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Applied Microbiology and Biotechnology (v.57, #5-6)

Bioinformatic tools for DNA/protein sequence analysis, functional assignment of genes and protein classification by B. Rehm (pp. 579-592).

The development of efficient DNA sequencing methods has led to the achievement of the DNA sequence of entire genomes from (to date) 55 prokaryotes, 5 eukaryotic organisms and 10 eukaryotic chromosomes. Thus, an enormous amount of DNA sequence data is available and even more will be forthcoming in the near future. Analysis of this overwhelming amount of data requires bioinformatic tools in order to identify genes that encode functional proteins or RNA. This is an important task, considering that even in the well-studied Escherichia coli more than 30% of the identified open reading frames are hypothetical genes. Future challenges of genome sequence analysis will include the understanding of gene regulation and metabolic pathway reconstruction including DNA chip technology, which holds tremendous potential for biomedicine and the biotechnological production of valuable compounds. The overwhelming volume of information often confuses scientists.This review intends to provide a guide to choosing the most efficient way to analyze a new sequence or to collect information on a gene or protein of interest by applying current publicly available databases and Web services. Recently developed tools that allow functional assignment of genes, mainly based on sequence similarity of the deduced amino acid sequence, using the currently available and increasing biological databases will be discussed.

Biotechnology and genetics of ergot alkaloids by P. Tudzynski; T. Correia; U. Keller (pp. 593-605).

Ergot alkaloids, i.e. ergoline-derived toxic metabolites, are produced by a wide range of fungi, predominantly by members of the grass-parasitizing family of the Clavicipitaceae. Naturally occurring alkaloids like the D-lysergic acid amides, produced by the "ergot fungus" Claviceps purpurea, have been used as medicinal agents for a long time. The pharmacological effects of the various ergot alkaloids and their derivatives are due to the structural similarity of the tetracyclic ring system to neurotransmitters such as noradrenaline, dopamine or serotonin. In addition to "classical" indications, e.g. migraine or blood pressure regulation, there is a wide spectrum of potential new applications of this interesting group of compounds. The biotechnology of ergot alkaloids has a long tradition, and efficient parasitic and submerse production processes have been developed; the biochemistry of the pathway and the physiology of production have been worked out in detail. The recent identification of a cluster of genes involved in ergot alkaloid biosynthesis in C. purpurea and the availability of molecular genetic techniques allow the development of strategies for rational drug design of ergoline-related drugs by enzyme engineering and by biocombinatorial approaches.

Current status of the anticoagulant hirudin: its biotechnological production and clinical practice by J. Sohn; H. Kang; K. Rao; C. Kim; E. Choi; B. Chung; S. Rhee (pp. 606-613).

Hirudin is a potent thrombin inhibitor originally derived from the medicinal leech, Hirudo medicinalis. Owing to its high affinity and specificity for thrombin, hirudin has been intensively investigated for research and therapeutic purposes. The investigation of hirudin has contributed greatly to the understanding of the mode of action of thrombin and the clotting system. Hirudin and several hirudin analogues have also been demonstrated to have several advantages as a highly specific anticoagulant over the most widely used drug, heparin. Due to the great demand for hirudin in physicochemical and clinical studies, various recombinant systems have been developed, using bacteria, yeasts, and higher eukaryotes, to obtain the biologically active hirudin in significant quantities. After 10 years of clinical applications, two recombinant hirudins and a hirudin analogue have gained marketing approval from the United States Food and Drug Administration, for several applications. Clinical trials are currently ongoing for other treatments for thrombotic disease. As a consequence, it is conceivable that hirudin may expand its therapeutic utility over heparin in the near future.

Antigiardial drugs by J. Harris; S. Plummer; D. Lloyd (pp. 614-619).

Giardia intestinalis is a world-wide cause of intestinal infection. Treatment of this debilitating disease is usually accomplished using one of several drugs. Metronidazole is the treatment of choice, but benzimidazoles are now being used more frequently. Other treatments include quinacrine, paromomycin and furazolidone. Even though these drugs are all used to treat the same disease, their modes of action differ in all cases. However, resistance is increasing and new alternatives are being sought. New wave antigiardials all appear to have their roots in natural herbal remedies. This mini-review looks at the current treatments available, their efficacy, side effects and different modes of action and addresses a possible way forward using natural products.

Microbial transformations of 2-substituted benzothiazoles by H. De Wever; P. Besse; H. Verachtert (pp. 620-625).

The occurrence of benzothiazoles in the environment seems to be restricted to aquatic compartments and is mainly associated with the manufacture and use of the rubber additive 2-mercaptobenzothiazole (MBT) and its derivatives. Although data on benzothiazole biotransformations in natural environments at ppb and ppt levels are scarce, the unsubstituted benzothiazole (BT) and 2-hydroxybenzothiazole (OBT) are generally considered to be biodegradable, whereas 2-methylthiobenzothiazole is recalcitrant. The fungicide 2-thiocyanomethylthiobenzothiazole is assumed to be hydrolysed to MBT, which is then further methylated. At higher concentration levels, similar conclusions can generally be drawn. In addition, BT, MBT, 2-aminobenzothiazole and benzothiazole-2-sulphonate can be biodegraded, although side- and end-products may form. For BT and MBT, threshold concentration were reported above which inhibitory effects on biological treatment processes occur. Due to the limited availability of axenic bacterial cultures capable of benzothiazole mineralization, only the initial steps of the degradation pathways have been elucidated so far.

