Characterization of recombinant human brain-derived neurotrophic factor variants

The purpose of this work was the chemical characterization of variants of the recombinant human brain derived neurotrophic factor (rHu-BDNF), expressed in Escherichia coli. This paper also addresses the question of the in vitro activity of these variants. Chemical characterization of the variants employed peptide mapping using Glu-C protease and cyanogen bromide digestion on reduced and alkylated variants followed by the analysis of the digested peptides using mass spectrometry and Edman sequencing. The BDNF variants in this work have been designated by the order of their elution as observed from the high temperature RPLC assay. It was determined that Peaks 1 and 2, which eluted just before the predominant BDNF peak, had methionine sulfoxide instead of methionine at positions 31 and 61, respectively. Peak 4, which is chromatographically a single peak, contained three variants. Two of these variants had norleucine instead of methionine, at positions 61 and 92, respectively, while the third had methionine sulfoxide instead of methionine at position 92. Peak 5 had norleucine at position 31 instead of methionine. All of these variants showed in vitro biological activity consistent with the BDNF standard, suggesting the preservation of the trkB receptor-ligand binding domain of the variants.     

Naked amoebae (Protozoa) of the Salton Sea, California

The Salton Sea is an inland lake in California with an average salinity of ca. 44 g l^–1. This productive water body, which supports substantial fish and migratory bird populations, is under threat because of increasing salinity levels. The present study was the first to examine the naked amoeboid protozoa of the Salton Sea and provide a first estimate of their numerical importance. Over a six-month sampling period (June–December, 1999), 45 different morphospecies (considered to be species) of amoebae were isolated. Wherever possible, isolates were identified to species or genus using diagnostic features recognizable by light microscopy. For each isolate, illustrations and brief notes on the diagnostic characters used in the identifications are given. These will allow this paper to be used as an identification guide to amoebae of the Salton Sea in future studies. Of the 45 taxa, around 18 of the isolates (i.e. 40%) are probably new to Science. Preliminary counts, based on enrichment cultivation methods, showed that amoebae in shoreline waters ranged from 14560 to 237120 cells l^–1 (mean 117312 ± 86075 S.D.). The ecological importance of high numbers and high diversity of amoebae is unknown. But it should be noted that several of the amoebae were actively grazing cyanobacterial and algal filaments and filaments of the bacterium Beggiatoa. Others were predominately associated with suspended particulates. As such, amoebae may be important in the cycling of carbon and nutrients in the Salton Sea.     

The question of uniqueness of ancient bacteria

Microorganisms are associated with a variety of ancient geological materials. However, conclusive proof that these organisms are as old as the geological material and not more recent introductions has generally been lacking. Over the years, numerous reports of the isolation of ancient bacteria from geological materials have appeared. Most of these have suffered from the fact that the protocol for the surface sterilization of the sample was either poorly defined, inadequate or rarely included data to validate the overall effectiveness of the sterilization protocol. With proper sterility validation and isolation protocol, a legitimate claim for the isolation of an ancient microbe can be made. Biochemical, physiological, or morphological data indicate that these ancient microbes are not significantly different from modern isolates. As the role (decomposition) of modern and ancient microbes has not changed over time, it is probably unreasonable to expect these organisms to be vastly different. A discussion on the reasons for the homogeneity of ancient and modern microbes is presented. Journal of Industrial Microbiology & Biotechnology (2002) 28, 32–41 DOI: 10.1038/sj/jim/7000174 Received 20 May 2001/ Accepted in revised form 16 June 2001     

