Principal Components Analysis as a Tool to Summarise Biotransformation Data: Influence on Cells of Solvent Type and Phase Ratio

The effect of some solvents, present in different amounts, upon whole cells of Rhodococcus erythropolis DCL14 carrying out the biotransformation of (-)-carveol to (-)-carvone was studied. The solvents tested were ethyl butyrate, n-hexane, cyclohexane, iso-octane, n-dodecane, dimethyl sulfoxide, bis(2-ethylhexyl) phthalate and FC-70. The volumes of each solvent corresponded to organic:aqueous phase ratios of 0.0005, 0.0025, 0.005, 0.025 and 0.2. To assess any potential solvent protection towards substrate toxicity, assays were carried out at two initial carveol concentrations (15 and 50 mM). Carvone accumulation was followed by gas chromatography. Cell viability, several aspects of cell morphology and the ability to form clusters were monitored by fluorescence microscopy. Principal components analysis (PCA) was used as a tool to explain the differences in the observations of the multidimensional data set obtained from the multiple conditions. PCA using the different volumes of each solvent as variable suggests that the variability of the observations can be summarised in six components which represent 79.4% of the variance of the data. Conversely, using cell and solvent data to perform the PCA, 97.1% of the variance of the data can be summarised in three components, the first two capturing 91.0% of the information. These components seem to represent solvent toxicity and a protective effect of the solvent from carveol toxicity.     

Principal Components Analysis as a Tool to Summarise Biotransformation Data: Influence on Cells of Solvent Type and Phase Ratio

The effect of some solvents, present in different amounts, upon whole cells of Rhodococcus erythropolis DCL14 carrying out the biotransformation of (?)-carveol to (?)-carvone was studied. The solvents tested were ethyl butyrate, n-hexane, cyclohexane, iso-octane, n-dodecane, dimethyl sulfoxide, bis(2-ethylhexyl) phthalate and FC-70. The volumes of each solvent corresponded to organic:aqueous phase ratios of 0.0005, 0.0025, 0.005, 0.025 and 0.2. To assess any potential solvent protection towards substrate toxicity, assays were carried out at two initial carveol concentrations (15 and 50 mM). Carvone accumulation was followed by gas chromatography. Cell viability, several aspects of cell morphology and the ability to form clusters were monitored by fluorescence microscopy. Principal components analysis (PCA) was used as a tool to explain the differences in the observations of the multidimensional data set obtained from the multiple conditions. PCA using the different volumes of each solvent as variable suggests that the variability of the observations can be summarised in six components which represent 79.4% of the variance of the data. Conversely, using cell and solvent data to perform the PCA, 97.1% of the variance of the data can be summarised in three components, the first two capturing 91.0% of the information. These components seem to represent solvent toxicity and a protective effect of the solvent from carveol toxicity.     

Principal component analysis applied to bacterial cell behaviour in the presence of organic solvents

The behaviour of cells of Rhodococcus erythropolis DCL14, Xanthobacter Py2, Arthrobacter simplex and Mycobacterium sp. NRRL B-3805, in biphasic systems containing different organic solvents was evaluated and compared. The data, obtained mainly by fluorescence microscopy and image analysis, was interpreted using principal components analysis (PCA). With this technique, the variability of the data could be summarised in 7 components, representing 75.8% of the variance of the data. Over a third of the variance could be explained by the first two principal components which represent solvent toxicity. Apparently this is the major factor influencing cell behaviour in an organic:aqueous system. However, factors such as substrate concentration, cell adaptation ability (resulting in morphological changes and aggregation or separation of cells) and membrane composition (specific to each strain) also play an important role in cell resistance to solvent toxicity. The results regarding cell shape indicate that loss of viability occurs, in the tested bacterial strains, after incorporation of molecules of solvent in the cellular membrane. This should result in an increase in membrane fluidity, and thus, in an alteration of cell shape. The ability to form “self-defence” clusters was observed to be different amongst the four strains. X. Py2 showed, in general, a low tendency to form aggregates under the tested conditions; A. simplex and R. erythropolis aggregated mainly in the presence of low log P solvents; and Mycobacterium. sp. cells showed a high ability to aggregate.     

