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Applied Microbiology and Biotechnology (v.88, #1)

Lactococcal membrane-permeabilizing antimicrobial peptides by Takeshi Zendo; Fuminori Yoneyama; Kenji Sonomoto (pp. 1-9).

A number of lactococcal antimicrobial peptides, bacteriocins have been discovered and characterized. Since Lactococcus spp. are generally regarded as safe bacteria, their bacteriocins are expected for various application uses. Most of lactococcal bacteriocins exert antimicrobial activity via membrane permeabilization. The most studied and prominent bacteriocin, nisin A is characterized in the high activity and has been utilized as food preservatives for more than half a century. Recently, other lactococcal bacteriocins such as lacticin Q were found to have distinguished features for further applications as the next generation to nisin.

Keywords: Antimicrobial peptide; Bacteriocin; Lactic acid bacteria; Lactococcus ; Nisin; Lacticin

On-line infrared spectroscopy for bioprocess monitoring by Daniel Landgrebe; Claas Haake; Tim Höpfner; Sascha Beutel; Bernd Hitzmann; Thomas Scheper; Martin Rhiel; Kenneth F. Reardon (pp. 11-22).

One of the major aims of bioprocess engineering is the real-time monitoring of important process variables. This is the basis of precise process control and is essential for high productivity as well as the exact documentation of the overall production process. Infrared spectroscopy is a powerful analytical technique to analyze a wide variety of organic compounds. Thus, infrared sensors are ideal instruments for bioprocess monitoring. The sensors are non-invasive, have no time delay due to sensor response times, and have no influence on the bioprocess itself. No sampling is necessary, and several components can be analyzed simultaneously. In general, the direct monitoring of substrates, products, metabolites, as well as the biomass itself is possible. In this review article, insights are provided into the different applications of infrared spectroscopy for bioprocess monitoring and the complex data interpretation. Different analytical techniques are presented as well as example applications in different areas.

Keywords: Infrared spectroscopy; Bioprocess; On-line measurement; On-line monitoring; Sensor

Enzyme systems for biodegradation of polychlorinated dibenzo-p-dioxins by Toshiyuki Sakaki; Eiji Munetsuna (pp. 23-30).

The angular dioxygenase, cytochrome P450, lignin peroxidase, and dehalogenase are known as dioxin-metabolizing enzymes. All of these enzymes have metal ions in their active centers, and the enzyme systems except for peroxidase have each distinct electron transport chain. Although the enzymatic properties of the angular dioxygenase, lignin peroxidase, and cytochrome P450 have been studied well, the information about dehalogenase is much less than other enzyme systems due to its instability under the aerobic conditions. However, this enzyme system appears to be quite promising from the viewpoint of practical use for bioremediation, because dehalogenases are capable of degradation of polychlorinated dibenzo-p-dioxins (PCDDs) with more than four chlorine substituents, whereas the other three enzyme systems prefer low-chlorinated PCDDs. On the other hand, protein engineering of angular dioxygenase, lignin peroxidase, and cytochrome P450 based on their tertiary structures has great potential to generate highly efficient dioxin-metabolizing enzymes. Actually, we successfully generated 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-metabolizing enzyme by site-directed mutagenesis of cytochrome P450. We hope that recombinant microorganisms harboring genetically engineered dioxin-metabolizing enzymes will be used for bioremediation of soil contaminated with PCDDs and polychlorinated dibenzofurans in the near future.

Keywords: Dioxin; Enzyme; Metabolism; Bioremediation; Microorganism

Yeast flocculation and its biotechnological relevance by Florian F. Bauer; Patrick Govender; Michael C. Bester (pp. 31-39).

Adhesion properties of microorganisms are crucial for many essential biological processes such as sexual reproduction, tissue or substrate invasion, biofilm formation and others. Most, if not all microbial adhesion phenotypes are controlled by factors such as nutrient availability or the presence of pheromones. One particular form of controlled cellular adhesion that occurs in liquid environments is a process of asexual aggregation of cells which is also referred to as flocculation. This process has been the subject of significant scientific and biotechnological interest because of its relevance for many industrial fermentation processes. Specifically adjusted flocculation properties of industrial microorganisms could indeed lead to significant improvements in the processing of biotechnological fermentation products such as foods, biofuels and industrially produced peptides. This review briefly summarises our current scientific knowledge on the regulation of flocculation-related phenotypes, their importance for different biotechnological industries, and possible future applications for microorganisms with improved flocculation properties.

Keywords: Flocculation; Microbial cell adhesion; Genetic engineering; Industrial bioprocesses; Yeast

Multiple roles of ATP:cob(I)alamin adenosyltransferases in the conversion of B₁₂ to coenzyme B₁₂ by Paola E. Mera; Jorge C. Escalante-Semerena (pp. 41-48).

Our mechanistic understanding of the conversion of vitamin B₁₂ into coenzyme B₁₂ (a.k.a. adenosylcobalamin, AdoCbl) has been substantially advanced in recent years. Insights into the multiple roles played by ATP:cob(I)alamin adenosyltransferase (ACA) enzymes have emerged through the crystallographic, spectroscopic, biochemical, and mutational analyses of wild-type and variant proteins. ACA enzymes circumvent the thermodynamic barrier posed by the very low redox potential associated with the reduction of cob(II)alamin to cob(I)alamin by generating a unique four-coordinate cob(II)alamin intermediate that is readily converted to cob(I)alamin by physiological reductants. ACA enzymes not only synthesize AdoCbl but also they deliver it to the enzymes that use it, and in some cases, enzymes in which its function is needed to maintain the fidelity of the AdoCbl delivery process have been identified. Advances in our understanding of ACA enzyme function have provided valuable insights into the role of specific residues, and into why substitutions of these residues have profound negative effects on human health. From an applied science standpoint, a better understanding of the adenosylation reaction may lead to more efficient ways of synthesizing AdoCbl.

Keywords: Coenzyme B₁₂ ; Adenosylcobalamin; Corrinoid adenosylation; Cyclic tetrapyrroles; Vitamin metabolism

One-pot, two-step enzymatic synthesis of amoxicillin by complexing with Zn²⁺ by Ye-Wang Zhang; Rui-Jiang Liu; Xi-Ming Xu (pp. 49-55).

A one-pot, two-step enzymatic synthesis of amoxicillin from penicillin G, using penicillin acylase, is presented. Immobilized penicillin acylase from Kluyvera citrophila was selected as the biocatalyst for its good pH stability and selectivity. Hydrolysis of penicillin G and synthesis of amoxicillin from the 6-aminopenicillanic acid formed and d-p-hydroxyphenylglycine methyl ester were catalyzed in situ by a single enzyme. Zinc ions can react with amoxicillin to form complexes, and the yield of 76.5% was obtained after optimization. In the combined one-pot synthesis process, zinc sulfate was added to remove produced amoxicillin as complex for shifting the equilibrium to the product in the second step. By controlling the conditions in two separated steps, the conversion of the first and second step was 93.8% and 76.2%, respectively. With one-pot continuous procedure, a 71.5% amoxicillin yield using penicillin G was obtained.

Keywords: Amoxicillin; Enzymatic synthesis; Complexing; Penicillin acylase; In situ product removal

Highly regioselective enzymatic synthesis of 5′-O-stearate of 1-β-D-arabinofuranosylcytosine in binary organic solvent mixtures by Xiao-feng Li; Min-hua Zong; Guang-lei Zhao (pp. 57-63).

