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Applied Microbiology and Biotechnology (v.73, #3)

Application of FISH technology for microbiological analysis: current state and prospects by Benedetta Bottari; Danilo Ercolini; Monica Gatti; Erasmo Neviani (pp. 485-494).

In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.

Magnetic particles for the separation and purification of nucleic acids by Sonja Berensmeier (pp. 495-504).

Nucleic acid separation is an increasingly important tool for molecular biology. Before modern technologies could be used, nucleic acid separation had been a time- and work-consuming process based on several extraction and centrifugation steps, often limited by small yields and low purities of the separation products, and not suited for automation and up-scaling. During the last few years, specifically functionalised magnetic particles were developed. Together with an appropriate buffer system, they allow for the quick and efficient purification directly after their extraction from crude cell extracts. Centrifugation steps were avoided. In addition, the new approach provided for an easy automation of the entire process and the isolation of nucleic acids from larger sample volumes. This review describes traditional methods and methods based on magnetic particles for nucleic acid purification. The synthesis of a variety of magnetic particles is presented in more detail. Various suppliers of magnetic particles for nucleic acid separation as well as suppliers offering particle-based kits for a variety of different sample materials are listed. Furthermore, commercially available manual magnetic separators and automated systems for magnetic particle handling and liquid handling are mentioned.

Keywords: Magnetic particles; Nucleic acid; Separators; Automation

Secretory production system of bionanocapsules using a stably transfected insect cell line by Takuya Shishido; Masaru Muraoka; Masakazu Ueda; Masaharu Seno; Katsuyuki Tanizawa; Shun’ichi Kuroda; Hideki Fukuda; Akihiko Kondo (pp. 505-511).

Bionanocapsules (BNCs) are hollow nanoscale particles composed of L protein of the hepatitis B virus surface antigen that represent specific affinity for human hepatocytes. BNCs can transfer genes and drugs into human hepatocytes efficiently and specifically. BNC can be expressed in yeast cells. In this study, we developed a new L particle production system using a stably transfected insect cell line. For this purpose, we established a host–vector system using the Trichoplusia ni insect cell line. L particles were efficiently secreted by the overexpression of the L protein, which was fused to the secretion signal peptide. The concentration of L particles was reached approximately 1.7 μg/ml in 5 days during cultivation in a serum-free medium without antibiotic selective pressure. The production of L particles was maintained for at least 75 days. The secretory production of L particles facilitated their easy purification by chromatography. Furthermore, it was demonstrated that purified L particles can transfect only human hepatocytes. Therefore, an insect cell expression system is an attractive tool for the production of BNC.

Tetramethylpyrazine production from glucose by a newly isolated Bacillus mutant by Z. J. Xiao; N. Z. Xie; P. H. Liu; D. L. Hua; P. Xu (pp. 512-518).

2,3,5,6-Tetramethylpyrazine (TTMP) was produced using a newly isolated Bacillus mutant. Culture medium optimization studies showed that soytone, an enzyme-hydrolysate of soybean meal, with the supplementation of vitamins, can fully replace yeast extract plus peptone in supporting TTMP production from glucose. In a 5-l fermenter, using the optimized medium which contained 20% glucose, 5% soytone, 3% (NH₄)₂HPO₄, and vitamin supplements, fermentations were carried out with stirring at 700 rpm, air flow at 1.0 vvm, controlled pH at 7.0, and temperature at 37 °C. TTMP reached 4.33 g l⁻¹ after 64.6 h cultivation. A product recovery method was described, which involved evaporation, crystallization, and lyophilization. The product purity was 99.88%, determined by GC with the normalization method. The main impurities were 2,3,5-trimethylpyrazine (0.09%) and 2-ethyl-3,5,6-trimethylpyrazine (0.02%), which were identified by GC/MS. ¹³C NMR determination also gave a consistent result. Natural and high purity of the product and the utilization of cheap green renewable materials make this process promising to compete with TTMP chemical synthetic methods.

Antioxidants enhanced production of destruxin E from cultivation of Metarhizium anisopliae by Yerra Koteswara Rao; Chia-Heng Tsou; Yew-Min Tzeng (pp. 519-524).

The effect of antioxidants on the production of an important cyclohexadepsipeptide congener destruxin E (dtx E) was investigated using the entomopathogenic fungus Metarhizium anisopliae F061. In shaker flask cultivations, 0.015% of menadione-enhanced dtx E production of 220.4 mg/l compared to the control cultivation 90.2 mg/l, which was illustrated by stimulation of dtx E biosynthesis through two electron reduction DT-diaphorase processes in cultivation of M. anisopliae. In 5-l stirred-tank bioreactor cultivation with menadione addition and of control pH 4.0, a yield of 454.6 mg/l of dtx E was obtained after 7 days, and was nearly 30 and 15-fold higher than that from no pH control, and controlled pH 2.0 cultivations, respectively. Further cultivation in a 20-l airlift bioreactor, at pH 4.0, dtx E obtained on the 9th day was 406.0 mg/l, which was much higher than the standard cultivation of no pH control yield 203.3 mg/l on the 11th day. Thus, the present study provides useful information for enhancing dtx E production in cultivation.

