A kinetic study on the bioremediation of sodium cyanide and acetonitrile by free and immobilized cells ofPseudomonas putida

Pseudomonas putida capable of utilizing organic nitrile (acetonitrile) and inorganic cyanide (sodium cyanide) as the sole source of carbon and nitrogen was isolated from contaminated industrial sites and waste water. The bacterium possesses nitrile aminohydrolase (EC 3.5.5.1) and amidase (EC 3.5.1.4), which are involved in the transformation of cyanides and nitriles into ammonia and CO₂ through the formation of amide as an intermediate. Both of the enzymes have a high selectivity and affinity toward the⁻Cn group. The rate of degradation of aceotnitrile and sodium cyanide to ammonia and CO₂ by the calcium-alginate immobilized cells ofP. putida was studied. The rate of reaction during the biodegradation of acetonitrile and sodium cyanide, and the substrate- and product-dependent kinetics of these toxic compounds were studied using free and immobilized cells ofP. putida and modeled using a simple Michaelis-Menten equation.     

Comparative study of amidase production by free and immobilized Escherichia coli cells

Escherichia coli NCIM 2569 was evaluated for its potential for amidase production under submerged fermentation. Among the various amide compounds screened, maximum substrate specificity and enzyme yield (8.1 U/mL) were obtained by using 1% acetamide. Fermentation was carried out at 30°C in shake-flask culture under optimized process conditions. A maximum of 0.52 U/mL of intracellular amidase activity was also obtained from cells incubated for 24 h. Studies were also performed to elucidate the optimal conditions (gel concentration, initial biomass, curing period of beads, and calcium ion concentration in the production medium) for immobilization of whole cells. By using E. coli cells entrapped in alginate, a maximum of 6.2 U/mL of enzyme activity was obtained after 12 h of incubation under optimized conditions. Using the immobilized cells, three repeated batches were carried out successfully, and 85% of the initial enzyme activity was retained in the second and third batches. The study indicated that the immobilized E. coli cells offered certain advantages such as less time for maximum enzyme production, more stability in the enzyme production rate, and repeated use of the biocatalyst.     

Preparation of N-unsubstituted β-ketoamides by Rhodococcus rhodochrous-catalysed hydration of β-ketonitriles

A varied set of N-unsubstituted β-ketoamides, hardly obtainable or non-accessible by non-enzymatic methods, have been synthesized, with good to excellent yields, by the generally fast hydration of the corresponding β-ketonitriles, catalysed by the bacterium Rhodococcus rhodochrous IFO 15564. This bacterium shows nitrile hydratase and amidase activities, the latter being inhibited during its growth phase with diethyl phosphoramidate (DEPA). Optimization of the processes and studies concerning large-scale biotransformations were also carried out. β-Ketoamides exist as keto-enol mixtures whose composition depends on their substituents and varies with solvent polarity.     

Use of nuclear magnetic resonance and gas-liquid chromatography for the study of microbial nitrile-hydratases and amidases

Some microbial strains can hydrolyse many nitriles to the corresponding organic acids by means of two enzymes: a nitrile-hydratase which hydrates the nitrile to the corresponding amide, and an amidase which hydrolyses the amide to the corresponding acid. Two methods are proposed for the assay of the enzymatic activities: proton magnetic resonance spectrometry (n.m.r.) and gas-liquid chromatography (g.l.c.). For the assay of these enzymatic activities (nitrile-hydratase and amidase), g.l.c, was better, because it was more precise and much more sensitive than the n.m.r, method. The examples of acetonitrile and acetamide are described in detail.     

Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media

Preliminary measurements have been made of the volatile compounds emitted by the bacterium E. coli JM109 cultured in the commonly used media Dulbecco's modified Eagle's medium (DMEM) and lysogeny broth (LB) using selected ion flow tube mass spectrometry, SIFT-MS, as a step towards the real time, non-invasive monitoring of accidental infections of mammalian cell cultures. In one procedure, the culture medium alone and the E. coli cells/medium combination were held at 37 °C in bottles sealed with septa for a given time period, usually overnight, to allow the bacterium to proliferate, after which the captured headspace was analysed directly by SIFT-MS. Several compounds were seen to be produced by the E. coli cells that depended on the liquid medium used: when cultured in DMEM, copious amounts of ethanol, acetaldehyde and hydrogen sulphide were produced; in LB ammonia is the major volatile product. In a second procedure, to ensure aerobic conditions prevailed in the cell culture, selected volatile compounds were monitored by SIFT-MS in real time for several hours above the open-to-air E. coli/DMEM culture held at close to 37 °C. The temporal variations in the concentrations of some compounds, which reflect their production rates in the culture, indicate maxima. Thus, the maxima in the ethanol and acetaldehyde production are a reflection of the reduction of glucose from the DMEM by the vigorous E. coli cells and the maximum in the hydrogen sulphide level is an indication of the loss of the sulphur-bearing amino acids from the DMEM. Serendipitously, emissions from DMEM inadvertently infected with the bacterium C. testosteroni were observed when large quantities of ammonia were seen to be produced. The results of this preliminary study suggest that monitoring volatile compounds might assist in the early detection of bacterial infection in large-scale bioreactors.     

Enzyme–Substrate Binding Landscapes in the Process of Nitrile Biodegradation Mediated by Nitrile Hydratase and Amidase

The continuing discharge of nitriles in various industrial processes has caused serious environmental consequences of nitrile pollution. Microorganisms possess several nitrile-degrading pathways by direct interactions of nitriles with nitrile-degrading enzymes. However, these interactions are largely unknown and difficult to experimentally determine but important for interpretation of nitrile metabolisms and design of nitrile-degrading enzymes with better nitrile-converting activity. Here, we undertook a molecular modeling study of enzyme–substrate binding modes in the bi-enzyme pathway for degradation of nitrile to acid. Docking results showed that the top substrates having favorable interactions with nitrile hydratase from Rhodococcus erythropolis AJ270 (ReNHase), nitrile hydratase from Pseudonocardia thermophila JCM 3095 (PtNHase), and amidase from Rhodococcus sp. N-771 (RhAmidase) were benzonitrile, 3-cyanopyridine, and l-methioninamide, respectively. We further analyzed the interactional profiles of these top poses with corresponding enzymes, showing that specific residues within the enzyme’s binding pockets formed diverse contacts with substrates. This information on binding landscapes and interactional profiles is of great importance for the design of nitrile-degrading enzyme mutants with better oxidation activity toward nitriles or amides in the process of pollutant treatments.     

Silica-carrageenan hybrids used for cell immobilization realizing high-temperature degradation of nitrile substrates

In this work the application of hybrid materials, containing TEOS as source of SiO2 and k-carrageenan in different percentage, synthesized by the sol-gel method at room temperature was studied. They were used as matrices for entrapment of whole Bacillus sp. UG-5B cells, producers of thermostable nitrilase. The effect of the surface area and size and quantity of pores in the synthesized materials on the enzyme activity was evaluated. The process of biodegradation of different concentrations of toxic, potentially carcinogenic and mutagenic substrates by the obtained biocatalysts was investigated. The enzyme reaction takes place by the nitrilase pathway, catalysing nitrile hydrolysis directly to the corresponding carboxylic acid, forming ammonia. At batch experiments the influence of the substrate concentration of different nitriles was tested and 20 mM concentration was found most suitable. A two-step biodegradation process in a laboratory-scale column bioreactor of o-, m- and p-tolunitrile as a mixture was followed. After operation of the system for nine hours for the mixture of substrates at a flow rate of 45 mL h⁻¹ and at 60°C, the overall conversion realized was above 90%, showing a good efficiency of the investigated process.     

