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RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process. Microorganisms 2021; 9:microorganisms9091888. [PMID: 34576783 PMCID: PMC8467165 DOI: 10.3390/microorganisms9091888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Azoarcus olearius BH72 is an endophyte capable of biological nitrogen fixation (BNF) and of supplying nitrogen to its host plant. Our previous microarray approach provided insights into the transcriptome of strain BH72 under N2-fixation in comparison to ammonium-grown conditions, which already indicated the induction of genes not related to the BNF process. Due to the known limitations of the technique, we might have missed additional differentially expressed genes (DEGs). Thus, we used directional RNA-Seq to better comprehend the transcriptional landscape under these growth conditions. RNA-Seq detected almost 24% of the annotated genes to be regulated, twice the amount identified by microarray. In addition to confirming entire regulated operons containing known DEGs, the new approach detected the induction of genes involved in carbon metabolism and flagellar and twitching motility. This may support N2-fixation by increasing energy production and by finding suitable microaerobic niches. On the other hand, energy expenditures were reduced by suppressing translation and vitamin biosynthesis. Nonetheless, strain BH72 does not appear to be content with N2-fixation but is primed for alternative economic N-sources, such as nitrate, urea or amino acids; a strong gene induction of machineries for their uptake and assimilation was detected. RNA-Seq has thus provided a better understanding of a lifestyle under limiting nitrogen sources by elucidating hitherto unknown regulated processes.
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Wang H, Waluk D, Dixon R, Nordlund S, Norén A. Energy shifts induce membrane sequestration of DraG in Rhodospirillum rubrum independent of the ammonium transporters and diazotrophic conditions. FEMS Microbiol Lett 2019; 365:5053809. [PMID: 30010831 PMCID: PMC6067124 DOI: 10.1093/femsle/fny176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/10/2018] [Indexed: 01/15/2023] Open
Abstract
Metabolic regulation of Rhodospirillum rubrum nitrogenase is mediated at the post-translational level by the enzymes DraT and DraG when subjected to changes in nitrogen or energy status. DraT is activated during switch-off, while DraG is inactivated by reversible membrane association. We confirm here that the ammonium transporter, AmtB1, rather than its paralog AmtB2, is required for ammonium induced switch-off. Amongst several substitutions at the N100 position in DraG, only N100K failed to locate to the membrane following ammonium shock, suggesting loss of interaction through charge repulsion. When switch-off was induced by lowering energy levels, either by darkness during photosynthetic growth or oxygen depletion under respiratory conditions, reversible membrane sequestration of DraG was independent of AmtB proteins and occurred even under non-diazotrophic conditions. We propose that under these conditions, changes in redox status or possibly membrane potential induce interactions between DraG and another membrane protein in response to the energy status.
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Affiliation(s)
- Helen Wang
- Department of Medical Biochemistry and Microbiology, Uppsala Biomedicinska Centrum, Husarg.3, S-75237 Uppsala, Sweden
| | - Dominik Waluk
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Svante Arrhenius v. 16C, Stockholm S-10691, Sweden
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich NR47 UH, UK
| | - Stefan Nordlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Svante Arrhenius v. 16C, Stockholm S-10691, Sweden
| | - Agneta Norén
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Svante Arrhenius v. 16C, Stockholm S-10691, Sweden
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3
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Moure VR, Siöberg CLB, Valdameri G, Nji E, Oliveira MAS, Gerdhardt ECM, Pedrosa FO, Mitchell DA, Seefeldt LC, Huergo LF, Högbom M, Nordlund S, Souza EM. The ammonium transporter AmtB and the PII signal transduction protein GlnZ are required to inhibit DraG in Azospirillum brasilense. FEBS J 2019; 286:1214-1229. [PMID: 30633437 DOI: 10.1111/febs.14745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 11/04/2018] [Accepted: 01/09/2019] [Indexed: 01/15/2023]
Abstract
The ammonium-dependent posttranslational regulation of nitrogenase activity in Azospirillum brasilense requires dinitrogenase reductase ADP-ribosyl transferase (DraT) and dinitrogenase reductase ADP-glycohydrolase (DraG). These enzymes are reciprocally regulated by interaction with the PII proteins, GlnB and GlnZ. In this study, purified ADP-ribosylated Fe-protein was used as substrate to study the mechanism involved in the regulation of A. brasilense DraG in vitro. The data show that DraG is partially inhibited by GlnZ and that DraG inhibition is further enhanced by the simultaneous presence of GlnZ and AmtB. These results are the first to demonstrate experimentally that DraG inactivation requires the formation of a ternary DraG-GlnZ-AmtB complex in vitro. Previous structural data have revealed that when the DraG-GlnZ complex associates with AmtB, the flexible T-loops of the trimeric GlnZ bind to AmtB and become rigid; these molecular events stabilize the DraG-GlnZ complex, resulting in DraG inactivation. To determine whether restraining the flexibility of the GlnZ T-loops is a limiting factor in DraG inhibition, we used a GlnZ variant that carries a partial deletion of the T-loop (GlnZΔ42-54). However, although the GlnZΔ42-54 variant was more effective in inhibiting DraG in vitro, it bound to DraG with a slightly lower affinity than does wild-type GlnZ and was not competent to completely inhibit DraG activity either in vitro or in vivo. We, therefore, conclude that the formation of a ternary complex between DraG-GlnZ-AmtB is necessary for the inactivation of DraG.
