requires prior hyperphosphorylation by the ATM protein kinase. SUMO-modified hyperphosphorylated CtIP is targeted by the SUMO-dependent E3 ubiquitin ligase RNF4 for polyubiquitination and subsequent degradation. Consequently, disruption of CtIP SUMOylation results in aberrant accumulation of CtIP at DSBs, which, in turn, causes uncontrolled excessive resection, defective HR, and increased cellular sensitivity to DSB-inducing agents. These findings reveal a previously unidentified regulatory mechanism that regulates CtIP activity at DSBs and thus the extent of end resection via ATM-dependent sequential posttranslational modification of CtIP.
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17
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Bouchard D, Wang W, Yang WC, He S, Garcia A, Matunis MJ. SUMO paralogue-specific functions revealed through systematic analysis of human knockout cell lines and gene expression data. Mol Biol Cell 2021; 32:1849-1866. [PMID: 34232706 PMCID: PMC8684707 DOI: 10.1091/mbc.e21-01-0031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The small ubiquitin-related modifiers (SUMOs) regulate nearly every aspect of cellular function, from gene expression in the nucleus to ion transport at the plasma membrane. In humans, the SUMO pathway has five SUMO paralogues with sequence homologies that range from 45% to 97%. SUMO1 and SUMO2 are the most distantly related paralogues and also the best studied. To what extent SUMO1, SUMO2, and the other paralogues impart unique and nonredundant effects on cellular functions, however, has not been systematically examined and is therefore not fully understood. For instance, knockout studies in mice have revealed conflicting requirements for the paralogues during development and studies in cell culture have relied largely on transient paralogue overexpression or knockdown. To address the existing gap in understanding, we first analyzed SUMO paralogue gene expression levels in normal human tissues and found unique patterns of SUMO1–3 expression across 30 tissue types, suggesting paralogue-specific functions in adult human tissues. To systematically identify and characterize unique and nonredundant functions of the SUMO paralogues in human cells, we next used CRISPR-Cas9 to knock out SUMO1 and SUMO2 expression in osteosarcoma (U2OS) cells. Analysis of these knockout cell lines revealed essential functions for SUMO1 and SUMO2 in regulating cellular morphology, promyelocytic leukemia (PML) nuclear body structure, responses to proteotoxic and genotoxic stress, and control of gene expression. Collectively, our findings reveal nonredundant regulatory roles for SUMO1 and SUMO2 in controlling essential cellular processes and provide a basis for more precise SUMO-targeting therapies.
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Affiliation(s)
- Danielle Bouchard
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Wei Wang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Wei-Chih Yang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Shuying He
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Anthony Garcia
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
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18
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Robinson NJ, Miyagi M, Scarborough JA, Scott JG, Taylor DJ, Schiemann WP. SLX4IP promotes RAP1 SUMOylation by PIAS1 to coordinate telomere maintenance through NF-κB and Notch signaling. Sci Signal 2021; 14:eabe9613. [PMID: 34187905 PMCID: PMC8353884 DOI: 10.1126/scisignal.abe9613] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The maintenance of telomere length supports repetitive cell division and therefore plays a central role in cancer development and progression. Telomeres are extended by either the enzyme telomerase or the alternative lengthening of telomeres (ALT) pathway. Here, we found that the telomere-associated protein SLX4IP dictates telomere proteome composition by recruiting and activating the E3 SUMO ligase PIAS1 to the SLX4 complex. PIAS1 SUMOylated the telomere-binding protein RAP1, which disrupted its interaction with the telomere-binding protein TRF2 and facilitated its nucleocytoplasmic shuttling. In the cytosol, RAP1 bound to IκB kinase (IKK), resulting in activation of the transcription factor NF-κB and its induction of Jagged-1 expression, which promoted Notch signaling and the institution of ALT. This axis could be targeted therapeutically in ALT-driven cancers and in tumor cells that develop resistance to antitelomerase therapies. Our results illuminate the mechanisms underlying SLX4IP-dependent telomere plasticity and demonstrate the role of telomere proteins in directly coordinating intracellular signaling and telomere maintenance dynamics.
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Affiliation(s)
- Nathaniel J Robinson
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jessica A Scarborough
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jacob G Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.
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19
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Chang YC, Oram MK, Bielinsky AK. SUMO-Targeted Ubiquitin Ligases and Their Functions in Maintaining Genome Stability. Int J Mol Sci 2021; 22:ijms22105391. [PMID: 34065507 PMCID: PMC8161396 DOI: 10.3390/ijms22105391] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/14/2021] [Accepted: 05/16/2021] [Indexed: 02/06/2023] Open
Abstract
Small ubiquitin-like modifier (SUMO)-targeted E3 ubiquitin ligases (STUbLs) are specialized enzymes that recognize SUMOylated proteins and attach ubiquitin to them. They therefore connect the cellular SUMOylation and ubiquitination circuits. STUbLs participate in diverse molecular processes that span cell cycle regulated events, including DNA repair, replication, mitosis, and transcription. They operate during unperturbed conditions and in response to challenges, such as genotoxic stress. These E3 ubiquitin ligases modify their target substrates by catalyzing ubiquitin chains that form different linkages, resulting in proteolytic or non-proteolytic outcomes. Often, STUbLs function in compartmentalized environments, such as the nuclear envelope or kinetochore, and actively aid in nuclear relocalization of damaged DNA and stalled replication forks to promote DNA repair or fork restart. Furthermore, STUbLs reside in the same vicinity as SUMO proteases and deubiquitinases (DUBs), providing spatiotemporal control of their targets. In this review, we focus on the molecular mechanisms by which STUbLs help to maintain genome stability across different species.
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20
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Ma X, Chen T, Peng Z, Wang Z, Liu J, Yang T, Wu L, Liu G, Zhou M, Tong M, Guan Y, Zhang X, Lin Y, Tang X, Li L, Tang Z, Pan T, Zhang H. Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies. EMBO J 2021; 40:e106632. [PMID: 33739466 PMCID: PMC8126954 DOI: 10.15252/embj.2020106632] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023] Open
Abstract
HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.
