The stereospecific bioconversion of α-aminopropionitrile to L-alanine by an immobilised bacterium isolated from soil

Summary Bacterial isolate APN grew on -aminoacetonitrile and -amino propionitrile (-APN) converting the -aminonitriles to glycine and alanine, respectively. The nitrilase had an apparent Km for -APN of 34mM in whole cells and 21mM when immobilised. The alanine formed from APN was 87% in the L-form and was produced for 45 days after immobilisation in alginate.     

Biotransformation of β-myrcene to geraniol by a strain of Rhodococcus erythropolis isolated by selective enrichment from hop plants

The biocatalytic generation of high-value chemicals from abundant, cheap and renewable feedstocks is an area of great contemporary interest. A strain of Rhodococcus erythropolis designated MLT1 was isolated by selective enrichment from the soil surrounding hop plants, using the abundant triene β-myrcene from hops as a sole carbon source for growth. Resting cells of the organism were challenged with β-myrcene, and the major product of biotransformation was determined by mass spectrometric analysis to be the monoterpene alcohol geraniol. Controls demonstrated that the product was biogenic and that an aerobic environment was required. The ability to transform β-myrcene was shown to be restricted to cells that had been grown on this substrate as sole carbon source. Pre-incubation of cells with the cytochrome P450 inhibitors metyrapone or 1-aminobenzotriazole reduced geraniol production by 23% and 73% respectively, but reduction in activity was found not to correlate with the inhibitor concentration. A comparative analysis of insoluble and soluble cell extracts derived from cells of MLT1 grown on either β-myrcene or glucose revealed at least four proteins that were clearly overproduced in response to growth on β-myrcene. Mass spectrometric analysis of tryptic digests of three of these protein bands suggested their identities as an aldehyde dehydrogenase, an acyl-CoA dehydrogenase and a chaperone-like protein, each of which has a precedented role in hydrocarbon metabolism clusters in Rhodococcus sp. and which may therefore participate in a β-myrcene degradation pathway in this organism.     

Antimicrobial susceptibilities of strains of Nocardia brasiliensis isolated from soil of Tucumán

The activity of antimicrobial agents against soil isolates of N. brasiliensis was studied by determination of the minimum inhibitory concentrations (MICs) and disk diffusion technique, according to the National Committee for Clinical Laboratory Standards (NCCLS). The objectives were: (a) to study the patterns of sensitivity among regional strains of N. brasiliensis isolated from natural sources (soil) of different zones of Tucumán province; (b) to correlate these results with those previously obtained with regional strains of N. brasiliensis isolated from human mycetomas, as a contribution in the evaluation of the importance of the natural reservoir area of the potentially pathogen strains. The results obtained by both methods identified strains of N. brasiliensis from soils with similar patterns of susceptibility to the strains N. brasiliensis isolated from human mycetomas. This showed strains sensitive and resistant to antibiotics. The majority of the isolates of N. brasiliensis from soils showed higher susceptibilities to antibiotics than the strains isolated from human mycetomas. Among the antibiotics studied, cefotaxime, ceftriaxone and gentamicin were the most effective against all the regional strains tested, and these results are correlated with those obtained with regional strains that cause human mycetomas. This revised version was published online in June 2006 with corrections to the Cover Date.     

Selective inhibition of toxic cyanobacteria by β-carboline-containing bacterium Bacillus flexus isolated from Saudi freshwaters

A bacterial strain SSZ01 isolated from a eutrophic lake in Saudi Arabia dominated by cyanobacterial blooms, showed an antialgal activity against cyanobacteria species. Based on the analysis of the 16S rDNA gene sequence, the isolated strain (SSZ01) most likely belonged to the genus Bacillus with a 99% similarity to Bacillus flexus strain EMGA5. The thin layer chromatography (TLC) analysis of the ethyl acetate extract of this bacterium revealed that this strain can produce harmine and norharmane compared to different β-carboline analog standards. Harmine and norharmane were also detected in considerable amounts in bacterial growth medium, indicating a potential excretion of these compounds into the aquatic environment. The crude extract of Bacillus flexus as well as pure materials of harmine and norharmane inhibited the growth of tested species of cyanobacteria. However, the bacterial crude extract has a higher toxicity against tested species of cyanobacteria than harmine and norharmane. In addition, harmine was more toxic to cyanobacteria than norharmane. On the other hand, neither pure compounds of harmine and norharmane nor crude bacterial extract showed any antialgal activity against tested species of green algae. The results of the present study suggest that B. flexus SSZ01 or its crude extract containing harmine and norharmane could be a candidate for the selective control of cyanobacterial blooms without affecting other algal species.     

