Reduction of nitro-substituted compounds by native and immobilized Escherichia coli cells

Reduction of nitro-substituted compounds, 1,4-benzodiazepine-2-ones, dibenzo[b,f]-1,4-diazepines, quinolones, and quinoxalinones, by Escherichia coli cells was studied. Physicochemical methods demonstrated the formation of corresponding amines. 4-(p-Nitrophenyl)-1H-6-R-quinolones-2 were nor reduced by Escherichia coli cells. Regiospecific reduction of 2,4-dinitro-5H-11-(p-R-phenyl)-dibenzo[b,f]-1,4-diazepines and 4-(2'-R-3',5'-dinitro)-benzoyl-3,4-dihydroquinoxalinones-2 was shown to result in the formation of 2-nitro-4-amino-5H-11-(p-R-phenyl)-dibenzo[b,f]-1,4-diazepines and 4-(2'-R-3'-nitro-5'-amino)-benzoyl-3,4-dihydroquinoxalinones-2, respectively. Methods for microbiological reduction of nitro compounds and immobilization of Escherichia coli cells into carrageenan and its modified forms were elaborated.     

Synthesis of novel selenium containing sulfa drugs and their antibacterial activities

Synthesis of 3-[4-(N-substituted sulfamoyl)phenyl]-3,4-dihydro-4-oxo-7,9-dimethylpyri-do[3′,2′:4,5]selenolo[3,2-d]pyrimidines,7-[4-(N-substituted sulfamoyl)phenyl]-7,8-dihydro-8-oxo-3,4-diphenylpyrimido[4′,5′:4,5]selenolo [2,3-c]pyridazines and 1-[4-(N-substituted sulfamoyl)phenyl]-1,11-dihydro 11-oxo-4-methylpyrimido[4′,5′:4,5]selenolo[2,3-b]quinolines is reported. 4-Amino-N-pyrimidine-2-ylbenzene sulfonamide (a), 4-amino-N-(2,6-dimethylpyrimidin-4-yl)benzene sulfonamide (b), N-[(4-aminophenyl)sulfonyl] acetamide (c) with N-ethoxymethyleneamino of selenolo pyridine, selenolo pyridazine and selenolo quinoline derivatives respectively were obtained starting from 1-amino-N ⁴-substituted sulfanilamides. Spectroscopic data (IR, ¹H NMR, ¹³C NMR and Mass spectral) confirmed the structure of the newly synthesized compounds. Substituted pyrimidines, pyridazines and quinolines were screened for antibacterial activity against gram-positive and gram-negative bacteria. Selenolo derivative of N-[(4-aminophenyl)sulfonyl] acetamide (substitutent of sulfacetamide c) showed strong bactericidal effect against all the tested organisms. Selenolo[3,2-d]pyrimidin (substitutent a) showed a good bactericidal effect against Serratia marcescens, Staphylococcus aureus and Escherichia coli. Compounds selenolo[2,3-c]pyridazine (substitutent b), selenolo[2,3-b]quinoline(substitutents c)) exhibited a moderate bactericidal effect against Serratia marcescens. None of the synthesized seleno pyridazines has a considerable antimicrobial activity against the tested organisms. The minimum inhibitory concentration (MIC) of the most active compound-3-[4-(N-acetyl sulfamoyl)phenyl]-3,4-dihydro-4-oxo-7,9-dimethylpyrido[3′,2′:4,5]selenolo [3,2-d]pyrimidine was 10 mg ml⁻¹.     

Specificity of recognition sequence forEscherichia coli primase

Summary We have surveyed the frequency of each of 64 trinucleotide permutations at every nucleotide frame located from 1 to 15 nucleotides upstream of primer RNA-DNA transition sites mapped within a 1.5 kb region of the bacteriophage lambda genome and a 1.4 kb region of theEscherichia coli genome. We have demonstrated that in both systems initiation of DNA synthesis strongly correlates with a CAG sequence located 11 nucleotides upstream of the DNA start sites. Based on the examination of various reports of the priming reaction catalyzed byE. coli primase in vivo and in vitro, we propose that (i)E. coli primase itself recognizes a 3′GTC 5′ sequence on the template strand, (ii) DnaB helicase releases the specificity ofE. coli primase and, (iii) the consensus recognition sequence forE. coli primase associated with DnaB helicase is 3′PuPyPy 5′.     

