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Applied Microbiology and Biotechnology (v.93, #1)

Engineering of routes to heparin and related polysaccharides by Ujjwal Bhaskar; Eric Sterner; Anne Marie Hickey; Akihiro Onishi; Fuming Zhang; Jonathan S. Dordick; Robert J. Linhardt (pp. 1-16).

Anticoagulant heparin has been shown to possess important biological functions that vary according to its fine structure. Variability within heparin’s structure occurs owing to its biosynthesis and animal tissue-based recovery and adds another dimension to its complex polymeric structure. The structural variations in chain length and sulfation patterns mediate its interaction with many heparin-binding proteins, thereby eliciting complex biological responses. The advent of novel chemical and enzymatic approaches for polysaccharide synthesis coupled with high throughput combinatorial approaches for drug discovery have facilitated an increased effort to understand heparin’s structure–activity relationships. An improved understanding would offer potential for new therapeutic development through the engineering of polysaccharides. Such a bioengineering approach requires the amalgamation of several different disciplines, including carbohydrate synthesis, applied enzymology, metabolic engineering, and process biochemistry.

Keywords: Bioengineered heparin; Applied enzymology; Biosynthesis; Chemical synthesis; Chemoenzymatic synthesis; Metabolic engineering

Efficient use of shrimp waste: present and future trends by Prameela Kandra; Murali Mohan Challa; Hemalatha Kalangi Padma Jyothi (pp. 17-29).

The production of shrimp waste from shrimp processing industries has undergone a dramatic increase in recent years. Continued production of this biomaterial without corresponding development of utilizing technology has resulted in waste collection, disposal, and pollution problems. Currently used chemical process releases toxic chemicals such as HCl, acetic acid, and NaOH into aquatic ecosystem as byproducts which will spoil the aquatic flora and fauna. Environmental protection regulations have become stricter. Now, there is a need to treat and utilize the waste in most efficient manner. The shrimp waste contains several bioactive compounds such as chitin, pigments, amino acids, and fatty acids. These bioactive compounds have a wide range of applications including medical, therapies, cosmetics, paper, pulp and textile industries, biotechnology, and food applications. This current review article present the utilization of shrimp waste as well as an alternative technology to replace hazardous chemical method that address the future trends in total utilization of shrimp waste for recovery of bioactive compounds.

Keywords: Shrimp waste; Toxic chemicals; Chitin; Pigments; Therapies

Protein secretion in Pichia pastoris and advances in protein production by Leonardo M. Damasceno; Chung-Jr Huang; Carl A. Batt (pp. 31-39).

Yeast expression systems have been successfully used for over 20 years for the production of recombinant proteins. With the growing interest in recombinant protein expression for various uses, yeast expression systems, such as the popular Pichia pastoris, are becoming increasingly important. Although P. pastoris has been successfully used in the production of many secreted and intracellular recombinant proteins, there is still room for improvement of this expression system. In particular, secretion of recombinant proteins is still one of the main reasons for using P. pastoris. Therefore, endoplasmic reticulum protein folding, correct glycosylation, vesicular transport to the plasma membrane, gene dosage, secretion signal sequences, and secretome studies are important considerations for improved recombinant protein production.

Keywords: Pichia pastoris ; Recombinant protein secretion; Unfolded protein response; Protein folding

Shuttling happens: soluble flavin mediators of extracellular electron transfer in Shewanella by Evan D. Brutinel; Jeffrey A. Gralnick (pp. 41-48).

The genus Shewanella contains Gram negative γ-proteobacteria capable of reducing a wide range of substrates, including insoluble metals and carbon electrodes. The utilization of insoluble respiratory substrates by bacteria requires a strategy that is quite different from a traditional respiratory strategy because the cell cannot take up the substrate. Electrons generated by cellular metabolism instead must be transported outside the cell, and perhaps beyond, in order to reduce an insoluble substrate. The primary focus of research in model organisms such as Shewanella has been the mechanisms underlying respiration of insoluble substrates. Electrons travel from the menaquinone pool in the cytoplasmic membrane to the surface of the bacterial cell through a series of proteins collectively described as the Mtr pathway. This review will focus on respiratory electron transfer from the surface of the bacterial cell to extracellular substrates. Shewanella sp. secrete redox-active flavin compounds able to transfer electrons between the cell surface and substrate in a cyclic fashion—a process termed electron shuttling. The production and secretion of flavins as well as the mechanisms of cell-mediated reduction will be discussed with emphasis on the experimental evidence for a shuttle-based mechanism. The ability to reduce extracellular substrates has sparked interest in using Shewanella sp. for applications in bioremediation, bioenergy, and synthetic biology.

Keywords: Shewanella ; Flavin; Respiration; Electron shuttle

Updates on naringinase: structural and biotechnological aspects by Munish Puri (pp. 49-60).

Naringinases has attracted a great deal of attention in recent years due to its hydrolytic activities which include the production of rhamnose, and prunin and debittering of citrus fruit juices. While this enzyme is widely distributed in fungi, its production from bacterial sources is less commonly known. Fungal naringinase are very important as they are used industrially in large amounts and have been extensively studied during the past decade. In this article, production of bacterial naringinase and potential biotechnological applications are discussed. Bacterial rhamnosidases are exotype enzymes that hydrolyse terminal non-reducing α-l-rhamnosyl groups from α-l-rhamnose containing polysaccharides and glycosides. Structurally, they are classified into family 78 of glycoside hydrolases and characterized by the presence of Asp567 and Glu841 in their active site. Optimization of fermentation conditions and enzyme engineering will allow the development of improved rhamnosidases for advancing suggested industrial applications.

Keywords: Family 78 glycosides hydrolases; Rhamnosidase; Rhamnose; Pruning; Debittering; Pro-drug

Enzyme immobilization for biodiesel production by Baohua Zhang; Yanqing Weng; Hong Xu; Zhiping Mao (pp. 61-70).

Biodiesel has attracted more and more attention in recent years because of its biodegradability, environmentally friendliness, and renewability. Contrary to the conventional chemical catalysis method to produce biodiesel, the biochemical catalysis method developed quickly in the past decade and many immobilized enzymes are commercially available to meet the large-scale industrialization of biodiesel. This review is focusing on the current status of biodiesel production by biochemical catalysis method, especially the commercial enzyme and its immobilization for biodiesel production. Consequently, we believe that biochemical catalysis with immobilized enzymes is bound to be an alternative method instead of chemical catalysis in biodiesel production in the near future.

Keywords: Biochemical catalysis; Biodiesel production; Enzyme; Immobilization; Review

Algal fucoidan: structural and size-dependent bioactivities and their perspectives by V. K. Morya; Jungeun Kim; Eun-Ki Kim (pp. 71-82).

