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1.
World J Microbiol Biotechnol ; 34(12): 184, 2018 Nov 28.
Article in English | MEDLINE | ID: mdl-30488133

ABSTRACT

Nitrogen fixation is one of the major biogeochemical contributions carried out by diazotrophic microorganisms. The goal of this research is study of posttranslational modification of dinitrogenase reductase (Fe protein), the involvement of malate and pyruvate in generation of reductant in Rhodospirillum rubrum. A procedure for the isolation of the Fe protein from cell extracts was developed and used to monitor the modification of the Fe protein in vivo. The subunit pattern of the isolated the Fe protein after sodium dodecyl sulfate-polyacrylamide gel electrophoresis was assayed by Western blot analysis. Whole-cell nitrogenase activity was also monitored during the Fe protein modification by gas chromatograpy, using the acetylene reduction assay. It has been shown, that the addition of fluoroacetate, ammonia and darkness resulted in the loss of whole-cell nitrogenase activity and the in vivo modification of the Fe protein. For fluoroacetate, ammonia and darkness, the rate of loss of nitrogenase activity was similar to that for the Fe protein modification. The addition of NADH and reillumination of a culture incubated in the dark resulted in the rapid restoration of nitrogenase activity and the demodification of the Fe protein. Fluoroacetate inhibited the nitrogenase activity of R. rubrum and resulted in the modification of the Fe protein in cells, grown on pyruvate or malate as the endogeneous electron source. The nitrogenase activity in draTG mutant (lacking DRAT/DRAG system) decreased after the addition of fluoroacetate, but the Fe protein remained completely unmodified. The results showed that the reduced state of cell, posttranslational modifications of the Fe protein and the DRAT/DRAG system are important for nitrogenase activity and the regulation of nitrogen fixation.


Subject(s)
Bacterial Proteins/metabolism , Dinitrogenase Reductase/metabolism , Fluoroacetates/metabolism , Rhodospirillum rubrum/enzymology , Bacterial Proteins/genetics , Dinitrogenase Reductase/genetics , Gene Expression Regulation, Bacterial , Nitrogen Fixation , Protein Processing, Post-Translational , Rhodospirillum rubrum/genetics , Rhodospirillum rubrum/metabolism
2.
ISME J ; 10(3): 678-92, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26394007

ABSTRACT

To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5'-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no (15)NH4(+) assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active 'free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. (15)N2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, (15)N2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced (15)N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.


Subject(s)
Archaea/isolation & purification , Bacteria/isolation & purification , Geologic Sediments/microbiology , Methane/metabolism , Transcription, Genetic , Archaea/classification , Archaea/genetics , Archaea/metabolism , Bacteria/classification , Bacteria/genetics , Bacteria/metabolism , Dinitrogenase Reductase/genetics , Dinitrogenase Reductase/metabolism , Ecosystem , In Situ Hybridization, Fluorescence , Mass Spectrometry , Nitrogen Fixation , Volcanic Eruptions/analysis
3.
Microb Ecol ; 71(1): 131-49, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26582318

ABSTRACT

Cyanobacteria are generally thought to be responsible for primary production and nitrogen fixation in the microbial communities that dominate Antarctic ecosystems. Recent studies of bacterial communities in terrestrial Antarctica, however, have shown that Cyanobacteria are sometimes only scarcely present, suggesting that other bacteria presumably take over their role as primary producers and diazotrophs. The diversity of key genes in these processes was studied in surface samples from the Sør Rondane Mountains, Dronning Maud Land, using clone libraries of the large subunit of ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL, cbbM) and dinitrogenase-reductase (nifH) genes. We recovered a large diversity of non-cyanobacterial cbbL type IC in addition to cyanobacterial type IB, suggesting that non-cyanobacterial autotrophs may contribute to primary production. The nifH diversity recovered was predominantly related to Cyanobacteria, particularly members of the Nostocales. We also investigated the occurrence of proteorhodopsin and anoxygenic phototrophy as mechanisms for non-Cyanobacteria to exploit solar energy. While proteorhodopsin genes were not detected, a large diversity of genes coding for the light and medium subunits of the type 2 phototrophic reaction center (pufLM) was observed, suggesting for the first time, that the aerobic photoheterotrophic lifestyle may be important in oligotrophic high-altitude ice-free terrestrial Antarctic habitats.


