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Journal of Bacteriology, March 2000, p. 1472-1480, Vol. 182, No. 6
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Three New NifA-Regulated Genes in the Bradyrhizobium japonicum Symbiotic Gene Region Discovered by Competitive DNA-RNA Hybridization

Andrea Nienaber,1 Alexander Huber,1,dagger Michael Göttfert,2 Hauke Hennecke,1 and Hans-Martin Fischer1,*

Institut für Mikrobiologie, Eidgenössische Hochschule, CH-8092 Zürich, Switzerland,1 and Institut für Genetik, Technische Universität Dresden, D-01062 Dresden, Germany2

Received 10 May 1999/Accepted 16 December 1999

The so-called symbiotic region of the Bradyrhizobium japonicum chromosome (C. Kündig, H. Hennecke, and M. Göttfert, J. Bacteriol. 175:613-622, 1993) was screened for the presence of genes controlled by the nitrogen fixation regulatory protein NifA. Southern blots of restriction enzyme-digested cosmids that represent an ordered, overlapping library of the symbiotic region were competitively hybridized with in vitro-labeled RNA from anaerobically grown wild-type cells and an excess of RNA isolated either from anaerobically grown nifA and rpoN mutant cells or from aerobically grown wild-type cells. In addition to the previously characterized nif and fix gene clusters, we identified three new NifA-regulated genes that were named nrgA, nrgB, and nrgC (nrg stands for NifA-regulated gene). The latter two probably form an operon, nrgBC. The proteins encoded by nrgC and nrgA exhibited amino acid sequence similarity to bacterial hydroxylases and N-acetyltransferases, respectively. The product of nrgB showed no significant similarity to any protein with a database entry. Primer extension experiments and expression studies with translational lacZ fusions revealed the presence of a functional -24/-12-type promoter upstream of nrgA and nrgBC and proved the NifA- and RpoN (sigma 54)-dependent transcription of the respective genes. Null mutations introduced into nrgA and nrgBC resulted in mutant strains that exhibited wild-type-like symbiotic properties, including nitrogen fixation, when tested on soybean, cowpea, or mung bean host plants. Thus, the discovery of nrgA and nrgBC further emphasizes the previously suggested role of NifA as an activator of anaerobically induced genes other than the classical nitrogen fixation genes.

* Corresponding author. Mailing address: Institut für Mikrobiologie, Eidgenössische Technische Hochschule, Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland. Phone: 41-1-632-44 19. Fax: 41-1-632 11 48. E-mail: fischerh{at}micro.biol.ethz.ch.

dagger Present address: Pharmakologie, Universität Zürich, CH-8057 Zürich, Switzerland.

Journal of Bacteriology, March 2000, p. 1472-1480, Vol. 182, No. 6
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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