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PubMed2005

Isolation and characterization of a novel polychlorinated biphenyl-degrading bacterium, Paenibacillus sp. KBC101.

The biphenyl-utilizing bacterial strain KBC101 has been newly isolated from soil. Biphenyl-grown cells of KBC101 efficiently degraded di- to nonachlorobiphenyls. The isolate was identified as Paenibacillus sp. with respect to its 16S rDNA sequence and fatty acid profiles, as well as various biological and physiological characteristics. In the case of highly chlorinated biphenyl (polychlorinated biphenyl; PCB) congeners, the degradation activities of this strain were superior to those of the previously reported strong PCB degrader, Rhodococcus sp. RHA1. Recalcitrant coplanar PCBs, such as 3,4,3',4'-CB, were also efficiently degraded by strain KBC101 cells. This is the first report of a representative of the genus Paenibacillus capable of degrading PCBs. In addition to growth on biphenyl, strain KBC101 could grow on dibenzofuran, xanthene, benzophenone, anthrone, phenanthrene, naphthalene, fluorene, fluoranthene, and chrysene as sole sources of carbon and energy. Paenibacillus sp. strain KBC101 presented heterogeneous degradation profiles toward various aromatic compounds.

Bacillaceae↗

PubMed2005

Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization.

A dibenzothiophene (DBT)-degrading bacterial strain able to utilize carbazole as the only source of nitrogen was identified as Gordonia sp. F.5.25.8 due to its 16S rRNA gene sequence and phenotypic characteristics. Gas chromatography (GC) and GC-mass spectroscopy analyses showed that strain F.5.25.8 transformed DBT into 2-hydroxybiphenyl (2-HBP). This strain was also able to grow using various organic sulfur or nitrogen compounds as the sole sulfur or nitrogen sources. Resting-cell studies indicated that desulfurization occurs either in cell-associated or in cell-free extracts of F.5.25.8. The biological responses of F.5.25.8 to a series of mutagens and environmental agents were also characterized. The results revealed that this strain is highly tolerant to DNA damage and also refractory to induced mutagenesis. Strain F.5.25.8 was also characterized genetically. Results showed that genes involved in desulfurization (dsz) are located in the chromosome, and PCR amplification was observed with primers dszA and dszB designed based on Rhodococcus genes. However, no amplification product was observed with the primer based on dszC.

Biotechnology↗

PubMed2006

Biotransformation of isoeugenol to vanillin by Pseudomonas putida IE27 cells.

The ability to produce vanillin and/or vanillic acid from isoeugenol was screened using resting cells of various bacteria. The vanillin- and/or vanillic-acid-producing activities were observed in strains belonging to the genera Achromobacter, Aeromonas, Agrobacerium, Alcaligenes, Arthrobacter, Bacillus, Micrococcus, Pseudomonas, Rhodobacter, and Rhodococcus. Strain IE27, a soil isolate showing the highest vanillin-producing activity, was identified as Pseudomonas putida. We optimized the culture and reaction conditions for vanillin production from isoeugenol using P. putida IE27 cells. The vanillin-producing activity was induced by adding isoeugenol to the culture medium but not vanillin or eugenol. Under the optimized reaction conditions, P. putida IE27 cells produced 16.1 g/l vanillin from 150 mM isoeugenol, with a molar conversion yield of 71% at 20 degrees C after a 24-h incubation in the presence of 10% (v/v) dimethyl sulfoxide.

Benzaldehydes↗

PubMed1998

Cloning and expression of a gene encoding cyanidase from Pseudomonas stutzeri AK61.