In this paper, highly regioselective enzymatic acylations of 1-β-D-arabinofuranosylcytosine (ara-C) with vinyl stearate (VS) in binary organic solvents were explored for the preparation of 5′-O-stearate of ara-C with potential antitumor activity. Twelve kinds of hydrolases were tested for the regioselective acylation reaction and the immobilized Candida antarctica lipase B (Novozym 435) showed the highest regioselectivity (>99.9%) towards the 5′-OH of ara-C. A comparative study showed that the lipase had much higher catalytic activity in the binary mixture of hexane and pyridine than in other tested co-solvent systems. To better understand lipase-mediated acylation conducted in the best binary organic solvent system, the effects of hydrophobic solvent content, molar ratio of VS to ara-C, initial water activity, and reaction temperature on the acylation reaction were studied. It was found that the most suitable hexane content, VS–ara-C molar ratio, initial water activity, and reaction temperature were shown to be 25% (v/v), 20:1, 0.07, and 50°C, respectively. Under these reaction conditions, the initial reaction rate, the maximum substrate conversion, and regioselectivity were as high as 86.0 mmol·L⁻¹h⁻¹, 96.6%, and >99.9%, respectively. The product of Novozym 435-catalyzed acylation was characterized by Carbon-13(¹³C) NMR and confirmed to be 5′-O-stearate of ara-C.

Keywords: 1-β-D-arabinofuranosylcytosine; Vinyl stearate; Lipases; Binary organic solvents

Impact of linoleic acid supplementation on lovastatin production in Aspergillus terreus cultures by Flavia Sorrentino; Ipsita Roy; Tajalli Keshavarz (pp. 65-73).

This work proposes a novel approach for enhancing the yield of lovastatin in Aspergillus terreus cultures by exploiting linoleic acid-derived signalling molecules, which are potentially involved in fungal cell–cell communication. High-performance liquid chromatography analysis revealed that production of lovastatin was enhanced up to 1.8-fold upon exogenous addition of the oxylipin precursor linoleic acid to low cell density cultures of A. terreus. Real-time PCR analysis showed that supplementation of linoleic acid also resulted in an increase in transcriptional levels of lovastatin biosynthetic genes lovB and lovF, indicating a transcriptional control of fatty acids (linoleic acid) on these genes in A. terreus. This study therefore demonstrates for the first time the potential of an oxylipin molecule as an enhancer of a fungal secondary metabolite production with positive impact for industrial exploitation.

Keywords: Lovastatin; Linoleic acid; Aspergillus terreus ; Yield enhancement; Cell–cell communication; Oxylipin

Extracellular accumulation of recombinant protein by Escherichia coli in a defined medium by Xiang-Yang Fu (pp. 75-86).

Extracellular accumulation of recombinant proteins in the culture medium of Escherichia coli is desirable but difficult to obtain. The inner or cytoplasmic membrane and the outer membrane of E. coli are two barriers for releasing recombinant proteins expressed in the cytoplasm into the culture medium. Even if recombinant proteins have been exported into the periplasm, a space between the outer membrane and the inner membrane, the outer membrane remains the last barrier for their extracellular release. However, when E. coli was cultured in a particular defined medium, recombinant proteins exported into the periplasm could diffuse into the culture medium automatically. If a nonionic detergent, Triton X-100, was added in the medium, recombinant proteins expressed in the cytoplasm could also be released into the culture medium. It was then that extracellular accumulation of recombinant proteins could be obtained by exporting them into the periplasm or releasing them from the cytoplasm with Triton X-100 addition. The tactics described herein provided simple and valuable methods for achieving extracellular production of recombinant proteins in E. coli.

Keywords: Chemical permeabilization; Extracellular production; Escherichia coli ; Recombinant protein; Membrane permeability; Secretion

Ethanol production from biomass by repetitive solid-state fed-batch fermentation with continuous recovery of ethanol by Churairat Moukamnerd; Masahiro Kino-oka; Minetaka Sugiyama; Yoshinobu Kaneko; Chuenchit Boonchird; Satoshi Harashima; Hideo Noda; Kazuaki Ninomiya; Suteaki Shioya; Yoshio Katakura (pp. 87-94).

To save cost and input energy for bioethanol production, a consolidated continuous solid-state fermentation system composed of a rotating drum reactor, a humidifier, and a condenser was developed. Biomass, saccharifying enzymes, yeast, and a minimum amount of water are introduced into the system. Ethanol produced by simultaneous saccharification and fermentation is continuously recovered as vapor from the headspace of the reactor, while the humidifier compensates for the water loss. From raw corn starch as a biomass model, 95 ± 3, 226 ± 9, 458 ± 26, and 509 ± 64 g l⁻¹ of ethanol solutions were recovered continuously when the ethanol content in reactor was controlled at 10–20, 30–50, 50–70 and 75–85 g kg-mixture⁻¹, respectively. The residue showed a lesser volume and higher solid content than that obtained by conventional liquid fermentation. The cost and energy for intensive waste water treatment are decreased, and the continuous fermentation enabled the sustainability of enzyme activity and yeast in the system.

Keywords: Bioethanol; Solid-state fermentation; Simultaneous saccharification and fermentation; Continuous recovery of ethanol

Recombinant production of an Aspergillus nidulans class I hydrophobin (DewA) in Hypocrea jecorina (Trichoderma reesei) is promoter-dependent by Monika Schmoll; Christian Seibel; Caroline Kotlowski; Frank Wöllert Genannt Vendt; Burghart Liebmann; Christian P. Kubicek (pp. 95-103).

Fungal hydrophobins have potential for several applications because of their abilities to change the hydrophobicity of different surfaces. Yet because of their tendency for aggregation and attachment to interfacial areas only few production processes have so far been reported. Towards the development of a heterologous production system, we report here the expression of a class I hydrophobin DewA of Aspergillus nidulans in Hypocrea jecorina (Trichoderma reesei). Using the H. jecorina hfb2 (class II hydrophobin-encoding) promoter and lactose as a carbon source, only a minor fraction of the DewA remained cell-wall-bound and the majority of it secreted into the medium with up to 15% of the total secreted protein. N-terminal amino acid sequencing showed that it was correctly processed. In contrast, no DewA was produced under the cel7A (cellobiohydrolase I) promoter, although its mRNA was abundantly detected in the cells. This lack of secretion is not due to trapping in the cell wall or to its degradation because of the unfolded protein response. Recombinant DewA could be conveniently precipitated from the culture filtrate, and its bioactivity proven by its ability to stably bind to hydrophilic and hydrophobic surfaces (glass and Teflon, respectively). We thus consider H. jecorina as a promising host for further optimization of DewA production.

Keywords: Trichoderma; Heterologous production; Hydrophobin; Aspergillus

Activation of diacylglycerol acyltransferase expressed in Saccharomyces cerevisiae: overexpression of Dga1p lacking the N-terminal region in the ∆snf2 disruptant produces a significant increase in its enzyme activity by Yasushi Kamisaka; Kazuyoshi Kimura; Hiroshi Uemura; Motonari Shibakami (pp. 105-115).

