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Klünemann T, Henke S, Blankenfeldt W. The crystal structure of the heme d 1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo. Acta Crystallogr D Struct Biol 2020; 76:375-384. [PMID: 32254062 PMCID: PMC7137109 DOI: 10.1107/s2059798320003101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/05/2020] [Indexed: 11/10/2022] Open
Abstract
Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa, has been determined. The crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution of 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of 11 NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D domain-swapped dimers, one of which shows pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between the high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison with similar proteins may offer new leads to unravel the unknown function of NirC.
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Affiliation(s)
- Thomas Klünemann
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Steffi Henke
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
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Bali S, Warren MJ, Ferguson SJ. NirF is a periplasmic protein that binds d1 heme as part of its essential role in d1 heme biogenesis. FEBS J 2010; 277:4944-55. [DOI: 10.1111/j.1742-4658.2010.07899.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Brindley AA, Zajicek R, Warren MJ, Ferguson SJ, Rigby SE. NirJ, a radical SAM family member of thed1heme biogenesis cluster. FEBS Lett 2010; 584:2461-6. [DOI: 10.1016/j.febslet.2010.04.053] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 04/16/2010] [Accepted: 04/19/2010] [Indexed: 11/28/2022]
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5
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Ghiglione JF, Richaume A, Philippot L, Lensi R. Relative involvement of nitrate and nitrite reduction in the competitiveness of Pseudomonas fluorescens in the rhizosphere of maize under non-limiting nitrate conditions. FEMS Microbiol Ecol 2009; 39:121-7. [PMID: 19709191 DOI: 10.1111/j.1574-6941.2002.tb00913.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Competition between different isogenic mutants of Pseudomonas fluorescens unable to carry out the first steps of the denitrification pathway was compared in soil micro-columns non-planted or planted with maize. A new isogenic mutant of P. fluorescens YT101 affected in both nitrate and nitrite respirations was constructed and used as a model of non-denitrifying strain (FM69MS strain). The outcome of the selection exerted by the plant after co-inoculation of FM69MS at the same ratio either with an isogenic denitrifier unable to reduce nitrate (Nar(-) mutant) or with an isogenic NO2 (-) accumulator (Nir(-) mutant) was investigated in non-limiting NO3 (-) conditions. Regardless of the inoculated mixture, both strains were able to grow in both rhizosphere and non-planted soil. The proportion of Nar(-) or Nir(-) strain in the Nar(-)+FM69MS or Nir(-)+FM69MS total introduced population remained stable in non-planted soil. In the rhizosphere, we observed a higher competitiveness of the Nir(-) mutant compared with FM69MS, whereas the latter showed the same competitiveness as the Nar(-) mutant. These results provide the first demonstration that NO3 (-) reduction is the main nitrogen-dissimilating step controlling the competitiveness of P. fluorescens in the rhizosphere.
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Affiliation(s)
- Jean-François Ghiglione
- Ecologie Microbienne, UMR CNRS 5557, Université Claude Bernard-Lyon1, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
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Zajicek RS, Bali S, Arnold S, Brindley AA, Warren MJ, Ferguson SJ. d(1) haem biogenesis - assessing the roles of three nir gene products. FEBS J 2009; 276:6399-411. [PMID: 19796169 DOI: 10.1111/j.1742-4658.2009.07354.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of the modified tetrapyrrole known as d(1) haem requires several dedicated proteins which are coded for by a set of genes that are often found adjacent to the structural gene, nirS, for cytochrome cd(1) nitrite reductase. NirE, the product of the first gene in the nir biogenesis operon, was anticipated to catalyse the conversion of uroporphyrinogen III into precorrin-2; this was confirmed, but it was shown that this enzyme is less sensitive to product inhibition than similar enzymes that function in other biosynthetic pathways. Sequence analysis suggesting that one of these proteins, NirN, is a c-type cytochrome, and has similarity to the part of cytochrome cd(1) that binds d(1), was validated by recombinant production and characterization of NirN. A NirN-d(1) haem complex was demonstrated to release the cofactor to a semi-apo form of cytochrome cd(1) from which d(1) was extracted, suggesting a role for NirN in the assembly of cytochrome cd(1) (NirS). However, inactivation of nirN surprisingly led to only a marginal attenuation of growth of Paracoccus pantotrophus under anaerobic denitrifying conditions. As predicted, NirC is a c-type cytochrome; it was shown in vitro to be an electron donor to the NirN-d(1) complex.
