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Park EN, Mackens-Kiani T, Berhane R, Esser H, Erdenebat C, Burroughs AM, Berninghausen O, Aravind L, Beckmann R, Green R, Buskirk AR. B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage. EMBO J 2024; 43:484-506. [PMID: 38177497 PMCID: PMC10897456 DOI: 10.1038/s44318-023-00010-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
Stalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. In E. coli, these pathways are triggered by ribosome collisions through the recruitment of SmrB, a nuclease that cleaves the mRNA. In B. subtilis, the related protein MutS2 was recently implicated in ribosome rescue. Here we show that MutS2 is recruited to collisions by its SMR and KOW domains, and we reveal the interaction of these domains with collided ribosomes by cryo-EM. Using a combination of in vivo and in vitro approaches, we show that MutS2 uses its ABC ATPase activity to split ribosomes, targeting the nascent peptide for degradation through the ribosome quality control pathway. However, unlike SmrB, which cleaves mRNA in E. coli, we see no evidence that MutS2 mediates mRNA cleavage or promotes ribosome rescue by tmRNA. These findings clarify the biochemical and cellular roles of MutS2 in ribosome rescue in B. subtilis and raise questions about how these pathways function differently in diverse bacteria.
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Affiliation(s)
- Esther N Park
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Timur Mackens-Kiani
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Rebekah Berhane
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hanna Esser
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - A Maxwell Burroughs
- Computational Biology Branch, Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Otto Berninghausen
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - L Aravind
- Computational Biology Branch, Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Magg T, Okano T, Koenig LM, Boehmer DFR, Schwartz SL, Inoue K, Heimall J, Licciardi F, Ley-Zaporozhan J, Ferdman RM, Caballero-Oteyza A, Park EN, Calderon BM, Dey D, Kanegane H, Cho K, Montin D, Reiter K, Griese M, Albert MH, Rohlfs M, Gray P, Walz C, Conn GL, Sullivan KE, Klein C, Morio T, Hauck F. Heterozygous OAS1 gain-of-function variants cause an autoinflammatory immunodeficiency. Sci Immunol 2021; 6:eabf9564. [PMID: 34145065 PMCID: PMC8392508 DOI: 10.1126/sciimmunol.abf9564] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/06/2021] [Indexed: 12/13/2022]
Abstract
Analysis of autoinflammatory and immunodeficiency disorders elucidates human immunity and fosters the development of targeted therapies. Oligoadenylate synthetase 1 is a type I interferon-induced, intracellular double-stranded RNA (dsRNA) sensor that generates 2'-5'-oligoadenylate to activate ribonuclease L (RNase L) as a means of antiviral defense. We identified four de novo heterozygous OAS1 gain-of-function variants in six patients with a polymorphic autoinflammatory immunodeficiency characterized by recurrent fever, dermatitis, inflammatory bowel disease, pulmonary alveolar proteinosis, and hypogammaglobulinemia. To establish causality, we applied genetic, molecular dynamics simulation, biochemical, and cellular functional analyses in heterologous, autologous, and inducible pluripotent stem cell-derived macrophages and/or monocytes and B cells. We found that upon interferon-induced expression, OAS1 variant proteins displayed dsRNA-independent activity, which resulted in RNase L-mediated RNA cleavage, transcriptomic alteration, translational arrest, and dysfunction and apoptosis of monocytes, macrophages, and B cells. RNase L inhibition with curcumin modulated and allogeneic hematopoietic cell transplantation cured the disorder. Together, these data suggest that human OAS1 is a regulator of interferon-induced hyperinflammatory monocyte, macrophage, and B cell pathophysiology.
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Affiliation(s)
- Thomas Magg
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tsubasa Okano
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Lars M Koenig
- Division of Clinical Pharmacology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniel F R Boehmer
- Division of Clinical Pharmacology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Kento Inoue
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Jennifer Heimall
- Department of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Francesco Licciardi
- Department of Pediatric and Public Health Sciences, University of Torino, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Julia Ley-Zaporozhan
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ronald M Ferdman
- Division of Clinical Immunology and Allergy, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Andrés Caballero-Oteyza
- Centre for Chronic Immunodeficiency (CCI) and Institute for Immunodeficiency (IFI), University Hospital Freiburg, Freiburg, Germany
| | - Esther N Park
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Brenda M Calderon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Hirokazu Kanegane
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazutoshi Cho
- Maternity and Perinatal Care Center, Hokkaido University Hospital, Hokkaido, Japan
| | - Davide Montin
- Department of Pediatric and Public Health Sciences, University of Torino, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Karl Reiter
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Lung Research (DZL), Munich, Germany
| | - Michael H Albert
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Meino Rohlfs
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul Gray
- Department of Immunology and Infectious Disease, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Kathleen E Sullivan
- Department of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
- Munich Centre for Rare Diseases (M-ZSE), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
- German Centre for Infection Research (DZIF), Munich, Germany
- Munich Centre for Rare Diseases (M-ZSE), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
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Schwartz SL, Park EN, Vachon VK, Danzy S, Lowen AC, Conn GL. Human OAS1 activation is highly dependent on both RNA sequence and context of activating RNA motifs. Nucleic Acids Res 2020; 48:7520-7531. [PMID: 32678884 PMCID: PMC7367156 DOI: 10.1093/nar/gkaa513] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
2′-5′-Oligoadenylate synthetases (OAS) are innate immune sensors of cytosolic double-stranded RNA (dsRNA) and play a critical role in limiting viral infection. dsRNA binding induces allosteric structural changes in OAS1 that reorganize its catalytic center to promote synthesis of 2′-5′-oligoadenylate and thus activation of endoribonuclease L. Specific RNA sequences and structural motifs can also enhance activation of OAS1 through currently undefined mechanisms. To better understand these drivers of OAS activation, we tested the impact of defined sequence changes within a short dsRNA that strongly activates OAS1. Both in vitro and in human A549 cells, appending a 3′-end single-stranded pyrimidine (3′-ssPy) can strongly enhance OAS1 activation or have no effect depending on its location, suggesting that other dsRNA features are necessary for correct presentation of the motif to OAS1. Consistent with this idea, we also find that the dsRNA binding position is dictated by an established consensus sequence (WWN9WG). Unexpectedly, however, not all sequences fitting this consensus activate OAS1 equivalently, with strong dependence on the identity of both partially conserved (W) and non-conserved (N9) residues. A picture thus emerges in which both specific RNA features and the context in which they are presented dictate the ability of short dsRNAs to activate OAS1.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, USA
| | - Esther N Park
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Virginia K Vachon
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.,Graduate Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Emory University, USA
| | - Shamika Danzy
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Anice C Lowen
- Graduate Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Emory University, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, USA.,Graduate Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Emory University, USA
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