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Affiliation(s)
- Xiancai Ma
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Chen
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhilin Peng
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ziwen Wang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jun Liu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Yang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Liyang Wu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Guangyan Liu
- College of Basic Medical SciencesShenyang Medical CollegeShenyangLiaoningChina
| | - Mo Zhou
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Muye Tong
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yuanjun Guan
- Core Laboratory Platform for Medical ScienceZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xu Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yingtong Lin
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xiaoping Tang
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Linghua Li
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Zhonghui Tang
- Department of BioinformaticsZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ting Pan
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Hui Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
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21
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SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization. Mol Cell Biol 2021; 41:MCB.00464-20. [PMID: 33526451 DOI: 10.1128/mcb.00464-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/20/2021] [Indexed: 12/29/2022] Open
Abstract
The nuclear and subnuclear compartmentalization of the telomerase-associated protein and H/ACA ribonucleoprotein component dyskerin is an important although incompletely understood aspect of H/ACA ribonucleoprotein function. Four SUMOylation sites were previously identified in the C-terminal nuclear/nucleolar localization signal (N/NoLS) of dyskerin. We found that a cytoplasmic localized C-terminal truncation variant of dyskerin lacking most of the C-terminal N/NoLS represents an under-SUMOylated variant of dyskerin compared to wild-type dyskerin. We demonstrate that mimicking constitutive SUMOylation of dyskerin using a SUMO3 fusion construct can drive nuclear accumulation of this variant and that the SUMO site K467 in this N/NoLS is particularly important for the subnuclear localization of dyskerin to the nucleolus in a mature H/ACA complex assembly- and SUMO-dependent manner. We also characterize a novel SUMO-interacting motif in the mature H/ACA complex component GAR1 that mediates the interaction between dyskerin and GAR1. Mislocalization of dyskerin, either in the cytoplasm or excluded from the nucleolus, disrupts dyskerin function and leads to reduced interaction of dyskerin with the telomerase RNA. These data indicate a role for dyskerin C-terminal N/NoLS SUMOylation in regulating the nuclear and subnuclear localization of dyskerin, which is essential for dyskerin function as both a telomerase-associated protein and as an H/ACA ribonucleoprotein.
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22
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Paakinaho V, Lempiäinen JK, Sigismondo G, Niskanen EA, Malinen M, Jääskeläinen T, Varjosalo M, Krijgsveld J, Palvimo J. SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites. Nucleic Acids Res 2021; 49:1951-1971. [PMID: 33524141 PMCID: PMC7913686 DOI: 10.1093/nar/gkab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of regulation has remained elusive. Here, we identify the protein network around chromatin-bound GR by using selective isolation of chromatin-associated proteins and show that the network is affected by receptor SUMOylation, with several nuclear receptor coregulators and chromatin modifiers preferring interaction with SUMOylation-deficient GR and proteins implicated in transcriptional repression preferring interaction with SUMOylation-competent GR. This difference is reflected in our chromatin binding, chromatin accessibility and gene expression data, showing that the SUMOylation-deficient GR is more potent in binding and opening chromatin at glucocorticoid-regulated enhancers and inducing expression of target loci. Blockage of SUMOylation by a SUMO-activating enzyme inhibitor (ML-792) phenocopied to a large extent the consequences of GR SUMOylation deficiency on chromatin binding and target gene expression. Our results thus show that SUMOylation modulates the specificity of GR by regulating its chromatin protein network and accessibility at GR-bound enhancers. We speculate that many other SUMOylated TFs utilize a similar regulatory mechanism.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | | | - Einari A Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marjo Malinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Tiina Jääskeläinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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23
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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24
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Arnold F, Gout J, Wiese H, Weissinger SE, Roger E, Perkhofer L, Walter K, Scheible J, Prelli Bozzo C, Lechel A, Ettrich TJ, Azoitei N, Hao L, Fürstberger A, Kaminska EK, Sparrer KMJ, Rasche V, Wiese S, Kestler HA, Möller P, Seufferlein T, Frappart PO, Kleger A. RINT1 Regulates SUMOylation and the DNA Damage Response to Preserve Cellular Homeostasis in Pancreatic Cancer. Cancer Res 2021; 81:1758-1774. [PMID: 33531371 DOI: 10.1158/0008-5472.can-20-2633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/14/2020] [Accepted: 01/28/2021] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) still presents with a dismal prognosis despite intense research. Better understanding of cellular homeostasis could identify druggable targets to improve therapy. Here we propose RAD50-interacting protein 1 (RINT1) as an essential mediator of cellular homeostasis in PDAC. In a cohort of resected PDAC, low RINT1 protein expression correlated significantly with better survival. Accordingly, RINT1 depletion caused severe growth defects in vitro associated with accumulation of DNA double-strand breaks (DSB), G2 cell cycle arrest, disruption of Golgi-endoplasmic reticulum homeostasis, and cell death. Time-resolved transcriptomics corroborated by quantitative proteome and interactome analyses pointed toward defective SUMOylation after RINT1 loss, impairing nucleocytoplasmic transport and DSB response. Subcutaneous xenografts confirmed tumor response by RINT1 depletion, also resulting in a survival benefit when transferred to an orthotopic model. Primary human PDAC organoids licensed RINT1 relevance for cell viability. Taken together, our data indicate that RINT1 loss affects PDAC cell fate by disturbing SUMOylation pathways. Therefore, a RINT1 interference strategy may represent a new putative therapeutic approach. SIGNIFICANCE: These findings provide new insights into the aggressive behavior of PDAC, showing that RINT1 directly correlates with survival in patients with PDAC by disturbing the SUMOylation process, a crucial modification in carcinogenesis.
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Affiliation(s)
- Frank Arnold
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Johann Gout
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Heike Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, Ulm, Germany
| | | | - Elodie Roger
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Lukas Perkhofer
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Karolin Walter
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Jeanette Scheible
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | | | - André Lechel
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Thomas J Ettrich
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Ninel Azoitei
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | - Li Hao
- Center for Translational Imaging (MoMAN), Ulm University, Ulm, Germany
| | - Axel Fürstberger
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Ewa K Kaminska
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Volker Rasche
- Center for Translational Imaging (MoMAN), Ulm University, Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, Ulm, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Peter Möller
- Institute of Pathology, University Medical Centre Ulm, Ulm, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany
| | | | - Alexander Kleger
- Department of Internal Medicine I, University Medical Centre Ulm, Ulm, Germany.
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25
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Locke AJ, Hossain L, McCrostie G, Ronato DA, Fitieh A, Rafique T, Mashayekhi F, Motamedi M, Masson JY, Ismail I. SUMOylation mediates CtIP's functions in DNA end resection and replication fork protection. Nucleic Acids Res 2021; 49:928-953. [PMID: 33406258 PMCID: PMC7826263 DOI: 10.1093/nar/gkaa1232] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
Double-strand breaks and stalled replication forks are a significant threat to genomic stability that can lead to chromosomal rearrangements or cell death. The protein CtIP promotes DNA end resection, an early step in homologous recombination repair, and has been found to protect perturbed forks from excessive nucleolytic degradation. However, it remains unknown how CtIP's function in fork protection is regulated. Here, we show that CtIP recruitment to sites of DNA damage and replication stress is impaired upon global inhibition of SUMOylation. We demonstrate that CtIP is a target for modification by SUMO-2 and that this occurs constitutively during S phase. The modification is dependent on the activities of cyclin-dependent kinases and the PI-3-kinase-related kinase ATR on CtIP's carboxyl-terminal region, an interaction with the replication factor PCNA, and the E3 SUMO ligase PIAS4. We also identify residue K578 as a key residue that contributes to CtIP SUMOylation. Functionally, a CtIP mutant where K578 is substituted with a non-SUMOylatable arginine residue is defective in promoting DNA end resection, homologous recombination, and in protecting stalled replication forks from excessive nucleolytic degradation. Our results shed further light on the tightly coordinated regulation of CtIP by SUMOylation in the maintenance of genome stability.