Continuous lactic acid fermentation using a plastic composite support biofilm reactor by J. Cotton; A. Pometto; J. Gvozdenovic-Jeremic (pp. 626-630).

An immobilized-cell biofilm reactor was used for the continuous production of lactic acid by Lactobacillus casei subsp. rhamnosus (ATCC 11443). At Iowa State University, a unique plastic composite support (PCS) that stimulates biofilm formation has been developed. The optimized PCS blend for Lactobacillus contains 50% (wt/wt) agricultural products [35% (wt/wt) ground soy hulls, 5% (wt/wt) soy flour, 5% (wt/wt) yeast extract, 5% (wt/wt) dried bovine albumin, and mineral salts] and 50% (wt/wt) polypropylene (PP) produced by high-temperature extrusion. The PCS tubes have a wall thickness of 3.5 mm, outer diameter of 10.5 mm, and were cut into 10-cm lengths. Six PCS tubes, three rows of two parallel tubes, were bound in a grid fashion to the agitator shaft of a 1.2-l vessel for a New Brunswick Bioflo 3000 fermentor. PCS stimulates biofilm formation, supplies nutrients to attached and suspended cells, and increases lactic acid production. Biofilm thickness on the PCS tubes was controlled by the agitation speed. The PCS biofilm reactor and PP control reactor achieved optimal average production rates of 9.0 and 5.8 g l^–1 h^–1, respectively, at 0.4 h^–1 dilution rate and 125-rpm agitation with yields of approximately 70%.

Potential inhibitors from wet oxidation of wheat straw and their effect on growth and ethanol production by Thermoanaerobacter mathranii by H. Klinke; A. Thomsen; B. Ahring (pp. 631-638).

Alkaline wet oxidation (WO) (using water, 6.5 g/l sodium carbonate, and 12 bar oxygen at 195 °C) was used for pre-treating wheat straw (60 g/l), resulting in a hemicellulose-rich hydrolysate and a cellulose-rich solid fraction. The hydrolysate consisted of soluble hemicellulose (9 g/l), aliphatic carboxylic acids (6 g/l), phenols (0.27 g/l or 1.7 mM), and 2-furoic acid (0.007 g/l). The wet-oxidized wheat straw hydrolysate caused no inhibition of ethanol yield by the anaerobic thermophilic bacterium Thermoanaerobacter mathranii. Nine phenols and 2-furoic acid, identified to be present in the hydrolysate, were each tested in concentrations of 10–100× the concentration found in the hydrolysate for their effect on fermentation by T. mathranii. At 2 mM, these aromatic compounds were not inhibitory to growth or ethanol yield in T. mathranii. When the concentration of aromatics was increased to 10 mM, the fermentation was severely inhibited by the phenol aldehydes and to a lesser extent by the phenol ketones. By adding the same aromatic compounds to WO hydrolysate (10 mM), synergistic inhibitory effects of all tested compounds with hydrolysate components were shown. When the hydrolysate was concentrated three- and six-fold, growth and fermentation with T. mathranii were inhibited. At a six-fold hydrolysate concentration, the total concentration of phenolic monomers was 17 mM; hence aromatic monomers are an important co-factor in hydrolysate inhibition.

Modelling and optimization of environmental conditions for kefiran production by Lactobacillus kefiranofaciens by B. Cheirsilp; H. Shimizu; S. Shioya (pp. 639-646).

A mathematical model for kefiran production by Lactobacillus kefiranofaciens was established, in which the effects of pH, substrate and product on cell growth, exopolysaccharide formation and substrate assimilation were considered. The model gave a good representation both of the formation of exopolysaccharides (which are not only attached to cells but also released into the medium) and of the time courses of the production of galactose and glucose in the medium (which are produced and consumed by the cells). Since pH and both lactose and lactic acid concentrations differently affected production and growth activity, the model included the effects of pH and the concentrations of lactose and lactic acid. Based on the mathematical model, an optimal pH profile for the maximum production of kefiran in batch culture was obtained. In this study, a simplified optimization method was developed, in which the optimal pH profile was determined at a particular final fermentation time. This was based on the principle that, at a certain time, switching from the maximum specific growth rate to the critical one (which yields the maximum specific production rate) results in maximum production. Maximum kefiran production was obtained, which was 20% higher than that obtained in the constant-pH control fermentation. A genetic algorithm (GA) was also applied to obtain the optimal pH profile; and it was found that practically the same solution was obtained using the GA.

High-efficiency synthesis of oligosaccharides with a truncated β-galactosidase from Bifidobacterium bifidum by F. Jørgensen; O. Hansen; P. Stougaard (pp. 647-652).

An exceptionally large β-galactosidase, BIF3, with a subunit molecular mass of 188 kDa (1,752 amino acid residues) was recently isolated from Bifidobacterium bifidum DSM20215 [Møller et al. (2001) Appl Environ Microbiol 67:2276–2283]. The BIF3 polypeptide comprises a signal peptide followed by an N-terminal β-galactosidase region and a C-terminal galactose-binding motif. We have investigated the functional importance of the C-terminal part of the BIF3 sequence by deletion mutagenesis and expression of truncated enzyme variants in Escherichia coli. Deletion of approximately 580 amino acid residues from the C-terminal end converted the enzyme from a normal, hydrolytic β-galactosidase into a highly efficient, transgalactosylating enzyme. Quantitative analysis showed that the truncated β-galactosidase utilised approximately 90% of the reacted lactose for the production of galacto-oligosaccharides, while hydrolysis constituted a 10% side reaction. This 9:1 ratio of transgalactosylation to hydrolysis was maintained at lactose concentrations ranging from 10% to 40%, implying that the truncated β-galactosidase behaved as a "true" transgalactosylase even at low lactose concentrations.

