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Many nitrogen fixation-associated genes in the soybean symbiontBradyrhizobium japonicum are regulated by the transcriptional activator NifA, whose activity is inhibited by aerobiosis. NifA is encoded in thefixR-nifA operon, which is expressed at a low level under aerobic conditions and induced approximately fivefold under low-oxygen tension. This induction depends on a −24/−12-type promoter (fixRp 1 ) that is recognized by the ς54 RNA polymerase and activated by NifA. Low-level aerobic expression and part of the anaerobic expression originates from a second promoter (fixRp 2 ) that overlaps withfixRp 1 and depends on an upstream DNA region (UAS) located around position −68 (H. Barrios, H. M. Fischer, H. Hennecke, and E. Morett, J. Bacteriol. 177:1760–1765, 1995). A protein binding to the UAS was previously postulated to act as an activator. This protein has now been purified, and the corresponding gene (regR ) has been cloned. On the basis of the predicted amino acid sequence, RegR belongs to the family of response regulators of two-component regulatory systems. We identified upstream of theregR gene an additional gene (regS ) encoding a putative sensor kinase. AregR mutant was constructed in which neither a specific UAS-binding activity norfixRp 2 -dependent transcript formation andfixR′-′lacZ expression was detected in aerobically grown cells. AnaerobicfixR′-′lacZ expression was also decreased inregR mutants to about 10% of the level observed in the wild type. Similarly,regR mutants showed only about 2% residual nitrogen fixation activity, but unlike nodules induced bynifA mutants, the morphology of those nodules was normal, displaying no signs of necrosis. WhileregR mutants grew only slightly slower in free-living, aerobic conditions, they displayed a strong growth defect under anaerobic conditions. The phenotypic properties ofregS mutants differed only marginally, if at all, from those of the wild type, suggesting the existence of a compensating sensor activity in these strains. The newly identified RegR protein may be regarded as a master regulator in the NifA-dependent network controllingnif andfix gene expression inB. japonicum .

Expression of the fixR-nifA Operon in Bradyrhizobium japonicum Depends on a New Response Regulator, RegR