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Affiliation(s)
- Vivian R Moure
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Catrine L B Siöberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Glaucio Valdameri
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emmanuel Nji
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Marco Aurelio S Oliveira
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Edileusa C M Gerdhardt
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Fabio O Pedrosa
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - David A Mitchell
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Luciano F Huergo
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil.,Setor Litoral, Universidade Federal do Paraná, Matinhos, Brazil
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Stefan Nordlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Emanuel M Souza
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
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Bustamante-Brito R, Vera-Ponce de León A, Rosenblueth M, Martínez-Romero JC, Martínez-Romero E. Metatranscriptomic Analysis of the Bacterial Symbiont Dactylopiibacterium carminicum from the Carmine Cochineal Dactylopius coccus (Hemiptera: Coccoidea: Dactylopiidae). Life (Basel) 2019; 9:life9010004. [PMID: 30609847 PMCID: PMC6463064 DOI: 10.3390/life9010004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/14/2018] [Accepted: 12/25/2018] [Indexed: 11/16/2022] Open
Abstract
The scale insect Dactylopius coccus produces high amounts of carminic acid, which has historically been used as a pigment by pre-Hispanic American cultures. Nowadays carmine is found in food, cosmetics, and textiles. Metagenomic approaches revealed that Dactylopius spp. cochineals contain two Wolbachia strains, a betaproteobacterium named Candidatus Dactylopiibacterium carminicum and Spiroplasma, in addition to different fungi. We describe here a transcriptomic analysis indicating that Dactylopiibacterium is metabolically active inside the insect host, and estimate that there are over twice as many Dactylopiibacterium cells in the hemolymph than in the gut, with even fewer in the ovary. Albeit scarce, the transcripts in the ovaries support the presence of Dactylopiibacterium in this tissue and a vertical mode of transmission. In the cochineal, Dactylopiibacterium may catabolize plant polysaccharides, and be active in carbon and nitrogen provisioning through its degradative activity and by fixing nitrogen. In most insects, nitrogen-fixing bacteria are found in the gut, but in this study they are shown to occur in the hemolymph, probably delivering essential amino acids and riboflavin to the host from nitrogen substrates derived from nitrogen fixation.
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Affiliation(s)
- Rafael Bustamante-Brito
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
| | - Arturo Vera-Ponce de León
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
- Department of Ecology, Evolution and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
| | - Julio César Martínez-Romero
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
| | - Esperanza Martínez-Romero
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
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Huergo LF, Chandra G, Merrick M. PIIsignal transduction proteins: nitrogen regulation and beyond. FEMS Microbiol Rev 2013; 37:251-83. [DOI: 10.1111/j.1574-6976.2012.00351.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/26/2012] [Accepted: 07/26/2012] [Indexed: 01/12/2023] Open
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Huergo LF, Pedrosa FO, Muller-Santos M, Chubatsu LS, Monteiro RA, Merrick M, Souza EM. PII signal transduction proteins: pivotal players in post-translational control of nitrogenase activity. MICROBIOLOGY-SGM 2012; 158:176-190. [PMID: 22210804 DOI: 10.1099/mic.0.049783-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The fixation of atmospheric nitrogen by the prokaryotic enzyme nitrogenase is an energy- expensive process and consequently it is tightly regulated at a variety of levels. In many diazotrophs this includes post-translational regulation of the enzyme's activity, which has been reported in both bacteria and archaea. The best understood response is the short-term inactivation of nitrogenase in response to a transient rise in ammonium levels in the environment. A number of proteobacteria species effect this regulation through reversible ADP-ribosylation of the enzyme, but other prokaryotes have evolved different mechanisms. Here we review current knowledge of post-translational control of nitrogenase and show that, for the response to ammonium, the P(II) signal transduction proteins act as key players.
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Affiliation(s)
- Luciano F Huergo
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Fábio O Pedrosa
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Marcelo Muller-Santos
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Leda S Chubatsu
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Rose A Monteiro
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Mike Merrick
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, UK
| | - Emanuel M Souza
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
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Sarkar A, Köhler J, Hurek T, Reinhold-Hurek B. A novel regulatory role of the Rnf complex of Azoarcus sp. strain BH72. Mol Microbiol 2011; 83:408-22. [DOI: 10.1111/j.1365-2958.2011.07940.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Kraiser T, Gras DE, Gutiérrez AG, González B, Gutiérrez RA. A holistic view of nitrogen acquisition in plants. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1455-66. [PMID: 21239377 PMCID: PMC3137434 DOI: 10.1093/jxb/erq425] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 11/29/2010] [Accepted: 11/30/2010] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is the mineral nutrient required in the greatest amount and its availability is a major factor limiting growth and development of plants. As sessile organisms, plants have evolved different strategies to adapt to changes in the availability and distribution of N in soils. These strategies include mechanisms that act at different levels of biological organization from the molecular to the ecosystem level. At the molecular level, plants can adjust their capacity to acquire different forms of N in a range of concentrations by modulating the expression and function of genes in different N uptake systems. Modulation of plant growth and development, most notably changes in the root system architecture, can also greatly impact plant N acquisition in the soil. At the organism and ecosystem levels, plants establish associations with diverse microorganisms to ensure adequate nutrition and N supply. These different adaptive mechanisms have been traditionally discussed separately in the literature. To understand plant N nutrition in the environment, an integrated view of all pathways contributing to plant N acquisition is required. Towards this goal, in this review the different mechanisms that plants utilize to maintain an adequate N supply are summarized and integrated.
