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Standke HG, Kim L, Owens CP. Purification and Biochemical Characterization of the DNA Binding Domain of the Nitrogenase Transcriptional Activator NifA from Gluconacetobacter diazotrophicus. Protein J 2023; 42:802-810. [PMID: 37787923 PMCID: PMC10590331 DOI: 10.1007/s10930-023-10158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
NifA is a σ54 activator that turns on bacterial nitrogen fixation under reducing conditions and when fixed cellular nitrogen levels are low. The redox sensing mechanism in NifA is poorly understood. In α- and β-proteobacteria, redox sensing involves two pairs of Cys residues within and immediately following the protein's central AAA+ domain. In this work, we examine if an additional Cys pair that is part of a C(X)5 C motif and located immediately upstream of the DNA binding domain of NifA from the α-proteobacterium Gluconacetobacter diazotrophicus (Gd) is involved in redox sensing. We hypothesize that the Cys residues' redox state may directly influence the DNA binding domain's DNA binding affinity and/or alter the protein's oligomeric sate. Two DNA binding domain constructs were generated, a longer construct (2C-DBD), consisting of the DNA binding domain with the upstream Cys pair, and a shorter construct (NC-DBD) that lacks the Cys pair. The Kd of NC-DBD for its cognate DNA sequence (nifH-UAS) is equal to 20.0 µM. The Kd of 2C-DBD for nifH-UAS when the Cys pair is oxidized is 34.5 µM. Reduction of the disulfide bond does not change the DNA binding affinity. Additional experiments indicate that the redox state of the Cys residues does not influence the secondary structure or oligomerization state of the NifA DNA binding domain. Together, these results demonstrate that the Cys pair upstream of the DNA binding domain of Gd-NifA does not regulate DNA binding or domain dimerization in a redox dependent manner.
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Affiliation(s)
- Heidi G Standke
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA
| | - Lois Kim
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA
| | - Cedric P Owens
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA.
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2
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Li X, Li Z. What determines symbiotic nitrogen fixation efficiency in rhizobium: recent insights into Rhizobium leguminosarum. Arch Microbiol 2023; 205:300. [PMID: 37542687 DOI: 10.1007/s00203-023-03640-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobium, a Gram-negative soil bacterium, is an essential component in the nitrogen cycle and is a sustainable green way to maintain soil fertility without chemical energy consumption. SNF, which results from the processes of nodulation, rhizobial infection, bacteroid differentiation and nitrogen-fixing reaction, requires the expression of various genes from both symbionts with adaptation to the changing environment. To achieve successful nitrogen fixation, rhizobia and their hosts cooperate closely for precise regulation of symbiotic genes, metabolic processes and internal environment homeostasis. Many researches have progressed to reveal the ample information about regulatory aspects of SNF during recent decades, but the major bottlenecks regarding improvement of nitrogen-fixing efficiency has proven to be complex. In this mini-review, we summarize recent advances that have contributed to understanding the rhizobial regulatory aspects that determine SNF efficiency, focusing on the coordinated regulatory mechanism of symbiotic genes, oxygen, carbon metabolism, amino acid metabolism, combined nitrogen, non-coding RNAs and internal environment homeostasis. Unraveling regulatory determinants of SNF in the nitrogen-fixing protagonist rhizobium is expected to promote an improvement of nitrogen-fixing efficiency in crop production.
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Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
| | - Zhangqun Li
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China
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3
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Zeng Q, Ding X, Wang J, Han X, Iqbal HMN, Bilal M. Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45089-45106. [PMID: 35474421 DOI: 10.1007/s11356-022-20399-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/19/2022] [Indexed: 02/08/2023]
Abstract
Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.
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Affiliation(s)
- Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China.
