Modulating DNA bending affects NodD-mediated transcriptional control in Rhizobium leguminosarum

Abstract

Rhizobium leguminosarum NodD binds to the nod box of the inducible nod gene nodA as a V-shaped tetramer and bends the nod box. In this work, we show that the nod gene inducer naringenin decreased gel mobility of nod box DNA–NodD complexes by sharpening the NodD-induced DNA bend, which correlated with nodA transcription activation. NodD can induce different DNA bends when the distance between the two half-sites of the nod box was modified, which severely affected NodD-mediated transcriptional control. One or two base pairs were deleted from, or inserted into, the two half-sites of the nod box of nodA. Circular permutation assays showed that such distance modulations allowed NodD to induce relaxed or sharpened DNA bending. In the case of 1 bp deletion, where the DNA bends were more relaxed than in the wild type, nodA transcription was repressed both in the absence and in the presence of inducer naringenin. In the cases of 1 and 2 bp insertion, where the DNA bends were much sharper than in wild type in the absence or presence of the inducer naringenin, nodA transcription was initiated constitutively with no requirement for the inducer naringenin or, even, the NodD regulating protein.

The Cation-Responsive Protein NhaR of Escherichia coli Activates pgaABCD Transcription, Required for Production of the Biofilm Adhesin Poly-β-1,6- N -Acetyl- d -Glucosamine

“…Coinducers typically do not increase promoter affinity but instead activate transcription via a conformational change in the LTTR-DNA complex (11,35,46,64). While NhaR activates gene expression in vivo in response to Na ϩ , K ϩ , or Li ϩ , this cation response has not been reconstituted in vitro (10,22,23,70).…”

Identification of Aromatic Residues Critical to the DNA Binding and Ligand Response of theBacillus subtilisQdoR (YxaF) Repressor Antagonized by Flavonoids

“…25) Besides these regulators, it has been reported that some bacterial transcriptional regulators recognize and respond to flavonoids. NodD regulators, which belong to the LysR family and control the transcription of the nod operons involved in the nodulation of Rhzobiales in response to flavonoid signals released by their leguminous hosts, have been characterized in detail, 26) but the domain structure of NodD accommodating the ligand flavonoid and its molecular mechanism for flavonoid recognition and response are not fully understood. It is plausible that the flavonoid-interacting domains in LmrA/QdoR, YetL, and NodD are structurally conserved.…”

Transcriptional Cross-Regulation between Gram-Negative and Gram-Positive Bacteria, Demonstrated Using ArgP- argO of Escherichia coli and LysG- lysE of Corynebacterium glutamicum

“…For many LTTRs, including CysB (15), OxyR (33), OccR (1, 31, 69), NocR (31), CatR (52), ClcR (40), and CbbR (18), DNA bending by the protein is more pronounced in the absence of the activating coeffector than in its presence, leading to the suggestion that bending is inversely correlated with gene activation. However, in a few cases, such as MetR (37), DntR (65), and TrpI (57), DNA bending that occurs upon protein binding is unaffected by coeffector addition, and for NodD (14), the bending is in fact increased in the presence of the coeffector. In the cases of CysB (15), TrpI (13), and MetR (37), the affinity of factor binding to target DNA is also increased upon coeffector addition, but this is not true for many of the other proteins.…”