Enzymatic synthesis of L-tryptophan from D,L-2-amino-Δ2-thiazoline-4-carboxylic acid and indole by Pseudomonas sp. TS1138 L-2-amino-Δ2-thiazoline-4-carboxylic acid hydrolase, S-carbamyl-L-cysteine amidohydrolase and Escherichia coli L-tryptophanase

L-Tryptophan (L-Trp) is an essential amino acid. It is widely used in medical, health and food products, so a low-cost supply is needed. There are 4 methods for L-Trp production: chemical synthesis, extraction, enzymatic synthesis, and fermentation. In this study, we produced a recombinant bacterial strain pET-tnaA of Escherichia coli which has the L-tryptophanase gene. Using the pET-tnaA E. coli and the strain TS1138 of Pseudomonas sp., a one-pot enzymatic synthesis of L-Trp was developed. Pseudomonas sp. TS1138 was added to a solution of D,L-2-amino-Δ2-thiazoline-4-carboxylic acid (DL-ATC) to convert it to L-cysteine (L-Cys). After concentration, E. coli BL21 (DE 3) cells including plasmid pET-tnaA, indole, and pyridoxal 5’-phosphate were added. At the optimum conditions, the conversion rates of DL-ATC and L-Cys were 95.4% and 92.1%, respectively. After purifying using macroporous resin S8 and NKA-II, 10.32 g of L-Trp of 98.3% purity was obtained. This study established methods for one-pot enzymatic synthesis and separation of L-Trp. This method of producing L-Trp is more environmentally sound than methods using chemical synthesis, and it lays the foundations for industrial production of L-Trp from dl-ATC and indole.     

Carbon source regulation of th ephenazine-α-carboxylic acid synthesis in Pseudomonas aureofaciens

Summary 1. Formation of phenazine--carbolic acid in Pseudomonas aureofaciens is closely related to the carbon sources in the culture medium. 2. With the exception of quinic acid only carbon sources with glyceraldehyde phosphate as metabolic intermediate seem to give rise to phenazine--carboxylic acid production. 3. Monoiodoacetate inhibits this pigment formation.     

Expression and homology modeling of 2′-aminobiphenyl-2,3-diol-1,2-dioxygenase from Pseudomonas stutzeri carbazole degradation pathway

The enzyme 2′-aminobiphenyl-2,3-diol-1,2-dioxygenase (CarB), encoded by two genes (carBa and carBb), is an α₂β₂ heterotetramer that presents meta-cleavage activity toward the hydroxylated aromatic ring in the carbazole degradation pathway from petroleum-degrader bacteria Pseudomonas spp. The 1082-base, pair polymerase chain reaction product corresponding to, carBaBb genes from Pseudomonas stutzeri ATCC 31258 was cloned by site-specific recombination and expressed in high levels in Escherichia coli BL21-SI with a histidine-tag and in native form. The CarB activity toward 2,3-dihydroxybiphenyl was similar for these two constructions. The α₂β₂ 3D model of CarB dioxygenase was proposed by homology modeling using the protocatechuate 4,5-dioxygenase (LigAB) structure as template. Accordingly, His12, His53, and Glu230 coordinate the Fe(II) in the catalytic site at the subunit CarBb. The model also indicates that His182 is the catalytic base responsible for deprotonating one of the hydroxyl group of the substrate by a hydrogen bond. The hydrophobic residues Trp257 and Phe258 in the CarB structure substituted the LigAB amino acid residues Ser269 and Asn270. These data could explain why the CarB was active for 2,3-dihydroxybiphenyl and not for protocatechuate.     

The dimerization of Δ1-piperidine-2-carboxylic acid

The l-amino acid oxidase of Mytilus edulis has been used to oxidize l-lysine on a large scale in the presence of catalase. The alpha-oxo acid derived from lysine cyclizes to a Schiff base, which readily dimerizes. The dimer undergoes spontaneous dehydration and decarboxylation to form 1,2,3,4,5,6,7,8-octahydropyrido[3,2-a]-indolizin-10(4bH)-one. This structure was established by a study of its molecular weight and infrared, nuclear-magnetic-resonance and mass spectra.     

