Ribonucleotide reductases (RNR) are indispensable enzymes that convert ribonucleotides to deoxyribonucleotides (dNTPs), the precursors to make up DNA. Because DNA synthesis is fundamental to cell survival, RNR activity must be tightly controlled. In bacteria, this control is exerted by a specialised transcriptional regulator, NrdR, which has no equivalent in eukaryotic organisms and therefore represents a potential selective target for antimicrobial development. Despite its central role, the structural basis of NrdR’s function and the mechanisms by which it senses cellular nucleotide levels and modulates RNR expression had remained only partially understood.
Now, this study addresses this gap by combining structural biology, biophysical characterisation and functional assays to delineate how NrdR’s quaternary structure responds to different nucleotide states and how these changes affect its regulatory activity. Researchers focused their study on two important bacterial pathogens: Escherichia coli , a key model pathogen for studying fundamental bacterial physiology, and Pseudomonas aeruginosa , an opportunistic pathogen recognized for its inherent resistance to many antibiotics and its role in chronic infections. The research work was led by the Bacterial infections: antimicrobial therapies group at the Institute for Bioengineering of Catalonia (IBEC) and the Structural Biology of Mitochondrial Macromolecules group at the Molecular Biology Institute of Barcelona (IBMB-CSIC), with participation of the Nanoscale bioelectrical characterization group at IBEC.
NrdR as a promising new target against bacterial infections
The comprehensive characterisation of NrdR’s structure and mechanism marks a significant advance in our understanding of bacterial transcriptional regulation. By revealing how bacteria regulate deoxyribonucleotide synthesis in response to nucleotide fluctuations, this work provides both conceptual and experimental groundwork for the identification of novel antibacterial targets and future therapeutic innovation.
Elucidating how NrdR senses nucleotide levels and controls the expression of essential RNR genes provides a new strategic entry point for antimicrobial development. Because NrdR is absent in human cells and plays a pivotal role in bacterial DNA precursor synthesis, the structural insights uncovered here offer a strong foundation for designing molecules that selectively disrupt bacterial nucleotide homeostasis. These insights position NrdR as a compelling antimicrobial target whose manipulation may inspire next‑generation strategies to combat resistant bacterial infections.
“Targeting such a central regulatory hub could weaken pathogenic bacteria or help restore their susceptibility to existing antibiotics, representing a promising avenue to counteract rising antimicrobial resistance”, explains Eduard Torrents, principal investigator of the Bacterial infections: antimicrobial therapies group at IBEC, Associate Professor at the University of Barcelona (UB), ICREA Academia member and author of the study.
Deciphering NrdR 3D structure and its biological significance
Researchers first identified which genes are controlled by NrdR in these bacteria by integrating transcriptomic data with motif analysis, providing a clearer picture of how this regulator influences essential cellular processes. The team then determined, by X-ray protein crystallography, the three-dimensional structure of the NrdR protein in E. coli , uncovering how individual protein molecules associate with each other to form assemblies. Though different techniques such as multi-angle light scattering (SEC-MALS) and atomic force microscopy, researchers also examined how these assemblies change in response to the presence of different nucleotides, revealing a highly dynamic system regulated by these metabolites. “After determining the crystal structure, the next crucial step is to decipher whether the interactions observed in the crystal are biologically meaningful — in this case, for how NrdR responds to nucleotides,” says Maria Solà, principal investigator of the Structural Biology of Mitochondrial Macromolecules group at the Molecular Biology Institute of Barcelona (IBMB-CSIC) and author of the study.
To address the impact of the structural states to DNA-binding activity and the regulatory outcomes, researchers performed functional validation of the protein-protein interactions observed in the crystal using point mutations, electrophoretic mobility shift assays and in vitro transcription assays. Importantly, the work clarifies how NrdR responds to intracellular signals — notably ATP and dATP — to switch between active and repressive states, thereby tuning RNR expression in accordance with cellular needs, explains Lucas Pedraz, co-first author of the study. These findings challenge earlier, more simplistic views of NrdR regulation, and reveal a finely tuned mechanism by which nucleotide binding drives structural transitions that directly influence DNA binding and gene repression.
Together, these results position NrdR as a compelling new target in the fight against antimicrobial resistance, offering a rare opportunity to disrupt a regulatory pathway essential for bacterial survival yet absent in humans. By defining NrdR’s structure and revealing how it governs nucleotide homeostasis, this work not only deepens our understanding of bacterial biology but also lays a strong foundation for the development of next‑generation therapeutics. As antibiotic resistance continues to rise globally, such mechanistic insights provide a crucial springboard for innovative strategies to weaken pathogenic bacteria and restore the effectiveness of existing treatments.
International Journal of Biological Macromolecules
10.1016/j.ijbiomac.2026.150647
Experimental study
Cells
Structure and mechanistic basis of NrdR, a bacterial master regulator of ribonucleotide reduction
4-Feb-2026
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.