Function of the Pseudomonas aeruginosa NrdR Transcription Factor: Global Transcriptomic Analysis and Its Role on Ribonucleotide Reductase Gene Expression

Abstract

Ribonucleotide reductases (RNRs) are a family of sophisticated enzymes responsible for the synthesis of the deoxyribonucleotides (dNTPs), the building blocks for DNA synthesis and repair. Although any living cell must contain one RNR activity to continue living, bacteria have the capacity to encode different RNR classes in the same genome, allowing them to adapt to different environments and growing conditions. Pseudomonas aeruginosa is well known for its adaptability and surprisingly encodes all three known RNR classes (Ia, II and III). There must be a complex transcriptional regulation network behind this RNR activity, dictating which RNR class will be expressed according to specific growing conditions. In this work, we aim to uncover the role of the transcriptional regulator NrdR in P. aeruginosa. We demonstrate that NrdR regulates all three RNR classes, being involved in differential control depending on whether the growth conditions are aerobic or anaerobic. Moreover, we also identify for the first time that NrdR is not only involved in controlling RNR expression but also regulates topoisomerase I (topA) transcription. Finally, to obtain the entire picture of NrdR regulon, we performed a global transcriptomic analysis comparing the transcription profile of wild-type and nrdR mutant strains. The results provide many new data about the regulatory network that controls P. aeruginosa RNR transcription, bringing us a step closer to the understanding of this complex system.

Role of Ribonucleotide Reductase in Bacillus subtilis Stress-Associated Mutagenesis

“…However, the intracellular amount of these enzymes is also regulated at the transcriptional level; such control is of particular relevance in bacterial species possessing different types of RNRs, including E. coli, Salmonella, and Pseudomonas aeruginosa (7,8,35). B. subtilis possesses one class Ib RNR, encoded by the nrdEF operon (3, 4).…”

“…This protein represses the expression of genes encoding the class 1b RNR in E. coli and other bacteria (7,8,35). B. subtilis contains a putative ortholog of this protein encoded by ytcG.…”

“…The N-terminal portion displays a zinc finger-like DNA-binding domain, whereas the C-terminal region encodes a putative class Ia ATP/dATP allosteric site (31)(32)(33). On the basis of these properties, it is proposed that increasing cellular levels of nucleotides activate the repressing properties of NrdR, which recognizes a palindromic element (NrdR box) located in the promoter region of the nrdEF operon (34,35). In fact, results from an in silico analysis revealed the presence of two potential NrdR boxes in the regulatory region that control the expression of the nrdIEF operon (34).…”

Gradual adaptation of facultative anaerobic pathogens to microaerobic and anaerobic conditions

“…This method used the family of plasmids derived from pETS130-GFP (see Supporting Information Table S1), which encode transcriptional fusions of the promoters of all nrd operons with GFP. 42,45 To evaluate the expression of these operons under different oxygenation conditions, a full experiment was conducted for each desired oxygen concentration using strains containing each transcriptional fusion, as well as one with a promoterless GFP plasmid to evaluate the fluorescence level of a blank reaction.…”

“…In bacteria, NrdR represses all RNR classes; this protein is absent in Archaea and Eukarya. 33,55,56 Although several studies have explored the mechanism of action of NrdR in different bacterial species, 45,[55][56][57] the biological purpose of this protein remains unknown.…”