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Ercole TG, Savi DC, Adamoski D, Kava VM, Hungria M, Galli-Terasawa LV. Diversity of maize (Zea mays L.) rhizobacteria with potential to promote plant growth. Braz J Microbiol 2021; 52:1807-1823. [PMID: 34458975 DOI: 10.1007/s42770-021-00596-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/15/2021] [Indexed: 11/30/2022] Open
Abstract
Plant growth-limiting factors, such as low nutrient availability and weak pathogen resistance, may hinder the production of several crops. Plant growth-promoting bacteria (PGPB) used in agriculture, which stimulate plant growth and development, can serve as a potential tool to mitigate or even circumvent these limitations. The present study evaluated the feasibility of using bacteria isolated from the maize rhizosphere as PGPB for the cultivation of this crop. A total of 282 isolates were collected and clustered into 57 groups based on their genetic similarity using BOX-PCR. A representative isolate from each group was selected and identified at the genus level with 16S rRNA sequencing. The identified genera included Bacillus (61.5% of the isolates), Lysinibacillus (30.52%), Pseudomonas (3.15%), Stenotrophomonas (2.91%), Paenibacillus (1.22%), Enterobacter (0.25%), Rhizobium (0.25%), and Atlantibacter (0.25%). Eleven isolates with the highest performance were selected for analyzing the possible pathways underlying plant growth promotion using biochemical and molecular techniques. Of the selected isolates, 90.9% were positive for indolepyruvate/phenylpyruvate decarboxylase, 54.4% for pyrroloquinoline quinine synthase, 36.4% for nitrogenase reductase, and 27.3% for nitrite reductase. Based on biochemical characterization, 9.1% isolates could fix nitrogen, 36.6% could solubilize phosphate, 54.5% could produce siderophores, and 90.9% could produce indole acetic acid. Enzymatic profiling revealed that the isolates could degrade starch (90.1%), cellulose (72.7%), pectin (81.8%), protein (90.9%), chitin (18.2%), urea (54.5%), and esters (45.4%). Based on the data obtained, we identified three Bacillus spp. (LGMB12, LGMB273, and LGMB426), one Stenotrophomonas sp. (LGMB417), and one Pseudomonas sp. (LGMB456) with the potential to serve as PGPB for maize. Further research is warranted to evaluate the biotechnological potential of these isolates as biofertilizers under field conditions.
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Affiliation(s)
- Tairine G Ercole
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil
| | - Daiani C Savi
- Department of Biomedicine, Centro Universitário Católica de Santa Catarina, R. Visconde de Taunay, 427. CEP, Joinville, SC, 89203-005, Brazil
| | - Douglas Adamoski
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Sao Paulo, Brazil
| | - Vanessa M Kava
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil
| | | | - Lygia V Galli-Terasawa
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil.
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The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense. mSystems 2020; 5:5/6/e00817-20. [PMID: 33144311 PMCID: PMC7646526 DOI: 10.1128/msystems.00817-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors. The PII family comprises a group of widely distributed signal transduction proteins ubiquitous in prokaryotes and in the chloroplasts of plants. PII proteins sense the levels of key metabolites ATP, ADP, and 2-oxoglutarate, which affect the PII protein structure and thereby the ability of PII to interact with a range of target proteins. Here, we performed multiple ligand fishing assays with the PII protein orthologue GlnZ from the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense to identify 37 proteins that are likely to be part of the PII protein-protein interaction network. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, coenzyme synthesis, RNA catabolism, and transcription. Direct binary PII-target complex was confirmed for 15 protein complexes using pulldown assays with recombinant proteins. Untargeted metabolome analysis showed that PII is required for proper homeostasis of important metabolites. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII-deficient strain showed reduced c-di-GMP levels and altered aerotaxis and flocculation behavior. These data support that PII acts as a major metabolic hub controlling important enzymes and the homeostasis of key metabolites such as c-di-GMP in response to the prevailing nutritional status. IMPORTANCE The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors.
