1
|
Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA. RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii. mBio 2023; 14:e0085223. [PMID: 37458473 PMCID: PMC10470531 DOI: 10.1128/mbio.00852-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii, an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3'-5' exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5'-3' exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identified in the archaeon Haloferax volcanii, which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3'-5' exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5'-3' exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.
Collapse
Affiliation(s)
- Huiyong Jia
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Swathi Dantuluri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Shae Margulies
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Lever
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
2
|
Ran M, Li Q, Xin Y, Ma S, Zhao R, Wang M, Xun L, Xia Y. Rhodaneses minimize the accumulation of cellular sulfane sulfur to avoid disulfide stress during sulfide oxidation in bacteria. Redox Biol 2022; 53:102345. [PMID: 35653932 PMCID: PMC9163753 DOI: 10.1016/j.redox.2022.102345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 10/27/2022] Open
|
3
|
Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås AC, Robinson NP, Baum B. The proteasome controls ESCRT-III-mediated cell division in an archaeon. Science 2020; 369:eaaz2532. [PMID: 32764038 PMCID: PMC7116001 DOI: 10.1126/science.aaz2532] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
Abstract
Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III-mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.
Collapse
Affiliation(s)
- Gabriel Tarrason Risa
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Fredrik Hurtig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sian Bray
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Anne E Hafner
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Lena Harker-Kirschneck
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Peter Faull
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Colin Davis
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Dimitra Papatziamou
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Delyan R Mutavchiev
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Catherine Fan
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Leticia Meneguello
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Gautam Dey
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Mairi Kilkenny
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Diorge P Souza
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Luca Pellegrini
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Robertus A M de Bruin
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Anđela Šarić
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Nicholas P Robinson
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK.
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK.
- Institute for the Physics of Living Systems, UCL, London, UK
| |
Collapse
|