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Affiliation(s)
- Andrew J Locke
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Lazina Hossain
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Glynnis McCrostie
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Daryl A Ronato
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec City, Québec, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine; Laval University Cancer Research Center, Université Laval, Québec City, Québec, G1V 0A6, Canada
| | - Amira Fitieh
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Tanzeem Ahmed Rafique
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Mobina Motamedi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Jean-Yves Masson
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec City, Québec, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine; Laval University Cancer Research Center, Université Laval, Québec City, Québec, G1V 0A6, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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26
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Barysch SV, Stankovic-Valentin N, Miedema T, Karaca S, Doppel J, Nait Achour T, Vasudeva A, Wolf L, Sticht C, Urlaub H, Melchior F. Transient deSUMOylation of IRF2BP proteins controls early transcription in EGFR signaling. EMBO Rep 2021; 22:e49651. [PMID: 33480129 PMCID: PMC7926235 DOI: 10.15252/embr.201949651] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
Molecular switches are essential modules in signaling networks and transcriptional reprogramming. Here, we describe a role for small ubiquitin‐related modifier SUMO as a molecular switch in epidermal growth factor receptor (EGFR) signaling. Using quantitative mass spectrometry, we compare the endogenous SUMO proteomes of HeLa cells before and after EGF stimulation. Thereby, we identify a small group of transcriptional coregulators including IRF2BP1, IRF2BP2, and IRF2BPL as novel players in EGFR signaling. Comparison of cells expressing wild type or SUMOylation‐deficient IRF2BP1 indicates that transient deSUMOylation of IRF2BP proteins is important for appropriate expression of immediate early genes including dual specificity phosphatase 1 (DUSP1, MKP‐1) and the transcription factor ATF3. We find that IRF2BP1 is a repressor, whose transient deSUMOylation on the DUSP1 promoter allows—and whose timely reSUMOylation restricts—DUSP1 transcription. Our work thus provides a paradigm how comparative SUMO proteome analyses serve to reveal novel regulators in signal transduction and transcription.
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Affiliation(s)
- Sina V Barysch
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Tim Miedema
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Samir Karaca
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Judith Doppel
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Thiziri Nait Achour
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Aarushi Vasudeva
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Lucie Wolf
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics, Heidelberg, Germany.,BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Carsten Sticht
- Center of Medical Research, Bioinformatic and Statistic, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
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27
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Cai H, Yu Y, Ni X, Li C, Hu Y, Wang J, Chen F, Xi S, Chen Z. LncRNA LINC00998 inhibits the malignant glioma phenotype via the CBX3-mediated c-Met/Akt/mTOR axis. Cell Death Dis 2020; 11:1032. [PMID: 33268783 PMCID: PMC7710718 DOI: 10.1038/s41419-020-03247-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022]
Abstract
Long noncoding RNAs (lncRNAs), once considered to be nonfunctional relics of evolution, are emerging as essential genes in tumor progression. However, the function and underlying mechanisms of lncRNAs in glioma remain unclear. This study aimed to investigate the role of LINC00998 in glioma progression. Through screening using TCGA database, we found that LINC00998 was downregulated in glioblastoma tissues and that low expression of LINC00998 was associated with poor prognosis. Overexpression of LINC00998 inhibited glioma cell proliferation in vitro and in vivo and blocked the G1/S cell cycle transition, which exerted a tumor-suppressive effect on glioma progression. Mechanistically, RNA pull-down and mass spectrometry results showed an interaction between LINC00998 and CBX3. IP assays demonstrated that LINC00998 could stabilize CBX3 and prevent its ubiquitination degradation. GSEA indicated that LINC00998 could regulate the c-Met/Akt/mTOR signaling pathway, which was further confirmed by a rescue assay using siRNA-mediated knockdown of CBX3 and the Akt inhibitor MK2206. In addition, dual-luciferase assays showed that miR-34c-5p could directly bind to LINC00998 and downregulate its expression. Our results identified LINC00998 as a novel tumor suppressor in glioma, and LINC00998 could be a novel prognostic biomarker, providing a strategy for precision therapy in glioma patients.
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Affiliation(s)
- Haiping Cai
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China
| | - Yanjiao Yu
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China
| | - Xiangrong Ni
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China
| | - Cong Li
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China
| | - Yuanjun Hu
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China
| | - Jing Wang
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China
| | - Furong Chen
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China
| | - Shaoyan Xi
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China.
| | - Zhongping Chen
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, PR China.
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28
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Mus81-Mms4 endonuclease is an Esc2-STUbL-Cullin8 mitotic substrate impacting on genome integrity. Nat Commun 2020; 11:5746. [PMID: 33184279 PMCID: PMC7665200 DOI: 10.1038/s41467-020-19503-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
The Mus81-Mms4 nuclease is activated in G2/M via Mms4 phosphorylation to allow resolution of persistent recombination structures. However, the fate of the activated phosphorylated Mms4 remains unknown. Here we find that Mms4 is engaged by (poly)SUMOylation and ubiquitylation and targeted for proteasome degradation, a process linked to the previously described Mms4 phosphorylation cycle. Mms4 is a mitotic substrate for the SUMO-Targeted Ubiquitin ligase Slx5/8, the SUMO-like domain-containing protein Esc2, and the Mms1-Cul8 ubiquitin ligase. In the absence of these activities, phosphorylated Mms4 accumulates on chromatin in an active state in the next G1, subsequently causing abnormal processing of replication-associated recombination intermediates and delaying the activation of the DNA damage checkpoint. Mus81-Mms4 mutants that stabilize phosphorylated Mms4 have similar detrimental effects on genome integrity. Overall, our findings highlight a replication protection function for Esc2-STUbL-Cul8 and emphasize the importance for genome stability of resetting phosphorylated Mms4 from one cycle to another. Mus81-Mms4 endonuclease is critical for processing various DNA recombination structures. Here the authors uncover a regulatory mechanism of the endonuclease via posttranslational modifications involving SUMOylation and ubiquitylation that impact on genome integrity.
