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

Abstract

The postreplicative mismatch repair (MMR) is an almost ubiquitous DNA repair essential for maintaining genome stability. Mycobacteria, a diverse group which includes the pathogen Mycobacterium tuberculosis, likely possess an alternative MMR in which NucS, an endonuclease with no structural homology to the canonical MMR proteins (MutS/MutL), is the key factor. Despite its major importance, the in vivo specificity and mutagenesis bias of this putative alternative MMR remained unknown. Spontaneous mutations accumulated in a neutral manner over thousands of generations by M. smegmatis and its MMR-deficient derivative (nucS) were analyzed. The base-pair substitution (BPS) rate per genome per generation are 0.004 and 0.165 (>40-fold higher) for wild-type and nucS, respectively. The nucS strain displays a mutational bias for A:T>G:C, indicating that this alternative MMR prevents further increase in the already G:C rich mycobacterial genome. Strikingly, despite the different evolutionary origin and the absence of structural homology, comparison of the efficiency of MutS/L- and NucS-based systems indicates that they display similar specificity and mutagenesis bias for BPSs, especially for transitions, revealing a functional evolutionary convergence. However, NucS does not repair indels in vivo, in contrast to the efficient correction catalysed by the MutS/MutL-dependent canonical MMR proteins. Our results provide an unparalleled view of how the mycobacterial MMR works in vivo to maintain genome stability and how it may affect Mycobacterium evolution.