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Applied Microbiology and Biotechnology (v.63, #4)
The challenge of multidrug resistance: actual strategies in the development of novel antibacterials by F. R. Schmidt (pp. 335-343).
Bacterial resistance against established antibiotics is becoming an increasingly important global healthcare problem. Despite enormous efforts, the number of therapeutically useful compounds that emerge from chemical derivatisation programs, which aim at circumventing mechanisms of resistance, is continuously decreasing and no truly novel class of compound has been introduced into therapy for nearly four decades. Hopes are now set on a thorough elucidation of bacterial cell functions to identify new bacterial target sites, and on the development of novel compounds with alternative modes of action. The pursuit of these strategies is rendered possible by employment of biotechnologically based methods such as in vivo modification of biosynthetic routes in antibiotic-producing organisms, large-scale screening assays with isolated bacterial targets, the molecular profiling of bacterial genomes and proteomes, and the development and clinical use of biochips as diagnostic tools for rapid identification and characterization of pathogenic strains. As one of the most promising class of compounds known to date with unique modes of action that escape most known mechanisms of resistance, peptic agents have recently came under the focus of anti-infective research, just as extracellular signalling molecules (autoinducer) have emerged as new bacterial target sites.
The biosynthesis of glycopeptide antibiotics—a model for complex, non-ribosomally synthesized, peptidic secondary metabolites by R. D. Süssmuth; W. Wohlleben (pp. 344-350).
Glycopeptide antibiotics are a class of widely known natural compounds produced by Actinomycetes. Vancomycin, the first member of the glycopeptide family to be discovered, was described in 1955 and used as an antibiotic soon thereafter. During the past 50 years numerous contributions on the structure, mode of action, and therapeutic features of vancomycin have been published. Recently, there has been considerable progress in elucidating the biosynthesis of glycopeptide antibiotics by combining molecular biology and analytical chemistry methods. Here, we provide an overview of the current knowledge regarding biosynthetic glycopeptide assembly.
Environmental and cultural stimulants in the production of carotenoids from microorganisms by P. Bhosale (pp. 351-361).
Commercial production of carotenoids from microorganisms competes mainly with synthetic manufacture by chemical procedures. Efficient stimulation of carotenoid biosynthesis is expected to promote accumulation of carotenoid by microbes. This review describes the variety of environmental and cultural stimulants studied during the last few decades which enhance volumetric production and cellular accumulation of commercially important carotenoids from microalgae, fungi and bacteria. Stimulation of carotenoid production by white-light illumination and temperature fluctuation is discussed along with supplementation of metal ions, salts, organic solvents, preformed precursors and several other chemicals in the culture broth. Reports on the improvements in yield are reviewed and assessed from a biotechnology point of view.
Biochemical properties and substrate specificities of alkaline and histidine acid phytases by B.-C. Oh; W.-C. Choi; S. Park; Y.-o. Kim; T.-K. Oh (pp. 362-372).
Phytases are a special class of phosphatase that catalyze the sequential hydrolysis of phytate to less-phosphorylated myo-inositol derivatives and inorganic phosphate. Phytases are added to animal feedstuff to reduce phosphate pollution in the environment, since monogastric animals such as pigs, poultry, and fish are unable to metabolize phytate. Based on biochemical properties and amino acid sequence alignment, phytases can be categorized into two major classes, the histidine acid phytases and the alkaline phytases. The histidine acid phosphatase class shows broad substrate specificity and hydrolyzes metal-free phytate at the acidic pH range and produces myo-inositol monophosphate as the final product. In contrast, the alkaline phytase class exhibits strict substrate specificity for the calcium–phytate complex and produces myo-inositol trisphosphate as the final product. This review describes recent findings that present novel viewpoints concerning the molecular basis of phytase classification.
Reductive dehalogenation of tetrachloroethylene by microorganisms: current knowledge and application strategies by G. Chen (pp. 373-377).
Reductive anaerobic dehalogenation is a useful method for remediation of sites contaminated by chlorinated ethylenes, where hydrogen concentration plays the key role. Under anaerobic conditions, dehalogenating bacteria compete best against methanogenic consortia when the hydrogen level is low; and methanogenic consortia outplay dehalogenating bacteria when the hydrogen level is high. Thus, in an anaerobic mixed culture, efficient use of hydrogen for dehalogenation can be achieved by strategies that maintain hydrogen at a certain low concentration. However, due to the role of acetate, expected dehalogenating results cannot be obtained and unexpected methane formation can be encountered in practice.