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Wrage N, van Groenigen JW, Oenema O, Baggs EM. A novel dual-isotope labelling method for distinguishing between soil sources of N2O. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:3298-306. [PMID: 16220527 DOI: 10.1002/rcm.2191] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present a novel 18O-15N-enrichment method for the distinction between nitrous oxide (N2O) from nitrification, nitrifier denitrification and denitrification based on a method with single- and double-15N-labelled ammonium nitrate. We added a new treatment with 18O-labelled water to quantify N2O from nitrifier denitrification. The theory behind this is that ammonia oxidisers use oxygen (O2) from soil air for the oxidation of ammonia (NH3), but use H2O for the oxidation of the resulting hydroxylamine (NH2OH) to nitrite (NO2-). Thus, N2O from nitrification would therefore be expected to reflect the 18O signature of soil O2, whereas the 18O signature of N2O from nitrifier denitrification would reflect that of both soil O2 and H2O. It was assumed that (a) there would be no preferential removal of 18O or 16O during nitrifier denitrification or denitrification, (b) the 18O signature of the applied 18O-labelled water would remain constant over the experimental period, and (c) any O exchange between H(2)18O and NO3- would be negligible under the chosen experimental conditions. These assumptions were tested and validated for a silt loam soil at 50% water-filled pore space (WFPS) following application of 400 mg N kg-1 dry soil. We compared the results of our new method with those of a conventional inhibition method using 0.02% v/v acetylene (C2H2) and 80% v/v O2 in helium. Both the 18O-15N-enrichment and inhibitor methods identified nitrifier denitrification to be a major source of N2O, accounting for 44 and 40%, respectively, of N2O production over 24 h. However, compared to our 18O-15N-method, the inhibitor method overestimated the contribution from nitrification at the expense of denitrification, probably due to incomplete inhibition of nitrifier denitrification and denitrification by large concentrations of O2 and a negative effect of C2H2 on denitrification. We consider our new 18O-15N-enrichment method to be more reliable than the use of inhibitors; it enables the distinction between more soil sources of N2O than was previously possible and has provided the first direct evidence of the significance of nitrifier denitrification as a source of N2O in fertilised arable soil.
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Affiliation(s)
- N Wrage
- School of Biological Sciences (Plant and Soil Science), University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK.
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Maron PA, Richaume A, Potier P, Lata JC, Lensi R. Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil. J Microbiol Methods 2004; 58:13-21. [PMID: 15177899 DOI: 10.1016/j.mimet.2004.02.013] [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: 02/05/2004] [Revised: 02/24/2004] [Accepted: 02/24/2004] [Indexed: 11/30/2022]
Abstract
This work describes an immunological method for detection and quantification in complex environments of the dissimilative nitrate reductase (NRA) responsible for the reduction of nitrate to nitrite, which plays an important role in ecosystem functioning. The alpha-catalytic subunit of the enzyme was purified from the denitrifying strain Pseudomonas fluorescens YT101 and used for the production of polyclonal antibodies. These antibodies were used to detect and quantify the NRA by a chemifluorescence technique on Western blots after separation of total proteins from pure cultures and soil samples. The specificity, detection threshold and reproducibility of the proposed method were evaluated. A soil experiment showed that our method can be applied to complex environmental samples.
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Affiliation(s)
- P-A Maron
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France.
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Körner H, Sofia HJ, Zumft WG. Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol Rev 2003; 27:559-92. [PMID: 14638413 DOI: 10.1016/s0168-6445(03)00066-4] [Citation(s) in RCA: 327] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The Crp-Fnr regulators, named after the first two identified members, are DNA-binding proteins which predominantly function as positive transcription factors, though roles of repressors are also important. Among over 1200 proteins with an N-terminally located nucleotide-binding domain similar to the cyclic adenosine monophosphate (cAMP) receptor protein, the distinctive additional trait of the Crp-Fnr superfamily is a C-terminally located helix-turn-helix motif for DNA binding. From a curated database of 369 family members exhibiting both features, we provide a protein tree of Crp-Fnr proteins according to their phylogenetic relationships. This results in the assembly of the regulators ArcR, CooA, CprK, Crp, Dnr, FixK, Flp, Fnr, FnrN, MalR, NnrR, NtcA, PrfA, and YeiL and their homologs in distinct clusters. Lead members and representatives of these groups are described, placing emphasis on the less well-known regulators and target processes. Several more groups consist of sequence-derived proteins of unknown physiological roles; some of them are tight clusters of highly similar members. The Crp-Fnr regulators stand out in responding to a broad spectrum of intracellular and exogenous signals such as cAMP, anoxia, the redox state, oxidative and nitrosative stress, nitric oxide, carbon monoxide, 2-oxoglutarate, or temperature. To accomplish their roles, Crp-Fnr members have intrinsic sensory modules allowing the binding of allosteric effector molecules, or have prosthetic groups for the interaction with the signal. The regulatory adaptability and structural flexibility represented in the Crp-Fnr scaffold has led to the evolution of an important group of physiologically versatile transcription factors.
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Affiliation(s)
- Heinz Körner
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, PF 6980, D-76128 Karlsruhe, Germany
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Maron PA, Coeur C, Pink C, Clays-Josserand A, Lensi R, Richaume A, Potier P. Use of polyclonal antibodies to detect and quantify the NOR protein of nitrite oxidizers in complex environments. J Microbiol Methods 2003; 53:87-95. [PMID: 12609727 DOI: 10.1016/s0167-7012(02)00231-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the approaches or models which aim to understand and/or predict how the functioning of ecosystems may be affected by perturbations or disturbances, little attention is generally given to microorganisms. Even when they are taken into account as indicators, variables which are poorly informative about the changes in the microbial functioning (microbial biomass or diversity or total number of microorganisms) are often used. To be able to estimate, in complex environments, the quantity of enzymes involved in key ecosystem processes may constitute a useful complementary tool. Here, we describe an immunological method for detecting and quantifying, in complex environments, the nitrite oxidoreductase (NOR), responsible for the oxidation of nitrite to nitrate. The alpha-catalytic subunit of the enzyme was purified from Nitrobacter hamburgensis and used for the production of polyclonal antibodies. These antibodies were used to detect and quantify the NOR by a chemifluorescence technique on Western blots after separation of total proteins from pure cultures and soil samples. They recognized the alpha-NOR of all the Nitrobacter species described to date, but no reaction was observed with members of other nitrite-oxidizing genera. The detection threshold and reproducibility of the proposed method were evaluated. The feasibility of its use to quantify NOR in a soil was tested.