A bioreaction–diffusion model for growth of marine sponge explants in bioreactors by F. Garcia Camacho; T. Chileh; M. C. Cerón García; A. Sánchez Mirón; E. H. Belarbi; Y. Chisti; E. Molina Grima (pp. 525-532).

Marine sponges are sources of high-value bioactives. Engineering aspects of in vitro culture of sponges from cuttings (explants) are poorly understood. This work develops a diffusion-controlled growth model for sponge explants. The model assumes that the explant growth is controlled by diffusive transport of at least some nutrients from the surrounding medium into the explant that generally has a poorly developed aquiferous system for internal irrigation during early stages of growth. Growth is assumed to obey Monod-type kinetics. The model is shown to satisfactorily explain the measured growth behavior of the marine sponge Crambe crambe in two different growth media. In addition, the model is generally consistent with published data for growth of explants of the sponges Disidea avara and Hemimycale columella. The model predicted that nutrient concentration profiles for nutrients, such as dissolved oxygen within the explant, are consistent with data published by independent researchers. In view of the proposed model’s ability to explain available data for growth of several species of sponge explants, diffusive transport does play a controlling role in explant growth at least until a fully developed aquiferous system has become established. According to the model and experimental observations, the instantaneous growth rate depends on the size of the explant and all those factors that influence the diffusion of critical nutrients within the explant. Growth follows a hyperbolic profile that is consistent with the Monod kinetics.

Optimization of multienzyme production by two mixed strains in solid-state fermentation by Xiu-Juan Wang; Ji-Gang Bai; Yun-Xiang Liang (pp. 533-540).

F₃ and F₄ strains of Aspergillus niger were screened from five strains of fungi to produce multienzyme preparations (containing cellulase, hemicellulase, glucoamylase, pectinase, and acidic proteinase) as dietary supplementation. Enzyme activities indicated that 1:4 (F₃ to F₄) was the optimum mixture proportion, and 0.3% (W/W) was the preferable pitching rate. In bran mash containing 54.5% (W/W) water, F₃ and F₄ could produce the supplementation better when cultured 30 to 36 h at 30 °C. Monofactorial and orthogonal experiments were performed to optimize media. Results of the variance and range analysis showed that the optimum medium contained 80 g of bran, 20 g of cottonseed powder, 1 g of (NH₄)₂SO₄, and 0.1 g of KH₂PO₄. When F₃ and F₄strains were cultured in the optimum medium containing 54.5% (W/W) water, the activity of cellulase, hemicellulase, glucoamylase, pectinase, and acidic proteinase reached 996; 15,863; 13,378; 7,621; and 5,583 U/g, respectively.

Keywords: Multienzyme supplementation; Aspergillus niger ; Mixed strains; Solid state fermentation; Optimization; Medium

Continuous gluconic acid production by the yeast-like Aureobasidium pullulans in a cascading operation of two bioreactors by Savas Anastassiadis; Hans-Jürgen Rehm (pp. 541-548).

The application of a new developed process for the continuous production of gluconic acid using a cascade of two bioreactors in a continuous process is shown reaching the highest concentration of gluconic acid described in the literature for continuous culture fermentation. Very high gluconic acid concentrations of 272–308 g/l have been achieved under continuous cultivation of free-growing cells of Aureobasidium pullulans in the first bioreactor at residence times (RT) between 19.5 and 24 h with formation rates for the generic product between 12.7 and 13.9 g/(l h). Gluconic acid, 350–370 g/l, was continuously reached in the second bioreactor at a total RT of 30.8–37 h with R _j of 9.2–12 g/(l h). The highest specific gluconic acid production (m _p) of 3.6 g/(g h) was found in the first bioreactor at the lowest RT of 19.5 h. The highest selectivity of 93.6% was determined in the first bioreactor as well. Complete glucose consumption was obtained at 37 h total residence time in the second bioreactor. Gluconic acid, 433 g/l, was continuously produced in the second bioreactor at a total RT of 37 h.

Keywords: Gluconic acid; Aureobasidium pullulans ; Continuous gluconic acid fermentation; Continuous fermentation; Continuous gluconic acid production; Gluconic acid production; Gluconic acid fermentation; Cascade of bioreactors

Simultaneous control of apparent extract and volatile compounds concentrations in low-malt beer fermentation by Michiko Kobayashi; Keisuke Nagahisa; Hiroshi Shimizu; Suteaki Shioya (pp. 549-558).

Volatile compounds cause undesirable flavor when their concentrations exceed threshold values in beer fermentation. The objective of this study is to develop a system for controlling apparent extract concentration, which indicates the fermentation degree and which should be decreased below a targeted value at a fixed time under a constraint of tolerable amounts of volatile compounds. In beer fermentation, even though the production of volatile compounds is suppressed by maintaining a low fermentation temperature, a low temperature causes a delay in the control of apparent extract concentration. Volatile compound concentration was estimated on-line, and the simulation of apparent extract consumption and volatile compound production was performed. To formulate various beer tastes and conserve energy for attemperation, optimal temperature profiles were determined using a genetic algorithm (GA). The developed feedback control of the brewing temperature profile was successfully applied, and apparent extract and volatile compound concentrations at a fixed time reached their target concentrations. Additionally, the control technique developed in this study enables us to brew a wide variety of beers with different tastes.