Splitting of the cyclic 3′, 5′-adenosine monophosphate in cell-free system ofEscherichia coli

Broken cells ofEscherichia coli contain an enzyme system breaking down cyclic 3′,5′-adenosine monophosphate (Ado-3′,5′-P). The enzyme splitting this nucleotide is located in the supernatant fraction at 20,000 ×g. Some characteristics of the enzyme were studied. In contrast with the animal enzyme theEscherichia coli enzyme is not inhibited by caffeine.     

Cis-2′, 3′-Dihydrodiol production on flavone B-Ring by Biphenyl Dioxygenase from Pseudomonas pseudoalcaligenes KF707 expressed in Escherichia coli

Escherichia coli JM109 strains expressing either toluene dioxygenase from Pseudomonas putida F1 or biphenyl dioxygenase from Pseudomonas pseudoalcaligenes KF707 were examined for their ability to catalyze flavones. Biphenyl dioxygenase produced metabolites from flavone and 5,7-dihydroxyflavone which were not found in the control experiments. The absorption maxima of UV-visible spectra for the metabolites from flavone and 5,7-dihydroxyflavone were found at 337 and 348 nm respectively by using a photodiode array detector in the HPLC. Liquid chromatography/mass spectroscopy (LC/MS) showed molecular weights 256 and 288 for the metabolites, respectively. The metabolite of flavone, which was isolated and purified from the bacterial culture, was further subjected to analysis by ¹H and ¹³C nuclear magnetic resonance (NMR) spectroscopy. Based on the LC/MS and NMR results, biphenyl dioxygenase inserted oxygen at C2′ and C3′ on the B-ring of flavone, resulting in the formation of flavone cis-2′, 3′-dihydrodiol (2-[3,4-dihydroxy-1.5-cyclohexadienyl]-4H-chromen-4-one). Since this product is not found in Chemical Abstracts, this compound is considered a novel one. In addition, biotransformation of flavones by biphenyl dioxygenase suggested a potential role of bacterial dioxygenase to synthesize novel compounds from plant secondary metabolites. This revised version was published online in June 2006 with corrections to the Cover Date.     

The preparation of a photoreactive analogue of 2′,3′-dideoxyuridine 5′-triphosphate and its use for photoaffinity modification of human replication protein A

A new reagent for photoaffinity modification of biopolymers, 5-[E-N-(2-nitro-5-azidobenzoyl)-3-amino-1-propen-1-yl]-2′,3′-dideoxyuridine 5′-triphosphate (NAB-ddUTP), was synthesized. Like a similar derivative of 2′-deoxyuridine 5′-triphosphate (NAB-dUTP), it was shown to be able to effectively substitute for dTTP in the synthesis of DNA catalyzed by eukaryotic DNA polymerase β and to terminate DNA synthesis. A 5′-³²P-labeled primer with a photoreactive group at the 3′-terminus was derived from NAB-ddUTP and used for photoaffinity labeling of the human replication protein A (RPA). The covalent attachment of RPA p32 and p70 subunits to the labeled primers was demonstrated. NAB-ddUTP is a promising tool for studying the interaction of proteins of the replicative complex with NA in cellular extracts and living cells during the termination of DNA synthesis.     

Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy

Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of ¹³C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using Escherichia coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on [3-¹³C]-pyruvate affords ribonucleotides with site specific labeling at C5′ (~95%) and C1′ (~42%) and minimal enrichment elsewhere in the ribose ring. Enrichment is also achieved at purine C2 and C8 (~95%) and pyrimidine C5 (~100%) positions with minimal labeling at pyrimidine C6 and purine C5 positions. These labeling patterns contrast with those obtained with DL323 E. coli grown on [1, 3-¹³C]-glycerol for which the ribose ring is labeled in all but the C4′ carbon position, leading to multiplet splitting of the C1′, C2′ and C3′ carbon atoms. The usefulness of these labeling patterns is demonstrated with a 27-nt RNA fragment derived from the 30S ribosomal subunit. Removal of the strong magnetic coupling within the ribose and base leads to increased sensitivity, substantial simplification of NMR spectra, and more precise and accurate dynamic parameters derived from NMR relaxation measurements. Thus these new labels offer valuable probes for characterizing the structure and dynamics of RNA that were previously limited by the constraint of uniformly labeled nucleotides.     

Biochemical retrosynthesis of 2′-deoxyribonucleosides from glucose, acetaldehyde, and a nucleobase

2′-Deoxyribonucleosides are important as building blocks for the synthesis of antisense drugs, antiviral nucleosides, and 2′-deoxyribonucleotides for polymerase chain reaction. The microbial production of 2′-deoxyribonucleosides from simple materials, glucose, acetaldehyde, and a nucleobase, through the reverse reactions of 2′-deoxyribonucleoside degradation and the glycolytic pathway, was investigated. The glycolytic pathway of baker’s yeast yielded fructose 1,6-diphosphate from glucose using the energy of adenosine 5′-triphosphate generated from adenosine 5′-monophosphate through alcoholic fermentation with the yeast. Fructose 1,6-diphosphate was further transformed to 2-deoxyribose 5-phosphate in the presence of acetaldehyde by deoxyriboaldolase-expressing Escherichia coli cells via d-glyceraldehyde 3-phosphate. E. coli transformants expressing phosphopentomutase and nucleoside phosphorylase produced 2′-deoxyribonucleosides from 2-deoxyribose 5-phosphate and a nucleobase via 2-deoxyribose 1-phosphate through the reverse reactions of 2′-deoxyribonucleoside degradation. Coupling of the glycolytic pathway and deoxyriboaldolase-catalyzing reaction efficiently supplied 2-deoxyribose 5-phosphate, which is a key intermediate for 2′-deoxyribonucleoside synthesis. 2′-Deoxyinosine (9.9 mM) was produced from glucose, acetaldehyde, and adenine through three-step reactions via fructose 1,6-diphosphate and then 2-deoxyribose 5-phosphate, the molar yield as to glucose being 17.8%.     

One-pot Microbial Synthesis of 2′-deoxyribonucleoside from Glucose, Acetaldehyde, and a Nucleobase

A one-pot enzymatic synthesis of 2′-deoxyribonucleoside from glucose, acetaldehyde, and a nucleobase was established. Glycolysis by baker’s yeast (Saccharomyces cerevisiae) generated ATP which was used to produce d-glyceraldehyde 3-phosphate production from glucose via fructose 1,6-diphosphate. The d-glyceraldehyde 3-phosphate produced was transformed to 2′-deoxyribonucleoside via 2-deoxyribose 5-phosphate and then 2-deoxyribose 1-phosphate in the presence of acetaldehyde and a nucleobase by deoxyriboaldolase, phosphopentomutase expressed in Escherichia coli, and a commercial nucleoside phosphorylase. About 33 mM 2′-deoxyinosine was produced from 600 mM glucose, 333 mM acetaldehyde and 100 mM adenine in 24 h. 2′-Deoxyinosine was produced from adenine due to the adenosine deaminase activity of E. coli transformants.     

Microbial Reductive Dechlorination of Weathered and Exogenous Co-planar Polychlorinated Biphenyls (PCBs) in an Anaerobic Sediment of Venice Lagoon