Isolation and genetic improvement of Pseudomonas sp. strain HUT-78, capable of enzymatic production of L-cysteine from DL-2-amino-Δ2-thiazoline-4-carboxylic acid

Microorganisms able to bioconvert DL-2-amino-Δ(2)-thiazoline-4-carboxylic acid (DL-ATC) into L-cysteine were originally isolated from 10 soil samples with DL-ATC as the sole nitrogen source. Ninety-seven L-cysteine-producing bacterial strains were screened out and obtained in pure culture. Among them, a strain, designated as HUT-78, was selected as the best producer, with a molar bioconversion rate of 60%. Based on the 16S rRNA gene sequence analysis, this isolate was placed within the genus Pseudomonas. A novel mutant of this strain with a significantly reduced activity of L-cysteine desulfhydrase, a L-cysteine-decomposing enzyme, was derived by UV-mutagenesis. This mutant, designated as mHUT-78, exhibited a 42% increase in L-cysteine producing activity. Moreover, the bioconversion reactions in both the parent and the mutant strain were significantly accelerated by co-overexpression of the two key enzymes, AtcB and AtcC, involved in the bioconversion reaction.     

Purification and characterization of a novel l-2-amino-Δ2-thiazoline-4-carboxylic acid hydrolase from Pseudomonas sp. strain ON-4a expressed in E. coli

l-2-Amino-Δ²-thiazoline-4-carboxylic acid hydrolase (ATC hydrolase) was purified and characterized from the crude extract of Escherichia coli, in which the gene for ATC hydrolase of Pseudomonas sp. strain ON-4a was expressed. The results of SDS–polyacrylamide gel electrophoresis and gel filtration on Sephacryl S-200 suggested that the ATC hydrolase was a tetrameric enzyme consisted of identical 25-kDa subunits. The optimum pH and temperature of the enzyme activity were pH 7.0 and 30–35°C, respectively. The enzyme did not require divalent cations for the expression of the activity, and Cu²⁺ and Mn²⁺ ions strongly inhibited the enzyme activity. An inhibition experiment by diethylpyrocarbonic acid, 2-hydroxy-5-nitrobenzyl bromide, and N-bromosuccinimide suggested that tryptophan, cysteine, or/and histidine residues may be involved in the catalytic site of this enzyme. The enzyme was strictly specific for the l-form of d,l-ATC and exhibited high activity for the hydrolysis of l-ATC with the values of K _m (0.35 mM) and V _max (69.0 U/mg protein). This enzyme could not cleave the ring structure of derivatives of thiazole, thiazoline, and thiazolidine tested, except for d,l- and l-ATC. These results show that the ATC hydrolase is a novel enzyme cleaving the carbon–sulfur bond in a ring structure of l-ATC to produce N-carbamoyl-l-cysteine.     

Polyhydroxyalkanoate copolyesters produced by Ralstonia eutropha PHB−4 harboring a low-substrate-specificity PHA synthase PhaC2Ps from Pseudomonas stutzeri 1317

Polyhydroxyalkanoate (PHA) copolymers consisting of short-chain-length (SCL) and medium-chain-length (MCL) 3-hydroxyalkanoates (3HA) were produced by recombinant Ralstonia eutropha PHB⁻4 harboring a low-substrate-specificity PHA synthase PhaC2_Ps from Pseudomonas stutzeri 1317. These polyesters, containing a wide range of chain length, were purified and characterized by acetone fractionation, nuclear magnetic resonance (NMR), gel-permeation chromatography (GPC), differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA) and mechanical property studies. The physical properties of the copolymers are dependent largely with 3-hydroxyoctanoate (3HO) content in all PHA.     