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29
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Srivastava M, Su D, Zhang H, Chen Z, Tang M, Nie L, Chen J. HMCES safeguards replication from oxidative stress and ensures error-free repair. EMBO Rep 2020; 21:e49123. [PMID: 32307824 DOI: 10.15252/embr.201949123] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 03/14/2020] [Accepted: 03/19/2020] [Indexed: 02/02/2023] Open
Abstract
Replication across oxidative DNA lesions can give rise to mutations that pose a threat to genome integrity. How such lesions, which escape base excision repair, get removed without error during replication remains unknown. Our PCNA-based screen to uncover changes in replisome composition under different replication stress conditions had revealed a previously unknown PCNA-interacting protein, HMCES/C3orf37. Here, we show that HMCES is a critical component of the replication stress response, mainly upon base misincorporation. We further demonstrate that the absence of HMCES imparts resistance to pemetrexed treatment due to error-prone bypass of oxidative damage. Furthermore, based on genetic screening, we show that homologous recombination repair proteins, such as CtIP, BRCA2, BRCA1, and PALB2, are indispensable for the survival of HMCES KO cells. Hence, HMCES, which is the sole member of the SRAP superfamily in higher eukaryotes known so far, acts as a proofreader on replication forks, facilitates resolution of oxidative base damage, and therefore ensures faithful DNA replication.
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Affiliation(s)
- Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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30
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Liebelt F, Schimmel J, Verlaan-de Vries M, Klemann E, van Royen ME, van der Weegen Y, Luijsterburg MS, Mullenders LH, Pines A, Vermeulen W, Vertegaal ACO. Transcription-coupled nucleotide excision repair is coordinated by ubiquitin and SUMO in response to ultraviolet irradiation. Nucleic Acids Res 2020; 48:231-248. [PMID: 31722399 PMCID: PMC7145520 DOI: 10.1093/nar/gkz977] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 12/04/2022] Open
Abstract
Cockayne Syndrome (CS) is a severe neurodegenerative and premature aging autosomal-recessive disease, caused by inherited defects in the CSA and CSB genes, leading to defects in transcription-coupled nucleotide excision repair (TC-NER) and consequently hypersensitivity to ultraviolet (UV) irradiation. TC-NER is initiated by lesion-stalled RNA polymerase II, which stabilizes the interaction with the SNF2/SWI2 ATPase CSB to facilitate recruitment of the CSA E3 Cullin ubiquitin ligase complex. However, the precise biochemical connections between CSA and CSB are unknown. The small ubiquitin-like modifier SUMO is important in the DNA damage response. We found that CSB, among an extensive set of other target proteins, is the most dynamically SUMOylated substrate in response to UV irradiation. Inhibiting SUMOylation reduced the accumulation of CSB at local sites of UV irradiation and reduced recovery of RNA synthesis. Interestingly, CSA is required for the efficient clearance of SUMOylated CSB. However, subsequent proteomic analysis of CSA-dependent ubiquitinated substrates revealed that CSA does not ubiquitinate CSB in a UV-dependent manner. Surprisingly, we found that CSA is required for the ubiquitination of the largest subunit of RNA polymerase II, RPB1. Combined, our results indicate that the CSA, CSB, RNA polymerase II triad is coordinated by ubiquitin and SUMO in response to UV irradiation. Furthermore, our work provides a resource of SUMO targets regulated in response to UV or ionizing radiation.
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Affiliation(s)
- Frauke Liebelt
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Joost Schimmel
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Matty Verlaan-de Vries
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Esra Klemann
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Cancer Treatment Screening Facility (CTSF), Erasmus Optical Imaging Centre (OIC), Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Leon H Mullenders
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands.,Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Japan
| | - Alex Pines
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
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31
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Nayak A, Amrute-Nayak M. SUMO system - a key regulator in sarcomere organization. FEBS J 2020; 287:2176-2190. [PMID: 32096922 DOI: 10.1111/febs.15263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/07/2020] [Accepted: 02/24/2020] [Indexed: 01/14/2023]
Abstract
Skeletal muscles constitute roughly 40% of human body mass. Muscles are specialized tissues that generate force to drive movements through ATP-driven cyclic interactions between the protein filaments, namely actin and myosin filaments. The filaments are organized in an intricate structure called the 'sarcomere', which is a fundamental contractile unit of striated skeletal and cardiac muscle, hosting a fine assembly of macromolecular protein complexes. The micrometer-sized sarcomere units are arranged in a reiterated array within myofibrils of muscle cells. The precise spatial organization of sarcomere is tightly controlled by several molecular mechanisms, indispensable for its force-generating function. Disorganized sarcomeres, either due to erroneous molecular signaling or due to mutations in the sarcomeric proteins, lead to human diseases such as cardiomyopathies and muscle atrophic conditions prevalent in cachexia. Protein post-translational modifications (PTMs) of the sarcomeric proteins serve a critical role in sarcomere formation (sarcomerogenesis), as well as in the steady-state maintenance of sarcomeres. PTMs such as phosphorylation, acetylation, ubiquitination, and SUMOylation provide cells with a swift and reversible means to adapt to an altered molecular and therefore cellular environment. Over the past years, SUMOylation has emerged as a crucial modification with implications for different aspects of cell function, including organizing higher-order protein assemblies. In this review, we highlight the fundamentals of the small ubiquitin-like modifiers (SUMO) pathway and its link specifically to the mechanisms of sarcomere assembly. Furthermore, we discuss recent studies connecting the SUMO pathway-modulated protein homeostasis with sarcomere organization and muscle-related pathologies.
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Affiliation(s)
- Arnab Nayak
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Mamta Amrute-Nayak
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
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32
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Hegde S, Soory A, Kaduskar B, Ratnaparkhi GS. SUMO conjugation regulates immune signalling. Fly (Austin) 2020; 14:62-79. [PMID: 32777975 PMCID: PMC7714519 DOI: 10.1080/19336934.2020.1808402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) are critical drivers and attenuators for proteins that regulate immune signalling cascades in host defence. In this review, we explore functional roles for one such PTM, the small ubiquitin-like modifier (SUMO). Very few of the SUMO conjugation targets identified by proteomic studies have been validated in terms of their roles in host defence. Here, we compare and contrast potential SUMO substrate proteins in immune signalling for flies and mammals, with an emphasis on NFκB pathways. We discuss, using the few mechanistic studies that exist for validated targets, the effect of SUMO conjugation on signalling and also explore current molecular models that explain regulation by SUMO. We also discuss in detail roles of evolutionary conservation of mechanisms, SUMO interaction motifs, crosstalk of SUMO with other PTMs, emerging concepts such as group SUMOylation and finally, the potentially transforming roles for genome-editing technologies in studying the effect of PTMs.