The gene coding for cyanidase, which catalyzes the hydrolysis of cyanide to formate and ammonia, was cloned from chromosomal DNA of Pseudomonas stutzeri AK61 into Escherichia coli. The cyanidase gene consisted of an open reading frame of 1004 bp, and it was predicted that cyanidase was composed of 334 amino acids with a calculated molecular mass of 37,518 Da. The amino acid sequence of cyanidase showed a 35.1% and 26.4% homology to aliphatic nitrilase from Rhodococcus rhodochrous K22 and cyanide hydratase from Fusarium lateritium, respectively. A unique cysteine residue of aliphatic nitrilase, which was suggested to play an essential role in the catalytic activity, was conserved in cyanidase. The active form of cyanidase was successfully expressed by a DNA clone containing the cyanidase gene in E. coli. Its productivity was approximately 230 times larger than that of P. stutzeri AK61. The characteristics of the expressed cyanidase, including optimum pH, optimum temperature. Michaelis constant (K(m)) for cyanide and specific activity, were similar to those of the native enzyme from P. stutzeri AK61.

Amino Acid Sequence↗

PubMed1999

Developments in destructive and non-destructive pathways for selective desulfurizations in oil-biorefining processes

Biocatalytic desulfurization is still not a commercial technology, but conceptual engineering and sensitivity analyses have shown that the approach is very promising. The purpose of this paper is to investigate further some aspects of the biodesulphurization pathways, discussing the non-destructive pathway with the well-known Rhodococcus rhodochrous IGTS8. Findings revealed byproducts, such as 2'-hydroxybiphenyl (HBP), sulfite and sulfate, obtained by the desulfurization of dibenzothiophene (DBT), to exert an inhibiting effect. The results suggest that IGTS8 may follow two different metabolic pathways in stationary-growth-phase cells or under growing conditions. The first pathway is characterized by oxidative steps, which convert DBT to DBT sulfoxide and to DBT sulfone. The sulfone is transformed to 2-(2'-hydroxyphenyl)benzene sulfinate and then to HBP and sulfite by a sulfinic acid hydrolase. In the second pathway the sulfone is further oxidized to 2-(2'-hydroxyphenyl)benzene sulfonate and then to HBP and sulfate by a sulfonic acid hydrolase. Experiments using benzene sulfonic acid suggest that the sulfonic acid hydrolase is an induced enzyme.

Journal Article↗

PubMed2002

Scale-down studies on the hydrodynamics of two-liquid phase biocatalytic reactors.

The maintenance of constant interfacial area per unit volume is a key parameter for the successful scale-up of two-liquid phase bioconversion processes. To date, however, there is little published information on the hydrodynamics of such systems and a suitable basis for scale-up has yet to be defined and verified. Here we report power input and hydrodynamic data for a whole-cell bioconversion process using resting cells of Rhodococcus R312 to catalyse the hydration of a poorly water-soluble substrate 1,3-dicyanobenzene (1,3-DCB). Experiments were performed in geometrically similar 3-L and 75-L reactors, each fitted with a three-stage Rushton turbine impeller system. The two-phase system used comprised of 20% v/v toluene dispersed in 0.1 M aqueous phosphate buffer containing up to 10 g(ww) x L(-1) of resuspended biocatalyst and 20 g x L(-1) 1,3-DCB. The power input to the 3-L reactor was first determined using an air-bearing technique for both single-phase and two-phase mixing. In both cases, the power number attained a constant value of 11 at Re>10,000, while the measured power inputs were in the range 0.15-3.25 kW x m(-3). Drop size distributions and Sauter mean drop diameters (d(32)) were subsequently measured on-line in both reactors, using an in-situ light-backscattering technique, for scale-up on the basis of either constant power input per unit volume or constant tip speed. At both scales d(32) decreased with increasing agitation rate, while the drop size distributions obtained were log-normal. All the measured d(32) values were in the range of 30-50 microm, with the lowest values being obtained in systems with biocatalyst present. In all cases, constant power input per unit volume was found to be the most suitable basis for scale-up. This gave virtually identical d(32) values and drop size distributions at both scales. A number of correlations were also identified that would allow reasonable prediction of d(32) values for various agitation rates at each scale. While the results obtained are for a particular phase system, the scale-down methodology presented here would allow the rapid evaluation of other bioconversion processes in the 3-L reactor with a 25-fold reduction in scale. In this way, potential problems that might be encountered at the larger scale, such as the carryover of antifoam from the fermentation stage, could be quickly and efficiently identified.