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Stefanello AA, Oliveira MASD, Souza EM, Pedrosa FO, Chubatsu LS, Huergo LF, Dixon R, Monteiro RA. Regulation of Herbaspirillum seropedicae NifA by the GlnK PII signal transduction protein is mediated by effectors binding to allosteric sites. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140348. [PMID: 31866507 DOI: 10.1016/j.bbapap.2019.140348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/19/2019] [Accepted: 12/17/2019] [Indexed: 10/25/2022]
Abstract
Herbaspirillum seropedicae is a plant growth promoting bacterium that is able to fix nitrogen and to colonize the surface and internal tissues of important crops. Nitrogen fixation in H. seropedicae is regulated at the transcriptional level by the prokaryotic enhancer binding protein NifA. The activity of NifA is negatively affected by oxygen and positively stimulated by interaction with GlnK, a PII signaling protein that monitors intracellular levels of the key metabolite 2-oxoglutarate (2-OG) and functions as an indirect sensor of the intracellular nitrogen status. GlnK is also subjected to a cycle of reversible uridylylation in response to intracellular levels of glutamine. Previous studies have established the role of the N-terminal GAF domain of NifA in intramolecular repression of NifA activity and the role of GlnK in relieving this inhibition under nitrogen-limiting conditions. However, the mechanism of this control of NifA activity is not fully understood. Here, we constructed a series of GlnK variants to elucidate the role of uridylylation and effector binding during the process of NifA activation. Our data support a model whereby GlnK uridylylation is not necessary to activate NifA. On the other hand, binding of 2-OG and MgATP to GlnK are very important for NifA activation and constitute the most important signal of cellular nitrogen status to NifA.
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Affiliation(s)
- Adriano Alves Stefanello
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CEP 81530-900 Curitiba, PR, Brazil
| | | | - Emanuel Maltempi Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CEP 81530-900 Curitiba, PR, Brazil
| | - Fábio Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CEP 81530-900 Curitiba, PR, Brazil
| | - Leda Satie Chubatsu
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CEP 81530-900 Curitiba, PR, Brazil
| | - Luciano Fernandes Huergo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CEP 81530-900 Curitiba, PR, Brazil; Setor Litoral, Universidade Federal do Paraná, Matinhos, PR, CEP 80060-000, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, NR4 7UH Norwich, UK
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CEP 81530-900 Curitiba, PR, Brazil.
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Inaba J, Thornton J, Huergo LF, Monteiro RA, Klassen G, Pedrosa FDO, Merrick M, de Souza EM. Mutational analysis of GlnB residues critical for NifA activation in Azospirillum brasilense. Microbiol Res 2014; 171:65-72. [PMID: 25644954 DOI: 10.1016/j.micres.2014.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 11/28/2022]
Abstract
PII proteins are signal transduction that sense cellular nitrogen status and relay this signals to other targets. Azospirillum brasilense is a nitrogen fixing bacterium, which associates with grasses and cereals promoting beneficial effects on plant growth and crop yields. A. brasilense contains two PII encoding genes, named glnB and glnZ. In this paper, glnB was mutagenised in order to identify amino acid residues involved in GlnB signaling. Two variants were obtained by random mutagenesis, GlnBL13P and GlnBV100A and a site directed mutant, GlnBY51F, was obtained. Their ability to complement nitrogenase activity of glnB mutant strains of A. brasilense were determined. The variant proteins were also overexpressed in Escherichia coli, purified and characterized biochemically. None of the GlnB variant forms was able to restore nitrogenase activity in glnB mutant strains of A. brasilense LFH3 and 7628. The purified GlnBY51F and GlnBL13P proteins could not be uridylylated by GlnD, whereas GlnBV100A was uridylylated but at only 20% of the rate for wild type GlnB. Biochemical and computational analyses suggest that residue Leu13, located in the α helix 1 of GlnB, is important to maintain GlnB trimeric structure and function. The substitution V100A led to a lower affinity for ATP binding. Together the results suggest that NifA activation requires uridylylated GlnB bound to ATP.