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Affiliation(s)
- Pierre-Alain Maron
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Université Claude Bernard Lyon 1, 69622 Villeurbanne cedex, France.
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11
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Delorme S, Philippot L, Edel-Hermann V, Deulvot C, Mougel C, Lemanceau P. Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent pseudomonads. Appl Environ Microbiol 2003; 69:1004-12. [PMID: 12571023 PMCID: PMC143668 DOI: 10.1128/aem.69.2.1004-1012.2003] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overall, there was a good correspondence between the reductase activities and the presence of the corresponding genes. Distribution in the different ribotypes of strains harboring both the narG and nosZ genes and of strains missing both genes suggests that these two groups of strains had different evolutionary histories. Both dissimilatory genes showed high polymorphism, with similarity indexes (Jaccard) of between 0.04 and 0.8, whereas those of the 16S rRNA gene only varied from 0.77 to 0.99. No correlation between the similarity indexes of 16S rRNA and dissimilatory genes was seen, suggesting that the evolution rates of ribosomal and functional genes differ. Pairwise comparison of similarity indexes of the narG and nosZ genes led to the delineation of two types of strains. Within the first type, the similarity indexes of both genes varied in the same range, suggesting that these two genes have followed a similar evolution. Within the second type of strain, the range of variations was higher for the nosZ than for the narG gene, suggesting that these genes have had a different evolutionary rate.
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Affiliation(s)
- Sandrine Delorme
- UMR INRA/Université de Bourgogne, Microbiologie et Géochimie du Sol, INRA-CMSE, 21065 Dijon Cedex, France
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12
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Hasegawa N, Arai H, Igarashi Y. Two c-type cytochromes, NirM and NirC, encoded in the nir gene cluster of Pseudomonas aeruginosa act as electron donors for nitrite reductase. Biochem Biophys Res Commun 2001; 288:1223-30. [PMID: 11700043 DOI: 10.1006/bbrc.2001.5919] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three c-type cytochromes, NirM, NirC, and NirN, are encoded in the nirSMCFDLGHJEN gene cluster for cytochrome cd(1)-type nitrite reductase (NIR) of Pseudomonas aeruginosa. nirS is the structural gene for NIR. NirM (cytochrome c(551)) is reported to be a physiological electron donor for nitrite reductase. The respective functions of NirC and NirN have remained unclear. In this study, we produced recombinant NirC and NirN in P. aeruginosa, and purified them from the periplasmic fraction. N-terminal amino acid sequences of the purified proteins showed that the N-terminal 31 and 18 residues of NirC and NirN precursors were cleaved, respectively, indicating that cleaved peptides act as signals for membrane translocation. In addition, the ability of NirC for electron donation to nitrite reductase was investigated. NirC, as well as NirM, was able to mediate the electron donation from the membrane electron pathway to NIR, suggesting that the structural gene for NIR is followed by the genes for two electron donors for NIR.
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Affiliation(s)
- N Hasegawa
- Department of Biotechnology, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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Demanèche S, Kay E, Gourbière F, Simonet P. Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil. Appl Environ Microbiol 2001; 67:2617-21. [PMID: 11375171 PMCID: PMC92915 DOI: 10.1128/aem.67.6.2617-2621.2001] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2000] [Accepted: 03/07/2001] [Indexed: 11/20/2022] Open
Abstract
Little information is available concerning the occurrence of natural transformation of bacteria in soil, the frequency of such events, and the actual role of this process on bacterial evolution. This is because few bacteria are known to possess the genes required to develop competence and because the tested bacteria are unable to reach this physiological state in situ. In this study we found that two soil bacteria, Agrobacterium tumefaciens and Pseudomonas fluorescens, can undergo transformation in soil microcosms without any specific physical or chemical treatment. Moreover, P. fluorescens produced transformants in both sterile and nonsterile soil microcosms but failed to do so in the various in vitro conditions we tested. A. tumefaciens could be transformed in vitro and in sterile soil samples. These results indicate that the number of transformable bacteria could be higher than previously thought and that these bacteria could find the conditions necessary for uptake of extracellular DNA in soil.
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Affiliation(s)
- S Demanèche
- Laboratoire d'Ecologie Microbienne, UMR 5557, Université Lyon I, 69622 Villeurbanne Cedex, France
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Vollack KU, Zumft WG. Nitric oxide signaling and transcriptional control of denitrification genes in Pseudomonas stutzeri. J Bacteriol 2001; 183:2516-26. [PMID: 11274111 PMCID: PMC95168 DOI: 10.1128/jb.183.8.2516-2526.2001] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The expression of denitrification by a facultatively anaerobic bacterium requires as exogenous signals a low oxygen tension concomitant with an N oxide. We have studied the role of nitric oxide (NO), nitrous oxide (N2O), and nitrite as signal molecules for the expression of the denitrification apparatus of Pseudomonas stutzeri. Transcriptional kinetics of structural genes were monitored by Northern blot analysis in a 60-min time frame after cells were exposed to an N oxide signal. To differentiate the inducer role of NO from that of nitrite, mRNA kinetics were monitored under anoxic conditions in a nirF strain, where NO generation from nitrite is prevented because of a defect in heme D(1) biosynthesis. NO-triggered responses were monitored from the nirSTB operon (encoding cytochrome cd(1) nitrite reductase), the norCB operon (encoding NO reductase), nosZ (encoding nitrous oxide reductase), and nosR (encoding a putative regulator). Transcription of nirSTB and norCB was activated by 5 to 50 nM NO, whereas the nosZ promoter required about 250 nM. Nitrite at 5 to 50 nM elicited no response. At a threshold concentration of 650 nM N2O, we observed in the anoxic cell the transient appearance of nosZ and nosR transcripts. Constant levels of transcripts of both genes were observed in an anoxic cell sparged with N2O. NO at 250 nM stimulated in this cell type the expression of nos genes severalfold. The transcription factor DnrD, a member of the FNR-CRP family, was found to be part of the NO-triggered signal transduction pathway. However, overexpression of dnrD in an engineered strain did not result in NirS synthesis, indicating a need for activation of DnrD. NO modified the transcriptional pattern of the dnrD operon by inducing the transcription of dnrN and dnrO, located upstream of dnrD. Insertional mutagenesis of dnrN altered the kinetic response of the nirSTB operon towards nitrite. Our data establish NO and DnrD as key elements in the regulatory network of denitrification in P. stutzeri. The NO response adds to the previously identified nitrate-nitrite response mediated by the NarXL two-component system for the expression of respiratory nitrate reductase encoded by the narGHJI operon.