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Affiliation(s)
- Tatiana Kraiser
- Center for Genome Regulation, Millennium Nucleus for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Diana E. Gras
- Center for Genome Regulation, Millennium Nucleus for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Alvaro G. Gutiérrez
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research – UFZ Permoser str. 15, 04318 Leipzig, Germany
| | - Bernardo González
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago 7941169, Chile
| | - Rodrigo A. Gutiérrez
- Center for Genome Regulation, Millennium Nucleus for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
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9
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Souza ALF, Invitti AL, Rego FGM, Monteiro RA, Klassen G, Souza EM, Chubatsu LS, Pedrosa FO, Rigo LU. The involvement of the nif-associated ferredoxin-like genes fdxA and fdxN of Herbaspirillum seropedicae in nitrogen fixation. J Microbiol 2010; 48:77-83. [PMID: 20221733 DOI: 10.1007/s12275-009-0077-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 07/26/2009] [Indexed: 10/19/2022]
Abstract
The pathway of electron transport to nitrogenase in the endophytic beta-Proteobacterium Herbaspirillum seropedicae has not been characterized. We have generated mutants in two nif-associated genes encoding putative ferredoxins, fdxA and fdxN. The fdxA gene is part of the operon nifHDKENXorf1orf2fdxAnifQmodABC and is transcribed from the nifH promoter, as revealed by lacZ gene fusion. The fdxN gene is probably cotranscribed with the nifB gene. Mutational analysis suggests that the FdxA protein is essential for maximum nitrogenase activity, since the nitrogenase activity of the fdxA mutant strain was reduced to about 30% of that of the wild-type strain. In addition, the fdxA mutation had no effect on the nitrogenase switch-off in response to ammonium. Nitrogenase activity of a mutant strain lacking the fdxN gene was completely abolished. This phenotype was reverted by complementation with fdxN expressed under lacZ promoter control. The results suggest that the products of both the fdxA and fdxN genes are probably involved in electron transfer during nitrogen fixation.
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Affiliation(s)
- André L F Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Brazil
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Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes. ISME JOURNAL 2009; 4:121-30. [PMID: 19741736 DOI: 10.1038/ismej.2009.99] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The filamentous, non-heterocystous cyanobacterium Microcoleus chthonoplastes is a cosmopolitan organism, known to build microbial mats in a variety of different environments. Although most of these cyanobacterial mats are known for their capacity to fix dinitrogen, M. chthonoplastes has not been assigned as a diazotrophic organism. None of the strains that were correctly identified as M. chthonoplastes has been shown to fix dinitrogen and it has repeatedly been reported that these organisms lacked the cyanobacterial nifH, the structural gene for dinitrogenase reductase. In this study, we show that a complete nif-gene cluster is present in the genome of M. chthonoplastes PCC 7420 and that the three structural nitrogenase genes, nifHDK, are present in a collection of axenic strains of M. chthonoplastes from distant locations. Phylogenetic analysis of nifHDK revealed that they cluster with the Deltaproteobacteria and that they are closely related to Desulfovibrio. The nif operon is flanked by typical cyanobacterial genes, suggesting that it is an integral part of the M. chthonoplastes genome. In this study, we provide evidence that the nif operon of M. chthonoplastes is acquired through horizontal gene transfer. Moreover, the presence of the same nif-cluster in M. chthonoplastes isolates derived from various sites around the world suggests that this horizontal gene transfer event must have occurred early in the evolution of M. chthonoplastes. We have been unable to express nitrogenase in cultures of M. chthonoplastes, but we show that these genes were expressed under natural conditions in the field.
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Oetjen J, Reinhold-Hurek B. Characterization of the DraT/DraG system for posttranslational regulation of nitrogenase in the endophytic betaproteobacterium Azoarcus sp. strain BH72. J Bacteriol 2009; 191:3726-35. [PMID: 19346301 PMCID: PMC2681912 DOI: 10.1128/jb.01720-08] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 03/29/2009] [Indexed: 11/20/2022] Open
Abstract
DraT/DraG-mediated posttranslational regulation of the nitrogenase Fe protein by ADP-ribosylation has been described for a few diazotrophic bacteria belonging to the class Alphaproteobacteria. Here we present for the first time the DraT/DraG system of a betaproteobacterium, Azoarcus sp. strain BH72, a diazotrophic grass endophyte. Its genome harbors one draT ortholog and two physically unlinked genes coding for ADP-ribosylhydrolases. Northern blot analysis revealed cotranscription of draT with two genes encoding hypothetical proteins. Furthermore, draT and draG2 were expressed under all studied conditions, whereas draG1 expression was nitrogen regulated. By using Western blot analysis of deletion mutants and nitrogenase assays in vivo, we demonstrated that DraT is required for the nitrogenase Fe protein modification but not for the physiological inactivation of nitrogenase activity. A second mechanism responsible for nitrogenase inactivation must operate in this bacterium, which is independent of DraT. Fe protein demodification was dependent mainly on DraG1, corroborating the assumption from phylogenetic analysis that DraG2 might be mostly involved in processes other than the posttranslational regulation of nitrogenase. Nitrogenase in vivo reactivation was impaired in a draG1 mutant and a mutant lacking both draG alleles after anaerobiosis shifts and subsequent adjustment to microaerobic conditions, suggesting that modified dinitrogenase reductase was inactive. Our results demonstrate that the DraT/DraG system, despite some differences, is functionally conserved in diazotrophic proteobacteria.
