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Daniel J. Arp - One of the best experts on this subject based on the ideXlab platform.
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interactions of Nitrosomonas europaea and nitrobacter winogradskyi grown in co culture
Archives of Microbiology, 2015Co-Authors: Jose Perez, Peter J. Bottomley, Daniel J. Arp, Alex Buchanan, Brett L Mellbye, Rebecca V Ferrell, Jeff H Chang, Frank W R Chaplen, Luis A SayavedrasotoAbstract:Nitrosomonas europaea and Nitrobacter winogradskyi were grown singly and in co-culture in chemostats to probe for physiological differences between the two growth conditions. Co-culture growth medium containing 60 mM NH4 (+) resulted in a cell density (0.20-0.29 OD600) greater than the sum of the densities in single chemostat cultures, i.e., 0.09-0.14 OD600 for N. europaea with 60 mM NH4 (+)and 0.04-0.06 OD600 for N. winogradskyi with 60 mM NO2 (-). The NO2 (-)- and NH4 (+)-dependent O2 uptake rates, qRT-PCR, and microscopic observations indicated that in co-culture, N. europaea contributed ~0.20 OD600 (~80 %) and N. winogradskyi ~0.05 OD600 (~20 %). In co-culture, the transcriptomes showed that the mRNA levels of 773 genes in N. europaea (30.2 % of the genes) and of 372 genes in N. winogradskyi (11.8 % of the genes) changed significantly. Total cell growth and the analysis of the transcriptome revealed that in co-culture, N. europaea benefits more than N. winogradskyi.
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Global analysis of the Nitrosomonas europaea iron starvation stimulon
Archives of Microbiology, 2012Co-Authors: Neeraja Vajrala, Luis A. Sayavedra-soto, Peter J. Bottomley, Daniel J. ArpAbstract:The importance of iron to the metabolism of the ammonia-oxidizing bacterium Nitrosomonas europaea is well known. However, the mechanisms by which N. europaea acquires iron under iron limitation are less well known. To obtain insight into these mechanisms, transcriptional profiling of N. europaea was performed during growth under different iron availabilities. Of 2,355 N. europaea genes on DNA microarrays, transcripts for 247 genes were identified as differentially expressed when cells were grown under iron limitation compared to cells grown under iron-replete conditions. Genes with higher transcript levels in response to iron limitation included those with confirmed or assigned roles in iron acquisition. Genes with lower transcript levels included those encoding iron-containing proteins. Our analysis identified several potentially novel iron acquisition systems in N. europaea and provided support for the primary involvement of a TonB-dependent heme receptor gene in N. europaea iron homeostasis. We demonstrated that hemoglobin can act as an iron source under iron-depleted conditions for N. europaea . In addition, we identified a hypothetical protein carrying a lipocalin-like domain that may have the ability to chelate iron for growth in iron-limited media.
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Role of a Fur homolog in iron metabolism in Nitrosomonas europaea
BMC microbiology, 2011Co-Authors: Neeraja Vajrala, Luis A. Sayavedra-soto, Peter J. Bottomley, Daniel J. ArpAbstract:Background In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of Nitrosomonas europaea, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family.
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Dissecting iron uptake and homeostasis in Nitrosomonas europaea.
Methods in enzymology, 2011Co-Authors: Luis A. Sayavedra-soto, Neeraja Vajrala, Daniel J. ArpAbstract:Abstract The chemolithoautotroph Nitrosomonas europaea oxidizes about 25 mol of NH 3 for each mole of CO 2 that is converted to biomass using an array of heme and nonheme Fe-containing proteins. Hence mechanisms of efficient iron (Fe) uptake and homeostasis are particularly important for this Betaproteobacterium. Among nitrifiers, N. europaea has been the most studied to date. Characteristics that make N . europaea a suitable model to study Fe uptake and homeostasis are as follows: (a) its sequenced genome, (b) its capability to grow relatively well in 0.2 μ M Fe in the absence of heterologous siderophores, and (c) its amenability to mutagenesis. In this chapter, we describe the methodology we use in our laboratory to dissect Fe uptake and homeostasis in the ammonia oxidizer N. europaea .
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Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea.
FEMS microbiology letters, 2010Co-Authors: Barbara O. Gvakharia, Luis A. Sayavedra-soto, Neeraja Vajrala, Brian Tjaden, Daniel J. ArpAbstract:Bacterial small noncoding RNAs (sRNAs) have been discovered in many genetically well-studied microorganisms and have been shown to regulate critical cellular processes at the post-transcriptional level. In this study, we used comparative genomics and microarray data to analyze the genome of the ammonia-oxidizing bacterium Nitrosomonas europaea for the presence and expression of sRNAs. Fifteen genes encoding putative sRNAs (psRNAs) were identified. Most of these genes showed altered expression in a variety of experimental conditions. The transcripts of two psRNAs were further characterized by mapping their 5'- and 3'-ends and by real-time PCR. The results of these analyses suggested that one of them, psRNA11, is involved in iron homeostasis in N. europaea.