Fucoidan is a complex-sulfated polysaccharide distributed in various marine organisms, and the brown algae are reported as the major producer. The fucoidan is important for their high bioactive properties, like antibacterial, anticoagulant, antiviral, anti-tumor, etc., and many more to be explored. There is a strong archival support for the bioactivity and promising properties of this molecule, which creates a hope for this molecule as future drug against thrombosis and some kind of cancers. Reports other than the above bioactive properties have also been a matter of interest for the design of signal or enzyme-arrested new class of drugs. In the past three decades, the research on isolation, molecular characterization, and screening of biological applications has significantly increased. One major issue associated with this molecule is the higher size and seasonal variation in their chemical composition; to resolve the issue and maintain its bioactivity, a prioritized and literal hydrolysis process is required to be developed. Here, in this mini-review, we have tried to summarize the algal fucoidan research and the bioactivities influenced by their molecular size.

Keywords: Fucoidan; Brown algae; Antioxidant; Anticoagulant; Antiviral; Anti-tumoral

l-Proline dehydrogenases in hyperthermophilic archaea: distribution, function, structure, and application by Ryushi Kawakami; Takenori Satomura; Haruhiko Sakuraba; Toshihisa Ohshima (pp. 83-93).

Dye-linked l-proline dehydrogenase (ProDH) catalyzes the oxidation of l-proline to ∆¹-pyrroline-5-carboxylate (P5C) in the presence of artificial electron acceptors. The enzyme is known to be widely distributed in bacteria and eukarya, together with nicotinamide adenine dinucleotide (phosphate)-dependent P5C dehydrogenase, and to function in the metabolism of l-proline to l-glutamate. In addition, over the course of the last decade, three other types of ProDH with molecular compositions completely different from previously known ones have been identified in hyperthermophilic archaea. The first is a heterotetrameric αβγδ-type ProDH, which exhibits both ProDH and reduced nicotinamide adenine dinucleotide dehydrogenase activity and includes two electron transfer proteins. The second is a heterooctameric α₄β₄-type ProDH, which uses flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate, and Fe as cofactors and creates a new electron transfer pathway. The third is a recently identified homodimeric ProDH, which exhibits the greatest thermostability among these archaeal ProDHs. This minireview focuses on the functional and structural properties of these three types of archaeal ProDH and their distribution in archaea. In addition, we will describe the specific application of hyperthermostable ProDH for use in a biosensor and for DNA sensing.

Keywords: Dye-linked l-proline dehydrogenase; Hyperthermophilic archaea; Enzyme complex structure; Flavoenzyme; Catalytic electrode; DNA sensing

Corynebacterium glutamicum as a potent biocatalyst for the bioconversion of pentose sugars to value-added products by Vipin Gopinath; Anusree Murali; Kiran S. Dhar; K. Madhavan Nampoothiri (pp. 95-106).

Corynebacterium glutamicum, the industrial microbe traditionally used for the production of amino acids, proved its value for the fermentative production of diverse products through genetic/metabolic engineering. A successful demonstration of the heterologous expression of arabinose and xylose utilization genes made them interesting biocatalysts for pentose fermentation, which are the main components in lignocellulosic hydrolysates. Its ability to withstand substantial amount of general growth inhibitors like furfurals, hydroxyl methyl furfurals and organic acids generated from the acid/alkali hydrolysis of lignocellulosics in growth arrested conditions and its ability to produce amino acids like glutamate and lysine in acid hydrolysates of rice straw and wheat bran, indicate the future prospective of this bacterium as a potent biocatalyst in fermentation biotechnology. However, the efforts so far on these lines have not yet been reviewed, and hence an attempt is made to look into the efficacy and prospects of C. glutamicum to utilize the normally non-fermentable pentose sugars from lignocellulosic biomass for the production of commodity chemicals.

Keywords: Corynebacterium glutamicum ; Pentose utilization; Lignocellulosic biomass; Metabolic engineering; Value-added products

Manipulation of heterogeneity product in 4′-demethylepipodophyllotoxin biotransformation process by using yeast extract as nitrogen source by Wei Zhao; Hong-Mei Li; Duan-Ji Wan; Ya-Jie Tang (pp. 107-115).

Manipulation of product heterogeneity was attempted by using yeast extract as nitrogen source in Alternaria alternata S-f6 transformation process of 4′-demethylepipodophyllotoxin. When the nitrogen source of NaNO₃ was replaced by yeast extract, the heterogeneity of biotransformation products was significantly varied from a single product (i.e., 4′-demethylpodophyllotoxone) to four podophyllum derivates. According to the kinetics of 4′-demethylepipodophyllotoxin biotransformation process by A. alternata S-f6, the starting substrate of 4′-demethylepipodophyllotoxin was preferentially transformed to produce 4′-demethylpodophyllotoxone (1) with an oxidation reaction. By the further comparison of products configuration, 4β-caprinoyl-4′-demethylepipodophyllotoxin (3) was produced from 4′-demethylpodophyllotoxone (1) instead of 4′-demethylisopicropodophyllone (2), which might be produced from 4′-demethylpodophyllotoxone (1) with the isomerization of lactone. Finally, 4′-demethylisopicropodophyllone (2) was hydrolyzed to produce 3α-hydroxymethyl-(6, 7)-dioxol-4-one-naphthalene (4). This work shows new information on the 4′-demethylepipodophyllotoxin biotransformation process by A. alternata S-f6 and provides a foundation for further studies on the structural diversification of a bioactive natural lead compound.

Keywords: Biotransformation product heterogeneity; Biotransformation metabolic pathway; Yeast extract; 4′-Demethylepipodophyllotoxin; Alternaria alternata S-f6

Hydrodynamic study of an internal airlift reactor for microalgae culture by Ana Rengel; Assaad Zoughaib; Dominique Dron; Denis Clodic (pp. 117-129).

Internal airlift reactors are closed systems considered today for microalgae cultivation. Several works have studied their hydrodynamics but based on important solid concentrations, not with biomass concentrations usually found in microalgae cultures. In this study, an internal airlift reactor has been built and tested in order to clarify the hydrodynamics of this system, based on microalgae typical concentrations. A model is proposed taking into account the variation of air bubble velocity according to volumetric air flow rate injected into the system. A relationship between riser and downcomer gas holdups is established, which varied slightly with solids concentrations. The repartition of solids along the reactor resulted to be homogenous for the range of concentrations and volumetric air flow rate studied here. Liquid velocities increase with volumetric air flow rate, and they vary slightly when solids are added to the system. Finally, liquid circulation time found in each section of the reactor is in concordance with those employed in microalgae culture.

