1
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Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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2
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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3
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Paulmann C, Spallek R, Karpiuk O, Heider M, Schäffer I, Zecha J, Klaeger S, Walzik M, Öllinger R, Engleitner T, Wirth M, Keller U, Krönke J, Rudelius M, Kossatz S, Rad R, Kuster B, Bassermann F. The OTUD6B-LIN28B-MYC axis determines the proliferative state in multiple myeloma. EMBO J 2022; 41:e110871. [PMID: 36059274 PMCID: PMC9574752 DOI: 10.15252/embj.2022110871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Deubiquitylases (DUBs) are therapeutically amenable components of the ubiquitin machinery that stabilize substrate proteins. Their inhibition can destabilize oncoproteins that may otherwise be undruggable. Here, we screened for DUB vulnerabilities in multiple myeloma, an incurable malignancy with dependency on the ubiquitin proteasome system and identified OTUD6B as an oncogene that drives the G1/S‐transition. LIN28B, a suppressor of microRNA biogenesis, is specified as a bona fide cell cycle‐specific substrate of OTUD6B. Stabilization of LIN28B drives MYC expression at G1/S, which in turn allows for rapid S‐phase entry. Silencing OTUD6B or LIN28B inhibits multiple myeloma outgrowth in vivo and high OTUD6B expression evolves in patients that progress to symptomatic multiple myeloma and results in an adverse outcome of the disease. Thus, we link proteolytic ubiquitylation with post‐transcriptional regulation and nominate OTUD6B as a potential mediator of the MGUS‐multiple myeloma transition, a central regulator of MYC, and an actionable vulnerability in multiple myeloma and other tumors with an activated OTUD6B‐LIN28B axis.
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Affiliation(s)
- Carmen Paulmann
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Ria Spallek
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Oleksandra Karpiuk
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Michael Heider
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Isabell Schäffer
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susan Klaeger
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Michaela Walzik
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Rupert Öllinger
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, Technical University of Munich, Munich, Germany
| | - Thomas Engleitner
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, Technical University of Munich, Munich, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany.,Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Martina Rudelius
- Institute of Pathology, Ludwigs Maximilians University, Munich, Germany
| | - Susanne Kossatz
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Nuclear Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Roland Rad
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, Technical University of Munich, Munich, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Florian Bassermann
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
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4
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Kalesh K, Wei W, Mantilla BS, Roumeliotis TI, Choudhary J, Denny PW. Transcriptome-Wide Identification of Coding and Noncoding RNA-Binding Proteins Defines the Comprehensive RNA Interactome of Leishmania mexicana. Microbiol Spectr 2022; 10:e0242221. [PMID: 35138191 PMCID: PMC8826732 DOI: 10.1128/spectrum.02422-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
Proteomic profiling of RNA-binding proteins in Leishmania is currently limited to polyadenylated mRNA-binding proteins, leaving proteins that interact with nonadenylated RNAs, including noncoding RNAs and pre-mRNAs, unidentified. Using a combination of unbiased orthogonal organic phase separation methodology and tandem mass tag-labeling-based high resolution quantitative proteomic mass spectrometry, we robustly identified 2,417 RNA-binding proteins, including 1289 putative novel non-poly(A)-RNA-binding proteins across the two main Leishmania life cycle stages. Eight out of 20 Leishmania deubiquitinases, including the recently characterized L. mexicana DUB2 with an elaborate RNA-binding protein interactome were exclusively identified in the non-poly(A)-RNA-interactome. Additionally, an increased representation of WD40 repeat domains were observed in the Leishmania non-poly(A)-RNA-interactome, thus uncovering potential involvement of this protein domain in RNA-protein interactions in Leishmania. We also characterize the protein-bound RNAs using RNA-sequencing and show that in addition to protein coding transcripts ncRNAs are also enriched in the protein-RNA interactome. Differential gene expression analysis revealed enrichment of 142 out of 195 total L. mexicana protein kinase genes in the protein-RNA-interactome, suggesting important role of protein-RNA interactions in the regulation of the Leishmania protein kinome. Additionally, we characterize the quantitative changes in RNA-protein interactions in hundreds of Leishmania proteins following inhibition of heat shock protein 90 (Hsp90). Our results show that the Hsp90 inhibition in Leishmania causes widespread disruption of RNA-protein interactions in ribosomal proteins, proteasomal proteins and translation factors in both life cycle stages, suggesting downstream effect of the inhibition on protein synthesis and degradation pathways in Leishmania. This study defines the comprehensive RNA interactome of Leishmania and provides in-depth insight into the widespread involvement of RNA-protein interactions in Leishmania biology. IMPORTANCE Advances in proteomics and mass spectrometry have revealed the mRNA-binding proteins in many eukaryotic organisms, including the protozoan parasites Leishmania spp., the causative agents of leishmaniasis, a major infectious disease in over 90 tropical and subtropical countries. However, in addition to mRNAs, which constitute only 2 to 5% of the total transcripts, many types of non-coding RNAs participate in crucial biological processes. In Leishmania, RNA-binding proteins serve as primary gene regulators. Therefore, transcriptome-wide identification of RNA-binding proteins is necessary for deciphering the distinctive posttranscriptional mechanisms of gene regulation in Leishmania. Using a combination of highly efficient orthogonal organic phase separation method and tandem mass tag-labeling-based quantitative proteomic mass spectrometry, we provide unprecedented comprehensive molecular definition of the total RNA interactome across the two main Leishmania life cycle stages. In addition, we characterize for the first time the quantitative changes in RNA-protein interactions in Leishmania following inhibition of heat shock protein 90, shedding light into hitherto unknown large-scale downstream molecular effect of the protein inhibition in the parasite. This work provides insight into the importance of total RNA-protein interactions in Leishmania, thus significantly expanding our knowledge of the emergence of RNA-protein interactions in Leishmania biology.
