A new nos gene downstream from nosDFY is essential for dissimilatory reduction of nitrous oxide by Rhizobium (Sinorhizobium) meliloti

Relative contributions of different substrates to soil N2O emission and their responses to N addition in a temperate forest

With increasing nitrogen (N) deposition, soil nitrous oxide (N₂O) emission is expected to increase, causing positive feedback to global warming. However, the substrates of soil N₂O emission, especially their responses to N addition, are still unclear. Here, we conducted an in situ ¹⁵N tracing experiment to study the substrates of N₂O (i.e., ammonium-derived, nitrate-derived and organic N-derived N₂O emission) under N addition treatment in a temperate forest in northeast China. Nitrate derived N₂O through denitrification contributed most to the total N₂O emission, pointing to the importance of denitrification under ambient N deposition. NH₄NO₃ addition of 50 kg N ha^-1 yr^-1 significantly increased organic N derived N₂O on the 6th day after N addition, which suggests that heterotrophic nitrification may be the dominating process with higher N deposition rate. However, because soil pH and the examined functional genes did not change after N addition, future studies should be carried out to understand if the increase of heterotrophic nitrification is transient. Our study emphasizes the role of organic N pool in soil N₂O emissions, highlighting the importance of considering the heterotrophic nitrification process while studying soil N cycling or modeling soil N₂O emission.

Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity

Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer.

Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N₂O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices.

IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.

nosX is essential for whole-cell N2O reduction in Paracoccus denitrificans but not for assembly of copper centres of nitrous oxide reductase

Nitrous oxide (N₂O) is a potent greenhouse gas that is produced naturally as an intermediate during the process of denitrification carried out by some soil bacteria. It is consumed by nitrous oxide reductase (N₂OR), the terminal enzyme of the denitrification pathway, which catalyses a reduction reaction to generate dinitrogen. N₂OR contains two important copper cofactors (Cu_A and Cu_Z centres) that are essential for activity, and in copper-limited environments, N₂OR fails to function, contributing to rising levels of atmospheric N₂O and a major environmental challenge. Here we report studies of nosX, one of eight genes in the nos cluster of the soil dwelling α-proteobaterium Paraccocus denitrificans. A P. denitrificans ΔnosX deletion mutant failed to reduce N₂O under both copper-sufficient and copper-limited conditions, demonstrating that NosX plays an essential role in N₂OR activity. N₂OR isolated from nosX-deficient cells was found to be unaffected in terms of the assembly of its copper cofactors, and to be active in in vitro assays, indicating that NosX is not required for the maturation of the enzyme; in particular, it plays no part in the assembly of either of the Cu_A and Cu_Z centres. Furthermore, quantitative Reverse Transcription PCR (qRT-PCR) studies showed that NosX does not significantly affect the expression of the N₂OR-encoding nosZ gene. NosX is a homologue of the FAD-binding protein ApbE from Pseudomonas stutzeri, which functions in the flavinylation of another N₂OR accessory protein, NosR. Thus, it is likely that NosX is a system-specific maturation factor of NosR, and so is indirectly involved in maintaining the reaction cycle of N₂OR and cellular N₂O reduction.

Simultaneous removal characteristics of ammonium and phenol by Alcaligenes faecalis strain WY-01 with the addition of acetate

In this study, simultaneous removal of ammonium plus phenol could be achieved by Alcaligenes faecalis strain WY-01 with the addition of acetate, although acetate delayed the phenol degradation, probably due to the delayed expression of phenol hydroxylase gene under the presence of acetate. Moreover, the successful expression of key enzyme genes in strain WY-01 provided some evidence to illustrate its metabolic pathways of ammonium and phenol under aerobic conditions. Furthermore, SEM was used to clarify the role of acetate in resisting phenol toxicity, and these results demonstrated that strain WY-01 has the ability to form cell flocs when sodium acetate is used as co-substrate for a high concentration of phenol, and these flocs could protect cells against the toxicity of phenol, further enhancing phenol degradation in a high concentration of phenol. All these will provide further insights into the efficacy of strain WY-01 for treating wastewater cocontaminated by ammonium and phenol.