Keywords: Airlift reactor; Hydrodynamic; Microalgae

Effect of alternative NAD⁺-regenerating pathways on the formation of primary and secondary aroma compounds in a Saccharomyces cerevisiae glycerol-defective mutant by Vishist K. Jain; Benoit Divol; Bernard A. Prior; Florian F. Bauer (pp. 131-141).

Saccharomyces cerevisiae maintains a redox balance under fermentative growth conditions by re-oxidizing NADH formed during glycolysis through ethanol formation. Excess NADH stimulates the synthesis of mainly glycerol, but also of other compounds. Here, we investigated the production of primary and secondary metabolites in S. cerevisiae strains where the glycerol production pathway was inactivated through deletion of the two glycerol-3-phosphate dehydrogenases genes (GPD1/GPD2) and replaced with alternative NAD⁺-generating pathways. While these modifications decreased fermentative ability compared to the wild-type strain, all improved growth and/or fermentative ability of the gpd1Δgpd2Δ strain in self-generated anaerobic high sugar medium. The partial NAD⁺ regeneration ability of the mutants resulted in significant amounts of alternative products, but at lower yields than glycerol. Compared to the wild-type strain, pyruvate production increased in most genetically manipulated strains, whereas acetate and succinate production decreased in all strains. Malate production was similar in all strains. Isobutanol production increased substantially in all genetically manipulated strains compared to the wild-type strain, whereas only mutant strains expressing the sorbitol producing SOR1 and srlD genes showed increases in isoamyl alcohol and 2-phenyl alcohol. A marked reduction in ethyl acetate concentration was observed in the genetically manipulated strains, while isobutyric acid increased. The synthesis of some primary and secondary metabolites appears more readily influenced by the NAD⁺/NADH availability. The data provide an initial assessment of the impact of redox balance on the production of primary and secondary metabolites which play an essential role in the flavour and aroma character of beverages.

Keywords: Redox; Saccharomyces cerevisiae ; Higher alcohol; Organic acids; Fermentation

A novel biocatalytic approach to acetylation of 1-β-d-arabinofuranosylcytosine by Aspergillus oryzae whole cell in organic solvents by Xiao-Feng Li; Zhen Zhu; Guang-Lei Zhao; Yi-Gang Yu; Fu-Rao Lai; Hui Wu (pp. 143-150).

Biocatalytic acylation of 1-β-d-arabinofuranosylcytosine (ara-C) was developed using whole cell of Aspergillus oryzae as a novel catalyst. ¹³C nuclear magnetic resonance (NMR) analysis indicated that the whole-cell biocatalyst had more specific activity toward the 3′-hydroxyl group than 5′-hydroxyl group among the available hydroxyl groups in sugar moiety of ara-C. Except for glucose and maltose, 11 carbon sources supplemented to basal media, including Spans, Tweens, olive oil and oleic acid, exhibited notable enhancement effects on both the cell growth and the acylation reactions. It was suggested that the carbon sources containing controlled-release oleic acid were the important substrates for the production of fungal cell-bound lipase with specific activity, partially due to a gradual induction effect of their released oleic acid on the cell-bound lipase production. Despite the low initial reaction rate and substrate conversion, the addition of 2.0 g/l Span 80 resulted in a higher 3′-regioselectivity of the cells than 81%. By using Tween 85 at its optimum concentration of 5.0 g/l, however, the highest initial rates (3.2 mmol/l h) and substrate conversion (76%) of the whole-cell catalyzed acylation of ara-C can be achieved. It was also found that the 3′-regioselectivity of the cells showed observable increase by extending the culture time. And the activity of cell-bound lipase drastically increased in the early stage of cell growth and then declined in the late culture stage, whatever the culture media used. Our results thus indicated that A. oryzae whole cell was a promising green tool for biosynthesis of nucleoside esters with potential bioactivities.

Keywords: Whole cell; Regioselectivity; Acylation; 1-β-d-Arabinofuranosylcytosine

Development of a low-cost sterilization biological indicator using Bacillus atrophaeus by solid-state fermentation by Sandra Regina B. R. Sella; Belquis P. Guizelini; Pedro H. Zanello; Luciana P. S. Vandenberghe; Ciro A. O. Ribeiro; João Carlos Minozzo; Carlos Ricardo Soccol (pp. 151-158).

The production of biological indicators involving bacterial sporulation and multi-step downstream processes has been described. The goal of the present work was to use fermented material as the final product in a biological indicator, thereby reducing processing steps and costs. The performance of three different inexpensive supports (vermiculite, sand, and sugarcane bagasse) was assessed by determining Bacillus atrophaeus sporulation during solid-state fermentation and by assessing the direct use of the fermentation products in the subsequent steps of the process. All three supports allowed spore production of between 10⁷ and 10⁹ CFU g⁻¹. Sand proved to be the best inert support enabling the direct use of the fermented product due to its easy homogenization, filling properties, and compatibility with recovery medium. Bacterial adhesion to the sand surface was supported by biofilm formation. The resistance to sterilization of the dried fermentation product was evaluated. For dry-heat resistance (160°C), the D value was 6.6 min, and for ethylene oxide resistance (650 mg/L), the D value was 6.5 min. The cost reduction of this process was at least 48%. No previous studies have been published on the application of sand as a support in solid-state fermentation for the production of biological indicators.

Keywords: Bacillus atrophaeus ; Spores; Biological indicator; Solid-state fermentation; Sand; Biofilm

Synthesis of green note aroma compounds by biotransformation of fatty acids using yeast cells coexpressing lipoxygenase and hydroperoxide lyase by Markus Buchhaupt; Jan Christopher Guder; Maria Magdalena Walburga Etschmann; Jens Schrader (pp. 159-168).

Green notes are substances that characterize the aroma of freshly cut grass, cucumbers, green apples, and foliage. In plants, they are synthesized by conversion of linolenic or linoleic acid via the enzymes lipoxygenase (LOX) and hydroperoxide lyase (HPL) to short-chained aldehydes. Current processes for production of natural green notes rely on plant homogenates as enzyme sources but are limited by low enzyme concentration and low specificity. In an alternative approach, soybean LOX2 and watermelon HPL were overexpressed in Saccharomyces cerevisiae. After optimization of the expression constructs, a yeast strain coexpressing LOX and HPL was applied in whole cell biotransformation experiments. Whereas addition of linolenic acid to growing cultures of this strain yielded no products, we were able to identify high green note concentrations when resting cells were used. The primary biotransformation product was 3(Z)-hexenal, a small amount of which isomerized to 2(E)-hexenal. Furthermore, both aldehydes were reduced to the corresponding green note alcohols by endogenous yeast alcohol dehydrogenase to some extent. As the cosolvent ethanol was the source of reducing equivalents for green note alcohol formation, the hexenal/hexenol ratio could be influenced by the use of alternative cosolvents. Further investigations to identify the underlying mechanism of the rather low biocatalyst stability revealed a high toxicity of linolenic acid to yeast cells. The whole cell catalyst containing LOX and HPL enzyme activity described here can be a promising approach towards a highly efficient microbial green note synthesis process.

