Abstract
Cell division is a central process in all living organisms and requires the coordinated action of many proteins and regulatory elements. In most bacteria, the division and cell wall (dcw) gene cluster is regulated by the first gene of the dcw operon, mraZ, a highly conserved DNA-binding transcriptional regulator. Here we report the structural basis of MraZ transcriptional regulation by the resolution of three different cryo-EM structures of MraZ in complex with the upstream promoter region of the dcw cluster from Mycoplasma genitalium at 3.36, 3.57 and 3.87 Å resolution. The structures reveal the specific interactions between MraZ DNA-binding motif and nucleobases of the binding boxes, which induces distortion in the MraZ octamer to enable the interaction with the four repetitive binding boxes of the promoter DNA. The “cradle-like” DNA-binding motif of MraZ exposes three highly conserved basic residues, Lys13, Arg15 and Arg86, which are essential for binding to the consensus sequence of its cognate promoter. Ultimately, the mechanism behind MraZ’s DNA binding and regulation of the dcw operon could be translated to other species, working as a general mechanism for the regulation of dcw gene cluster in bacteria.
Data availability
Coordinates from crystal structures reported here have been deposited in the Protein Data Bank under accession codes 9QLG (MraZ octamer) and 9QLR (MraZ nonamer). CryoEM coordinates and maps have been deposited in the Protein Data Bank under accession codes 9R4J and EMD-53569 (MraZ Fiber 1), 9SZ7 and EMD-55361 (MraZ Fiber 2), and 9SX6 and EMD-55332 (MraZ Octamer-DNA). Other Protein Data Bank accession codes used in this study: 1N0E (MraZ M.pneumoniae), 2W1T (SpoVT), 1Z0R (AbrB) and 2FY9] (AbH). All other data supporting the findings of this study are available within the article and its supplementary information files. Source data are provided in this paper.
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Acknowledgements
This work was supported by the Spanish Ministry of Science and Innovation (MICINN) PID2024-160233OB-I00 to D.R., PID2024-156687OB-I00 to V.A. and PID2024-159663OB-C21 to J.P.; and by ICREA to DR, ICREA-Academia-2022, from Generalitat de Catalunya. L.S.A. acknowledges her FPI fellowship from the Spanish Government (PRE2019-088509). D.R. acknowledges support from the Serra Hunter program from Generalitat de Catalunya. X-ray experiments were performed at BL-13 XALOC beamline at ALBA Synchrotron with the collaboration of ALBA staff. This work benefited from access to IGBMC, an Instruct-ERIC Center. Financial support was provided by Instruct-ERIC internship APPID 3074 and PID 27465. We thank the Microscopy Services (UAB). We thank Nils Marechal (IGBMC-CBI) for his help with cryoEM sample preparation, data collection and insightful discussions. We also thank Pablo Guerra (IBMB-CSIC, JEMCA, ALBA Synchrotron) for his help in obtaining preliminary cryoEM data.
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L.S.A. conducted crystallization experiments. A.D, L.S.A., and J.G.P. performed the cryoEM analysis. J.P. analyzed the promotor sequences. L.S.A. and N.V. conducted all in vitro activity assays. M.C-C. and V.A. conducted qPCR analysis. D.R., N.V., and L.S.A. contributed to the correction and writing of the manuscript.
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Sánchez-Alba, L., Varejão, N., Durand, A. et al. Structural basis for transcriptional regulation by the cell division regulator MraZ in Mycoplasma genitalium. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68809-2
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DOI: https://doi.org/10.1038/s41467-026-68809-2