A novel thermostable branching enzyme from an extremely thermophilic bacterial species, Rhodothermus obamensis by Mari L. Shinohara; Michiko Ihara; Masanobu Abo; Miyoko Hashida; Shinobu Takagi; Thomas C. Beck (pp. 653-659).

A branching enzyme (EC 2.4.1.18) gene was isolated from an extremely thermophilic bacterium, Rhodothermus obamensis. The predicted protein encodes a polypeptide of 621 amino acids with a predicted molecular mass of 72 kDa. The deduced amino acid sequence shares 42–50% similarity to known bacterial branching enzyme sequences. Similar to the Bacillus branching enzymes, the predicted protein has a shorter N-terminal amino acid extension than that of the Escherichia coli branching enzyme. The deduced amino acid sequence does not appear to contain a signal sequence, suggesting that it is an intracellular enzyme. The R. obamensis branching enzyme was successfully expressed both in E. coli and a filamentous fungus, Aspergillus oryzae. The enzyme showed optimum catalytic activity at pH 6.0–6.5 and 65 °C. The enzyme was stable after 30 min at 80 °C and retained 50% of activity at 80 °C after 16 h. Branching activity of the enzyme was higher toward amylose than toward amylopectin. This is the first thermostable branching enzyme isolated from an extreme thermophile.

Sequence of celQ and properties of CelQ, a component of the Clostridium thermocellum cellulosome by T. Arai; H. Ohara; S. Karita; T. Kimura; K. Sakka; K. Ohmiya (pp. 660-666).

The nucleotide sequence of the Clostridium thermocellum F1 celQ gene, which codes for the endoglucanase CelQ, consists of 2,130 bp encoding 710 amino acids. The precursor form of CelQ has a molecular weight of 79,809 and is composed of a signal peptide, a family 9 cellulase domain, a family IIIc carbohydrate-binding module (CBM), and a dockerin domain. Truncated derivatives of CelQ were constructed: CelQΔdoc consisted of the catalytic domain and the CBM; CelQcat consisted of the catalytic domain only. CelQΔdoc showed strong activity toward carboxymethylcellulose (CMC) and barley β-glucan and low activity toward Avicel, acid-swollen cellulose, lichenan, and xylan. The V _max and K _m values were 235 µmol/min/mg and 3.3 mg/ml, respectively, for CMC. By contrast, CelQcat, which was devoid of the CBM, showed negligible activity toward CMC, i.e., about 1/1,000 of the activity of CelQΔdoc, supporting the previously proposed idea that family IIIc CBMs participate in the catalytic function of the enzyme. Immunological analysis using an antiserum raised against CelQΔdoc confirmed that CelQ is a component of the C. thermocellum cellulosome.

Metabolic redirection of carbon flow toward isoleucine by expressing a catabolic threonine dehydratase in a threonine-overproducing Corynebacterium glutamicum by S. Guillouet; A. Rodal; G-H. An; N. Gorret; P. Lessard; A. Sinskey (pp. 667-673).

Carbon destined for lysine synthesis in Corynebacterium glutamicum ATCC 21799 can be diverted toward threonine by overexpression of genes encoding a feedback-insensitive homoserine dehydrogenase (hom ^dr) and homoserine kinase (thrB). We studied the effects of introducing two different threonine dehydratase genes into this threonine-producing system to gauge their effects on isoleucine production. Co-expression of hom ^dr, thrB, and ilvA, which encodes a native threonine dehydratase, caused isoleucine to accumulate to a final concentration of 2.2±0.2 g l^–1, five-fold more than accumulates in the wild-type strain, and approximately twice as much as accumulates in the strain expressing only hom ^dr and thrB. Comparing these data with previous results, we found that overexpression of the three genes, hom ^dr, thrB, and ilvA, in C. glutamicum ATCC 21799 is no better in terms of isoleucine production than the expression of a single gene, tdcB, encoding a catabolic threonine dehydratase from Escherichia coli. Co-expression of hom ^dr, thrB, and tdcB, however, caused the concentration of isoleucine to increase 20-fold compared to the wild-type strain, about four times more than the corresponding ilvA-expressing strain. In this system, the apparent yield of isoleucine production was multiplied by a factor of two [2.1 mmol (g dry cell weight)^–1]. While the balance of excreted metabolites showed that the carbon flow in this strain was completely redirected from the lysine pathway into the isoleucine pathway, it also showed that more pyruvate was diverted into amino acid synthesis.

An improved procedure for production of human epidermal growth factor from recombinant E. coli by W.-Y. Tong; S.-J. Yao; Z.-Q. Zhu; J. Yu (pp. 674-679).

An improved procedure for the fermentation and purification of human epidermal growth factor (hEGF) was developed. Recombinant Escherichia coli HB-101 [lacUV5omp08hEGF] harboring plasmid lacUV5omp08hEGF encoding hEGF was used in fermentation to increase levels of hEGF. Medium composition, and the levels of inoculum, inducer (isopropyl-β-D-thiogalactoside) and ampicillin were optimized with respect to volumetric fermentation of hEGF. As a result, the hEGF concentration reached a high value of 242 mg l^–1 and the amount of heterogeneous protein decreased by 62% compared with that before optimization in batch fermentation. High-quality hEGF was purified from the fermentation culture by centrifugation, salting-out, resuspension, re-centrifugation and finally gel chromatography on a GradiFrac System using Sephadex G-50 superfine. The purity of hEGF and the total yield were more than 94% and higher than 36%, respectively, and SDS-PAGE of the purified hEGF demonstrated a single band corresponding to an hEGF standard. In particular, a very important phenomenon was found, i.e. that the amount of heterogenous protein in fermentation broths cultured in media with high concentrations of lactose is far less than that cultured in media with high concentrations of glucose.