Journal Article↗

PubMed2004

Solvent toxicity in organic-aqueous systems analysed by multivariate analysis.

The effect of several solvents present in a biphasic reaction system on cells of Rhodococcus erythropolis DCL14, Xanthobacter Py2, Arthrobacter simplex and Mycobacterium sp. NRRL B-3805 was evaluated. These four strains have been widely exploited, from bioremediation to the production of fine chemicals, in two-phase reaction media. The solvents tested were ethyl butyrate, n-hexane, cyclohexane, iso-octane, n-dodecane, DMSO, bis(2-ethylhexyl) phthalate and fluorinert FC-70. The cell population was monitored by fluorescence microscopy and analysis of the images captured provided single-cell-level information on cell viability, morphological factors of both viable and non-viable cells, and on the number of viable cells in clusters. These data, and those concerning the initial carveol concentration, the carbon source used during growth, the adaptation time to the solvent prior to substrate addition, and the properties of the organic solvent, were interpreted using principal components analysis (PCA). For R. erythropolis, X. Py2, and A. simplex, between 70.1 and 80.4% of the variability of the data could be explained by six principal components, while 86.7% of the variance in the results obtained with Mycobacterium sp. could be represented by seven principal components. In all cases, solvent toxicity could explain over a third of the variability in the data. R. erythropolis cells were able to maintain their viability under harsh conditions. A period of contact between cells and solvent, prior to the addition of substrate, was prejudicial for R. erythropolis and A. simplex cells, at least for the most toxic solvents, but was beneficial for X. Py2 cells. The number of Mycobacterium sp. cells in clusters was lower after an adaptation period compared to the number of cells in aggregates when the substrate was added at time zero. The substrates transformed by R. erythropolis and A. simplex cells increased the toxicity of the system by decreasing the log P of the reaction mixture. Hydrocortisone was responsible for a reduction in the ability of A. simplex to respond to stress conditions. Mycobacterium sp. cells were apparently unaffected by beta-sitosterol. The results obtained are useful for the design of more efficient two-phase reaction systems where solvent toxicity may be overcome in order to increase cell productivity.

Algorithms↗

PubMed2003

Frozen cancellous bone allografts: positive cultures of implanted grafts in posterior fusions of the spine.

We have carried out a study on the behaviour pattern of implanted allografts initially stored in perfect conditions (aseptically processed, culture-negative and stored at -80 degrees C) but which presented positive cultures at the implantation stage. There is no information available on how to deal with this type of situation, so our aim was to set guidelines on the course of action which would be required in such a case. This was a retrospective study of 112 patients who underwent a spinal arthrodesis and in whom a total of 189 allograft pieces were used. All previous bone and blood cultures and tests for hepatitis B and C, syphilis and HIV (via PCR techniques) were negative. The allografts were stored by freezing them at -80 degrees C. A sample of the allograft was taken for culture in the operating theatre just before its implantation in all cases. The results of the cultures were obtained 3-5 days after the operation. There were 22 allografts with positive culture results (12%) after implantation. These allografts were implanted in 16 patients (14%). Cultures were positive for staphylococci coagulase negative (ECN) in 10 grafts (46%), Pseudomonas stutzeri in two grafts (9%), Corynebacterium jeikeium in two grafts (9%), staphylococci coagulase positive in two grafts (9%) and for each of the following organisms in one case each (4%): Corynebacterium spp., Actinomyces odontolyticus, Streptococcus mitis, Peptostreptococcus spp., Rhodococcus equi and Bacillus spp. No clinical infection was seen in any of these patients. Positive cultures could be caused by non-detected contamination at harvesting, storing or during manipulation before implantation. The lack of clinical signs of infection during the follow-up of our patients may indicate that no specific treatment different from our antibiotic protocol is required in the case of positive culture results of a graft piece after implantation.

Adolescent↗

PubMed2006

Bioremediation of hydrocarbon-contaminated polar soils.