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Affiliation(s)
- K U Vollack
- Lehrstuhl für Mikrobiologie der Universität Karlsruhe, D-76128 Karlsruhe, Germany
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15
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Ghiglione JF, Gourbiere F, Potier P, Philippot L, Lensi R. Role of respiratory nitrate reductase in ability of Pseudomonas fluorescens YT101 to colonize the rhizosphere of maize. Appl Environ Microbiol 2000; 66:4012-6. [PMID: 10966422 PMCID: PMC92252 DOI: 10.1128/aem.66.9.4012-4016.2000] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Selection of the denitrifying community by plant roots (i.e., increase in the denitrifier/total heterotroph ratio in the rhizosphere) has been reported by several authors. However, very few studies to evaluate the role of the denitrifying function itself in the selection of microorganisms in the rhizosphere have been performed. In the present study, we compared the rhizosphere survival of the denitrifying Pseudomonas fluorescens YT101 strain with that of its isogenic mutant deficient in the ability to synthesize the respiratory nitrate reductase, coinoculated in nonplanted or planted soil. We demonstrated that under nonlimiting nitrate conditions, the denitrifying wild-type strain had an advantage in the ability to colonize the rhizosphere of maize. Investigations of the effect of the inoculum characteristics (density of the total inoculum and relative proportions of mutant and wild-type strains) on the outcome of the selection demonstrated that the selective effect of the plant was expressed only during the phase of bacterial multiplication and that the intensity of selection was dependent on the magnitude of this phase. Moreover, application of the de Wit replacement series technique to our results suggests that the advantage of the wild-type strain was maximal when the ratio between the two strains in the inoculum was close to 1:1. This work constitutes the first direct demonstration that the presence of a functional structural gene encoding the respiratory nitrate reductase confers higher rhizosphere competence to a microorganism.
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Affiliation(s)
- J F Ghiglione
- Laboratoire d'Ecologie Microbienne, UMR-CNRS 5557, Université Claude-Bernard Lyon I, 69622 Villeurbanne Cedex, France
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16
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Kukimoto M, Nishiyama M, Tanokura M, Horinouchi S. Gene organization for nitric oxide reduction in Alcaligenes faecalis S-6. Biosci Biotechnol Biochem 2000; 64:852-7. [PMID: 10830505 DOI: 10.1271/bbb.64.852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
norB and norC encoding the cytochrome b-containing subunit and the cytochrome c-containing subunit, respectively, of the nitric oxide reductase (NOR) in Alcaligenes faecalis S-6 were cloned and sequenced. Both NorB and NorC showed more than 40% sequence identity to the corresponding subunits of cytochrome bc-type NORs in other denitrifying bacteria. norCB was in a gene cluster containing seven other genes; these were named dnr, orf2, orf3, norE, norF, norQ, and norD on the basis of their similarity with NOR systems in other bacteria. Potential FNR-binding sites were present in front of norCB, norEF, and/or orf2/orf3, suggesting that most of these genes are regulated simultaneously by an FNR-related protein. NorB and NorC proteins produced in the membrane fraction in Escherichia coli showed no enzyme activity, probably due to lack of NorQ and NorD, which appear to perform some essential function for activation of the NorB-NorC complex in the recombinant E. coli.
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Affiliation(s)
- M Kukimoto
- Department of Biotechnology, The University of Tokyo, Japan
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17
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Michotey V, Méjean V, Bonin P. Comparison of methods for quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples. Appl Environ Microbiol 2000; 66:1564-71. [PMID: 10742243 PMCID: PMC92024 DOI: 10.1128/aem.66.4.1564-1571.2000] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two PCR primer sets were developed for the detection and quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples. The specificity and sensitivity of these primers were tested. Both primer sets were suitable for detection, but only one set, cd3F-cd4R, was suitable for the quantification and enumeration of the functional community using most-probable-number PCR and competitive PCR techniques. Quantification of cytochrome cd(1) denitrifiers taken from marine sediment and water samples was achieved using two different molecular techniques which target the nirS gene, and the results were compared to those obtained by using the classical cultivation method. Enumerations using both molecular techniques yielded similar results in seawater and sediment samples. However, both molecular techniques showed 1,000 or 10 times more cytochrome cd(1) denitrifiers in the sediment or water samples, respectively, than were found by use of the conventional cultivation method for counting.