Biosynthesis of fructo-oligosaccharides by Sporotrichum thermophile during submerged batch cultivation in high sucrose media by P. Katapodis; E. Kalogeris; D. Kekos; B. J. Macris; P. Christakopoulos (pp. 378-382).
Biosynthesis of fructo-oligosaccharides (FOS) was observed during growth of the thermophilic fungus Sporotrichum thermophile on media containing high sucrose concentrations. Submerged batch cultivation with the optimum initial sucrose concentration of 250 g/l allowed the production of 12.5 g FOS/l. The FOS mixture obtained was composed of three sugars, which were isolated by size-exclusion chromatography. They were characterized by acid hydrolysis and HPLC as 1-kestose, 6-kestose and neokestose. The mechanism of osmotic adaptation of S. thermophile was investigated and sugars and amino acids were found to be the predominant compatible solutes. The fungus accumulated glutamic acid, arginine, alanine, leucine and lysine, in order to balance the outer osmotic pressure. Fatty acid analysis of the membrane lipids showed a relatively high percentage of unsaturated lipids, which is known to be associated with high membrane fluidity.
Characteristics of fungal phytases from Aspergillus fumigatus and Sartorya fumigata by R. Brugger; C. Simões Nunes; D. Hug; K. Vogel; P. Guggenbuhl; F. Mascarello; S. Augem; M. Wyss; A. P. G. M. van Loon; L. Pasamontes (pp. 383-389).
Aspergillus fumigatus phytase has previously been identified as a phytase with a series of favourable properties that may be relevant in animal and human nutrition, both for maximising phytic acid degradation and for increasing mineral and amino acid availability. To study the natural variability in amino acid sequence and its impact on the catalytic properties of the enzyme, we cloned and overexpressed the phytase genes and proteins from six new purported A. fumigatus isolates. Five of these phytases displayed ≤2 amino acid substitutions and had virtually identical stability and catalytic properties when compared with the previously described A. fumigatus ATCC 13073 phytase. In contrast, the phytase from isolate ATCC 32239 (Sartorya fumigata, the anamorph of which was identified as A. fumigatus) was more divergent (only 86% amino acid sequence identity), had a higher specific activity with phytic acid, and displayed distinct differences in substrate specificity and pH-activity profile. Finally, comparative experiments confirmed the favourable stability and catalytic properties of A. fumigatus phytase.
Improved recovery of active recombinant laccase from maize seed by M. R. Bailey; S. L. Woodard; E. Callaway; K. Beifuss; M. Magallanes-Lundback; J. R. Lane; M. E. Horn; H. Mallubhotla; D. D. Delaney; M. Ward; F. Van Gastel; J. A. Howard; E. E. Hood (pp. 390-397).
Lignolytic enzymes such as laccase have been difficult to over-express in an active form. This paper describes the expression, characterization, and application of a fungal laccase in maize seed. The transgenic seed contains immobilized and extractable laccase. Fifty ppm dry weight of aqueously extractable laccase was obtained, and the remaining solids contained a significant amount of immobilized laccase that was active. Although a portion of the extractable laccase was produced as inactive apoenzyme, laccase activity was recovered by treatment with copper and chloride. In addition to allowing the apoenzyme to regain activity, treatment with copper also provided a partial purification step by precipitating other endogenous corn proteins while leaving >90% of the laccase in solution. The data also demonstrate the application of maize-produced laccase as a polymerization agent. The apparent concentration of laccase in ground, defatted corn germ is approximately 0.20% of dry weight.
A chitinase with high activity toward partially N-acetylated chitosan from a new, moderately thermophilic, chitin-degrading bacterium, Ralstonia sp. A-471 by A. Sutrisno; M. Ueda; Y. Abe; M. Nakazawa; K. Miyatake (pp. 398-406).