We previously found that overexpression of DGA1 encoding diacylglycerol acyltransferase (DGAT) in the ∆snf2 disruptant of Saccharomyces cerevisiae caused a significant increase in lipid accumulation and DGAT activity. The present study was conducted to investigate how Dga1p is activated in the ∆snf2 disruptant. To analyze the expression of Dga1p in wild type and the ∆snf2 disruptant, we overexpressed Dga1p with a 6x His tag at the N-terminus and a FLAG tag at the C-terminus. Immunoblotting using anti-6x His and anti-FLAG antibodies revealed that, in addition to full-length protein, Dga1p lacking the N-terminus was produced only in the ∆snf2 disruptant. Full-length Dga1p and N-terminally truncated Dga1p were separated and purified from the lipid body fraction by using anti-FLAG M2 agarose and TALON metal affinity resin. Major DGAT activity was recovered in the purified fraction of N-terminally truncated Dga1p, indicating that proteolytic cleavage at the N-terminal region is involved in DGAT activation in the ∆snf2 disruptant. Analysis of the cleavage site of N-terminally truncated Dga1p revealed a major site between Lys-29 and Ser-30. We then overexpressed truncated Dga1p variants that lacked different N-terminal amino acids and had a FLAG tag at the C-terminus. The homogenate and lipid body fraction of the ∆snf2 disruptant overexpressing Dga1p lacking the N-terminal 29 amino acids (Dga1∆N2p) had higher DGAT activity than that overexpressing Dga1p, indicating that Dga1∆N2p is activated Dga1p. Dga1∆N2p-FLAG(C-terminus) was purified to near homogeneity by anti-FLAG M2 agarose chromatography and maintained significant DGAT activity. These results provide a new strategy to engineer expression of DGAT.

Keywords: DGA1 ; Diacylglycerol acyltransferase; Lipid body fraction; Proteolytic cleavage; Saccharomyces cerevisiae ; SNF2 ; Yeast

Engineering of glycerol dehydrogenase for improved activity towards 1, 3-butanediol by Hongfang Zhang; George T. Lountos; Chi Bun Ching; Rongrong Jiang (pp. 117-124).

The objective of this study was to use protein engineering techniques to enhance the catalytic activity of glycerol dehydrogenase (GlyDH) on racemic 1, 3-butanediol (1, 3-BDO) for the bioproduction of the important pharmaceutical intermediate 4-hydroxy-2-butanone. Three GlyDH genes (gldA) from Escherichia coli K-12, Salmonella enterica, and Klebsiella pneumoniae MGH78578 were shuffled to generate a random mutagenesis library. The nitroblue tetrazolium/phenazine methosulfate high throughput screening protocol was used to select four chimeric enzymes with up to a 2.6-fold improved activity towards 1, 3-BDO. A rational design method was also employed to further improve the enzyme activity after DNA shuffling. Based on the homology model of GlyDH (Escherichia coli), Asp121 was predicted to influence 1, 3-BDO binding and replaced with Ala by site-directed mutagenesis. Combination of the mutations from both DNA shuffling and rational design produced the best mutant with a V _max value of 126.6 U/mg, a 26-fold activity increase compared with that of the wild type GlyDH from E. coli.

Keywords: Glycerol dehydrogenase; Protein engineering; 1, 3-butanediol; 4-hydroxy-2-butanone

An intramolecular disulfide bond is required for the thermostability of methyl parathion hydrolase, OPHC2 by Xiao-yu Chu; Jian Tian; Ning-feng Wu; Yun-liu Fan (pp. 125-131).

OPHC2, a methyl parathion hydrolase (MPH) from Pseudomonas pseudoalcaligenes C2-1 (CGMCC 1150), can degrade a wide range of organophosphate pesticides. Compared with other MPHs, OPHC2 exhibits high thermostability. Its thermostability mechanism, however, remains unknown. In the present study, sequence analysis demonstrated that two cysteines (Cys110 and Cys146) exist in OPHC2, but not in other MPHs. The three-dimensional structural model of OPHC2 performed by computer-assisted homology modelling revealed a potential stacking network with residues Cys110 and Cys146, which probably formed an intramolecular disulfide bond. Furthermore, both sodium dodecyl sulphate-polyacrylamide gel electrophoresis and thiol-titration analyses indicated that OPHC2 contains a disulfide bond. Substitution of the disulfide bond-forming cysteines with alanine, leucine or methionine residues substantially decreased the thermostability of OPHC2, suggesting that disulfide bond formation affects conformational stability. These results, combined with three-dimensional structural modelling, demonstrated that the formation of a C110-C146 disulfide bond may stabilise the conformation of OPHC2, contributing to its thermostability.

Keywords: Methyl parathion hydrolase; Disulfide bond; Site-directed mutagenesis; Thermostability

Biochemical and molecular characterization of Coriolopsis rigida laccases involved in transformation of the solid waste from olive oil production by Rosario Díaz; Mario C. N. Saparrat; Miguel Jurado; Inmaculada García-Romera; Juan Antonio Ocampo; María Jesús Martínez (pp. 133-142).

Two laccase isoenzymes were purified and characterized from the basidiomycete Coriolopsis rigida during transformation of the water-soluble fraction of “alpeorujo” (WSFA), a solid residue derived from the olive oil production containing high levels of toxic compounds. Zymogram assays of laccases secreted by the fungus growing on WSFA and WSFA supplemented with glucose showed two bands with isoelectric points of 3.3 and 3.4. The kinetic studies of the two purified isoenzymes showed similar affinity on 2,6-dimethoxyphenol and 2,2′-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid), used as phenolic and non-phenolic model substrate, respectively. The molecular mass of both proteins was 66 kDa with 9% N-linked carbohydrate. Physico-chemical properties of the purified laccases from media containing WSFA were similar to those obtained from medium with glucose as the main carbon source. In-vitro studies performed with the purified laccases revealed a 42% phenol reduction of WSFA, as well as changes in the molecular mass distribution. These findings indicate that these laccases are involved in the process of transformation, via polymerization by the oxidation of phenolic compounds present in WSFA. A single laccase gene, containing an open reading frame of 1,488 bp, was obtained in PCR amplifications performed with cDNA extracted from mycelia grown on WSFA. The product of the gene shares 90% identity (95% similarity) with a laccase from Trametes trogii and 89% identity (95% similarity) with a laccase from Coriolopsis gallica. This is the first report on purification and molecular characterization of laccases directly involved in the transformation of olive oil residues.

Keywords: Olive-mill waste; Basidiomycetes; Phenol; Gene sequence

Structural and biochemical characterization of a nitrilase from the thermophilic bacterium, Geobacillus pallidus RAPc8 by Dael S. Williamson; Kyle C. Dent; Brandon W. Weber; Arvind Varsani; Joni Frederick; Robert N. Thuku; Rory A. Cameron; Johan H. van Heerden; Donald A. Cowan; B. Trevor Sewell (pp. 143-153).

Geobacillus pallidus RAPc8 (NRRL: B-59396) is a moderately thermophilic gram-positive bacterium, originally isolated from Australian lake sediment. The G. pallidus RAPc8 gene encoding an inducible nitrilase was located and cloned using degenerate primers coding for well-conserved nitrilase sequences, coupled with inverse PCR. The nitrilase open reading frame was cloned into an expression plasmid and the expressed recombinant enzyme purified and characterized. The protein had a monomer molecular weight of 35,790 Da, and the purified functional enzyme had an apparent molecular weight of ~600 kDa by size exclusion chromatography. Similar to several plant nitrilases and some bacterial nitrilases, the recombinant G. pallidus RAPc8 enzyme produced both acid and amide products from nitrile substrates. The ratios of acid to amide produced from the substrates we tested are significantly different to those reported for other enzymes, and this has implications for our understanding of the mechanism of the nitrilases which may assist with rational design of these enzymes. Electron microscopy and image classification showed complexes having crescent-like, “c-shaped”, circular and “figure-8” shapes. Protein models suggested that the various complexes were composed of 6, 8, 10 and 20 subunits, respectively.