Keywords: Beer fermentation; Apparent extract; Volatile compounds; Automatic control; Temperature profile

Expression and characterization of a thermostable sarcosine oxidase (SOX) from Bacillus sp. in Escherichia coli by Kangping Guo; Xiaohang Ma; Guiqin Sun; Yuhua Zhao; Xia Li; Weifeng Zhao; Lei Kai (pp. 559-566).

A heat-stable sarcosine oxidase produced by Bacillus sp. BSD-8 (SOX) had been studied and its complete gene sequence, which contained 1,164 bp nucleotides and encoded a protein of 387 amino acids, was obtained by DNA Walking method. The sox gene was cloned and functionally overexpressed in E. coli and the recombinant SOX (rSOX) was purified to homogeneity, its properties was studied and compared with the wild type of SOX. The rSOX as well as SOX was stable at 60°C and at pH 7.0∼10.0, respectively. The optimal temperature for this enzyme was 60°C and at pH 8.5, it showed its highest activity. The Km and Kcat of the enzyme was 3.1 mM and 20.3/s, respectively. The difference between the properties of the SOX and rSOX was that the SOX contained noncovalent FAD, whereas the rSOX contained covalent FAD. The study also showed that an increased number of alanine residues in the rSOX might have some contribution in the enzymatic thermostability.

Purification and characterization of a nitrilase from Aspergillus niger K10 by Ondřej Kaplan; Vojtěch Vejvoda; Ondřej Plíhal; Petr Pompach; Daniel Kavan; Pavla Bojarová; Karel Bezouška; Martina Macková; Maria Cantarella; Vladimír Jirků; Vladimír Křen; Ludmila Martínková (pp. 567-575).

Aspergillus niger K10 cultivated on 2-cyanopyridine produced high levels of an intracellular nitrilase, which was partially purified (18.6-fold) with a 24% yield. The N-terminal amino acid sequence of the enzyme was highly homologous with that of a putative nitrilase from Aspergillus fumigatus Af293. The enzyme was copurified with two proteins, the N-terminal amino acid sequences of which revealed high homology with those of hsp60 and an ubiquitin-conjugating enzyme. The nitrilase exhibited maximum activity (91.6 U mg^-1) at 45°C and pH 8.0. Its preferred substrates, in the descending order, were 4-cyanopyridine, benzonitrile, 1,4-dicyanobenzene, thiophen-2-acetonitrile, 3-chlorobenzonitrile, 3-cyanopyridine, and 4-chlorobenzonitrile. Formation of amides as by-products was most intensive, in the descending order, for 2-cyanopyridine, 4-chlorobenzonitrile, 4-cyanopyridine, and 1,4-dicyanobenzene. The enzyme stability was markedly improved in the presence of d-sorbitol or xylitol (20% w/v each). p-Hydroxymercuribenzoate and heavy metal ions were the most powerful inhibitors of the enzyme.

Keywords: Nitrilase; Aspergillus niger ; Enzymatic nitrile hydrolysis

An antifungal peptide from baby lima bean by H. X. Wang; T. B. Ng (pp. 576-581).

A 6-kDa antifungal peptide with inhibitory activity on mycelial growth in Fusarium oxysporum, Mycosphaerella arachidicola, and Physalospora piricola was isolated from baby lima beans. The peptide suppressed growth in M. arachidicola with an IC₅₀ of 0.87 μM and inhibited activity of HIV-1 reverse transcriptase with an IC₅₀ of 4 μM. The peptide exhibited an N-terminal amino acid sequence similar to those of leguminous defensins. The isolation procedure comprised ion exchange chromatography on diethylaminoethyl (DEAE)-cellulose, affinity chromatography on Affi-gel blue gel, ion exchange chromatography on carboxymethyl (CM)-cellulose, and gel filtration by fast protein liquid chromatography on Superdex 75. The peptide was unadsorbed on DEAE-cellulose and Affi-gel blue gel but was adsorbed on CM-cellulose.

Keywords: Lima bean; Isolation; Antifungal peptide

Expression in Escherichia coli and characterization of β-xylosidases GH39 and GH-43 from Bacillus halodurans C-125 by Issam Smaali; Caroline Rémond; Michael J. O’Donohue (pp. 582-590).