Cloning and characterization of genes from Agrobacterium sp. IP I-671 involved in hydantoin degradation by M. Hils; P. Münch; J. Altenbuchner; C. Syldatk; R. Mattes (pp. 680-688).

Cloning and sequencing of a 7.1 kb DNA fragment from Agrobacterium sp IP I-671 revealed seven open reading frames (ORFs) encoding D-hydantoinase, D-carbamoylase and putative hydantoin racemase, D-amino acid oxidase and NAD(P)H-flavin oxidoreductase. Two incomplete ORFs flanking the hydantoin utilization genes showed similarities to genes involved in transposition. Expression of the D-hydantoinase and D-carbamoylase gene in Escherichia coli gave mainly inactive protein concentrated in inclusion bodies, whereas homologous expression on an RSF1010 derivative increased hydantoinase and D-carbamoylase activity 2.5-fold and 10-fold, respectively, in this strain. Inactivation of the D-carbamoylase gene in Agrobacterium sp IP I-671 led to a complete loss of detectable carbamoylase activity whereas the low hydantoinase activity remaining after inactivation of the D-hydantoinase gene indicated the presence of a second hydantoinase-encoding gene. Two plasmids of 80 kb and 190 kb in size were identified by pulsed-field gel electrophoresis and the cloned hydantoin utilization genes were found to be localized on the 190 kb plasmid.

Effects of transcription induction homogeneity and transcript stability on expression of two genes in a constructed operon by C. Smolke; A. Khlebnikov; J. Keasling (pp. 689-696).

A synthetic operon was constructed using the reporter genes gfp and lacZ and the arabinose-inducible araBAD promoter. DNA cassettes encoding mRNA secondary structures were placed at the 3′ and 5′ ends of the genes and a putative RNase E site was placed between the genes. These mRNA control elements have been shown to affect transcript processing and decay, resulting in altered protein levels. These constructs were transformed into cells harboring the native arabinose-inducible araE gene encoding the arabinose transport protein and engineered cells harboring a constitutively expressed araE. In the strains with arabinose-dependent transport the linear response in the production of both reporter proteins to inducer concentration occurred over a narrow range of arabinose concentrations. In the strains with constitutive transport the linear range of gene expression occurred over a much larger arabinose concentration range than in strains with the arabinose-inducible transport. Strains with the arabinose-inducible transport harboring different operon constructs produced the two reporter proteins at very different levels at low arabinose concentrations; as inducer concentrations increased, differences in relative expression levels decreased. In contrast, strains with constitutive transport harboring different operon constructs produced the reporter proteins at very different levels across the entire range of inducer concentrations, pointing to the importance of optimizing gene expression control at various levels to control the production of heterologous proteins.

Cell surface-engineered yeast displaying a histidine oligopeptide (hexa-His) has enhanced adsorption of and tolerance to heavy metal ions by K. Kuroda; S. Shibasaki; M. Ueda; A. Tanaka (pp. 697-701).

A histidine oligopeptide (hexa-His) with the ability to chelate divalent heavy metal ions was displayed on the yeast cell surface for the purpose of enhanced adsorption of heavy metal ions. We genetically fused a hexa-His-encoding gene with the gene encoding the C-terminal half of α-agglutinin that includes a glycosylphosphatidylinositol anchor attachment signal sequence and attached the hexa-His peptide on the cell wall of Saccharomyces cerevisiae. This surface-engineered yeast adsorbed three to eight times more copper ions than the parent strain and was more resistant to copper (4 mM) than the parent (below 1 mM at pH 7.8). It was possible to recover about a half of the copper ions adsorbed by whole cells with EDTA treatment without disintegrating the cells. Thus, we succeeded in constructing a novel yeast cell with both tolerance to toxic contaminants and enhanced adsorption of metal ions onto the cell surface.

Intelligent yeast strains with the ability to self-monitor the concentrations of intra- and extracellular phosphate or ammonium ion by emission of fluorescence from the cell surface by S. Shibasaki; Y. Ninomiya; M. Ueda; M. Iwahashi; T. Katsuragi; Y. Tani; S. Harashima; A. Tanaka (pp. 702-707).

Saccharomyces cerevisiae strains that respond to environmental changes and transmit the information by emission of fluorescence from the cell surface were constructed. The technique of cell surface engineering enabled the yeast cells to display enhanced cyan blue fluorescent protein (ECFP) or enhanced yellow fluorescent protein (EYFP) on the surface under the control of promoters that sense environmental changes. Two model promoters were examined in this study. For monitoring the intra- and extracellular concentrations of phosphate ion, the PHO5 promoter was chosen to display ECFP. The MEP2 promoter was used to display EYFP to sense the concentrations of ammonium ion. Fluorescence was observed by fluorescence microscopy and immunofluorescence microscopy, and the intensity was measured by a flow cytometer. The relationship between ion concentration inside and outside the cells was evaluated by the change in the rate of fluorescence. This S. cerevisiae system enables environmental changes to be transmitted as intra- and extracellular information using a suitable promoter functioning at real time and in a non-invasive manner.