A moderately thermophilic bacterium, strain A-471, capable of degrading chitin was isolated from a composting system of chitin-containing waste. Analysis of the 16S rDNA sequence revealed that the bacterium belongs to the genus Ralstonia. A thermostable chitinase A (Ra-ChiA) was purified from culture fluid of the bacterium grown in colloidal chitin medium. Purification of the enzyme was achieved mainly by exploiting its binding to the colloidal chitin. The molecular mass of the enzyme was estimated to be 70 kDa and the isoelectric point approximately 4.7. N-terminal amino acid sequencing revealed a sequence of ADPYLKVAYYP, which had high homology (66% identity) with that of chitinase A1 from Bacillus circulans WL-12. The pH and temperature optima were determined to be 5.0 and 70°C, respectively. The enzyme was classified as a retaining glycosyl hydrolase and was most active against partially N-acetylated chitosans. Its activities towards the partially N-acetylated chitosans, i.e. chitosan 7B, chitosan 8B, and chitosan 9B, were about 11-fold, 9-fold, and 5-fold higher than towards colloidal chitin, respectively. Ra-ChiA cleaved (GlcNAc)6 almost exclusively into (GlcNAc)2. Activation of Ra-ChiA was observed by the addition of 1 mM Cu2+, Mn2+, Ca2+ , or Mg2+. Degradation of the partially N-acetylated chitosan produced oligosaccharides with a degree of polymerization ranging from 1–8; these are products that offer potential application for functional oligosaccharide production.
Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations by K. Al Zaid Siddiquee; M. J. Arauzo-Bravo; K. Shimizu (pp. 407-417).
Metabolic flux analysis based on 13C-labeling experiments followed by the measurement of intracellular isotope distribution using both 2D NMR and GC-MS was carried out to investigate the effect of pyruvate kinase (pyk) gene knockout on the metabolism of Escherichia coli in continuous culture. In addition, the activities of 16 enzymes, and the concentrations of 5 intracellular metabolites, were measured as a function of time in batch culture as well as continuous culture. It was found that flux through phosphoenol pyruvate carboxylase and malic enzyme were up-regulated in the pykF − mutant as compared with the wild type, and acetate formation was significantly reduced in the mutant. In addition, flux through the phosphofructose kinase pathway was reduced and that through the oxidative pentose phosphate (PP) pathway increased in the mutant. This was evidenced by the corresponding enzyme activities, and the increase in the concentrations of phosphoenol pyruvate, glucose-6-phosphate and 6-phosphogluconate, etc. It was also found for continuous cultivation that the enzyme activities of the oxidative PP and Entner-Doudoroff pathways increased as the dilution rate increased for the pykF − mutant. To clarify the metabolism quantitatively, it was found to be quite important to integrate the information on intracellular metabolic flux distribution, enzyme activities and intracellular metabolite concentrations.
Development of a bisphenol A-adsorbing yeast by surface display of the Kluyveromyces yellow enzyme on Pichia pastoris by M. Mergler; K. Wolf; M. Zimmermann (pp. 418-421).
A novel surface-engineered strain of yeast Pichia pastoris was constructed that displays at its surface Kluyveromyces lactis Yellow Enzyme (KYE) fused to the C-terminal half of Saccharomyces cerevisiae α-agglutinin. The expression of the fusion protein was controlled by the AOX1-promoter. The new strain showed an increased sorption of the xenoestrogen Bisphenol A (BPA). It was shown that sorption of BPA depended on the presence of methanol in the growth medium and on the pH of the binding assays. The binding kinetics were typical for binding at a surface. The present results demonstrate that the α-agglutinin surface display system can be used in the yeast P. pastoris.
Characterization of Aspergillus oryzae fermentation extract effects on the rumen fungus Neocallimastix frontalis, EB 188. Part 1. Zoospore development and physiology by J. A. Schmidt; S. Albright; K.-P. Tsai; G. M. Calza; J. S. Chang; R. E. Calza (pp. 422-430).
Experiments were performed to determine the effect of Aspergillus oryzae (AO) fermentation extract on zoospore development in the rumen fungus Neocallimastix frontalis EB 188. Powdered product, or liquid extract prepared from such powder, was added at the recommended value for supplementation in dairy cattle. Stationary and stirred cultures were periodically sampled and assayed for extracellular and intracellular protein and enzymes, gas production, zoospore production and maturation, and carbon source utilization. Soluble extract increased fungal physiology when grown in stirred vessels or stationary cultures. Treated cultures produced higher levels of enzymes (nearly double). Mobile zoospores matured into germination entities more rapidly in treated cultures, and when powdered product was used, nearly 3 times more motile zoospores were produced at 56 h of fungal growth. Levels of the intracellular enzyme malate dehydrogenase increased by 6-fold in the presence of powdered product. Product wheat bran carrier used as soluble extract or powder had very little effect on fungal cultures. Medium cellulose was completely hydrolyzed in all cultures but this occurred earlier in those containing AO treatment.