Biocatalytic Synthesis of Highly Enantiopure 1,4-Benzodioxane-2-carboxylic Acid and Amide

Catalyzed by Rhodococcus erythropolis AJ270, a nitrile hydratase and amidase containing microbial whole-cell catalyst, at 10 ℃ and with the use of methanol as a co-solvent, nitrile and amide biotransformations produce 2S-1,4-benzodioxane-2-carboxamide and 2R-1,4-benzodioxane-2-carboxylic acid in high yields with excellent enantioselectivity.     

Whole‐Cell Biotransformation of Benzene to Phenol Catalysed by Intracellular Cytochrome P450BM3 Activated by External Additives

An Escherichia coli whole‐cell biocatalyst for the direct hydroxylation of benzene to phenol has been developed. By adding amino acid derivatives as decoy molecules to the culture medium, wild‐type cytochrome P450BM3 (P450BM3) expressed in E.coli can be activated and non‐native substrates hydroxylated, without supplementing with NADPH. The yield of phenol reached 59 % when N‐heptyl‐l ‐prolyl‐l ‐phenylalanine (C7‐Pro‐Phe) was employed as the decoy molecule. It was shown that decoy molecules, especially those lacking fluorination, reached the cytosol of E. coli, thus imparting in vivo catalytic activity for the oxyfunctionalisation of non‐native substrates to intracellular P450BM3.     

Partial Molar Volumes and Refractions of Cobalt(III) Complexes, Part 2: Homologous Series of Nitrilopentaamminecobalt(III) Complexes

Both the partial molar volumes (V° _2m refractions (R° _2m ) of the solutes at infinite dilution have been determined at 20 °C for a series of six octahedral N₆-coordinated cobalt(III) species featuring five coordinated ammonia ligands along with a sixth N-coordinated organonitrile of increasing ligand size (from acetonitrile to sebaconitrile). The experimental values for V° _2m are consistent with the relative sizes of the ligands but show larger values than those generated by computer modeling as the size of the cation increases, presumably due to the void space of the cation which increases with the size of the nitrile ligand.     

Stereoselective hydration of (RS)-phenylglycine nitrile by new whole cell biocatalysts

Five new bacterial isolates with stereoselective nitrile hydratase activity against (RS)-2-phenylpropionitrile and (RS)-phenylglycine nitrile were investigated. The permeabilized whole cell isolates selectively hydrate the (S)-enantiomer of phenylglycine nitrile with E values of 1.2–5.4. One isolate, which was identified as Pantoea endophytica, produced pure (S)-phenylglycine (>99% ee) as a result of hydrolysis of (S)-phenylglycine amide by an (S)-specific amidase. Surprisingly, in the hydrolysis of (RS)-phenylglycine nitrile, it was found that the (R)-amide was accumulated in excess (21% ee) despite the nitrile hydratase produced by Pantoea endophytica was (S)-selective. The synthesis of pure (R)-phenylglycine (>99% ee) was achieved in time course studies using another Pantoea sp. with (R)-selective amidase. In the case of Nocardioides sp. the intermediate product, (S)-phenylglycine amide, could be produced (52% ee) without its subsequent hydrolysis into the acid due to the apparent absence of any amidase activity.     

A technique for mycelial development of ectomycorrhizal fungi on agar media

A technique was established to study ectomycorrhizal fungi on agar media. Petri dishes, 60 mm in diameter, containing 10 mL of culture medium covered with a cellophane disk were used for easy collection of the mycelium after growth. For analysis of fungal biomass production, a sterilized cellophane sheet was placed on the medium’s surface. Inoculation was achieved by placing a mycelial block onto the center of the cellophane sheet and then incubating at 25°C in the dark. Colony radial growth was measured and biomass dry wt was determined. Fresh mycelia were homogenized with 10 mL of acetate buffer (pH 5.5) for enzyme analysis. A crude extract was obtained by adding all culture medium to 90 mL of distilled water and homogenizing in a Potter. Reducing sugars, enzyme concentration, and pH were determined. Three fungal strains, Suillus collinitus, Pisosithus arrhizus, and Hebeloma cylindrosporum, were grown in different culture media (potato dextrose agar or Pintro’s medium). Parameters measured over time included glucose concentration, phosphatase activity, biomass, and pH.     