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Affiliation(s)
- Juliana Inaba
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. Gal. Carlos Cavalcanti, 4748, CEP 84030-900 Ponta Grossa, PR, Brazil.
| | - Jeremy Thornton
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom.
| | - Luciano Fernandes Huergo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, CEP 81531-990 Curitiba, PR, Brazil.
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, CEP 81531-990 Curitiba, PR, Brazil.
| | - Giseli Klassen
- Department of Basic Pathology, Universidade Federal do Paraná, CP 19046, CEP 81531-990 Curitiba, PR, Brazil.
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, CEP 81531-990 Curitiba, PR, Brazil.
| | - Mike Merrick
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom.
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, CEP 81531-990 Curitiba, PR, Brazil.
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Sotomaior P, Araújo LM, Nishikawa CY, Huergo LF, Monteiro RA, Pedrosa FO, Chubatsu LS, Souza EM. Effect of ATP and 2-oxoglutarate on the in vitro interaction between the NifA GAF domain and the GlnB protein of Azospirillum brasilense. Braz J Med Biol Res 2012; 45:1135-40. [PMID: 22983183 PMCID: PMC3854208 DOI: 10.1590/s0100-879x2012007500146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/27/2012] [Indexed: 12/03/2022] Open
Abstract
Azospirillum brasilense is a diazotroph that associates with important agricultural crops and thus has potential to be a nitrogen biofertilizer. The A. brasilense transcription regulator NifA, which seems to be constitutively expressed, activates the transcription of nitrogen fixation genes. It has been suggested that the nitrogen status-signaling protein GlnB regulates NifA activity by direct interaction with the NifA N-terminal GAF domain, preventing the inhibitory effect of this domain under conditions of nitrogen fixation. In the present study, we show that an N-terminal truncated form of NifA no longer required GlnB for activity and lost regulation by ammonium. On the other hand, in trans co-expression of the N-terminal GAF domain inhibited the N-truncated protein in response to fixed nitrogen levels. We also used pull-down assays to show in vitro interaction between the purified N-terminal GAF domain of NifA and the GlnB protein. The results showed that A. brasilense GlnB interacts directly with the NifA N-terminal domain and this interaction is dependent on the presence of ATP and 2-oxoglutarate.
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Affiliation(s)
- P Sotomaior
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Interaction of GlnK with the GAF domain of Herbaspirillum seropedicae NifA mediates NH4+-regulation. Biochimie 2012; 94:1041-7. [DOI: 10.1016/j.biochi.2012.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 01/10/2012] [Indexed: 11/21/2022]
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Nishikawa CY, Araújo LM, Kadowaki MAS, Monteiro RA, Steffens MBR, Pedrosa FO, Souza EM, Chubatsu LS. Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense. Braz J Med Biol Res 2012; 45:113-7. [PMID: 22267004 PMCID: PMC3854256 DOI: 10.1590/s0100-879x2012007500006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/09/2012] [Indexed: 12/03/2022] Open
Abstract
Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ54 factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH4Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.