To develop xylosidases as tools for the hydrolysis of wheat bran arabinoxylans, two β-xylosidases from Bacillus halodurans C-125 have been cloned and expressed in Escherichia coli. The recombinant (His)₆-tagged enzymes, designated as XylBH39 and XylBH43, were efficiently purified using Ni²⁺-affinity chromatography. Determination of native molecular masses indicated that XylBH43 is dimeric in solution, whereas a similar analysis of XylBH39 did not allow differentiation between the dimeric and trimeric states. Both enzymes had similar pH and temperature optima (pH 7.5 and 55 °C for XylBH39 and pH 8 and 60 °C for XylBH43) and were relatively stable over the pH range of 3.5–8.5. In contrast, XylBH39 was more thermostable. At 60 °C, XylBH39 and XylBH43 displayed approximate half-life values of 2.40 and 0.05 h, respectively. The comparison of the ratio k _cat/K _M revealed that XylBH43 hydrolyzed p-nitrophenyl-β-d-xyloside more efficiently (4.6-fold) than XylBH39. Similarly, while XylBH43 was 18-fold less active on p-nitrophenyl-α-l-arabinofuranoside, XylBH39 was essentially inactive on this substrate. Using either p-nitrophenyl-β-d-xyloside or xylotriose, XylBH39 performed transglycosylation, while xylobiose proved to be a poor substrate for both hydrolysis and transglycosylation. The use of XylBH39 and XylBH43 for the posttreatment of endoxylanase-generated wheat bran hydrolysates revealed that XylBH43 efficiently produced xylose monomers (385 μg/ml after 330 min incubation). Its activity was improved by the simultaneous deployment of an α-l-arabinofuranosidase. Together, these enzymes were able to release 521 μg/ml of xylose after 330 min. This constitutes an approximate yield improvement of 35%.

Keywords: -Xylosidase; Heterologous expression; Hemicelluloses; Bioconversion; Bacillus halodurans C-125

Purification and characterization of a maltooligosaccharide-forming α-amylase from a new Bacillus subtilis KCC103 by Dilli Rani Nagarajan; Gobinath Rajagopalan; Chandraraj Krishnan (pp. 591-597).

A maltooligosaccharide-forming α-amylase was produced by a new soil isolate Bacillus subtilis KCC103. In contrast to other Bacillus species, the synthesis of α-amylase in KCC103 was not catabolite-repressed. The α-amylase was purified in one step using anion exchange chromatography after concentration of crude enzyme by acetone precipitation. The purified α-amylase had a molecular mass of 53 kDa. It was highly active over a broad pH range from 5 to 7 and stable in a wide pH range between 4 and 9. Though optimum temperature was 65–70 °C, it was rapidly deactivated at 70 °C with a half-life of 7 min and at 50 °C, the half-life was 94 min. The K _m and V _max for starch hydrolysis were 2.6 mg ml⁻¹ and 909 U mg⁻¹, respectively. Ca²⁺ did not enhance the activity and stability of the enzyme; however, EDTA (50 mM) abolished 50% of the activity. Hg²⁺, Ag²⁺, and p-hydroxymercurybenzoate severely inhibited the activity indicating the role of sulfydryl group in catalysis. The α-amylase displayed endolytic activity and formed maltooligosaccharides on hydrolysis of soluble starch at pH 4 and 7. Small maltooligosaccharides (D2–D4) were formed more predominantly than larger maltooligosaccharides (D5–D7). This maltooligosaccharide forming endo-α-amylase is useful in bread making as an antistaling agent and it can be produced economically using low-cost sugarcane bagasse.

Keywords: Amylase; Glucose effect; Maltooligosaccharide; Antistaling agent; Sugarcane bagasse; Bacillus subtilis

Arthrobacter sp. lipase immobilization for improvement in stability and enantioselectivity by Asha Chaubey; Rajinder Parshad; Surrinder Koul; Subhash C. Taneja; Ghulam N. Qazi (pp. 598-606).

Arthrobacter sp. lipase (ABL, MTCC no. 5125) is being recognized as an efficient enzyme for the resolution of drugs and their intermediates. The immobilization of ABL on various matrices for its enantioselectivity, stability, and reusability has been studied. Immobilization by covalent bonding on sepharose and silica afforded a maximum of 380 and 40 IU/g activity, respectively, whereas sol–gel entrapment provided a maximum of 150 IU/g activity in dry powder. The immobilized enzyme displayed excellent stability in the pH range of 4–10 and even at higher temperature, i.e., 50–60°C, compared to free enzyme, which is unstable under extreme conditions. The resolution of racemic auxiliaries like 1-phenyl ethanol and an intermediate of antidepressant drug fluoxetine, i.e., ethyl 3-hydroxy-3-phenylpropanoate alkyl acylates, provided exclusively R-(+) products (∼99% ee, E=646 and 473), compared to cell free extract/whole cells which gave a product with ∼96% ee (E=106 and 150). The repeated use (ten times) of covalently immobilized and entrapped ABL resulted in no loss in activity, thus demonstrating its prospects for commercial applications.

Keywords: Arthrobacter sp.; Lipase; Immobilization; Resolution; Enantioselectivity

Modified substrate specificity of pyrroloquinoline quinone glucose dehydrogenase by biased mutation assembling with optimized amino acid substitution by Norio Hamamatsu; Akitoshi Suzumura; Yukiko Nomiya; Masaaki Sato; Takuyo Aita; Motowo Nakajima; Yuzuru Husimi; Yasuhiko Shibanaka (pp. 607-617).