Stereo- and Regioselective Hydroxylation of α-Ionone by Streptomyces Strains

A total of 215 Streptomyces strains were screened for their capacity to regio- and stereoselectively hydroxylate β- and/or α-ionone to the respective 3-hydroxy derivatives. With β-ionone as the substrate, 15 strains showed little conversion to 4-hydroxy- and none showed conversion to the 3-hydroxy product as desired. Among these 15 Streptomyces strains, S. fradiae Tü 27, S. arenae Tü 495, S. griseus ATCC 13273, S. violaceoniger Tü 38, and S. antibioticus Tü 4 and Tü 46 converted α-ionone to 3-hydroxy-α-ionone with significantly higher hydroxylation activity compared to that of β-ionone. Hydroxylation of racemic α-ionone [(6R)-(−)/(6S)-(+)] resulted in the exclusive formation of only the two enantiomers (3R,6R)- and (3S,6S)-hydroxy-α-ionone. Thus, the enzymatic hydroxylation of α-ionone by the Streptomyces strains tested proceeds with both high regio- and stereoselectivity.Ionones and their derivatives are important intermediates in the metabolism of terpenoids, e.g., in carotenoid biosynthesis, and have been isolated from many sources (1a, 11). Compounds with a trimethylcyclohexane building block constitute essential aroma elements in many plant oils and thus have attracted the attention of the flavor and fragrance industry (3). Further, ionone derivatives, e.g., 3-hydroxy-β-ionone, could prove valuable intermediates for the chemoenzymatic synthesis of carotenoids, e.g., for astaxanthin and zeaxanthin (5).Microbial transformation of α- and/or β-ionone to a number of hydroxy and oxo derivatives has been reported for several fungal strains (2, 4, 8, 9, 18), mainly of the genus Aspergillus, but not for bacterial strains. 3-Hydroxy-α-ionone was observed, among other metabolites, when Cunninghamella blakesleeana ATCC 8688 (2) or Aspergillus niger JTS 191 (18) was used.Many species of the order Actinomycetes are known to catalyze a broad spectrum of xenobiotic transformations. Several cytochrome P-450-dependent monooxygenases from Streptomyces strains, which catalyze the hydroxylation of a wide range of substrates, have been investigated on the molecular level (12) and thus provide an interesting potential as biocatalysts for specific hydroxylation reactions by recombinant techniques.As a first step in this direction, we now report the screening of 215 Streptomyces strains for their capacity to hydroxylate β- and/or α-ionone to the respective 3-hydroxy derivatives in a regio- and stereoselective manner. The structure and stereochemistry of the main biotransformation product were characterized unequivocally by nuclear magnetic resonance (NMR) spectroscopy.     

High level, context dependent misincorporation of lysine for arginine in Saccharomyces cerevisiae a1 homeodomain expressed in Escherichia coli.

The Saccharomyces cerevisiae a1 homeodomain is expressed as a soluble protein in Escherichia coli when cultured in minimal medium. Nuclear magnetic resonance (NMR) spectra of previously prepared a1 homeodomain samples contained a subset of doubled and broadened resonances. Mass spectroscopic and NMR analysis demonstrates that the heterogeneity is largely due to a lysine misincorporation at the arginine (Arg) 115 site. Arg 115 is coded by the 5'-AGA-3' sequence, which is quite rare in E. coli genes. Lower level mistranslation at three other rare arginine codons also occurs. The percentage of lysine for arginine misincorporation in a1 homeodomain production is dependent on media composition. The dnaY gene, which encodes the rare 5'-AGA-3' tRNA(ARG), was co-expressed in E. coli with the a1-encoding plasmid to produce a homogeneous recombinant a1 homeodomain. Co-expression of the dnaY gene completely blocks mistranslation of arginine to lysine during a1 overexpression in minimal media, and homogeneous protein is produced.     

The Tn5 bleomycin resistance gene confers improved survival and growth advantage on Escherichia coli

The bleomycin resistance gene (ble) of transposon Tn5 is known to decrease the death rate of Escherichia coli during stationary phase. Bleomycin is a DNA-damaging agent and bleomycin resistance is produced by improved DNA repair which also requires the host genes aidC and polA coding, respectively, for an alkylation-inducible gene product and DNA polymerase I. In the absence of the drug, this DNA repair system is believed to cause the slower death rate of bleomycin-resistant bacteria. In this study, the effect of ble and aidC genes on the viability of bacteria and their growth rate in chemostat competitions was studied. The results indicate, that bleomycin-resistant bacteria display greater fitness under these conditions. Another beneficial effect of transposon Tn5 had been previously attributed to the insertion sequence IS50R. We were not able to reproduce this result with IS50R, however, the complete transposon was beneficial under similar conditions. Moreover, we showed the Tn5 fitness effect to be aidC-dependent. The ble gene was discovered after the fitness effect of IS50R had been established; it has not previously been considered to mediate the beneficial effect of Tn5. This possibility is discussed based on the molecular mechanism of bleomycin resistance.     

