Transcription start sites for syrM and nodD3 flank an insertion sequence relic in Rhizobium meliloti

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