Alan B Hooper - One of the best experts on this subject based on the ideXlab platform.
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EXPRESSION OF TWO Nitrosomonas europaea PROTEINS, HYDROXYLAMINE OXIDOREDUCTASE AND NE0961, IN ESCHERICHIA COLI
2012Co-Authors: Pankaj Mehrotra, Alan B Hooper, Kelli Brunson, David BergmannAbstract:We describe the heterologous expression of the Nitrosomonas europaea genes for hydroxylamine oxidoreductase (HAO) and a membrane protein, NE0961, in Escherichia coli strain BL21(de3), which also constitutively expressed the E. coli ccmA-H genes for c-cytochrome maturation and transport. Both HAO and NE0961 were expressed only in the membrane fraction of cells; only slight insertion of heme into HAO was observed. Co-expression of the genes for HAO and NE0961 was not sufficient for HAO transport to the periplasm or for complete heme insertion.
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Expression, purification, crystallization and preliminary X-ray diffraction of a novel Nitrosomonas europaea cytochrome, cytochrome P460
Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2006Co-Authors: Bradley O. Elmore, Arwen R. Pearson, Carrie M. Wilmot, Alan B HooperAbstract:Cytochrome P460 from Nitrosomonas europaea, a novel mono-heme protein containing an unusual cross-link between a conserved lysine and the porphyrin ring, has been recombinantly expressed and purified from Escherichia coli. The protein crystallizes readily and diffraction to 1.7 A has been obtained in-house. The crystals belong to the trigonal space group P31/221, with unit-cell parameters a = b = 53.3, c = 127.1 A, and contain one monomer in the asymmetric unit.
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nitrosocyanin a red cupredoxin like protein from Nitrosomonas europaea
Biochemistry, 2002Co-Authors: David M. Arciero, Brad S Pierce, Michael P Hendrich, Alan B HooperAbstract:Nitrosocyanin (NC), a soluble, red Cu protein isolated from the ammonia-oxidizing autotrophic bacterium Nitrosomonas europaea, is shown to be a homo-oligomer of 12 kDa Cu-containing monomers. Oligonucleotides based on the amino acid sequence of the N-terminus and of the C-terminal tryptic peptide were used to sequence the gene by PCR. The translated protein sequence was significantly homologous with the mononuclear cupredoxins such as plastocyanin, azurin, or rusticyanin, the type 1 copper-binding region of nitrite reductase, and the binuclear CuA binding region of N2O reductase or cytochrome oxidase. The gene for NC contains a leader sequence indicating a periplasmic location. Optical bands for the red Cu center at 280, 390, 500, and 720 nm have extinction coefficients of 13.9, 7.0, 2.2, and 0.9 mM-1, respectively. The reduction potential of NC (85 mV vs SHE) is much lower than those for known cupredoxins. Sequence alignments with homologous blue copper proteins suggested copper ligation by Cys95, His98,...
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Characterisation of Cytochrome c-552 from Nitrosomonas europaea with EPR and Mössbauer spectroscopy
Hyperfine Interactions (C), 2002Co-Authors: Thomas Teschner, Alan B Hooper, David M. Arciero, R. Benda, V. Schünemann, A. X. Trautwein, Kristoffer K. AnderssonAbstract:The mono-heme protein cytochrome c-552 from Nitrosomonas europaea has been studied by EPR as well as low temperature Mossbauer spectroscopy in fields up to 7 T. The obtained data have been analyzed within the model of Oosterhuis and Lang in the reference frame of Taylor for ferric low spin hemes. Our analysis yields δ = 0.26 mm/s, ΔEQ = 2.06 mm/s, η = 0.9, α = 90°, A/gNμN = (−33, 28, 76) T and g = (1.31, 1.77, 3.34) consistent with an electronic (dxy)2 (dxz)2(dyz)1 ground state typical for Type I model hemes
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Novel bacterial triterpenoids of the hopane series from Nitrosomonas europaea and their significance for the formation of the C35 bacteriohopane skeleton
Tetrahedron Letters, 1999Co-Authors: Myriam Seemann, Alan B Hooper, Philippe Bisseret, Jean-philippe Tritz, Michel RohmerAbstract:Abstract In addition to aminobacteriohopanetriol and adenosylhopane, three new hopanoids were isolated from the bacterium Nitrosomonas europaea: two N-acylaminobacteriohopanetriols, a hopanoid presenting a carbon carbon bond between ribonolactone and hopane and related to a putative intermediate involved in the formation of the C35 bacteriohopane skeleton and finally a condensation product between aminobacteriohopanetriol and trinorbacteriohopan-32-al, an artifact resulting from the autoxidation of the aminotriol.