Growth inhibition of a Fusarium verticillioides GUS strain in corn kernels of aflatoxin-resistant genotypes by R. Brown; T. Cleveland; C. Woloshuk; G. Payne; D. Bhatnagar (pp. 708-711).

Two corn genotypes, GT-MAS:gk and MI82, resistant to Aspergillus flavus infection/aflatoxin contamination, were tested for their ability to limit growth of Fusarium verticillioides. An F. verticillioides strain was transformed with a β-glucuronidase (GUS) reporter gene (uidA) construct to facilitate fungal growth quantification and then inoculated onto endosperm-wounded and non-wounded kernels of the above-corn lines. To serve as a control, an A. flavus strain containing the same reporter gene construct was inoculated onto non-wounded kernels of GT-MAS:gk. Results showed that, as in a previous study, non-wounded GT-MAS:gk kernels supported less growth (six- to ten-fold) of A. flavus than did kernels of a susceptible control. Also, non-wounded kernels of GT-MAS:gk and MI82 supported less growth (two- to four-fold) of F. verticillioides than did susceptible kernels. Wounding, however, increased F. verticillioides infection of MI82, but not that of GT-MAS:gk. This is in contrast to a previous study of A. flavus, where wounding increased infection of GT-MAS:gk rather than MI82 kernels. Further study is needed to explain genotypic variation in the kernel response to A. flavus and F. verticillioides kernel infections. Also, the potential for aflatoxin-resistant corn lines to likewise inhibit growth of F. verticillioides needs to be confirmed in the field.

Assessment of heavy metal bioavailability using Escherichia coli zntAp::lux and copAp::lux-based biosensors by K. Riether; M.-A. Dollard; P. Billard (pp. 712-716).

To determine the amount of metals detectable by bacteria, two plasmids were constructed in which the metal-inducible zntA and copA promoters from Escherichia coli were fused to a promoterless Vibrio fischeri luxCDABE operon. The luminescence response of E. coli bearing these constructs was studied as a function of the concentration of several heavy metals and was shown to be influenced by cell growth phase. The zntAp::lux fusion is induced mainly by salts of cadmium, lead, mercury and zinc, with significant induction by other metal ions, whereas the specificity of copA induction is restricted to copper and silver. In optimized assay conditions, metals could be detected at threshold concentrations ranging from nanomolar to micromolar, with maximal induction observed after only 60–100 min incubation. The ability of these biosensor strains to distinguish bioavailable quantities of metals in a sample makes them good candidates as useful tools to monitor metal contamination in environmental samples.

Major proteins related to chlortetracycline biosynthesis in a Streptomyces aureofaciens production strain studied by quantitative proteomics by X.-M. Li; J. Novotná; J. Vohradský; J. Weiser (pp. 717-724).

Changes in synthesis and abundance of proteins associated with chlortetracycline (CTC) production in Streptomyces aureofaciens were investigated by two-dimensional polyacrylamide gel electrophoresis of proteins pulse-labelled in vivo with L-[³⁵S]methionine. Eleven individual protein spots were selected as being related to formation of the antibiotic. Expression of these prominent proteins was not observed in the non-producing mutant; moreover, they were overexpressed in cultures grown in the presence of benzyl thiocyanate, a specific stimulator of CTC biosynthesis used in industrial fermentations. The expression kinetics of the selected proteins was assessed using the technique of computer-assisted image analysis with the EQIAS software and the elongation factor Tu as an internal standard. Interestingly, the kinetic profiles were generally not identical, including those of anhydrotetracycline monooxygenase and the 13-kDa subunit of tetracycline dehydrogenase, two enzymes involved in the terminal sequential steps of the CTC biosynthetic pathway. The presence of more forms of these enzymes with different charge characteristics was observed. The data presented demonstrated how dramatically the industrial microorganism can change its protein repertoire during the production phase; at least five proteins were nearly comparable in level to the most prominent proteins, exemplified by elongation factor Tu.

Evidence of a new biotransformation pathway of p-coumaric acid into p-hydroxybenzaldehyde in Pycnoporus cinnabarinus by I. Estrada Alvarado; A. Lomascolo; D. Navarro; M. Delattre; M. Asther; L. Lesage-Meessen (pp. 725-730).

Pycnoporus cinnabarinus MUCL39533 was shown to be able to convert p-coumaric acid into p-hydroxybenzaldehyde, a component of high organoleptic note present in natural vanilla aroma. Use of phospholipid-enriched medium led to high-density cultures of P. cinnabarinus, since dry mycelial biomass was increased three-fold as compared to glucose medium. In the presence of phospholipids, 155 mg l^–1 p-hydroxybenzaldehyde was produced as the major compound on culture day 13 with a molar yield of 26%. The degradation pathways of p-coumaric acid were investigated. Based on the different metabolites identified, an oxidative side-chain degradation pathway of p-coumaric acid conversion to p-hydroxybenzoic acid was suggested. This acid was further reduced to p-hydroxybenzaldehyde and p-hydroxybenzyl alcohol, or hydroxylated and reduced to protocatechyl derivatives. Additionally, a reductive pathway of p-coumaric acid with 3-(4-hydroxyphenyl)-propanol as the terminal product occurred.

Geraniol biotransformation-pathway in spores of Penicillium digitatum by W. Wolken; M. van der Werf (pp. 731-737).

