DNA-stimulated liquid-liquid phase separation by eukaryotic topoisomerase II modulates catalytic function
- Johns Hopkins University, United States
- The University of Texas Southwestern Medical Center, United States
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 - e.g., 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.
Data availability
Dataset information was uploaded to Dryad.DOI: https://doi.org/10.5061/dryad.z08kprrgc
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DNA-stimulated liquid-liquid phase separation by eukaryotic topoisomerase II modulates catalytic functionDryad Digital Repository, doi:10.5061/dryad.z08kprrgc.
Article and author information
Author details
Funding
National Institute of General Medical Sciences (T32-GM7445-43)
- Joshua Jeong
National Cancer Institute (R35-CA263778)
- James M Berger
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Jeong et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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DNA-stimulated liquid-liquid phase separation by eukaryotic topoisomerase II modulates catalytic function
eLife 11:e81786.
https://doi.org/10.7554/eLife.81786
Further reading
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- Biochemistry and Chemical Biology
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Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular condensates are exemplified here by experimental and theoretical investigations of the different salt- and ATP-dependent LLPSs of an IDR of messenger RNA-regulating protein Caprin1 and its phosphorylated variant pY-Caprin1, exhibiting, for example, reentrant behaviors in some instances but not others. Experimental data are rationalized by physical modeling using analytical theory, molecular dynamics, and polymer field-theoretic simulations, indicating that interchain ion bridges enhance LLPS of polyelectrolytes such as Caprin1 and the high valency of ATP-magnesium is a significant factor for its colocalization with the condensed phases, as similar trends are observed for other IDRs. The electrostatic nature of these features complements ATP’s involvement in π-related interactions and as an amphiphilic hydrotrope, underscoring a general role of biomolecular condensates in modulating ion concentrations and its functional ramifications.
