Open AccessComprehensive Assessment of the Regulons Controlled by the FixLJ-FixK 2 -FixK 1 Cascade in Bradyrhizobium japonicum
Author(s) -
Socorro Mesa,
Felix Hauser,
Markus Friberg,
Emmanuelle Malaguti,
HansMartin Fischer,
Hauke Hennecke
Publication year - 2008
Publication title -
journal of bacteriology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.652
H-Index - 246
eISSN - 1067-8832
pISSN - 0021-9193
DOI - 10.1128/jb.00748-08
Subject(s) - regulon , biology , sigma factor , gene , operon , bradyrhizobium japonicum , promoter , rpon , genetics , transcription factor , rna polymerase , bradyrhizobium , transcription (linguistics) , gene expression , symbiosis , rna , rhizobiaceae , rhizobium , mutant , linguistics , philosophy , bacteria
Symbiotic N2 fixation inBradyrhizobium 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 thefixK 2 gene. The FixK2 protein then activates not only a number of genes essential for microoxic respiration in symbiosis (fixNOQP andfixGHIS ) but also further regulatory genes (rpoN 1 ,nnrR , andfixK 1 ). 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 orientedfixK 1 andcycS 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 thecycS promoter required an intactfixK 1 gene and either microoxic or anoxic, denitrifying conditions. We present evidence thatcycS codes for ac -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.