Luis A. Sayavedra-soto - One of the best experts on this subject based on the ideXlab platform.
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Global analysis of the Nitrosomonas europaea iron starvation stimulon
Archives of Microbiology, 2012Co-Authors: Neeraja Vajrala, Luis A. Sayavedra-soto, Peter J. Bottomley, Daniel J. ArpAbstract:The importance of iron to the metabolism of the ammonia-oxidizing bacterium Nitrosomonas europaea is well known. However, the mechanisms by which N. europaea acquires iron under iron limitation are less well known. To obtain insight into these mechanisms, transcriptional profiling of N. europaea was performed during growth under different iron availabilities. Of 2,355 N. europaea genes on DNA microarrays, transcripts for 247 genes were identified as differentially expressed when cells were grown under iron limitation compared to cells grown under iron-replete conditions. Genes with higher transcript levels in response to iron limitation included those with confirmed or assigned roles in iron acquisition. Genes with lower transcript levels included those encoding iron-containing proteins. Our analysis identified several potentially novel iron acquisition systems in N. europaea and provided support for the primary involvement of a TonB-dependent heme receptor gene in N. europaea iron homeostasis. We demonstrated that hemoglobin can act as an iron source under iron-depleted conditions for N. europaea . In addition, we identified a hypothetical protein carrying a lipocalin-like domain that may have the ability to chelate iron for growth in iron-limited media.
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Role of a Fur homolog in iron metabolism in Nitrosomonas europaea
BMC microbiology, 2011Co-Authors: Neeraja Vajrala, Luis A. Sayavedra-soto, Peter J. Bottomley, Daniel J. ArpAbstract:Background In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of Nitrosomonas europaea, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family.
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Dissecting iron uptake and homeostasis in Nitrosomonas europaea.
Methods in enzymology, 2011Co-Authors: Luis A. Sayavedra-soto, Neeraja Vajrala, Daniel J. ArpAbstract:Abstract The chemolithoautotroph Nitrosomonas europaea oxidizes about 25 mol of NH 3 for each mole of CO 2 that is converted to biomass using an array of heme and nonheme Fe-containing proteins. Hence mechanisms of efficient iron (Fe) uptake and homeostasis are particularly important for this Betaproteobacterium. Among nitrifiers, N. europaea has been the most studied to date. Characteristics that make N . europaea a suitable model to study Fe uptake and homeostasis are as follows: (a) its sequenced genome, (b) its capability to grow relatively well in 0.2 μ M Fe in the absence of heterologous siderophores, and (c) its amenability to mutagenesis. In this chapter, we describe the methodology we use in our laboratory to dissect Fe uptake and homeostasis in the ammonia oxidizer N. europaea .
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Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea.
FEMS microbiology letters, 2010Co-Authors: Barbara O. Gvakharia, Luis A. Sayavedra-soto, Neeraja Vajrala, Brian Tjaden, Daniel J. ArpAbstract:Bacterial small noncoding RNAs (sRNAs) have been discovered in many genetically well-studied microorganisms and have been shown to regulate critical cellular processes at the post-transcriptional level. In this study, we used comparative genomics and microarray data to analyze the genome of the ammonia-oxidizing bacterium Nitrosomonas europaea for the presence and expression of sRNAs. Fifteen genes encoding putative sRNAs (psRNAs) were identified. Most of these genes showed altered expression in a variety of experimental conditions. The transcripts of two psRNAs were further characterized by mapping their 5'- and 3'-ends and by real-time PCR. The results of these analyses suggested that one of them, psRNA11, is involved in iron homeostasis in N. europaea.
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Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane.
Applied and environmental microbiology, 2007Co-Authors: Barbara O. Gvakharia, Luis A. Sayavedra-soto, Peter J. Bottomley, Elizabeth A. Permina, Mikhail S. Gelfand, Daniel J. ArpAbstract:Upon exposure of Nitrosomonas europaea to chloroform (7 μM, 1 h), transcripts for 175 of 2,460 genes were found at higher levels in treated cells than in untreated cells and transcripts for 501 genes were found at lower levels. With chloromethane (3.2 mM, 1 h), transcripts for 67 genes were at higher levels and transcripts for 148 genes were at lower levels. Transcripts for 37 genes were at higher levels following both treatments and included genes for heat shock proteins, σ-factors of the extracytoplasmic function subfamily, and toxin-antitoxin loci. N. europaea has higher levels of transcripts for a variety of defense genes when exposed to chloroform or chloromethane.
