Real-time Monitoring of Replication Errors' Fate Reveals the Origin and Dynamics of Spontaneous Mutations

Overview

Journal Nat Commun

Specialty Biology

Date 2024 Mar 28

PMID 38538613

Authors

Chiara Enrico Bena

Jean Ollion

Marianne De Paepe

Magali Ventroux

Lydia Robert

Marina Elez

Affiliations

Soon will be listed here.

Abstract

The efficiency of replication error repair is a critical factor governing the emergence of mutations. However, it has so far been impossible to study this efficiency at the level of individual cells and to investigate if it varies within isogenic cell populations. In addition, why some errors escape repair remains unknown. Here we apply a combination of fluorescent labelling of the Escherichia coli Mismatch Repair (MMR) complex, microfluidics, and time-lapse microscopy, to monitor in real-time the fate of >20000 replication errors. We show that i) many mutations result from errors that are detected by MMR but inefficiently repaired ii) this limited repair efficiency is due to a temporal constraint imposed by the transient nature of the DNA strand discrimination signal, a constraint that is likely conserved across organisms, and iii) repair capacity varies from cell to cell, resulting in a subpopulation of cells with higher mutation rate. Such variations could influence the fitness and adaptability of populations, accelerating for instance the emergence of antibiotic resistance.

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References

Wang P, Robert L, Pelletier J, Dang W, Taddei F, Wright A . Robust growth of Escherichia coli. Curr Biol. 2010; 20(12):1099-103. PMC: 2902570. DOI: 10.1016/j.cub.2010.04.045. View

Elez M, Murray A, Bi L, Zhang X, Matic I, Radman M . Seeing mutations in living cells. Curr Biol. 2010; 20(16):1432-7. PMC: 3612896. DOI: 10.1016/j.cub.2010.06.071. View

Elez M, Radman M, Matic I . The frequency and structure of recombinant products is determined by the cellular level of MutL. Proc Natl Acad Sci U S A. 2007; 104(21):8935-40. PMC: 1885606. DOI: 10.1073/pnas.0610149104. View

Damagnez V, Doutriaux M, Radman M . Saturation of mismatch repair in the mutD5 mutator strain of Escherichia coli. J Bacteriol. 1989; 171(8):4494-7. PMC: 210230. DOI: 10.1128/jb.171.8.4494-4497.1989. View

Hombauer H, Campbell C, Smith C, Desai A, Kolodner R . Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates. Cell. 2011; 147(5):1040-53. PMC: 3478091. DOI: 10.1016/j.cell.2011.10.025. View

Harris R, Feng G, Ross K, Sidhu R, Thulin C, Longerich S . Mismatch repair protein MutL becomes limiting during stationary-phase mutation. Genes Dev. 1997; 11(18):2426-37. PMC: 316514. DOI: 10.1101/gad.11.18.2426. View

Reyes G, Kolodziejczak A, Devakumar L, Kubota T, Kolodner R, Putnam C . Ligation of newly replicated DNA controls the timing of DNA mismatch repair. Curr Biol. 2021; 31(6):1268-1276.e6. PMC: 8281387. DOI: 10.1016/j.cub.2020.12.018. View

Lahue R, Su S, Modrich P . Requirement for d(GATC) sequences in Escherichia coli mutHLS mismatch correction. Proc Natl Acad Sci U S A. 1987; 84(6):1482-6. PMC: 304458. DOI: 10.1073/pnas.84.6.1482. View

Mardenborough Y, Nitsenko K, Laffeber C, Duboc C, Sahin E, Quessada-Vial A . The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair. Nucleic Acids Res. 2019; 47(22):11667-11680. PMC: 6902014. DOI: 10.1093/nar/gkz834. View

10.

Ollion J, Elez M, Robert L . High-throughput detection and tracking of cells and intracellular spots in mother machine experiments. Nat Protoc. 2019; 14(11):3144-3161. DOI: 10.1038/s41596-019-0216-9. View

11.

Guarne A . The functions of MutL in mismatch repair: the power of multitasking. Prog Mol Biol Transl Sci. 2012; 110:41-70. DOI: 10.1016/B978-0-12-387665-2.00003-1. View

12.

Robert L, Ollion J, Robert J, Song X, Matic I, Elez M . Mutation dynamics and fitness effects followed in single cells. Science. 2018; 359(6381):1283-1286. DOI: 10.1126/science.aan0797. View

13.

Galan J, Turrientes M, Baquero M, Rodriguez-Alcayna M, Martinez-Amado J, Martinez J . Mutation rate is reduced by increased dosage of mutL gene in Escherichia coli K-12. FEMS Microbiol Lett. 2007; 275(2):263-9. DOI: 10.1111/j.1574-6968.2007.00902.x. View

14.

Learn B, Grafstrom R . Methyl-directed repair of frameshift heteroduplexes in cell extracts from Escherichia coli. J Bacteriol. 1989; 171(12):6473-81. PMC: 210536. DOI: 10.1128/jb.171.12.6473-6481.1989. View

15.

Negishi K, Loakes D, Schaaper R . Saturation of DNA mismatch repair and error catastrophe by a base analogue in Escherichia coli. Genetics. 2002; 161(4):1363-71. PMC: 1462219. DOI: 10.1093/genetics/161.4.1363. View

16.

Campbell J, Kleckner N . The rate of Dam-mediated DNA adenine methylation in Escherichia coli. Gene. 1988; 74(1):189-90. DOI: 10.1016/0378-1119(88)90283-1. View

17.

Feng G, Tsui H, Winkler M . Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells. J Bacteriol. 1996; 178(8):2388-96. PMC: 177950. DOI: 10.1128/jb.178.8.2388-2396.1996. View

18.

Putnam C . Evolution of the methyl directed mismatch repair system in Escherichia coli. DNA Repair (Amst). 2015; 38:32-41. PMC: 4740232. DOI: 10.1016/j.dnarep.2015.11.016. View

19.

Hermans N, Laffeber C, Cristovao M, Artola-Boran M, Mardenborough Y, Ikpa P . Dual daughter strand incision is processive and increases the efficiency of DNA mismatch repair. Nucleic Acids Res. 2016; 44(14):6770-86. PMC: 5001592. DOI: 10.1093/nar/gkw411. View

20.

Ninio J . Transient mutators: a semiquantitative analysis of the influence of translation and transcription errors on mutation rates. Genetics. 1991; 129(3):957-62. PMC: 1204761. DOI: 10.1093/genetics/129.3.957. View