Characterization of Aspergillus oryzae fermentation extract effects on the rumen fungus Neocallimastix frontalis, EB 188. Part 2. Carbon source utilization and effects on zoospore production by J. A. Schmidt; S. Albright; G. M. Calza; R. E. Calza (pp. 431-437).
The effect of a commercial Aspergillus oryzae fermentation extract on the utilization of carbon source and zoospore production by the rumen fungus Neocallimastix frontalis EB 188 was determined. In addition, the composition of a soluble extract prepared from the commercial product was analyzed. This extract was added to N. frontalis EB 188 cultures grown on a variety of substrates and periodically assayed for protein, enzymes, zoospore production, and carbon source utilization. The powdered product contained 93% dry matter, more than 3,000 A. oryzaespores per gram, and did not contain strong buffers or high concentrations of salt. Measurable concentrations of DNA, protein, carbohydrate and several enzymes including cellulase and amylase were also found. Soluble extract increased fungal physiology and treated cultures produced significantly higher levels of supernatant protein and enzymes including amylase, cellulase and β-glucosidase. The fungal response depended on culture carbon source. However, culture zoospore production was increased regardless of substrate provided. Culture utilization of glucose was more rapid in treated cultures, yet high levels of the extract greatly inhibited glucose utilization.
Screening of tetrachlorodibenzo-p-dioxin-degrading fungi capable of producing extracellular peroxidases under various conditions by S. Manji; A. Ishihara (pp. 438-444).
Forty-six pulp-bleaching fungi were screened for production of key enzymes for conversion of polychlorinated dibenzo-p-dioxins—lignin peroxidase (LiP), manganese peroxidase (MnP), and manganese-independent peroxidase (MiP)—under various conditions that would allow their utilization in the environment. Of 38 MnP-producing strains with MiP activity, 22 produced LiP. Three of the new isolates, Bjerkandera sp. strains MS191, MS325, and MS1167, were the best producers of the three different peroxidases, and had reasonable growth rates. The most promising Bjerkandera sp. strain, MS325, exhibited significant levels of LiP and MnP activities under various conditions, e.g., nutrient nitrogen-sufficient or -limited conditions, conditions with or without Mn(II), and changes in temperature (15–37°C). Furthermore, the ability of this strain to degrade 1,3,6,8-tetrachlorodibenzo-p-dioxin was confirmed. The results presented here indicate that utilization of Bjerkandera sp. strain MS325 on a practical scale in the environment has several advantages over many white rot fungi, which produce extracellular peroxidases only under specific conditions such as nutrient limitation.
Inorganic tin and organotin interactions with Candida maltosa by J. S. White; J. M. Tobin (pp. 445-451).
As a consequence of the widespread industrial and agricultural applications of organotins, contamination of various ecosystems has occurred in recent decades. Understanding how these compounds interact with microorganisms is important in assessing the risks of organotin pollution. The organotins, tributyltin (TBT), trimethyltin (TMT) and inorganic tin, Sn(IV), were investigated for their physical interactions with non-metabolising cells and protoplasts of the yeast Candida maltosa, an organism that is often associated with contaminated environments. Uptake, toxicity and membrane-acting effects of these compounds, at concentrations approximating those found in polluted environments, were assessed. Sn(IV) and TBT uptake occurred by different mechanisms. Uptake of Sn(IV) was 2-fold greater in intact cells than protoplasts, underlining the importance of cell wall binding, whereas TBT uptake levels by both cell types were similar. TBT uptake resulted in cell death and extensive K+ leakage, while Sn(IV) uptake had no effect. TMT did not interact with cells. Of the three compounds, TBT alone altered membrane fluidity, as measured by the fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene incorporated into cells. Anisotropy of 1-(4-trimethylaminophenyl-6-phenyl-1,3,5-hexatriene) was not affected, implying that TBT is not confined to the surface of the cytoplasmic membrane, but acts within membrane lipids. These results indicate that the cell wall is the dominant site of Sn(IV) interactions with yeast, while lipophilic interactions play an important role in uptake and toxicity of TBT.
Evaluation of bacterial strategies to promote the bioavailability of polycyclic aromatic hydrocarbons by A. R. Johnsen; U. Karlson (pp. 452-459).