Spores of Penicillium digitatum ATCC 201167 transform geraniol, nerol, citral, and geranic acid into methylheptenone. Spore extracts of P. digitatum convert geraniol and nerol NAD⁺-dependently into citral. Spore extract also converts citral NAD⁺-dependently into geranic acid. Furthermore, a novel enzymatic activity, citral lyase, which cofactor-independently converts citral into methylheptenone and acetaldehyde, was detected. These result show that spores of P. digitatum convert geraniol via a novel biotransformation pathway. This is the first time a biotransformation pathway in fungal spores has been substantiated by biochemical studies. Geraniol and nerol are converted into citral by citrol dehydrogenase activity. The citral formed is subsequently deacetylated by citral lyase activity, forming methylheptenone. Moreover, citral is converted reversibly into geranic acid by citral dehydrogenase activity.

Metabolic study of the adaptation of the yeast Candida guilliermondii to sugarcane bagasse hydrolysate by L. Sene; A. Converti; M. Zilli; M. Felipe; S. Silva (pp. 738-743).

Batch xylitol production from concentrated sugarcane bagasse hydrolysate by Candida guilliermondii was performed by progressively adapting the cells to the medium. Samples were analyzed to monitor sugar and acetic acid consumption, xylitol, arabitol, ethanol, and carbon dioxide production, as well as cell growth. Both xylitol yield and volumetric productivity remarkably increased with the number of adaptations, demonstrating that the more adapted the cells, the better the capacity of the yeast to reduce xylose to xylitol in hemicellulose hydrolysates. Substrate and product concentrations were used in carbon material balances to study in which way the different carbon sources were utilized by this yeast under microaerobic conditions, as well as to shed light on the effect of the progressive adaptation to the medium on its fermentative activity. Such a theoretical means allowed estimation for the first time of the relative contribution of each medium component to the formation of the main products of this fermentation system.

Determination of the kinetic parameters of the phenol-degrading thermophile Bacillus themoleovorans sp. A2 by H. Feitkenhauer; S. Schnicke; R. Müller; H. Märkl (pp. 744-750).

Phenolic compounds are pollutants in many wastewaters, e.g. from crude oil refineries, coal gasification plants or olive oil mills. Phenol removal is a key process for the biodegradation of pollutants at high temperatures because even low concentrations of phenol can inhibit microorganisms severely. Bacillus thermoleovorans sp. A2, a recently isolated thermophilic strain (temperature optimum 65 °C), was investigated for its capacity to degrade phenol. The experiments revealed that growth rates were about four times higher than those of mesophilic microorganisms such as Pseudomonas putida. Very high specific growth rates of 2.8 h^–1 were measured at phenol concentrations of 15 mg/l, while at phenol concentrations of 100–500 mg/l growth rates were still in the range of 1 h^–1. The growth kinetics of the thermophilic Bacillus thermoleovorans sp. A2 on phenol as sole carbon and energy source can be described using a three-parameter model developed in enzyme kinetics. The yield coefficient Y _x/s of 0.8–1 g cell dry weight/g phenol was considerably higher than cell yields of mesophilic bacteria (Y _x/s 0.40–0.52 g cell dry weight/g phenol). The highest growth rate was found at pH 6. Bacillus thermoleovorans sp. A2 was found to be insensitive to hydrodynamic shear stress in stirred bioreactor experiments (despite possible membrane damage caused by phenol) and flourished at an ionic strength of the medium of 0.25–1 mol/l (equivalent to about 15–60 g NaCl/l). These exceptional properties make Bacillus thermoleovorans sp. A2 an excellent candidate for technical applications.

Evidence for three distinct hydrogenase activities in Rhodospirillum rubrum by P.-C. Maness; P. Weaver (pp. 751-756).

Inducer, inhibitor, and mutant studies on three hydrogenase activities of Rhodospirillum rubrum indicate that they are mediated by three distinct hydrogenase enzymes. Uptake hydrogenase mediates H₂ uptake to an unknown physiological acceptor or methylene blue and is maximally synthesized during autotrophic growth in light. Formate-linked hydrogenase is synthesized primarily during growth in darkness or when light becomes limiting, and links formate oxidation to H₂ production. Carbon-monoxide-linked hydrogenase is induced whenever CO is present and couples CO oxidation to H₂ evolution. The enzymes can be expressed singly or conjointly depending on growth conditions, and the inhibitor or inducer added. All three hydrogenases can use methyl viologen as the mediator for both the H₂ evolution and H₂ uptake reactions while displaying distinct pH optima, reversibility, and sensitivity to C₂H₂ gas. Yet, we present evidence that the CO-linked hydrogenase, unlike the uptake hydrogenase, does not link to methylene blue as the electron acceptor. These differences allow conditions to be established to quantitatively assay each hydrogenase independently of the others both in vivo and in vitro.

Luminescent method for the detection of antibacterial activities by L. Simon; C. Fremaux; Y. Cenatiempo; J.-M. Berjeaud (pp. 757-763).

A new rapid and sensitive method for the detection of antibacterial activities was based on luminescent indicator strains. Listeria innocua 8811 and Enterococcus faecalis 32 were transformed with plasmid carrying bacterial luciferase genes. Subsequent strains became capable to emit light during the exponential growth phase. The addition of bacteriocin containing culture supernatants to such cultures induced a drop of their light emission which was correlated to the combined antibacterial activity of acid stress and bacteriocin. The detection of antagonistic activity is independent of its mode of action, i.e. bactericidal or bacteriostatic. This method allowed to directly visualize the antagonistic activity of bacteriocin producer strains toward target strains in co-culture experiments. However, a control co-culture with non-producing bacteriocin mutant was necessary in order to distinguish between nutrients competition and bacteriocin activity. Finally, five class IIa bacteriocins were purified from culture supernatants of eight strains detected in 3 days from a 120 lactic acid bacteria collection.

