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

10 páginas, 3 figuras, 3 tablas. Material suplementario en: https://advances.sciencemag.org/content/suppl/2020/02/10/6.7.eaay4453.DC1The 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.This work was supported by Plan Nacional de I + D + i 2013–2016 and the Instituto de Salud Carlos III, Subdireccion General de Redes y Centros de Investigacion Cooperativa, Ministerio de Economia, Industria y Competitividad, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0009)—cofinanced by the European Development Regional Fund “A Way to Achieve Europe”—by Operative Program Intelligent Growth 2014-2020 and grants FIS PI17/00159 from the Instituto de Salud Carlos III and SAF2015-72793-EXP from the Spanish Ministry of Science and Competitiveness (MINECO)-FEDER. E.C.-S. was the recipient of a PFIS predoctoral research fellowship (FI18/00036) cofinanced by the Instituto de Salud Carlos III and the European Social Fund. I.C., A.C.-O., and M.T.-P. are funded by projects of the 581 European Research Council (ERC) (638553-TB-ACCELERATE) and Ministerio de Economía y Competitividad research grant SAF2016-77346-R.Peer reviewe