Polycyclic aromatic hydrocarbon (PAHs)-degrading bacteria may enhance the bioavailability of PAHs by excreting biosurfactants, by production of extracellular polymeric substances, or by forming biofilms. We tested these hypotheses in pure cultures of PAHs-degrading bacterial strains. Most of the strains did not substantially reduce the surface tension when grown on PAHs in liquid shaken cultures. Thus, pseudo-solubilization of PAHs in biosurfactant micelles seems not to be a general strategy for these isolates to enhance PAHs-bioavailability. Three semi-colloid Sphingomonas polysaccharides all increased the solubility of PAHs (Gellan 1.3- to 5.4-fold, Welan 1.8- to 6.0-fold and Rhamsan 2.4- to 9.0-fold). The increases were most pronounced for the more hydrophobic PAHs. The polysaccharide-sorbed PAHs were bioavailable. Mineralization rates of 9-[14C]-phenanthrene and 3-[14C]-fluoranthene by Sphingobium EPA505, were similar with and without sphingans, indicating that mass-transfer rates from PAHs crystals to the bulk liquid were unaffected by the polysaccharides. Biofilm formation on PAHs crystals may favor the diffusive mass transfer of PAHs from crystals to the bacterial cells. A majority of the PAHs-degraders tested formed biofilms in microtiter wells coated with PAHs crystals. For strains capable of growing on different PAHs; the more soluble the PAHs, the lower the percentage of cells attached. Biofilm formation on PAHs-sources was the predominant mechanism among the tested bacteria to overcome mass transfer limitations when growing on poorly soluble PAHs.
Bioavailability of pentachlorophenol to acclimatised bacteria under batch and flow-through conditions by Y. Dudal; A. R. Jacobson; R. Samson; L. Deschênes (pp. 460-465).
Biodegradation of organic contaminants in multi-phase systems, such as soils and aquifers, is often limited by the extent and the rate of contaminant sorption onto the solid matrix. However, information about biodegradation in complex matrices is largely limited to studies of closed systems under batch conditions in which potential bioavailability is characterised by the aqueous-phase concentration of a contaminant. There is little knowledge regarding the influence of flow-through conditions on the availability of contaminants to microbes (contaminant bioavailability). Thus, the aim of this study was to assess and compare contaminant bioavailability, in the presence of a sorptive medium, under both batch and flow-through conditions. Accordingly, experiments were designed in which pentachlorophenol (PCP) was introduced into a mixture of inoculated silica sand and a PCP-retaining resin, under either batch or flow-through (columns) conditions. The results indicated that an increase in the amount of resin (0.1–0.2 g) clearly lowered PCP availability to microbes after 170 h under batch conditions (30 and 45% respectively); whereas, the initial decrease in bioavailability observed under flow-through conditions (45 and 70% respectively) was reversed and no longer observable after 170 h. This increase in PCP availability was linked to an improvement in the contaminant biodegradation capacity from 0.03 to 0.13 mg·l−1·h−1 over 200 h.
Community structure of microbial biofilms associated with membrane-based water purification processes as revealed using a polyphasic approach by C.-L. Chen; W.-T. Liu; M.-L. Chong; M.-T. Wong; S. L. Ong; H. Seah; W. J. Ng (pp. 466-473).
The microbial communities of membrane biofilms occurring in two full-scale water purification processes employing microfiltration (MF) and reverse osmosis (RO) membranes were characterized using a polyphasic approach that employed bacterial cultivation, 16S rDNA clone library and fluorescence in situ hybridization techniques. All methods showed that the α-Proteobacteria was the largest microbial fraction in the samples, followed by the γ-Proteobacteria. This suggested that members of these two groups could be responsible for the biofouling on the membranes studied. Furthermore, the microbial community structures between the MF and RO samples were considerably different in composition of the most predominant 16S rDNA clones and bacterial isolates from the α-Proteobacteria and only shared two common groups (Bradyrhizobium, Bosea) out of more than 17 different bacterial groups observed. The MF and RO samples further contained Planctomycetes and Fibroacter/Acidobacteria as the second predominant bacterial clones, respectively, and differed in minor bacterial clones and isolates. The community structure differences were mainly attributed to differences in feed water, process configurations and operating environments, such as the pressure and hydrodynamic conditions present in the water purification systems.