Isolation of Bacillus subtilis (chungkookjang), a poly-^γ-glutamate producer with high genetic competence by M. Ashiuchi; T. Kamei; D.-H. Baek; S.-Y. Shin; M.-H. Sung; K. Soda; T. Yagi; H. Misono (pp. 764-769).

A bacterium with high poly-γ-glutamate (PGA) productivity was isolated from the traditional Korean seasoning, Chung-Kook-Jang. This bacterium could be classified as a Bacillus subtilis, but sporulation in culture was infrequent in the absence of Mn²⁺. It was judged to be a variety of B. subtilis and designated B. subtilis (chungkookjang). L-Glutamate significantly induced PGA production, and highly elongated PGAs were synthesized. The volumetric yield reached 13.5 mg ml^–1 in the presence of 2% L-glutamate. The D-glutamate content was over 50% in every PGA produced under the conditions used. During PGA production, glutamate racemase activity was found in the cells, suggesting that the enzyme is involved in the D-glutamate supply. Molecular sizes of PGAs were changed by the salt concentration in the medium; PGAs with comparatively low molecular masses were produced in culture media containing high concentrations of NaCl. B. subtilis (chungkookjang) harbors no plasmid and is the first B. subtilis strain reported with both naturally high PGA productivity and high genetic competence.

Controlled release of water-soluble polymeric complexes of sorbic acid with antifungal activities by E. Charvalos; M. Tzatzarakis; A. Tsatsakis; G. Petrikkos (pp. 770-775).

We synthesized six water-soluble polymeric complexes of sorbic acid with polyvinylpyrrolidone of different molecular weight (mol wt). As shown by infrared absorption spectrum analysis, the complexes were formed by hydrogen bonding. The complexes (SC1, with mol wt=10 kDa, SC2 with mol wt=25 kDa, SC3 with mol wt=30 kDa, SC4 with mol wt=40 kDa, SC5 with mol wt=90 kDa, and SC6 with mol wt=360 kDa) were characterized as low mol wt (SC1, SC2, and SC3) and high mol wt (SC4, SC5, and SC6). The antifungal potencies of the complexes were tested by the macrodilution susceptibility method against environmental and clinically important fungi. Sorbic acid as well as the complexes exhibited minimum inhibitory concentrations (MICs) lower than potassium sorbate against all the strains tested. MICs of SC1, SC2, and SC3 were shown to be 2- to 4-fold lower for yeast and 1.5- to 3-fold lower than those of sorbic acid for moulds, respectively. The MICs of SC4 and SC5 against both of the Candida species tested ranged from 500 to 800 µg/ml, whereas for SC6 and sorbic acid they were about 1 mg/ml. The potencies of the high mol wt complexes against moulds were decreased by increasing the mol wt. For both of the moulds tested, the MICs of SC4 were slightly lower than those of sorbate. The MICs of sorbic acid and SC5 were equal to 300 µg/ml and 500 µg/ml respectively for Aspergillus parasiticus and for Penicillum viridicatum. The susceptibility to SC6 of all of the hyphomycetes tested was higher than that to sorbic acid. The low mol wt complexes and the sorbic acid exhibited minimal fungicidal concentrations (MFCs) 2 and 3 times higher respectively than the MICs. Sorbic acid and SC3 at a concentration of 2.5 mg/ml in an in vitro time kill curve study of Candida tropicalis were shown to be fungistatic, whereas SC1 and SC2 were fungicidal at the same concentrations. For Aspergillus parasiticus sorbic acid at 2.5 mg/ml was fungistatic for a 24-h period, whereas SC1, SC2, and SC3 were fungicidal.

Keywords: Sorbate Polyvinylpyrrolidone Antifungal Controlled release complexes

Analysis of the microbial communities on corroded concrete sewer pipes – a case study by E. Vincke; N. Boon; W. Verstraete (pp. 776-785).

Conventional as well as molecular techniques have been used to determine the microbial communities present on the concrete walls of sewer pipes. The genetic fingerprint of the microbiota on corroded concrete sewer pipes was obtained by means of denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. The DGGE profiles of the bacterial communities present on the concrete surface changed as observed by shifts occurring at the level of the dominance of bands from non-corroded places to the most severely corroded places. By means of statistical tools, it was possible to distinguish two different groups, corresponding to the microbial communities on corroded and non-corroded surfaces, respectively. Characterization of the microbial communities indicated that the sequences of typical bands showed the highest level of identity to sequences from the bacterial strains Thiobacillus thiooxidans, Acidithiobacillus sp., Mycobacterium sp. and different heterotrophs belonging to the α-, β- and γ-Proteobacteria, Acidobacteria and Actinobacteria. In addition, the presence of N-acyl-homoserine lactone signal molecules was shown by two bio-assays of the biofilm on the concrete under the water level and at the most severely corroded places on the concrete surface of the sewer pipe.

Anaerobic reductive dechlorination of chlorinated dioxins in estuarine sediments by C. Vargas; D. Fennell; M. Häggblom (pp. 786-790).