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Affiliation(s)
- Sushmitha Hegde
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
| | - Amarendranath Soory
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
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33
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Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ. Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability. Nucleic Acids Res 2019; 47:8004-8018. [PMID: 31180492 PMCID: PMC6735892 DOI: 10.1093/nar/gkz510] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/27/2019] [Accepted: 05/30/2019] [Indexed: 01/31/2023] Open
Abstract
Common fragile sites (CFSs) are conserved genomic regions prone to break under conditions of replication stress (RS). Thus, CFSs are hotspots for rearrangements in cancer and contribute to its chromosomal instability. Here, we have performed a global analysis of proteins that recruit to CFSs upon mild RS to identify novel players in CFS stability. To this end, we performed Chromatin Immunoprecipitation (ChIP) of FANCD2, a protein that localizes specifically to CFSs in G2/M, coupled to mass spectrometry to acquire a CFS interactome. Our strategy was validated by the enrichment of many known regulators of CFS maintenance, including Fanconi Anemia, DNA repair and replication proteins. Among the proteins identified with unknown functions at CFSs was the chromatin remodeler ATRX. Here we demonstrate that ATRX forms foci at a fraction of CFSs upon RS, and that ATRX depletion increases the occurrence of chromosomal breaks, a phenotype further exacerbated under mild RS conditions. Accordingly, ATRX depletion increases the number of 53BP1 bodies and micronuclei, overall indicating that ATRX is required for CFS stability. Overall, our study provides the first proteomic characterization of CFSs as a valuable resource for the identification of novel regulators of CFS stability.
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Affiliation(s)
- David Pladevall-Morera
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark
| | - Stephanie Munk
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark.,Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andreas Ingham
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark
| | - Lorenza Garribba
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark
| | - Eliene Albers
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark
| | - Ying Liu
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andres J Lopez-Contreras
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark
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Abstract
The homologous recombination (HR) machinery plays multiple roles in genome maintenance. Best studied in the context of DNA double-stranded break (DSB) repair, recombination enzymes can cleave, pair, and unwind DNA molecules, and collaborate with regulatory proteins to execute multiple DNA processing steps before generating specific repair products. HR proteins also help to cope with problems arising from DNA replication, modulating impaired replication forks or filling DNA gaps. Given these important roles, it is not surprising that each HR step is subject to complex regulation to adjust repair efficiency and outcomes as well as to limit toxic intermediates. Recent studies have revealed intricate regulation of all steps of HR by the protein modifier SUMO, which has been increasingly recognized for its broad influence in nuclear functions. This review aims to connect established roles of SUMO with its newly identified effects on recombinational repair and stimulate further thought on many unanswered questions.
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Affiliation(s)
- Nalini Dhingra
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Nguéa P A, Robertson J, Herrera MC, Chymkowitch P, Enserink JM. Desumoylation of RNA polymerase III lies at the core of the Sumo stress response in yeast. J Biol Chem 2019; 294:18784-18795. [PMID: 31676685 DOI: 10.1074/jbc.ra119.009721] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/30/2019] [Indexed: 12/14/2022] Open
Abstract
Post-translational modification by small ubiquitin-like modifier (Sumo) regulates many cellular processes, including the adaptive response to various types of stress, referred to as the Sumo stress response (SSR). However, it remains unclear whether the SSR involves a common set of core proteins regardless of the type of stress or whether each particular type of stress induces a stress-specific SSR that targets a unique, largely nonoverlapping set of Sumo substrates. In this study, we used MS and a Gene Ontology approach to identify differentially sumoylated proteins during heat stress, hyperosmotic stress, oxidative stress, nitrogen starvation, and DNA alkylation in Saccharomyces cerevisiae cells. Our results indicate that each stress triggers a specific SSR signature centered on proteins involved in transcription, translation, and chromatin regulation. Strikingly, whereas the various stress-specific SSRs were largely nonoverlapping, all types of stress tested here resulted in desumoylation of subunits of RNA polymerase III, which correlated with a decrease in tRNA synthesis. We conclude that desumoylation and subsequent inhibition of RNA polymerase III constitutes the core of all stress-specific SSRs in yeast.
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Affiliation(s)
- Aurélie Nguéa P
- Department of Molecular Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway
| | - Joseph Robertson
- Department of Molecular Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway
| | - Maria Carmen Herrera
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway
| | - Pierre Chymkowitch
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway.
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Sha Z, Blyszcz T, González-Prieto R, Vertegaal ACO, Goldberg AL. Inhibiting ubiquitination causes an accumulation of SUMOylated newly synthesized nuclear proteins at PML bodies. J Biol Chem 2019; 294:15218-15234. [PMID: 31285264 PMCID: PMC6802522 DOI: 10.1074/jbc.ra119.009147] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/21/2019] [Indexed: 12/31/2022] Open
Abstract
Protein ubiquitination and SUMOylation are required for the maintenance of cellular protein homeostasis, and both increase in proteotoxic conditions (e.g. heat shock or proteasome inhibition). However, we found that when ubiquitination was blocked in several human cell lines by inhibiting the ubiquitin-activating enzyme with TAK243, there was an unexpected, large accumulation of proteins modified by SUMO2/3 chains or SUMO1, but not by several other ubiquitin-like proteins. This buildup of SUMOylated proteins was evident within 3–4 h. It required the small ubiquitin-like modifier (SUMO)-conjugating enzyme, UBC9, and the promyelocytic leukemia protein (PML) and thus was not due to nonspecific SUMO conjugation by ubiquitination enzymes. The SUMOylated proteins accumulated predominantly bound to chromatin and were localized to PML nuclear bodies. Because blocking protein synthesis with cycloheximide prevented the buildup of SUMOylated proteins, they appeared to be newly-synthesized proteins. The proteins SUMOylated after inhibition of ubiquitination were purified and analyzed by MS. In HeLa and U2OS cells, there was a cycloheximide-sensitive increase in a similar set of SUMOylated proteins (including transcription factors and proteins involved in DNA damage repair). Surprisingly, the inhibition of ubiquitination also caused a cycloheximide-sensitive decrease in a distinct set of SUMOylated proteins (including proteins for chromosome modification and mRNA splicing). More than 80% of the SUMOylated proteins whose levels rose or fell upon inhibiting ubiquitination inhibition underwent similar cycloheximide-sensitive increases or decreases upon proteasome inhibition. Thus, when nuclear substrates of the ubiquitin–proteasome pathway are not efficiently degraded, many become SUMO-modified and accumulate in PML bodies.
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Affiliation(s)
- Zhe Sha
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Tamara Blyszcz
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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Chachami G, Stankovic-Valentin N, Karagiota A, Basagianni A, Plessmann U, Urlaub H, Melchior F, Simos G. Hypoxia-induced Changes in SUMO Conjugation Affect Transcriptional Regulation Under Low Oxygen. Mol Cell Proteomics 2019; 18:1197-1209. [PMID: 30926672 PMCID: PMC6553927 DOI: 10.1074/mcp.ra119.001401] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
Hypoxia occurs in pathological conditions, such as cancer, as a result of the imbalance between oxygen supply and consumption by proliferating cells. HIFs are critical molecular mediators of the physiological response to hypoxia but also regulate multiple steps of carcinogenesis including tumor progression and metastasis. Recent data support that sumoylation, the covalent attachment of the Small Ubiquitin-related MOdifier (SUMO) to proteins, is involved in the activation of the hypoxic response and the ensuing signaling cascade. To gain insights into differences of the SUMO1 and SUMO2/3 proteome of HeLa cells under normoxia and cells grown for 48 h under hypoxic conditions, we employed endogenous SUMO-immunoprecipitation in combination with quantitative mass spectrometry (SILAC). The group of proteins whose abundance was increased both in the total proteome and in the SUMO IPs from hypoxic conditions was enriched in enzymes linked to the hypoxic response. In contrast, proteins whose SUMOylation status changed without concomitant change in abundance were predominantly transcriptions factors or transcription regulators. Particularly interesting was transcription factor TFAP2A (Activating enhancer binding Protein 2 alpha), whose sumoylation decreased on hypoxia. TFAP2A is known to interact with HIF-1 and we provide evidence that deSUMOylation of TFAP2A enhances the transcriptional activity of HIF-1 under hypoxic conditions. Overall, these results support the notion that SUMO-regulated signaling pathways contribute at many distinct levels to the cellular response to low oxygen.