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Affiliation(s)
- C Y Nishikawa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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8
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Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction. Proc Natl Acad Sci U S A 2011; 108:18972-6. [PMID: 22074780 DOI: 10.1073/pnas.1108038108] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogen metabolism in bacteria and archaea is regulated by a ubiquitous class of proteins belonging to the P(II)family. P(II) proteins act as sensors of cellular nitrogen, carbon, and energy levels, and they control the activities of a wide range of target proteins by protein-protein interaction. The sensing mechanism relies on conformational changes induced by the binding of small molecules to P(II) and also by P(II) posttranslational modifications. In the diazotrophic bacterium Azospirillum brasilense, high levels of extracellular ammonium inactivate the nitrogenase regulatory enzyme DraG by relocalizing it from the cytoplasm to the cell membrane. Membrane localization of DraG occurs through the formation of a ternary complex in which the P(II) protein GlnZ interacts simultaneously with DraG and the ammonia channel AmtB. Here we describe the crystal structure of the GlnZ-DraG complex at 2.1 Å resolution, and confirm the physiological relevance of the structural data by site-directed mutagenesis. In contrast to other known P(II) complexes, the majority of contacts with the target protein do not involve the T-loop region of P(II). Hence this structure identifies a different mode of P(II) interaction with a target protein and demonstrates the potential for P(II) proteins to interact simultaneously with two different targets. A structural model of the AmtB-GlnZ-DraG ternary complex is presented. The results explain how the intracellular levels of ATP, ADP, and 2-oxoglutarate regulate the interaction between these three proteins and how DraG discriminates GlnZ from its close paralogue GlnB.
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Sant'anna FH, Andrade DS, Trentini DB, Weber SS, Schrank IS. Tools for genetic manipulation of the plant growth-promoting bacterium Azospirillum amazonense. BMC Microbiol 2011; 11:107. [PMID: 21575234 PMCID: PMC3111374 DOI: 10.1186/1471-2180-11-107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/16/2011] [Indexed: 12/16/2022] Open
Abstract
Background Azospirillum amazonense has potential to be used as agricultural inoculant since it promotes plant growth without causing pollution, unlike industrial fertilizers. Owing to this fact, the study of this species has gained interest. However, a detailed understanding of its genetics and physiology is limited by the absence of appropriate genetic tools for the study of this species. Results Conjugation and electrotransformation methods were established utilizing vectors with broad host-replication origins (pVS1 and pBBR1). Two genes of interest - glnK and glnB, encoding PII regulatory proteins - were isolated. Furthermore, glnK-specific A. amazonense mutants were generated utilizing the pK19MOBSACB vector system. Finally, a promoter analysis protocol based on fluorescent protein expression was optimized to aid genetic regulation studies on this bacterium. Conclusion In this work, genetic tools that can support the study of A. amazonense were described. These methods could provide a better understanding of the genetic mechanisms of this species that underlie its plant growth promotion.
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Affiliation(s)
- Fernando H Sant'anna
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Campus do Vale, Porto Alegre, RS, Brazil
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Selao TT, Branca R, Chae PS, Lehtiö J, Gellman SH, Rasmussen SGF, Nordlund S, Norén A. Identification of chromatophore membrane protein complexes formed under different nitrogen availability conditions in Rhodospirillum rubrum. J Proteome Res 2011; 10:2703-14. [PMID: 21443180 DOI: 10.1021/pr100838x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The chromatophore membrane of the photosynthetic diazotroph Rhodospirillum rubrum is of vital importance for a number of central processes, including nitrogen fixation. Using a novel amphiphile, we have identified protein complexes present under different nitrogen availability conditions by the use of two-dimensional Blue Native/SDS-PAGE and NSI-LC-LTQ-Orbitrap mass spectrometry. We have identified several membrane protein complexes, including components of the ATP synthase, reaction center, light harvesting, and NADH dehydrogenase complexes. Additionally, we have identified differentially expressed proteins, such as subunits of the succinate dehydrogenase complex and other TCA cycle enzymes that are usually found in the cytosol, thus hinting at a possible association to the membrane in response to nitrogen deficiency. We propose a redox sensing mechanism that can influence the membrane subproteome in response to nitrogen availability.