Subject(s)
Bacteria/isolation & purification , Bacteria/metabolism , Bacterial Proteins/genetics , Biodiversity , Dinitrogenase Reductase/genetics , Ribulose-Bisphosphate Carboxylase/genetics , Soil Microbiology , Antarctic Regions , Autotrophic Processes , Bacteria/classification , Bacteria/genetics , DNA, Bacterial/genetics , Phototrophic Processes , Phylogeny , RNA, Ribosomal, 16S/genetics , Soil/chemistry
4.
ISME J ; 9(2): 485-96, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25303712

ABSTRACT

Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N2 fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community in intertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N2 fixation, whereas (15)N2 tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N2-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N2 fixation in the intertidal mats, whereas support for significant N2 fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.


Subject(s)
Bacteria/metabolism , Cyanobacteria/metabolism , Nitrogen Fixation , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Biodiversity , Cyanobacteria/classification , Cyanobacteria/genetics , Cyanobacteria/isolation & purification , Dinitrogenase Reductase/genetics , Ecosystem , Mexico , Nitrogen Fixation/genetics , Single-Cell Analysis
5.
J Basic Microbiol ; 55(4): 462-70, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25400035

ABSTRACT

The aim of this work was to determine the genetic structure of Rhizobium leguminosarum bv. trifolii population isolated from root nodules of Trifolium repens growing in heavy metal contaminated Boleslaw waste-heap area and compare it with that of an unpolluted control Bolestraszyce population. The 684-bp long dinitrogenase reductase (nifH) gene fragments were amplified in a PCR reaction and then sequenced. An analysis of nifH gene amplicons of 21 rhizobial strains from each of the studied populations revealed substantially reduced genotype (h) and nucleotide (π) diversities in the metallicolous Boleslaw population in comparison to the non-metallicolous Bolestraszyce one, and showed a significant genetic differentiation between these populations (F(ST) = 0.159, p = 0.018). Among the strains under investigation, six genotypes (A-F) with 95-99% nifH gene sequence identities were distinguished. Studied T. repens nodule isolates indicated the highest nifH gene sequence similarities (95-100%) with R. leguminosarum bv. trifolii reference strains and on nifH phylogram all these strains formed monophyletic, highly supported clade (100%). The decreased genotype and nucleotide diversities of the waste-heap R. leguminosarum bv. trifolii population, compared to that from the control area and substantial genetic differentiation between populations of nifH gene, is arguably the consequence of the random genetic drift (Tajima's D = 2.042, p = 0.99).


Subject(s)
Dinitrogenase Reductase/genetics , Genetic Variation , Rhizobium leguminosarum/genetics , Rhizobium leguminosarum/isolation & purification , Root Nodules, Plant/microbiology , Symbiosis , Trifolium/microbiology , Waste Disposal Facilities , Genetic Drift , Lead , Metals, Heavy , Poland , Polymerase Chain Reaction , Rhizobium leguminosarum/classification , Sequence Analysis, DNA , Zinc
6.
Funct Integr Genomics ; 14(3): 571-80, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24781142