Keywords: Green notes; Saccharomyces cerevisiae ; Lipoxygenase; Hydroperoxide lyase; Fatty acid; Biotransformation

Insight into the roles of hypoxanthine and thydimine on cultivating antibody-producing CHO cells: cell growth, antibody production and long-term stability by Fei Chen; Li Fan; Jiaqi Wang; Yan Zhou; Zhaoyang Ye; Liang Zhao; Wen-Song Tan (pp. 169-178).

The potential of hypoxanthine and thymidine (H&T) to promote growth of CHO cells and production of monoclonal antibody (mAb) was explored in this study. It was demonstrated that H&T stimulated the initial cell growth and enhanced volumetric production of anti-human CD20 mAb by 22%, mainly through the elevated integrated viable cell concentration (IVCC). The moderate alteration in cell cycle distribution might partially account for the increased cell growth. Subsequent long-term stability studies indicated that H&T did not accelerate decay kinetics in mAb productivity. Specifically, cells under both nucleic acids-replete (H&T supplementation) and nucleic acids-hungry (methotrexate treatment) culture conditions showed similar stable mAb production during the first 2 months, followed by a gradual decline in the specific production rate (q _mAb) with a 40% drop at the fourth month. In addition, the decreased transcript level of intracellular heavy chain (HC) of anti-human CD20 mAb correlated well with the decreased q _mAb. Furthermore, genomic mutation rate regarding the loss-of-function occurrence of the hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene was determined, showing that H&T repressed the HPRT spontaneous mutation rate while methotrexate (MTX) provoked the mutation rate. Collectively, our data illustrated that H&T as potential medium additives promoted both initial cell growth and volumetric production of mAb, while not affecting the long-term stability of antibody-producing CHO cells.

Keywords: Chinese hamster ovary cells; Hypoxanthine; Thymidine; Methotrexate; Long-term stability; Monoclonal antibody

Highly sensitive field test lateral flow immunodiagnostics of PVX infection by Yuri F. Drygin; Anatoly N. Blintsov; Vitaly G. Grigorenko; Irina P. Andreeva; Alexander P. Osipov; Yuri A. Varitzev; Alexander I. Uskov; Dmitry V. Kravchenko; Joseph G. Atabekov (pp. 179-189).

A test system is described and expanded upon for mass field immunochromatography assay on porous membrane carriers for rapid diagnostics of potato virus X (PVX) in potato leaf tissue and sprout extracts using colloidal gold nanoparticles as a marker. Sensitivity of the assay developed for PVX identification is found to be comparable to the sensitivity of solid-phase sandwich-ELISA. Complete assay time does not exceed 15 min, and the lower limit of the PVX detection in non-clarified leaf extract is 2 ng/ml. A single measurement requires 0.1–0.2 ml (3–5 drops) of tested solution only (extracted from 10–20 mg of potato leaf tissue or sprouts). The simplicity and reliability of the method makes it especially efficient in direct rapid monitoring of many infected potato specimens in the field, as verified by field trials of 360 clones of 28 domestic and foreign cultivars of potato. A diagnostic kit for routine analyses of potato viral infections both in the laboratory and in the field is described and expanded upon.

Keywords: Colloidal gold; ELISA; Molecular diagnostics; Potato virus X; Test-strip

The purification and characterization of a novel hypersensitive-like response-inducing elicitor from Verticillium dahliae that induces resistance responses in tobacco by Bingnan Wang; Xiufen Yang; Hongmei Zeng; Hua Liu; Tingting Zhou; Beibei Tan; Jingjing Yuan; Lihua Guo; Dewen Qiu (pp. 191-201).

PevD1, a novel protein elicitor from the pathogenic cotton verticillium wilt fungus, Verticillium dahliae, induced a hypersensitive response in tobacco plants. In this paper, the elicitor was purified and analyzed using de novo sequencing. The protein-encoding pevD1 gene consists of a 468-bp open reading frame that produces a polypeptide of 155 amino acids, with a theoretical molecular weight of 16.23 kDa. The sequence of elicitor protein PevD1 was matched to the genomic sequence (GenBank accession no. ABJE 01000445.1) of a putative protein from V. dahliae strain vdls.17, but a function had not yet been reported. The pevD1 gene was expressed in Escherichia coli, and the recombinant protein was characterized for its ability to confer systemic acquired resistance to tobacco mosaic virus (TMV). Recombinant PevD1-treated plants exhibited enhanced systemic resistance compared to control, including a significant reduction in the number and size of TMV lesions on tobacco leaves. The elicitor protein-induced hydrogen peroxide production, extracellular-medium alkalization, callose deposition, phenolics metabolism, and lignin synthesis in tobacco. Our results demonstrate that elicitor-PevD1 triggers defense responses in intact tobacco plants.

Keywords: Elicitor; Purification; Hypersensitive response; Resistance response; Verticillium dahliae

Recombinant expression, activity screening and functional characterization identifies three novel endo-1,4-β-glucanases that efficiently hydrolyse cellulosic substrates by José Humberto Tambor; Huanan Ren; Sophia Ushinsky; Yun Zheng; Anja Riemens; Christopher St-Francois; Adrian Tsang; Justin Powlowski; Reginald Storms (pp. 203-214).

The hydrolysis of cellulose into fermentable sugars is a costly and rate-limiting step in the production of biofuels from renewable feedstocks. Developing new cellulase systems capable of increased cellulose hydrolysis rates would reduce biofuel production costs. With this in mind, we screened 55 fungal endoglucanases for their abilities to be expressed at high levels by Aspergillus niger and to hydrolyze amorphous cellulose at rates significantly greater than that obtained with TrCel5A, one of the major endoglucanases in the Trichoderma reesei cellulase system. This screen identified three endoglucanases, Aureobasidium pullulans ApCel5A, Gloeophyllum trabeum GtCel12A and Sporotrichum thermophile StCel5A. We determined that A. niger expressed the three endoglucanases at relatively high levels (≥0.3 g/l) and that the hydrolysis rate of ApCel5A and StCel5A with carboxymethylcellulose 4M as substrate was five and two times greater than the T. reesei Cel5A. The ApCel5A, GtCel12A and StCel5A enzymes also demonstrated significant synergy with Cel7A/CbhI, the major exoglucanase in the T. reesei cellulase system. The three endoglucanases characterized in this study are, therefore, promising candidate endoglucanases for developing new cellulase systems with increased rates of cellulose saccharification.

