CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS

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Abstract

Faithful segregation of bacterial chromosomes relies on the ParABS partitioning system and the SMC complex. In this work, we used single molecule techniques to investigate the role of cytidine triphosphate (CTP) binding and hydrolysis in the critical interaction between centromere-like parS DNA sequences and the ParB CTPase. Using a combined optical tweezers confocal microscope, we observe the specific interaction of ParB with parS directly. Binding around parS is enhanced by the presence of CTP or the non-hydrolysable analogue CTPgS. However, ParB proteins are also detected at a lower density in distal non-specific DNA. This requires the presence of a parS loading site and is prevented by protein roadblocks, consistent with one dimensional diffusion by a sliding clamp. ParB diffusion on non-specific DNA is corroborated by direct visualization and quantification of movement of individual quantum-dot labelled ParB. Magnetic tweezers experiments show that the spreading activity, which has an absolute requirement for CTP binding but not hydrolysis, results in the condensation of parS-containing DNA molecules at low nanomolar protein concentrations.

Data availability

All DNA sequences used are included in Supplementary Information.Data sets for Fig. 1E, 1F; Fig. 1-S1B, Fig.1-S1C; Fig.1-S4C, Fig1-S4D; Fig. 2C, 2G; Fig. 4C, 4D, 4E, 4F, 4G; Fig. 4-S1A, Fig. 4-S1B, Fig. 4-S1C; Fig. 5A, 5B; Fig. 6A, 6B, 6D, 6F, have been provided.

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Francisco de Asis Balaguer

Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain

Competing interests
The authors declare that no competing interests exist.
Clara Aicart-Ramos

Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain

Competing interests
The authors declare that no competing interests exist.
Gemma LM Fisher

School of Biochemistry, University of Bristol, Bristol, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Sara de Bragança

Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4039-1993
Eva M Martin-Cuevas

Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain

Competing interests
The authors declare that no competing interests exist.
Cesar L Pastrana

Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain

Competing interests
The authors declare that no competing interests exist.
Mark Simon Dillingham

School of Biochemistry, University of Bristol, Bristol, United Kingdom

For correspondence
mark.dillingham@bristol.ac.uk

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4612-7141
Fernando Moreno-Herrero

Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain

For correspondence
fernando.moreno@cnb.csic.es

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4083-1709

Funding

European Research Council (681299)

Fernando Moreno-Herrero

Wellcome Trust (100401/Z/12/Z)

Mark Simon Dillingham

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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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.