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Affiliation(s)
- Georgia Chachami
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece;
- ‡‡Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany
| | - Nicolas Stankovic-Valentin
- §Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany
| | - Angeliki Karagiota
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
| | - Angeliki Basagianni
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
| | - Uwe Plessmann
- ¶Bioanalytical Mass Spectrometry Group Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Henning Urlaub
- ¶Bioanalytical Mass Spectrometry Group Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- ‖Bioanalytics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Frauke Melchior
- §Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany
| | - George Simos
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
- **Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, Canada
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Antoniou-Kourounioti M, Mimmack ML, Porter ACG, Farr CJ. The Impact of the C-Terminal Region on the Interaction of Topoisomerase II Alpha with Mitotic Chromatin. Int J Mol Sci 2019; 20:ijms20051238. [PMID: 30871006 PMCID: PMC6429393 DOI: 10.3390/ijms20051238] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
Type II topoisomerase enzymes are essential for resolving DNA topology problems arising through various aspects of DNA metabolism. In vertebrates two isoforms are present, one of which (TOP2A) accumulates on chromatin during mitosis. Moreover, TOP2A targets the mitotic centromere during prophase, persisting there until anaphase onset. It is the catalytically-dispensable C-terminal domain of TOP2 that is crucial in determining this isoform-specific behaviour. In this study we show that, in addition to the recently identified chromatin tether domain, several other features of the alpha-C-Terminal Domain (CTD). influence the mitotic localisation of TOP2A. Lysine 1240 is a major SUMOylation target in cycling human cells and the efficiency of this modification appears to be influenced by T1244 and S1247 phosphorylation. Replacement of K1240 by arginine results in fewer cells displaying centromeric TOP2A accumulation during prometaphase-metaphase. The same phenotype is displayed by cells expressing TOP2A in which either of the mitotic phosphorylation sites S1213 or S1247 has been substituted by alanine. Conversely, constitutive modification of TOP2A by fusion to SUMO2 exerts the opposite effect. FRAP analysis of protein mobility indicates that post-translational modification of TOP2A can influence the enzyme's residence time on mitotic chromatin, as well as its subcellular localisation.
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Affiliation(s)
- Melissa Antoniou-Kourounioti
- Department of Genetics, University of Cambridge, Downing St, Cambridge CB2 3EH, UK.
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Michael L Mimmack
- Department of Genetics, University of Cambridge, Downing St, Cambridge CB2 3EH, UK.
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Andrew C G Porter
- Centre for Haematology, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Rd, London W12 0NN, UK.
| | - Christine J Farr
- Department of Genetics, University of Cambridge, Downing St, Cambridge CB2 3EH, UK.
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Wright CM, Whitaker RH, Onuiri JE, Blackburn T, McGarity S, Bjornsti MA, Placzek WJ. UBC9 Mutant Reveals the Impact of Protein Dynamics on Substrate Selectivity and SUMO Chain Linkages. Biochemistry 2019; 58:621-632. [PMID: 30574775 DOI: 10.1021/acs.biochem.8b01045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SUMO, a conserved ubiquitin-like protein, is conjugated to a multitude of cellular proteins to maintain genomic integrity and resist genotoxic stress. Studies of the SUMO E2 conjugating enzyme mutant, UBC9P123L, suggested that altered substrate specificity enhances cell sensitivity to DNA damaging agents. Using nuclear magnetic resonance chemical shift studies, we confirm that the mutation does not alter the core globular fold of UBC9, while 15N relaxation measurements demonstrate mutant-induced stabilization of distinct chemical states in residues near the active site cysteine and substrate recognition motifs. We further demonstrate that the P123L substitution induces a switch from the preferential addition of SUMO to lysine residues in unstructured sites to acceptor lysines embedded in secondary structures, thereby also inducing alterations in SUMO chain linkages. Our results provide new insights regarding the impact that structural dynamics of UBC9 have on substrate selection and specifically SUMO chain formation. These findings highlight the potential contribution of nonconsensus SUMO targets and/or alternative SUMO chain linkages on DNA damage response and chemotherapeutic sensitivity.
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40
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Umbaugh CS, Figueiredo ML. Lysines residing in putative Small Ubiquitin-like MOdifier (SUMO) motifs regulate fate and function of 37 KDa laminin receptor. Biochimie 2019; 156:92-99. [DOI: 10.1016/j.biochi.2018.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 10/06/2018] [Indexed: 01/17/2023]
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Bennetzen MV, Kosar M, Bunkenborg J, Payne MR, Bartkova J, Lindström MS, Lukas J, Andersen JS, Bartek J, Larsen DH. DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy. Cell Cycle 2018; 17:2146-2163. [PMID: 30196736 DOI: 10.1080/15384101.2018.1515552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Ionizing radiation (IR) causes DNA double-strand breaks (DSBs) and activates a versatile cellular response regulating DNA repair, cell-cycle progression, transcription, DNA replication and other processes. In recent years proteomics has emerged as a powerful tool deepening our understanding of this multifaceted response. In this study we use SILAC-based proteomics to specifically investigate dynamic changes in cytoplasmic protein abundance after ionizing radiation; we present in-depth bioinformatics analysis and show that levels of proteins involved in autophagy (cathepsins and other lysosomal proteins), proteasomal degradation (Ubiquitin-related proteins), energy metabolism (mitochondrial proteins) and particularly translation (ribosomal proteins and translation factors) are regulated after cellular exposure to ionizing radiation. Downregulation of no less than 68 ribosomal proteins shows rapid changes in the translation pattern after IR. Additionally, we provide evidence of compartmental cytosol-nuclear translocation of numerous DNA damage related proteins using protein correlation profiling. In conclusion, these results highlight unexpected cytoplasmic processes actively orchestrated after genotoxic insults and protein translocation from the cytoplasm to the nucleus as a fundamental regulatory mechanism employed to aid cell survival and preservation of genome integrity.