Keywords: Nitrilase; Geobacillus pallidus ; Tetrahedral intermediate

A novel metagenome-derived β-galactosidase: gene cloning, overexpression, purification and characterization by Kui Wang; Gang Li; Shi Qin Yu; Chen Ting Zhang; Yu Huan Liu (pp. 155-165).

A novel β-galactosidase gene, zd410, was isolated by screening a soil metagenomic library. Sequence analysis revealed that zd410 encodes a protein of 672 amino acids with a predicted molecular weight of 78.6 kDa. The recombinant ZD410 was expressed and purified in Pichia pastoris, with a yield of ca. 300 mg from 1 L culture. The purified enzyme displayed optimal activity at 38°C and pH 7.0. Given that the enzyme had 54% of the maximal activity at 20°C and 11% of the maximal activity at close to 0°C, ZD410 was regarded as a cold-adapted β-galactosidase. ZD410 displays high enzymatic activity for its synthetic substrate-ONPG (o-nitrophenyl-β-d-galactopyranoside, 243 U/mg) and its natural substrate-lactose (25.4 U/mg), while its activity was slightly stimulated by addition of Na⁺, K⁺, or Ca²⁺ at low concentrations. ZD410 is a good candidate of β-galactosidases for food industry after further study.

Keywords: β-galactosidase; Cold-adapted activity; Gene cloning; Enzyme characterization; Metagenome

High level expression and purification of antimicrobial human cathelicidin LL-37 in Escherichia coli by Ján Krahulec; Marcela Hyršová; Stanislav Pepeliaev; Jana Jílková; Zbyněk Černý; Jana Machálková (pp. 167-175).

The human antimicrobial peptide LL-37 is a cationic peptide with antimicrobial activity against both Gram-positive and Gram-negative microorganisms. This work describes the development of an expression system based on Escherichia coli capable of high production of the recombinant LL-37. The fusion protein Trx-LL-37 was expressed under control of T7 promoter. The expression of T7 polymerase in the E. coli strain constructed in this work was controlled by regulation mechanisms of the arabinose promoter. The expression plasmid was stabilized by the presence of parB locus which ensured higher homology of the culture during cultivation without antibiotic selection pressure. This system was capable of producing up to 1 g of fusion protein per 1 l of culture. The subsequent semipreparative HPLC allowed us to isolate 40 mg of pure LL-37. LL-37 showed high antimicrobial activity against both Gram-negative and Gram-positive microorganisms. Its activity against Candida albicans was practically nonexistent. Minimal Inhibition Concentration (MIC) determined for E. coli was 1.65 μM; for Staphylococcus aureus 2.31 μM, and for Enterococcus faecalis 5.54 μM. The effects of cathelicidin on E. coli included the ability to permeabilize both cell membranes, as could be observed by the increase of β-galactosidase activity in extracellular space in time. Physiological changes were studied by scanning electron microscopy; Gram-positive microorganisms did not show any visible changes in cell shapes while the changes observed on E. coli cells were evident. The results of this work show that the herein designed expression system is capable of producing adequate quantities of active human antimicrobial peptide LL-37.

Keywords: Human; Recombinant; Antimicrobial peptide; Cathelicidin

Recombinant expression of bioactive peptide lunasin in Escherichia coli by Chin-Feng Liu; Tzu-Ming Pan (pp. 177-186).

Lunasin, a cancer-preventive peptide, was isolated from soybean, barley, and wheat. Previous studies showed that this 43-amino acid peptide has the ability to suppress chemical carcinogen-induced transformation in mammalian cells and skin carcinogenesis in mice. In this study, we attempted to use the Escherichia coli T7 expression system for expression of lunasin. The lunasin gene was synthesized by overlapping extension polymerase chain reaction and expressed in E. coli BL21(DE3) with the use of vector pET29a. The recombinant lunasin containing his-tag at the C-terminus was expressed in soluble form which could be purified by immobilized metal affinity chromatography. After 4 h, the expression level is above 4.73 mg of recombinant his-tagged lunasin/L of Luria–Bertani broth. It does not affect the bacterial growth and expression levels. This is the first study that successfully uses E. coli as a host to produce valuable bioactive lunasin. The result of in vitro bioassay showed that the purified recombinant lunasin can inhibit histone acetylation. Recombinant lunasin also inhibits the release of pro-inflammatory cytokines (tumor necrosis factor-α, interleukin-1β, and nitric oxide production). Compared with other research methods on extraction or chemical synthesis to produce lunasin, our method is very efficient in saving time and cost. In the future, it could be applied in medicine and structure–function determination.

Keywords: Lunasin; Escherichia coli ; Overlapping extension polymerase chain reaction; Core histone acetylation

Mutations in maltose-binding protein that alter affinity and solubility properties by Iris H. Walker; Pei-chung Hsieh; Paul D. Riggs (pp. 187-197).

Maltose-binding protein (MBP) from Escherichia coli has been shown to be a good substrate for protein engineering leading to altered binding (Marvin and Hellinga, Proc Natl Acad Sci U S A 98:4955–4960, 2001a) and increased affinity (Marvin and Hellinga, Nat Struct Biol 8:795–798, 2001b; Telmer and Shilton, J Biol Chem 278:34555–34567, 2003). It is also used in recombinant protein expression as both an affinity tag and a solubility tag. We isolated mutations in MBP that enhance binding to maltodextrins 1.3 to 15-fold, using random mutagenesis followed by screening for enhanced yield in a microplate-based affinity purification. We tested the mutations for their ability to enhance the yield of a fusion protein that binds poorly to immobilized amylose and their ability to enhance the solubility of one or more aggregation-prone recombinant proteins. We also measured dissociation constants of the mutant MBPs that retain the solubility-enhancing properties of MBP and combined two of the mutations to produce an MBP with a dissociation constant 10-fold tighter than wild-type MBP. Some of the mutations we obtained can be rationalized based on the previous work, while others indicate new ways in which the function of MBP can be modified.

Keywords: Maltose-binding protein; Periplasmic binding proteins; Altered affinity; Mutational analysis; Recombinant fusion proteins; Solubility enhancement

Metabolic engineering to improve ethanol production in Thermoanaerobacter mathranii by Shuo Yao; Marie Just Mikkelsen (pp. 199-208).