Spontaneous Mutations in the Nitrate Reductase Gene napC Drive the Emergence of Eco-friendly Low-N2O-Emitting Alfalfa Rhizobia in Regions with Different Climates

We have recently shown that commercial alfalfa inoculants (e.g., Sinorhizobium meliloti B399), which are closely related to the denitrifier model strain Sinorhizobium meliloti 1021, have conserved nitrate, nitrite, and nitric oxide reductases associated with the production of the greenhouse gas nitrous oxide (N₂O) from nitrate but lost the N₂O reductase related to the degradation of N₂O to gas nitrogen. Here, we screened a library of nitrogen-fixing alfalfa symbionts originating from different ecoregions and containing N₂O reductase genes and identified novel rhizobia (Sinorhizobium meliloti INTA1-6) exhibiting exceptionally low N₂O emissions. To understand the genetic basis of this novel eco-friendly phenotype, we sequenced and analyzed the genomes of these strains, focusing on their denitrification genes, and found mutations only in the nitrate reductase structural gene napC. The evolutionary analysis supported that, in these natural strains, the denitrification genes were inherited by vertical transfer and that their defective nitrate reductase napC alleles emerged by independent spontaneous mutations. In silico analyses showed that mutations in this gene occurred in ssDNA loop structures with high negative free energy (-ΔG) and that the resulting mutated stem-loop structures exhibited increased stability, suggesting the occurrence of transcription-associated mutation events. In vivo assays supported that at least one of these ssDNA sites is a mutational hot spot under denitrification conditions. Similar benefits from nitrogen fixation were observed when plants were inoculated with the commercial inoculant B399 and strains INTA4-6, suggesting that the low-N₂O-emitting rhizobia can be an ecological alternative to the current inoculants without resigning economic profitability.

NosL is a dedicated copper chaperone for assembly of the CuZ center of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the terminal enzyme of the denitrification pathway of soil bacteria that reduces the greenhouse gas nitrous oxide (N₂O) to dinitrogen. In addition to a binuclear Cu_A site that functions in electron transfer, the active site of N₂OR features a unique tetranuclear copper cluster bridged by inorganic sulfide, termed Cu_Z. In copper-limited environments, N₂OR fails to function, resulting in truncation of denitrification and rising levels of N₂O released by cells to the atmosphere, presenting a major environmental challenge. Here we report studies of nosL from Paracoccus denitrificans, which is part of the nos gene cluster, and encodes a putative copper binding protein. A Paracoccus denitrificans ΔnosL mutant strain had no denitrification phenotype under copper-sufficient conditions but failed to reduce N₂O under copper-limited conditions. N₂OR isolated from ΔnosL cells was found to be deficient in copper and to exhibit attenuated activity. UV-visible absorbance spectroscopy revealed that bands due to the Cu_A center were unaffected, while those corresponding to the Cu_Z center were significantly reduced in intensity. In vitro studies of a soluble form of NosL without its predicted membrane anchor showed that it binds one Cu(i) ion per protein with attomolar affinity, but does not bind Cu(ii). Together, the data demonstrate that NosL is a copper-binding protein specifically required for assembly of the Cu_Z center of N₂OR, and thus represents the first characterised assembly factor for the Cu_Z active site of this key environmental enzyme, which is globally responsible for the destruction of a potent greenhouse gas.

The impact of post-fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil

Forest fires are a regular occurrence in the Mediterranean basin. High severity fires and post-fire management can affect biological, chemical and physical properties of soil, including the composition and abundance of soil microbial communities. Salvage logging is a post-fire management strategy, which involves the removal of burnt wood from land after a fire. The main objective of this work was to evaluate the impact of post-fire salvage logging and microaggregation on soil microbial communities, specifically on the abundance of nitrogen cyclers and, thus, the potential of the soil for microbial nitrogen cycling. The abundance of nitrogen cyclers was assessed by quantification of microbial nitrogen cycling genes in soil DNA, including nifH (involved in nitrogen fixation), nirS/K and nosZ (involved in denitrification), amoA-B and amoA-Arch (involved in bacterial and archaeal nitrification, respectively). It was demonstrated that salvage logging reduced bacterial load post-fire when compared to tree retention control and resulted in significant changes to the abundance of functional bacteria involved in nitrogen cycling. Microbial gene pools involved in various stages of the nitrogen cycle were larger in control soil than in soil subjected to post-fire salvage logging and were significantly correlated with organic matter, available phosphorous, nitrogen and aggregate stability. The microaggregate fraction of the soil, which has been associated with greater organic carbon, was shown to be a hotspot for nitrogen cyclers particularly under salvage logging. The impact of post-fire management strategies on soil microbial communities needs to be considered in relation to maintaining ecosystem productivity, resilience and potential impact on climate change.

Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia

Proteorhodopsin (PR) is a light-driven proton pump that is found in diverse bacteria and archaea species, and is widespread in marine microbial ecosystems. To date, many studies have suggested the advantage of PR for microorganisms in sunlit environments. The ecophysiological significance of PR is still not fully understood however, including the drivers of PR gene gain, retention, and loss in different marine microbial species. To explore this question we sequenced 21 marine Flavobacteriia genomes of polyphyletic origin, which encompassed both PR-possessing as well as PR-lacking strains. Here, we show that the possession or alternatively the lack of PR genes reflects one of two fundamental adaptive strategies in marine bacteria. Specifically, while PR-possessing bacteria utilize light energy ("solar-panel strategy"), PR-lacking bacteria exclusively possess UV-screening pigment synthesis genes to avoid UV damage and would adapt to microaerobic environment ("parasol strategy"), which also helps explain why PR-possessing bacteria have smaller genomes than those of PR-lacking bacteria. Collectively, our results highlight the different strategies of dealing with light, DNA repair, and oxygen availability that relate to the presence or absence of PR phototrophy.

Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica

Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.

Denitrification in Sinorhizobium meliloti

Denitrification is the complete reduction of nitrate or nitrite to N2, via the intermediates nitric oxide (NO) and nitrous oxide (N2O), and is coupled to energy conservation and growth under O2-limiting conditions. In Bradyrhizobium japonicum, this process occurs through the action of the napEDABC, nirK, norCBQD and nosRZDFYLX gene products. DNA sequences showing homology with nap, nirK, nor and nos genes have been found in the genome of the symbiotic plasmid pSymA of Sinorhizobium meliloti strain 1021. Whole-genome transcriptomic analyses have demonstrated that S. meliloti denitrification genes are induced under micro-oxic conditions. Furthermore, S. meliloti has also been shown to possess denitrifying activities in both free-living and symbiotic forms. Despite possessing and expressing the complete set of denitrification genes, S. meliloti is considered a partial denitrifier since it does not grow under anaerobic conditions with nitrate or nitrite as terminal electron acceptors. In the present paper, we show that, under micro-oxic conditions, S. meliloti is able to grow by using nitrate or nitrite as respiratory substrates, which indicates that, in contrast with anaerobic denitrifiers, O2 is necessary for denitrification by S. meliloti. Current knowledge of the regulation of S. meliloti denitrification genes is also included.

FAD binding by ApbE protein from Salmonella enterica: a new class of FAD-binding proteins

The periplasmic protein ApbE was identified through the analysis of several mutants defective in thiamine biosynthesis and was implicated as having a role in iron-sulfur cluster biosynthesis or repair. While mutations in apbE cause decreased activity of several iron-sulfur enzymes in vivo, the specific role of ApbE remains unknown. Members of the AbpE family include NosX and RnfF, which have been implicated in oxidation-reduction associated with nitrous oxide and nitrogen metabolism, respectively. In this work, we show that ApbE binds one FAD molecule per monomeric unit. The structure of ApbE in the presence of bound FAD reveals a new FAD-binding motif. Protein variants that are nonfunctional in vivo were generated by random and targeted mutagenesis. Each variant was substituted in the environment of the FAD and analyzed for FAD binding after reconstitution. The variant that altered a key tyrosine residue involved in FAD binding prevented reconstitution of the protein.

Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach

We characterized operons encoding enzymes involved in denitrification, a nitrogen-cycling process involved in nitrogen losses and greenhouse gas emission, using a metagenomic approach which combines molecular screening and pyrosequencing. Screening of 77,000 clones from a soil metagenomic library led to the identification and the subsequent characterization of nine denitrification gene clusters.

Anaerobic purification, characterization and preliminary mechanistic study of recombinant nitrous oxide reductase from Achromobacter cycloclastes

An overexpression system for nitrous oxide reductase (N(2)OR), an enzyme that catalyzes the conversion of N(2)O to N(2) and H(2)O, has been developed in Achromobacter cycloclastes. Anaerobically purified A. cycloclastes recombinant N(2)OR (AcN(2)OR) has on average 4.5 Cu and 1.2 S per monomer. Upon reduction by methyl viologen, AcN(2)OR displays a high specific activity: 124 U/mg at 25 degrees C. Anaerobically purified AcN(2)OR displays a unique absorption spectrum. UV-visible and EPR spectra, combined with kinetics studies, indicate that the as-purified form of the enzyme is predominately a mixture of the fully-reduced Cu(Z)=[4Cu(I)] state and the Cu(Z)=[3Cu(I).Cu(II)] state, with the latter readily reducible by reduced forms of viologens. CD spectra of the as-purified AcN(2)OR over a range of pH values reveal perturbations of the protein conformation induced by pH variations, although the principal secondary structure elements are largely unaltered. Further, the activity of AcN(2)OR in D(2)O is significantly decreased compared with that in H(2)O, indicative of a significant solvent isotope effect on N(2)O reduction. These data are in good agreement with conclusions reached in recent studies on the effect of pH on catalysis by N(2)OR [K. Fujita, D.M. Dooley, Inorg. Chem. 46 (2007) 613-615].

Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea

N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.

A highly conserved Sinorhizobium meliloti operon is induced microaerobically via the FixLJ system and by nitric oxide (NO) via NnrR

A previously generated collection of 11 Tn5-luxAB insertion mutants of Sinorhizobium meliloti harbouring lux reporter gene fusions induced under microaerobic (1% O2) conditions was further characterized and mapped on the sequenced S. meliloti genome. One highly induced gene fusion from this collection (loe-7) was found to be located in the intergenic region between sma1292, encoding a putative protease/collagenase, and a gene of unknown function (sma1294). The loe-7 fusion had been shown previously to be partially controlled by the oxygen sensor/regulator FixLJ system, but significant ( approximately 40%) Lux activity remained in a fixLJ mutant background. Therefore, a secondary Tn1721 mutagenesis of the loe-7 strain was carried out. Nine Tn1721 ('dark') insertions completely abolishing the Lux activity of the loe-7 fusion under microaerobic conditions were isolated. Surprisingly, five dark insertions mapped in denitrification genes [napA, napC, nirK--two insertions--and sma1245 encoding a NnrR-like transcriptional regulator controlling denitrification in response to nitric oxide (NO)]; Tn1721 insertions in the respiration genes fixG and fixP resulted in a reduced expression of the loe-7-lux fusion, and insertions in the regulatory genes fixJ and fixK1 resulted in low, but still detectable Lux activity. On the contrary, insertions in the norD or norQ genes resulted in constitutive Lux activity. In these mutant strains, NO would be expected to accumulate under microaerobic conditions. NO was found to be able to strongly induce the loe-7-luxAB fusion under microaerobic and aerobic conditions, but only in the presence of the functional nnrR-like gene (sma1245). These results suggest that NO, via the NnrR regulator, can serve as a signal molecule to induce the loe-7-luxAB fusion in concert with the FixLJ system.

Biogenesis of the bacterial respiratory CuA, Cu-S enzyme nitrous oxide reductase

Nitrous oxide reductase (NosZ, EC 1.7.99.6) is the terminal oxidoreductase of a respiratory electron transfer chain that transforms nitrous oxide to dinitrogen. The enzyme carries six Cu atoms. Two are arranged in the mixed-valent binuclear CuA site, and four make up the mu4-sulfide-bridged Cu cluster, CuZ. The biogenesis of a catalytically active NosZ requires auxiliary functions for metal center assembly in the periplasm. Both Tat and Sec pathways share the task to transport the various Nos proteins to their functional sites. Biogenesis of NosZ requires an ABC transporter complex and the periplasmic Cu chaperone NosL. Sustaining whole-cell NosZ function depends on the periplasmic, FAD-containing protein NosX, and the membrane-bound iron-sulfur flavoprotein NosR. Most components with a biogenetic function are now amenable to structural studies.

