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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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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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Oliveira MA, Baura VA, Aquino B, Huergo LF, Kadowaki MA, Chubatsu LS, Souza EM, Dixon R, Pedrosa FO, Wassem R, Monteiro RA. Role of conserved cysteine residues in Herbaspirillum seropedicae NifA activity. Res Microbiol 2009; 160:389-95. [DOI: 10.1016/j.resmic.2009.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 05/29/2009] [Accepted: 06/10/2009] [Indexed: 11/24/2022]
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Baldani JI, Baldani VLD. History on the biological nitrogen fixation research in graminaceous plants: special emphasis on the Brazilian experience. AN ACAD BRAS CIENC 2005; 77:549-79. [PMID: 16127558 DOI: 10.1590/s0001-37652005000300014] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review covers the history on Biological Nitrogen Fixation (BNF) in Graminaceous plants grown in Brazil, and describes research progress made over the last 40 years, most of whichwas coordinated by Johanna Döbereiner. One notable accomplishment during this period was the discovery of several nitrogen-fixing bacteria such as the rhizospheric (Beijerinckia fluminensis and Azotobacter paspali), associative (Azospirillum lipoferum, A. brasilense, A. amazonense) and the endophytic (Herbaspirillum seropedicae, H. rubrisubalbicans, Gluconacetobacter diazotrophicus, Burkholderia brasilensis and B. tropica). The role of these diazotrophs in association with grasses, mainly with cereal plants, has been studied and a lot of progress has been achieved in the ecological, physiological, biochemical, and genetic aspects. The mechanisms of colonization and infection of the plant tissues are better understood, and the BNF contribution to the soil/plant system has been determined. Inoculation studies with diazotrophs showed that endophytic bacteria have a much higher BNF contribution potential than associative diazotrophs. In addition, it was found that the plant genotype influences the plant/bacteria association. Recent data suggest that more studies should be conducted on the endophytic association to strengthen the BNF potential. The ongoing genome sequencing programs: RIOGENE (Gluconacetobacter diazotrophicus) and GENOPAR (Herbaspirillum seropedicae) reflect the commitment to the BNF study in Brazil and should allow the country to continue in the forefront of research related to the BNF process in Graminaceous plants.
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Affiliation(s)
- José I Baldani
- Embrapa Agrobiologia, Seropédica, Rio de Janeiro, 23851-970, Brazil.
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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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Araújo LM, Monteiro RA, Souza EM, Steffens MBR, Rigo LU, Pedrosa FO, Chubatsu LS. GlnB is specifically required for Azospirillum brasilense NifA activity in Escherichia coli. Res Microbiol 2004; 155:491-5. [PMID: 15249067 DOI: 10.1016/j.resmic.2004.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Accepted: 03/11/2004] [Indexed: 10/26/2022]
Abstract
The Azospirillum brasilense transcription regulator NifA and the nitrogen-status signaling proteins GlnB, GlnZ and GlnK were expressed in Escherichia coli and analyzed for their ability to activate nif gene expression. When expressed separately, none of the proteins were able to activate nifH promoter expression in any tested conditions; in contrast, nifH expression was observed in cells grown in the absence of ammonium and oxygen and when expressing simultaneously NifA and GlnB proteins, but not when expressing NifA and GlnZ or GlnK. Our results show that the GlnB protein is required for transcription activation by Azospirillum brasilense NifA and it cannot be replaced by GlnZ or GlnK.
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Affiliation(s)
- Luiza M Araújo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-990 Curitiba, PR, Brazil
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Monteiro RA, de Souza EM, Yates MG, Pedrosa FO, Chubatsu LS. Fnr is involved in oxygen control of Herbaspirillum seropedicae N-truncated NifA protein activity in Escherichia coli. Appl Environ Microbiol 2003; 69:1527-31. [PMID: 12620839 PMCID: PMC150060 DOI: 10.1128/aem.69.3.1527-1531.2003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herbaspirillum seropedicae is an endophytic diazotroph belonging to the beta-subclass of the class Proteobacteria, which colonizes many members of the Gramineae. The activity of the NifA protein, a transcriptional activator of nif genes in H. seropedicae, is controlled by ammonium ions through its N-terminal domain and by oxygen through mechanisms that are not well understood. Here we report that the NifA protein of H. seropedicae is inactive and more susceptible to degradation in an fnr Escherichia coli background. Both effects correlate with oxygen exposure and iron deprivation. Our results suggest that the oxygen sensitivity and iron requirement for H. seropedicae NifA activity involve the Fnr protein.