Keywords: Glycosyl hydrolase family 5 endoglucanase; Glycosyl hydrolase family 12 endoglucanase; Cellulase; Heterologous expression; Synergy; Fungus

Identification of a periplasmic AlgK–AlgX–MucD multiprotein complex in Pseudomonas aeruginosa involved in biosynthesis and regulation of alginate by Iain David Hay; Oliver Schmidt; Jana Filitcheva; Bernd H. A. Rehm (pp. 215-227).

The opportunistic human pathogen Pseudomonas aeruginosa produces an extracellular polysaccharide called alginate. This is especially relevant in pulmonary infection of cystic fibrosis patients where it protects the bacteria from the hosts’ immune system and the diffusion of antibiotics. Here a connection between the stability of a proposed alginate polymerisation/secretion complex and the regulation of the operon encoding these proteins was assessed. Experimental evidence was provided for a periplasmic multiprotein complex composed of AlgX, AlgK, and the regulatory protein MucD. Disruption of the alginate machinery in a mucoid strain, either by removal, or over production of various essential proteins resulted in an at least 2-fold increase in transcription of a lacZ reporter under the control of the algD promoter. Instability of the complex was indicated by an increase in secretion of alginate degradation products. This increase in transcription was found to be dependent on the negative regulatory protein MucD. Surprisingly, over production of MucD leads to a 3.3-fold increase in transcription from the alginate promoter and a 1.7-fold increase in the levels of alginate produced, suggesting an additional positive regulatory role for MucD in mucoid strains. Overall, this study provided experimental evidence for the proposed periplasmic multiprotein complex and established a link of a constituent of this complex, MucD, to transcriptional regulation of alginate biosynthesis genes.

Keywords: Alginate; Alginate biosynthesis; Pseudomonas aeruginosa

Identification and comparison of cutinases for synthetic polyester degradation by Peter James Baker; Christopher Poultney; Zhiqiang Liu; Richard Gross; Jin Kim Montclare (pp. 229-240).

Cutinases have been exploited for a broad range of reactions, from hydrolysis of soluble and insoluble esters to polymer synthesis. To further expand the biotechnological applications of cutinases for synthetic polyester degradation, we perform a comparative activity and stability analysis of five cutinases from Alternaria brassicicola (AbC), Aspergillus fumigatus (AfC), Aspergillus oryzae (AoC), Humicola insolens (HiC), and the well-characterized Fusarium solani (FsC). Of the cutinases, HiC demonstrated enhanced poly(ε-caprolactone) hydrolysis at high temperatures and under all pH values, followed by AoC and AfC. Both AbC and FsC are least stable and function poorly at high temperatures as well as at acidic pH conditions. Surface charge calculations and phylogenetic analysis reveal two important modes of cutinase stabilization: (1) an overall neutral surface charge within the “crowning area” by the active site and (2) additional disulfide bond formation. These studies provide insights useful for reengineering such enzymes with improved function and stability for a wide range of biotransformations.

Keywords: Cutinase; Hydrolysis; Polymer degradation; Thermostability; pH stability; Residual activity

Functional characterization of Class II 5-enopyruvylshikimate-3-phosphate synthase from Halothermothrix orenii H168 in Escherichia coli and transgenic Arabidopsis by Yong-Sheng Tian; Jing Xu; Ai-Sheng Xiong; Wei Zhao; Feng Gao; Xiao-Yan Fu; Ri-He Peng; Quan-Hong Yao (pp. 241-250).

Although a large number of AroA enzymes (5-enopyruvylshikimate-3-phosphate synthase [EPSPS]) have been identified, cloned and tested for glyphosate resistance, only AroA variants derived from Agrobacterium tumefaciens strain CP4 have been successfully used commercially. We have now used a polymerase chain reaction (PCR)-based two-step DNA synthesis (PTDS) method to synthesize an aroA gene (aroA H. orenii) from Halothermothrix orenii H168 encoding a new EPSPS similar to AroA A. tumefaciens_CP4. AroA H. orenii was then expressed in Escherichia coli and key kinetic values of the purified enzyme were determined. Kinetic analysis of AroA H. orenii indicated that the full-length enzyme exhibited increased tolerance to glyphosate compared with E. coli AroA E. coli while retaining a high affinity for the substrate phosphoenolpyruvate. Transgenic Arabidopsis plants containing aroA H. orenii were resistant to 15 mM glyphosate. Site-directed mutagenesis showed that residues Thr355Ser affected the affinity of AroA H. orenii for glyphosate, providing further evidence that specific amino acid residues are responsible for differences in enzymatic behavior among different AroA enzymes.

Keywords: 5-Enopyruvylshikimate-3-phosphate synthase; Halothermothrix orenii ; Enzyme kinetic values; Transgenic Arabidopsis

Development of fluorescent probes for the detection of fucosylated N-glycans using an Aspergillus oryzae lectin by Ji-Young Mun; Kyung Jin Lee; Yu Jin Kim; Ohsuk Kwon; Su-Jin Kim; Seung-Goo Lee; Wei Sun Park; Won Do Heo; Doo-Byoung Oh (pp. 251-260).

The α(1,6)-fucose attached to the core N-glycan (core fucose) of glycoproteins has been known to play essential roles in various pathophysiological events, including oncogenesis and metastasis. Aspergillus oryzae lectin (AOL) encoded by the fleA gene has been reported to bind to N-glycans containing core fucose. The fleA gene encoding AOL was cloned into an Escherichia coli expression vector and then fused with genes of fluorescent proteins for production of fusion proteins. The resulting FleA-fluorescent fusion proteins were expressed well in E. coli and shown to detect glycoproteins containing N-glycans with core fucose by lectin blot assay. It was also shown to bind to the surface of cancer cells highly expressing the fucosyltransferase VIII for attachment of core fucose. Surprisingly, we found that FleA-fluorescent fusion proteins could be internalized into the intracellular compartment, early endosome, when applied to live cells. This internalization was shown to occur through a clathrin-mediated pathway by endocytosis inhibitor assay. Taken together, these results suggest that FleA-fluorescent fusion proteins can be employed as a valuable fluorescent probe for the detection of fucosylated glycans and/or a useful vehicle for delivery of substances to the inside of cells.

Keywords: Core fucose; AOL; Fluorescent proteins; Endocytosis; Clathrin-mediated

Sequencing and analysis of three plasmids from Lactobacillus casei TISTR1341 and development of plasmid-derived Escherichia coli–L. casei shuttle vectors by Marutpong Panya; Viraphong Lulitanond; Sithichoke Tangphatsornruang; Wises Namwat; Rungnapha Wannasutta; Namfon Suebwongsa; Baltasar Mayo (pp. 261-272).