Principal component analysis applied to bacterial cell behaviour in the presence of organic solvents

The behaviour of cells of Rhodococcus erythropolis DCL14, Xanthobacter Py2, Arthrobacter simplex and Mycobacterium sp. NRRL B-3805, in biphasic systems containing different organic solvents was evaluated and compared. The data, obtained mainly by fluorescence microscopy and image analysis, was interpreted using principal components analysis (PCA). With this technique, the variability of the data could be summarised in 7 components, representing 75.8% of the variance of the data. Over a third of the variance could be explained by the first two principal components which represent solvent toxicity. Apparently this is the major factor influencing cell behaviour in an organic:aqueous system. However, factors such as substrate concentration, cell adaptation ability (resulting in morphological changes and aggregation or separation of cells) and membrane composition (specific to each strain) also play an important role in cell resistance to solvent toxicity. The results regarding cell shape indicate that loss of viability occurs, in the tested bacterial strains, after incorporation of molecules of solvent in the cellular membrane. This should result in an increase in membrane fluidity, and thus, in an alteration of cell shape. The ability to form “self-defence” clusters was observed to be different amongst the four strains. X. Py2 showed, in general, a low tendency to form aggregates under the tested conditions; A. simplex and R. erythropolis aggregated mainly in the presence of low log P solvents; and Mycobacterium. sp. cells showed a high ability to aggregate.     

Molecular Dynamics Simulation of Linear Polymers in a Solvent

This paper reports a series of simulations of a single linear polymer chain in solution. Both the monomer units and the solvent particles are represented by “beads” which interact via a purely repulsive shifted Lennard-Jones potential; the chains themselves are constructed by linking beads with relatively stiff elastic bonds. The chain lenghts range from 8 to 48 beads, and the total system size is between 1000 and 14000 beads. The static and dynamic properties of the polymer chains obtained from long simulations of these systems (over 10⁶ timesteps) are discussed, and the size and density dependence of the chain behavior examined.     

非水相脂肪酶催化有机硅醇的酯化反应

非水相酶催化是酶工程研究热点之一。本文介绍了来自Ｃ．ｃｙｌｉｎｄｒａｃｅａ的脂肪酶催化有机硅醇和脂肪酸的酯化反应。该酶可催化有机硅醇与脂肪酸的酯化反应,并对不同链长的脂肪酸底物、有机溶剂极性及水含量等进行了初步研究。     

Monitoring surface chemical changes in the bacterial cell wall: multivariate analysis of cryo-x-ray photoelectron spectroscopy data

Gram-negative bacteria can alter the composition of the lipopolysaccharide (LPS) layer of the outer membrane as a response to different growth conditions and external stimuli. These alterations can, for example, promote attachment to surfaces and biofilm formation. The changes occur in the outermost layer of the cell and may consequently influence interactions between bacterial cells and surrounding host tissue, as well as other surfaces. Microscopic analyses, fractionation of bacterial cells, or other traditional microbiological assays have previously been used to study these alterations. These methods can, however, be time consuming and do not always give detailed chemical information about the bacterial cell surface. We here present an analytical method that provides chemical information on the outermost portion of bacterial cells with respect to protein, peptidoglycan, lipid, and polysaccharide content. The method involves cryo-x-ray photoelectron spectroscopy analyses of the outermost portion (within ～10 nm of the surface) of intact bacterial cells followed by a multivariate curve resolution analysis of carbon spectra. It can be used as a tool for characterizing and monitoring variations in the chemical composition of bacterial cell walls or of isolated outer membrane vesicles, variations that result from e.g. mutations or external stimuli. The method enabled us to predict accurately the alterations in polysaccharide content and surface chemistries of a set of well characterized Escherichia coli LPS mutants. The described approach may moreover be applied to monitor surface chemical composition of other biological samples.     

Enzymatic Production of Alkyl Esters Through Lipase-Catalyzed Transesterification Reactions in Organic Solvents: Solvent Effects and Prediction Capabilities of Equilibrium Conversions

The solvent effect on the equilibrium position of the transesterification reaction of hexanol with ethyl acetate catalyzed by a lipase has been investigated in a variety of non-polar and polar solvents - and binary mixtures. The results obtained indicate that the solvent effect on the equilibrium conversion is very small as compared to that for the direct esterification reactions.

