Speed variations of bacterial replisomes

Abstract
Data availability
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Abstract

Replisomes are multi-protein complexes that replicate genomes with remarkable speed and accuracy. Despite their importance, their dynamics is poorly characterized, especially in vivo. In this paper, we present an approach to infer the replisome dynamics from the DNA abundance distribution measured in a growing bacterial population. Our method is sensitive enough to detect subtle variations of the replisome speed along the genome. As an application, we experimentally measured the DNA abundance distribution in Escherichia coli populations growing at different temperatures using deep sequencing. We find that the average replisome speed increases nearly five-fold between 17°C and 37°C. Further, we observe wave-like variations of the replisome speed along the genome. These variations correlate with previously observed variations of the mutation rate, suggesting a common dynamical origin. Our approach has the potential to elucidate replication dynamics in E. coli mutants and in other bacterial species.

Data availability

Sequence reads were deposited in the NCBI Sequence Read Archive with links to BioProject accession number PRJNA772106. Corresponding read frequencies along the genome were deposited in Zenodo (DOI:10.5281/zenodo.5577986).

The following data sets were generated

(2022) Escherichia coli DNA replication study
NCBI BioProject, PRJNA772106.

https://dataview.ncbi.nlm.nih.gov/object/PRJNA772106?reviewer=lkimmuqg1d5cfjrrh625j30286
(2022) Escherichia coli DNA replication study: processed alignment data
doi: 10.5281/zenodo.5577986.

https://zenodo.org/record/5577986#.Yi96nRDP3s0

Article and author information

Author details

Deepak Bhat

Biological Complexity Unit, Okinawa Institute of Science and Technology, Onna, Japan

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9387-4951
Samuel Hauf

Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology, Onna, Japan

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3034-8441
Charles Plessy

Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Onna, Japan

Competing interests
The authors declare that no competing interests exist.
Yohei Yokobayashi

Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology, Onna, Japan

Competing interests
The authors declare that no competing interests exist.
Simone Pigolotti

Biological Complexity Unit, Okinawa Institute of Science and Technology, Onna, Japan

For correspondence
simone.pigolotti@oist.jp

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6157-6906

Funding

Japan Society for the Promotion of Science (JP18K03473)

Simone Pigolotti

Deutsche Forschungsgemeinschaft (Projektnummer 452628014,Geschätszeichen: HA9374/1-1)

Samuel Hauf

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

Copyright

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.