Pyrosequencing followed by conventional PCR and sequencing was used to determine the complete nucleotide sequence of three plasmids (pRCEID2.9, pRCEID3.2, and pRCEID13.9) from the Lactobacillus casei strain TISTR1341. The plasmid sequences were found to be almost identical, respectively, to those of pLA106, pLA105, and pLA103 from Lactobacillus acidophilus strain TK8912, suggesting that these strains may be related. Sequence analysis and comparison indicated that pRCEID2.9 replicates by a rolling circle (RC) mechanism, while pRCEID3.2 and pRCEID13.9 probably follow a theta-type mode of replication. Replicons of pRCEID2.9 and pRCEID13.9 were used to develop Escherichia coli/L. casei compatible shuttle vectors, which were stably maintained in different genetic backgrounds. Real-time quantitative PCR analysis showed copy numbers of around 4 and 15, respectively, for the pRCEID13.9- and pRCEID2.9-derived shuttle vectors per chromosome equivalent. The functionality of vector pRCEID-LC13.9 was proved by cloning and expressing in L. casei of a green fluorescent protein gene variant from Aequorea victoria under the control of the promoter from a homologous lactate dehydrogenase gene. The new vectors might complement those currently in use for the exploitation of L. casei as a cellular factory and in other biotechnological applications.

Keywords: Lactobacillus casei ; Plasmid; Cloning vectors; Lactic acid bacteria; Probiotics

Biosynthesis of polyhydroxyalkanoates containing 2-hydroxybutyrate from unrelated carbon source by metabolically engineered Escherichia coli by Si Jae Park; Tae Woo Lee; Sung-Chul Lim; Tae Wan Kim; Hyuk Lee; Min Kyung Kim; Seung Hwan Lee; Bong Keun Song; Sang Yup Lee (pp. 273-283).

We have previously reported in vivo biosynthesis of polylactic acid (PLA) and poly(3-hydroxybutyrate-co-lactate) [P(3HB-co-LA)] employing metabolically engineered Escherichia coli strains by the introduction of evolved Clostridium propionicum propionyl-CoA transferase (Pct Cp) and Pseudomonas sp. MBEL 6-19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1 Ps_6-19). Using this in vivo PLA biosynthesis system, we presently report the biosynthesis of PHAs containing 2-hydroxybutyrate (2HB) monomer by direct fermentation of a metabolically engineered E. coli strain. The recombinant E. coli ldhA mutant XLdh strain expressing PhaC1 Ps_6-19 and Pct Cp was developed and cultured in a chemically defined medium containing 20 g/L of glucose and varying concentrations of 2HB and 3HB. PHAs consisting of 2HB, 3HB, and a small fraction of lactate were synthesized. Their monomer compositions were dependent on the concentrations of 2HB and 3HB added to the culture medium. Even though the ldhA gene was completely deleted in the chromosome of E. coli, up to 6 mol% of lactate was found to be incorporated into the polymer depending on the culture condition. In order to synthesize PHAs containing 2HB monomer without feeding 2HB into the culture medium, a heterologous metabolic pathway for the generation of 2HB from glucose was constructed via the citramalate pathway, in which 2-ketobutyrate is synthesized directly from pyruvate and acetyl-CoA. Introduction of the Lactococcus lactis subsp. lactis Il1403 2HB dehydrogenase gene (panE) into E. coli allowed in vivo conversion of 2-ketobutyrate to 2HB. The metabolically engineered E. coli XLdh strain expressing the phaC1437, pct540, cimA3.7, and leuBCD genes together with the L. lactis Il1403 panE gene successfully produced PHAs consisting of 2HB, 3HB, and a small fraction of lactate by varying the 3HB concentration in the culture medium. As the 3HB concentration in the medium increased the 3HB monomer fraction in the polymer, the polymer content increased. When Ralstonia eutropha phaAB genes were additionally expressed in this recombinant E. coli XLdh strain, P(2HB-co-3HB-co-LA) having small amounts of 2HB and LA monomers could also be produced from glucose as a sole carbon source. The metabolic engineering strategy reported here should be useful for the production of PHAs containing 2HB monomer.

Keywords: Polyhydroxyalkanoate (PHA); 2-hydroxybutyrate (2HB); PHA synthase; Recombinant E. coli

A broader role for AmyR in Aspergillus niger: regulation of the utilisation of d-glucose or d-galactose containing oligo- and polysaccharides by Patricia A. vanKuyk; Jaques A. E. Benen; Han A. B. Wösten; Jaap Visser; Ronald P. de Vries (pp. 285-293).

AmyR is commonly considered a regulator of starch degradation whose activity is induced by the presence of maltose, the disaccharide building block of starch. In this study, we demonstrate that the role of AmyR extends beyond starch degradation. Enzyme activity assays, genes expression analysis and growth profiling on d-glucose- and d-galactose-containing oligo- and polysaccharides showed that AmyR regulates the expression of some of the Aspergillus niger genes encoding α- and β-glucosidases, α- and β- galactosidases, as well as genes encoding α-amlyases and glucoamylases. In addition, we provide evidence that d-glucose or a metabolic product thereof may be the inducer of the AmyR system in A. niger and not maltose, as is commonly assumed.

Keywords: Aspergillus niger ; AmyR; Polysaccharide degradation; Gene regulation

Site-specific genome integration in alphaproteobacteria mediated by TG1 integrase by Kentaro Morita; Kohji Morimura; Naoki Fusada; Mamoru Komatsu; Haruo Ikeda; Nobutaka Hirano; Hideo Takahashi (pp. 295-304).

The serine-type phage integrase is an enzyme that catalyzes site-specific recombination between two attachment sites of phage and host bacterial genomes (attP and attB, respectively) having relatively short but distinct sequences without host auxiliary factor(s). Previously, we have established in vivo and in vitro site-specific recombination systems based on the serine-type integrase produced by actinophage TG1 and determined the minimal sizes of attP TG1 and attB TG1 sites required for the in vitro TG1 integrase reaction as 43- and 39-bp, respectively. Here, DNA databases were surveyed by FASTA program with the authentic attB TG1 sequence of Streptomyces avermitilis as a query. As a result, possible attB TG1 sequences were extracted from genomes of bacterial strains belonging to Class Alphaproteobacteria in addition to those of Class Actinobacteria. Those sequences extracted with a high similarity score and high sequence identity (we took arbitrarily more than 80% identity) turned out to be located within a conserved region of dapC or related genes encoding aminotransferases and proved to be actually recognized as the cognate substrate of attP TG1 site by the in vitro TG1 integrase assay. Furthermore, the possible attB TG1 site of Rhodospirillum rubrum revealed to be used actually as a native (endogenous) attachment site for the in vivo TG1-based integration system. These features are distinct from other serine-type phage integrases and advantageous for a tool of genome technology in varied industrially important bacteria belonging to Class Alphaproteobacteria.

