The nodD locus from Azorhizobium caulinodans is flanked by two repetitive elements

The sequence surrounding the Azorhizobium caulinodans (Ac) regulatory nodD gene was analyzed. Upstream from nodD and in the opposite orientation, two small open reading frames were identified (ORF1 and ORF2). The DNA sequence corresponding to ORF1, termed epsilon 1, is similar to a part of the insertion element IS51 from Pseudomonas savastanoi. Immediately downstream from nodD, a repeated element, delta 1, has been described [Goethals et al., Mol. Plant-Microbe Interact. 5 (1992) 405-411]. The elements epsilon 1 and delta 1 form the borders of a shift in GC content between nodD and its surrounding sequences. delta 1 and the ORF1+ORF2 sequence both occur as two copies in the Ac genome. Based on these observations, we postulate that the repeated elements played a role in the horizontal transfer of nodD during evolution. Insertion mutations in epsilon 1 and delta 1 did not influence the induction of the nodulation operon, nodABCSUIJ, and had no effect on the nodulation behavior on Sesbania rostrata. lacZ fusion studies suggested that nodD is constitutively transcribed and that the promoter driving nodD expression overlaps with the ORF1 sequence. In contrast, promoter activity in the direction of ORF1 and ORF2 was not observed. In the nodD-ORF1-intervening sequence, a nod box-related motif was recognized that deviates from active nod boxes by the absence of an ATC-9-bp-GAT palindrome, i.e., a sequence involved in NodD-mediated transcription stimulation [Goethals et al., Proc. Natl. Acad. Sci. USA 89 (1992) 1646-1650].