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Affiliation(s)
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Brian S. Mantilla
- Department of Biosciences, Durham University, Durham, United Kingdom
| | | | - Jyoti Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, United Kingdom
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom
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5
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Klaric JA, Wüst S, Panier S. New Faces of old Friends: Emerging new Roles of RNA-Binding Proteins in the DNA Double-Strand Break Response. Front Mol Biosci 2021; 8:668821. [PMID: 34026839 PMCID: PMC8138124 DOI: 10.3389/fmolb.2021.668821] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. To protect genomic stability and ensure cell homeostasis, cells mount a complex signaling-based response that not only coordinates the repair of the broken DNA strand but also activates cell cycle checkpoints and, if necessary, induces cell death. The last decade has seen a flurry of studies that have identified RNA-binding proteins (RBPs) as novel regulators of the DSB response. While many of these RBPs have well-characterized roles in gene expression, it is becoming increasingly clear that they also have non-canonical functions in the DSB response that go well beyond transcription, splicing and mRNA processing. Here, we review the current understanding of how RBPs are integrated into the cellular response to DSBs and describe how these proteins directly participate in signal transduction, amplification and repair at damaged chromatin. In addition, we discuss the implications of an RBP-mediated DSB response for genome instability and age-associated diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Julie A Klaric
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stas Wüst
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stephanie Panier
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, University of Cologne, Cologne, Germany
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6
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Goyani S, Roy M, Singh R. TRIM-NHL as RNA Binding Ubiquitin E3 Ligase (RBUL): Implication in development and disease pathogenesis. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166066. [PMID: 33418035 DOI: 10.1016/j.bbadis.2020.166066] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/14/2020] [Accepted: 12/27/2020] [Indexed: 12/20/2022]
Abstract
TRIM proteins are RING domain-containing modular ubiquitin ligases, unique due to their stimuli specific expression, localization, and turnover. The TRIM family consists of more than 76 proteins, including the TRIM-NHL sub-family which possesses RNA binding ability along with the inherent E3 Ligase activity, hence can be classified as a unique class of RNA Binding Ubiquitin Ligases (RBULs). Having these two abilities, TRIM-NHL proteins can play important role in a wide variety of cellular processes and their dysregulation can lead to complex and systemic pathological conditions. Increasing evidence suggests that TRIM-NHL proteins regulate RNA at the transcriptional and post-transcriptional level having implications in differentiation, development, and many pathological conditions. This review explores the evolving role of TRIM-NHL proteins as TRIM-RBULs, their ubiquitin ligase and RNA binding ability regulating cellular processes, and their possible role in different pathophysiological conditions.
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Affiliation(s)
- Shanikumar Goyani
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India
| | - Milton Roy
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India
| | - Rajesh Singh
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India.