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Affiliation(s)
- Janina Oetjen
- General Microbiology, Faculty of Biology and Chemistry, University Bremen, Postfach 33 04 40, D-28334 Bremen, Germany
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12
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Oetjen J, Rexroth S, Reinhold-Hurek B. Mass spectrometric characterization of the covalent modification of the nitrogenase Fe-protein in Azoarcus sp. BH72. FEBS J 2009; 276:3618-27. [PMID: 19490119 DOI: 10.1111/j.1742-4658.2009.07081.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogenase Fe-protein modification was analyzed in the endophytic beta-proteobacterium Azoarcus sp. BH72. Application of modern MS techniques localized the modification in the peptide sequence and revealed it to be an ADP-ribosylation on Arg102 of one subunit of nitrogenase Fe-protein. A double digest with trypsin and endoproteinase Asp-N was necessary to obtain an analyzable peptide because the modification blocked the trypsin cleavage site at this residue. Furthermore, a peptide extraction protocol without trifluoroacetic acid was crucial to acquire the modified peptide, indicating an acid lability of the ADP-ribosylation. This finding was supported by the presence of a truncated version of the original peptide with Arg102 exchanged by ornithine. Site-directed mutagenesis verified that the ADP-ribosylation occurred on Arg102. With our approach, we were able to localize a labile modification within a large peptide of 31 amino acid residues. The present study provides a method suitable for the identification of so far unknown protein modifications on nitrogenases or other proteins. It represents a new tool for the MS analysis of protein mono-ADP-ribosylations.
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Affiliation(s)
- Janina Oetjen
- General Microbiology, Faculty of Biology and Chemistry, University Bremen, Germany
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13
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PII, the key regulator of nitrogen metabolism in the cyanobacteria. ACTA ACUST UNITED AC 2008; 51:1056-65. [PMID: 19093078 DOI: 10.1007/s11427-008-0148-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Accepted: 11/15/2008] [Indexed: 10/21/2022]
Abstract
PII proteins are a protein family important to signal transduction in bacteria and plants. PII plays a critical role in regulation of carbon and nitrogen metabolism in cyanobacteria. Through conformation change and covalent modification, which are regulated by 2-oxoglutarate, PII interacts with different target proteins in response to changes of cellular energy status and carbon and nitrogen sources in cyanobacteria and regulates cellular metabolism. This article reports recent progress in PII research in cyanobacteria and discusses the mechanism of PII regulation of cellular metabolism.
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14
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Huergo LF, Merrick M, Pedrosa FO, Chubatsu LS, Araujo LM, Souza EM. Ternary complex formation between AmtB, GlnZ and the nitrogenase regulatory enzyme DraG reveals a novel facet of nitrogen regulation in bacteria. Mol Microbiol 2007; 66:1523-35. [PMID: 18028310 DOI: 10.1111/j.1365-2958.2007.06016.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ammonium movement across biological membranes is facilitated by a class of ubiquitous channel proteins from the Amt/Rh family. Amt proteins have also been implicated in cellular responses to ammonium availability in many organisms. Ammonium sensing by Amt in bacteria is mediated by complex formation with cytosolic proteins of the P(II) family. In this study we have characterized in vitro complex formation between the AmtB and P(II) proteins (GlnB and GlnZ) from the diazotrophic plant-associative bacterium Azospirillum brasilense. AmtB-P(II) complex formation only occurred in the presence of adenine nucleotides and was sensitive to 2-oxoglutarate when Mg(2+) and ATP were present, but not when ATP was substituted by ADP. We have also shown in vitro complex formation between GlnZ and the nitrogenase regulatory enzyme DraG, which was stimulated by ADP. The stoichiometry of this complex was 1:1 (DraG monomer : GlnZ trimer). We have previously reported that in vivo high levels of extracellular ammonium cause DraG to be sequestered to the cell membrane in an AmtB and GlnZ-dependent manner. We now report the reconstitution of a ternary complex involving AmtB, GlnZ and DraG in vitro. Sequestration of a regulatory protein by the membrane-bound AmtB-P(II) complex defines a new regulatory role for Amt proteins in Prokaryotes.