A biased mutation-assembling method—that is, a directed evolution strategy to facilitate an optimal accumulation of multiple mutations on the basis of additivity principles, was applied to the directed evolution of water-soluble PQQ glucose dehydrogenase (PQQGDH-B) to reduce its maltose oxidation activity, which can lead to errors in blood glucose determination. Mutations appropriate for the reduction without fatal deterioration of its glucose oxidation activity were developed by an error-prone PCR method coupled with a saturation mutagenesis method. Moreover, two types of incorporation frequency based on their contribution were assigned to the mutations: high (80%) and evens (50%), in constructing a multiple mutant library. The best mutant created showed a marked reduction in maltose oxidation activity, corresponding to 4% of that of the wild-type enzyme, with 35% retention of glucose oxidation activity. In addition, this mutant showed a reduction in galactose oxidation activity corresponding to 5% of that of the wild-type enzyme. In conclusion, we succeeded in developing the PQQGDH-B mutants with improved substrate specificity and validated our method coupled with optimized mutations and their contribution-based incorporation frequencies by applying it to the development.

Keywords: Biased mutation-assembling method; Directed evolution; Saturation mutagenesis; Soluble pyrroloquinoline quinone glucose dehydrogenase; Substrate specificity

A cel44C-man26A gene of endophytic Paenibacillus polymyxa GS01 has multi-glycosyl hydrolases in two catalytic domains by Kye Man Cho; Su Young Hong; Sun Mi Lee; Yong Hee Kim; Goon Gjung Kahng; Hoon Kim; Han Dae Yun (pp. 618-630).

A bacterial strain Paenibacillus polymyxa GS01 was isolated from the interior of the roots of Korean cultivars of ginseng (Panax ginseng C. A. Meyer). The cel44C-man26A gene was cloned from this endophytic strain. This 4,056-bp gene encodes for a 1,352-aa protein which, based on BLAST search homologies, contains a glycosyl hydrolase family 44 (GH44) catalytic domain, a fibronectin domain type 3, a glycosyl hydrolase family 26 (GH26) catalytic domain, and a cellulose-binding module type 3. The multifunctional enzyme domain GH44 possesses cellulase, xylanase, and lichenase activities, while the enzyme domain GH26 possesses mannanase activity. The Cel44C enzyme expressed in and purified from Escherichia coli has an optimum pH of 7.0 for cellulase and lichenase activities, but is at an optimum pH of 5.0 for xylanase and mannanase activities. The optimum temperature for enzymatic activity was 50°C for all substrates. No detectable enzymatic activity was detected for the Cel44C-Man26A mutants E91A and E222A. These results suggest that the amino acid residues Glu₉₁ and Glu₂₂₂ may play an important role in the glycosyl hydrolases activity of Cel44C-Man26A.

Keywords: Paenibacillus polymyxa GS01; Glycosyl hydrolases; Rhizobacterium

Xylitol dehydrogenase from Candida tropicalis: molecular cloning of the gene and structural analysis of the protein by Luanne Helena Augusto Lima; Cristiano Guimarães do Amaral Pinheiro; Lídia Maria Pepe de Moraes; Sonia Maria de Freitas; Fernando Araripe Gonçalves Torres (pp. 631-639).

Yeasts can metabolize xylose by the action of two key enzymes: xylose reductase and xylitol dehydrogenase. In this work, we present data concerning the cloning of the XYL2 gene encoding xylitol dehydrogenase from the yeast Candida tropicalis. The gene is present as a single copy in the genome and is controlled at the transcriptional level by the presence of the inducer xylose. XYL2 was functionally tested by heterologous expression in Saccharomyces cerevisiae to develop a yeast strain capable of producing ethanol from xylose. Structural analysis of C. tropicalis xylitol dehydrogenase, Xyl2, suggests that it is a member of the medium-chain dehydrogenase (MDR) family. This is supported by the presence of the amino acid signature [GHE]xx[G]xxxxx[G]xx[V] in its primary sequence and a typical alcohol dehydrogenase Rossmann fold pattern composed by NAD⁺ and zinc ion binding domains.

Keywords: Xylitol dehydrogenase; Candida tropicalis ; Molecular modeling; Protein structure; Medium-chain dehydrogenase family

Cloning and characterization of a β-galactosidase encoding region in Lactobacillus coryniformis CECT 5711 by J. M. Corral; O. Bañuelos; J. L. Adrio; J. Velasco (pp. 640-646).

A chromosomal DNA fragment of 7.8 kb from Lactobacillus coryniformis CECT 5711 was cloned in Escherichia coli K-12 and was found to express a functional β-galactosidase. Nucleotide sequence analysis showed that this fragment contained two partially overlapping genes, the lacL (1,881 bp) and the lacM (960 bp), that encode the subunits of a heterodimeric β-galactosidase, with estimated molecular masses of 72,129 and 35,233 Da, respectively. Other three incomplete open reading frames showing homology to another β-galactosidase, an α-galactosidase, and a galactokinase, respectively, were also found. The L. coryniformis β-galactosidase was overproduced in E. coli by using an isopropyl-β-d-thiogalactopyranoside (IPTG) expression system. Two new proteins with an estimated M _r s of approximately 72,000 and 35,000 appeared upon induction with IPTG, and extracts of the recombinant E. coli strain showed β-galactosidase activity.