NosX function connects to nitrous oxide (N2O) reduction by affecting the CuZcenter of NosZ and its activity in vivo

The effect of loss of the 34-kDa periplasmic NosX protein on the properties of N2O reductase was investigated with an N2O-respiration negative, double mutant of the paralogous genes nosX and nirX of Paracoccus denitrificans. In spite of absence of whole-cell N2O-reducing activity, the purified reductase was catalytically active, which attributes NosX a physiological role in sustaining the reaction cycle. N2O reductase exhibited the spectroscopic features of Cu(A) and the redox-inert, paramagnetic state, Cu(Z)*, of the catalytic center. Cu(Z)*, hitherto considered the result of spontaneous reaction of the reductase with dioxygen, attains cellular significance.

Role of a nosX homolog in Streptococcus gordonii in aerobic growth and biofilm formation

Oral streptococci such as Streptococcus gordonii are facultative anaerobes that initiate biofilm formation on tooth surfaces. An isolated S. gordonii::Tn917-lac biofilm-defective mutant contained a transposon insertion in an open reading frame (ORF) encoding a homolog of NosX of Ralstonia eutropha, a putative maturation factor of nitrous oxide reductase. Located downstream are two genes, qor1 and qor2, predicted to encode two putative NADPH quinone oxidoreductases. These three genes are cotranscribed, forming a putative oxidative stress response (osr) operon in S. gordonii. Inactivation of nosX, qor1, or qor2 resulted in biofilm-defective phenotypes. Expression of nosX, measured by the beta-galactosidase activity of the nosX::Tn917-lac mutant, was growth-phase dependent and enhanced when grown under aerobic conditions or in the presence of paraquat. Real-time reverse transcription-PCR revealed that nosX-specific mRNA levels were increased approximately 8.4 and 3.5 fold in biofilm-derived cells grown on plastic and glass, respectively, when compared to planktonic cells. Expression of nosX increased 19.9 fold in cells grown under aerated aerobic conditions and 4.7 fold in cells grown under static aerobic conditions. Two ORFs immediately adjacent to the osr operon encode a putative NADH oxidase (Nox) and a putative thiol-specific antioxidant enzyme (AhpC, for alkyl hydroperoxide peroxidase C). Expression of nox and ahpC was also significantly increased in cells grown under aerated and static aerobic conditions when compared to anaerobic conditions. In addition, nox expression was increased in biofilm cells compared to planktonic cells. These genes may be part of an island that deals with oxidoreductive response, some of which may be important in S. gordonii biofilm formation.

Experimental evidence for plasmid-bornenor-nirgenes inSinorhizobium melilotiJJ1c10

In denitrification, nir and nor genes are respectively required for the sequential dissimilatory reduction of nitrite and nitric oxide to form nitrous oxide. Their location on the pSymA megaplasmid of Sinorhizobium meliloti was confirmed by Southern hybridization of its clones with specific structural gene probes for nirK and norCB. A 20-kb region of pSymA containing the nor-nir genes was delineated by nucleotide sequence analysis. These genes were linked to the nap genes encoding periplasmic proteins involved in nitrate reduction. The nor-nir-nap segment is situated within 30 kb downstream from the nos genes encoding nitrous oxide reduction, with a fix cluster intervening between nir and nos. Most of these predicted nor-nir and accessory gene products are highly homologous with those of related proteobacterial denitrifiers. Functional tests of Tn5 mutants confirmed the requirement of the nirV product and 1 unidentified protein for nitrite reduction as well as the norB-D products and another unidentified protein for nitric oxide reduction. Overall comparative analysis of the derived amino acid sequences of the S. meliloti gene products suggested a close relationship between this symbiotic N2fixer and the free-living non-N2-fixing denitrifier Pseudomonas G-179, despite differences in their genetic organization. This relationship may be due to lateral gene transfer of denitrification genes from a common donor followed by rearrangement and recombination of these genes.Key words: denitrification genes, nitric oxide reductase, nitrite reductase, Rhizobiaceae, Sinorhizobium meliloti.

