Journal article

Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

Christopher R Horne, Hariprasad Venugopal, Santosh Panjikar, David M Wood, Amy Henrickson, Emre Brookes, Rachel A North, James M Murphy, Rosmarie Friemann, Michael DW Griffin, Georg Ramm, Borries Demeler, Renwick CJ Dobson

Nature Communications | NATURE RESEARCH | Published : 2021

Abstract

Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-p..

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Grants

Awarded by New Zealand Royal Society Marsden Fund


Awarded by Ministry of Business, Innovation and Employment Smart Ideas grant


Awarded by ARC LIEF grants


Awarded by Swedish Governmental Agency for Innovation Systems


Awarded by NHMRC


Awarded by NIH


Awarded by NSF/XSEDE


Awarded by University of Texas


Awarded by Canada Foundation for Innovation


Funding Acknowledgements

We thank staff at the Australian Synchrotron MX2 and SAXS/WAXS beamlines for their assistance in data collection and the New Zealand Synchrotron Group for enabling access; Janet Newman (Collaborative Crystallisation Centre) for assistance with protein crystallization, Yee-Foong Mok (Bio21 Institute, University of Melbourne) for his assistance with analytical ultracentrifugation experiments; and Tim Cooper (Massey University) for critical reading of the manuscript. We are grateful to the Biomolecular Interaction Centre (University of Canterbury), the Canterbury Medical Research Foundation, and the Maurice Wilkins Centre for scholarship support to C.R.H. We acknowledge the New Zealand Royal Society Marsden Fund (to R.C.J.D., UOC1506), Ministry of Business, Innovation and Employment Smart Ideas grant (to R.C.J.D., UOCX1706), ARC LIEF grants (to G.R., LE120100090 and LE200100045), Swedish Governmental Agency for Innovation Systems (to R.F., 2017-00180), Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg (to R.F.), NHMRC grants (to J.M.M., 1172929 and 9000653), and the Victorian Government Operational Infrastructure Support Scheme (to J.M.M.). Funding to B.D. from NIH for grant and UltraScan multiwavelength development support (GM120600 and NSF-ACI-1339649), NSF/XSEDE grant for support towards UltraScan supercomputer calculations (TG-MCB070039N), and University of Texas grant (TG457201) is acknowledged. This research was undertaken in part using the SAXS/WAXS and MX2 beamlines at the Australian Synchrotron, part of ANSTO, and made use of the ACRF detector; the Monash Ramaciotti Centre for Cryo-Electron Microscopy (a node of Microscopy Australia) and made use of the Multi-modal Australian ScienceS Imaging and Visualisation Environment (www.massive.org.au) for data processing; and the Canadian Center for Hydrodynamics, University of Lethbridge for MWL-SV experiments, with support from the Canada Foundation for Innovation Grant CFI-37589 (to B.D.).