Mechanism of NanR transcriptional activation of sialic acid metabolism in Streptococcus pneumoniae

Wood, DM; Johns, AS; Tillett, ZD; Shearer, HL; Panjikar, S; Mok, YF; Griffin, MDW; Allison, TM; North, RA; Pace, PE; Demeler, B; Hampton, MB; Dobson, RCJ; Horne, CR

Author(s): Wood, DM; Johns, AS; Tillett, ZD; Shearer, HL; Panjikar, S; Mok, YF; Griffin, MDW; Allison, TM; North, RA; Pace, PE; Demeler, B; Hampton, MB; Dobson, RCJ; Horne, CR;
Details: Publication Year 2026-09-22,Volume 54,Issue #18,Page gkag953
Journal Title: Nucleic Acids Research
Abstract: In Streptococcus pneumoniae, the RpiR transcriptional regulator NanR (SpNanR) senses sialic acid in the environment and upregulates transcription of the nan and sia A operons to increase uptake and metabolism of sialic acid. The molecular basis of this activation is unknown. Here, we demonstrate that SpNanR binds N-acetylmannosamine-6-phosphate, a metabolite of sialic acid catabolism. SpNanR exists in a dimer-tetramer equilibrium, and N-acetylmannosamine-6-phosphate binding strongly stabilizes the tetramer. Crystal structures and site-specific substitutions demonstrate that N-acetylmannosamine-6-phosphate bridges and stabilizes the SpNanR tetramer. SpNanR binds its DNA recognition sequence with nanomolar affinity. Notably, the effector N-acetylmannosamine-6-phosphate does not affect the affinity of SpNanR for DNA. The DNA-binding domains are not structurally coupled to the sugar isomerase domains, explaining why N-acetylmannosamine-6-phosphate binding does not affect DNA binding. Structural analysis reveals that sequence specificity arises through distortion of B-DNA and an unusual π-stack formed by two arginine residues in the minor groove, while affinity is driven by backbone contacts. We propose a mechanism by which S. pneumoniae regulates sialic acid metabolism, consistent with our biophysical experiments and in vivo regulatory behavior. These findings define a unique activation mechanism for an RpiR regulator and provide new insights into carbohydrate-responsive gene regulation in pneumococci.
Publisher: Oxford Academic
Keywords: *Streptococcus pneumoniae/genetics/metabolism; *Transcriptional Activation; *Bacterial Proteins/chemistry/metabolism/genetics; *N-Acetylneuraminic Acid/metabolism; Hexosamines/metabolism/chemistry; Protein Binding; Models, Molecular; Gene Expression Regulation, Bacterial; Binding Sites; Crystallography, X-Ray; Protein Multimerization; DNA, Bacterial/metabolism/chemistry; *Transcription Factors/metabolism/chemistry/genetics
Research Division(s): Inflammation
PubMed ID: 42831430
Publisher's Version: https://doi.org/10.1093/nar/gkag953
Open Access at Publisher's Site: https://doi.org/10.1093/nar/gkag953
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2026-10-12 01:25:24

Last Modified: 2026-10-12 01:25:31