Enantioselective Hydrolysis of (RS)-2-Isopropyl-4′-chlorophenylacetonitrile by Pseudomonas sp. B21C9

Pseudomonas sp. B21C9, a new nitrile-degrading microorganism, was isolated from a soil sample. By the hydrolysis of (RS)-iso-propyl- 4´-chlorophenylacetonitrile using cells of B21C9, (S)-2- isopropyl-4´ -chlorophenylacetic acid having excellent optically purity could be obtained. It appeared that the microbial hydrolysis proceeded via stepwise reactions by a nitrile hydratase having poor (S)-selectivity and an amidase having strict (S)-selectivity     

Recruitment of divalent metal ions by incorporation of 4-thio-2′-deoxythymidine or 4-thio-2′-deoxyuridine into DNA

The modified nucleosides 4-thio-2-deoxyuridine (s⁴dU) and 4-thio-2-deoxythymidine (s⁴dT) are incorporated into dinucleosides, and s⁴dT is incorporated into a DNA hairpin loop to provide divalent metal ion binding sites. Binding of two different metal ions to these sites is studied, including Cd(II) as an NMR spectroscopy probe and Cu(II) as a reactive metal ion for DNA cleavage. Binding of Cd(II) to 4-thiouridine (s⁴U) and s⁴dT nucleosides, s⁴dU- and s⁴dT-containing dinucleosides, and a hairpin loop oligonucleotide containing s⁴dT is monitored by following the change in UV-vis absorbance of the thionucleosides at 340 nm and 21 °C in solutions containing 20.0–40 mM buffer, 1.00 M NaCl, and 15.0 mM BaCl₂. Cd(II) binds to the N(3) deprotonated form of s⁴dT with a binding constant (K=1.1×10⁴ M^–1) that is similar to that for Cd(II) binding to d(Tps⁴T) (K=9.2×10³ M^–1). Apparent binding constants (K_app) at pH 7.7 of Cd(II) to dinucleosides d(Gps⁴T), d(s⁴TpG), and d(Gps⁴U) are similar to those of their respective nucleosides s⁴U and s⁴dT, suggesting that neither the phosphate diester nor the second nucleoside has a major effect on Cd(II) binding. Binding of Cd(II) to s⁴U and d(Gps⁴U) is studied by use of ¹¹³Cd NMR and ¹H NMR spectroscopy, respectively. Binding strength and stoichiometry of the Cd(II) complex with d(Gps⁴U) as studied by ¹H NMR spectroscopy are similar to that obtained by UV-vis spectroscopy. Cd(II) binds strongly to s⁴dT in the loop portion of a DNA hairpin loop (K_app=2.7×10³ M^–1 at pH 7.7). However, the hairpin loop is moderately destabilized by Cd(II) binding, with a decrease in T_m of 14 °C in the presence of 10.0 mM Cd(II) as determined by optical melting experiments. Cu(II) oxidizes s⁴dT to form the disulfide of s⁴dT, limiting the usefulness of further studies with Cu(II).Electronic Supplementary Material Supplementary material is available in the online version of this article at .Abbreviations s⁴dU 4-thio-2-deoxyuridine - s⁴dT 4-thio-2-deoxythymidine - s⁴U 4-thiouridine     

Degradation of polyester polyurethane by newly isolated Pseudomonas aeruginosa strain MZA-85 and analysis of degradation products by GC–MS

In this report, a polyester polyurethane (PU) degrading bacterium, designated as strain MZA-85, was isolated from soil through enrichment. The bacterium was identified through 16S rRNA gene sequencing; it was completely matched with Pseudomonas aeruginosa type strain. The degradation of PU film pieces by P. aeruginosa strain MZA-85 was investigated by scanning electron microscopy (SEM), Fourier transformed infra-red spectroscopy (FT-IR) and gel permeation chromatography (GPC). SEM micrographs of PU film pieces, treated with strain MZA-85, revealed changes in the surface morphology. FTIR spectrum showed increase in organic acid functionality and corresponding decrease in ester functional group. GPC results revealed increase in polydispersity, which shows that long chains of polyurethane polymer are cleaved into shorter chains by microbial action. The bacterium was found to produce cell associated esterases based on p-Nitrophenyl acetate (pNPA) hydrolysis assay. 1,4-Butanediol and adipic acid monomers were detected by gas chromatography–mass spectrometry (GC–MS), which were produced as a result of hydrolysis of ester linkages in PU by cell bound esterases. Strain MZA-85 not only depolymerized PU but also mineralized it into CO₂ and H₂O, as indicated by increase in cells growth in the presence of degradation products as well as detection of CO₂ evolution through Sturm test. From the results presented above, it is finally concluded that P. aeruginosa strain MZA-85, as well as its enzymes, can be applied in the process of biochemical monomerization for the pure monomers recycling.     