Equilibrium conversions were then predicted using the equilibrium constant for the reaction obtained from Gibbs free energy of formation information for reactants and products in combination with the UNIFAC activity coefficient model. A solvent independent equilibrium conversion was obtained, which was in good agreement with the observed average value for all solvents. This indicates that UNIFAC provides satisfactory estimates of the activity coefficients but its group contribution structure does not allow the prediction of the small differences in conversion among the solvents examined.

Finally plots of these conversions versus the solvent octanol/water partition coefficient or the solubility of water in the solvent, that provide the correct trend in direct esterification reactions, did not achieve the same for transesterification.     

Variation in leaves and petals of Ranunculus subgenus Batrachium on the Aegean Islands, analysed by multivariate analysis

Variation in leaves and petals was studied using canonical variate and cluster analyseS. In total of 33 populations from eight islands leaf variation in laminar, floating leaves was studied in Ranunculus peltatus subsp. peltatus, subsp. baudotii and subsp. saniculifolius, and in R. Tripartitus, all of which are heterophyllous in the Aegean area. The petal data set also included the homophyllous R. Trichophyllus. The results of the analyses show that the populations are morphologically well differentiated and that petal shape has a tendency to discriminate between the populations somewhat better than leaf shape does. There was no basis for subdividing the populations into taxa on these characterS. Analyses showed that up to 70% of the variation was distributed between populations, the remainder (5–18%) being within populations.     

Immobilization of Lipase from Rhizopus Niveus: A Way to Enhance its Synthetic Activity in Organic Solvent

Lipase (EC 3.1.1.3) from Rhizopus niveus was immobilized by physical adsorption on various carriers, including different types of Celite, Spherosil and Duolite. After the enzyme immobilization, the recovered hydrolytic and synthetic activities on the different carriers were then determined. The results showed that the highest synthetic activity was obtained when Duolite XAD 761 was used as the carrier. However the recovered hydrolytic activity after the immobilization on this resin was relatively low although this carrier showed the best protein loading capacity. The highest recovered hydrolytic activity was observed when the lipase was immobilized on Celite Hyflo-Supercel using an immobilization buffer adjusted to pH 4. The comparison of the free and immobilized lipase specific activities suggest that the immobilization on Celite Hyflo-Supercel, Spherosil XOA 200 and silica has enhanced the lipase hydrolytic activity. On the other hand, the use of the lipase immobilized on Duolite XAD 761 as biocatalyst of synthetic reaction, compared to that of the free enzyme, allows the reaction initial velocity to be increased 12.2-fold. In addition, the synthetic activity of the lipase immobilized on Duolite XAD 761 was shown to be maximum at a water activity in the range of 0.32-0.52.     

加速溶剂提取法提取娑罗子中的七叶皂苷

为了探讨快速溶剂提取法(ASE)提取娑罗子中七叶皂苷的可行性,并比较该方法与回流提取法和超声提取法的优越性。本文以娑罗子中的四种七叶皂苷的提取率为指标,以高效液相色谱法(HPLC)为检测方法,用单因素考察法对加速溶剂提取法从娑罗子中提取七叶皂苷的工艺条件进行优化。结果通过实验我们优选出加速溶剂提取法从娑罗子中提取七叶皂苷的最佳条件,即提取溶剂为70%甲醇,提取温度为100℃,静态提取时间为7 min,提取次数为1次。由此可以定论加速溶剂提取法可以快速、高效地提取娑罗子中的七叶皂苷类化合物。     

Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis

A proteomics approach combined with multivariate data analysis was used to examine the hepatotoxic effect of hydrazine in 30 male Sprague Dawley rats, assigned to four treatment groups and two control groups. Liver samples from the individual animals were resolved by two-dimensional differential gel electrophoresis (2-D DIGE) and protein patterns from the 2-D gels were analyzed by principal component analysis (PCA) and partial least squares regression (PLSR). The PCA plot was able to describe the variation in the protein expression related to dose and time, by separation or clustering of different animal groups. PLSR followed by variable selection (Jack-knifing) was used to select proteins that varied significantly in relation to the dose related response of the hydrazine treatment. The 10 up-regulated and 10 down-regulated proteins with highest rank in the PLSR model were identified by mass spectrometry. Hydrazine treatment induced altered expression of proteins related to lipid metabolism, Ca(2+) homeostasis, thyroid hormone pathways and stress response. Several of the identified proteins have not previously been implicated in hydrazine toxicity and may thus be regarded as new potential biomarkers of induced liver toxicity.     

