TRANSCRIPTION START SITES FOR SYRM AND NODD3 FLANK AN INSERTION-SEQUENCE RELIC IN RHIZOBIUM-MELILOTI

In Rhizobium meliloti the syrM regulatory gene positively controls nod D3 and syrA, and nodD3 positively controls syrM and nod regulon genes such as nodABC. syrM and nodD3 are divergently transcribed and are sep arated by approximately 2.8 kb of DNA. The 885-bp SphI DNA fragment be tween syrM and nodD3 was subcloned and sequenced. Analysis of this int ergenic region showed two open reading frames similar to those found i n insertion elements of the IS3 family. We determined transcription in itiation sites for both syrM and nodD3 using primer extension. The syr M transcription initiation site is 499 bp upstream of the syrM protein -coding region and downstream of a nod box which shows several differe nces from the R. meliloti nod box consensus sequence. We demonstrated binding of NodD3 to DNA containing the syrM nod box. The nodD3 start s ite maps 659 bp upstream of the nodD3 translation initiation site. A p utative SyrM binding site was identified upstream of the nodD3 start s ite on the basis of sequence similarity to the upstream region of syrA , another locus regulated by SyrM.