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Affiliation(s)
- V Michotey
- Laboratoire d'Océanologie et de Biogeochimie, CNRS-UMR 6535, Centre d'Océanologie de Marseille, Campus de Luminy, 13288 Marseille cedex 9, France.
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18
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Ghiglione JF, Philippot L, Normand P, Lensi R, Potier P. Disruption of narG, the gene encoding the catalytic subunit of respiratory nitrate reductase, also affects nitrite respiration in Pseudomonas fluorescens YT101. J Bacteriol 1999; 181:5099-102. [PMID: 10438786 PMCID: PMC94003 DOI: 10.1128/jb.181.16.5099-5102.1999] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Pseudomonas fluorescens YT101 gene narG, which encodes the catalytic alpha subunit of the respiratory nitrate reductase, was disrupted by insertion of a gentamicin resistance cassette. In the Nar(-) mutants, nitrate reductase activity was not detectable under all the conditions tested, suggesting that P. fluorescens YT101 contains only one membrane-bound nitrate reductase and no periplasmic nitrate reductase. Whereas N(2)O respiration was not affected, anaerobic growth with NO(2) as the sole electron acceptor was delayed for all of the Nar(-) mutants following a transfer from oxic to anoxic conditions. These results provide the first demonstration of a regulatory link between nitrate and nitrite respiration in the denitrifying pathway.
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Affiliation(s)
- J F Ghiglione
- Laboratoire d'Ecologie Microbienne du Sol, UMR C.N.R.S. 5557, Université Claude Bernard, Lyon 1, 69622 Villeurbanne Cedex, France
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19
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Abstract
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
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20
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Abstract
Biogenesis of respiratory cytochromes is defined as consisting of the posttranslational processes that are necessary to assemble apoprotein, heme, and sometimes additional cofactors into mature enzyme complexes with electron transfer functions. Different biochemical reactions take place during maturation: (i) targeting of the apoprotein to or through the cytoplasmic membrane to its subcellular destination; (ii) proteolytic processing of precursor forms; (iii) assembly of subunits in the membrane and oligomerization; (iv) translocation and/or modification of heme and covalent or noncovalent binding to the protein moiety; (v) transport, processing, and incorporation of other cofactors; and (vi) folding and stabilization of the protein. These steps are discussed for the maturation of different oxidoreductase complexes, and they are arranged in a linear pathway to best account for experimental findings from studies concerning cytochrome biogenesis. The example of the best-studied case, i.e., maturation of cytochrome c, appears to consist of a pathway that requires at least nine specific genes and more general cellular functions such as protein secretion or the control of the redox state in the periplasm. Covalent attachment of heme appears to be enzyme catalyzed and takes place in the periplasm after translocation of the precursor through the membrane. The genetic characterization and the putative biochemical functions of cytochrome c-specific maturation proteins suggest that they may be organized in a membrane-bound maturase complex. Formation of the multisubunit cytochrome bc, complex and several terminal oxidases of the bo3, bd, aa3, and cbb3 types is discussed in detail, and models for linear maturation pathways are proposed wherever possible.
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Affiliation(s)
- L Thöny-Meyer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH Zentrum, Zürich, Switzerland.
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21
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Philippot L, Clays-Josserand A, Lensi R, Trinsoutreau I, Normand P, Potier P. Purification of the dissimilative nitrate reductase of Pseudomonas fluorescens and the cloning and sequencing of its corresponding genes. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1350:272-6. [PMID: 9061022 DOI: 10.1016/s0167-4781(97)00007-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The dissimilative membrane-bound nitrate reductase from Pseudomonas fluorescens strain AK15 was purified and the alpha subunit of the enzyme partially sequenced. On the basis of this partial amino acid sequence and of conserved stretches of amino acids between Escherichia coli and Bacillus subtilis, degenerate primers were design to amplify the narG gene and part of the narH gene in a PCR approach. The deduced amino acid sequence of narG shows 72% and 52% and narH 78% and 62% identity to the homologous subunit of E. coli and B. subtilis, respectively.
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Affiliation(s)
- L Philippot
- UMR CNRS 5557, Laboratoire d'Ecologie Microbienne du Sol, Université Claude Bernard, Lyon, Villeurbanne, France
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22
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Tosques IE, Kwiatkowski AV, Shi J, Shapleigh JP. Characterization and regulation of the gene encoding nitrite reductase in Rhodobacter sphaeroides 2.4.3. J Bacteriol 1997; 179:1090-5. [PMID: 9023188 PMCID: PMC178802 DOI: 10.1128/jb.179.4.1090-1095.1997] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Nitrite reductase catalyzes the reduction of nitrite to nitric oxide, the first step in denitrification to produce a gaseous product. We have cloned the gene nirK, which encodes the copper-type nitrite reductase from a denitrifying variant of Rhodobacter sphaeroides, strain 2.4.3. The deduced open reading frame has significant identity with other copper-type nitrite reductases. Analysis of the promoter region shows that transcription initiates 31 bases upstream of the translation start codon. The transcription initiation site is 43.5 bases downstream of a putative binding site for a transcriptional activator. Maximal expression of a nirK-lacZ construct in 2.4.3 requires both a low level of oxygen and the presence of a nitrogen oxide. nirK-lacZ expression was severely impaired in a nitrite reductase-deficient strain of 2.4.3. This suggests that nirK expression is dependent on nitrite reduction. The inability of microaerobically grown nitrite reductase-deficient cells to induce nirK-lacZ expression above basal levels in medium unamended with nitrate demonstrates that changes in oxygen concentrations are not sufficient to modulate nirK expression.