Thermoanaerobacter mathranii can produce ethanol from lignocellulosic biomass at high temperatures, but its biotechnological exploitation will require metabolic engineering to increase its ethanol yield. With a cofactor-dependent ethanol production pathway in T. mathranii, it may become crucial to regenerate cofactor to increase the ethanol yield. Feeding the cells with a more reduced carbon source, such as mannitol, was shown to increase ethanol yield beyond that obtained with glucose and xylose. The ldh gene coding for lactate dehydrogenase was previously deleted from T. mathranii to eliminate an NADH oxidation pathway. To further facilitate NADH regeneration used for ethanol formation, a heterologous gene gldA encoding an NAD⁺-dependent glycerol dehydrogenase was expressed in T. mathranii. One of the resulting recombinant strains, T. mathranii BG1G1 (Δldh, P xylGldA), showed increased ethanol yield in the presence of glycerol using xylose as a substrate. With an inactivated lactate pathway and expressed glycerol dehydrogenase activity, the metabolism of the cells was shifted toward the production of ethanol over acetate, hence restoring the redox balance. It was also shown that strain BG1G1 acquired the capability to utilize glycerol as an extra carbon source in the presence of xylose, and utilization of the more reduced substrate glycerol resulted in a higher ethanol yield.

Keywords: Metabolic engineering; Ethanol production; Thermoanaerobacter; Glycerol dehydrogenase; Lactate dehydrogenase

Broad-host-range plasmid-mediated metabolic perturbations in Pseudomonas fluorescens 13525 by Aditi D. Buch; G. Archana; G. Naresh Kumar (pp. 209-218).

Genetic engineering of fluorescent pseudomonads for various industrially, agriculturally and environmentally important bioprocesses often involves the use of suitable plasmids. Plasmid-mediated alterations in host physiology and metabolism are poorly understood for this group of organisms. Thus, we investigated the metabolic perturbations in Pseudomonas fluorescens 13525 due to the independent and combined presence of broad-host-range plasmids, pBBR1MCS-2 (copy number 30) and pUCPM18 derived pAB4 and pAB8 (copy number 14-16). Presence of pAB4 and pAB8 not only significantly increased the growth rate and glucose utilization of P. fluorescens 13525, but also increased glucose dehydrogenase activity and gluconic acid production indicating enhanced direct oxidative pathway for glucose catabolism. Additionally, increased secretion of pyruvic, acetic, and citric acids caused faster media acidification in presence of pAB4 and pAB8. Simultaneous presence of pAB4/pAB8 in Pf (pAB48) and pAB4/pBBR1MCS-2 in Pf (pAB4BBR1MCS-2) reduced their respective copy numbers to nearly half. Pf (pAB48) demonstrated further increase in direct oxidation pathway without altering growth and glucose depletion rates, as compared with single transformants. Conversely, pBBR1MCS-2 plasmid did not greatly alter P. fluorescens 13525 metabolism when present independently but masked the effects imposed by pAB4 when present in its combination. In conclusion, P. fluorescens 13525 redesigns its metabolism in response to the presence of plasmids irrespective of their nature, by enhancing anaplerosis with a simultaneous reduction in catabolism as indicated by increased pyruvate carboxylase and decreased citrate synthase activities, respectively. Such information will be helpful for vector designing during genetic engineering of fluorescent pseudomonads.

Keywords: Broad-host-range plasmids; Metabolic load; Pseudomonas fluorescens ; Glucose metabolism; Genetic engineering

Allicin-induced global gene expression profile of Saccharomyces cerevisiae by Lu Yu; Na Guo; Rizeng Meng; Bin Liu; Xudong Tang; Jing Jin; Yumei Cui; Xuming Deng (pp. 219-229).

To understand the response mechanisms of fungus cells upon exposure to the natural fungicide allicin, we performed commercial oligonucleotide microarrays to determine the overall transcriptional response of allicin-treated Saccharomyces cerevisiae strain L1190. Compared with the transcriptional profiles of untreated cultures, 147 genes were significantly upregulated, and 145 genes were significantly downregulated in the allicin-treated cells. We interpreted the microarray data with the hierarchical clustering tool, T-profiler. Major transcriptional responses were induced by allicin and included the following: first, Rpn4p-mediated responses involved in proteasome gene expression; second, the Rsc1p-mediated response involved in iron ion transporter activity; third, the Gcn4p-mediated response, also known as general amino acid control; finally, the Yap1p-, Msn2/4p-, Crz1p-, and Cin5p-mediated multiple stress response. Interestingly, allicin treatment, similar to mycotoxin patulin and artificial fungicide thiuram treatment, was found to induce genes involved in sulfur amino acid metabolism and the defense system for oxidative stress, especially DNA repair, which suggests a potential mutagenicity for allicin. Quantitative real-time reverse transcription-polymerase chain reaction was performed for selected genes to verify the microarray results. To our knowledge, this is the first report of the global transcriptional profiling of allicin-treated S. cerevisiae by microarray.

Keywords: Saccharomyces cerevisiae ; Microarrays; Allicin; Gene expression

Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae by Dragana Stanley; Paul J. Chambers; Grant A. Stanley; Anthony Borneman; Sarah Fraser (pp. 231-239).

Saccharomyces spp. are widely used for ethanol production; however, fermentation productivity is negatively affected by the impact of ethanol accumulation on yeast metabolic rate and viability. This study used microarray and statistical two-way ANOVA analysis to compare and evaluate gene expression profiles of two previously generated ethanol-tolerant mutants, CM1 and SM1, with their parent, Saccharomyces cerevisiae W303-1A, in the presence and absence of ethanol stress. Although sharing the same parentage, the mutants were created differently: SM1 by adaptive evolution involving long-term exposure to ethanol stress and CM1 using chemical mutagenesis followed by adaptive evolution-based screening. Compared to the parent, differences in the expression levels of genes associated with a number of gene ontology categories in the mutants suggest that their improved ethanol stress response is a consequence of increased mitochondrial and NADH oxidation activities, stimulating glycolysis and other energy-yielding pathways. This leads to increased activity of energy-demanding processes associated with the production of proteins and plasma membrane components, which are necessary for acclimation to ethanol stress. It is suggested that a key function of the ethanol stress response is restoration of the NAD⁺/NADH redox balance, which increases glyceraldehyde-3-phosphate dehydrogenase activity, and higher glycolytic flux in the ethanol-stressed cell. Both mutants achieved this by a constitutive increase in carbon flux in the glycerol pathway as a means of increasing NADH oxidation.

Keywords: Saccharomyces ; Ethanol; Stress; Gene expression; Mutants

Production and derivate composition of trisporoids in extended fermentation of Blakeslea trispora by Doreen Schachtschabel; Klaus-Dieter Menzel; Gudrun Krauter; Anja David; Martin Roth; Uwe Horn; Wilhelm Boland; Johannes Wöstemeyer; Christine Schimek (pp. 241-249).

Trisporic acid, its precursors and derivatives are used within zygomycete fungi as communication signals and sexual regulators, and also influence the production rate of the parent compound, β-carotene. Cultivation parameters during growth and the trisporoid production phase of Blakeslea trispora were studied in two-step shake flask cultures and up-scaled fermentations. Comparison of various fermentation protocols allowed the definition of parameters governing trisporoid production. Highest yields were obtained when the initial growth phase allowed for both rapid growth and fast exhaustion of nitrogen and phosporous sources. Onset of trisporoid production is accompanied by a pH drop in the medium and triggered by nutrient limitation, nitrogen depletion being the most important factor. Supplementation of cultures with carbon at low concentration after onset of trisporoid production led to prolonged growth and higher final product accumulation. B. trispora produces trisporoids in two major series, B and C. During a first peak in trisporic acid accumulation, production of trisporic acid B exceeds that of trisporic acid C, which later accumulates at the expense of the trisporic acid B, indicating a variable regulation of the ratio between these metabolites. These data are valuable for tailoring production systems for enrichment of specific intermediates of this complex signal family.