Biodegradation of α- and β-endosulfan by soil bacteria

Extensive applications of persistent organochlorine pesticides like endosulfan on cotton have led to the contamination of soil and water environments at several sites in Pakistan. Microbial degradation offers an effective approach to remove such toxicants from the environment. This study reports the isolation of highly efficient endosulfan degrading bacterial strains from soil. A total of 29 bacterial strains were isolated through enrichment technique from 15 specific sites using endosulfan as sole sulfur source. The strains differed substantially in their potential to degrade endosulfan in vitro ranging from 40 to 93% of the spiked amount (100 mg l⁻¹). During the initial 3 days of incubation, there was very little degradation but it got accelerated as the incubation period proceeded. Biodegradation of endosulfan by these bacteria also resulted in substantial decrease in pH of the broth from 8.2 to 3.7 within 14 days of incubation. The utilization of endosulfan was accompanied by increased optical densities (OD₅₉₅) of the broth ranging from 0.511 to 0.890. High performance liquid chromatography analyses revealed that endosulfan diol and endosulfan ether were among the products of endosulfan metabolism by these bacterial strains while endosulfan sulfate, a persistent and toxic metabolite of endosulfan, was not detected in any case. The presence of endosulfan diol and endosulfan ether in the bacterial metabolites was further confirmed by GC-MS. Abiotic degradation contributed up to 21% of the spiked amount. The three bacterial strains, Pseudomonas spinosa, P. aeruginosa, and Burkholderia cepacia, were the most efficient degraders of both α- and β-endosulfan as they consumed more than 90% of the spiked amount (100 mg l⁻¹) in the broth within 14 days of incubation. Maximum biodegradation by these three selected efficient bacterial strains was observed at an initial pH of 8.0 and at an incubation temperature of 30°C. The results of this study may imply that these bacterial strains could be employed for bioremediation of endosulfan polluted soil and water environments.     

Characterisation of Arthrobacter sp. S1 that can degrade α and β-haloalkanoic acids isolated from contaminated soil

A bacterium identified as Arthrobacter sp. S1 by 16S rRNA was isolated from contaminated soil. This is the first reported study that Arthrobacter could utilize both α-halocarboxylix acid (αHA) [2,2-dichloropropionic acid (2,2-DCP) and D,L-2-chloropropionic acid (D,L-2-CP)] and β-halocarboxylix acid (βHA) [3-chloropropionic acid (3CP)] as sole source of carbon with cell doubling times of 5?±?0.2, 7?±?0.1, and 10?±?0.1 h, respectively. More than 85 % chloride ion released was detected in the growth medium suggesting the substrates used were utilized. To identify the presence of dehalogenase gene in the microorganism, a molecular tool that included the use of oligonucleotide primers specific to microorganisms that can grow in halogenated compounds was adapted. A partial putative dehalogenase gene was determined by direct sequencing of the PCR-amplified genomic DNA of the bacterium. A comparative analysis of the deduced amino acid sequence data revealed that the amino acid sequence has a low identity of less than 15 % to both group I and group II dehalogenases, suggesting that the current putative dehalogenase amino acid sequence was completely distinct from both α-haloacids and β-haloacids dehalogenases. This investigation is useful in studying the microbial populations in order to monitor the presence of specific dehalogenase genes and to provide a better understanding of the microbial populations that are present in soil or in water systems treating halogenated compounds.     