Bioremediation is increasingly viewed as an appropriate remediation technology for hydrocarbon-contaminated polar soils. As for all soils, the successful application of bioremediation depends on appropriate biodegradative microbes and environmental conditions in situ. Laboratory studies have confirmed that hydrocarbon-degrading bacteria typically assigned to the genera Rhodococcus, Sphingomonas or Pseudomonas are present in contaminated polar soils. However, as indicated by the persistence of spilled hydrocarbons, environmental conditions in situ are suboptimal for biodegradation in polar soils. Therefore, it is likely that ex situ bioremediation will be the method of choice for ameliorating and controlling the factors limiting microbial activity, i.e. low and fluctuating soil temperatures, low levels of nutrients, and possible alkalinity and low moisture. Care must be taken when adding nutrients to the coarse-textured, low-moisture soils prevalent in continental Antarctica and the high Arctic because excess levels can inhibit hydrocarbon biodegradation by decreasing soil water potentials. Bioremediation experiments conducted on site in the Arctic indicate that land farming and biopiles may be useful approaches for bioremediation of polar soils.

Antarctic Regions↗

PubMed2005

Diversity of cultivable actinobacteria in geographically widespread marine sediments.

Reports describing actinobacteria isolated from marine environments have been dominated by Micromonospora, Rhodococcus and Streptomyces species. Recent culture-independent studies have shown that marine environments contain a high diversity of actinobacterial species that are rarely, if at all, recovered by cultivation-based methods. In this study, it is shown that cultivation-independent methods can be used to guide the application of selective isolation methods. The detection of marine-derived actinobacterial species that have previously only been reported from terrestrial habitats is highlighted. This study provides good evidence that the previously described low diversity of actinobacterial species isolated from marine environments does not reflect an actual low species diversity, and that the use of informed selective isolation procedures can aid in the isolation of members of novel taxa.

Actinobacteria↗

PubMed2006

Culturable actinobacteria from the marine sponge Hymeniacidon perleve: isolation and phylogenetic diversity by 16S rRNA gene-RFLP analysis.

A total of 106 actinobacteria associated with the marine sponge Hymeniacidon perleve collected from the Yellow Sea, China were isolated using eight different media. The number of species and genera of actinobacteria recovered from the different media varied significantly, underlining the importance of optimizing the isolation conditions. The phylogenetic diversity of the actinobacteria isolates was assessed using 16S rRNA gene amplification-restriction fragment length polymorphism (RFLP) analysis of the 106 strains with different morphologies. The RFLP fingerprinting of selected strains by HhaI-digestion of the 16S rRNA genes resulted in 11 different patterns. The HhaI-RFLP analysis gave good resolution for the identification of the actinobacteria isolates at the genus level. A phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates belonged to seven genera of culturable actinobacteria including Actinoalloteichus, Micromonospora, Nocardia, Nocardiopsis, Pseudonocardia, Rhodococcus, and Streptomyces. The dominant genus was Streptomyces, which represented 74% of the isolates. Three of the strains identified are candidates for new species.

Actinobacteria↗

PubMed2006

Catabolic pathways and biotechnological applications of microbial caffeine degradation.

Catabolism of caffeine (1,3,7-trimethylxanthine) in microorganisms commences via two possible mechanisms: demethylation and oxidation. Through the demethylation route, the major metabolite formed in fungi is theophylline (1,3-dimethylxanthine), whereas theobromine (3,7-dimethylxanthine) is the major metabolite in bacteria. In certain bacterial species, caffeine has also been oxidized directly to trimethyl uric acid in a single step. The conversion of caffeine to its metabolites is primarily brought about by N-demethylases (such as caffeine demethylase, theobromine demethylase and heteroxanthinedemethylase), caffeine oxidase and xanthine oxidase that are produced by several caffeine-degrading bacterial species such as Pseudomonas putida and species within the genera Alcaligenes, Rhodococcus and Klebsiella. Development of biodecaffeination techniques using these enzymes or using whole cells offers an attractive alternative to the present existing chemical and physical methods removal of caffeine, which are costly, toxic and non-specific to caffeine. This review mainly focuses on the biochemistry of microbial caffeine degradation, presenting recent advances and the potential biotechnological application of caffeine-degrading enzymes.