The occurrence of reductive dechlorination processes towards pre-existing PCBs and five exogenous coplanar PCBs were investigated in a contaminated sediment of Porto Marghera (Venice Lagoon, Italy) suspended, under strictly anaerobic conditions, in water collected from the same site. PCB dechlorination started after five months of incubation, when sulfate initially occurring in the microcosms was completely depleted and methanogenesis was in progress. It was ascribed to sulfate-reducing bacteria. Several pre-existing hexa-, penta- and tetra-chlorinated biphenyls were slowly bioconverted into tri- and di-, ortho-substituted PCBs from the 5th to the 16th month of experiment. Spiked coplanar PCBs, i.e., 3,3′,4,4′-tetrachlorobiphenyl, 3,3′,4,4′,5- and 2,3′,4,4′,5-pentachlorobiphenyls, 3,3′,4,4′,5,5′- and 2,3,3′,4,4′,5-hexachlorobiphenyls, were extensively transformed (by about 90%) into lower chlorinated congeners, such as 3,3′,5,5′-/2,3′,4,4′-tetrachlorobiphenyl, 3,3′,5-, 2,4,4′-, 2,3′,4- and 2,3′,5-trichlorobiphenyl, 3,4-/3,4′- and 3,3′-dichlorobiphenyl and 2-chlorobiphenyl. The reductive dechlorination of spiked PCBs did not influence significantly the biotransformation rate and extent of pre-existing PCBs.     

Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases

A metagenomic cosmid library was prepared in Escherichia coli from DNA extracted from the contents of rabbit cecum and screened for cellulase activities. Eleven independent clones expressing cellulase activities (four endo-β-1,4-glucanases and seven β-glucosidases) were isolated. Subcloning and sequencing analysis of these clones identified 11 cellulase genes; the encoded products of which shared less than 50% identities and 70% similarities to cellulases in the databases. All four endo-β-1,4-glucanases and all seven β-glucosidases, respectively, belonged to glycosyl hydrolase family 5 (GHF 5) and family 3 (GHF 3) and formed two separate branches in the phylogenetic tree. Ten of the 11 cloned cellulases exhibited highest activities at pH 5.5 ∼ 7.0 and 40 ∼ 55°C, a condition similar to that in the rabbit cecum. All the four endo-β-1,4-glucanases could hydrolyze a wide range of β-1,4-, β-1,4/β-1,3- or β-1,3/β-1,6-linked polysaccharides. One endo-β-1, 4-glucanase gene, umcel5G, was overexpressed in E. coli, and the purified recombinant enzyme was characterized in detail. The enzymes cloned in this work represented at least some of the cellulases operating efficiently in the rabbit cecum. This work provides the first snapshot on the cellulases produced by bacteria in rabbit cecum.     

Isolation and potential cancer chemopreventive activities of phenolic compounds of beer

Beer contains a variety of phenolic compounds. During the brewing process, some of these compounds are removed by polyvinylpolypyrrolidone (PVPP) to prevent haze formation. We have analyzed the phytochemical composition of a PVPP residue as well as of unstabilized beer and isolated a total of 51 compounds. Eight structures were identified as novel, i.e., 2-(4′-hydroxyphenyl)-3,5-dihydroxybenzoic acid (6), 2′-(4″-hydroxyphenyl)isoferulic acid ester (12), 1,2,5,7-tetrahydroxyanthraquinone (23) and 4,7-dihydroxy-5-(2′,4′,6′-trihydroxyphenyl)-indan-1,2-dione (24) from the PVPP residue, and catechin-7-O-β-(6″-O-nicotinoyl)-β-D-glucopyranoside (41), ent-epigallo-catechin-(4αto8, 2αtoOto7)catechin (44), ent-epigallocatechin (4αto6, 2αtoOto7)catechin (45) and 2,3-cis-3,4-trans-2-[2,3-trans-3,3′,4′,5,7-pentahydroxyflavan-8-yl]-4-(3,4-dihydroxyphenyl)3,5,7-trihydroxybenzopyran (46) from the unstabilized beer. Most of the compounds were tested for potential cancer chemopreventive activities in in vitro test systems detecting a modulation of carcinogen metabolism (inhibition of phase 1 cytochrome P450 1A (Cyp1A) activity, induction of NAD(P)H:quinone oxidoreductase (QR) activity) and anti-inflammatory mechanisms (inhibition of lipopolysaccharide (LPS)-mediated induction of inducible nitric oxide synthase (iNOS), inhibition of cyclooxygenase 1 (Cox-1) activity). 1,2,5,7-Tetrahydroxyanthraquinone (23) and xanthohumol (25), a prenylated chalcone derived from hop, were identified as the most potent compounds and were additionally tested for inhibition of chemically-induced preneoplastic lesions in an ex vivo mouse mammary gland organ culture model (MMOC). Importantly, both agents inhibited lesion formation with halfmaximal inhibitory concentrations (IC₅₀) of 0.1 and 0.02 μM, respectively. Our results demonstrate that beer is an interesting source of potential cancer chemopreventive agents and should be further investigated with this respect. This revised version was published online in June 2006 with corrections to the Cover Date.     