Conversion of 5′-inosinic acid to inosine by Streptomyces aureus

The production of inosine by microbial conversion of 5′-inosinic acid (IMP) was investigated. Among the various strains of Streptomyces and Bacillus tested, Streptomyces aureus NCIB 9803 was selected for the microbial conversion process due to its high IMP-degrading activity. A maximum conversion yield of 0.43 (86% of the theoretical value) was obtained when IMP was added to the culture medium at 24 h. Kinetic studies with [8-¹⁴C] IMP showed that the difference from the theoretical values mainly attributable to the uptake of inosine by S. aureus.     

Isolation of Microorganisms Growing on Phthalate Esters and Degradation of Phthalate Esters by Pseudomonas acidovorans 256–1

Many microorganisms (17 strains of gram-positive bacteria, 8 strains of gram-negative bacteria, 2 strains of fungi) capable of assimilating di-2-ethyl hexyl phthalate (DEHP) were isolated from soil and other natural sources. When Pseudomonas acidovorans 256–1 among these microorganisms was aerobically cultured in media containing 0.5 % of DEHP, DEHP disappeared completely in 72 hr when assayed gaschromatographically. Most of phthalate esters could be assimilated, regardless of their side-chain types. In addition, branched-alkyl phthalate was assimilated better than n-alkyl phthalate. Based on degradation rate of n-alkyl phthalate in relation to its side chain and carbon number, two peaks were observed in n-alkyl phthalate with four and seven carbon number on its side-chain.     

Kinetics of modification of the mitochondrial succinate-ubiquinone reductase by 5,5′-dithiobis-(2-nitro-benzoic acid)

The kinetic theory of the substrate reaction during modification of enzyme activity previously described by Tsou [Tsou (1988),Adv. Enzymol. Relat. Areas Mol. Biol. 61, 381–436] has been applied to a study of the kinetics of the course of inactivation of the mitochondrial succinate-ubiquinone reductase by 5,5′-dithiobis-(2-nitro-benzoic acid) (DTNB). The results show that the inactivation of this enzyme by DTNB is a conformation-change-type inhibition which involves a conformational change of the enzyme before inactivation. The microscopic rate constants were determined for the reaction of the inactivator with the enzyme. The presence of the substrate provides marked protection of this enzyme against inactivation by DTNB. The modification reaction of the enzyme using DTNB was shown to follow a triphasic course by following the absorption at 412 nm. Among these reactive thiol groups, the fast-reaction thiol group is essential for the enzyme activity. The results suggest that the essential thiol group is situated at the succinate-binding site of the mitochondrial succinate-ubiquinone reductase.     

N-(5′-Phosphopyridoxyl)glutamic acid and N-(5′-phosphopyridoxyl)-2-oxopyrrolidine-5-carboxylic acid and their action on the apoenzyme of aspartate aminotransferase

1. N-(5'-Phosphopyridoxyl)-l-glutamic acid (P-Pxy-Glu, compound I) is readily converted at pH3 into a substance (P-Pxy-Glp, compound II) characterized as N-(5'-phosphopyridoxyl)-2-oxopyrrolidine-5-carboxylic acid. 2. The u.v., i.r. and fluorescence spectra of P-Pxy-Glu and P-Pxy-Glp have been determined; from the u.v. spectra their pK values have been found and compared. 3. The apoenzyme of aspartate aminotransferase is rapidly and irreversibly inactivated by P-Pxy-Glu, but is inactivated more slowly by P-Pxy-Glp. The complex with P-Pxy-Glp is stable enough to be isolated, but it is slowly reactivated in the presence of excess of pyridoxal phosphate. 4. The u.v. spectrum of the complex of apoenzyme and P-Pxy-Glp suggests that it contains a hydrogen bond between the phenolic hydroxyl group and the pyrrolidone nitrogen; this specifies the conformation of most of the molecule of P-Pxy-Glp. This conformation is similar to that previously postulated for the enzyme-glutamate complex except for the side chain of glutamate. Hence both the affinity of P-Pxy-Glp for the apoenzyme and the fact that it is more easily removed than P-Pxy-Glu are explicable.     