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Affiliation(s)
- Tiago Toscano Selao
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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11
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Noindorf L, Bonatto AC, Monteiro RA, Souza EM, Rigo LU, Pedrosa FO, Steffens MBR, Chubatsu LS. Role of PII proteins in nitrogen fixation control of Herbaspirillum seropedicae strain SmR1. BMC Microbiol 2011; 11:8. [PMID: 21223584 PMCID: PMC3023670 DOI: 10.1186/1471-2180-11-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 01/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The PII protein family comprises homotrimeric proteins which act as transducers of the cellular nitrogen and carbon status in prokaryotes and plants. In Herbaspirillum seropedicae, two PII-like proteins (GlnB and GlnK), encoded by the genes glnB and glnK, were identified. The glnB gene is monocistronic and its expression is constitutive, while glnK is located in the nlmAglnKamtB operon and is expressed under nitrogen-limiting conditions. RESULTS In order to determine the involvement of the H. seropedicae glnB and glnK gene products in nitrogen fixation, a series of mutant strains were constructed and characterized. The glnK- mutants were deficient in nitrogen fixation and they were complemented by plasmids expressing the GlnK protein or an N-truncated form of NifA. The nitrogenase post-translational control by ammonium was studied and the results showed that the glnK mutant is partially defective in nitrogenase inactivation upon addition of ammonium while the glnB mutant has a wild-type phenotype. CONCLUSIONS Our results indicate that GlnK is mainly responsible for NifA activity regulation and ammonium-dependent post-translational regulation of nitrogenase in H. seropedicae.
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Affiliation(s)
- Lilian Noindorf
- National Institute of Science and Technology for Biological Nitrogen Fixation, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, Curitiba, PR, 81531-980, Brazil
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12
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Functional analysis of the fixL/fixJ and fixK genes in Azospirillum brasilense Sp7. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0065-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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13
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Zou X, Zhu Y, Pohlmann EL, Li J, Zhang Y, Roberts GP. Identification and functional characterization of NifA variants that are independent of GlnB activation in the photosynthetic bacterium Rhodospirillum rubrum. MICROBIOLOGY-SGM 2008; 154:2689-2699. [PMID: 18757802 DOI: 10.1099/mic.0.2008/019406-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The activity of NifA, the transcriptional activator of the nitrogen fixation (nif) gene, is tightly regulated in response to ammonium and oxygen. However, the mechanisms for the regulation of NifA activity are quite different among various nitrogen-fixing bacteria. Unlike the well-studied NifL-NifA regulatory systems in Klebsiella pneumoniae and Azotobacter vinelandii, in Rhodospirillum rubrum NifA is activated by a direct protein-protein interaction with the uridylylated form of GlnB, which in turn causes a conformational change in NifA. We report the identification of several substitutions in the N-terminal GAF domain of R. rubrum NifA that allow NifA to be activated in the absence of GlnB. Presumably these substitutions cause conformational changes in NifA necessary for activation, without interaction with GlnB. We also found that wild-type NifA can be activated in a GlnB-independent manner under certain growth conditions, suggesting that some other effector(s) can also activate NifA. An attempt to use Tn5 mutagenesis to obtain mutants that altered the pool of these presumptive effector(s) failed, though much rarer spontaneous mutations in nifA were detected. This suggests that the necessary alteration of the pool of effector(s) for NifA activation cannot be obtained by knockout mutations.
