A low Smc flux avoids collisions and facilitates chromosome organization in B. subtilis
- University of Lausanne, Switzerland
- Université Paris-Saclay, France
- Max Planck Institute of Biochemistry, Germany
Abstract
SMC complexes are widely conserved ATP-powered DNA-loop-extrusion motors indispensable for organizing and faithfully segregating chromosomes. How SMC complexes translocate along DNA for loop extrusion and what happens when two complexes meet on the same DNA molecule is largely unknown. Revealing the origins and the consequences of SMC encounters is crucial for understanding the folding process not only of bacterial, but also of eukaryotic chromosomes. Here, we uncover several factors that influence bacterial chromosome organization by modulating the probability of such clashes. These factors include the number, the strength, and the distribution of Smc loading sites, the residency time on the chromosome, the translocation rate, and the cellular abundance of Smc complexes. By studying various mutants, we show that these parameters are fine-tuned to reduce the frequency of encounters between Smc complexes, presumably as a risk mitigation strategy. Mild perturbations hamper chromosome organization by causing Smc collisions, implying that the cellular capacity to resolve them is limited. Altogether, we identify mechanisms that help to avoid Smc collisions and their resolution by Smc traversal or other potentially risky molecular transactions.
Data availability
All deep sequencing data has been deposited to the NCBI GEO database and will be available at GEO Accession number: GSE163573All other raw data will be made available via Mendeley Data DOI:10.17632/kvjd6nj2bh.2
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GEO_Smc_collisionsNCBI GEO, GSE163573.
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Smc_collisionsMendeley Data, V2, doi: 10.17632/kvjd6nj2bh.2.
Article and author information
Author details
Funding
European Reserach Council Horizon 2020 (724482)
- Stephan Gruber
Agence Nationale de la Recherche (ANR-CE12-0013-01)
- Frederic Boccard
Assocation pour la Recherche contre le Cancer
- Frederic Boccard
Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg
- Anita Minnen
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Anchimiuk 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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A low Smc flux avoids collisions and facilitates chromosome organization in B. subtilis
eLife 10:e65467.
https://doi.org/10.7554/eLife.65467
Further reading
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- Chromosomes and Gene Expression
Specialized magnetic beads that bind target proteins to a cryogenic electron microscopy grid make it possible to study the structure of protein complexes from dilute samples.
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- Chromosomes and Gene Expression
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Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
