Strong conservation of spacer lengths in NrdR repressor DNA binding sites

Abstract

The ribonucleotide reductase-specific repressor NrdR, from the human pathogens Listeria monocytogenes and Streptococcus pneumoniae, form tetramers that bind to DNA when loaded with dATP and ATP. If loaded with only ATP they form different oligomeric complexes that cannot bind to DNA. The DNA binding site in L. monocytogenes is a pair of NrdR boxes separated by 15-16 bp, whereas in Streptococcus pneumoniae the NrdR boxes are separated by 25-26 bp. However, Streptococcus pneumoniae NrdR binds stronger to the related Streptococcus thermophilus binding sites with NrdR boxes separated by 15-16 bp. This observation triggered a comprehensive binding study of four NrdRs from L. monocytogenes, Streptococcus pneumoniae, Escherichia coli and Streptomyces coelicolor to a series of synthetic dsDNA fragments where the NrdR boxes were separated by 12-27 bp. All four NrdRs bound well to NrdR boxes separated by 14-17 bp, and also to NrdR boxes separated by 24-27 bp. The worst binding occurred when NrdR boxes were separated by 20 bp. The in vitro results were confirmed in vivo in E. coli for spacer distances 12-27 bp. We conclude that NrdR repressors bind most efficiently when there is an integer number of DNA turns between the center of the two NrdR boxes.