title: The global response regulator RegR controls expression of denitrification genes in Bradyrhizobium japonicum.
abstract: Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544) or cy2 (bll2388), and genes involved in nitric oxide detoxification (blr2806-09) and copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130, which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5'end of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS.
authors.affiliation: Estación Experimental del Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Torres
authors.affiliation: Departamento de Microbiología y Parasitología, Universidad de Sevilla, Sevilla, Spain.
authors.forename: Montserrat
authors.initials: M
authors.lastname: Argandoña
authors.affiliation: Departamento de Microbiología y Parasitología, Universidad de Sevilla, Sevilla, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Vargas
authors.affiliation: Estación Experimental del Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
authors.forename: Eulogio J
authors.initials: EJ
authors.lastname: Bedmar
authors.affiliation: ETH Zurich, Institute of Microbiology, Zurich, Switzerland.
authors.forename: Hans-Martin
authors.initials: HM
authors.lastname: Fischer
authors.affiliation: Estación Experimental del Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
authors.forename: Socorro
authors.initials: S
authors.lastname: Mesa
authors.affiliation: Estación Experimental del Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
authors.forename: María J
authors.initials: MJ
authors.lastname: Delgado
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000235:genetics; D020369:Bradyrhizobium / Q000235:genetics* / Q000378:metabolism; D058440:Denitrification / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D009569:Nitric Oxide / Q000235:genetics / Q000378:metabolism; D009586:Nitrogen Fixation / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; C113722:RegR protein, bacteria; D014157:Transcription Factors; D009569:Nitric Oxide; D010088:Oxidoreductases; C022763:nitrous oxide reductase