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiangchuan Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Xuejiao Han
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
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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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Aquino B, Stefanello AA, Oliveira MAS, Pedrosa FO, Souza EM, Monteiro RA, Chubatsu LS. Effect of point mutations on Herbaspirillum seropedicae NifA activity. ACTA ACUST UNITED AC 2015; 48:683-90. [PMID: 26176311 PMCID: PMC4541686 DOI: 10.1590/1414-431x20154522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/26/2015] [Indexed: 11/21/2022]
Abstract
NifA is the transcriptional activator of the nif genes in
Proteobacteria. It is usually regulated by nitrogen and oxygen, allowing biological
nitrogen fixation to occur under appropriate conditions. NifA proteins have a typical
three-domain structure, including a regulatory N-terminal GAF domain, which is
involved in control by fixed nitrogen and not strictly required for activity, a
catalytic AAA+ central domain, which catalyzes open complex formation, and a
C-terminal domain involved in DNA-binding. In Herbaspirillum
seropedicae, a β-proteobacterium capable of colonizing Graminae of
agricultural importance, NifA regulation by ammonium involves its N-terminal GAF
domain and the signal transduction protein GlnK. When the GAF domain is removed, the
protein can still activate nif genes transcription; however,
ammonium regulation is lost. In this work, we generated eight constructs resulting in
point mutations in H. seropedicae NifA and analyzed their effect on
nifH transcription in Escherichia coli and
H. seropedicae. Mutations K22V, T160E, M161V, L172R, and A215D
resulted in inactive proteins. Mutations Q216I and S220I produced partially active
proteins with activity control similar to wild-type NifA. However, mutation G25E,
located in the GAF domain, resulted in an active protein that did not require GlnK
for activity and was partially sensitive to ammonium. This suggested that G25E may
affect the negative interaction between the N-terminal GAF domain and the catalytic
central domain under high ammonium concentrations, thus rendering the protein
constitutively active, or that G25E could lead to a conformational change comparable
with that when GlnK interacts with the GAF domain.
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Affiliation(s)
- B Aquino
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A A Stefanello
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - M A S Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - F O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - E M Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - R A Monteiro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L S Chubatsu
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Batista MB, Wassem R, Pedrosa FDO, de Souza EM, Dixon R, Monteiro RA. Enhanced oxygen consumption in Herbaspirillum seropedicae fnr mutants leads to increased NifA mediated transcriptional activation. BMC Microbiol 2015; 15:95. [PMID: 25947294 PMCID: PMC4422417 DOI: 10.1186/s12866-015-0432-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Orthologous proteins of the Crp/Fnr family have been previously implicated in controlling expression and/or activity of the NifA transcriptional activator in some diazotrophs. This study aimed to address the role of three Fnr-like proteins from H. seropedicae SmR1 in controlling NifA activity and consequent NifA-mediated transcription activation. RESULTS The activity of NifA-dependent transcriptional fusions (nifA::lacZ and nifB::lacZ) was analysed in a series of H. seropedicae fnr deletion mutant backgrounds. We found that combined deletions in both the fnr1 and fnr3 genes lead to higher expression of both the nifA and nifB genes and also an increased level of nifH transcripts. Expression profiles of nifB under different oxygen concentrations, together with oxygen consumption measurements suggest that the triple fnr mutant has higher respiratory activity when compared to the wild type, which we believe to be responsible for greater stability of the oxygen sensitive NifA protein. This conclusion was further substantiated by measuring the levels of NifA protein and its activity in fnr deletion strains in comparison with the wild-type. CONCLUSIONS Fnr proteins are indirectly involved in controlling the activity of NifA in H. seropedicae, probably as a consequence of their influence on respiratory activity in relation to oxygen availability. Additionally we can suggest that there is some redundancy in the physiological function of the three Fnr paralogs in this organism, since altered respiration and effects on NifA activity are only observed in deletion strains lacking both fnr1 and fnr3.
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Affiliation(s)
- Marcelo Bueno Batista
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná, P.O. Box 19071, Curitiba, PR, 81531-990, Brazil.
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR, 81531-990, Brazil.
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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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Abstract
Alternative σ-factors of bacteria bind core RNA polymerase to program the specific promoter selectivity of the holoenzyme. Signal-responsive changes in the availability of different σ-factors redistribute the RNA polymerase among the distinct promoter classes in the genome for appropriate adaptive, developmental and survival responses. The σ(54) -factor is structurally and functionally distinct from all other σ-factors. Consequently, binding of σ(54) to RNA polymerase confers unique features on the cognate holoenzyme, which requires activation by an unusual class of mechano-transcriptional activators, whose activities are highly regulated in response to environmental cues. This review summarizes the current understanding of the mechanisms of transcriptional activation by σ(54) -RNA polymerase and highlights the impact of global regulatory factors on transcriptional efficiency from σ(54) -dependent promoters. These global factors include the DNA-bending proteins IHF and CRP, the nucleotide alarmone ppGpp, and the RNA polymerase-targeting protein DksA.
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