ABSTRACT

The enzyme nitrogenase complex is a key component conferring nitrogen fixation in all known diazotrophs. This study for the first time examines the impact of As, Na, Cd, Cu and butachlor on component II (dinitrogenase reductase, nifH1) of nitrogenase from diazotrophic cyanobacterium Anabaena sp. PCC7120 using in silico and wet lab approaches. The nifH1 of Anabaena is a glycine-rich stable protein having DNA-binding properties and shows close similarity with free living compared with symbiotic diazotrophs. Phylogenetic tree revealed an adverse effect of the selected stresses on close homologs across the diazotroph community. The protein interaction network demonstrated the presence of nirA, glnA, glnB, alr4255 and alr2485 proteins besides nif proteins, suggesting their involvement in nitrogen fixation along with nifH1. Homology modelling and docking under As, Na, Cd, Cu and butachlor revealed an interaction between stressors and nifH1 protein which was further validated by a transcript of the gene through quantitative real-time PCR (qRT-PCR). Presence of binding sites for As, Na, Cd and Cu on oxyR promoter attested their adverse affects on nifH1. Maximum down-regulation of nifH1 in Cd and As followed by salt, copper and butachlor revealed that arsenic and cadmium were most potential inhibitors of nitrogenase of diazotrophic community, which might negatively affect crop yield.


Subject(s)
Anabaena/enzymology , Arsenic/pharmacology , Bacterial Proteins/genetics , Cadmium/pharmacology , Dinitrogenase Reductase/genetics , Anabaena/genetics , Bacterial Proteins/biosynthesis , Bacterial Proteins/chemistry , Dinitrogenase Reductase/biosynthesis , Dinitrogenase Reductase/chemistry , Gene Expression/drug effects , Models, Molecular , Nitrogen Fixation , Phylogeny , Promoter Regions, Genetic , Structural Homology, Protein
7.
PLoS One ; 9(2): e88141, 2014.
Article in English | MEDLINE | ID: mdl-24505405

ABSTRACT

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.


Subject(s)
Bacterial Physiological Phenomena , Fagus/microbiology , Fungi/physiology , Nitrogen Fixation , Picea/microbiology , Wood/microbiology , Amino Acid Sequence , Bacteria/chemistry , Bacteria/enzymology , Bacteria/isolation & purification , Dinitrogenase Reductase/chemistry , Dinitrogenase Reductase/genetics , Ecology , Fungi/isolation & purification , Molecular Sequence Data , Phylogeny
8.
J Proteome Res ; 12(11): 4757-68, 2013 Nov 01.
Article in English | MEDLINE | ID: mdl-23971515

ABSTRACT

Although the use of plant growth-promoting bacteria in agriculture is a reality, the molecular basis of plant-bacterial interaction is still poorly understood. We used a proteomic approach to study the mechanisms of interaction of Herbaspirillum seropedicae SmR1 with rice. Root proteins of rice seedlings inoculated or noninoculated with H. seropedicae were separated by 2-D electrophoresis. Differentially expressed proteins were identified by MALDI-TOF/TOF and MASCOT program. Among the identified proteins of H. seropedicae, the dinitrogenase reductase NifH and glutamine synthetase GlnA, which participate in nitrogen fixation and ammonium assimilation, respectively, were the most abundant. The rice proteins up-regulated included the S-adenosylmethionine synthetase, methylthioribose kinase, and acireductone dioxygenase 1, all of which are involved in the methionine recycling. S-Adenosylmethionine synthetase catalyzes the synthesis of S-adenosylmethionine, an intermediate used in transmethylation reactions and in ethylene, polyamine, and phytosiderophore biosynthesis. RT-qPCR analysis also confirmed that the methionine recycling and phytosiderophore biosynthesis genes were up-regulated, while ACC oxidase mRNA level was down-regulated in rice roots colonized by bacteria. In agreement with these results, ethylene production was reduced approximately three-fold in rice roots colonized by H. seropedicae. The results suggest that H. seropedicae stimulates methionine recycling and phytosiderophore synthesis and diminishes ethylene synthesis in rice roots.