The Tn5 bleomycin resistance gene confers improved survival and growth advantage on Escherichia coli

The bleomycin resistance gene (ble) of transposon Tn5 is known to decrease the death rate of Escherichia coli during stationary phase. Bleomycin is a DNA-damaging agent and bleomycin resistance is produced by improved DNA repair which also requires the host genes aidC and polA coding, respectively, for an alkylation-inducible gene product and DNA polymerase I. In the absence of the drug, this DNA repair system is believed to cause the slower death rate of bleomycin-resistant bacteria. In this study, the effect of ble and aidC genes on the viability of bacteria and their growth rate in chemostat competitions was studied. The results indicate, that bleomycin-resistant bacteria display greater fitness under these conditions. Another beneficial effect of transposon Tn5 had been previously attributed to the insertion sequence IS50R. We were not able to reproduce this result with IS50R, however, the complete transposon was beneficial under similar conditions. Moreover, we showed the Tn5 fitness effect to be aidC-dependent. The ble gene was discovered after the fitness effect of IS50R had been established; it has not previously been considered to mediate the beneficial effect of Tn5. This possibility is discussed based on the molecular mechanism of bleomycin resistance.     

Proton pumps of the plasmalemma of the yeast Rhodotorula gracilis Their coupling to fluxes of potassium and other ions

(1) Intact cells of the obligatory aerobic yeast Rhodotorula gracilis (glutinis) generate a difference of the electrochemical proton potential (Δμ_H⁺) across the plasmalemma. In the range from pH 4.0 to 7.0 its value remains close to 12 kJ/mol. At pH 4.0 it is composed of the pH difference (inside alkaline) alone, at pH 7.0 of the membrane potential alone. (2) Both components of Δμ_H⁺ are generated by an active process, as shown by their rapid dissipation under anaerobic conditions. (3) In order to find out by which type of mechanism Δμ_H⁺ is generated the effect of a number of inhibitors of transport-ATPases (among them ouabain, triphenyltin chloride, quercetin, oligomycin, venturicidin, dicyclohexylcarbodiimide, Dio-9) were tested both on the generation of the membrane potential and on the extrusion of protons either in the absence or the presence of potassium ions. We found that all three processes were inhibited by Dio-9 and dicyclohexylcarbodiimide, which are specific for H⁺-ATPases. Triphenyltin chloride inhibited the K⁺/H⁺-exchange without having any effect either on the extrusion of H⁺ alone or on the membrane potential. (4) Dicyclohexylcarbodiimide and Dio-9, but not triphenyltin chloride inhibited at pH 4.0 the active transport of sugars. This class of substrates has been shown earlier to be transported by an electrogenic H⁺ symport driven by Δμ_H⁺ across the cell membrane. (5) Neither the rate of respiration nor the intracellular level of ATP were significantly decreased by any of these inhibitors (except for venturicidin). (6) We conclude that in Rhodotorula gracilis the difference of the electrochemical potential of H⁺ is created by an electrogenic proton pump, presumably in ATPase. The extrusion of protons in exchange against potassium is catalyzed by a different energy-dependent but electroneutral system. This conclusion is based on the observation that the H⁺/K⁺ exchange does not work under conditions where the membrane potential is large, and vice versa.     

Kinetic analysis and modelling of enzymatic (R)-phenylacetylcarbinol batch biotransformation process

Initial rate and biotransformation studies were applied to refine and validate a mathematical model for enzymatic (R)-phenylacetylcarbinol (PAC) production from pyruvate and benzaldehyde using Candida utilis pyruvate decarboxylase (PDC). The rate of PAC formation was directly proportional to the enzyme activity level up to 5.0 U ml-1 carboligase. Michaelis-Menten kinetics were determined for the effect of pyruvate concentration on the reaction rate. The effect of benzaldehyde followed the sigmoidal shape of the Monod-Wyman-Changeux (MWC) model. The biotransformation model, which also included a term for PDC inactivation by benzaldehyde, was used to determine the overall rate constants for the formation of PAC, acetaldehyde, and acetoin. These values were determined from data for three batch biotransformations performed over a range of initial concentrations (viz. 50-150 mM benzaldehyde, 60-180 mM pyruvate, 1.1-3.4 U ml-1 enzyme activity). The finalized model was then used to predict a batch biotransformation profile at 120/100 mM initial pyruvate/benzaldehyde (initial enzyme activity 3.0 U ml-1). The simulated kinetics gave acceptable fitting (R2 = 0.9963) to the time courses of these latter experimental data for substrates pyruvate and benzaldehyde, product PAC, by-products acetaldehyde and acetoin, as well as enzyme activity level.