Bacterial Proteins↗

PubMed2006

Biodegradation kinetics of the nitramine explosive CL-20 in soil and microbial cultures.

The cyclic nitramine explosive CL-20 (C(6)H(6)N(12)O(12), 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12 -hexaazaisowurtzitane) is a relatively new energetic compound which could be a persistent organic pollutant. To follow its biodegradation dynamics, CL-20 was added to soil alone or together with organic co-substrates and N-source and incubated under oxic and anoxic conditions. Without co-substrates, the CL-20 degradation was detectable only under anoxic conditions. The highest degradation rate was found under aerobic conditions and with the addition of co-substrates, succinate and pyruvate being more efficient than acetate, glucose, starch or yeast extract. When added to intact soil, CL-20 degradation was not affected by the N content, but in soil serially diluted with N-free succinate-mineral medium, the process became N-limited. About 40% of randomly selected bacterial colonies grown on succinate agar medium were able to decompose CL-20. Based on 16S rDNA gene sequence and cell morphology, they were affiliated to Pseudomonas, Rhodococcus, Ochrobactrum, Mycobacterium and Ralstonia. In the pure culture of Pseudomonas sp. MS-P grown on the succinate-mineral N(+) medium, the degradation kinetics were first order with the same apparent kinetic constant throughout growth and decline phases of the batch culture. The observed kinetics agreed with the model that supposes co-metabolic transformation of CL-20 uncoupled from cell growth, which can be carried out by several constitutive cellular enzymes with wide substrate specificity.

Aerobiosis↗

PubMed2006

Association between the presence of bacterial 16S RNA in prostate specimens taken during transurethral resection of prostate and subsequent risk of prostate cancer (Sweden).

OBJECTIVE: To study bacterial 16S RNA in archival prostate samples from 352 patients with benign prostate hyperplasia (BPH) and evaluate whether the presence of bacterial DNA was different in those who later developed prostate cancer (n = 171) and in the matched controls that did not progress to cancer (n = 181). METHODS: 16S DNA PCR followed by cloning and sequencing the positive samples. RESULTS: In 96/352 (27%) of the prostate tissue specimens 16S RNA were detected. Sequence analysis revealed Propionibacterium acnes as the predominant microorganism (23% of 16S RNA positive patients). The second most frequent isolate-Escherichia coli was found in 12 (12%) patients. The other isolates included Pseudomonas sp. (3 patients), Actinomyces sp. (2), Streptococcus mutans (1), Corynebacterium sp. (2), Nocardioides sp. (1), Rhodococcus sp. (1) Veillonella sp. (2). In P. acnes positive samples 62% exhibited severe histological inflammation versus 50% in the bacteria-negative group (p = 0.602). The presence of P. acnes in the prostate was associated with prostate cancer development (OR 2.17, 95% CI 0.77-6.95). CONCLUSIONS: This study has revealed P. acnes as the most common bacteria in the prostate in BPH. Further studies are needed to clarify its role in contributing to the development of prostatic inflammation and prostate cancer.

Aged↗

PubMed2006

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.

1,2,3-Trichloropropane (TCP) is a highly toxic, recalcitrant byproduct of epichlorohydrin manufacture. Haloalkane dehalogenase (DhaA) from Rhodococcus sp. hydrolyses the carbon-halogen bond in various halogenated compounds including TCP, but with low efficiency (k (cat)/K (m )= 36 s(-1) M(-1)). A Cys176Tyr-DhaA mutant with a threefold higher catalytic efficiency for TCP dehalogenation has been previously obtained by error-prone PCR. We have used molecular simulations and quantum mechanical calculations to elucidate the molecular mechanisms involved in the improved catalysis of the mutant, and enantioselectivity of DhaA toward TCP. The Cys176Tyr mutation modifies the protein access and export routes. Substitution of the Cys residue by the bulkier Tyr narrows the upper tunnel, making the second tunnel "slot" the preferred route. TCP can adopt two major orientations in the DhaA enzyme, in one of which the halide-stabilizing residue Asn41 forms a hydrogen bond with the terminal halogen atom of the TCP molecule, while in the other it bonds with the central halogen atom. The differences in these binding patterns explain the preferential formation of the (R)- over the (S)-enantiomer of 2,3-dichloropropane-1-ol in the reaction catalyzed by the enzyme.