Subject(s)
Herbaspirillum/enzymology , Methionine/metabolism , Oryza/metabolism , Oryza/microbiology , Plant Roots/microbiology , Proteomics/methods , Symbiosis , Dinitrogenase Reductase/metabolism , Electrophoresis, Gel, Two-Dimensional , Glutamate-Ammonia Ligase/metabolism , Methionine Adenosyltransferase/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Seedlings/metabolism , Siderophores/biosynthesis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
9.
ISME J ; 6(7): 1427-39, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22237543

ABSTRACT

N(2) fixation is a key process in photosynthetic microbial mats to support the nitrogen demands associated with primary production. Despite its importance, groups that actively fix N(2) and contribute to the input of organic N in these ecosystems still remain largely unclear. To investigate the active diazotrophic community in microbial mats from the Elkhorn Slough estuary, Monterey Bay, CA, USA, we conducted an extensive combined approach, including biogeochemical, molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. Detailed analysis of dinitrogenase reductase (nifH) transcript clone libraries from mat samples that fixed N(2) at night indicated that cyanobacterial nifH transcripts were abundant and formed a novel monophyletic lineage. Independent NanoSIMS analysis of (15)N(2)-incubated samples revealed significant incorporation of (15)N into small, non-heterocystous cyanobacterial filaments. Mat-derived enrichment cultures yielded a unicyanobacterial culture with similar filaments (named Elkhorn Slough Filamentous Cyanobacterium-1 (ESFC-1)) that contained nifH gene sequences grouping with the novel cyanobacterial lineage identified in the transcript clone libraries, displaying up to 100% amino-acid sequence identity. The 16S rRNA gene sequence recovered from this enrichment allowed for the identification of related sequences from Elkhorn Slough mats and revealed great sequence diversity in this cluster. Furthermore, by combining (15)N(2) tracer experiments, fluorescence in situ hybridization and NanoSIMS, in situ N(2) fixation activity by the novel ESFC-1 group was demonstrated, suggesting that this group may be the most active cyanobacterial diazotroph in the Elkhorn Slough mat. Pyrotag sequences affiliated with ESFC-1 were recovered from mat samples throughout 2009, demonstrating the prevalence of this group. This work illustrates that combining standard and single-cell analyses can link phylogeny and function to identify previously unknown key functional groups in complex ecosystems.


Subject(s)
Cyanobacteria/classification , Cyanobacteria/isolation & purification , Estuaries , Cyanobacteria/genetics , Cyanobacteria/metabolism , DNA, Bacterial/genetics , Dinitrogenase Reductase/genetics , In Situ Hybridization, Fluorescence , Mass Spectrometry , Molecular Sequence Data , Phylogeny , Single-Cell Analysis
10.
FEMS Microbiol Ecol ; 73(3): 514-25, 2010 Sep.
Article in English | MEDLINE | ID: mdl-20618861

ABSTRACT

The structure of the microbial community and the diversity of the functional gene for dinitrogenase reductase and its transcripts were investigated by analyzing >1400 16S rRNA gene and nifH sequences from two microbial mats situated in the intertidal zone of the Dutch barrier island Schiermonnikoog. Although both microbial mat communities were dominated by Cyanobacteria, they differed with respect to the composition of the total bacterial community. Proteobacteria-related sequences were retrieved as the second most abundant group higher up in the littoral (Station I), whereas Bacteroidetes were the second most abundant group at the low water mark (Station II). The diazotrophic (nitrogen-fixing) communities at both stations were also different, but had more operational taxonomic units in common than the total bacterial community. Denaturing gradient gel electrophoresis also revealed differences in the total bacterial and diazotrophic community in two consecutive years. Analysis of the expression of nifH at Station I showed a discrepancy between the present and the active diazotrophic community. Transcript abundances of the different diazotrophs changed over a 24-h cycle and were dominated by cyanobacterial lineages in the daytime, while Gammaproteobacteria peaked at night. These variations might be responsible for the pattern in nitrogenase activity observed in these mats.


