Signal structure for transcriptional activation in the upstream regions of virulence genes on the hairy-root-inducing plasmid A4.

The inducibility of the vir genes (virA, -B, -C, -D, -E, and -G) on pRiA4 was examined at the transcriptional level, and the RNA-starting sites were determined by S1-nuclease mapping and primer-extension experiments. All of these genes were inducible, while virA, -E, and -G were transcribed even under noninducing conditions. Each transcription of virB, -C, -D, and -E was initiated at one particular site, but that of virA and -G occurred at two and three sites, respectively, depending on the conditions used. In the DNA region upstream from each inducible transcript, one or more blocks of six base-pairs, 5'TGATAACT3' (vir box), were found to be placed characteristically. These blocks were phasing with an interval of 11 base-pairs, and the most upstream one in each upstream region was preceded by an additional block in the inverted orientation. Although the distance between the block(s) and the promoter varied with the vir gene, every block was placed in a phase nearly opposite to the -35 and -10 regions of the promoter.