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Affiliation(s)
- Luciano F Huergo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba-PR, Brazil
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15
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Tremblay PL, Drepper T, Masepohl B, Hallenbeck PC. Membrane sequestration of PII proteins and nitrogenase regulation in the photosynthetic bacterium Rhodobacter capsulatus. J Bacteriol 2007; 189:5850-9. [PMID: 17586647 PMCID: PMC1952044 DOI: 10.1128/jb.00680-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Both Rhodobacter capsulatus PII homologs GlnB and GlnK were found to be necessary for the proper regulation of nitrogenase activity and modification in response to an ammonium shock. As previously reported for several other bacteria, ammonium addition triggered the AmtB-dependent association of GlnK with the R. capsulatus membrane. Native polyacrylamide gel electrophoresis analysis indicates that the modification/demodification of one PII homolog is aberrant in the absence of the other. In a glnK mutant, more GlnB was found to be membrane associated under these conditions. In a glnB mutant, GlnK fails to be significantly sequestered by AmtB, even though it appears to be fully deuridylylated. Additionally, the ammonium-induced enhanced sequestration by AmtB of the unmodifiable GlnK variant GlnK-Y51F follows the wild-type GlnK pattern with a high level in the cytoplasm without the addition of ammonium and an increased level in the membrane fraction after ammonium treatment. These results suggest that factors other than PII modification are driving its association with AmtB in the membrane in R. capsulatus.
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Affiliation(s)
- Pier-Luc Tremblay
- Département de Microbiologie et Immunologie, Université de Montréal, CP 6128, Succursale Centre-ville, Montréal, Québec, Canada
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16
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Huergo LF, Chubatsu LS, Souza EM, Pedrosa FO, Steffens MBR, Merrick M. Interactions between PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense. FEBS Lett 2006; 580:5232-6. [PMID: 16963029 DOI: 10.1016/j.febslet.2006.08.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 08/17/2006] [Accepted: 08/17/2006] [Indexed: 11/16/2022]
Abstract
In Azospirillum brasilense ADP-ribosylation of dinitrogenase reductase (NifH) occurs in response to addition of ammonium to the extracellular medium and is mediated by dinitrogenase reductase ADP-ribosyltransferase (DraT) and reversed by dinitrogenase reductase glycohydrolase (DraG). The P(II) proteins GlnB and GlnZ have been implicated in regulation of DraT and DraG by an as yet unknown mechanism. Using pull-down experiments with His-tagged versions of DraT and DraG we have now shown that DraT binds to GlnB, but only to the deuridylylated form, and that DraG binds to both the uridylylated and deuridylylated forms of GlnZ. The demonstration of these specific protein complexes, together with our recent report of the ability of deuridylylated GlnZ to be sequestered to the cell membrane by the ammonia channel protein AmtB, offers new insights into the control of NifH ADP-ribosylation.
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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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Zhang Y, Wolfe DM, Pohlmann EL, Conrad MC, Roberts GP. Effect of AmtB homologues on the post-translational regulation of nitrogenase activity in response to ammonium and energy signals in Rhodospirillum rubrum. MICROBIOLOGY-SGM 2006; 152:2075-2089. [PMID: 16804182 DOI: 10.1099/mic.0.28903-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The AmtB protein transports uncharged NH(3) into the cell, but it also interacts with the nitrogen regulatory protein P(II), which in turn regulates a variety of proteins involved in nitrogen fixation and utilization. Three P(II) homologues, GlnB, GlnK and GlnJ, have been identified in the photosynthetic bacterium Rhodospirillum rubrum, and they have roles in at least four overlapping and distinct functions, one of which is the post-translational regulation of nitrogenase activity. In R. rubrum, nitrogenase activity is tightly regulated in response to addition or energy depletion (shift to darkness), and this regulation is catalysed by the post-translational regulatory system encoded by draTG. Two amtB homologues, amtB(1) and amtB(2), have been identified in R. rubrum, and they are linked with glnJ and glnK, respectively. Mutants lacking AmtB(1) are defective in their response to both addition and darkness, while mutants lacking AmtB(2) show little effect on the regulation of nitrogenase activity. These responses to darkness and appear to involve different signal transduction pathways, and the poor response to darkness does not seem to be an indirect result of perturbation of internal pools of nitrogen. It is also shown that AmtB(1) is necessary to sequester detectable amounts GlnJ to the cell membrane. These results suggest that some element of the AmtB(1)-P(II) regulatory system senses energy deprivation and a consistent model for the integration of nitrogen, carbon and energy signals by P(II) is proposed. Other results demonstrate a degree of specificity in interaction of AmtB(1) with the different P(II) homologues in R. rubrum. Such interaction specificity might be important in explaining the way in which P(II) proteins regulate processes involved in nitrogen acquisition and utilization.
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Affiliation(s)
- Yaoping Zhang
- Department of Bacteriology and the Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David M Wolfe
- 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
| | - Mary C Conrad
- Department of Bacteriology and the Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - 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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18
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Zhang Y, Pohlmann EL, Conrad MC, Roberts GP. The poor growth of Rhodospirillum rubrum mutants lacking PII proteins is due to an excess of glutamine synthetase activity. Mol Microbiol 2006; 61:497-510. [PMID: 16762025 DOI: 10.1111/j.1365-2958.2006.05251.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The P(II) family of proteins is found in all three domains of life and serves as a central regulator of the function of proteins involved in nitrogen metabolism, reflecting the nitrogen and carbon balance in the cell. The genetic elimination of the genes encoding these proteins typically leads to severe growth problems, but the basis of this effect has been unknown except with Escherichia coli. We have analysed a number of the suppressor mutations that correct such growth problems in Rhodospirillum rubrum mutants lacking P(II) proteins. These suppressors map to nifR3, ntrB, ntrC, amtB(1) and the glnA region and all have the common property of decreasing total activity of glutamine synthetase (GS). We also show that GS activity is very high in the poorly growing parental strains lacking P(II) proteins. Consistent with this, overexpression of GS in glnE mutants (lacking adenylyltransferase activity) also causes poor growth. All of these results strongly imply that elevated GS activity is the causative basis for the poor growth seen in R. rubrum mutants lacking P(II) and presumably in mutants of some other organisms with similar genotypes. The result underscores the importance of proper regulation of GS activity for cell growth.