Subject(s)
Bacteroidetes/genetics , Biodiversity , Cyanobacteria/genetics , Nitrogen Fixation , Proteobacteria/genetics , Bacteroidetes/classification , Bacteroidetes/enzymology , Cluster Analysis , Cyanobacteria/classification , Cyanobacteria/enzymology , DNA, Bacterial/genetics , Dinitrogenase Reductase/genetics , Gene Library , Netherlands , Proteobacteria/classification , Proteobacteria/enzymology , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
11.
Curr Microbiol ; 56(6): 563-8, 2008 Jun.
Article in English | MEDLINE | ID: mdl-18324437

ABSTRACT

Periphyton mats are an important component of many wetland ecosystems, performing a range of vital ecosystem functions, including nitrogen fixation. The composition and integrity of these mats are affected by nutrient additions, which might result in changes in their function. The overall objective of this study was to investigate the distribution of nifH sequences in floating periphyton mats collected along a nutrient gradient in the Florida Everglades. Distribution of nifH clone libraries indicated nutrient enrichment selected primarily for sequences branching deeply within the heterocystous cyanobacteria and within a novel group of cyanobacteria; sequences from low-nutrient sites were broadly distributed, with no clear dominance of sequences associated with heterocystous and nonheterocystous cyanobacteria and alpha-, gamma-, and delta-proteobacteria. The dominance of heterocystous cyanobacteria in nutrient-enriched sites and the lack of clear dominance by heterocystous cyanobacteria is consistent with previously reported diurnal cycles of nitrogen fixation rates in these systems. Sequences clustering with those harbored by methanotrophs were also identified; sequences from nutrient-impacted and transition regions clustered with those characteristic of type II methanotrophs, and sequences from oligotrophic regions clustered with type I methanotrophs.


Subject(s)
Cyanobacteria/classification , Dinitrogenase Reductase/genetics , Plankton/classification , Proteobacteria/classification , Soil Microbiology , Water Microbiology , Wetlands , Bacterial Proteins/genetics , Cyanobacteria/enzymology , Cyanobacteria/genetics , Cyanobacteria/isolation & purification , Florida , Genetic Variation , Molecular Sequence Data , Phosphorus/metabolism , Phylogeny , Plankton/enzymology , Plankton/genetics , Proteobacteria/enzymology , Proteobacteria/genetics , Proteobacteria/isolation & purification
12.
Curr Microbiol ; 53(4): 317-23, 2006 Oct.
Article in English | MEDLINE | ID: mdl-16972125

ABSTRACT

Azospirillum brasilense is a nitrogen-fixing, root-colonizing bacterium that brings about plant-growth-promoting effects mainly because of its ability to produce phytohormones. Ethylenediamine (EDA)-resistant mutants of A. brasilense were isolated and screened for their higher ability to decrease acetylene and release ammonia in the medium. One of the mutants showed considerably higher levels of acetylene decrease and ammonia excretion. Nitrogenase activity of this mutant was relatively resistant to inhibition by NH(4)Cl. Adenosine triphosphate ribosylation of dinitrogenase reductase in the mutant did not increase even in presence of 10 mM NH(4)Cl. Although the mutant showed decreased glutamine synthetase (GS) activity, neither the levels of GS synthesized by the mutant nor the NH (4) (+) -binding site in the GS differed from those of the parent. The main reason for the release of ammonia by the mutant seems to be the fixation of higher levels of nitrogen than its GS can assimilate, as well as higher levels of adenylylation of GS, which may decrease ammonia assimilation.


Subject(s)
Ammonia/metabolism , Apyrase/metabolism , Azospirillum brasilense/genetics , Azospirillum brasilense/metabolism , Glutamate-Ammonia Ligase/metabolism , Adenosine Diphosphate Ribose/metabolism , Ammonium Chloride/pharmacology , Azospirillum brasilense/drug effects , Azospirillum brasilense/growth & development , Dinitrogenase Reductase/metabolism , Drug Resistance, Bacterial , Ethylenediamines/pharmacology , Mutation , Nitrogen Fixation
13.
Biochem Soc Trans ; 34(Pt 1): 160-1, 2006 Feb.
Article in English | MEDLINE | ID: mdl-16417510

ABSTRACT

Nitrogenase activity in Rhodospirillum rubrum is post-translationally regulated by DRAG (dinitrogenase reductase glycohydrolase) and DRAT (dinitrogenase reductase ADP-ribosylation transferase). When a sudden increase in fixed nitrogen concentration or energy depletion is sensed by the cells, DRAG is inactivated and DRAT activated. We propose that the regulation of DRAG is dependent on its location in the cell and the presence of an ammonium-sensing protein.