H Saiki - One of the best experts on this subject based on the ideXlab platform.
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Distribution of Nitrosomonas europaea and Paracoccus denitrificans Immobilized in Tubular Polymeric Gel for Nitrogen Removal
Applied and environmental microbiology, 2000Co-Authors: Hiroaki Uemoto, H SaikiAbstract:To improve the cooperative removal of nitrogen by Nitrosomonas europaea and Paracoccus denitrificans, we controlled their distribution in a tubular gel. When ethanol was supplied inside the tubular gel as an electron donor, their distributions overlapped in the external region of the gel. By changing the electron donor from ethanol to gaseous hydrogen, the distribution of P. denitrificans shifted to the inside of the tube and was separated from that of N. europaea. The separation resulted in an increase of the oxidation rate of ammonia by 25%.
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Nitrogen removal by tubular gel containing Nitrosomonas europaea and Paracoccus denitrificans.
Applied and environmental microbiology, 1996Co-Authors: Hiroaki Uemoto, H SaikiAbstract:A new bioreactor for the removal of nitrogen from wastewater is described which consists of a tubular polymeric gel containing Nitrosomonas europaea and Paracoccus denitrificans. The outer surface of the tube is in aerobic contact with wastewater containing ammonia, while the inside of the tube is in anaerobic contact with ethanol flowing through the tube. N. europaea oxidizes ammonia to nitrite in the gel, and then P. denitrificans reduces the nitrite to nitrogen gas in the same gel. This concept would be effective for simplifying nitrogen removal systems requiring aerobic and anaerobic operations.
Lisa Y Stein - One of the best experts on this subject based on the ideXlab platform.
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Transcriptome of a Nitrosomonas europaea Mutant with a Disrupted Nitrite Reductase Gene (nirK)
Applied and environmental microbiology, 2006Co-Authors: Catherine Mee-hie Cho, Tingfen Yan, Xueduan Liu, Jizhong Zhou, Lisa Y SteinAbstract:Global gene expression was compared between the Nitrosomonas europaea wild type and a nitrite reductase-deficient mutant using a genomic microarray. Forty-one genes were differentially regulated between the wild type and the nirK mutant, including the nirK operon, genes for cytochrome c oxidase, and seven iron uptake genes. Relationships of differentially regulated genes to the nirK mutant phenotype are discussed.
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Differential regulation of amoA and amoB gene copies in Nitrosomonas europaea
FEMS microbiology letters, 2000Co-Authors: Lisa Y Stein, Luis A. Sayavedra-soto, Norman G Hommes, Daniel J. ArpAbstract:Nitrosomonas europaea contains two nearly identical copies of the operon, amoCAB, which encodes the ammonia monooxygenase (AMO) enzyme. Cells of N. europaea containing single mutations in either amoA or amoB gene copies were incubated in ammonium both prior to and after exposure to acetylene or light. For each strain, the O2 consumption rates and amounts of AmoA polypeptide, the active site-containing subunit of AMO, produced in each strain were determined. Strains carrying a mutation in either the amoA2 or amoB2 genes responded similarly to wild-type cells, but the strains carrying mutations in the amoA1 or amoB1 genes responded differently from the wild-type, or from each other. These results suggest that the copies of amoA and amoB are differentially regulated upon exposure to different external stimuli.
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Loss of Ammonia Monooxygenase Activity in Nitrosomonas europaea upon Exposure to Nitrite
Applied and environmental microbiology, 1998Co-Authors: Lisa Y Stein, Daniel J. ArpAbstract:Nitrosomonas europaea, an obligate ammonia-oxidizing bacterium, lost an increasing amount of ammonia oxidation activity upon exposure to increasing concentrations of nitrite, the primary product of ammonia-oxidizing metabolism. The loss of activity was specific to the ammonia monooxygenase (AMO) enzyme, as confirmed by a decreased rate of NH4+-dependent O2 consumption, some loss of active AMO molecules observed by polypeptide labeling with 14C2H2, the protection of activity by substrates of AMO, and the requirement for copper. The loss of AMO activity via nitrite occurred under both aerobic and anaerobic conditions, and more activity was lost under alkaline than under acidic conditions except in the presence of large concentrations (20 mM) of nitrite. These results indicate that nitrite toxicity in N. europaea is mediated by a unique mechanism that is specific for AMO.