Keywords: Fermentation; Trisporic acid; Zygomycota; Fungus; Development; Mating; Nutrient starvation; Blakeslea trispora

Interaction between tobramycin and CSA-13 on clinical isolates of Pseudomonas aeruginosa in a model of young and mature biofilms by Carole Nagant; Marie Tré-Hardy; Malika El-Ouaaliti; Paul Savage; Michel Devleeschouwer; Jean-Paul Dehaye (pp. 251-263).

The bactericidal activity of a cholic acid antimicrobial derivative, CSA-13, was tested against eight strains of Pseudomonas aeruginosa (both reference and clinical strains) and compared with the response to tobramycin. In planktonic cultures, the minimal inhibitory and minimal bactericidal concentrations of CSA-13 and tobramycin were in the 1–25 mg/L range except for one mucoid clinical strain which was much less sensitive to tobramycin (minimal bactericidal concentration, 65–125 mg/L). In young (24 h) biofilms, the sensitivity to CSA-13 was reduced (half-maximal concentration CSA-13 averaged 88 mg/L) and varied among the eight strains. The sensitivity to tobramycin was also very variable among the strains and some were fully resistant to the aminoglycoside. The combination of tobramycin with CSA-13 was synergistic in five strains. Only one strain showed antagonism between the two drugs at low concentrations of CSA-13. One reference and five clinical strains were tested in mature (12 days) biofilms. The effect of CSA-13 was delayed, some strains requiring 9 days exposure to the drug to observe a bactericidal effect. All the strains were tolerant to tobramycin but the addition of CSA-13 with tobramycin was synergistic in three strains. CSA-13 permeabilized the outer membrane of the bacteria (half-maximal concentration, 4.4 mg/L). At concentrations higher than 20 mg/L, it also permeabilized the plasma membrane of human umbilical vein endothelial cells. In conclusion, CSA-13 has bactericidal activity against P. aeruginosa even in mature biofilms and cationic steroid antibiotics can thus be considered as potential candidates for the treatment of chronic pulmonary infections of patients with cystic fibrosis. Considering its interaction with the plasma membrane of eukaryotic cells, less toxic derivatives of CSA-13 should be developed.

Keywords: Cystic fibrosis; Antimicrobial peptides; Aminoglycoside

Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli by Curt R. Fischer; Hsien-Chung Tseng; Mitchell Tai; Kristala L. J. Prather; Gregory Stephanopoulos (pp. 265-275).

In clostridia, n-butanol production from carbohydrates at yields of up to 76% of the theoretical maximum and at titers of up to 13 g/L has been reported. However, in Escherichia coli, several groups have reported butyric acid or butanol production from recombinant expression of clostridial genes, at much lower titers and yields. To pinpoint deficient steps in the recombinant pathway, we developed an analytical procedure for the determination of intracellular pools of key pathway intermediates and applied the technique to the analysis of three sets of E. coli strains expressing various combinations of butyrate biosynthesis genes. Low expression levels of the hbd-encoded S-3-hydroxybutyryl-CoA dehydrogenase were insufficient to convert acetyl-CoA to 3-hydroxybutyryl-CoA, indicating that hbd was a rate-limiting step in the production of butyryl-CoA. Increasing hbd expression alleviated this bottleneck, but in resulting strains, our pool size measurements and thermodynamic analysis showed that the reaction step catalyzed by the bcd-encoded butyryl-CoA dehydrogenase was rate-limiting. E. coli strains expressing both hbd and ptb-buk produced crotonic acid as a byproduct, but this byproduct was not observed with expression of related genes from non-clostridial organisms. Our thermodynamic interpretation of pool size measurements is applicable to the analysis of other metabolic pathways.

Keywords: Butanol; Clostridium acetobutylicum ; Clostridia; Synthetic biology; Metabolic engineering; Butyric acid

Vacuolar morphology of Saccharomyces cerevisiae during the process of wine making and Japanese sake brewing by Shingo Izawa; Kayo Ikeda; Takeo Miki; Yoshinori Wakai; Yoshiharu Inoue (pp. 277-282).

Although ethanol and osmotic stress affect the vacuolar morphology of Saccharomyces cerevisiae, little information is available about changes in vacuolar morphology during the processes of wine making and Japanese sake (rice wine) brewing. Here, we elucidated changes in the morphology of yeast vacuoles using Zrc1p-GFP, a vacuolar membrane protein, so as to better understand yeast physiology during the brewing process. Wine yeast cells (OC-2 and EC1118) contained highly fragmented vacuoles in the sake mash (moromi) as well as in the grape must. Although sake yeast cells (Kyokai no. 9 and no. 10) also contained highly fragmented vacuoles during the wine-making process, they showed quite a distinct vacuolar morphology during sake brewing. Since the environment surrounding sake yeast cells in the sake mash did not differ much from that surrounding wine yeast cells, the difference in vacuolar morphology during sake brewing between wine yeast and sake yeast was likely caused by innate characters.

Keywords: Wine making; Sake brewing; Vacuolar morphology; Ethanol stress; Saccharomyces cerevisiae

Functional characterization of starvation-induced lysosomal activity in Saccharomyces cerevisiae by Jihee Yoon; Suk-Tai Chang; Jin-Soo Park; Yang-Hoon Kim; Jiho Min (pp. 283-289).

Starvation induces significant alterations in lysosomal enzymes, and reduced concentrations of glucose increases the activity of several lysosomal enzymes. Therefore, to evaluate the lysosomal antimicrobial activity under starvation conditions, we added 0, 5, 10, 20, or 40 g/l of glucose (0%, 0.5%, 1%, 2%, or 4% glucose) supplemented YP medium to cultured Saccharomyces cerevisiae, and lysosomal fractions were isolated from S. cerevisiae grown under the various culture conditions. The lysosomes isolated from each condition exhibited increased antimicrobial activity against Escherichia coli as determined by a decrease in glucose concentration. In addition, a starvation-dependent increase in lysosomal activity coincided with increased lysosome intensity at the cytosol and distinct protein expression from lysosomes in S. cerevisiae. It also was determined found that the lysosomes have antimicrobial activity against seven different microorganisms, including E. coli, and starvation-induced lysosomes showed enhanced antimicrobial activity compared to those from normal lysosomes. These results suggest the possibility that lysosomal alterations during starvation may induce conditions that activate lysosomes for future development of efficient antimicrobial agents.

Keywords: Starvation; Glucose; Lysosomes; Organelle; Antimicrobial activity; S. cerevisiae

A simple and effective plating method to screen polycyclic aromatic hydrocarbon-degrading bacteria under various redox conditions by Youngsoon Um; Matthew Wook Chang; Tracey Pulliam Holoman (pp. 291-297).

Agar plates with a polycyclic aromatic hydrocarbon (PAH) layer have been used to screen for microorganisms that degrade PAHs, leaving clear zones around colonies; however, there are several problems with previous methods such as undesired contamination in the fume hood and difficulty in controlling the amount of PAH on the plates. In this study, we developed a modified screening method to address the drawbacks encountered with previous screening methods. A uniform white layer of PAHs was generated by spreading PAHs dissolved in volatile solvents over a surface of solidified agar medium, followed by the evaporation of the solvents. An inoculation was then performed by spreading a molten agar medium containing microbial samples over the solidified agar medium with a PAH layer. Subsequently, the white PAH layer migrated to the surface of the molten agar medium. This essential modification enabled us not only to solve problems of the previous screening methods but also to prepare an agar plate with a PAH layer without a complicated experimental scheme in the anaerobic chamber. After solidification of the molten agar medium and incubation of the plates, clear zones were successfully detected around colonies with aerobic and anaerobic PAH-degrading microbial cultures.

