1
|
Jeong J, Lee JH, Carcamo CC, Parker MW, Berger JM. DNA-Stimulated Liquid-Liquid phase separation by eukaryotic topoisomerase ii modulates catalytic function. eLife 2022; 11:e81786. [PMID: 36342377 PMCID: PMC9674351 DOI: 10.7554/elife.81786] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Type II topoisomerases modulate chromosome supercoiling, condensation, and catenation by moving one double-stranded DNA segment through a transient break in a second duplex. How DNA strands are chosen and selectively passed to yield appropriate topological outcomes - for example, decatenation vs. catenation - is poorly understood. Here, we show that at physiological enzyme concentrations, eukaryotic type IIA topoisomerases (topo IIs) readily coalesce into condensed bodies. DNA stimulates condensation and fluidizes these assemblies to impart liquid-like behavior. Condensation induces both budding yeast and human topo IIs to switch from DNA unlinking to active DNA catenation, and depends on an unstructured C-terminal region, the loss of which leads to high levels of knotting and reduced catenation. Our findings establish that local protein concentration and phase separation can regulate how topo II creates or dissolves DNA links, behaviors that can account for the varied roles of the enzyme in supporting transcription, replication, and chromosome compaction.
Collapse
Affiliation(s)
- Joshua Jeong
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Joyce H Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Claudia C Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Matthew W Parker
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| |
Collapse
|
2
|
Kozuki T, Chikamori K, Surleac MD, Micluta MA, Petrescu AJ, Norris EJ, Elson P, Hoeltge GA, Grabowski DR, Porter ACG, Ganapathi RN, Ganapathi MK. Roles of the C-terminal domains of topoisomerase IIα and topoisomerase IIβ in regulation of the decatenation checkpoint. Nucleic Acids Res 2017; 45:5995-6010. [PMID: 28472494 PMCID: PMC5449615 DOI: 10.1093/nar/gkx325] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/14/2017] [Indexed: 12/13/2022] Open
Abstract
Topoisomerase (topo) IIα and IIβ maintain genome stability and are targets for anti-tumor drugs. In this study, we demonstrate that the decatenation checkpoint is regulated, not only by topo IIα, as previously reported, but also by topo IIβ. The decatenation checkpoint is most efficient when both isoforms are present. Regulation of this checkpoint and sensitivity to topo II-targeted drugs is influenced by the C-terminal domain (CTD) of the topo II isoforms and by a conserved non-catalytic tyrosine, Y640 in topo IIα and Y656 in topo IIβ. Deletion of most of the CTD of topo IIα, while preserving the nuclear localization signal (NLS), enhances the decatenation checkpoint and sensitivity to topo II-targeted drugs. In contrast, deletion of most of the CTD of topo IIβ, while preserving the NLS, and mutation of Y640 in topo IIα and Y656 in topo IIβ inhibits these activities. Structural studies suggest that the differential impact of the CTD on topo IIα and topo IIβ function may be due to differences in CTD charge distribution and differential alignment of the CTD with reference to transport DNA. Together these results suggest that topo IIα and topo IIβ cooperate to maintain genome stability, which may be distinctly modulated by their CTDs.
Collapse
Affiliation(s)
- Toshiyuki Kozuki
- Taussig Cancer Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Kenichi Chikamori
- Taussig Cancer Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Marius D Surleac
- Department of Bioinformatics, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Marius A Micluta
- Department of Bioinformatics, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Andrei J Petrescu
- Department of Bioinformatics, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Eric J Norris
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, 1021 Morehead Medical Drive, Charlotte, NC 28204, USA
| | - Paul Elson
- Taussig Cancer Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Gerald A Hoeltge
- Clinical Pathology, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Dale R Grabowski
- Taussig Cancer Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Andrew C G Porter
- Imperial College Faculty of Medicine, Hammersmith Hospital, London W10 ONN, UK
| | - Ram N Ganapathi
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, 1021 Morehead Medical Drive, Charlotte, NC 28204, USA
| | - Mahrukh K Ganapathi
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, 1021 Morehead Medical Drive, Charlotte, NC 28204, USA
| |
Collapse
|
3
|
Liu H, Lichti CF, Mirfattah B, Frahm J, Nilsson CL. A modified database search strategy leads to improved identification of in vitro brominated peptides spiked into a complex proteomic sample. J Proteome Res 2013; 12:4248-54. [PMID: 23898862 DOI: 10.1021/pr400472c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inflammation leads to activation of immune cells, resulting in production of hypobromous acid. Few investigations have been performed on protein bromination on a proteomic scale, even though bromination is a relatively abundant protein modification in endogenously brominated proteomes. Such studies have been hampered by the lack of an optimized database search strategy. In order to address this issue, we performed nano-LC-MS/MS analysis of an in vitro generated, trypsin-digested brominated human serum albumin standard, spiked into a complex trypsin-digested proteomic background, in an LTQ-Orbitrap instrument. We found that brominated peptides spiked in at a 1-10% ratio (mass:mass) were easily identified by manual inspection when higher-energy collisional dissociation (HCD) and collision induced dissociation (CID) were employed as the dissociation mode; however, confident assignment of brominated peptides from protein database searches required a novel approach. By addition of a custom modification, corresponding to the substitution of a single bromine with 81Br rather than 79Br for dibromotyrosine (79Br81BrY), the number of validated assignments for peptides containing dibromotyrosine increased significantly when analyzing both high resolution and low resolution MS/MS data. This new approach will facilitate the identification of proteins derived from endogenously brominated proteomes, providing further knowledge about the role of protein bromination in various pathological states.
Collapse
Affiliation(s)
- Huiling Liu
- University of Texas Medical Branch, Department of Pharmacology and Toxicology, 301 University Boulevard, Galveston, Texas 77555-0617, United States
| | | | | | | | | |
Collapse
|