Solvent tolerant Pseudomonads as a source of novel lipases for applications in non-aqueous systems

Abstract

Lipases (triacylglycerol acylhydrolases, EC 3.1.1.3) are ubiquitous biocatalysts known to catalyze the hydrolysis of water insoluble triglycerides in aqueous medium and carry out the reverse reaction (synthesis) under organic solvent rich medium. Microbial lipases have received a great deal of attention in the field of food technology, pharmaceutical sciences, chemical and detergent industries due to their stability, selectivity, mild operation conditions and broad substrate specificity. Despite these advantages, low activity and stability displayed in organic medium has restricted their commercial application in organic synthesis. Researchers have explored alternative ways to modify the enzymes making them suitable for use in non-conventional media. In this context, harvesting lipases from “Solvent Tolerant Microbes” has recently become an attractive approach. These microbes are able to grow in the presence of high concentrations of organic solvents, generally known to have detrimental effect on microorganisms. Such microbes survive through novel adaptation mechanisms and secretion of solvent stable enzymes having efficient functionality in solvent-rich media. These enzymes could be useful for bioconversion in non-conventional media. In the current review, this approach is described with an emphasis on characteristics, applications and genetic aspect of lipases from the genus Pseudomonas.     

Peculiarities of direct bioelectrocatalysis by laccase in aqueous-nonaqueous mixtures

The effect of concentration of ethanol and dimethyl sulfoxide on the catalytic activity of laccase is studied for the enzymatic reaction of catechol oxidation and bioelectrocatalytic reaction of oxygen reduction under the conditions of direct electron transfer. Laccase-Nafion composite is elaborated ensuring the enzyme stability in a wide potential range and a content of organic solvents. Based on the STM measurements, the structure of composite layer is proposed. It is shown that the mechanism of oxygen reduction reaction by laccase in organo-aqueous mixtures is similar to that earlier proposed for aqueous solutions. A decrease in the electrocatalytic activity of laccase in the oxygen reduction correlates with a decrease in the laccase enzymatic activity in the substrate oxidation. However, a decrease in the laccase activity in the composite is observed at a higher content of organic solvent in the mixture. The mechanism of laccase inactivation by organic solvents is proposed.     

Solvent effects on biocatalysis in organic systems: equilibrium position and rates of lipase catalyzed esterification

Porcine pancreatic lipase immobilized on celite particles has been employed as a catalyst for the esterification of dodecanol and decanoic acid in a predominantly organic system. Solvent influence on the equilibrium position and on the catalyst activity has been studied using 20 solvents, including aliphatic and aromatic hydrocarbons, ethers, ketones, nitro- and halogenated hydrocarbons, and esters. The equilibrium constant for esterification correlates well with the solubility of water in the organic solvent, which in turn shows a good relationship with a function of Guttman's donor number and the electron pair acceptance index number of the solvent. This may be rationalized in terms of the requirements for solvation of water and of the reactants. The catalyst activity, measured as the initial rate of the esterification reaction, is best correlated as a function of both n-octanol-water partition coefficient (log P) and either the electron pair acceptance index or the polarizability.     

Purification of Saponin Compounds in Bupleurum falcatum by Solvent Partitioning and Preparative LC

Saponin compounds (saikosaponin c, a, and d) in Bupleurum falcatum were partially purified by solvent partitioning of the herbal extract using diethyl ether, distilled water, n-butanol, and acetone. After separation of the saponins by preparative LC, the purity of each saikosaponin was more than 94%. The identities of purified individual saikosaponins were confirmed by TLC, analytical LC, and fast-atom bombardment mass spectrometry.     