Keywords: β-Galactosidase; Lactobacillus coryniformis ; Probiotic

Improvement of the activity of arylmalonate decarboxylase by random mutagenesis by Y. Terao; K. Miyamoto; H. Ohta (pp. 647-653).

Arylmalonate decarboxylase (EC 4.1.1.76) catalyzes enantioselective decarboxylation of α-aryl-α-methylmalonates to give optically pure α-arylpropionates. Recently, we have succeeded in creating a double mutant enzyme that gave opposite enantionmer as the product. Unfortunately, however, the activity of the mutant decreased far lower than that of the native enzyme. Thus, we performed the directed evolution of the mutant via the random mutagenesis method employing the mutator strain Escherichia coli XL1-Red. About 50,000 mutants were screened on color assay plate, and one mutant with higher activity was obtained. Gene analysis of this mutant indicated that the obtained enzyme had an S36N mutation in addition to its original G74C/C188S mutations. The activity of the triple mutant enzyme was tenfold higher than that of the starting doubly mutated enzyme.

Keywords: Arylmalonate decarboxylase; Random-mutagenesis; XL1-Red; Activity

Substrate preference of Bifidobacterium adolescentis MB 239: compared growth on single and mixed carbohydrates by Alberto Amaretti; Elena Tamburini; Tatiana Bernardi; Anna Pompei; Simona Zanoni; Giuseppe Vaccari; Diego Matteuzzi; Maddalena Rossi (pp. 654-662).

The utilization of mono-, di-, and oligosaccharides by Bifidobacterium adolescentis MB 239 was investigated. Raffinose, fructooligosaccharides (FOS), lactose, and the monomeric moieties glucose and fructose were used. To establish a hierarchy of sugars preference, the kinetics of growth and sugar consumption were determined on individual and mixed carbohydrates. On single carbon sources, higher specific growth rates and cell yields were attained on di- and oligosaccharides compared to monosaccharides. Analysis of the carbohydrates in steady-state chemostat cultures, growing at the same dilution rate on FOS, lactose, or raffinose, showed that monomeric units and hydrolysis products were present. In chemostat cultures on individual carbohydrates, B. adolescentis MB 239 simultaneously displayed α-galactosidase, β-galactosidase, and β-fructofuranosidase activities on all the sugars, including monosaccharides. Glycosyl hydrolytic activities were found in cytosol, cell surface, and growth medium. Batch experiments on mixtures of carbohydrates showed that they were co-metabolized by B. adolescentis MB 239, even if different disappearance kinetics were registered. When mono-, di-, and oligosaccharides were simultaneously present in the medium, no precedence for monosaccharides utilization was observed, and di- and oligosaccharides were consumed before their constitutive moieties.

Keywords: Bifidobacterium; Prebiotics; Sugar mixtures; Chemostat; Glycosyl hydrolases; HPTLC-AMD

Hydrogen peroxide-induced astaxanthin biosynthesis and catalase activity in Xanthophyllomyces dendrorhous by Yuan Shuai Liu; Jian Yong Wu (pp. 663-668).

Xanthophyllomyces dendrorhous (formerly Phaffia rhodozyma) in shake-flask cultures was exposed to 10–20 mmol/L H₂O₂ at various culture stages, and the astaxanthin production was significantly increased by H₂O₂ fed at 0 or 24 h (exponential phase), but only slightly at 48 h (near stationary phase). The astaxanthin production was enhanced most significantly with double feeding of 10 mmol/L H₂O₂ at 0 and 24 h, reaching a cellular content of 1.30 mg/g cell and a volumetric yield of 10.4 mg/L, which were 83 and 65% higher, respectively, than those of the control (0.71 mg/g cell and 6.3 mg/L). The intracellular catalase (CAT) activity was also increased after H₂O₂ treatment. The increases in CAT and astaxanthin of cells could be detected within 4 h of H₂O₂ treatment. The increase in the astaxanthin content of cells was concomitant with a notable decrease in the β-carotene content. The older yeast cells at late culture stage (120 h), due perhaps in part to their higher astaxanthin contents, were more tolerant to H₂O₂ toxicity than the younger cells (24 h). No enhancement of the astaxanthin biosynthesis was attained when H₂O₂ was added to the yeast culture together with a sufficient amount of exogenous CAT. The results suggest that astaxanthin biosynthesis in X. dendrorhous can be stimulated by H₂O₂ as an antioxidative response.

Keywords: Xanthophyllomyces dendrorhous ; Astaxanthin; β-carotene; Hydrogen peroxide; Catalase; Antioxidant

Bacterial quorum sensing and cell surface electrokinetic properties by K. E. Eboigbodin; J. R. A. Newton; A. F. Routh; C. A. Biggs (pp. 669-675).