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Affiliation(s)
- I E Tosques
- Section of Microbiology, Cornell University, Ithaca, New York 14853, USA
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23
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Glockner AB, Zumft WG. Sequence analysis of an internal 9.72-kb segment from the 30-kb denitrification gene cluster of Pseudomonas stutzeri. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1277:6-12. [PMID: 8950369 DOI: 10.1016/s0005-2728(96)00108-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The DNA segment was sequenced that links the nir-nor and nos gene clusters for denitrification of Pseudomonas stutzeri ATCC 14405. Of 10 predicted gene products, four are putative membrane proteins. Sequence similarity was detected with the subunit III of cytochrome-c oxidase (ORF175), PQQ3 of the biosynthetic pathway for pyrrolo-quinoline quinone (ORF393), S-adenosylmethionine-dependent uroporphyrinogen-III C-methyltransferase (ORF278), the cytochrome cd1 nitrite reductase and the NirF protein involved in the biosynthesis of heme d1 (ORF507), LysR type transcriptional regulators (ORF286), short-chain alcohol dehydrogenases (ORF247), and a hypothetical protein, YBEC, of Escherichia coli (ORF57). The current data together with previous work establish a contiguous DNA sequence of 29.2 kb comprising the supercluster of nos-nir-nor genes for denitrification in this bacterium.
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Affiliation(s)
- A B Glockner
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
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24
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Kwiatkowski AV, Shapleigh JP. Requirement of nitric oxide for induction of genes whose products are involved in nitric oxide metabolism in Rhodobacter sphaeroides 2.4.3. J Biol Chem 1996; 271:24382-8. [PMID: 8798693 DOI: 10.1074/jbc.271.40.24382] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
During denitrification, freely diffusible nitric oxide (NO) is generated for use as a terminal electron acceptor. NO is produced by nitrite reductase (Nir) and reduced to nitrous oxide by nitric oxide reductase (Nor). Using Nir and Nor-deficient mutants of Rhodobacter sphaeroides 2.4.3, we have shown that the endogenous production of NO or the addition of exogenous NO induces transcription of certain genes encoding Nir and Nor. A Nor-deficient strain was found to be capable of expressing wild type levels of nirK-lacZ and norB-lacZ fusions in medium unamended with nitrogen oxides. When this experiment is performed in the presence of hemoglobin, fusion expression is eliminated. NO and the NO-generator, sodium nitroprusside, can induce expression of both fusions in a strain lacking Nir and the consequent ability to produce NO. Sodium nitroprusside cannot induce expression of nirK-lacZ in a strain lacking the transcriptional activator NnrR (nitrite and nitric oxide reductase regulator). Addition of the cyclic nucleotides cAMP and 8-bromoguanosine-cGMP does not result in expression of either fusion. These results demonstrate that denitrifying bacteria produce NO as a signal molecule to activate expression of the genes encoding proteins required for NO metabolism.
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Affiliation(s)
- A V Kwiatkowski
- Department of Microbiology, Cornell University, Ithaca, New York 14853, USA
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25
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26
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Kawasaki S, Arai H, Igarashi Y, Kodama T. Sequencing and characterization of the downstream region of the genes encoding nitrite reductase and cytochrome c-551 (nirSM) from Pseudomonas aeruginosa: identification of the gene necessary for biosynthesis of heme d1. Gene 1995; 167:87-91. [PMID: 8566817 DOI: 10.1016/0378-1119(95)00641-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The nirC and nirF genes were identified downstream from nirSM, the structural genes encoding nitrite reductase (NIR) and cytochrome c-551 from Pseudomonas aeruginosa (Pa). The nirC gene encodes a probable c-type cytochrome with a signal sequence for membrane translocation. The nirF gene codes for a protein of 392 amino acids. A nirF mutant of Pa, constructed by marker exchange mutagenesis, synthesized an inactive NIR protein whose activity was restored by adding purified heme d1. The mutant strain produced an active NIR, when it was transformed by a broad-host-range plasmid carrying nirF. These results showed that the product of nirF was essential for the biosynthesis of heme d1 in Pa.
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Affiliation(s)
- S Kawasaki
- Department of Biotechnology, University of Tokyo, Japan
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27
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Berks BC, Ferguson SJ, Moir JW, Richardson DJ. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1232:97-173. [PMID: 8534676 DOI: 10.1016/0005-2728(95)00092-5] [Citation(s) in RCA: 390] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- B C Berks
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich, UK
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28
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Palmedo G, Seither P, Korner H, Matthews JC, Burkhalter RS, Timkovich R, Zumft WG. Resolution of the nirD Locus for Heme d1, Synthesis of Cytochrome cd1, (Respiratory Nitrite Reductase) from Pseudomonas Stutzeri. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.tb20868.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Abstract
Although the biological conversion of nitrite to nitrate is a well-known process, studies of Nitrobacter populations are hindered by their physiological characteristics. This report describes a new method for detecting and counting Nitrobacter populations in situ with the PCR. Two primers from the 16S rRNA gene were used to generate a 397-bp fragment by amplification of Nitrobacter species DNA. No signal was detected from their phylogenetic neighbors or the common soil bacteria tested. Extraction and purification steps were optimized for minimal loss and maximal purity of soil DNA. The detection threshold and accuracy of the molecular method were determined from soil inoculated with 10, 10(2), or 10(3) Nitrobacter hamburgensis cells per g of soil. Counts were also done by the most-probable-number (MPN)-Griess and fluorescent antibody methods. PCR had a lower detection threshold (10(2) Nitrobacter cells per g of soil) than did the MPN-Griess or fluorescent antibody method. When PCR amplification was coupled with the MPN method, the counting rate reached 65 to 72% of inoculated Nitrobacter cells. Tested on nonsterile soil, this rapid procedure was proved efficient.