Keywords: Streptomyces ; TG1 integrase; Attachment site; Integration vector; Alphaproteobacteria

Conserved and specific responses to hypoxia in Aspergillus oryzae and Aspergillus nidulans determined by comparative transcriptomics by Yasunobu Terabayashi; Motoyuki Shimizu; Tatsuya Kitazume; Shunsuke Masuo; Tatsuya Fujii; Naoki Takaya (pp. 305-317).

Hypoxia imposes stress on filamentous fungi that require oxygen to proliferate. Global transcription analysis of Aspergillus oryzae grown under hypoxic conditions found that the expression of about 50% of 4,244 affected genes was either induced or repressed more than 2-fold. A comparison of these genes with the hypoxically regulated genes of Aspergillus nidulans based on their predicted amino acid sequences classified them as bi-directional best hit (BBH), one-way best hit (extra homolog, EH), and no-hit (non-syntenic genes, NSG) genes. Clustering analysis of the BBH genes indicated that A. oryzae and A. nidulans down-regulated global translation and transcription under hypoxic conditions, respectively. Under hypoxic conditions, both fungi up-regulated genes for alcohol fermentation and the γ-aminobutyrate shunt of the tricarboxylate cycle, whereas A. oryzae up-regulated the glyoxylate pathway, indicating that both fungi eliminate NADH accumulation under hypoxic conditions. The A. oryzae NS genes included specific genes for secondary and nitric oxide metabolism under hypoxic conditions. This comparative transcriptomic analysis discovered common and strain-specific responses to hypoxia in hypoxic Aspergillus species.

Keywords: DNA microarray; Glycolysis; Gluconeogenesis; Fermentation; Environmental stress; Denitrification

Bioleaching in brackish waters—effect of chloride ions on the acidophile population and proteomes of model species by Carla M. Zammit; Stefanie Mangold; Venkateswara rao Jonna; Lesley A. Mutch; Helen R. Watling; Mark Dopson; Elizabeth L. J. Watkin (pp. 319-329).

High concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to Western Australian and Chilean biomining operations. Despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. This study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics to elucidate how two species from this mixed culture alter their proteomes under chloride stress. A mixture consisting of well-known biomining microorganisms and an enrichment culture obtained from an acidic saline drain were tested for their ability to bioleach pyrite in the presence of 0, 3.5, 7, and 20 g L⁻¹ NaCl. Microorganisms from the enrichment culture were found to out-compete the known biomining microorganisms, independent of the chloride ion concentration. The proteomes of the Gram-positive acidophile Acidimicrobium ferrooxidans and the Gram-negative acidophile Acidithiobacillus caldus grown in the presence or absence of chloride ions were investigated. Analysis of differential expression showed that acidophilic microorganisms adopted several changes in their proteomes in the presence of chloride ions, suggesting the following strategies to combat the NaCl stress: adaptation of the cell membrane, the accumulation of amino acids possibly as a form of osmoprotectant, and the expression of a YceI family protein involved in acid and osmotic-related stress.

Keywords: Biomining; Chloride; Proteomics; Brackish; Membrane

The complete genome sequence of Pantoea ananatis AJ13355, an organism with great biotechnological potential by Yoshihiko Hara; Naoki Kadotani; Hiroshi Izui; Joanna I. Katashkina; Tatiana M. Kuvaeva; Irina G. Andreeva; Lyubov I. Golubeva; Dmitry B. Malko; Vsevolod J. Makeev; Sergey V. Mashko; Yurii I. Kozlov (pp. 331-341).

Pantoea ananatis AJ13355 is a newly identified member of the Enterobacteriaceae family with promising biotechnological applications. This bacterium is able to grow at an acidic pH and is resistant to saturating concentrations of L-glutamic acid, making this organism a suitable host for the production of L-glutamate. In the current study, the complete genomic sequence of P. ananatis AJ13355 was determined. The genome was found to consist of a single circular chromosome consisting of 4,555,536 bp [DDBJ: AP012032] and a circular plasmid, pEA320, of 321,744 bp [DDBJ: AP012033]. After automated annotation, 4,071 protein-coding sequences were identified in the P. ananatis AJ13355 genome. For 4,025 of these genes, functions were assigned based on homologies to known proteins. A high level of nucleotide sequence identity (99%) was revealed between the genome of P. ananatis AJ13355 and the previously published genome of P. ananatis LMG 20103. Short colinear regions, which are identical to DNA sequences in the Escherichia coli MG1655 chromosome, were found to be widely dispersed along the P. ananatis AJ13355 genome. Conjugal gene transfer from E. coli to P. ananatis, mediated by homologous recombination between short identical sequences, was also experimentally demonstrated. The determination of the genome sequence has paved the way for the directed metabolic engineering of P. ananatis to produce biotechnologically relevant compounds.

Keywords: Central carbon metabolism; Interspecies conjugation; Genome backbone; Genome sequencing; Genome synteny; Megaplasmid

Identification of phenylalkane derivatives when Mycobacterium neoaurum and Rhodococcus erythropolis were cultured in the presence of various phenylalkanes by Susanne Herter; Annett Mikolasch; Frieder Schauer (pp. 343-355).

Phenylalkanes are ubiquitously found in nature as pollutants originating from oil, gas oil and petrol. Rising commercial demand for mineral oil fractions has led to the increased prevalence of environmental contamination, whereby these particular hydrocarbons are encountered by bacteria which have subsequently developed sophisticated metabolic routes for purposes of degradation. Herein a detailed analysis of these metabolic pathways in the degradation of phenylalkanes by Mycobacterium neoaurum and Rhodococcus erythropolis highlighted preponderance for the formation of certain metabolites of which 17 were identified and whereby striking differences were noticed depending specifically upon the length of the substrate’s alkyl chain. Although the degradation of even-numbered phenylalkane substrates was assumed to result in the generation of phenylacetic acid formed due to substrate terminal oxidation and subsequent β-oxidation, cultures of M. neoaurum and R. erythropolis were determined in an extracellular accumulation of odd-numbered acidic metabolites, suggesting a simultaneous presence of sub-terminal degradation mechanisms. However, results obtained from biotransformation assays containing even-chained phenylalkanoic acid intermediates as substrates revealed exclusive β-oxidative mechanisms and no generation of odd-numbered degradation products. R. erythropolis in contrast to M. neoaurum also proved viable for hydroxylation of the aromatic ring of metabolites. Interestingly, the generation of phenylacetic acid and subsequently 2-hydroxyphenyl acetic acid was monitored and entailed the presence of the lactone intermediate 2-coumaranone. These results enhance our understanding of the degradation of phenylalkanes and illustrate the potential application of such species in the bioremediation of these common environmental pollutants and in the strains’ diverse abilities to transform mineral oil compounds to new valuable products.