Enantioselective biotransformations of racemic α-substituted phenylacetonitriles and phenylacetamides using Rhodococcus sp. AJ270

Rhodococcus sp. AJ270 is an efficient whole-cell system able to catalyze the stereoselective conversions of racemic α-substituted phenylacetonitriles and amides under very mild conditions into enantiopure carboxylic acids and derivatives. The nitrile hydratase involved generally has a broad substrate spectrum against phenylacetonitriles irrespective of the electronic nature of the α-substituent while the amidase is very sensitive to both the electronic and steric factors of the substituent of amides. The overall enantioselectivity of nitrile hydrolysis is mainly determined by the combination of selectivities of nitrile hydratase and of amidase, with the latter being a major contributor. The amidase has high S-enantiocontrol against amides while the nitrile hydratase exhibits low R-selectivity against nitriles. The scope and limitations of this enantioselective biotransformation process are discussed.     

Characteristics of Sulfobacin A from a Soil Isolate Chryseobacterium gleum

A nonmotile, nonspore-forming, Gram-negative, aerobic, small rod-shaped bacterium, isolated from soil, was identified as Chryseobacterium gleum on the basis of 16S rRNA gene sequence analysis. It was observed to grow luxuriously at pH 9 and tolerate highly alkaline environment up to pH 12. Orange red color was a peculiar character of these cells which on purification obtained 60–80 mg/l and found to be sphingosine type of sulfonolipid “sulfobacin A” on the basis of infrared, nuclear magnetic resonance, and mass spectral data. Inhibition of sulfobacin A synthesis by incorporation of l-cycloserine in culture growth medium suggested presence of serine palmitoyl transferase which is one of the important enzymes involved in its biosynthesis. Sulfobacin A from C. gleum LMG P-22264 exhibited cytotoxicity against four cell lines tested. Maximum activity against human mammary adenocarcinoma cells was indicative of its potential as an anticancer agent.     

Rhodococcus rhodochrous IFO 15564-mediated hydrolysis of alicyclic nitriles and amides: stereoselectivity and use for kinetic resolution and asymmetrization

The stereocourse and the selectivity of the hydrolysis of alicyclic mono- and dinitriles and amides mediated by Rhodococcus rhodochrous IFO 15564 has been examined. The stereochemistry of the substrates, as well as the nature of substituents and presence of double bonds in alicyclic rings greatly affected the rate of hydrolysis by nitrile hydratase and amidase. The rate difference between enantiomers or enantiotopic groups, in some cases, enabled kinetic resolution or asymmetrization. The highest enantioselectivity of amidase was observed in the hydrolysis of 5-benzoyloxy-3-cyclohexene-1-carboxamide (E>200), and both enantiomers of methyl 5-hydroxy-3-cyclohexene-1-carboxylate thus became readily available.     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Purification and characterization of a laccase from the white-rot fungus Trametes multicolor

The wood-degrading fungus Trametes multicolor secretes several laccase isoforms when grown on a simple medium containing copper in the millimolar range for stimulating laccase synthesis. The main isoenzyme laccase II was purified to apparent homogeneity from the culture supernatant by using anion-exchange chromatography and gel filtration. Laccase II is a monomeric glycoprotein with a molecular mass of 63 kDa as determined by sodium dodecylsulfate polyacrylamide gel electrophoresis, contains 18% glycosylation, and has a pI of 3.0. It oxidizes a variety of phenolic substrates as well as ferrocyanide and iodide. The pH optimum depends on the substrate employed and shows a bell-shaped pH activity profile with an optimum of 4.0 to 5.0 for the phenolic substrates, while the nonphenolic substrates ferrocyanide and 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonate) show a monotonic pH profile with a rate decreasing with increasing pH.     

