Disparate Oxygen Responsiveness of Two Regulatory Cascades That Control Expression of Symbiotic Genes in
            <i>Bradyrhizobium japonicum</i>

Sciotti, Michel-Angelo; Chanfon, Astrid; Hennecke, Hauke; Fischer, Hans‐Martin

doi:10.1128/jb.185.18.5639-5642.2003

Cited by 79 publications

(82 citation statements)

References 29 publications

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“…S1, lanes 1-3). This result was unexpected, because previous studies showed a clear induction of fixK 2 gene expression in response to decreased oxygen concentrations, although a basal level of fixK 2 expression had been noticed even in aerobiosis (16,17,20 H2O2 sensitivity of the B. japonicum WT and the C183A-FixK2-expressing mutant strain 8854. Soft agar (0.9%) plates with PSY medium were inoculated with the indicated B. japonicum strains.…”

Section: Analysis Of the In Vivo Status Of The Fixk2contrasting

confidence: 39%

Posttranslational control of transcription factor FixK ₂ , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

Mesa

Reutimann

Fischer

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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Rhizobial FixK-like proteins play essential roles in activating genes for endosymbiotic life in legume root nodules, such as genes for micro-oxic respiration. In the facultative soybean symbiont, Bradyrhizobium japonicum, the FixK 2 protein is the key player in a complex regulatory network. The fixK 2 gene itself is activated by the 2-component regulatory system FixLJ in response to a moderate decrease of the oxygen tension, and the FixK 2 protein distributes and amplifies this response to the level of approximately 200 target genes. Unlike other members of the cAMP receptor protein family, to which FixK 2 belongs, the FixK2 protein does not appear to be modulated by small effector molecules. Here, we show that a critical, single cysteine residue (C183) near the DNA-binding domain of FixK 2 confers sensitivity to oxidizing agents and reactive oxygen species. Oxidation-dependent inactivation occurs not only in vitro, as shown with cell-free transcription assays, but also in vivo, as shown by microarray-assisted transcriptome analysis of the FixK 2 regulon. The oxidation mechanism may involve a reversible dimerization by intermolecular disulfide-bridge formation and a direct, irreversible oxidation at the cysteine thiol, depending on the oxidizing agent. Mutational exchange of C183 to alanine renders FixK 2 resistant to oxidation, yet allows full activity, shown again both in vitro and in vivo. We hypothesize that posttranslational modification by reactive oxygen species is a means to counterbalance the cellular pool of active FixK 2, which would otherwise fill unrestrictedly through FixLJ-dependent synthesis.CPR/FNR ͉ gene regulation ͉ nitrogen fixation ͉ nodules ͉ rhizobia T he cAMP receptor protein (CRP)/fumarate-nitrate reductase regulator (FNR) family comprises transcription factors that mainly act as activators in a wide range of bacteria (reviewed in ref. 1). In all cases studied, the active form consists of homodimeric proteins in which each monomer contains an N-terminal sensor domain linked to the C-terminal DNA binding domain via a long ␣-helix that causes dimerization. These regulators control expression of specific sets of genes implicated in a broad spectrum of processes such as oxidative stress response, micro-oxic and anoxic metabolism, carbon catabolism, and stationary phase survival. The response to the respective environmental or intracellular stimuli is usually transduced through an interaction between a signaling molecule and the sensory domain, whereby a conformational change is induced that leads to the binding of the active dimer to operators near the promoters of the target genes (reviewed in ref.2). Three modes of signal perception have been described: (i) direct perception of a stressor, as in the Lactobacillus casei FLP protein (3); (ii) dependency on a prosthetic group such as a [4Fe-4S] 2ϩ cluster or heme in Escherichia coli FNR (4) or Rhodospirillum rubrum CooA (5), respectively; and (iii) binding of a small effector molecule like cAMP for E. coli CRP (6) or 2-oxoglutarate for cyanob...