The biotransformation of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-tetraCDD) under anaerobic sulfate-reducing, methanogenic, and iron-reducing conditions was examined with anaerobic enrichment cultures established with sediment from an estuarine intertidal strait in the New York/New Jersey harbor. In addition, the effect of prior enrichment on 2-bromophenol or a mixture of 2-, 3-, and 4-bromophenol on dioxin dechlorination was examined. All enrichments were spiked with 1 ppm 1,2,3,4-tetraCDD and monitored by gas chromatography-mass spectrometry for up to a 3-year period. Reductive dechlorination was initially observed only under methanogenic conditions in the cultures enriched on all three bromophenol isomers. 1,2,3,4-TetraCDD was dechlorinated in the lateral position to 1,2,4-triCDD. The initial appearance of 1,2,4-triCDD was observed after 2 months, with further dechlorination to 1,3-diCDD within 17 months.

Ammonia removal from prawn aquaculture water using immobilized nitrifying bacteria by H. Shan; J. Obbard (pp. 791-798).

Intensive prawn aquaculture in tropical regions is associated with high concentrations of total ammoniacal nitrogen (TAN) as a result of high rates of prawn excretion and feed loading. Excessive TAN can adversely effect productivity and result in adverse impacts on coastal waters. Cultures of indigenous nitrifying bacteria were enriched from intensive prawn aquaculture pond water using continuous and batch enrichment techniques. Cultures were capable of TAN removal over a wide range of initial TAN concentrations – up to 200 mg/l. Cultures were immobilized onto porous clay pellets to enhance cell density and applied to culture medium and TAN-augmented pond water under aerobic conditions to determine TAN removal proficiency. Immobilized cultures were able to achieve a high TAN removal proficiency in pond water – even at a low density of 0.1 pellet per liter. A concentration of less than 0.5 mg TAN/l could be maintained under a fed-batch condition of 3.2 mg TAN/l per day, after an initial 2-day lag phase. A simplified and effective culture enrichment process was developed for culture immobilization onto pellets using TAN-augmented pond water. Overall, pellet immobilization of indigenous nitrifying bacteria represents a potentially effective TAN control system for prawn aquaculture in low-cost, but intensive tropical prawn farms.

Assay for determination of α-glucosidase and peptidase activity and location in a nitrifying trickling filter by N. Mustafa; F. Sörensson (pp. 799-802).

Enzymatic α-glucosidase and peptidase activity in a nitrifying trickling filter (NTF) at the Rya wastewater treatment plant, Göteborg, Sweden, was investigated to evaluate whether these activities can be used as indicators of heterotrophic activity and polymer degradation. Samples of the biofilm were taken from the NTF and incubated in sterile filtered effluent water from the NTF with the addition of soluble starch, peptone, and ammonium chloride. In order to determine the distribution of enzyme activities, the α-glucosidase and peptidase activities were measured in the biofilm samples, in the filtered effluent water from the NTF and in the water phase in which the biofilm was incubated. Activities of both enzymes were found both in the effluent water from the NTF and in the biofilm. The enzyme activities were elevated in the samples when starch and peptone were present. In addition, there was a significant inhibition of ammonium oxidation in samples incubated with starch and peptone. Thus, the presence of starch, peptone and ammonium resulted in increased activity of heterotrophs, which lead to an inhibition of the nitrifiers, probably via competition for available oxygen.

Basic examinations on chemical pre-oxidation by ozone for enhancing bioremediation of phenanthrene contaminated soils by J. Stehr; T. Müller; K. Svensson; C. Kamnerdpetch; T. Scheper (pp. 803-809).

Biological treatment of polycyclic aromatic hydrocarbons (PAH) has been demonstrated to be a feasible and common remediation technology which has been successfully applied to the clean-up of contaminated soils. Because bioavailability of the contaminants is of great importance for a successful bioremediation, a chemical pre-oxidation step by ozone was tested to enhance the subsequent biodegradation steps. Oxidation of PAH by ozone should result in reaction products that have a better solubility in water and thus a better bioavailability. A major part of this work was done by examinations of the model substance phenanthrene as a typical compound of PAH. After initial ozonation of phenanthrene, analysis by GC-MS showed at least seven identified conversion-products of phenanthrene. In comparison with phenanthrene these conversion products were more efficiently biodegraded by Sphingomonas yanoikuyae or mixed cultures when the ozonation process resulted in monoaromatic compounds. Primary ozonation products with biphenylic structures were found not to be biodegradable. Investigations into the toxicity of contaminated and ozonated soils were carried out by well-established toxicity assays using Bacillus subtilis and garden cress. The ozonated soils surprisingly showed higher toxic or inhibitory effects towards different organisms than the phenanthrene or PAH itself. The microbial degradation of phenanthrene in slurry reactors by S. yanoikuyae was not enhanced significantly by pre-ozonation of the contaminated soil.

Studies on the decolourisation of an artificial textile-effluent by white-rot fungi in N-rich and N-limited media by T. Robinson; B. Chandran; P. Nigam (pp. 810-814).

Coriolopsis gallica and Phanerochaete chrysosporium were selected for their potential ability to degrade five dyes in an artificial effluent. Degradation experiments were carried out in N-rich (C:N ratio 11.6:1) and N-limited (116:1) conditions at an effluent concentration of 100 mg l^–1. P. chrysosporium decolourised 53.6% of the effluent in N-rich conditions and 48% in N-limited conditions. C. gallica decolourised 80.7% in N-rich conditions and 86.9% in N-limited conditions. Nitrogen supplementation improved enzyme activities and dye decolourisation for P. chrysosporium. Additional nitrogen increased enzyme activities for C. gallica but did not improve decolourisation. The results highlight the potential of C. gallica for textile dye degradation.

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Applied Microbiology and Biotechnology (v.57, #5-6)

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Applied Microbiology and Biotechnology (v.57, #5-6)