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Affiliation(s)
- Yaoping Zhang
- Department of Bacteriology, Center for the Study of Nitrogen Fixation, University of Wisconsin-Madison, Madison, WI 53706, USA
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19
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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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20
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Noindorf L, Rego FGM, Baura VA, Monteiro RA, Wassem R, Cruz LM, Rigo LU, Souza EM, Steffens MBR, Pedrosa FO, Chubatsu LS. Characterization of the orf1glnKamtB operon of Herbaspirillum seropedicae. Arch Microbiol 2005; 185:55-62. [PMID: 16331441 DOI: 10.1007/s00203-005-0066-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 10/21/2005] [Accepted: 11/11/2005] [Indexed: 10/25/2022]
Abstract
Herbaspirillum seropedicae is an endophytic nitrogen-fixing bacterium that colonizes economically important grasses. In this organism, the amtB gene is co-transcribed with two other genes: glnK that codes for a PII-like protein and orf1 that codes for a probable periplasmatic protein of unknown function. The expression of the orf1glnKamtB operon is increased under nitrogen-limiting conditions and is dependent on NtrC. An amtB mutant failed to transport methylammonium. Post-translational control of nitrogenase was also partially impaired in this mutant, since a complete switch-off of nitrogenase after ammonium addition was not observed. This result suggests that the AmtB protein is involved in the signaling pathway for the reversible inactivation of nitrogenase in H. seropedicae.
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Affiliation(s)
- Lilian Noindorf
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-990, Curitiba, Brazil
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21
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Klassen G, Souza EM, Yates MG, Rigo LU, Costa RM, Inaba J, Pedrosa FO. Nitrogenase switch-off by ammonium ions in Azospirillum brasilense requires the GlnB nitrogen signal-transducing protein. Appl Environ Microbiol 2005; 71:5637-41. [PMID: 16151168 PMCID: PMC1214662 DOI: 10.1128/aem.71.9.5637-5641.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogenase activity in several diazotrophs is switched off by ammonium and reactivated after consumption. The signaling pathway to this system in Azospirillum brasilense is not understood. We show that ammonium-dependent switch-off through ADP-ribosylation of Fe protein was partial in a glnB mutant of A. brasilense but absent in a glnB glnZ double mutant. Triggering of inactivation by anaerobic conditions was not affected in either mutant. The results suggest that glnB is necessary for full ammonium-dependent nitrogenase switch-off in A. brasilense.
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Affiliation(s)
- Giseli Klassen
- Universidade Federal do Paraná, Departamento de Bioquímica e Biologia Molecular, Caixa Postal 19046 CEP-81531-990, Curitiba, Paraná, Brazil
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22
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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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23
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Dodsworth JA, Cady NC, Leigh JA. 2-Oxoglutarate and the PII homologues NifI1and NifI2regulate nitrogenase activity in cell extracts ofMethanococcus maripaludis. Mol Microbiol 2005; 56:1527-38. [PMID: 15916603 DOI: 10.1111/j.1365-2958.2005.04621.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Summary Post-translational regulation of nitrogen fixation, or switch-off, in the methanogenic archaeon Methanococcus maripaludis does not involve detectable covalent modification of the dinitrogenase reductase as in some bacteria, and the genes encoding the PII homologues NifI(1) and NifI(2) are both required, indicating a novel mechanism. To further understand the mechanism of switch-off, we assayed nitrogenase activity in cell extracts from wild-type and nifI mutant strains in the absence or presence of potential signals of nitrogen status. Activity in extracts from a DeltanifI(1)nifI(2) strain was sixfold higher than in extracts from wild-type cells. Addition of 2-oxoglutarate to wild-type extracts enhanced activity up to fivefold, a level similar to that observed in DeltanifI(1)nifI(2) extracts. 2-Oxoglutarate did not affect activity in DeltanifI(1)nifI(2) or single nifI mutant extracts. Furthermore, extracts from genetically complimented nifI mutants regained wild-type characteristics, indicating an in vitro correlation with in vivo effects. Extraction and quantification of 2-oxoglutarate indicated concentrations 10-fold higher in nitrogen-fixing cells than in switched-off and ammonium-grown cells. We propose a model for switch-off where the NifI proteins have an inhibitory effect on nitrogenase activity that is counteracted by high levels of 2-oxoglutarate, which acts as a signal of nitrogen limitation.
