Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events

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Abstract

The spread of antimicrobial resistance and vaccine escape in the human pathogen Streptococcus pneumoniae can be largely attributed to competence-induced transformation. Here, we studied this process at the single-cell level. We show that within isogenic populations, all cells become naturally competent and bind exogenous DNA. We find that transformation is highly efficient and that the chromosomal location of the integration site or whether the transformed gene is encoded on the leading or lagging strand has limited influence on recombination efficiency. Indeed, we have observed multiple recombination events in single recipients in real-time. However, because of saturation and because a single stranded donor DNA replaces the original allele, transformation efficiency has an upper threshold of approximately 50% of the population. The fixed mechanism of transformation results in a fail-safe strategy for the population as half of the population generally keeps an intact copy of the original genome.

Data availability

This work is mainly based upon microscopy and snap shots and movies of most experiments are included in the manuscript and supporting files. Raw microscopy images will be made available at the BioImages Archive (accession S-BIAD26).

Article and author information

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Jun Kurushima

Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Nathalie Campo

UMR 5100, Laboratoire de Microbiologie et Genetique Moleculaires, Toulouse, France

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2917-930X
Renske van Raaphorst

Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Guillaume Cerckel

Biochemistry and Molecular Genetics of Bacteria (BBGM), Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium

Competing interests
The authors declare that no competing interests exist.
Patrice Polard

LMGM-UMR5100, CNRS, Toulouse, France

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0365-4347
Jan-Willem Veening

Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland

For correspondence
Jan-Willem.Veening@unil.ch

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3162-6634

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_172861)

Jan-Willem Veening

European Commission (771534- PneumoCaTChER.)

Jan-Willem Veening

Agence Nationale de la Recherche (ANR-10-BLAN-1331)

Patrice Polard

Naito Foundation

Jun Kurushima

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (40AR40_185533)

Jan-Willem Veening

Agence Nationale de la Recherche (EXStasis-17-CE13-0031-01)

Patrice Polard

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.