Subject(s)
Dinitrogenase Reductase/metabolism , Nitrogen Fixation , Rhodospirillum rubrum/metabolism , Enzyme Activation , Gene Expression Regulation, Bacterial , Nitrogenase/genetics , Nitrogenase/metabolism
14.
FEBS Lett ; 579(25): 5751-8, 2005 Oct 24.
Article in English | MEDLINE | ID: mdl-16225869

ABSTRACT

Nitrogenase activity in the photosynthetic bacterium Rhodospirillum rubrum is reversibly regulated by ADP-ribosylation of a specific arginine residue of dinitrogenase reductase based on the cellular nitrogen or energy status. In this paper, we have investigated the ability of nicotinamide adenine dinucleotide, NAD (the physiological ADP-ribose donor), and its analogs to support covalent modification of dinitrogenase reductase in vitro. R. rubrum dinitrogenase reductase can be modified by DRAT in the presence of 2 mM NAD, but not with 2 mM nicotinamide mononucleotide (NMN) or nicotinamide adenine dinucleotide phosphate (NADP). We also found that the apo- and the all-ferrous forms of R. rubrum dinitrogenase reductase are not substrates for covalent modification. In contrast, Azotobacter vinelandii dinitrogenase reductase can be modified by the dinitrogenase reductase ADP-ribosyl transferase (DRAT) in vitro in the presence of either 2 mM NAD, NMN or NADP as nucleotide donors. We found that: (1) a simple ribose sugar in the modification site of the A. vinelandii dinitrogenase reductase is sufficient to inactivate the enzyme, (2) phosphoADP-ribose is the modifying unit in the NADP-modified enzyme, and (3) the NMN-modified enzyme carries two ribose-phosphate units in one modification site. This is the first report of NADP- or NMN-dependent modification of a target protein by an ADP-ribosyl transferase.


Subject(s)
Azotobacter vinelandii/enzymology , Dinitrogenase Reductase/metabolism , Rhodospirillum rubrum/enzymology , Ribonucleotides/pharmacology , Adenosine Diphosphate Ribose/chemistry , Dinitrogenase Reductase/chemistry , Dinitrogenase Reductase/drug effects , NAD/chemistry , NAD/pharmacology , NADP/chemistry , NADP/pharmacology , Nicotinamide Mononucleotide/chemistry , Nicotinamide Mononucleotide/pharmacology , Ribonucleotides/chemistry
15.
Mol Ecol ; 14(9): 2637-43, 2005 Aug.
Article in English | MEDLINE | ID: mdl-16029466

ABSTRACT

Nitrogen, although abundant in the atmosphere, is paradoxically a limited resource for multicellular organisms. In the Animalia, biological nitrogen fixation has solely been demonstrated in termites. We found that all individuals of field-collected Mediterranean fruit flies (Ceratitis capitata) harbour large diazotrophic enterobacterial populations that express dinitrogen reductase in the gut. Moreover, nitrogen fixation was demonstrated in isolated guts and in live flies and may significantly contribute to the fly's nitrogen intake. The presence of similar bacterial consortia in additional insect orders suggests that nitrogen fixation occurs in vast pools of terrestrial insects. On such a large scale, this phenomenon may have a considerable impact on the nitrogen cycle.


Subject(s)
Ceratitis capitata/metabolism , Ceratitis capitata/microbiology , Enterobacteriaceae/genetics , Nitrogen/metabolism , Phylogeny , Animals , Base Sequence , DNA Primers , Dinitrogenase Reductase/metabolism , Enterobacteriaceae/metabolism , Gastrointestinal Tract/metabolism , Gastrointestinal Tract/microbiology , Likelihood Functions , Models, Genetic , Molecular Sequence Data , Oxidoreductases/genetics , RNA, Ribosomal, 16S/genetics , Reverse Transcriptase Polymerase Chain Reaction , Sequence Analysis, DNA
16.
Proc Natl Acad Sci U S A ; 102(18): 6291-6, 2005 May 03.
Article in English | MEDLINE | ID: mdl-15845763