Characterization of β2-microglobulin transcripts from two teleost species

Using degenerate primers based on published ₂-microglobulin sequences we were able to obtain an expected 111 base pairs (bp) polymerase chain reaction (PCR) fragment from tilapia genomic DNA. The sequence of this fragment showed a high degree of similarity to mouse ₂-microglobulin at the protein level. We used these primers in an anchored PCR to obtain a 213 bp PCR fragment from a carp cDNA library. This was then used to clone a full-length ₂-microglobulin cDNA from carp. The carp sequence showed the highest similarity to rabbit ₂-microglobulin. Both sequences showed strong similarities to all previously published vertebrate ₂-microglobulin sequences. The predicted protein secondary structure of both the carp and tilapia clones was almost identical to the corresponding regions of previously known vertebrate ₂-microglobulin protein sequences. When either the carp or tilapia probes were used against corresponding northern blots, they hybridized to a message of approximately 800–1000 bases long, which corresponds to the previously published lengths of ₂-microglobulin mRNAs. Southern blotting indicated that ₂-microglobulin was encoded by a single copy gene in both cases. Phylogenetic analysis indicated that the sequences were related to the ₂-microglobulins of higher vertebrates but grouped together in an ancestral position.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers L05536 (carp), L05537 (tilapia).     

Characterization of a novel β-glucosidase-like activity from a soil metagenome

We report the cloning of a novel β-glucosidase-like gene by function-based screening of a metagenomic library from uncultured soil microorganisms. The gene was named bgllC and has an open reading frame of 1,443 base pairs. It encodes a 481 amino acid polypeptide with a predicted molecular mass of about 57.8 kDa. The deduced amino acid sequence did not show any homology with known β-glucosidases. The putative β-glucosidase gene was subcloned into the pETBlue-2 vector and overexpressed in E. coli Tuner (DE3) pLacI; the recombinant protein was purified to homogeneity. Functional characterization with a high performance liquid chromatography method demonstrated that the recombinant BgllC protein hydrolyzed d-glucosyl-β-(l–4)-d-glucose to glucose. The maximum activity for BgllC protein occurred at pH 8.0 and 42°C using p-nitrophenyl-β-d-glucoside as the substrate. A CaCl₂ concentration of 1 mM was required for optimal activity. The putative β-glucosidase had an apparent K _m value of 0.19 mM, a V _max value of 4.75 U/mg and a k _cat value of 316.7/min under the optimal reaction conditions. The biochemical characterization of BgllC has enlarged our understanding of the novel enzymes that can be isolated from the soil metagenome.     

Enzymatic synthesis of β-xylosyl-oligosaccharides by transxylosylation using two β-xylosidases of glycoside hydrolase family 3 from Aspergillus nidulans FGSC A4

Two β-xylosidases of glycoside hydrolase family 3 (GH 3) from Aspergillus nidulans FGSC A4, BxlA and BxlB were produced recombinantly in Pichia pastoris and secreted to the culture supernatants in yields of 16 and 118 mg/L, respectively. BxlA showed about sixfold higher catalytic efficiency (k_cat/K_m) than BxlB towards para-nitrophenyl β-d-xylopyranoside (pNPX) and β-1,4-xylo-oligosaccharides (degree of polymerisation 2–6). For both enzymes k_cat/K_m decreased with increasing β-1,4-xylo-oligosaccharide chain length. Using pNPX as donor with 9 monosaccharides, 7 disaccharides and two sugar alcohols as acceptors 18 different β-xylosyl-oligosaccharides were synthesised in 2–36% (BxlA) and 6–66% (BxlB) yields by transxylosylation. BxlA utilised the monosaccharides d-mannose, d-lyxose, d-talose, d-xylose, d-arabinose, l-fucose, d-glucose, d-galactose and d-fructose as acceptors, whereas BxlB used the same except for d-lyxose, d-arabinose and l-fucose. BxlB transxylosylated the disaccharides xylobiose, lactulose, sucrose, lactose and turanose in upto 35% yield, while BxlA gave inferior yields on these acceptors. The regioselectivity was acceptor dependent and primarily involved β-1,4 or 1,6 product linkage formation although minor products with different linkages were also obtained. Five of the 18 transxylosylation products obtained from d-lyxose, d-galactose, turanose and sucrose (two products) as acceptors were novel xylosyl-oligosaccharides, β-d-Xylp-(1→4)-d-Lyxp, β-d-Xylp-(1→6)-d-Galp, β-d-Xylp-(1→4)-α-d-Glcp-(1→3)-β-d-Fruf, β-d-Xylp-(1→4)-α-d-Glcp-(1→2)-β-d-Fruf, and β-d-Xylp-(1→6)-β-d-Fruf-(2→1)-α-d-Glcp, as structure-determined by 2D NMR, indicating that GH3 β-xylosidases are able to transxylosylate a larger variety of carbohydrate acceptors than earlier reported. Furthermore, transxylosylation of certain acceptors resulted in mixtures. Some of these products are also novel, but the structures of the individual products could not be determined.     