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Affiliation(s)
- Xiaoxiao Zou
- Department of Microbiology and Immunology, College of Biological Sciences and State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, PR China
| | - Yu Zhu
- Department of Bacteriology and the Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Edward L Pohlmann
- Department of Bacteriology and the Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jilun Li
- Department of Microbiology and Immunology, College of Biological Sciences and State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, PR China
| | - Yaoping Zhang
- Department of Bacteriology and the Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Microbiology and Immunology, College of Biological Sciences and State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, PR China
| | - Gary P Roberts
- Department of Bacteriology and the Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, WI 53706, USA
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Araújo LM, Huergo LF, Invitti AL, Gimenes CI, Bonatto AC, Monteiro RA, Souza EM, Pedrosa FO, Chubatsu LS. Different responses of the GlnB and GlnZ proteins upon in vitro uridylylation by the Azospirillum brasilense GlnD protein. Braz J Med Biol Res 2008; 41:289-94. [PMID: 18392451 DOI: 10.1590/s0100-879x2008000400006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 02/29/2008] [Indexed: 11/22/2022] Open
Abstract
Azospirillum brasilense is a diazotroph found in association with important agricultural crops. In this organism, the regulation of nitrogen fixation by ammonium ions involves several proteins including the uridylyltransferase/uridylyl-removing enzyme, GlnD, which reversibly uridylylates the two PII proteins, GlnB and GlnZ, in response to the concentration of ammonium ions. In the present study, the uridylylation/deuridylylation cycle of A. brasilense GlnB and GlnZ proteins by GlnD was reconstituted in vitro using the purified proteins. The uridylylation assay was analyzed using non-denaturing polyacrylamide gel electrophoresis and fluorescent protein detection. Our results show that the purified A. brasilense GlnB and GlnZ proteins were uridylylated by the purified A. brasilense GlnD protein in a process dependent on ATP and 2-oxoglutarate. The dependence on ATP for uridylylation was similar for both proteins. On the other hand, at micromolar concentration of 2-oxoglutarate (up to 100 microM), GlnB uridylylation was almost twice that of GlnZ, an effect that was not observed at higher concentrations of 2-oxoglutarate (up to 10 mM). Glutamine inhibited uridylylation and stimulated deuridylylation of both GlnB and GlnZ. However, glutamine seemed to inhibit GlnZ uridylylation more efficiently. Our results suggest that the differences in the uridylylation pattern of GlnB and GlnZ might be important for fine-tuning of the signaling pathway of cellular nitrogen status in A. brasilense.
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Affiliation(s)
- L M Araújo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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15
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Selao TT, Nordlund S, Norén A. Comparative Proteomic Studies in Rhodospirillum rubrum Grown under Different Nitrogen Conditions. J Proteome Res 2008; 7:3267-75. [DOI: 10.1021/pr700771u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tiago T. Selao
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
| | - Stefan Nordlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
| | - Agneta Norén
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
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16
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Huergo LF, Souza EM, Araujo MS, Pedrosa FO, Chubatsu LS, Steffens MBR, Merrick M. ADP-ribosylation of dinitrogenase reductase in Azospirillum brasilense is regulated by AmtB-dependent membrane sequestration of DraG. Mol Microbiol 2006; 59:326-37. [PMID: 16359338 DOI: 10.1111/j.1365-2958.2005.04944.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Nitrogen fixation in some diazotrophic bacteria is regulated by mono-ADP-ribosylation of dinitrogenase reductase (NifH) that occurs in response to addition of ammonium to the extracellular medium. This process is mediated by dinitrogenase reductase ADP-ribosyltransferase (DraT) and reversed by dinitrogenase reductase glycohydrolase (DraG), but the means by which the activities of these enzymes are regulated are unknown. We have investigated the role of the P(II) proteins (GlnB and GlnZ), the ammonia channel protein AmtB and the cellular localization of DraG in the regulation of the NifH-modification process in Azospirillum brasilense. GlnB, GlnZ and DraG were all membrane-associated after an ammonium shock, and both this membrane sequestration and ADP-ribosylation of NifH were defective in an amtB mutant. We now propose a model in which membrane association of DraG after an ammonium shock creates a physical separation from its cytoplasmic substrate NifH thereby inhibiting ADP-ribosyl-removal. Our observations identify a novel role for an ammonia channel (Amt) protein in the regulation of bacterial nitrogen metabolism by mediating membrane sequestration of a protein other than a P(II) family member. They also suggest a model for control of ADP-ribosylation that is likely to be applicable to all diazotrophs that exhibit such post-translational regulation of nitrogenase.