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7
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Kolapalli SP, Sahu R, Chauhan NR, Jena KK, Mehto S, Das SK, Jain A, Rout M, Dash R, Swain RK, Lee DY, Rusten TE, Chauhan S, Chauhan S. RNA-Binding RING E3-Ligase DZIP3/hRUL138 Stabilizes Cyclin D1 to Drive Cell-Cycle and Cancer Progression. Cancer Res 2020; 81:315-331. [PMID: 33067265 DOI: 10.1158/0008-5472.can-20-1871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/02/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022]
Abstract
DZIP3/hRUL138 is a poorly characterized RNA-binding RING E3-ubiquitin ligase with functions in embryonic development. Here we demonstrate that DZIP3 is a crucial driver of cancer cell growth, migration, and invasion. In mice and zebrafish cancer models, DZIP3 promoted tumor growth and metastasis. In line with these results, DZIP3 was frequently overexpressed in several cancer types. Depletion of DZIP3 from cells resulted in reduced expression of Cyclin D1 and a subsequent G1 arrest and defect in cell growth. Mechanistically, DZIP3 utilized its two different domains to interact and stabilize Cyclin D1 both at mRNA and protein levels. Using an RNA-binding lysine-rich region, DZIP3 interacted with the AU-rich region in 3' untranslated region of Cyclin D1 mRNA and stabilized it. Using a RING E3-ligase domain, DZIP3 interacted and increased K63-linked ubiquitination of Cyclin D1 protein to stabilize it. Remarkably, DZIP3 interacted with, ubiquitinated, and stabilized Cyclin D1 predominantly in the G1 phase of the cell cycle, where it is needed for cell-cycle progression. In agreement with this, a strong positive correlation of mRNA expression between DZIP3 and Cyclin D1 in different cancer types was observed. Additionally, DZIP3 regulated several cell cycle proteins by modulating the Cyclin D1-E2F axes. Taken together, this study demonstrates for the first time that DZIP3 uses a unique two-pronged mechanism in its stabilization of Cyclin D1 to drive cell-cycle and cancer progression. SIGNIFICANCE: These findings show that DZIP3 is a novel driver of cell-cycle and cancer progression via its control of Cyclin D1 mRNA and protein stability in a cell-cycle phase-dependent manner. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/2/315/F1.large.jpg.
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Affiliation(s)
| | - Rinku Sahu
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Nishant R Chauhan
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Kautilya K Jena
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Subhash Mehto
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Saroj K Das
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Ashish Jain
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo; Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Manaswini Rout
- Vascular Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Rupesh Dash
- Gene Therapy and Cancer Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Rajeeb K Swain
- Vascular Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - David Y Lee
- Department of Internal Medicine, Radiation Oncology, and University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Tor Erik Rusten
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo; Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Santosh Chauhan
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Swati Chauhan
- Gene Therapy and Cancer Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
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8
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Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE. Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins. Nucleic Acids Res 2020; 48:4725-4740. [PMID: 32313943 PMCID: PMC7229827 DOI: 10.1093/nar/gkaa256] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular stress causes multifaceted reactions to trigger adaptive responses to environmental cues at all levels of the gene expression pathway. RNA-binding proteins (RBP) are key contributors to stress-induced regulation of RNA fate and function. Here, we uncover the plasticity of the RNA interactome in stressed cells, differentiating between responses in the nucleus and in the cytoplasm. We applied enhanced RNA interactome capture (eRIC) analysis preceded by nucleo-cytoplasmic fractionation following arsenite-induced oxidative stress. The data reveal unexpectedly compartmentalized RNA interactomes and their responses to stress, including differential responses of RBPs in the nucleus versus the cytoplasm, which would have been missed by whole cell analyses.
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Affiliation(s)
- Michael Backlund
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 564555;
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Joel I Perez-Perri
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Annika Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence may also be addressed to Matthias W. Hentze.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Correspondence may also be addressed to Andreas E. Kulozik.
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9
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MKRN2 Physically Interacts with GLE1 to Regulate mRNA Export and Zebrafish Retinal Development. Cell Rep 2020; 31:107693. [DOI: 10.1016/j.celrep.2020.107693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/25/2020] [Accepted: 05/05/2020] [Indexed: 12/31/2022] Open
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10
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Dold A, Han H, Liu N, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY, Lasko P. Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLoS Genet 2020; 16:e1008581. [PMID: 31978041 PMCID: PMC7001992 DOI: 10.1371/journal.pgen.1008581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 02/05/2020] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila, maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar (osk). We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3’ UTR in a region adjacent to A-rich sequences. Using Drosophila S2R+ cultured cells we show that this binding site overlaps with a Bruno1 (Bru1) responsive element (BREs) that regulates osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3’ UTR. To ensure accurate development of the Drosophila embryo, proteins and mRNAs are positioned at specific sites within the embryo. Many of these factors are produced and localized during the development of the egg in the mother. One protein essential for this process that has been heavily studied is Oskar (Osk), which is positioned at the posterior pole. During the localization of osk mRNA, its translation is repressed by the RNA-binding protein Bruno1 (Bru1), ensuring that Osk protein is not present outside of the posterior where it is harmful. At the posterior pole, osk mRNA is activated through mechanisms that are not yet understood. In this work, we show that the conserved protein Makorin 1 (Mkrn1) is a novel factor involved in the translational activation of osk. Mkrn1 binds specifically to osk mRNA, overlapping with a binding site of Bru1, thus alleviating the association of Bru1 with osk. Moreover, Mkrn1 is stabilized by poly(A) binding protein (pAbp), a translational activator that binds osk mRNA in close proximity to one Mkrn1 binding site. Our work thus helps to answer a long-standing question in the field, providing insight about the function of Mkrn1 and more generally into embryonic patterning in animals.