Occurrence and metabolism of 1′,4′-trans-diol of abscisic acid

The 1′,4′-trans-diol of abscisic acid was first identified in higher plants with GC-ECD and GC-SIM. The ²H-labelled derivative was converted into abscisic acid (ABA) in pea and avocado, but ²H-labelled ABA was not converted into the diol. These results suggest that the diol is one of the precursors of ABA in higher plants.     

Metabolic Pathway of l-Cysteine Formation from dl-2-Amino-Δ2-Thiazoline-4-Carboxylic Acid by Pseudomonas

Replication factor C (RFC) catalyzes the assembly of circular proliferating cell nuclear antigen (PCNA) clamps around primed DNA, enabling processive synthesis by DNA polymerase. The RFC-like genes, arranged in tandem in the Thermococcus kodakaraensis KOD1 genome, were cloned individually and co-expressed in Escherichia coli cells. T. kodakaraensis KOD1 RFC homologue (Tk-RFC) consists of the small subunit (Tk-RFCS: MW=37.2 kDa) and the large subunit (Tk-RFCL: MW=57.2 kDa). The DNA elongation rate of the family B DNA polymerase from T. kodakaraensis KOD1 (KOD DNA polymerase), which has the highest elongation rate in all thermostable DNA polymerases, was increased about 1.7 times, when T. kodakaraensis KOD1 PCNA (Tk-PCNA) and the Tk-RFC at the equal molar ratio of KOD DNA polymerase were reacted with primed DNA.     

Spectral differentiation of 3,3′-di-O-methylellagic acid from 4,4′-di-O-methylellagic acid

3,3′-and 4,4′-di-O-methylellagic acid were synthesized, and their spectra (IR, UV, ¹³CFT-NMR) were compared with each other. UV and ¹³C FT-NMR spectra were the most useful for distinguishing them.     

Reaction of 3′,5′-di-O-acetyl-2′-deoxyguansoine with hypobromous acid

Hypobromous acid (HOBr) is formed by eosinophil peroxidase and myeloperoxidase in the presence of H₂O₂, Cl^?, and Br^? in the host defense system of humans, protecting against invading bacteria. However, the formed HOBr may cause damage to DNA and its components in the host. When a guanine nucleoside (3′,5′-di-O-acetyl-2′-deoxyguansoine) was treated with HOBr at pH 7.4, spiroiminodihydantoin, guanidinohydantoin/iminoallantoin, dehydro-iminoallantoin, diimino-imidazole, amino-imidazolone, and diamino-oxazolone nucleosides were generated in addition to an 8-bromoguanine nucleoside. The major products were spiroiminodihydantoin under neutral conditions and guanidinohydantoin/iminoallantoin under mildly acidic conditions. All the products were formed in the reaction with HOCl in the presence of Br^?. These products were also produced by eosinophil peroxidase or myeloperoxidase in the presence of H₂O₂, Cl^?, and Br^?. The results suggest that the products other than 8-bromoguanine may also have importance for mutagenesis by the reaction of HOBr with guanine residues in nucleotides and DNA.     

Stabilization of RNA Bulges by Oligonucleotides Containing 2′-Naphthylmethyl-2′-deoxytubercidine

Abstract

A novel nucleoside analogue, 2′-naphthylmethyl-2′-deoxytubercidine, is synthesized and incorporated in oligonucleotides that stabilize bulges in partially complementary RNA.     

Study of the methylation and lack of deamination of deoxyribonucleic acid by N-methyl-N′-nitro-N-nitrosoguanidine

1. DNA labelled with (14)C in the purine residues was prepared by treating newborn rats with [(14)C]formate and killing them for preparation of nucleic acids at 11-17 months. This DNA was incubated with N-methyl-N'-nitro-N-nitrosoguanidine, and then analysed for products of methylation and deamination reactions. 2. Evidence was found for the formation of 7-methylguanine and a smaller amount of 3-methyladenine, and, after preliminary denaturation of the DNA, 1-methyladenine was detected. The presence of cysteine increased the extent of methylation. No evidence was found for the formation of xanthine or hypoxanthine, even at pH5.5.