Previous Article | Next Article 
Journal of Bacteriology, October 2008, p. 6568-6579, Vol. 190, No. 20
0021-9193/08/$08.00+0 doi:10.1128/JB.00748-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK2-FixK1 Cascade in Bradyrhizobium japonicum
,
Socorro Mesa,1*
Felix Hauser,1,
Markus Friberg,2
Emmanuelle Malaguti,1
Hans-Martin Fischer,1 and
Hauke Hennecke1
Institute of Microbiology, ETH, Zürich, Switzerland,1 Institute of Computational Science, ETH, Zürich, Switzerland2
Received 26 May 2008/ Accepted 28 July 2008
Symbiotic N2 fixation in Bradyrhizobium japonicum is controlled by a complex transcription factor network. Part of it is a hierarchically arranged cascade in which the two-component regulatory system FixLJ, in response to a moderate decrease in oxygen concentration, activates the fixK2 gene. The FixK2 protein then activates not only a number of genes essential for microoxic respiration in symbiosis (fixNOQP and fixGHIS) but also further regulatory genes (rpoN1, nnrR, and fixK1). The results of transcriptome analyses described here have led to a comprehensive and expanded definition of the FixJ, FixK2, and FixK1 regulons, which, respectively, consist of 26, 204, and 29 genes specifically regulated in microoxically grown cells. Most of these genes are subject to positive control. Particular attention was addressed to the FixK2-dependent genes, which included a bioinformatics search for putative FixK2 binding sites on DNA (FixK2 boxes). Using an in vitro transcription assay with RNA polymerase holoenzyme and purified FixK2 as the activator, we validated as direct targets eight new genes. Interestingly, the adjacent but divergently oriented fixK1 and cycS genes shared the same FixK2 box for the activation of transcription in both directions. This recognition site may also be a direct target for the FixK1 protein, because activation of the cycS promoter required an intact fixK1 gene and either microoxic or anoxic, denitrifying conditions. We present evidence that cycS codes for a c-type cytochrome which is important, but not essential, for nitrate respiration. Two other, unexpected results emerged from this study: (i) specifically FixK1 seemed to exert a negative control on genes that are normally activated by the N2 fixation-specific transcription factor NifA, and (ii) a larger number of genes are expressed in a FixK2-dependent manner in endosymbiotic bacteroids than in culture-grown cells, pointing to a possible symbiosis-specific control.
* Corresponding author. Mailing address: Institute of Microbiology, ETH, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland. Phone: 41 44 632 3330. Fax: 41 44 632 1378. E-mail: mesam{at}micro.biol.ethz.ch
Published ahead of print on 8 August 2008.
Supplemental material for this article may be found at http://jb.asm.org/.
Present address: Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116.
Journal of Bacteriology, October 2008, p. 6568-6579, Vol. 190, No. 20
0021-9193/08/$08.00+0 doi:10.1128/JB.00748-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»