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Section: Analysis Of the In Vivo Status Of The Fixk2contrasting

confidence: 39%

Posttranslational control of transcription factor FixK ₂ , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

Mesa

Reutimann

Fischer

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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“…Upon a switch to low-oxygen or anoxic conditions, the redox-responsive NifA protein in concert with RNA polymerase containing RpoN ( 54 ) enhances its own synthesis via activation of the Ϫ24/Ϫ12-type P1 promoter. This results in maximal expression not only of the fixR-nifA operon but also of other target genes (11,51). Most recently, the NifA-RpoN regulon of B. japonicum was unraveled by a genome-wide transcriptome analysis, which identified numerous new NifA-RpoN-dependent genes (25).…”

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confidence: 99%

New Target Genes Controlled by the Bradyrhizobium japonicum Two-Component Regulatory System RegSR

et al. 2007

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RegSR-like proteins, members of the family of two-component regulatory systems, are present in a large number of proteobacteria in which they globally control gene expression mostly in a redox-responsive manner. The controlled target genes feature an enormous functional diversity. In Bradyrhizobium japonicum, the facultative root nodule symbiont of soybean, RegSR activate the transcription of the nitrogen fixation regulatory gene nifA, thus forming a RegSR-NifA cascade which is part of a complex regulatory network for gene regulation in response to changing oxygen concentrations. Whole-genome transcription profiling was performed here in order to assess the full regulatory scope of RegSR. The comparative analysis of wild-type and ⌬regR cells grown under oxic and microoxic conditions revealed that expression of almost 250 genes is dependent on RegR, a result that underscores the important contribution of RegR to oxygen-or redoxregulated gene expression in B. japonicum. Furthermore, transcription profiling of ⌬regR bacteroids compared with wild-type bacteroids revealed expression changes for about 1,200 genes in young and mature bacteroids. Incidentally, many of these were found to be induced in symbiosis when wild-type bacteroids were compared with free-living, culture-grown wild-type cells, and they appeared to encode diverse functions possibly related to symbiosis and nitrogen fixation. We demonstrated direct RegR-mediated control at promoter regions of several selected target genes by means of DNA binding experiments and in vitro transcription assays, which revealed six novel direct RegR target promoters.

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“…In these two cascades, different oxygen-sensing mechanisms are responsible for a stepwise activation of downstream events (63). In the RegSR-NifA cascade, the low-oxygen-responsive NifA protein activates the transcription of essential symbiotic nitrogen fixation genes at an oxygen concentration at or below 0.5% oxygen in the gas phase over a culture.…”

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Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK₂-FixK₁Cascade inBradyrhizobium japonicum

et al. 2008

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Symbiotic N 2 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 fixK 2 gene. The FixK 2 protein then activates not only a number of genes essential for microoxic respiration in symbiosis (fixNOQP and fixGHIS) but also further regulatory genes (rpoN 1 , nnrR, and fixK 1 ). The results of transcriptome analyses described here have led to a comprehensive and expanded definition of the FixJ, FixK 2 , and FixK 1 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 FixK 2 -dependent genes, which included a bioinformatics search for putative FixK 2 binding sites on DNA (FixK 2 boxes). Using an in vitro transcription assay with RNA polymerase holoenzyme and purified FixK 2 as the activator, we validated as direct targets eight new genes. Interestingly, the adjacent but divergently oriented fixK 1 and cycS genes shared the same FixK 2 box for the activation of transcription in both directions. This recognition site may also be a direct target for the FixK 1 protein, because activation of the cycS promoter required an intact fixK 1 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 FixK 1 seemed to exert a negative control on genes that are normally activated by the N 2 fixation-specific transcription factor NifA, and (ii) a larger number of genes are expressed in a FixK 2 -dependent manner in endosymbiotic bacteroids than in culture-grown cells, pointing to a possible symbiosisspecific control.

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Disparate Oxygen Responsiveness of Two Regulatory Cascades That Control Expression of Symbiotic Genes in Bradyrhizobium japonicum

Cited by 79 publications

References 29 publications

Posttranslational control of transcription factor FixK ₂ , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

Posttranslational control of transcription factor FixK ₂ , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

New Target Genes Controlled by the Bradyrhizobium japonicum Two-Component Regulatory System RegSR

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK₂-FixK₁Cascade inBradyrhizobium japonicum

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Disparate Oxygen Responsiveness of Two Regulatory Cascades That Control Expression of Symbiotic Genes in Bradyrhizobium japonicum

Cited by 79 publications

References 29 publications

Posttranslational control of transcription factor FixK 2 , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

Posttranslational control of transcription factor FixK 2 , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

New Target Genes Controlled by the Bradyrhizobium japonicum Two-Component Regulatory System RegSR

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK2-FixK1Cascade inBradyrhizobium japonicum

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Resources

About

Posttranslational control of transcription factor FixK ₂ , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

Posttranslational control of transcription factor FixK ₂ , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK₂-FixK₁Cascade inBradyrhizobium japonicum