Dinitrogen Production from Nitrite by a Nitrosomonas Isolate

A chemolithotrophic ammonium-oxidizing bacterium that was able to reduce ¹⁵NO₂⁻ to ¹⁵N₂ (m/z 30) while oxidizing ammonium under conditions of oxygen stress was isolated from stream sediments. Energy was derived from ammonium oxidation, as evidence by growth, with CO₂ serving as the sole C source. The organism was a gram-negative, motile, short rod that failed to grow either aerobically or anaerobically in heterotroph media. The organism was identified as a Nitrosomonas sp.     

Characterization of 2,2',3-trihydroxybiphenyl dioxygenase, an extradiol dioxygenase from the dibenzofuran- and dibenzo-p-dioxin-degrading bacterium Sphingomonas sp. strain RW1.

A key enzyme in the degradation pathways of dibenzo-p-dioxin and dibenzofuran, namely, 2,2',3-trihydroxybiphenyl dioxygenase, which is responsible for meta cleavage of the first aromatic ring, has been genetically and biochemically analyzed. The dbfB gene of this enzyme has been cloned from a cosmid library of the dibenzo-p-dioxin- and dibenzofuran-degrading bacterium Sphingomonas sp. strain RW1 (R. M. Wittich, H. Wilkes, V. Sinnwell, W. Francke, and P. Fortnagel, Appl. Environ. Microbiol. 58:1005-1010, 1992) and sequenced. The amino acid sequence of this enzyme is typical of those of extradiol dioxygenases. This enzyme, which is extremely oxygen labile, was purified anaerobically to apparent homogeneity from an Escherichia coli strain that had been engineered to hyperexpress dbfB. Unlike most extradiol dioxygenases, which have an oligomeric quaternary structure, the 2,2',3-trihydroxybiphenyl dioxygenase is a monomeric protein. Kinetic measurements with the purified enzyme produced similar Km values for 2,2',3-trihydroxybiphenyl and 2,3-dihydroxybiphenyl, and both of these compounds exhibited strong substrate inhibition. 2,2',3-Trihydroxydiphenyl ether, catechol, 3-methylcatechol, and 4-methylcatechol were oxidized less efficiently and 3,4-dihydroxybiphenyl was oxidized considerably less efficiently.     

Determination of substituted indole derivatives by ion suppression-reverse-phase high-performance liquid chromatography

A method for the separation of substituted indole derivatives has been developed by the use of ion suppression-reversed-phase high-performance liquid chromatography (IS-HPLC). Signal response, selectivity (alpha), retention times (tR), and capacity factors (k') were monitored by varying the mobile phase with respect to methanol composition and pH. Chromatographic parameters including tR, k', K (distribution coefficients), alpha, number of theoretical plates, height equivalent to theoretical plates, and column resolution were calculated and assessed in regard to the suitability of four stationary phases in the analysis of 20 substituted indole derivatives. This work has established the chromatographic foundation needed to analyze over 10 specific enzyme reactions involved in the microbial and plant metabolism of auxins. Quantitative studies on the stability of auxins were possible by employing IS chromatography (ISC). The application of the developed IS chromatographic technique was employed to detect indole-3-acetic acid derived from L-tryptophan in a fluorescent pseudomonad culture.     

Crystallization and initial X-ray diffraction analysis of the multi-domain Brucella blue light-activated histidine kinase LOV-HK in its illuminated state

The pathogenic bacterium Brucella abortus codes for a multi-domain dimeric cytoplasmic histidine kinase called LOV-HK, which is a key blue light-activated virulence factor in this microorganism. The structural basis of the light activation mechanism of this protein remains unclear. In this work, full-length LOV-HK was cloned, expressed and purified. The protein was activated by light and crystallized under a controlled illumination environment. The merge of 14 individual native data sets collected on a single crystal resulted in a complete X-ray diffraction data set to a resolution of 3.70 Å with over 2 million reflections. Crystals belong to space group P2₁2₁2₁, with unit-cell parameters a = 95.96, b = 105.30, c = 164.49 Å with a dimer in the asymmetric unit. Molecular replacement with Phaser using the individual domains as search models allowed for the reconstruction of almost the whole protein. Very recently, improved LOV-HK crystals led to a 3.25-Å resolution dataset. Refinement and model building is underway. This crystal model will represent one of the very few examples of a multi-domain histidine kinase with known structure.     