Large-scale production of CMP-NeuAc and sialylated oligosaccharides through bacterial coupling

A large-scale production system of cytidine 5′-monophospho-N-acetylneuraminic acid (CMP-NeuAc) and sialyloligosaccharides was established by a whole-cell reaction through the combination of recombinant Escherichia coli strains and Corynebacterium ammoniagenes. For the production of CMP-NeuAc, two recombinant E. coli strains were generated that overexpressed the genes of CMP-NeuAc synthetase and CTP synthetase, respectively. C. ammoniagenes contributed to the formation of UTP from orotic acid. CMP-NeuAc was accumulated at 27 mM (17 g/l) after a 27-h reaction starting with orotic acid and N-acetylneuraminic acid. When E. coli cells that overexpressed the α-(2 → 3)-sialyltransferase gene of Neisseria gonorrhoeae were put into the CMP-NeuAc production system, 3′-sialyllactose was accumulated at 52 mM (33 g/l) after an 11-h reaction starting with orotic acid, N-acetylneuraminic acid, and lactose. Almost no oligosaccharide byproducts other than 3′-sialyllactose were observed after the reaction. The production of 3′-sialyllactose at a 5-l jar fermenter scale was almost the same as that at a beaker scale, which indicated the high potential of the 3′-sialyllactose production on an industrial scale. Received: 9 July 1999 / Received revision: 17 September 1999 / Accepted: 10 October 1999     

A critical evaluation of metal-promoted Klenow 3′-5′ exonuclease activity: calorimetric and kinetic analyses support a one-metal-ion mechanism

 Metal-mediated hydrolysis of phosphate esters is a common catalytic pathway in nucleic acid biochemistry. Two distinct models are principally invoked in mechanistic discussions of these reactions for magnesium-dependent nuclease activation: namely, the one-versus two-metal-ion pathways. The 3′-5′ exonuclease domain of the Klenow fragment of Escherichia coli DNA polymerase I is a paradigm for the two-metal-ion mechanism; however, this reaction model is principally based on structural and kinetics experiments employing high concentrations of transition metal analogues and high concentrations of background ammonium sulfate during doping experiments. This prompted us to re-evaluate the metal cofactor stoichiometry of the 3′-5′ exonuclease mechanism for the Klenow fragment by solution kinetics and isothermal titration calorimetry using the natural Mg²⁺ cofactor and salt conditions. Both solution calorimetric and kinetics experiments strongly indicate binding of only one metal ion to the exonuclease active site. Comparative studies with Mn²⁺ also indicate a requirement for one metal ion to effect 3′-5′ exonuclease activity. Received, accepted: 16 March 1998     

Site-specific labeling of nucleotides for making RNA for high resolution NMR studies using an <Emphasis Type="Italic">E. coli</Emphasis> strain disabled in the oxidative pentose phosphate pathway