ABSTRACT

Rnf proteins are proposed to form membrane-protein complexes involved in the reduction of target proteins such as the transcriptional regulator SoxR or the dinitrogenase reductase component of nitrogenase. In this work, we investigate the role of rnf genes in the nitrogen-fixing bacterium Azotobacter vinelandii. We show that A. vinelandii has two clusters of rnf-like genes: rnf1, whose expression is nif-regulated, and rnf2, which is expressed independently of the nitrogen source in the medium. Deletion of each of these gene clusters produces a time delay in nitrogen-fixing capacity and, consequently, in diazotrophic growth. Deltarnf mutations cause two distinguishable effects on the nitrogenase system: (i), slower nifHDK gene expression and (ii), impairment of nitrogenase function. In these mutants, dinitrogenase reductase activity is lowered, whereas dinitrogenase activity remains essentially unaltered. Further analysis indicates that deltarnf mutants accumulate an inactive and iron-deficient form of NifH because they have lower rates of incorporation of [4Fe-4S] into NifH. Deltarnf mutations also cause a noticeable decrease in aconitase activity; however, they do not produce general oxidative stress or modification of Fe metabolism in A. vinelandii. Our results suggest the existence of a redox regulatory mechanism in A. vinelandii that controls the rate of expression and maturation of nitrogenase by the activity of the Rnf protein complexes. rnf1 plays a major and more specific role in this scheme, but the additive effects of mutations in rnf1 and rnf2 indicate the existence of functional complementation between the two homologous systems.


Subject(s)
Azotobacter vinelandii/genetics , Gene Expression Regulation, Bacterial , Genes, Bacterial/genetics , Nitrogen Fixation/genetics , Nitrogenase/metabolism , Azotobacter vinelandii/enzymology , Azotobacter vinelandii/growth & development , Dinitrogenase Reductase/metabolism , Electrophoresis, Polyacrylamide Gel , Gene Components , Iron Radioisotopes , Nitrogenase/genetics
18.
J Biosci ; 29(2): 153-61, 2004 Jun.
Article in English | MEDLINE | ID: mdl-15286412

ABSTRACT

Potassium deficiency enhanced the synthesis of fifteen proteins in the nitrogen-fixing cyanobacterium Anabaena torulosa and of nine proteins in Escherichia coli. These were termed potassium deficiency-induced proteins or PDPs and constitute hitherto unknown potassium deficiency-induced stimulons. Potassium deficiency also enhanced the synthesis of certain osmotic stress-induced proteins. Addition of K+ repressed the synthesis of a majority of the osmotic stress-induced proteins and of PDPs in these bacteria. These proteins contrast with the dinitrogenase reductase of A. torulosa and the glycine betaine-binding protein of E. coli, both of which were osmo-induced to a higher level in potassium-supplemented conditions. The data demonstrate the occurrence of novel potassium deficiency-induced stimulons and a wider role of K+ in regulation of gene expression and stress responses in bacteria


Subject(s)
Anabaena/drug effects , Bacterial Proteins/biosynthesis , Potassium/physiology , Protein Biosynthesis , Anabaena/metabolism , Bacterial Proteins/genetics , Dinitrogenase Reductase/biosynthesis , Dinitrogenase Reductase/genetics , Escherichia coli/drug effects , Escherichia coli/metabolism , Escherichia coli Proteins/biosynthesis , Escherichia coli Proteins/genetics , Gene Expression Regulation, Bacterial/drug effects , Membrane Transport Proteins/biosynthesis , Membrane Transport Proteins/genetics , Osmotic Pressure , Periplasmic Binding Proteins/biosynthesis , Periplasmic Binding Proteins/genetics , Potassium/pharmacology , Protein Biosynthesis/drug effects
19.
FEBS Lett ; 559(1-3): 84-8, 2004 Feb 13.
Article in English | MEDLINE | ID: mdl-14960312

ABSTRACT

In Rhodospirillum rubrum, nitrogenase activity is subject to posttranslational regulation through the adenosine diphosphate (ADP)-ribosylation of dinitrogenase reductase by dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase-activating glycohydrolase (DRAG). To study the posttranslational regulation of DRAG, its gene was mutagenized and colonies screened for altered DRAG regulation. Three different mutants were found and the DRAG variants displayed different biochemical properties including an altered affinity for divalent metal ions. Taken together, the results suggest that the site involved in regulation is physically near the metal binding site of DRAG.