Requirements for Cu(A) and Cu-S center assembly of nitrous oxide reductase deduced from complete periplasmic enzyme maturation in the nondenitrifier Pseudomonas putida

Bacterial nitrous oxide (N(2)O) reductase is the terminal oxidoreductase of a respiratory process that generates dinitrogen from N(2)O. To attain its functional state, the enzyme is subjected to a maturation process which involves the protein-driven synthesis of a unique copper-sulfur cluster and metallation of the binuclear Cu(A) site in the periplasm. There are seven putative maturation factors, encoded by nosA, nosD, nosF, nosY, nosL, nosX, and sco. We wanted to determine the indispensable proteins by expressing nos genes from Pseudomonas stutzeri in the nondenitrifying organism Pseudomonas putida. An in silico study of denitrifying bacteria revealed that nosL, nosX (or a homologous gene, apbE), and sco, but not nosA, coexist consistently with the N(2)O reductase structural gene and other maturation genes. Nevertheless, we found that expression of only three maturation factors (periplasmic protein NosD, cytoplasmic NosF ATPase, and the six-helix integral membrane protein NosY) together with nosRZ in trans was sufficient to produce catalytically active holo-N(2)O reductase in the nondenitrifying background. We suggest that these obligatory factors are required for Cu-S center assembly. Using a mutational approach with P. stutzeri, we also studied NosA, the Cu-containing outer membrane protein previously thought to have Cu insertase function, and ScoP, a putative membrane-anchored chaperone for Cu(A) metallation. Both of these were found to be dispensable elements for N(2)O reductase biosynthesis. Our experimental and in silico data were integrated in a model of N(2)O reductase maturation.

Lack of the ApbC or ApbE protein results in a defect in Fe-S cluster metabolism in Salmonella enterica serovar Typhimurium

The isc genes function in the assembly of Fe-S clusters and are conserved in many prokaryotic and eukaryotic organisms. In most bacteria studied, the isc operon can be deleted without loss of cell viability, indicating that additional systems for Fe-S cluster assembly must exist. Several laboratories have described nutritional and biochemical defects resulting from mutations in the isc operon. Here we demonstrate that null mutations in two genes of unknown function, apbC and apbE, result in similar cellular deficiencies. Exogenous ferric chloride suppressed these deficiencies in the apbC and apbE mutants, distinguishing them from previously described isc mutants. The deficiencies caused by the apbC and isc mutations were additive, which is consistent with Isc and ApbC's having redundant functions or with Isc and ApbC's functioning in different areas of Fe-S cluster metabolism (e.g., Fe-S cluster assembly and Fe-S cluster repair). Both the ApbC and ApbE proteins are similar in sequence to proteins that function in metal cofactor assembly. Like the enzymes with sequence similarity to ApbC, purified ApbC protein was able to hydrolyze ATP. The data herein are consistent with the hypothesis that the ApbC and ApbE proteins function in Fe-S cluster metabolism in vivo.

Denitrifying genes in bacterial and Archaeal genomes

Denitrification, the reduction of nitrate or nitrite to nitrous oxide or dinitrogen, is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Although the denitrifying ability has been found in microorganisms belonging to numerous groups of bacteria and Archaea, the genes encoding the denitrifying reductases have been studied in only few species. Recent investigations have led to the identification of new classes of denitrifying reductases, indicating a more complex genetic basis of this process than previously recognized. The increasing number of genome sequencing projects has opened a new way to study the genetics of the denitrifying process in bacteria and Archaea. In this review, we summarized the current knowledge on denitrifying genes and compared their genetic organizations by using new sequences resulting from the analysis of finished and unfinished microbial genomes with a special attention paid to the clustering of genes encoding different classes of reductases. In addition, some evolutionary relationships between the structural genes are presented.