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Affiliation(s)
- Jeremy A Dodsworth
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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24
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Huergo LF, Souza EM, Steffens MBR, Yates MG, Pedrosa FO, Chubatsu LS. Effects of over-expression of the regulatory enzymes DraT and DraG on the ammonium-dependent post-translational regulation of nitrogenase reductase in Azospirillum brasilense. Arch Microbiol 2005; 183:209-17. [PMID: 15723223 DOI: 10.1007/s00203-005-0763-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Revised: 01/20/2005] [Accepted: 01/28/2005] [Indexed: 10/25/2022]
Abstract
Nitrogen fixation in Azospirillum brasilense is regulated at transcriptional and post-translational levels. Post-translational control occurs through the reversible ADP-ribosylation of dinitrogenase reductase (Fe Protein), mediated by the dinitrogenase reductase ADP-ribosyltransferase (DraT) and dinitrogenase reductase glycohydrolase (DraG). Although the DraT and DraG activities are regulated in vivo, the molecules responsible for such regulation remain unknown. We have constructed broad-host-range plasmids capable of over-expressing, upon IPTG induction, the regulatory enzymes DraT and DraG as six-histidine-N-terminal fused proteins (His). Both DraT-His and DraG-His are functional in vivo. We have analyzed the effects of DraT-His and DraG-His over-expression on the post-translational modification of Fe Protein. The DraT-His over-expression led to Fe Protein modification in the absence of ammonium addition, while cells over-expressing DraG-His showed only partial ADP-ribosylation of Fe Protein by adding ammonium. These results suggest that both DraT-His and DraG-His lose their regulation upon over-expression, possible by titrating out negative regulators.
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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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25
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Laurent S, Forchhammer K, Gonzalez L, Heulin T, Zhang CC, Bédu S. Cell-type specific modification of PII is involved in the regulation of nitrogen metabolism in the cyanobacterium Anabaena PCC 7120. FEBS Lett 2004; 576:261-5. [PMID: 15474048 DOI: 10.1016/j.febslet.2004.09.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Revised: 09/04/2004] [Accepted: 09/04/2004] [Indexed: 10/26/2022]
Abstract
In the heterocystous cyanobacterium Anabaena PCC 7120, the modification state of the signalling PII protein is regulated according to the nitrogen regime of the cells, as already observed in some unicellular cyanobacteria. However, during the adaptation to diazotrophic growth conditions, PII is phosphorylated in vegetative cells while unphosphorylated in heterocysts. Isolation of mutants affected on PII modification state and analysis of their phenotypes allow us to show the implication of PII in the regulation of molecular nitrogen assimilation and more specifically, the requirement of unmodified state of PII in the formation of polar nodules of cyanophycin in heterocysts.
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Affiliation(s)
- Sophie Laurent
- Laboratoire de Chimie Bactérienne, CNRS-UPR9043, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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26
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Forchhammer K. Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets. FEMS Microbiol Rev 2004; 28:319-33. [PMID: 15449606 DOI: 10.1016/j.femsre.2003.11.001] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
PII signal transduction plays a pervasive role in microbial nitrogen control. Different phylogenetic lineages have developed various signal transduction schemes around the highly conserved core of the signalling system, which consists of the PII proteins. Among all various bacterial PII signalling systems, the one in cyanobacteria is so far unique: in unicellular strains, the mode of covalent modification is by serine phosphorylation and the interpretation of the cellular nitrogen status occurs by measuring the 2-oxoglutarate levels. Recent advances have been the identification of the phospho-PII phosphatase, the resolution of the crystal structure of PII proteins from Synechococcus and Synechocystis strains and the identification of novel functions of PII regulation in cyanobacteria, which highlight the central role of PII signalling for the acclimation to changing carbon-nitrogen regimes.
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Affiliation(s)
- Karl Forchhammer
- Institut für Mikrobiologie und Molekularbiologie, Interdisziplinäres Forschungszentrum der Universität Giessen, Heinrich-Buff-Ring 26-32, Giessen 35392, Germany.
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27
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Wirén NV, Merrick M. Regulation and function of ammonium carriers in bacteria, fungi, and plants. MOLECULAR MECHANISMS CONTROLLING TRANSMEMBRANE TRANSPORT 2004. [DOI: 10.1007/b95775] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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Abstract
The availability of nitrogen often limits plant growth in terrestrial ecosystems. The only biological reaction counterbalancing the loss of N from soils or ecosystems is biological nitrogen fixation, the enzymatic reduction of N2 to ammonia. Some gramineous crops such as certain Brazilian sugar cane cultivars or Kallar grass can derive a substantial part of the plant nitrogen from biological nitrogen fixation. Our research on grass-associated diazotrophs focuses on endophytic bacteria, microorganisms that multiply and spread inside plants without causing damage of the host plants or conferring an ecological threat to the plant. This review summarizes the current knowledge on the diazotrophic endophyte Azoarcus sp. BH72, which is capable of colonizing the interior of rice roots, one of the globally most important crops.
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Affiliation(s)
- Thomas Hurek
- Laboratory of General Microbiology, University of Bremen, D-28334 Bremen, Germany
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29
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Tan Z, Hurek T, Reinhold-Hurek B. Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice. Environ Microbiol 2003; 5:1009-15. [PMID: 14510855 DOI: 10.1046/j.1462-2920.2003.00491.x] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified nitrogenase gene (nifH) fragments is a rapid technique for profiling of diazotrophic microbial communities without the necessity of cultures for study. Here, we examined the impact of N-fertilization, plant genotype and environmental conditions on diazotrophic microbial populations in association with roots of rice (Oryza species) by T-RFLP community profiling and found marked effects on the composition of the microbial community. We found a rapid change of the diazotrophic population structure within 15 days after application of nitrogen fertilizer and a strong effect of environmental conditions and plant genotype. Control experiments revealed that phylogenetically distantly related nifH genes were proportionately amplified, and that signal strength reflected the relative abundance of nifH genes in the sample within a 10-fold range of template concentrations. These results clearly demonstrated that our T-RFLP method was suitable to reflect compositional differences in the diazotrophic community in a semiquantitative manner and that the diazotrophic rhizosphere communities of rice are not static but presumably rather highly dynamic.