Subject(s)
ADP Ribose Transferases/metabolism , N-Glycosyl Hydrolases/metabolism , Protein Processing, Post-Translational/genetics , Rhodospirillum rubrum/enzymology , ADP Ribose Transferases/genetics , Adenosine Diphosphate Ribose/metabolism , Binding Sites , Cations, Divalent/metabolism , Dinitrogenase Reductase/metabolism , Mutagenesis , Mutation , N-Glycosyl Hydrolases/genetics
20.
Biochemistry ; 42(13): 3846-57, 2003 Apr 08.
Article in English | MEDLINE | ID: mdl-12667075

ABSTRACT

In the phototrophic non-sulfur bacterium Rhodobacter capsulatus, the biosynthesis of the conventional Mo-nitrogenase is strictly Mo-regulated. Significant amounts of both dinitrogenase and dinitrogenase reductase were only formed when the growth medium was supplemented with molybdate (1 microM). During cell growth under Mo-deficient conditions, tungstate, at high concentrations (1 mM), was capable of partially (approximately 25%) substituting for molybdate in the induction of nitrogenase synthesis. On the basis of such conditions, a tungsten-substituted nitrogenase was isolated from R. capsulatus with the aid of anfA (Fe-only nitrogenase defective) mutant cells and partially purified by Q-sepharose chromatography. Metal analyses revealed the protein to contain an average of 1 W-, 16 Fe-, and less than 0.01 Mo atoms per alpha(2)beta(2)-tetramer. The tungsten-substituted (WFe) protein was inactive in reducing N(2) and marginally active in acetylene reduction, but it was found to show considerable activity with respect to the generation of H(2) from protons. The EPR spectrum of the WFe protein, recorded at 4 K, exhibited three distinct signals: (i) an S = 3/2 signal, which dominates the low-field region of the spectrum (g = 4.19, 3.93) and is indicative of a tungsten-substituted cofactor (termed FeWco), (ii) a marginal S = 3/2 signal (g = 4.29, 3.67) that can be attributed to residual amounts of FeMoco present in the protein, and (iii) a broad S = 1/2 signal (g = 2.09, 1.95, 1.86) arising from at least two paramagnetic species. Redox titrational analysis of the WFe protein revealed the midpoint potential of the FeWco (E(m) < -200 mV) to be shifted to distinctly lower potentials as compared to that of the FeMoco (E(m) approximately -50 mV) present in the native enzyme. The P clusters of both the WFe and the MoFe protein appear indistinguishable with respect to their midpoint potentials. EPR spectra recorded with the WFe protein under turnover conditions exhibited a 20% decrease in the intensity of the FeWco signal, indicating that the cofactor can be enzymatically reduced only to a small extent. The data presented in the current study demonstrate the pivotal role of molybdenum in optimal N(2) fixation and provides direct evidence that the inability of a tungsten-substituted nitrogenase to reduce N(2) is due to the difficulty to effectively reduce the FeW cofactor beyond its semi-reduced state.


Subject(s)
Nitrogenase/chemistry , Rhodobacter capsulatus/enzymology , Tungsten/chemistry , Blotting, Western , Cell Division , Dinitrogenase Reductase , Electron Spin Resonance Spectroscopy , Iron/metabolism , Molybdenum/chemistry , Molybdenum/metabolism , Molybdoferredoxin , Nitrogenase/isolation & purification , Nitrogenase/metabolism , Oxidation-Reduction , Tungsten/metabolism
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