The NosX and NirX proteins of Paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase

The nos (nitrous oxide reductase) operon of Paracoccus denitrificans contains a nosX gene homologous to those found in the nos operons of other denitrifiers. NosX is also homologous to NirX, which is so far unique to P. denitrificans. Single mutations of these genes did not result in any apparent phenotype, but a double nosX nirX mutant was unable to reduce nitrous oxide. Promoter-lacZ assays and immunoblotting against nitrous oxide reductase showed that the defect was not due to failure of expression of nosZ, the structural gene for nitrous oxide reductase. Electron paramagnetic resonance spectroscopy showed that nitrous oxide reductase in cells of the double mutant lacked the Cu(A) center. A twin-arginine motif in both NosX and NirX suggests that the NosX proteins are exported to the periplasm via the TAT translocon.

High-resolution physical map of the Sinorhizobium meliloti 1021 pSyma megaplasmid

To facilitate sequencing of the Sinorhizobium meliloti 1021 pSyma megaplasmid, a high-resolution map was constructed by ordering 113 overlapping bacterial artificial chromosome clones with 192 markers. The 157 anonymous sequence tagged site markers (81,072 bases) reveal hypothetical functions encoded by the replicon.

Transcription regulation of the nir gene cluster encoding nitrite reductase of Paracoccus denitrificans involves NNR and NirI, a novel type of membrane protein

The nirIX gene cluster of Paracoccus denitrificans is located between the nir and nor gene clusters encoding nitrite and nitric oxide reductases respectively. The NirI sequence corresponds to that of a membrane-bound protein with six transmembrane helices, a large periplasmic domain and cysteine-rich cytoplasmic domains that resemble the binding sites of [4Fe-4S] clusters in many ferredoxin-like proteins. NirX is soluble and apparently located in the periplasm, as judged by the predicted signal sequence. NirI and NirX are homologues of NosR and NosX, proteins involved in regulation of the expression of the nos gene cluster encoding nitrous oxide reductase in Pseudomonas stutzeri and Sinorhizobium meliloti. Analysis of a NirI-deficient mutant strain revealed that NirI is involved in transcription activation of the nir gene cluster in response to oxygen limitation and the presence of N-oxides. The NirX-deficient mutant transiently accumulated nitrite in the growth medium, but it had a final growth yield similar to that of the wild type. Transcription of the nirIX gene cluster itself was controlled by NNR, a member of the family of FNR-like transcriptional activators. An NNR binding sequence is located in the middle of the intergenic region between the nirI and nirS genes with its centre located at position -41.5 relative to the transcription start sites of both genes. Attempts to complement the NirI mutation via cloning of the nirIX gene cluster on a broad-host-range vector were unsuccessful, the ability to express nitrite reductase being restored only when the nirIX gene cluster was reintegrated into the chromosome of the NirI-deficient mutant via homologous recombination in such a way that the wild-type nirI gene was present directly upstream of the nir operon.

The nos (nitrous oxide reductase) gene cluster from the soil bacterium Achromobacter cycloclastes: cloning, sequence analysis, and expression

The nitrous oxide (N2O) reductase (nos) gene cluster from Achromobacter cycloclastes has been cloned and sequenced. Seven protein coding regions corresponding to nosR, nosZ (structural N2O reductase gene), nosD, nosF, nosY, nosL, and nosX are detected, indicating a genetic organization similar to that of Rhizobium meliloti. To aid homology studies, nosR from R. meliloti has also been sequenced. Comparison of the deduced amino acid sequences with corresponding sequences from other organisms has also allowed structural and functional inferences to be made. The heterologous expression of NosD, NosZ (N2O reductase), and NosL is also reported. A model of the CuA site in N2O reductase, based on the crystal structure of this site in bovine heart cytochrome c oxidase, is presented. The model suggests that a His residue of the CuA domain may be a ligand to the catalytic CuZ site. In addition, the origin of the spectroscopically-observed Cys coordination to CuZ is discussed in terms of the sequence alignment of seven N2O reductases.

Cell biology and molecular basis of denitrification

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.