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Affiliation(s)
- Martin V Bennetzen
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Martin Kosar
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark
| | - Jakob Bunkenborg
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Mark Ronald Payne
- c National Institute of Aquatic Resources , Technical University of Denmark , Lyngby , Denmark
| | - Jirina Bartkova
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Mikael S Lindström
- d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Jiri Lukas
- e Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research , Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen , Denmark
| | - Jens S Andersen
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Jiri Bartek
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Dorthe Helena Larsen
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,f Nucleolar Stress and Disease Group, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark
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Site-specific characterization of endogenous SUMOylation across species and organs. Nat Commun 2018; 9:2456. [PMID: 29942033 PMCID: PMC6018634 DOI: 10.1038/s41467-018-04957-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/05/2018] [Indexed: 12/30/2022] Open
Abstract
Small ubiquitin-like modifiers (SUMOs) are post-translational modifications that play crucial roles in most cellular processes. While methods exist to study exogenous SUMOylation, large-scale characterization of endogenous SUMO2/3 has remained technically daunting. Here, we describe a proteomics approach facilitating system-wide and in vivo identification of lysines modified by endogenous and native SUMO2. Using a peptide-level immunoprecipitation enrichment strategy, we identify 14,869 endogenous SUMO2/3 sites in human cells during heat stress and proteasomal inhibition, and quantitatively map 1963 SUMO sites across eight mouse tissues. Characterization of the SUMO equilibrium highlights striking differences in SUMO metabolism between cultured cancer cells and normal tissues. Targeting preferences of SUMO2/3 vary across different organ types, coinciding with markedly differential SUMOylation states of all enzymes involved in the SUMO conjugation cascade. Collectively, our systemic investigation details the SUMOylation architecture across species and organs and provides a resource of endogenous SUMOylation sites on factors important in organ-specific functions. Proteomics is a powerful method to study protein SUMOylation, but system-wide insights into endogenous SUMO2/3 modification events are still sparse. Here, the authors develop a more sensitive SUMO proteomics approach, providing detailed maps of endogenous SUMO2/3 sites in human cells and mouse tissues.
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43
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Munk S, Sigurðsson JO, Xiao Z, Batth TS, Franciosa G, von Stechow L, Lopez-Contreras AJ, Vertegaal ACO, Olsen JV. Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress. Cell Rep 2018; 21:546-558. [PMID: 29020638 DOI: 10.1016/j.celrep.2017.09.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/11/2017] [Accepted: 09/18/2017] [Indexed: 11/20/2022] Open
Abstract
The mechanisms that protect eukaryotic DNA during the cumbersome task of replication depend on the precise coordination of several post-translational modification (PTM)-based signaling networks. Phosphorylation is a well-known regulator of the replication stress response, and recently an essential role for SUMOs (small ubiquitin-like modifiers) has also been established. Here, we investigate the global interplay between phosphorylation and SUMOylation in response to replication stress. Using SUMO and phosphoproteomic technologies, we identify thousands of regulated modification sites. We find co-regulation of central DNA damage and replication stress responders, of which the ATR-activating factor TOPBP1 is the most highly regulated. Using pharmacological inhibition of the DNA damage response kinases ATR and ATM, we find that these factors regulate global protein SUMOylation in the protein networks that protect DNA upon replication stress and fork breakage, pointing to integration between phosphorylation and SUMOylation in the cellular systems that protect DNA integrity.
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Affiliation(s)
- Stephanie Munk
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Center for Chromosome Stability and Center for Healthy Aging, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jón Otti Sigurðsson
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Zhenyu Xiao
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Tanveer Singh Batth
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giulia Franciosa
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Louise von Stechow
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andres Joaquin Lopez-Contreras
- Center for Chromosome Stability and Center for Healthy Aging, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Jesper Velgaard Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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44
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Xu HD, Wang LN, Wen PP, Shi SP, Qiu JD. Site-Specific Systematic Analysis of Lysine Modification Crosstalk. Proteomics 2018. [DOI: 10.1002/pmic.201700292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hao-Dong Xu
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Li-Na Wang
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Ping-Ping Wen
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Shao-Ping Shi
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
| | - Jian-Ding Qiu
- Department of Chemistry; Nanchang University; No. 999 Xuefu Road Nanchang Honggutan New District Jiangxi Province 330031 P. R. China
- Department of Materials and Chemical Engineering; Pingxiang University; Pingxiang P. R. China
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45
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Association of Proteomics Changes with Al-Sensitive Root Zones in Switchgrass. Proteomes 2018; 6:proteomes6020015. [PMID: 29565292 PMCID: PMC6027131 DOI: 10.3390/proteomes6020015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/13/2018] [Accepted: 03/21/2018] [Indexed: 12/25/2022] Open
Abstract
In this paper, we report on aluminum (Al)-induced root proteomic changes in switchgrass. After growth in a hydroponic culture system supplemented with 400 μM of Al, plants began to show signs of physiological stress such as a reduction in photosynthetic rate. At this time, the basal 2-cm long root tips were harvested and divided into two segments, each of 1-cm in length, for protein extraction. Al-induced changes in proteomes were identified using tandem mass tags mass spectrometry (TMT-MS)-based quantitative proteomics analysis. A total of 216 proteins (approximately 3.6% of total proteins) showed significant differences between non-Al treated control and treated groups with significant fold change (twice the standard deviation; FDR adjusted p-value < 0.05). The apical root tip tissues expressed more dramatic proteome changes (164 significantly changed proteins; 3.9% of total proteins quantified) compared to the elongation/maturation zones (52 significantly changed proteins, 1.1% of total proteins quantified). Significantly changed proteins from the apical 1-cm root apex tissues were clustered into 25 biological pathways; proteins involved in the cell cycle (rotamase FKBP 1 isoforms, and CDC48 protein) were all at a reduced abundance level compared to the non-treated control group. In the root elongation/maturation zone tissues, the identified proteins were placed into 18 pathways, among which proteins involved in secondary metabolism (lignin biosynthesis) were identified. Several STRING protein interaction networks were developed for these Al-induced significantly changed proteins. This study has identified a large number of Al-responsive proteins, including transcription factors, which will be used for exploring new Al tolerance genes and mechanisms. Data are available via ProteomeXchange with identifiers PXD008882 and PXD009125.
