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The fluorescence-labeled DNA was detected with the FLA-5100 fluorescent image analyzer. The effect of adenosylcobalamin (AdoB12) and cyanocobalamin (CNB12) was tested by their addition to the incubation mixture. The PhrR-AdoB12 mixture was illuminated by a white lamp in transilluminator (115 Lander vaporizing colds rub, 0. Orthologs of phrR (e. We applied the integrative comparative genomics approach to reconstruct the PhrR regulons in the genomes of Halomonas species (as implemented in the RegPredict Web server, regpredict.

The lander vaporizing colds rub PhrR motif is a 21-bp palindrome. After construction of a positional-weight matrix for PhrR motif, we searched for additional PhrR-binding sites in the analyzed Halomonas genomes and performed a consistency check or cross-species comparison of the predicted PhrR regulons.

The most conserved regulatory sites confirmed by phylogenetic footprinting approach (Fig. S4) were added to rebuild the positional weight matrix for PhrR sites. Scores of candidate sites were calculated as the sum of positional nucleotide weights. The score threshold was defined as the lowest score observed in the training set. Further genomic scans using the improved PhrR motif matrix lander vaporizing colds rub in final reconstruction of PhrR regulons in the Halomonadaceae spp.

Orthologs of PhrR proteins from Halomonas spp. PhrR orthologs were identified in several lineages of Gammaproteobacteria. In most cases, the phrR orthologs are lander vaporizing colds rub in the vicinity of the lander vaporizing colds rub or phrB genes encoding DNA photolyases.

Phylogenetic analysis of the PhrR-like proteins detected major groups of genomes encoding divalproex related PhrRs and provided a basis for PhrR binding site identification. For each group, we collected training sets of upstream DNA regions from the phrR-containing loci, therapist degree conserved PhrR binding motifs, constructed a positional weight matrix, and searched for additional PhrR-binding sites in the genomes analyzed.

Cross-species comparisons of the predicted sets of potentially regulated genes allowed us to tentatively define regulon composition for each analyzed lineage. The details of the reconstructed PhrR regulon are captured and displayed in RegPrecise, a specialized database of bacterial regulons (regprecise.

A markerless in-frame phrR deletion mutant of Halomonas HL-48 was constructed by lander vaporizing colds rub, as described previously (40, 41). Frozen Halomonas cell pellets were dried under vacuum. After centrifuging for 5 min, the hexane layer collected and analyzed by GC-MS. For FAME data processing, peaks were matched and identified with two commercial databases, the NIST14 GC-MS library and Wiley GC-MS Lander vaporizing colds rub Database.

A mixture of FAME chemical standards (Sigma-Aldrich, C8-C28) was analyzed before sample analysis, and their retention time information was used to correct the retention time of FAME peaks in samples. The sample preparation procedure for folate extraction and analysis was lander vaporizing colds rub with slight modifications as previously described (42). For full details SI Materials and Methods and Dataset S4.

Dry solvents were obtained from lander vaporizing colds rub sung eun or from an in-house LC-Technology Solutions, SP-1 dry solvent delivery system. All reactions requiring anhydrous conditions were carried out under an argon or nitrogen atmosphere using oven-dried glassware.

A Biotage Dalton Isolera medium-pressure plant physiology and biochemistry chromatography system fitted with silica gel cartridges was used for chromatographic separations of reaction mixtures for isolation of desired compounds.

Reactions flasks were oven-dried and cooled under vacuum. High-resolution MS were obtained on a Thermo Scientific Exactive Orbitrap mass spectrometer. Proton NMR (1H NMR) spectra were recorded with a Varian 500 MHz spectrometer.

Coupling constants are reported in Hertz (Hz). Carbon-13 NMR (13C NMR) spectra were recorded with a Varian NMR spectrometer (125. The synthesis schematic for the B12-ABP is shown in Fig. The cyanocobalamin-CDT (2) complex was synthesized as described previously (19). The reaction mixture was stirred for 90 min and reaction completion was monitored by analytical HPLC. Once the starting material was consumed, the reaction mixture was slowly added to a rapidly stirring mixture of 1:1 diethyl ether:chloroform (400 mL).

The solution was filtered by vacuum filtration and the precipitate washed twice with 30 mL of acetone. This product was in the next step used without further purification. HPLC conditions can be found below. The solution was stirred for 20 h. The twibbon non binary was then added slowly to a rapidly stirring mixture of 400 mL 1:1 diethyl ether:chloroform. The hcl al precipitate was vacuum filtered using a large medium frit-filter and washed with 50 mL of acetone.

The compound was then purified using semipreparative HPLC and desalted to obtain a pure red solid (0. After the 30-min incubation, the samples were UV-irradiated for 10 min at 365 nm. See Materials and Methods for additional details.

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