Keywords: Polycyclic aromatic hydrocarbon; Biodegradation; Screening method; Anaerobic condition

Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods by Louise Vanysacker; Steven A. J. Declerck; Bart Hellemans; Luc De Meester; Ivo Vankelecom; Priscilla Declerck (pp. 299-307).

The effectiveness of three commercially available direct DNA isolation kits (Mobio, Fast, Qiagen) and one published direct DNA extraction protocol (Bead) for extracting bacterial DNA from different types of activated sludge was investigated and mutually compared. The DNA quantity and purity were determined using real-time PCR targeting the bacterial 16S rDNA gene. Microbial community fingerprints were assessed by automated ribosomal intergenic spacer analysis. The resulting community profiles were analyzed with canonical correspondence analysis. Our results clearly demonstrate that direct DNA extraction methods can significantly influence the DNA quantity, purity, and observed community patterns of microbiota in activated sludge. Fast and Mobio generated high amounts of good quality DNA compared to Bead and Qiagen. Mobio also resulted in the detection of the highest number of species while Fast scored the best in discriminating between the community patterns of different activated sludge types. With respect to the characterization of community profiles, our analyses demonstrated a strong sludge type dependent variability among methods. Taking into account our results, we recommend Fast as the most suitable DNA extraction method for activated sludge samples used for bacterial community studies.

Keywords: Activated sludge; ARISA; Community fingerprinting; Direct DNA extraction; Real-time PCR

Assessment of MTBE biodegradation pathways by two-dimensional isotope analysis in mixed bacterial consortia under different redox conditions by Laura K. G. Youngster; Mònica Rosell; Hans H. Richnow; Max M. Häggblom (pp. 309-317).

The fuel oxygenate, methyl tert-butyl ether (MTBE), although now widely banned or substituted, remains a persistent groundwater contaminant. Multidimensional compound-specific isotope analysis (CSIA) of carbon and hydrogen is being developed for determining the extent of MTBE loss due to biodegradation and can also potentially distinguish between different biodegradation pathways. Carbon and hydrogen isotopic fractionation factors were determined for MTBE degradation in aerobic and anaerobic laboratory cultures. The carbon isotopic enrichment factor (εC) for aerobic MTBE degradation by a bacterial consortium containing the aerobic MTBE-degrading bacterium, Variovorax paradoxus, was −1.1 ± 0.2‰ and the hydrogen isotope enrichment factor (εH) was −15 ± 2‰. This corresponds to an approximated lambda value (Λ = εH/εC) of 14. Carbon isotope enrichment factors for anaerobic MTBE-degrading enrichment cultures were −7.0 ± 0.2‰ and did not vary based on the original inoculum source, redox condition of the enrichment, or supplementation with syringic acid as a co-substrate. The hydrogen enrichment factors of cultures without syringic acid were insignificant, however a strong hydrogen enrichment factor of −41 ± 3‰ was observed for cultures which were fed syringic acid during MTBE degradation. The Λ = 6 obtained for NYsyr cultures might be diagnostic for the stimulation of anaerobic MTBE degradation by methoxylated compounds by an as yet unknown pathway and mechanism. The stable-isotope enrichment factors determined in this study will enhance the use of CSIA for monitoring anaerobic and aerobic MTBE biodegradation in situ.

Keywords: MTBE; Fuel oxygenate; CSIA (compound-specific stable isotope analysis); Aerobic and anaerobic biodegradation; Variovorax paradoxus strain CL-8

Reactive iron barriers: a niche enabling microbial dehalorespiration of 1,2-dichloroethane by Olivier Zemb; Matthew Lee; Adrian Low; Mike Manefield (pp. 319-325).

A reactive iron barrier in a contaminated aquifer with low pH was found to dechlorinate 1,2-dichloroethane (1,2-DCA) in situ. This chlorinated ethane is known to resist abiotic reduction by zero valent iron. Samples taken up-gradient and within the barrier were used to inoculate anaerobic batch cultures amended with various electron donors. Cultures inoculated with groundwater from within the reactive iron barrier reduced 1,2-DCA to ethene. The same effect could be achieved by simultaneously supplying hydrogen while neutralising pH. The presence of iron or hydrogen at neutral pH had negligible effects on 1,2-DCA reduction in cultures inoculated with groundwater sampled up-gradient of the barrier. Molecular microbial community characterisation revealed that Dehalobacter species were more abundant in groundwater sampled from within the barrier. These findings suggest reactive iron barriers represent a remediation technology for 1,2-DCA degradation acting through in situ recruitment of 1,2-DCA reducing bacteria such as Dehalobacter.

Keywords: SSCP; Reactive iron barrier; Dehalorespiration; 1,2-dichloroethane; Microbial ecology; Electron transfer; Biotechnology; Dechlorination

Assessing bioavailability of the solubilization of organic compound in nonionic surfactant micelles by dose–response analysis by Zewen Dai; Zhilong Wang; Jian-He Xu; Hanshi Qi (pp. 327-339).

It is uncertain in some extent that organic compounds solubilized in micelles of a nonionic surfactant aqueous solution are bioavailable directly by the microbes in an extractive microbial transformation or biodegradation process. In this work, a dose–response method, where a bioequivalence concept is introduced to evaluate the synergic toxicity of the nonionic surfactants and the organic compounds, was applied to analyze the inhibition effect of organic compounds (naphthalene, phenyl ether, 2-phenylethanol, and 1-butanol) in nonionic surfactant Triton X-100 micelle aqueous solutions and Triton X-114 in aqueous solutions forming cloud point systems. Based on the result, a mole solubilization ratio of organic compounds in micelle was also determined, which consisted very well with those of classic semi-equilibrium dialysis experiments. The results exhibit that bioavailability of organic compounds solubilized in micelles to microbial cells is negligible, which provides a guideline for application of nonionic surfactant micelle aqueous solutions or cloud point systems as novel media for microbial transformations or biodegradations.

Keywords: Bioavailability; Dose–response analysis; Micelle; Nonionic surfactant; Cloud point system

Marine bacterial isolates inhibit biofilm formation and disrupt mature biofilms of Pseudomonas aeruginosa PAO1 by Chari Nithya; Mansur Farzana Begum; Shunmugiah Karutha Pandian (pp. 341-358).