Synthesis of alkyl esters by cutinase in miniemulsion and organic solvent media

The main objective of this work was studying and testing the nature and influence of reaction media (organic solvent vs. miniemulsion system) on the synthesis of alkyl esters catalyzed by Fusarium solani pisi cutinase. Ester synthesis and cutinase selectivity for different chain length of acids and alcohols (ethyl and hexyl) were evaluated. In iso-octane, after 1 h of reaction, cutinase exhibits rates of esterification between 0.24 μmol x mg^–1 x min^–1 for ethyl oleate and 1.15 μmol x mg^–1 x min^–1 for ethyl butyrate, while in a miniemulsion system the rates were from 0.05 for ethyl heptanoate to 0.76 μmol x mg^–1 x min^–1 for ethyl decanoate. The reaction rate for the synthesis of hexyl esters in a miniemulsion system was from 0.19 for hexyl heptanoate to 1.07 μmol x mg^–1 x min^–1 for hexyl decanoate. High conversion yields of 95% at equilibrium after 8 h of reaction in iso-octane for pentanoic acid (C₅) with ethanol at equimolar concentration (0.1 M) was achieved. Additionally, this work showed that a significant and unexpected shift in cutinase selectivity occurred towards longer chain length carboxylic acids (C₈–C₁₀) in miniemulsion system as compared to organic solvent (iso-octane) and previous studies in reverse micellar systems. The possibility of working with higher concentration of substrates, without inhibitory effect on the enzyme, was another advantage of the miniemulsion system.     

Bioinformatic analysis and in vitro site-directed mutagenesis of conserved amino acids in BphK, a specific bacterial glutathione transferase

Glutathione transferases [GSTs: EC 2.5.1.18)] are ubiquitous multifunctional prokaryotic and eukaryotic enzymes involved in the cellular detoxification and excretion of a large variety of compounds. However, our understanding of the role of bacterial GSTs in metabolism is still in its infancy. The association of bacterial GST DNA with other genes involved in degradation of toxic pollutants, including polychlorinated biphenyls (PCBs), indirectly suggests a role for bacterial GSTs in biodegradation. Previously, in this laboratory, a specific bacterial GST, BphK^LB400 isolated from Burkholderia xenovorans LB400, was shown to be capable of dehalogenating chlorinated organic substrates rendering them less toxic. However, little is known about the specific amino acids in BphK^LB400 involved in catalysis in vitro. In this study, bioinformatic analysis of BphK^LB400 and other bacterial GSTs, including PCB degraders, identified a number of amino acids that were identical in all bacterial GST sequences analysed. Two amino acids, Cys10 and His106, were selected for in vitro site-directed mutagenesis studies. In vitro GST activity assay results suggest that these two amino acids play a role in determining the catalytic activity of BphK^LB400. Studies of bacterial cell extracts expressing BphK^LB400 (wildtype and mutant) identified a specific mutant, Cys10Phe, with increased GST activity towards 1-chloro-2,4-dinitrobenzene (the model substrate for GSTs). BphK^LB400 (mutant) with increased activity towards toxic chlorinated organic compounds could have potential for bioremediation of contaminated soil in the environment.     

Ribosome Modulation Factor,an Important Protein for Cell Viability Encoded by the Polyamine Modulon

We searched for proteins whose synthesis is enhanced by polyamines at the stationary phase of cell growth using an Escherichia coli polyamine-requiring mutant in which cell viability is greatly decreased by polyamine deficiency. The synthesis of ribosome modulation factor (RMF) was strongly enhanced by polyamines at the level of translation at the stationary phase of cell growth. In rmf mRNA, a Shine-Dalgarno (SD) sequence is located 11 nucleotides upstream of the initiation codon AUG. When the SD sequence was moved to the more common position 8 nucleotides upstream of the initiation codon, the degree of polyamine stimulation was reduced, although the level of RMF synthesis was markedly increased. Polyamine stimulation of RMF synthesis was found to be caused by a selective structural change of the bulged-out region of the initiation site of rmf mRNA. The decrease in cell viability caused by polyamine deficiency was prevented by the addition of a modified rmf gene whose synthesis is not influenced by polyamines. The results indicate that polyamines enhance cell viability of E. coli at least in part by enhancing RMF synthesis.