Hydrolases↗

PubMed2005

Characterization of clinical isolates of pathogenic Nocardia strains and related actinomycetes in Thailand from 1996 to 2003.

In Thailand from 1996 to 2003, 171 strains of pathogenic aerobic actinomycetes from clinical specimens were isolated. Of those strains, 134 were mycolic acid containing actinomycetes, including 96 strains of Nocardia species. Others included 10 strains of Gordonia, 14 strains of Rhodococcus, and 22 strains of Mycobacterium. One strain each of the genera Tsukamurella and Corynebacterium were also isolated. Also identified were 27 strains of non-mycolic acid containing actinomycetes. Our identification studies of 96 strains of Nocardia species showed that significant pathogens in Thailand were N. beijingensis (18 strains), N. cyriacigeorgica (13 strains), and N. farcinica (34 strains); the most prevalent species was N. farcinica (35.4%). We also isolated four strains of N. asiatica, five strains of N. asteroides sensu stricto, four strains of N. nova, seven strains of N. otitidiscaviarum, eight strains of N. transvalensis, and two strains of N. pseudobrasiliensis.

Actinobacteria↗

PubMed1993

New method for the isolation of polyglycosylceramides from human erythrocyte membranes.

A new procedure was developed for the isolation of long-chain, highly polar glycosphingolipids from human erythrocytes. The membrane material left after extraction of membrane lipids with organic solvents was peracetylated in a mixture of formamide, pyridine and acetic anhydride, and the acetylated products were then extracted with chloroform. The material was fractionated and purified by means of Sephadex LH-20, Sephadex LH-60 and silica-gel chromatography. The final preparations were mixtures of highly polar glycosphingolipids containing from 7 to 31 sugar residues relative to sphingosine. GC-MS analysis of the sugar part of the isolated fractions showed the presence of branched polyglycosyl chains of N-acetyllactosaminyl type. Endo-beta-galactosidase (Bacteroides fragilis) liberated from the deacetylated material two glycosphingolipids, which were identified by fast atom bombardment-mass spectrometry as Hex-Cer and HexNAc-Hex-Hex-Cer with sphingosine and mainly 24 and 22 carbon fatty acids. Endoglycoceramidase (Rhodococcus) degraded polyglycosylceramides to free ceramides and free polysaccharides. The released sugars were fractionated by high-pH ion-exchange chromatography into fractions differing in sialic acid content. The procedure presented in this paper can be used for large and small scale preparations of complex glycosphingolipids. It proved to be especially suitable for screening for polyglycosylceramides in different tissues.

Carbohydrate Sequence↗

PubMed1992

Light-induced oxidation of iron atoms in a photosensitive nitrile hydratase.

The photoactivation process of a photosensitive nitrile hydratase (NHase) from Rhodococcus sp. N-771 has been investigated by 57Fe Mössbauer spectroscopy and magnetic susceptibility measurements in order to clarify the behavior of iron atoms in the enzyme. Mössbauer spectra of inactive NHase gave two symmetric-doublet components indicating the presence of two iron species, while that of the active NHase gave a single symmetric doublet indicating the presence of a single iron species. Magnetic susceptibility measurements of the inactive and active HNase both showed small effective magnetic moments. These results led us to conclude that one of the two iron atoms incorporated in the NHase is oxidized during photoactivation, namely from a low spin ferrous to a low spin ferric state. This is the first observation of an intramolecular photooxidation phenomena involving iron in a single protein molecule.

Enzyme Activation↗