The hypothesis tested in this paper is that quorum sensing influences the microbial surface electrokinetic properties. Escherichia coli MG1655 and MG1655 LuxS- mutant (lacking quorum-sensing gene for Autoinducer synthase AI-2) were used for this study. AI-2 production (or lack of) in both strains was analyzed using the Vibrio harveyi bioassay. The levels of extracellular AI-2 with and without glucose in the growth medium were consistent with previously published work. The surface electrokinetic properties were determined for each strain of E. coli MG1655 by measuring the electrophoretic mobility using a phase amplitude light-scattering (PALS) Zeta potential analyser. The findings show that the surface charge of the cells is dependent upon the stage in the growth phase as well as the ability to participate in quorum sensing. In addition, significant differences in the electrophoretic mobility were observed between both strains of E. coli. These findings suggest that quorum sensing plays a significant role in the surface chemistry of bacteria during their growth.

Keywords: Cell surface charge; Electrokinetic potential; Quorum sensing; Escherichia coli ; Aggregation

Lipids of Cunninghamella echinulata with emphasis to γ-linolenic acid distribution among lipid classes by Stylianos Fakas; Seraphim Papanikolaou; Maria Galiotou-Panayotou; Michael Komaitis; George Aggelis (pp. 676-683).

Changes in lipid composition of the oleaginous fungus Cunninghamella echinulata were monitored during growth. Lipid fractions and individual lipid classes varied in amount, relative proportions, and fatty acid profile depending on the developmental stage. Neutral lipids (N), comprised mainly of triacylglycerol, were accumulated in the fungal mycelium during both the late exponential and the stationary growth phases with a concomitant decrease in the amount of polar lipids. While fatty acid composition of N fraction remained almost constant, individual N classes showed a noticeable alteration in γ-linolenic acid (GLA) concentration. The glycolipid plus sphingolipid (G+S) fraction consisted mainly of monoglycosylglycerol and diglycosylglycerol. The sugar composition of G+S fraction was analyzed and showed a partial replacement of galactose for glucose as growth proceeded. Phospholipid (P) major classes were phosphatidylcholine (PC) and phosphatidylethanolamine, followed by phosphatidylinositol, phosphatidylserine, and diphosphatidylglycerol. P fatty acid composition showed significant changes with time, resulting in a considerable drop in the unsaturation index of this fraction. While in mid exponential growth phase, all P classes contained more than 20% w/w GLA of total fatty acids, and their concentration decreased to 12–17% w/w, except for the PC class where GLA concentration remained at high levels (e.g., more than 20% w/w). The constant level of GLA in PC at all growth phases suggests that PC was the major source of GLA. Sterol analysis showed that their concentration increased during growth, whereas ergosterol was the major component.

Keywords: Microbial lipid; GLA

Producing mechanism of an algicidal compound against red tide phytoplankton in a marine bacterium γ-proteobacterium by Takuji Nakashima; Yousuke Miyazaki; Yukihiko Matsuyama; Wataru Muraoka; Kenichi Yamaguchi; Tatsuya Oda (pp. 684-690).

Strain MS-02-063, γ-proteobacterium, isolated from a coast area of Nagasaki, Japan, produced a red pigment which belongs to prodigiosin members. This pigment, PG-L-1, showed potent algicidal activity against various red tide phytoplanktons in a concentration-dependent manner. An understanding of a mechanism of PG-L-1 production by this marine bacterium may yield important new insights and strategies for preventing blooms of harmful flagellate algae in natural marine environments. Therefore, we analyzed the mechanisms of PG-L-1 production. In our previous study, the pigment production by this marine bacterium was completely inhibited at 1.56 μg/ml of erythromycin or 3.13 μg/ml of chloramphenicol, while minimal inhibitory concentrations for cell growth of erythromycin and chloramphenicol against this bacterium were >100 and 25 μg/ml, respectively. It is interesting to note that the ability of the pigment production in erythromycin-treated bacterium recovered by an addition of homoserine lactone. In fact, the pigment production was inhibited by β-cyclodextrin that inhibits autoinducer activities by a complex with N-acyl homoserine lactones. N-acyl homoserine lactones with autoinducer activities are ubiquitous bacterial signaling molecules that regulate gene expression in a cell density dependent process known as quorum sensing. Therefore, it was suggested that PG-L-1 produced by strain MS-02-063 is controlled by the homoserine lactone quorum sensing. It is speculated that this quorum sensing is involved in the production of algicidal agents of other marine bacteria. This bacterium and other algicidal bacteria might be concerned in regulating the blooms of harmful flagellate algae through the quorum sensing system.

Keywords: Algicidal activity; Harmful algal bloom; Prodigiosin; γ-proteobacterium ; Homoserine lactone

Expression of gentisate 1,2-dioxygenase (gdoA) genes involved in aromatic degradation in two haloarchaeal genera by D. J. Fairley; G. Wang; C. Rensing; I. L. Pepper; M. J. Larkin (pp. 691-695).