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Affiliation(s)
- Luciano F Huergo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-990 Curitiba, PR, Brazil
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17
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Huergo LF, Filipaki A, Chubatsu LS, Yates MG, Steffens MB, Pedrosa FO, Souza EM. Effect of the over-expression of PII and PZ proteins on the nitrogenase activity of Azospirillum brasilense. FEMS Microbiol Lett 2005; 253:47-54. [PMID: 16239079 DOI: 10.1016/j.femsle.2005.09.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 09/12/2005] [Indexed: 11/30/2022] Open
Abstract
The Azospirillum brasilense PII and PZ proteins, encoded by the glnB and glnZ genes respectively, are intracellular transducers of nitrogen levels with distinct functions. The PII protein participates in nif regulation by controlling the activity of the transcriptional regulator NifA. PII is also involved in transducing the prevailing nitrogen levels to the Fe-protein ADP-ribosylation system. PZ regulates negatively ammonium transport and is involved in nitrogenase reactivation. To further investigate the role of PII and PZ in the regulation of nitrogen fixation, broad-host-range plasmids capable of over-expressing the glnB and glnZ genes under control of the ptac promoter were constructed and introduced into A. brasilense. The nitrogenase activity and nitrate-dependent growth was impaired in A. brasilense cells over-expressing the PII protein. Using immunoblot analysis we observed that the reduction of nitrogenase activity in cells over-expressing PII was due to partial ADP-ribosylation of the Fe-protein under derepressing conditions and a reduction in the amount of Fe-protein. These results support the hypothesis that the unmodified PII protein act as a signal to the DraT enzyme to ADP-ribosylate the Fe-protein in response to ammonium shock, and that it also inhibits nif gene expression. In cells over-expressing the PZ protein the nitrogenase reactivation after an ammonium shock was delayed indicating that the PZ protein is involved in regulation of DraG activity.
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Affiliation(s)
- Luciano F Huergo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-990, Curitiba, PR, Brazil
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18
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Chen S, Liu L, Zhou X, Elmerich C, Li JL. Functional analysis of the GAF domain of NifA in Azospirillum brasilense: effects of Tyr→Phe mutations on NifA and its interaction with GlnB. Mol Genet Genomics 2005; 273:415-22. [PMID: 15887032 DOI: 10.1007/s00438-005-1146-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 03/17/2005] [Indexed: 10/25/2022]
Abstract
Regulation of NifA activity in Azospirillum brasilense depends on GlnB (a PII protein), and it was previously reported that the target of GlnB activity is the N-terminal domain of NifA. Furthermore, mutation of the Tyr residue at position 18 in the N-terminal domain resulted in a NifA protein that did not require GlnB for activity under nitrogen fixation conditions. We report here that a NifA double mutant in which the Tyr residues at positions 18 and 53 of NifA N-were simultaneously replaced by Phe (NifA-Y1853F) displays high nitrogenase activity, which is still regulatable by ammonia, but not by GlnB. The yeast two-hybrid technique was used to investigate whether GlnB can physically interact with wild-type and mutant NifA proteins. GlnB was found to interact directly with the N-terminal GAF domain of wild-type NifA, but not with its central or C-terminal domain. GlnB could still bind to the single NifA mutants Y18F and Y53F. In contrast, no interaction was detected between GlnB and the double mutant NifA-Y18/53F or between GlnB and NifA-Y43.
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Affiliation(s)
- Sanfeng Chen
- Department of Microbiology and National Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100094, China
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Huergo LF, Assumpção MC, Souza EM, Steffens MBR, Yates MG, Chubatsu LS, Pedrosa FO. Repressor mutant forms of the Azospirillum brasilense NtrC protein. Appl Environ Microbiol 2004; 70:6320-3. [PMID: 15466584 PMCID: PMC522079 DOI: 10.1128/aem.70.10.6320-6323.2004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Azospirillum brasilense mutant strains FP8 and FP9, after treatment with nitrosoguanidine, showed a null Nif phenotype and were unable to use nitrate as their sole nitrogen source. Sequencing of the ntrC genes revealed single nucleotide mutations in the NtrC nucleotide-binding site. The phenotypes of these strains are discussed in relation to their genotypes.
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Affiliation(s)
- Luciano F Huergo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-990 Curitiba, Paraná, Brazil
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