The mycobacterial ImuA'-ImuB-DnaE2 mutasome: composition and recruitment in live cells
- University of Cape Town, South Africa
- Howard Hughes Medical Institute, United States
- Leiden University Medical Center, Netherlands
- University of Saskatchewan, Canada
- Umeå University, Sweden
- Helmholtz Institute for Pharmaceutical Research Saarland, Germany
- Swiss Federal Institute of Technology in Lausanne, Switzerland
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States
- Vilnius University, Lithuania
Abstract
A DNA damage-inducible mutagenic gene cassette has been implicated in the emergence of drug resistance in Mycobacterium tuberculosis during anti-tuberculosis (TB) chemotherapy. However, the molecular composition and operation of the encoded 'mycobacterial mutasome' - minimally comprising DnaE2 polymerase and ImuA′ and ImuB accessory proteins - remain elusive. Following exposure of mycobacteria to DNA damaging agents, we observe that DnaE2 and ImuB co-localize with the DNA polymerase III β subunit (β clamp) in distinct intracellular foci. Notably, genetic inactivation of the mutasome in an imuBAAAAGG mutant containing a disrupted β clamp-binding motif abolishes ImuB-β clamp focus formation, a phenotype recapitulated pharmacologically by treating bacilli with griselimycin and in biochemical assays in which this β clamp-binding antibiotic collapses pre-formed ImuB-β clamp complexes. These observations establish the essentiality of the ImuB-β clamp interaction for mutagenic DNA repair in mycobacteria, identifying the mutasome as target for adjunctive therapeutics designed to protect anti-TB drugs against emerging resistance.
Data availability
Source data for all figures contained in the manuscript and SI have been deposited in Dryad; see https://datadryad.org/stash/share/fjhwiXFEIIM5-6liMtXIQn0Ehq4NIKZ3690FiR8lWyI.
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Data from: The mycobacterial ImuA'-ImuB-DnaE2 mutasome: composition and recruitment in live cellsDryad Digital Repository, doi:10.5061/dryad.76hdr7szc.
Article and author information
Author details
Meindert Hugo Lamers
Funding
Eunice Kennedy Shriver National Institute of Child Health and Human Development (U01HD085531)
- Roger Woodgate
- Digby F Warner
Norges Forskningsråd (261669)
- Digby F Warner
South African Medical Research Council (SHIP and Extramural Unit)
- Valerie Mizrahi
- Digby F Warner
National Research Foundation
- Valerie Mizrahi
- Digby F Warner
Howard Hughes Medical Institute (Senior International Research Scholars)
- Valerie Mizrahi
Leids Universitair Medisch Centrum (LUMC Fellowship)
- Meindert Hugo Lamers
National Research Foundation (104683)
- Michael Anton Reiche
David and Elaine Potter Foundation (PhD Fellowship)
- Zela Alexandria-Mae Martin
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Further reading
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Glutamine synthetases (GS) are central enzymes essential for the nitrogen metabolism across all domains of life. Consequently, they have been extensively studied for more than half a century. Based on the ATP-dependent ammonium assimilation generating glutamine, GS expression and activity are strictly regulated in all organisms. In the methanogenic archaeon Methanosarcina mazei, it has been shown that the metabolite 2-oxoglutarate (2-OG) directly induces the GS activity. Besides, modulation of the activity by interaction with small proteins (GlnK1 and sP26) has been reported. Here, we show that the strong activation of M. mazei GS (GlnA1) by 2-OG is based on the 2-OG dependent dodecamer assembly of GlnA1 by using mass photometry (MP) and single particle cryo-electron microscopy (cryo-EM) analysis of purified strep-tagged GlnA1. The dodecamer assembly from dimers occurred without any detectable intermediate oligomeric state and was not affected in the presence of GlnK1. The 2.39 Å cryo-EM structure of the dodecameric complex in the presence of 12.5 mM 2-OG demonstrated that 2-OG is binding between two monomers. Thereby, 2-OG appears to induce the dodecameric assembly in a cooperative way. Furthermore, the active site is primed by an allosteric interaction cascade caused by 2-OG-binding towards an adaption of an open active state conformation. In the presence of additional glutamine, strong feedback inhibition of GS activity was observed. Since glutamine dependent disassembly of the dodecamer was excluded by MP, feedback inhibition most likely relies on the binding of glutamine to the catalytic site. Based on our findings, we propose that under nitrogen limitation the induction of M. mazei GS into a catalytically active dodecamer is not affected by GlnK1 and crucially depends on the presence of 2-OG.
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