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Affiliation(s)
- Zhiyuan Tan
- Universit Bremen, Faculty of Biology, PO Box 33 04 40, D-28334 Bremen, Germany
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30
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Pawlowski A, Riedel KU, Klipp W, Dreiskemper P, Gross S, Bierhoff H, Drepper T, Masepohl B. Yeast two-hybrid studies on interaction of proteins involved in regulation of nitrogen fixation in the phototrophic bacterium Rhodobacter capsulatus. J Bacteriol 2003; 185:5240-7. [PMID: 12923097 PMCID: PMC181009 DOI: 10.1128/jb.185.17.5240-5247.2003] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter capsulatus contains two PII-like proteins, GlnB and GlnK, which play central roles in controlling the synthesis and activity of nitrogenase in response to ammonium availability. Here we used the yeast two-hybrid system to probe interactions between these PII-like proteins and proteins known to be involved in regulating nitrogen fixation. Analysis of defined protein pairs demonstrated the following interactions: GlnB-NtrB, GlnB-NifA1, GlnB-NifA2, GlnB-DraT, GlnK-NifA1, GlnK-NifA2, and GlnK-DraT. These results corroborate earlier genetic data and in addition show that PII-dependent ammonium regulation of nitrogen fixation in R. capsulatus does not require additional proteins, like NifL in Klebsiella pneumoniae. In addition, we found interactions for the protein pairs GlnB-GlnB, GlnB-GlnK, NifA1-NifA1, NifA2-NifA2, and NifA1-NifA2, suggesting that fine tuning of the nitrogen fixation process in R. capsulatus may involve the formation of GlnB-GlnK heterotrimers as well as NifA1-NifA2 heterodimers. In order to identify new proteins that interact with GlnB and GlnK, we constructed an R. capsulatus genomic library for use in yeast two-hybrid studies. Screening of this library identified the ATP-dependent helicase PcrA as a new putative protein that interacts with GlnB and the Ras-like protein Era as a new protein that interacts with GlnK.
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Affiliation(s)
- Alice Pawlowski
- Lehrstuhl für Biologie der Mikroorganismen, Fakultät für Biologie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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31
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Drepper T, Groß S, Yakunin AF, Hallenbeck PC, Masepohl B, Klipp W. Role of GlnB and GlnK in ammonium control of both nitrogenase systems in the phototrophic bacterium Rhodobacter capsulatus. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2203-2212. [PMID: 12904560 DOI: 10.1099/mic.0.26235-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In most bacteria, nitrogen metabolism is tightly regulated and P(II) proteins play a pivotal role in the regulatory processes. Rhodobacter capsulatus possesses two genes (glnB and glnK) encoding P(II)-like proteins. The glnB gene forms part of a glnB-glnA operon and the glnK gene is located immediately upstream of amtB, encoding a (methyl-) ammonium transporter. Expression of glnK is activated by NtrC under nitrogen-limiting conditions. The synthesis and activity of the molybdenum and iron nitrogenases of R. capsulatus are regulated by ammonium on at least three levels, including the transcriptional activation of nifA1, nifA2 and anfA by NtrC, the regulation of NifA and AnfA activity by two different NtrC-independent mechanisms, and the post-translational control of the activity of both nitrogenases by reversible ADP-ribosylation of NifH and AnfH as well as by ADP-ribosylation independent switch-off. Mutational analysis revealed that both P(II)-like proteins are involved in the ammonium regulation of the two nitrogenase systems. A mutation in glnB results in the constitutive expression of nifA and anfA. In addition, the post-translational ammonium inhibition of NifA activity is completely abolished in a glnB-glnK double mutant. However, AnfA activity was still suppressed by ammonium in the glnB-glnK double mutant. Furthermore, the P(II)-like proteins are involved in ammonium control of nitrogenase activity via ADP-ribosylation and the switch-off response. Remarkably, in the glnB-glnK double mutant, all three levels of the ammonium regulation of the molybdenum (but not of the alternative) nitrogenase are completely circumvented, resulting in the synthesis of active molybdenum nitrogenase even in the presence of high concentrations of ammonium.
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Affiliation(s)
- Thomas Drepper
- Ruhr-Universität Bochum, Lehrstuhl für Biologie der Mikroorganismen, D-44780 Bochum, Germany
| | - Silke Groß
- Ruhr-Universität Bochum, Lehrstuhl für Biologie der Mikroorganismen, D-44780 Bochum, Germany
| | - Alexander F Yakunin
- Université de Montréal, Département de microbiologie et immunologie, CP 6128, succursale Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Patrick C Hallenbeck
- Université de Montréal, Département de microbiologie et immunologie, CP 6128, succursale Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Bernd Masepohl
- Ruhr-Universität Bochum, Lehrstuhl für Biologie der Mikroorganismen, D-44780 Bochum, Germany
| | - Werner Klipp
- Ruhr-Universität Bochum, Lehrstuhl für Biologie der Mikroorganismen, D-44780 Bochum, Germany
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