Gentisate-1,2-dioxygenase genes (gdoA), with homology to a number of bacterial dioxygenases, and genes encoding a putative coenzyme A (CoA)-synthetase subunit (acdB) and a CoA-thioesterase (tieA) were identified in two haloarchaeal isolates. In Haloarcula sp. D1, gdoA was expressed during growth on 4-hydroxybenzoate but not benzoate, and acdB and tieA were not expressed during growth on any of the aromatic substrates tested. In contrast, gdoA was expressed in Haloferax sp. D1227 during growth on benzoate, 3-hydroxybenzoate, cinnamate and phenylpropionate, and both acdB and tieA were expressed during growth on benzoate, cinnamate and phenylpropionate, but not on 3-hydroxybenzoate. This pattern of induction is consistent with these genes encoding steps in a CoA-mediated benzoate pathway in this strain.

Keywords: Haloarchaea; Aromatic; Catabolism; Haloferax; Benzoate; 3-Hydroxybenzoate

Quantification of methanogens by fluorescence in situ hybridization with oligonucleotide probe by O. Stabnikova; X.-Y. Liu; J.-Y. Wang; V. Ivanov (pp. 696-702).

To monitor anaerobic environmental engineering system, new method of quantification for methanogens was tested. It is based on the measurement of specific binding (hybridization) of 16S rRNA-targeted oligonucleotide probe Arc915, performed by fluorescence in situ hybridization (FISH) and quantified by fluorescence spectrometry. Average specific binding of Arc915 probe was 13.4±0.5 amol/cell of autofluorescent methanogens. It was 14.3, 13.3, and 12.9 amol/cell at the log phase, at stationary phase and at the period of cell lysis of batch culture, respectively. Specific binding of Arc915 probe per 1 ml of microbial sludge suspension from anaerobic digester linearly correlated with concentration of autofluorescent cells of methanogens. Coefficient of correlation was 0.95. Specific binding of oligonucleotide probe Arc915 can be used for the comparative estimation of methanogens during anaerobic digestion of organic waste. Specific binding of Arc915 probe was linear function of anaerobic sludge concentration when it was between 1.4 and 14.0 mg/ml. Accuracy of the measurements in this region was from 5 to 12%.

Bacterial survival in evaporating deposited droplets on a teflon-coated surface by Xiaojian Xie; Yuguo Li; Tong Zhang; Herbert H. P. Fang (pp. 703-712).

Understanding of bacterial survival in aerosols is crucial for controlling infection transmission via airborne aerosols and/or large droplets routes. The cell viability changes of four bacteria species (Escherichia coli K12 JM109; Acinetobacter sp. 5A5; Pseudomonas oleovorans X5; and Staphylococcus aureus X8), three Gram-negative and one Gram-positive, in a large evaporating droplet of size 1,800 μm in diameter on teflon-coated slides were measured using the LIVE/DEAD BacLight solution and a microscope. Droplets of three levels of salinity (0, 0.9, and 36% w/v) were tested. All four species survived well during the droplet evaporation process, but died mostly at the time when droplets were dried out at 40–45 min. The final bacteria survival rate after droplets were completely dried was dependent on bacteria species and the salinity of the suspension solution. Droplet evaporation over the first 35–40 min had no adverse effect on bacterial survival for the droplets tested. The lethal effect of desiccation was found to be the most important death mechanism.

Keywords: Droplet; Bacterial survival; Evaporation effect; Desiccation effect; Salinity effect

Rapid intrinsic biodegradation of benzene, toluene, and xylenes at the boundary of a gasoline-contaminated plume under natural attenuation by Yoh Takahata; Yuki Kasai; Toshihiro Hoaki; Kazuya Watanabe (pp. 713-722).

A groundwater plume contaminated with gasoline constituents [mainly benzene, toluene, and xylenes (BTX)] had been treated by pumping and aeration for approximately 10 years, and the treatment strategy was recently changed to monitored natural attenuation (MNA). To gain information on the feasibility of using MNA to control the spread of BTX, chemical and microbiological parameters in groundwater samples obtained inside and outside the contaminated plume were measured over the course of 73 weeks. The depletion of electron acceptors (i.e., dissolved oxygen, nitrate, and sulfate) and increase of soluble iron were observed in the contaminated zone. Laboratory incubation tests revealed that groundwater obtained immediately outside the contaminated zone (the boundary zone) exhibited much higher potential for BTX degradation than those in the contaminated zone and in uncontaminated background zones. The boundary zone was a former contaminated area where BTX were no longer detected. Denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR)-amplified bacterial 16S rRNA gene fragments revealed that DGGE profiles for groundwater samples obtained from the contaminated zone were clustered together and distinct from those from uncontaminated zones. In addition, unique bacterial rRNA types were observed in the boundary zone. These results indicate that the boundary zone in the contaminant plumes served as a natural barrier for preventing the BTX contamination from spreading out.

Keywords: Bioremediation; Gasoline-contaminated groundwater

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Applied Microbiology and Biotechnology (v.73, #3)