Localization of β-oxidation enzymes in peroxisomes isolated from nonfatty plant tissues

Peroxisomes from spinach leaves, mungbean hypocotyls, and potato tubers catalyze a palmitoyl-CoA-dependent, KCN-insensitive O₂ uptake. In the course of this reaction O₂ is reduced to H₂O₂ in a 1:1 stoichiometry and palmitoyl-CoA oxidized, in a 1:1 stoichiometry, to a product serving as substrate for enoyl-CoA hydratase. These findings demonstrate the existence of a peroxisomal acyl-CoA oxidase in these tissues. Enoyl-CoA hydratase (EC 4.2.1.17), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), and thiolase (EC 2.3.1.9) are also associated with the peroxisomes from mung-bean hypocotyls and potato tubers (as well as with spinach leaf peroxisomes as recently reported; Gerhardt 1981, FEBS Lett. 126, 71). The low activities of these enzymes in mitochondrial fractions seem to be due to contaminating peroxisomes since the ratio of β-oxidation enzyme activities to catalase activity did not significantly differ between peroxisomal and mitochondrial fractions isolated on sucrose density gradients. The proof of localization of β-oxidation enzymes in peroxisomes without glyoxysomal function leads to the concept that fatty-acid oxidation is a consistent basic function of the peroxisome in cells of higher plants.     

Antimicrobial mechanism of β-glycyrrhetinic acid isolated from licorice, Glycyrrhiza glabra

-Glycyrrhetinic acid isolated from Glycyrrhiza glabra had an antibacterial activity of 7.6 and 12.5 g ml^–1 against Bacillus subtilis and Staphylococcus epidermidis without causing hemolysis of human erythrocytes, whereas it was not inhibitory against Escherichia coli, Proteus vulgaris and various fungi. Confocal microscopy showed that -glycyrrhetinic acid was located within the bacteria but had not caused membrane disruption. It then inhibited synthesis of DNA, RNA and protein.     

Degradation of polypropylene–poly-L-lactide blend by bacteria isolated from compost

Abstract

Polypropylene (PP) degrading bacteria (P1 to P16) were isolated from compost using enrichment technique. Five isolates (P3, P6, P8, P10, and P13) were selected based on their degradation abilities. These isolates were identified as Bacillus spp. through biochemical characteristics and 16S rDNA sequence analysis. The isolates were tested for their ability to degrade blends of PP and poly-L-lactide (PLLA) (PP80 and PP80C6) in minimal media as well as in soil. In minimal media, the growth of bacteria increased with time, showing utilization of blend as carbon source. The protein content was estimated at the end of 15?days and maximum amount was secreted by isolate P8 indicating maximum potential to degrade polymers compared to other isolates. Scanning electron microscopy (SEM) results revealed the formation of biofilm on the polymer surface. Fourier-transform infrared spectroscopy (FTIR) analysis showed the formation of new bond at 2123?cm^?1 and breakage of old C=O ester bond at 1757?cm^?1 in case of polymer PP80C6. Thermogravimetric analysis (TGA) showed decrease in thermal stability of polymers after degradation. The carbon dioxide evolved from sample was measured and biodegradation degree was also calculated. The degree of biodegradation shown by the isolate P8 was 12% and the P6 was 10%. The results demonstrated that Bacillus species isolated from composted samples in this study provided promising evidence for the biodegradation of polypropylene and poly-L-lactide (PP-PLLA) blends in the environment.     