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Affiliation(s)
- Annabelle Dold
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Hong Han
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Niankun Liu
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andrea Hildebrandt
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany.,Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Cornelia Rücklé
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Heike Hänel
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Anke Busch
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Petra Beli
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julian König
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Jean-Yves Roignant
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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11
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Thapa P, Shanmugam N, Pokrzywa W. Ubiquitin Signaling Regulates RNA Biogenesis, Processing, and Metabolism. Bioessays 2019; 42:e1900171. [PMID: 31778250 DOI: 10.1002/bies.201900171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/29/2019] [Indexed: 12/17/2022]
Abstract
The fate of eukaryotic proteins, from their synthesis to destruction, is supervised by the ubiquitin-proteasome system (UPS). The UPS is the primary pathway responsible for selective proteolysis of intracellular proteins, which is guided by covalent attachment of ubiquitin to target proteins by E1 (activating), E2 (conjugating), and E3 (ligating) enzymes in a process known as ubiquitylation. The UPS can also regulate protein synthesis by influencing multiple steps of RNA (ribonucleic acid) metabolism. Here, recent publications concerning the interplay between the UPS and different types of RNA are reviewed. This interplay mainly involves specific RNA-binding E3 ligases that link RNA-dependent processes with protein ubiquitylation. The emerging understanding of their modes of RNA binding, their RNA targets, and their molecular and cellular functions are primarily focused on. It is discussed how the UPS adapted to interact with different types of RNA and how RNA molecules influence the ubiquitin signaling components.
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Affiliation(s)
- Pankaj Thapa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
| | - Nilesh Shanmugam
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
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12
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Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P. The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol 2019; 20:216. [PMID: 31640799 PMCID: PMC6805484 DOI: 10.1186/s13059-019-1814-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide via ribosome-associated quality control. RESULTS Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at poly(A) sequences during ribosome-associated quality control. We show that MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) and associates with polysomes. MKRN1 is positioned upstream of poly(A) tails in mRNAs in a PABPC1-dependent manner. Ubiquitin remnant profiling and in vitro ubiquitylation assays uncover PABPC1 and ribosomal protein RPS10 as direct ubiquitylation substrates of MKRN1. CONCLUSIONS We propose that MKRN1 mediates the recognition of poly(A) tails to prevent the production of erroneous proteins from prematurely polyadenylated transcripts, thereby maintaining proteome integrity.
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Affiliation(s)
- Andrea Hildebrandt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Cornelia Rücklé
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Martin M Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | | | - Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Annabelle Dold
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Génopode Building, CH-1015, Lausanne, Switzerland
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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13
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Abstract
3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. In addition, 3' UTRs can establish 3' UTR-mediated protein-protein interactions (PPIs), and thus can transmit genetic information encoded in 3' UTRs to proteins. This function has been shown to regulate diverse protein features, including protein complex formation or posttranslational modifications, but is also expected to alter protein conformations. Therefore, 3' UTR-mediated information transfer can regulate protein features that are not encoded in the amino acid sequence. This review summarizes both 3' UTR functions-the regulation of mRNA and protein-based processes-and highlights how each 3' UTR function was discovered with a focus on experimental approaches used and the concepts that were learned. This review also discusses novel approaches to study 3' UTR functions in the future by taking advantage of recent advances in technology.
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Affiliation(s)
- Christine Mayr
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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14
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Proteins that physically interact with the phosphatase Cdc14 in Candida albicans have diverse roles in the cell cycle. Sci Rep 2019; 9:6258. [PMID: 31000734 PMCID: PMC6472416 DOI: 10.1038/s41598-019-42530-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
The chromosome complement of the human fungal pathogen Candida albicans is unusually unstable, suggesting that the process of nuclear division is error prone. The Cdc14 phosphatase plays a key role in organising the intricate choreography of mitosis and cell division. In order to understand the role of Cdc14 in C. albicans we used quantitative proteomics to identify proteins that physically interact with Cdc14. To distinguish genuine Cdc14-interactors from proteins that bound non-specifically to the affinity matrix, we used a substrate trapping mutant combined with mass spectrometry analysis using Stable Isotope Labelling with Amino Acids in Cell Culture (SILAC). The results identified 126 proteins that interact with Cdc14 of which 80% have not previously been identified as Cdc14 interactors in C. albicans or S. cerevisiae. In this set, 55 proteins are known from previous research in S. cerevisiae and S. pombe to play roles in the cell cycle, regulating the attachment of the mitotic spindle to kinetochores, mitotic exit, cytokinesis, licensing of DNA replication by re-activating pre-replication complexes, and DNA repair. Five Cdc14-interacting proteins with previously unknown functions localised to the Spindle Pole Bodies (SPBs). Thus, we have greatly increased the number of proteins that physically interact with Cdc14 in C. albicans.
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