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Herbelet S, De Vlieghere E, Gonçalves A, De Paepe B, Schmidt K, Nys E, Weynants L, Weis J, Van Peer G, Vandesompele J, Schmidt J, De Wever O, De Bleecker JL. Localization and Expression of Nuclear Factor of Activated T-Cells 5 in Myoblasts Exposed to Pro-inflammatory Cytokines or Hyperosmolar Stress and in Biopsies from Myositis Patients. Front Physiol 2018. [PMID: 29515464 PMCID: PMC5826317 DOI: 10.3389/fphys.2018.00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Aims: Regeneration in skeletal muscle relies on regulated myoblast migration and differentiation, in which the transcription factor nuclear factor of activated T-cells 5 (NFAT5) participates. Impaired muscle regeneration and chronic inflammation are prevalent in myositis. Little is known about the impact of inflammation on NFAT5 localization and expression in this group of diseases. The goal of this study was to investigate NFAT5 physiology in unaffected myoblasts exposed to cytokine or hyperosmolar stress and in myositis. Methods: NFAT5 intracellular localization and expression were studied in vitro using a cell culture model of myositis. Myoblasts were exposed to DMEM solutions enriched with pro-inflammatory cytokines IFN-γ with IL-1β or hyperosmolar DMEM obtained by NaCl supplementation. NFAT5 localization was visualized using immunohistochemistry (IHC) and Western blotting (WB) in fractionated cell lysates. NFAT5 expression was assessed by WB and RT-qPCR. In vivo localization and expression of NFAT5 were studied in muscle biopsies of patients diagnosed with polymyositis (n = 6), dermatomyositis (n = 10), inclusion body myositis (n = 11) and were compared to NFAT5 localization and expression in non-myopathic controls (n = 13). Muscle biopsies were studied by means of quantitative IHC and WB of total protein extracts. Results: In unaffected myoblasts, hyperosmolar stress ensues in NFAT5 nuclear translocation and increased NFAT5 mRNA and protein expression. In contrast, pro-inflammatory cytokines did not lead to NFAT5 nuclear translocation nor increased expression. Cytokines IL-1β with IFN-γ induced colocalization of NFAT5 with histone deacetylase 6 (HDAC6), involved in cell motility. In muscle biopsies from dermatomyositis and polymyositis patients, NFAT5 colocalized with HDAC6, while in IBM, this was often absent. Conclusions: Our data suggest impaired NFAT5 localization and expression in unaffected myoblasts in response to inflammation. This disturbed myogenic NFAT5 physiology could possibly explain deleterious effects on muscle regeneration in myositis.
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Affiliation(s)
- Sandrine Herbelet
- Department of Neurology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Elly De Vlieghere
- Cancer Research Institute Ghent and Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Amanda Gonçalves
- VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,VIB Bio Imaging Core Gent, Ghent, Belgium
| | - Boel De Paepe
- Department of Neurology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Karsten Schmidt
- Department of Neurology and Department of Experimental and Clinical Neuroimmunology, University of Göttingen, Göttingen, Germany
| | - Eline Nys
- Department of Neurology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Laurens Weynants
- Department of Neurology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen Medical School, Aachen, Germany
| | - Gert Van Peer
- Center for Medical Genetics and Cancer Research Institute Ghent, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics and Cancer Research Institute Ghent, Ghent, Belgium
| | - Jens Schmidt
- Department of Neurology and Department of Experimental and Clinical Neuroimmunology, University of Göttingen, Göttingen, Germany
| | - Olivier De Wever
- Cancer Research Institute Ghent and Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Jan L De Bleecker
- Department of Neurology, Ghent University and Ghent University Hospital, Ghent, Belgium
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Rytz TC, Miller MJ, Vierstra RD. Purification of SUMO Conjugates from Arabidopsis for Mass Spectrometry Analysis. Methods Mol Biol 2018; 1475:257-81. [PMID: 27631811 DOI: 10.1007/978-1-4939-6358-4_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The posttranslational modification of proteins with small ubiquitin-related modifier (SUMO) is a rapid, robust, and reversible mechanism that impacts a host of eukaryotic processes important to both normal cellular functions and survival during various abiotic and biotic challenges. Essential to defining the breadth of events impacted by SUMOylation is the development of full catalogues of protein targets. Here, we describe a stringent affinity method to purify native SUMO conjugates from the model plant Arabidopsis thaliana based on the expression of modified SUMOs bearing epitope tags. When combined with standard and quantitative mass spectrometric methods, deep datasets of SUMOylated proteins can be acquired. Functional analysis of these lists links SUMO to numerous regulatory events, with an emphasis on those associated with transcription, DNA replication and repair, and chromatin assembly/accessibility.
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Affiliation(s)
- Thérèse C Rytz
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA.,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA
| | - Marcus J Miller
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA. .,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA.
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Xu C, Fang L, Kong Y, Xiao C, Yang M, Du LQ, Liu Q. Knockdown of RMI1 impairs DNA repair under DNA replication stress. Biochem Biophys Res Commun 2017; 494:158-164. [DOI: 10.1016/j.bbrc.2017.10.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022]
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49
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The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery. Nat Commun 2017; 8:1809. [PMID: 29180619 PMCID: PMC5703878 DOI: 10.1038/s41467-017-01900-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/23/2017] [Indexed: 12/14/2022] Open
Abstract
SUMO-targeted ubiquitin ligases (STUbLs) mediate the ubiquitylation of SUMOylated proteins to modulate their functions. In search of direct targets for the STUbL RNF4, we have developed TULIP (targets for ubiquitin ligases identified by proteomics) to covalently trap targets for ubiquitin E3 ligases. TULIP methodology could be widely employed to delineate E3 substrate wiring. Here we report that the single SUMO E2 Ubc9 and the SUMO E3 ligases PIAS1, PIAS2, PIAS3, ZNF451, and NSMCE2 are direct RNF4 targets. We confirm PIAS1 as a key RNF4 substrate. Furthermore, we establish the ubiquitin E3 ligase BARD1, a tumor suppressor and partner of BRCA1, as an indirect RNF4 target, regulated by PIAS1. Interestingly, accumulation of BARD1 at local sites of DNA damage increases upon knockdown of RNF4. Combined, we provide an insight into the role of the STUbL RNF4 to balance the role of SUMO signaling by directly targeting Ubc9 and SUMO E3 ligases. SUMO and ubiquitin are key signal transducers in several cellular processes including the DNA-damage response. Here the authors describe a method for selective enrichment of ubiquitin substrates for E3 ligases from complex cellular proteomes and identify the SUMO conjugation machinery as direct RNF4 substrates.
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50
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Zilio N, Eifler-Olivi K, Ulrich HD. Functions of SUMO in the Maintenance of Genome Stability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:51-87. [PMID: 28197906 DOI: 10.1007/978-3-319-50044-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like in most other areas of cellular metabolism, the functions of the ubiquitin-like modifier SUMO in the maintenance of genome stability are manifold and varied. Perturbations of global sumoylation causes a wide spectrum of phenotypes associated with defects in DNA maintenance, such as hypersensitivity to DNA-damaging agents, gross chromosomal rearrangements and loss of entire chromosomes. Consistent with these observations, many key factors involved in various DNA repair pathways have been identified as SUMO substrates. However, establishing a functional connection between a given SUMO target, the cognate SUMO ligase and a relevant phenotype has remained a challenge, mainly because of the difficulties involved in identifying important modification sites and downstream effectors that specifically recognize the target in its sumoylated state. This review will give an overview over the major pathways of DNA repair and genome maintenance influenced by the SUMO system and discuss selected examples of SUMO's actions in these pathways where the biological consequences of the modification have been elucidated.
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Affiliation(s)
- Nicola Zilio
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | | | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
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