Alternative oxygen‐dependent and oxygen‐independent ribonucleotide reductases in Streptomyces: cross‐regulation and physiological role in response to oxygen limitation

Abstract

SummaryRibonucleotide reductases (RNRs) catalyse the conversion of ribonucleotides to deoxyribonucleotides and are essential for de novo DNA synthesis and repair. Streptomyces spp. contain genes coding for two RNRs. We show here that the Streptomyces coelicolor M145 nrdAB genes encoding an oxygendependent class I RNR are co-transcribed with nrdS , which encodes an AraC-like regulatory protein. Likewise, the class II oxygen-independent RNR nrdJ gene forms an operon with a likely regulatory gene, nrdR , which encodes a protein possessing an ATP-cone domain like those present in the allosteric activity site of many class Ia RNRs. Deletions in nrdB and nrdJ had no discernible effect on growth individually, but abolition of both RNR systems, using hydroxyurea to inactivate the class Ia RNR (NrdAB) in the nrdJ deletion mutant, was lethal, establishing that S. coelicolor possesses just two functional RNR systems. The class II RNR (NrdJ) may function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and/or for immediate growth after restoration of oxygen, as the nrdJ mutant was slower in growth recovery than the nrdB mutant or the parent strain. The class Ia and class II RNR genes show complex regulation. The nrdRJ genes were transcribed some five-to sixfold higher than the nrdABS genes in vegetative growth, but when nrdJ was deleted, nrdABS transcription was upregulated by 13-fold. In a reciprocal experiment, deletion of nrdB had little effect on nrdRJ transcription. Deletion of nrdR caused a dramatic increase in transcription of nrdJ and to a less extent nrdABS , whereas disruption of cobN , a gene required for synthesis of coenzyme B12 a cofactor for the class II RNR, caused similar upregulation of transcription of nrdRJ and nrdABS . In contrast, deletion of nrdS had no detectable effect on transcription of either set of RNR genes. These results establish the existence of control mechanisms that sense and regulate overall RNR gene expression.

Two Proteins Mediate Class II Ribonucleotide Reductase Activity in Pseudomonas aeruginosa

“…Our HU induction experiments also suggest that expression of class II RNR is not under vitamin B 12 control, as suggested for several other RNRs (28,39,40), because the addition of AdoCbl made no difference to the induction of nrdJ. Elegant studies in Streptomyces coelicolor recently identified the regulatory gene nrdR upstream of the nrdJ gene, forming an operon in this species (41). This regulatory protein is responsible for the coordinated transcription of class I and II RNRs in S. coelicolor.…”

“…Apparently, the nrdR gene is ubiquitous and can be found together with, for example, the lexA operon in several other microorganisms (41). P. aeruginosa encodes an nrdR gene next to the rib genes for riboflavin biosynthesis (41,42). It is therefore premature to speculate on how the differential expression of class I and II RNR is controlled in P. aeruginosa, and further work is necessary to evaluate whether nrdR is involved in the transcriptional control of the RNRs also in this species.…”

“…Similar gene arrangements are found throughout the Streptomycetes. Apparently, the nrdR gene is ubiquitous and can be found together with, for example, the lexA operon in several other microorganisms (41). P. aeruginosa encodes an nrdR gene next to the rib genes for riboflavin biosynthesis (41,42).…”

Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays

“…The lexA gene (cg2114) of C. glutamicum ATCC 13032 is located in a head-to-head arrangement with the divS-nrdR (cg2113-cg2112) transcription unit (Fig. 1a), encoding a cell division suppressor and a regulator of deoxyribonucleotide biosynthesis (Borovok et al, 2004;Ogino et al, 2008;Rodionov & Gelfand, 2005). Downstream of the nrdR gene, a coding region for a putative ATP-dependent helicase has been predicted ( Fig.…”

“…The remaining genes encode hypothetical proteins with unknown functions, including secreted proteins, putative membrane proteins and potential transporters (Tables 2, 3 and 4). The only regulatory genes directly controlled by the LexA protein are lexA itself and the divergently oriented divS and nrdR genes, encoding a regulator of cell division and a DNA binding transcription regulator of ribonucleotide reductase, respectively (Borovok et al, 2004;Ogino et al, 2008;Rodionov & Gelfand, 2005). Interestingly, the three regulatory genes are located in a highly conserved gene region of the hitherto sequenced corynebacterial genomes (Fig.…”