15N Kinetic Analysis of N2O Production by Nitrosomonas europaea: an Examination of Nitrifier Denitrification

A series of ¹⁵N isotope tracer experiments showed that Nitrosomonas europaea produces nitrous oxide only under oxygen-limiting conditions and that the labeled N from nitrite, but not nitrate, is incorporated into nitrous oxide, indicating the presence of the “denitrifying enzyme” nitrite reductase. A kinetic analysis of the m/z 44, 45, and 46 nitrous oxide produced by washed cell suspensions of N. europaea when incubated with 4 mM ammonium (99% ¹⁴N) and 0.4 mM nitrite (99% ¹⁵N) was performed. No labeled nitrite was reduced to ammonium. All labeled material added was accounted for as either nitrite or nitrous oxide. The hypothesis that nitrous oxide is produced directly from nitrification was rejected since (i) it does not allow for the large amounts of double-labeled (m/z 46) nitrous oxide observed; (ii) the observed patterns of m/z 44, 45, and 46 nitrous oxide were completely consistent with a kinetic analysis based on denitrification as the sole mechanism of nitrous oxide production but not with a kinetic analysis based on both mechanisms; (iii) the asymptotic ratio of m/z 45 to m/z 46 nitrous oxide was consistent with denitrification kinetics but inconsistent with nitrification kinetics, which predicted no limit to m/z 45 production. It is concluded that N. europaea is a denitrifier which, under conditions of oxygen stress, uses nitrite as a terminal electron acceptor and produces nitrous oxide.     

Antioxidants and antioxidative enzymes in wild-type and transgenic Lycopersicon genotypes of different chilling tolerance

The Mehler–Ascorbate–Peroxidase cycle is a protection system against reactive oxygen species (ROS) occurring during over-excitation of the photosynthetic apparatus. In the cultivated tomato, Lycopersicon esculentum, long-term chilling under moderate light leads to oxidation of the Calvin cycle key enzyme, ribulose-1,5-bisphosphate carboxylase (rubisco), presumably by generation of ROS. In contrast, high-altitude lines of the wild tomato species L. peruvianum were tolerant against the same chilling stress. In the present study, we analysed leaf contents of antioxidants (ascorbate, glutathione) and activities of enzymes of the Mehler–Ascorbate–Peroxidase cycle in the two Lycopersicon species. While antioxidant levels and activities of chloroplast superoxide dismutase (SOD) and ascorbate peroxidase (APX), both inducible by chilling stress, were similar in chilling-tolerant and chilling-sensitive genotypes, chilled L. esculentum showed lower glutathione reductase (GR) activities than high-altitude L. peruvianum. We constructed transgenic plants overexpressing an Escherichia coli GR in the chloroplast (approximately 60-fold of the wild-type (WT) activity). However, these plants resembled identical chilling sensitivity of the photosynthetic apparatus as WT plants as measured after a photoinhibition treatment and by the effect of long-term chilling on rubisco activity. We conclude that the Mehler–Ascorbate–Peroxidase cycle is not the limiting factor for the sensitivity of the photosynthetic apparatus of L. esculentum towards long-term chilling under moderate light. We suggest that a possible cause for the higher chilling tolerance of L. peruvianum is prevention of ROS formation by better conversion of light energy to photochemistry at suboptimal temperatures.     

Photo catalogue for the classification of foci in the BALB/c 3T3 cell transformation assay

This catalogue is a display of focus photos representative of the BALB/c 3T3 cell transformation assay (CTA). It is intended as a visual aid for the identification and the scoring of foci in the conduct of the assay. A proper training from experienced personnel together with the protocol reported in this issue and the present photo catalogue will support method transfer and consistency in the assay results.     

Analysis of the human casein phosphoproteome by 2-D electrophoresis and MALDI-TOF/TOF MS reveals new phosphoforms

Mammalian breast milk contains an array of proteins and other nutrients essential for the development of the newborn. In human milk, the caseins (alpha S1, beta and kappa) are a major class of proteins; however, the dynamic range of concentrations in which the various isoforms of each casein exist presents challenges in their characterization. To study human milk casein phosphoforms, we applied traditional two-dimensional polyacrylamide gel electrophoretic (2-DE) separation combined with matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) tandem mass spectroscopic analysis. The abundant beta-casein was resolved as a train of 6 spots differing in phosphorylation level with 0-5 phosphates attached. To study the less abundant alpha S1-casein, a cysteine-tagging enrichment treatment was used prior to 2-DE. A train of 9 spots with 4.4 < p I < 5.3 were identified as alpha S1-casein. This included five previously uncharacterized phosphoforms with up to 8 phosphate groups located in two serine-rich tryptic phosphopeptides ( (27)L-R (51), (69)N-K (98)) consistent with alpha-caseins from various ruminant species. MS/MS analysis of the phosphopeptides released by tryptic digestion enabled identification of the residue-specific order of phosphorylation among the 6 beta-casein and 9 alpha S1-casein phosphoforms. Deamidation of N (47) of alpha S1-casein was also a feature of the MS analysis. This study represents the first comprehensive analysis of the human casein phosphoproteome and reveals a much higher level of phosphorylation than previously recognized. It also highlights the advantages of 2-DE for examining the global pattern of protein phosphoforms and the limitations of attempting to estimate phosphorylation site occupancies from "bottom-up" studies.