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Affiliation(s)
- V Degrange
- Laboratoire d'Ecologie Microbienne, URA Centre National de la Recherche Scientifique 1450, Université Claude Bernard Lyon, Villeurbanne, France
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30
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Philippot L, Clays-Josserand A, Lensi R. Use of tn5 mutants to assess the role of the dissimilatory nitrite reductase in the competitive abilities of two pseudomonas strains in soil. Appl Environ Microbiol 1995; 61:1426-30. [PMID: 16534994 PMCID: PMC1388412 DOI: 10.1128/aem.61.4.1426-1430.1995] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the influence of soil aeration state and plant root presence on the comparative survival of wild-type bacteria and isogenic Tn5 (Nir(sup-)) mutants lacking the ability to synthesize nitrite reductase. Two denitrifying Pseudomonas strains with different nitrite reductase types were used. Enumeration of bacteria in sterile and nonsterile soils was based on differential antibiotic resistance. The validity of the bacterial models studied (i.e., equal growth of wild-type and mutant bacteria under aerobic conditions and significantly better growth of wild-type bacteria under denitrifying conditions) was verified in pure-culture studies. In sterile soil, both strains survived better under aerobic than under anaerobic conditions. The lower efficiency of denitrification than O(inf2) respiration in supporting bacterial growth explained this result, and the physical heterogeneity of soil did not strongly modify the results obtained in pure-culture studies. In nonsterile soil, one of the Pseudomonas strains survived better under anaerobic conditions while the other competed equally with the indigenous soil microflora under aerobic and anaerobic conditions. However, when the Nir(sup-)-to-total inoculant ratios (wild type plus Nir(sup-) mutant) were analyzed, it appeared that the presence of nitrite reductase conferred on both Pseudomonas strains a competitive advantage for anaerobic environment or rhizosphere colonization. This is the first attempt to demonstrate with isogenic nondenitrifying mutants that denitrification can contribute to the persistence and distribution of bacteria in fluctuating soil environments.
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31
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Ye RW, Averill BA, Tiedje JM. Denitrification: production and consumption of nitric oxide. Appl Environ Microbiol 1994; 60:1053-8. [PMID: 8017903 PMCID: PMC201439 DOI: 10.1128/aem.60.4.1053-1058.1994] [Citation(s) in RCA: 162] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- R W Ye
- Department of Microbiology, Michigan State University, East Lansing 48824
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32
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de Boer AP, Reijnders WN, Kuenen JG, Stouthamer AH, van Spanning RJ. Isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in Paracoccus denitrificans. Antonie Van Leeuwenhoek 1994; 66:111-27. [PMID: 7747927 DOI: 10.1007/bf00871635] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
By using the gene encoding the C-terminal part of the cd1-type nitrite reductase of Pseudomonas stutzeri JM300 as a heterologous probe, the corresponding gene from Paracoccus denitrificans was isolated. This gene, nirS, codes for a mature protein of 63144 Da having high homology with cd1-type nitrite reductases from other bacteria. Directly downstream from nirS, three other nir genes were found in the order nirECF. The organization of the nir gene cluster in Pa. denitrificans is different from the organization of nir clusters in some Pseudomonads. nirE has high homology with a S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase (uro'gen III methylase). This methylase is most likely involved in the heme d1 biosynthesis in Pa. denitrificans. The third gene, nirC, codes for a small cytochrome c of 9.3 kDa having high homology with cytochrome c55X of Ps. stutzeri ZoBell. The 4th gene, nirF, has no homology with other genes in the sequence databases and has no relevant motifs. Inactivation of either of these 4 genes resulted in the loss of nitrite and nitric oxide reductase activities but not of nitrous oxide reductase activity. nirS mutants lack the cd1-type nitrite reductase while nirE, nirC and nirF mutants produce a small amount of cd1-type nitrite reductase, inactive due to the absence of heme d1. Upstream from the nirS gene the start of a gene was identified which has limited homology with nosR, a putative regulatory gene involved in nitrous oxide reduction. A potential FNR box was identified between this gene and nirS.