According to the Centers for Disease Control and Prevention, biofilms cause 65% of infections in developed countries. Pseudomonas aeruginosa biofilm cause life threatening infections in cystic fibrosis infection and they are 1,000 times more tolerant to antibiotic than the planktonic cells. As quorum sensing, hydrophobicity index and extracellular polysaccharide play a crucial role in biofilm formation, extracts from 46 marine bacterial isolates were screened against these factors in P. aeruginosa. Eleven extracts showed antibiofilm activity. Extracts of S6-01 (Bacillus indicus = MTCC 5559) and S6-15 (Bacillus pumilus = MTCC 5560) inhibited the formation of PAO1 biofilm up to 95% in their Biofilm Inhibitory Concentration(BIC) of 50 and 60 μg/ml and 85% and 64% in the subinhibitory concentrations (1/4 and 1/8 of the BIC, respectively). Furthermore, the mature biofilm was disrupted to 70–74% in their BIC. The antibiofilm compound from S6-15 was partially purified using solvent extraction followed by TLC and silica column and further characterized by IR analysis. Current study for the first time reveals the antibiofilm and antiquorum-sensing activity of B. pumilus, B. indicus, Bacillus arsenicus, Halobacillus trueperi, Ferrimonas balearica, and Marinobacter hydrocarbonoclasticus from marine habitat.

Keywords: PAO1 biofilm; Antibiofilm; Marine bacteria; B. pumilus ; Hydrophobicity index; Quorum sensing

Free nitrous acid (FNA) inhibition on denitrifying poly-phosphate accumulating organisms (DPAOs) by Yan Zhou; Lily Ganda; Melvin Lim; Zhiguo Yuan; Staffan Kjelleberg; Wun Jern Ng (pp. 359-369).

Free nitrous acid (FNA) has been identified to be a ubiquitous inhibitor of a wide range of microorganisms, including bacteria involved in wastewater treatment. The FNA-induced inhibition on the anoxic (nitrite as electron acceptor) metabolism of denitrifying poly-phosphate accumulating organisms (DPAOs) was investigated using sludge from a sequencing batch reactor performing carbon, nitrogen, and phosphorus removal from synthetic wastewater. We found that FNA had a much stronger inhibitory effect on phosphorus (P) uptake and glycogen production than on poly-β-hydroxyalkanoate degradation and nitrite reduction. The intracellular adenosine triphosphate levels decreased sharply during the FNA incubation, and the decreasing rates were positively correlated with increasing FNA concentrations. The electron transport activity of DPAOs when exposed to FNA displayed a similar trend. Further, at FNA concentrations above 0.044 mg HNO₂-N/L, the anaerobic metabolism of DPAOs was initiated despite of the presence of nitrite, as evidenced by the release of phosphorus and the consumption of glycogen. DPAO metabolism did not recover completely from FNA inhibition in the subsequent FNA-free environment. The recovery rate depended on the concentration of FNA applied in the previous anoxic period. These results suggest that the inhibitory effects are diverse and may be attributable to different mechanisms operating simultaneously.

Keywords: Free nitrous acid (FNA); Denitrifying poly-phosphate accumulating organisms (DPAOs); Inhibition; Intracellular adenosine triphosphate (ATP); Phosphate uptake; Glycogen consumption

Anodic biofilms in microbial fuel cells harbor low numbers of higher-power-producing bacteria than abundant genera by Patrick D. Kiely; Douglas F. Call; Matthew D. Yates; John M. Regan; Bruce E. Logan (pp. 371-380).

Microbial fuel cell (MFC) anode communities often reveal just a few genera, but it is not known to what extent less abundant bacteria could be important for improving performance. We examined the microbial community in an MFC fed with formic acid for more than 1 year and determined using 16S rRNA gene cloning and fluorescent in situ hybridization that members of the Paracoccus genus comprised most (~30%) of the anode community. A Paracoccus isolate obtained from this biofilm (Paracoccus denitrificans strain PS-1) produced only 5.6 mW/m², whereas the original mixed culture produced up to 10 mW/m². Despite the absence of any Shewanella species in the clone library, we isolated a strain of Shewanella putrefaciens (strain PS-2) from the same biofilm capable of producing a higher-power density (17.4 mW/m²) than the mixed culture, although voltage generation was variable. Our results suggest that the numerical abundance of microorganisms in biofilms cannot be assumed a priori to correlate to capacities of these predominant species for high-power production. Detailed screening of bacterial biofilms may therefore be needed to identify important strains capable of high-power generation for specific substrates.

Keywords: Microbial fuel cell; Paracoccus denitrificans ; Formic acid; Community analysis

Direct ethanol production from cellulosic materials at high temperature using the thermotolerant yeast Kluyveromyces marxianus displaying cellulolytic enzymes by Shuhei Yanase; Tomohisa Hasunuma; Ryosuke Yamada; Tsutomu Tanaka; Chiaki Ogino; Hideki Fukuda; Akihiko Kondo (pp. 381-388).

To exploit cellulosic materials for fuel ethanol production, a microorganism capable of high temperature and simultaneous saccharification–fermentation has been required. However, a major drawback is the optimum temperature for the saccharification and fermentation. Most ethanol-fermenting microbes have an optimum temperature for ethanol fermentation ranging between 28 °C and 37 °C, while the activity of cellulolytic enzymes is highest at around 50 °C and significantly decreases with a decrease in temperature. Therefore, in the present study, a thermotolerant yeast, Kluyveromyces marxianus, which has high growth and fermentation at elevated temperatures, was used as a producer of ethanol from cellulose. The strain was genetically engineered to display Trichoderma reesei endoglucanase and Aspergillus aculeatus β-glucosidase on the cell surface, which successfully converts a cellulosic β-glucan to ethanol directly at 48 °C with a yield of 4.24 g/l from 10 g/l within 12 h. The yield (in grams of ethanol produced per gram of β-glucan consumed) was 0.47 g/g, which corresponds to 92.2% of the theoretical yield. This indicates that high-temperature cellulose fermentation to ethanol can be efficiently accomplished using a recombinant K. marxianus strain displaying thermostable cellulolytic enzymes on the cell surface.

Keywords: Bioethanol; Thermotolerant yeast; Cellulose; Cellulase; Cell surface display; Kluyveromyces marxianus

Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production by Emily B. Hollister; Andrea K. Forrest; Heather H. Wilkinson; Daniel J. Ebbole; Stephanie A. Malfatti; Susannah G. Tringe; Mark T. Holtzapple; Terry J. Gentry (pp. 389-399).

The carboxylate platform utilizes a mixed microbial community to convert lignocellulosic biomass into chemicals and fuels. While much of the platform is well understood, little is known about its microbiology. Mesophilic (40 °C) and thermophilic (55 °C) fermentations employing a sorghum feedstock and marine sediment inoculum were profiled using 16S rRNA tag-pyrosequencing over the course of a 30-day incubation. The contrasting fermentation temperatures converted similar amounts of biomass, but the mesophilic community was significantly more productive, and the two temperatures differed significantly with respect to propionic and butyric acid production. Pyrotag sequencing revealed the presence of dynamic communities that responded rapidly to temperature and changed substantially over time. Both temperatures were dominated by bacteria resembling Clostridia, but they shared few taxa in common. The species-rich mesophilic community harbored a variety of Bacteroidetes, Actinobacteria, and γ-Proteobacteria, whereas the thermophilic community was composed mainly of Clostridia and Bacilli. Despite differences in composition and productivity, similar patterns of functional class dynamics were observed. Over time, organisms resembling known cellulose degraders decreased in abundance, while organisms resembling known xylose degraders increased. Improved understanding of the carboxylate platform’s microbiology will help refine platform performance and contribute to our growing knowledge regarding biomass conversion and biofuel production processes.

Keywords: Mixed alcohol bioreactor; Lignocellulosic biofuels; Tag-pyrosequencing; Microbial communities; Carboxylate platform

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Applied Microbiology and Biotechnology (v.88, #1)