The induction of autophagy in isolated insect fat body by β-ecdysone

The fat body in Calpodes undergoes sequential organelle specific autophagy as a first step in the cell remodeling process necessary for metamorphosis to the pupa. This autophagy begins at about 36 hr before pupation and coincides with a critical period after which an isolated abdomen will pupate without further influence from the prothoracic glands. This suggested that autophagy might be induced by ecdysone. Fat body taken before the critical period and cultured in a medium containing β-ecdysone undergoes autophagy. Fat body from the same animal maintained in hormone-free medium retains the pre-critical period morphology with no autophagy. Autophagy is therefore directly induced by β-ecdysone. Fat body taken soon after the critical period continues with the autophagic sequence in hormone-free medium. Therefore the entire autophagic sequence is induced and does not require the continuing presence of hormone. Protein storage granule formation and cell dissociation, which occur in fat body at metamorphosis, are also induced by β-ecdysone.     

Catalysis by isolated β-subunits of the ATP Synthase/ATPase from Thermophilic bacillus PS3. Hydrolysis of Pyrophosphate

Although the capacity of isolated β-subunits of the ATP synthase/ATPase to perform catalysis has been extensively studied, the results have not conclusively shown that the subunits are catalytically active. Since soluble F₁ of mitochondrial H⁺-ATPase can bind inorganic pyrophosphate (PP_i) and synthesize PP_i from medium phosphate, we examined if purified His-tagged β-subunits from Thermophilic bacillus PS3 can hydrolyze PP_i. The difference spectra in the near UV CD of β-subunits with and without PP_i show that PP_i binds to the subunits. Other studies show that β-subunits hydrolyze [³²P] PP_i through a Mg²⁺-dependent process with an optimal pH of 8.3. Free Mg²⁺ is required for maximal hydrolytic rates. The Km for PP_i is 75 μM and the Vmax is 800 pmol/min/mg. ATP is a weak inhibitor of the reaction, it diminishes the Vmax and increases the Km for PP_i. Thus, isolated β-subunits are catalytically competent with PP_i as substrate; apparently, the assembly of β-subunits into the ATPase complex changes substrate specificity, and leads to an increase in catalytic rates.     

Pseudo-homology of protein standard structures formed by two consecutive β-strands

Protein standard structures formed by two consecutive β-strands connected by short loops are considered in this paper. A stereochemical analysis of each standard structure has been performed to determine the necessary conditions which must be fulfilled in the amino acid sequence encoding the standard structure. It is shown that amino acid sequences coding for the same standard structure in ditterent proteins have practically the same order of hydrophobic, hydrophilic and glycine residues. The results of the stereochemical analysis are confirmed by a large number of examples from known protein structures.     

A thermostable β-glucosidase isolated from a bacterial species of the genus Thermus

Summary An extremely thermophilic aerobic bacterium which produced -glucosidase was isolated from soil collected at the Yudanaka hot spring in Japan. It was identified as belonging to the genus Thermus. Production of -glucosidase by this bacterium was stimulated by the addition of cellobiose or laminaribiose to the medium. The optimum pH and temperature of the enzyme were 4.5–6.5 and 85° C respectively. The enzyme was stable in the pH range of 4.5–7.0 at 70° C for 2 h and the half-life at 75° C was 5 days. The K _m value of the enzyme for p-nitrophenyl--d-glucopyranoside, determined at 70° C in 0.1 M sodium phosphate buffer (pH 6.5), was 0.28 mM while the K _m was 2.0 mM for cellobiose. The enzyme effectively hydrolysed cellobiose at 70° C and the conversion yields of cellobiose to glucose were 95%, 93% and 90% at substrate concentrations of 5%, 10% and 15%, respectively.     