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Affiliation(s)
- A P de Boer
- Department of Molecular and Cellular Biology, BioCentrum Amsterdam, Vrije Universiteit, The Netherlands
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33
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Zumft WG, Braun C, Cuypers H. Nitric oxide reductase from Pseudomonas stutzeri. Primary structure and gene organization of a novel bacterial cytochrome bc complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 219:481-90. [PMID: 7508388 DOI: 10.1111/j.1432-1033.1994.tb19962.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nitric oxide (NO) reductase is an integral membrane component of the anaerobic respiratory chain of Pseudomonas stutzeri that transforms nitrate to dinitrogen (denitrification). The enzyme catalyzes the reduction of NO to nitrous oxide. The structural genes for the NO reductase complex, norC and norB, were sequenced and their organization established by primer extension and Northern blot analysis. The norCB genes encoding the cytochrome c and cytochrome b subunits of the enzyme are contiguous and transcribed as a single 2.0-kb transcript. The promoter region has a canonical recognition motif for the transcriptional activator protein Fnr, centered at -40.5 nucleotides from the initiation site of transcription. No similarity of the derived gene products to known cytochromes of b- or c-type was found in a data bank search. Post-translational processing of the two subunits was limited to the removal of the terminal methionine to leave an N-terminal serine in either subunit. The mature cytochrome c subunit (16508Da, 145 residues) is predicted to be a bitopic protein with a single membrane anchor. The mature cytochrome b subunit (53006Da, 473 residues) is a putatively polytopic, strongly hydrophobic membrane-bound protein with 12 potential transmembrane segments. Several histidine and proline residues were identified with potentially structural and/or functional importance. Mutational inactivation of NO reductase by deletion of norB or the norCB genes affected strongly the in vivo activity of respiratory nitrite reductase (cytochrome cd1), but to a much lesser extent the expression level of this enzyme. In turn, mutational inactivation of the structural gene for cytochrome cd1, nirS, or loss of in vivo nitrite reduction by mutation of the nirT gene, encoding a presumed tetraheme cytochrome, lowered the expression level of NO reductase to 5-20%, but hardly its catalytic activity. The cellular concentration of NO reductase increased again on restoration of nitrite reduction in the nirS::Tn5 mutant MK202 by complementation with nirS or with the heterologous nirK gene, encoding the Cu-containing nitrite reductase from Pseudomonas aureofaciens. Thus, NO may be required as an inducer for its own reductase. Our results show that the nitrite-reducing system and the NO-reducing system are not operating independently from each other but are interlaced by activity modulation and regulation of enzyme synthesis.
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, Germany
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34
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Abstract
Denitrification in bacteria comprises a series of four reduction reactions; for nitrate, nitrite, nitric oxide and nitrous oxide. Nitrogen gas is the final product. The nature of the enzymes catalysing these reactions is described along with the the properties of the underlying electron transport systems. The factors influencing the expression of the reductases for the four reactions are reviewed along with the effect of oxygen on the activities of the enzymes of denitrification. The main emphasis is on observations made with Paracoccus denitrificans and Pseudomonas stutzeri.
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Affiliation(s)
- S J Ferguson
- Department of Biochemistry, University of Oxford, UK
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35
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Jones AM, Hollocher TC. Nitric oxide reductase of Achromobacter cycloclastes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1993. [DOI: 10.1016/0005-2728(93)90121-u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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36
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, Germany
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37
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Jüngst A, Zumft WG. Interdependence of respiratory NO reduction and nitrite reduction revealed by mutagenesis of nirQ, a novel gene in the denitrification gene cluster of Pseudomonas stutzeri. FEBS Lett 1992; 314:308-14. [PMID: 1468562 DOI: 10.1016/0014-5793(92)81495-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An open reading frame, designated nirQ, was identified upstream of nirS, the structural gene for the respiratory nitrite reductase of Pseudomonas stutzeri ZoBell. Its derived gene product (275 amino acids, M(r) = 30,554) shows similarity to the NtrC protein family of transcriptional activators. Deletion-replacement mutagenesis of the nirQ gene resulted in the simultaneous loss of nitrite reduction and NO reduction in vivo. However, both reductases were still synthesized, with only nitrite reductase being active in vitro. NO reductase was overproduced by a factor of about 2. Our results indicate that the systems for nitrite reduction and NO reduction are functionally coupled.
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Affiliation(s)
- A Jüngst
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, Germany
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38
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Ye RW, Averill BA, Tiedje JM. Characterization of Tn5 mutants deficient in dissimilatory nitrite reduction in Pseudomonas sp. strain G-179, which contains a copper nitrite reductase. J Bacteriol 1992; 174:6653-8. [PMID: 1328160 PMCID: PMC207644 DOI: 10.1128/jb.174.20.6653-6658.1992] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Tn5 was used to generate mutants that were deficient in the dissimilatory reduction of nitrite for Pseudomonas sp. strain G-179, which contains a copper nitrite reductase. Three types of mutants were isolated. The first type showed a lack of growth on nitrate, nitrite, and nitrous oxide. The second type grew on nitrate and nitrous oxide but not on nitrite (Nir-). The two mutants of this type accumulated nitrite, showed no nitrite reductase activity, and had no detectable nitrite reductase protein bands in a Western blot (immunoblot). Tn5 insertions in these two mutants were clustered in the same region and were within the structural gene for nitrite reductase. The third type of mutant grew on nitrate but not on nitrite or nitrous oxide (N2O). The mutant of this type accumulated significant amounts of nitrite, NO, and N2O during anaerobic growth on nitrate and showed a slower growth rate than the wild type. Diethyldithiocarbamic acid, which inhibited nitrite reductase activity in the wild type, did not affect NO reductase activity, indicating that nitrite reductase did not participate in NO reduction. NO reductase activity in Nir- mutants was lower than that in the wild type when the strains were grown on nitrate but was the same as that in the wild type when the strains were grown on nitrous oxide. These results suggest that the reduction of NO and N2O was carried out by two distinct processes and that mutations affecting nitrite reduction resulted in reduced NO reductase activity following anaerobic growth with nitrate.
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Affiliation(s)
- R W Ye
- Department of Microbiology and Public Health, Michigan State University, East Lansing 48824
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