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Affiliation(s)
- Rose A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, Curitiba, PR 81531-990, Brazil
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Monteiro RA, Souza EM, Geoffrey Yates M, Steffens MBR, Pedrosa FO, Chubatsu LS. Expression, purification, and functional analysis of the C-terminal domain of Herbaspirillum seropedicae NifA protein. Protein Expr Purif 2003; 27:313-8. [PMID: 12597891 DOI: 10.1016/s1046-5928(02)00635-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Herbaspirillum seropedicae NifA protein is responsible for nif gene expression. The C-terminal domain of the H. seropedicae NifA protein, fused to a His-Tag sequence (His-Tag-C-terminal), was over-expressed and purified by metal-affinity chromatography to yield a highly purified and active protein. Band-shift assays showed that the NifA His-Tag-C-terminal bound specifically to the H. seropedicae nifB promoter region in vitro. In vivo analysis showed that this protein inhibited the Central + C-terminal domains of NifA protein from activating the nifH promoter of K. pneumoniae in Escherichia coli, indicating that the protein must be bound to the NifA-binding site (UAS site) at the nifH promoter region to activate transcription.
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Affiliation(s)
- Rose A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná CP 19046, Curitiba, PR 81531-990, Brazil
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Monteiro RA, de Souza EM, Wassem R, Yates MG, Pedrosa FO, Chubatsu LS. Inter-domain cross-talk controls the NifA protein activity of Herbaspirillum seropedicae. FEBS Lett 2001; 508:1-4. [PMID: 11707257 DOI: 10.1016/s0014-5793(01)03017-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herbaspirillum seropedicae is an endophytic diazotroph, which colonizes sugar cane, wheat, rice and maize. The activity of NifA, a transcriptional activator of nif genes in H. seropedicae, is controlled by ammonium ions through a mechanism involving its N-terminal domain. Here we show that this domain interacts specifically in vitro with the N-truncated NifA protein, as revealed by protection against proteolysis, and this interaction caused an inhibitory effect on both the ATPase and DNA-binding activities of the N-truncated NifA protein. We suggest that the N-terminal domain inhibits NifA-dependent transcriptional activation by an inter-domain cross-talk between the catalytic domain of the NifA protein and its regulatory N-terminal domain in response to fixed nitrogen.
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Affiliation(s)
- R A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, P.O. Box 19046, Curitiba, PR 81531-990, Brazil
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Paschen A, Drepper T, Masepohl B, Klipp W. Rhodobacter capsulatus nifA mutants mediating nif gene expression in the presence of ammonium. FEMS Microbiol Lett 2001; 200:207-13. [PMID: 11425477 DOI: 10.1111/j.1574-6968.2001.tb10717.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Expression of nitrogen fixation genes in Rhodobacter capsulatus is repressed by ammonium at different regulatory levels including an NtrC-independent mechanism controlling NifA activity. In contrast to R. capsulatus NifA, heterologous NifA proteins of Klebsiella pneumoniae and Rhizobium meliloti, respectively, were not subjected to this posttranslational ammonium control in R. capsulatus. The characterization of ammonium-tolerant R. capsulatus NifA1 mutants indicated that the N-terminal domain of NifA was involved in posttranslational regulation. Analysis of a double mutant carrying amino acid substitutions in both the N-terminal domain and the C-terminal DNA-binding domain gave rise to the hypothesis that an interaction between these two domains might be involved in ammonium regulation of NifA activity. Western analysis demonstrated that both constitutively expressed wild-type and ammonium-tolerant NifA1 proteins exhibited high stability and accumulated to comparable levels in cells grown in the presence of ammonium excluding the possibility that proteolytic degradation was responsible for ammonium-dependent inactivation of NifA.
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Affiliation(s)
- A Paschen
- Fakultät für Biologie, Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, D-44780, Bochum, Germany
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Arcondéguy T, Jack R, Merrick M. P(II) signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol Mol Biol Rev 2001; 65:80-105. [PMID: 11238986 PMCID: PMC99019 DOI: 10.1128/mmbr.65.1.80-105.2001] [Citation(s) in RCA: 312] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The P(II) family of signal transduction proteins are among the most widely distributed signal proteins in the bacterial world. First identified in 1969 as a component of the glutamine synthetase regulatory apparatus, P(II) proteins have since been recognized as playing a pivotal role in control of prokaryotic nitrogen metabolism. More recently, members of the family have been found in higher plants, where they also potentially play a role in nitrogen control. The P(II) proteins can function in the regulation of both gene transcription, by modulating the activity of regulatory proteins, and the catalytic activity of enzymes involved in nitrogen metabolism. There is also emerging evidence that they may regulate the activity of proteins required for transport of nitrogen compounds into the cell. In this review we discuss the history of the P(II) proteins, their structures and biochemistry, and their distribution and functions in prokaryotes. We survey data emerging from bacterial genome sequences and consider other likely or potential targets for control by P(II) proteins.
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Affiliation(s)
- T Arcondéguy
- Department of Microbiology, John Innes Centre, Norwich, United Kingdom
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