Unbiased Homeologous Recombination During Pneumococcal Transformation Allows for Multiple Chromosomal Integration Events

Overview

Journal Elife

Specialty Biology

Date 2020 Sep 23

PMID 32965219

Citations 12

Authors

Jun Kurushima

Nathalie Campo

Renske van Raaphorst

Guillaume Cerckel

Patrice Polard

Jan-Willem Veening

Affiliations

Soon will be listed here.

Abstract

The spread of antimicrobial resistance and vaccine escape in the human pathogen 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.

Citing Articles

Pneumococcal competence is a populational health sensor driving multilevel heterogeneity in response to antibiotics.

Prudhomme M, Johnston C, Soulet A, Boyeldieu A, De Lemos D, Campo N Nat Commun. 2024; 15(1):5625.

PMID: 38987237 PMC: 11237056. DOI: 10.1038/s41467-024-49853-2.

Triggering Toll-Like Receptor 5 Signaling During Pneumococcal Superinfection Prevents the Selection of Antibiotic Resistance.

Costa C, Sirard J, Gibson P, Veening J, Gjini E, Baldry M J Infect Dis. 2024; 230(5):e1126-e1135.

PMID: 38716762 PMC: 11566229. DOI: 10.1093/infdis/jiae239.

Airway proteolytic control of pneumococcal competence.

Echlin H, Iverson A, Sardo U, Rosch J PLoS Pathog. 2023; 19(5):e1011421.

PMID: 37256908 PMC: 10259803. DOI: 10.1371/journal.ppat.1011421.

DNA modifications impact natural transformation of Acinetobacter baumannii.

Vesel N, Iseli C, Guex N, Lemopoulos A, Blokesch M Nucleic Acids Res. 2023; 51(11):5661-5677.

PMID: 37178001 PMC: 10287943. DOI: 10.1093/nar/gkad377.

Programming bacteria for multiplexed DNA detection.

Cheng Y, Chen Z, Cao X, Ross T, Falbel T, Burton B Nat Commun. 2023; 14(1):2001.

PMID: 37037805 PMC: 10086068. DOI: 10.1038/s41467-023-37582-x.

References

Cowley L, Petersen F, Junges R, Jimson D Jimenez M, Morrison D, Hanage W . Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS Genet. 2018; 14(6):e1007410. PMC: 6016952. DOI: 10.1371/journal.pgen.1007410. View

Croucher N, Lochen A, Bentley S . Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles. Annu Rev Microbiol. 2018; 72:521-549. DOI: 10.1146/annurev-micro-090817-062338. View

Chewapreecha C, Harris S, Croucher N, Turner C, Marttinen P, Cheng L . Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014; 46(3):305-309. PMC: 3970364. DOI: 10.1038/ng.2895. View

Campbell E, Choi S, Masure H . A competence regulon in Streptococcus pneumoniae revealed by genomic analysis. Mol Microbiol. 1998; 27(5):929-39. DOI: 10.1046/j.1365-2958.1998.00737.x. View

Ouldali N, Levy C, Varon E, Bonacorsi S, Bechet S, Cohen R . Incidence of paediatric pneumococcal meningitis and emergence of new serotypes: a time-series analysis of a 16-year French national survey. Lancet Infect Dis. 2018; 18(9):983-991. DOI: 10.1016/S1473-3099(18)30349-9. View

van Raaphorst R, Kjos M, Veening J . BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data. Mol Microbiol. 2019; 113(1):297-308. PMC: 7027861. DOI: 10.1111/mmi.14417. View

Paintdakhi A, Parry B, Campos M, Irnov I, Elf J, Surovtsev I . Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis. Mol Microbiol. 2015; 99(4):767-77. PMC: 4752901. DOI: 10.1111/mmi.13264. View

Ephrussi-Taylor H . Genetic recombination in DNA-induced transformation of Pneumococcus. IV. The pattern of transmission and phenotypic expression of high and low-efficiency donor sites in the amiA locus. Genetics. 1966; 54(1):211-22. PMC: 1211102. DOI: 10.1093/genetics/54.1.211. View

Mortier-Barriere I, Velten M, Dupaigne P, Mirouze N, Pietrement O, McGovern S . A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell. 2007; 130(5):824-36. DOI: 10.1016/j.cell.2007.07.038. View

10.

Fox M, Allen M . ON THE MECHANISM OF DEOXYRIBONUCLEATE INTEGRATION IN PNEUMOCOCCAL TRANSFORMATION. Proc Natl Acad Sci U S A. 1964; 52:412-9. PMC: 300292. DOI: 10.1073/pnas.52.2.412. View

11.

Chen I, Dubnau D . DNA uptake during bacterial transformation. Nat Rev Microbiol. 2004; 2(3):241-9. DOI: 10.1038/nrmicro844. View

12.

Havarstein L, Coomaraswamy G, Morrison D . An unmodified heptadecapeptide pheromone induces competence for genetic transformation in Streptococcus pneumoniae. Proc Natl Acad Sci U S A. 1995; 92(24):11140-4. PMC: 40587. DOI: 10.1073/pnas.92.24.11140. View

13.

Mortier-Barriere I, de Saizieu A, Claverys J, Martin B . Competence-specific induction of recA is required for full recombination proficiency during transformation in Streptococcus pneumoniae. Mol Microbiol. 1998; 27(1):159-70. DOI: 10.1046/j.1365-2958.1998.00668.x. View

14.

Domenech A, Brochado A, Sender V, Hentrich K, Henriques-Normark B, Typas A . Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer. Cell Host Microbe. 2020; 27(4):544-555.e3. DOI: 10.1016/j.chom.2020.02.002. View

15.

Dubnau D, Blokesch M . Mechanisms of DNA Uptake by Naturally Competent Bacteria. Annu Rev Genet. 2019; 53:217-237. DOI: 10.1146/annurev-genet-112618-043641. View

16.

Sorg R, Kuipers O, Veening J . Gene expression platform for synthetic biology in the human pathogen Streptococcus pneumoniae. ACS Synth Biol. 2014; 4(3):228-39. DOI: 10.1021/sb500229s. View

17.

Berge M, Kamgoue A, Martin B, Polard P, Campo N, Claverys J . Midcell recruitment of the DNA uptake and virulence nuclease, EndA, for pneumococcal transformation. PLoS Pathog. 2013; 9(9):e1003596. PMC: 3764208. DOI: 10.1371/journal.ppat.1003596. View

18.

Carrasco B, Serrano E, Sanchez H, Wyman C, Alonso J . Chromosomal transformation in Bacillus subtilis is a non-polar recombination reaction. Nucleic Acids Res. 2016; 44(6):2754-68. PMC: 4824099. DOI: 10.1093/nar/gkv1546. View

19.

Puyet A, Greenberg B, Lacks S . Genetic and structural characterization of endA. A membrane-bound nuclease required for transformation of Streptococcus pneumoniae. J Mol Biol. 1990; 213(4):727-38. DOI: 10.1016/S0022-2836(05)80259-1. View

20.

Shanker E, Federle M . Quorum Sensing Regulation of Competence and Bacteriocins in Streptococcus pneumoniae and mutans. Genes (Basel). 2017; 8(1). PMC: 5295010. DOI: 10.3390/genes8010015. View