An Lrp-type transcriptional regulator from Agrobacterium tumefaciens condenses more than 100 nucleotides of DNA into globular nucleoprotein complexes

The PutR protein of Agrobacterium tumefaciens positively regulates expression of the putA gene in response to exogenous proline, resulting in the utilization of proline as a source of carbon and nitrogen. PutR activity required a region of DNA extending more than 106 nt upstream of the putA transcription start site. Purified PutR bound to this region with high degree of affinity and repressed expression of the putR promoter in vitro. PutR also activated the putA promoter in vitro in the presence of proline, though less strongly than in whole cells. PutR protected a DNA interval extending from nucleotides -30 to -140, but protected only one helical face over most of this interval, suggesting that it may bind only to this face of the DNA. The addition of proline caused a slight decrease in binding affinity and altered DNase I protection patterns along the entire length of the binding site. PutR-DNA complexes were found by atomic force microscopy to be globular rather than elongated. Although the DNA fragment in these complexes was 190 nm in length, the length of the visible DNA was only 150 nm, indicating that 40 nm of DNA (115 nt) must be condensed with protein. PutR caused a net bend of this binding site, and under some conditions, proline shifted the center of this bend by one helical turn.