The Iron Control Element, Acting in Positive and Negative Control of Iron-Regulated Bradyrh.pdf

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The Iron Control Element, Acting in Positive and Negative Control of Iron-Regulated Bradyrh.pdf

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The Iron Control Element, Acting in Positive and Negative Control of Iron-Regulated Bradyrh

JOURNAL OF BACTERIOLOGY, Jan. 2006, p. 733–744 Vol. 188, No. 2 0021-9193/06/$08.000 doi:10.1128/JB.188.2.733–744.2006 Copyright ? 2006, American Society for Microbiology. All Rights Reserved. The Iron Control Element, Acting in Positive and Negative Control of Iron-Regulated Bradyrhizobium japonicum Genes, Is a Target for the Irr Protein? Gesine Rudolph,1 Geo Semini,1 Felix Hauser,1 Andrea Lindemann,1 Markus Friberg,2 Hauke Hennecke,1 and Hans-Martin Fischer1* Institute of Microbiology1 and Institute of Computational Science,2 Eidgeno?ssische Technische Hochschule, Zu?rich, Switzerland Received 16 August 2005/Accepted 27 October 2005 Bradyrhizobium japonicum, the nitrogen-fixing soybean symbiont, possesses a heme uptake system encoded by the gene cluster hmuVUT-hmuR-exbBD-tonB. Transcription of the divergently oriented hmuT and hmuR genes was previously found to be induced by iron limitation and to depend on a 21-bp promoter-upstream iron control element (ICE). Here, we show by deletion analysis that the full-length ICE is needed for this type of positive control. Additional genes associated with ICE-like motifs were identified in the B. japonicum genome, of which bll6680 and blr7895 code for bacterioferritin and rubrerythrin homologs, respectively. Transcription start site mapping revealed that their ICEs directly overlap with either the 10 promoter region or the transcription initiation site, suggesting an involvement of the ICE in negative control of both genes. Consistent with this inference was the observed down- regulation of both genes under iron limitation, which in the case of bll6680 was shown to require an intact ICE motif. Using a yeast one-hybrid system, we demonstrated in vivo interaction of the iron response regulator (Irr) with all three ICEs. Moreover, specific in vitro binding of purified Irr protein to the ICE motifs of bll6680 and blr7895 was shown in electrophoretic mobility shift experiments. A genome-wide survey for iron-regulated genes with