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. 2020 Feb 12;6(7):eaay4453.
doi: 10.1126/sciadv.aay4453. eCollection 2020 Feb.

Specificity and mutagenesis bias of the mycobacterial alternative mismatch repair analyzed by mutation accumulation studies

A Castañeda-García  1 , I Martín-Blecua  1 , E Cebrián-Sastre  1 , A Chiner-Oms  2 , M Torres-Puente  2 , I Comas  2   3 , J Blázquez  1
Affiliations

Specificity and mutagenesis bias of the mycobacterial alternative mismatch repair analyzed by mutation accumulation studies

A Castañeda-García et al. Sci Adv. .

Abstract

The postreplicative mismatch repair (MMR) is an almost ubiquitous DNA repair essential for maintaining genome stability. It has been suggested that Mycobacteria have an alternative MMR in which NucS, an endonuclease with no structural homology to the canonical MMR proteins (MutS/MutL), is the key factor. Here, we analyze the spontaneous mutations accumulated in a neutral manner over thousands of generations by Mycobacterium smegmatis and its MMR-deficient derivative (ΔnucS). The base pair substitution rates per genome per generation are 0.004 and 0.165 for wild type and ΔnucS, respectively. By comparing the activity of different bacterial MMR pathways, we demonstrate that both MutS/L- and NucS-based systems display similar specificity and mutagenesis bias, revealing a functional evolutionary convergence. However, NucS is not able to repair indels in vivo. Our results provide an unparalleled view of how this mycobacterial system works in vivo to maintain genome stability and how it may affect Mycobacterium evolution.

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Figures

Fig. 1
Fig. 1. Whole-genome mutations of the evolved strains.
Total number of mutations (A), BPSs (B), and indels (C) of the evolved wild-type M. smegmatis mc2 155 (blue circles) and ∆nucS (red circles) strains after performing the MA experiment. The horizontal straight segment represents the median value of mutations in each case.
Fig. 2
Fig. 2. Assembly of reporter plasmids.
Integrative plasmid constructs used to measure KanR reversion events are shown. Modified bases are shown in green, and indels are shown in orange.
Fig. 3
Fig. 3. Mutation rates for KanR reversion events.
Rates of spontaneous mutations per cell per generation conferring kanamycin resistance for M. smegmatis mc2 155 (wild type) (blue) and its ΔnucS derivative (red) are shown. Ninety-five percent confidence intervals are shown. The limit of detection was around 10−10, as inferred by observed mutation rates of A:T>T:A transversion.
See this image and copyright information in PMC

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