Process Optimisation Studies and Aminonitrile Substrate Evaluation of Rhodococcus erythropolis SET1, A Nitrile Hydrolyzing Bacterium

A comprehensive series of optimization studies including pH, solvent and temperature were completed on the nitrile hydrolyzing Rhodococcus erythropolis bacterium SET1 with the substrate 3-hydroxybutyronitrile. These identified temperature of 25 °C and pH of 7 as the best conditions to retain enantioselectivity and activity. The effect of the addition of organic solvents to the biotransformation mixture was also determined. The results of the study suggested that SET1 is suitable for use in selected organo-aqueous media at specific ratios only. The functional group tolerance of the isolate with unprotected and protected β-aminonitriles, structural analogues of β-hydroxynitriles was also investigated with disappointingly poor isolated yields and selectivity obtained. The isolate was further evaluated with the α- aminonitrile phenylglycinonitrile generating acid in excellent yield and ee (>99 % (S) – isomer and 50 % yield). A series of pH studies with this substrate indicated pH 7 to be the optimum pH to avoid product and substrate degradation.     

Synthesis of Linear (Z)‐α,β‐Unsaturated Esters by Catalytic Cross‐Metathesis. The Influence of Acetonitrile

Kinetically controlled catalytic cross‐metathesis reactions that generate (Z)‐α,β‐unsaturated esters selectively are disclosed. A key finding is that the presence of acetonitrile obviates the need for using excess amounts of a more valuable terminal alkene substrates. On the basis of X‐ray structure and spectroscopic investigations a rationale for the positive impact of acetonitrile is provided. Transformations leading to various E,Z‐dienoates are highly Z‐selective as well. Utility is highlighted by application to stereoselective synthesis of the C1–C12 fragment of biologically active natural product (?)‐laulimalide.     

Production,Purification and Characterization of the Hen Egg-White Lysozyme Inhibitor from Enterobacter cloacae M-1002

Three hen egg-white lysozyme inhibitor producing strains, Enterobacter cloacae M-1002, E. sakazakii M-1204, and Erwinia rhapontici H-55, were isolated from the soils of Taiwan. E. cloacae M-1002 appeared to be a promising inhibitor producing strain. One inhibitor was isolated from the culture broth of this strain. Maximum lysozyme inhibitory activity was obtained when the bacterium was grown aerobically in a medium consisting of 0.75% glucose, 0.25% beef extract, 1.0% polypeptone, and 0.25% sodium L-glutamate (pH 70) at 37 °C after 36–48 hrs. A hen egg-white lysozyme inhibitor was isolated from the culture broth of this strain. The inhibitor was purified from the culture supernatant of E. cloacae M-1002 by ammonium sulfate fractionation, DEAE-Sepharose CL-6B column chromatography and Fractogel TSK HW-55 (S) gel chromatography. Molecular weight of the purified lysozyme inhibitor was estimated to be 18, 000–20, 000 by SDS-PAGE and HPLC, and was composed of 71% amino acid and 23% total sugar. Serine, glycine, and alanine in a 3:2:1 molar ratio were the major amino acids, calculated to be 32.8, 20.3, and 11.4% (mol%), respectively. Glucose and mannose were the major sugar components of the inhibitor. The inhibitor was stable at pH 5 to 8 and was stable under 50 °C. Only hen egg-white lysozyme was inhibited by the purified inhibitor but not the other tested enzymes such as lysozyme of celery, turnip; lytic enzyme of Pseudomonas aeruginosa M-1001; chitinase/lysozyme of P. aeruginosa K-187; or cellulase and xylanase of Streptomyces actuosus A-151 and Aspergillus sp. G-393. The inhibition of lysozyme to the bacterial cell lytic activity by the purified inhibitor was 100%.