Escherichia coli (E. coli) is a versatile organism for making nucleotides labeled with stable isotopes (¹³C, ¹⁵N, and/or ²H) for structural and molecular dynamics characterizations. Growth of a mutant E. coli strain deficient in the pentose phosphate pathway enzyme glucose-6-phosphate dehydrogenase (K10-1516) on 2-¹³C-glycerol and ¹⁵N-ammonium sulfate in Studier minimal medium enables labeling at sites useful for NMR spectroscopy. However, ¹³C-sodium formate combined with ¹³C-2-glycerol in the growth media adds labels to new positions. In the absence of labeled formate, both C5 and C6 positions of the pyrimidine rings are labeled with minimal multiplet splitting due to ¹J_C5C6 scalar coupling. However, the C2/C8 sites within purine rings and the C1′/C3′/C5′ positions within the ribose rings have reduced labeling. Addition of ¹³C-labeled formate leads to increased labeling at the base C2/C8 and the ribose C1′/C3′/C5′ positions; these new specific labels result in two- to three-fold increase in the number of resolved resonances. This use of formate and ¹⁵N-ammonium sulfate promises to extend further the utility of these alternate site specific labels to make labeled RNA for downstream biophysical applications such as structural, dynamics and functional studies of interesting biologically relevant RNAs.     

Cation dependent O-methyltransferases from rice

Two lower molecular mass OMT genes (ROMT-15 and -17) were cloned from rice and expressed in Escherichia coli as glutathione S-transferase fusion proteins. ROMT-15 and -17 metabolized caffeoyl-CoA, flavones and flavonols containing two vicinal hydroxyl groups, although they exhibited different substrate specificities. The position of methylation in both luteolin and quercetin was determined to be the 3′ hydroxyl group and myricetin and tricetin were methylated not only at 3′ but also at 5′ hydroxyl groups. ROMT-15 and -17 are cation-dependent and mutation of the predicted metal binding sites resulted in the loss of the enzyme activity, indicating that the metal ion has a critical role in the enzymatic methylation.     

Characterisation of the flavin-free oxygen-tolerant azoreductase from Xenophilus azovorans KF46F in comparison to flavin-containing azoreductases

The flavin-free azoreductase from Xenophilus azovorans KF46F (AzoB), which has been the very first characterized oxygen-tolerant azoreductase, was analyzed in comparison to various recently described flavin-containing azoreductases from different bacterial sources. Sequence comparisons demonstrated that the azoreductase from X. azovorans KF46F is a member of the NmrA family of proteins and demonstrates 30% sequence identity with a NADPH-dependent quinone oxidoreductase from Escherichia coli (encoded by ytfG). In contrast, it was found that the flavin-containing azoreductases from E. coli OY1-2 (AZR), Bacillus sp. OY1-2 (AZR) and related azoreductases all belong to the FMN_red superfamily of enzymes. The substrate specificity of AzoB was reanalyzed in respect to the recently characterized flavin-containing azoreductases, and it was found that purified AzoB converted in addition to different ortho-hydroxy azo compounds [such as Orange II = 1-(4′-sulfophenylazo)-2-naphthol] also the simple non-hydroxylated non-sulfonated azo dye Methyl Red (4′-dimethylaminoazobenzene-2-carboxylic acid), but no indications for the conversion of quinones were obtained. Significant differences were observed in the substrate specificities between AzoB and the flavin-containing azoreductases. The kinetic analysis of the turn-over of Orange II by AzoB suggested an ordered bireactant reaction mechanism which was different from the ping-pong mechanism suggested for the flavin-containing azoreductases.     

Structure of the O-antigen and characterization of the O-antigen gene cluster of Escherichia coli O108 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-d-galacto-non-2-ulosonic (8-epilegionaminic) acid

On mild acid degradation of the lipopolysaccharide of Escherichia coli O108, the O-polysaccharide was isolated and studied by sugar analysis and one- and two-dimensional ¹H- and ¹³C-NMR spectroscopy. The polysaccharide was found to contain an unusual higher sugar, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-d-galacto-non-2-ulosonic acid (di-N-acetyl-8-epilegionaminic acid, 8eLeg5Ac7Ac). The following structure of the tetrasaccharide repeating unit of the polysac-charide was established: →4)-α-8eLegp5Ac7Ac-(2→6)-α-D-Galp-(1→3)-α-L-FucpNAc-(1→3)-α-D-GlcpNAc-(1→. Functions of the E. coli O108 antigen biosynthetic genes, including seven putative genes for synthesis of 8eLeg5Ac7Ac, were assigned by sequencing the O-antigen gene cluster along with comparison with gene databases and known biosynthetic pathways for related nonulosonic acids.