An alkaline β-glucosidase isolated from an olive brine strain of Wickerhamomyces anomalus

An efficient β-glucosidase (βG)-producing strain, Wickerhamomyces anomalus BS81, was isolated from naturally fermented olive brine and identified based on PCR/restriction fragment length polymorphism of the rDNA internal transcribed spacer and sequence analysis of the D1/D2 region of the 26S rRNA gene. The hydrolytic activity of the βG had an optimum pH of 8.5 and an optimum temperature of 35 °C. The enzyme had high substrate specificity and high catalytic efficiency (K(m) 0.99 mM, V(max) 14 U g(-1) of cells) for p-nitrophenyl-β-d-glucopyranoside. The enzyme was activated by increasing concentrations of NaCl, with maximum activity at 150 g L(-1) NaCl. Although βGs have been purified and characterized from several other sources, the W. anomalusβG is unique among βGs because its relative maximum activity occurs at alkaline pH and 35 °C. Moreover, the yeast strain has esterase activity that acts synergistically with βG to degrade oleuropein to debitter table olives and olive oil.     

Molecular characterization of β-lactam-resistant Escherichia coli isolated from Fu River, China

The present study aims to demonstrate the β-lactam resistance phenotypes and genotypes of Escherichia coli isolates from the Fu River in Chengdu, southwestern China. We obtained 108 E. coli isolates from nine sampling sites during May and December 2010. The total bacterial count varied from 79 colony-forming units (CFU)/ml to 14,550 CFU/ml, and coliform group number from 13 to 1,435 MPN/ml. Among the 108 isolates, 0-31.48% were resistant to β-lactams and β-lactam inhibitors, 1.85-7.40% to aminoglycoside, 1-20% to fluoroquinolone, and 50% to trimethoprim- sulfamethoxazole. The total bacterial count and antimicrobial resistance of different sites were significantly correlated (P < 0.05). Among the 34 ampicillin-resistant isolates, polymerase chain reaction (PCR) amplification and DNA sequencing showed that bla (TEM), bla (SHV), and bla (CTX-M) were detected in 85.29% (n = 29), 41.18% (n = 14), and 5.88% (n = 2) of the isolates, respectively, whereas bla (KPC) and bla (GES) were not observed in any of the isolates. Enterobacterial repetitive intergenic consensus-PCR patterns revealed that the 34 ampicillin-resistant E. coli isolates belonged to three distinct groups. Plasmid DNAs from the 14 SHV producer isolates yielded one to five bands of ca. 0.15-40 kb. To our knowledge, the current study is the first to describe the phenotypic and genetic characterizations of β-lactam resistance in E. coli isolates of river water origin from the Fu River, Chengdu, southwestern China. Results of the present study suggest that the river water may be considered as a reservoir for antibiotic resistance genes.     

Relaxation by β3-adrenoceptor agonists of the isolated human internal anal sphincter

AimsIn this study, responses of β₃-adrenoceptor agonists were examined on human isolated internal anal sphincter (IAS) in order to explore their relaxant effects on hypertonicity of IAS.Main methodsThe relaxant efficacy (E_max) and potency (? logIC₅₀) of BRL37344 and SR58611A, β₃-adrenoceptor agonists, were examined in contracted IAS muscle strips. The presence of β₃-adrenoceptors, and changes in intracellular calcium and cyclic nucleotide levels in IAS muscle were tested by Western blotting, epifluorescence microscopy and enzyme immunoassay, respectively.Key findingsBRL37344 and SR58611A relaxed contracted IAS muscle (E_max = 27 ± 3% and 35 ± 3%; -logIC₅₀ = 6.26 ± 0.24 and 4.87 ± 0.13; respectively). These relaxant responses were blocked by SR59230A, a selective β₃-antagonist but not by β₁/β₂-selective antagonists, neuronal inhibitor or inhibition of nitric oxide synthase. The E_max of β₃-agonists was similar to that of β₂-selective agonists but smaller than that of isoprenaline (nonselective agonist) or β₁-selective agonists. BRL37344 (100 μM) increased cAMP (1.5-fold) without cGMP change, and depressed intracellular calcium signal. β₃-Adrenoceptor expression was smaller than that of β₁- and β₂-adrenoceptors.SignificanceThis is the first study demonstrating the presence of β₃-adrenoceptor in human IAS muscle and β₃-mediated relaxation of augmented sphincter tone. However, direct β₃-relaxation appears smaller than that obtained for nonselective agonists which may limit their potential use in the treatment of anorectal hypertonicity disorders.