title: The NtrY-NtrX two-component system is involved in controlling nitrate assimilation in Herbaspirillum seropedicae strain SmR1.
abstract: Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated with gramineae (Poaceae or graminaceous plants) such as rice, sorghum and sugar cane. In this work we show that nitrate-dependent growth in this organism is regulated by the master nitrogen regulatory two-component system NtrB-NtrC, and by NtrY-NtrX, which functions to specifically regulate nitrate metabolism. NtrY is a histidine kinase sensor protein predicted to be associated with the membrane and NtrX is the response regulator partner. The ntrYntrX genes are widely distributed in Proteobacteria. In α-Proteobacteria they are frequently located downstream from ntrBC, whereas in β-Proteobacteria these genes are located downstream from genes encoding an RNA methyltransferase and a proline-rich protein with unknown function. The NtrX protein of α-Proteobacteria has an AAA+ domain, absent in those from β-Proteobacteria. An ntrY mutant of H. seropedicae showed the wild-type nitrogen fixation phenotype, but the nitrate-dependent growth was abolished. Gene fusion assays indicated that NtrY is involved in the expression of genes coding for the assimilatory nitrate reductase as well as the nitrate-responsive two-component system NarX-NarL (narK and narX promoters, respectively). The purified NtrX protein was capable of binding the narK and narX promoters, and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed similar sequences in other promoter regions of H. seropedicae that are related to nitrate assimilation, supporting the role of the NtrY-NtrX system in regulating nitrate metabolism in H. seropedicae.
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Paloma
authors.initials: P
authors.lastname: Bonato
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Lysangela R
authors.initials: LR
authors.lastname: Alves
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Juliana H
authors.initials: JH
authors.lastname: Osaki
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Liu U
authors.initials: LU
authors.lastname: Rigo
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Fabio O
authors.initials: FO
authors.lastname: Pedrosa
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Emanuel M
authors.initials: EM
authors.lastname: Souza
authors.affiliation: Department of Life Sciences, Imperial College London, UK.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Department of Life Sciences, Imperial College London, UK.
authors.forename: Jörg
authors.initials: J
authors.lastname: Schumacher
authors.affiliation: Department of Life Sciences, Imperial College London, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Buck
authors.affiliation: Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Roseli
authors.initials: R
authors.lastname: Wassem
authors.affiliation: Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.
authors.forename: Leda S
authors.initials: LS
authors.lastname: Chubatsu
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D042803:Herbaspirillum / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D009154:Mutation; D009566:Nitrates / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D000072417:Protein Domains; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D009566:Nitrates
keywords: 
  Herbaspirillum seropedicae
  ; NtrX; NtrY; nitrate metabolism; two-component system