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

• Published in: Nature communications 2021-03, Vol.12 (1), p.1988-1988, Article 1988
• Main Authors: Horne, Christopher R., Venugopal, Hariprasad, Panjikar, Santosh, Wood, David M., Henrickson, Amy, Brookes, Emre, North, Rachel A., Murphy, James M., Friemann, Rosmarie, Griffin, Michael D. W., Ramm, Georg, Demeler, Borries, Dobson, Renwick C. J.
• Format: Article
• Language: English
• Subjects: 101/28; 631/1647/2204; 631/337/572; 631/45/147; 631/535/1258/1259; 631/535/1266; 82/16; 82/80; 82/83; Allosteric properties; Allosteric Regulation; Bacteria; Base Sequence; Binding; Binding Sites - genetics; Cell and Molecular Biology; Cell- och molekylärbiologi; Coliforms; Crystal structure; Crystallography, X-Ray; Deoxyribonucleic acid; Dimers; DNA; DNA structure; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Domains; E coli; Electron microscopy; Environmental changes; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene Expression Regulation, Bacterial; Genes; Humanities and Social Sciences; Metabolism; Models, Molecular; multidisciplinary; N-Acetylneuraminic Acid - metabolism; Nucleotide Motifs - genetics; Prokaryotes; Protein Binding; Protein Conformation; Protein interaction; Protein Multimerization; Protein structure; Proteins; Repressor Proteins - genetics; Repressor Proteins - metabolism; Science; Science & Technology - Other Topics; Science (multidisciplinary); Sialic acids; Sialic Acids - metabolism; Transcription factors
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-22253-6

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-protein interactions between NanR dimers via their N-terminal extensions. The effector, N -acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N -acetylneuraminate reveals a domain rearrangement upon N -acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.