Keywords: Hydrocarbons; Degradation; Mineral oil components; Environmental pollution; n-Alkanes; 2-Coumaranone

Biotechnological conversion of glycerol to 2-amino-1,3-propanediol (serinol) in recombinant Escherichia coli by Björn Andreeßen; Alexander Steinbüchel (pp. 357-365).

Microbial conversion is an important technology for the refinement of renewable resources. Here, we describe the biotechnological conversion of glycerol to 2-amino-1,3-propanediol (serinol), a relevant intermediate in several chemical syntheses processes. Either the dihydroxyacetone phosphate aminotransferase/dihydrorhizobitoxine synthase (RtxA) of Bradyrhizobium elkanii USD94 or only the N-terminal domain (RtxA513) comprising the first reaction, respectively, was expressed in recombinant Escherichia coli. Serinol contents of up to 3.3 g/l were achieved in batch cultures. We could further clarify that glutamic acid is the preferred cosubstrate for the transamination of dihydroxyacetone phosphate to serinolphosphate, which is the essential step in serinol synthesis. An in vivo detoxification of serinol employing wax ester synthase/acyl-CoA:diacyl-glycerol acyl transferase from Acinetobacter baylyi ADP1 was not accomplished. This study paves the way for biotechnological production of serinol from glycerol derived from the biodiesel industry.

Keywords: 2-Amino-1,3-propanediol; Bradyrhizobium elkanii ; Dihydrorhizobitoxine synthase; Glycerol; RtxA; Serinol

Improved curdlan fermentation process based on optimization of dissolved oxygen combined with pH control and metabolic characterization of Agrobacterium sp. ATCC 31749 by Hong-Tao Zhang; Xiao-Bei Zhan; Zhi-Yong Zheng; Jian-Rong Wu; Nike English; Xiao-Bin Yu; Chi-Chung Lin (pp. 367-379).

A significant problem in scale-down cultures, rarely studied for metabolic characterization and curdlan-producing Agrobacterium sp. ATCC 31749, is the presence of dissolved oxygen (DO) gradients combined with pH control. Constant DO, between 5% and 75%, was maintained during batch fermentations by manipulating the agitation with PID system. Fermentation, metabolic and kinetic characterization studies were conducted in a scale-down system. The curdlan yield, intracellular nucleotide levels and glucose conversion efficiency into curdlan were significantly affected by DO concentrations. The optimum DO concentrations for curdlan production were 45–60%. The average curdlan yield, curdlan productivity and glucose conversion efficiency into curdlan were enhanced by 80%, 66% and 32%, respectively, compared to that at 15% DO. No apparent difference in the gel strength of the resulting curdlan was detected. The comparison of curdlan biosynthesis and cellular nucleotide levels showed that curdlan production had positive relationship with intracellular levels of UTP, ADP, AMP, NAD⁺, NADH and UDP-glucose. The curdlan productivity under 45% DO and 60% DO was different during 20–50 h. However, after 60 h curdlan productivity of both conditions was similar. On that basis, a simple and reproducible two-stage DO control process for curdlan production was developed. Curdlan production yield reached 42.8 g/l, an increase of 30% compared to that of the single agitation speed control process.

Keywords: Agrobacterium sp. ATCC 31749; Curdlan; Dissolved oxygen; Two-stage DO control strategy; Kinetic characterization

Suitability of different β-galactosidases as reporter enzymes in Bacillus subtilis by Norma Welsch; Georg Homuth; Thomas Schweder (pp. 381-392).

The suitability of three β-galactosidases as reporter enzymes for promoter expression analyses was investigated in Bacillus subtilis with respect to various temperature conditions during cultivation and assay procedures. Starting from the hypothesis that proteins derived from diverse habitats have different advantages as reporters at different growth temperatures, the beta-galactosidases from the thermophilic organism Bacillus stearothermophilus, from the mesophilic bacterium Escherichia coli and from the psychrophilic organism Pseudoalteromonas haloplanktis TAE79 were analysed under control of the constitutive B. subtilis lepA promoter. Subsequent expression of the β-galactosidase genes and determination of specific activities was performed at different cultivation and assay temperatures using B. subtilis as host. Surprisingly, the obtained results demonstrated that the highest activities over a broad cultivation temperature range were obtained using the β-galactosidase from the mesophilic bacterium E. coli whereas the enzymes from the thermophilic and psychrophilic bacteria revealed a more restricted usability in terms of cultivation temperature.

Keywords: β-galactosidase; Reporter enzymes; Bacillus subtilis ; Recombinant expression

Luciferase and fluorescent protein as dual reporters analyzing the effect of n-dodecyltrimethylammonium bromide on the physiology of Pseudomonas putida by Chong Zhang; Feng-Yi Su; Jian-Feng Zhang; Sang-Tian Yan; Xin-Hui Xing (pp. 393-400).

With the growing interest in using surfactants to improve microbial cell performance for whole-cell biocatalysis and bioremediation, understanding the interactions between surfactants and bacteria is of great importance. By using cyanine fluorescent protein (CFP) and bacterial luciferase (LUX) as dual bioreporters, the effects of n-dodecyltrimethylammonium bromide (DTAB) on the whole cells and intracellular proteins in Pseudomonas putida cultures were quantitatively and systematically studied. The dual reporter system was shown to be a useful indicator to assess the effect of DTAB treatment on whole-cell metabolic activity, membrane permeability, and cellular enzyme activity. CFP was useful to assess the leakage of intracellular enzymes and the lysis of cells and was able to reflect the activities of most cellular enzymes, while LUX reflected the permeability of cell membranes and cellular metabolic activity. The validity of CFP–LUX dual bioreporters was further confirmed by detecting changes in extracellular proteins, membrane potential, oxygen consumption rate (OUR), and intracellular catechol 2,3-dioxygenase (C23O) activity with the addition of DTAB. The dual LUX–CFP bioreporter is a useful tool for analyzing the surfactant–bacterium interactions for biotechnological applications.

Keywords: Bioreporter; Bacterial luciferase; Cationic surfactant; Cyanine fluorescent protein; P. putida

Analysis of ammonia-oxidizing bacteria dominating in lab-scale bioreactors with high ammonium bicarbonate loading by Dana Vejmelkova; Dimitry Y. Sorokin; Ben Abbas; Olga L. Kovaleva; Robbert Kleerebezem; Marlies J. Kampschreur; Gerard Muyzer; Mark C. M. van Loosdrecht (pp. 401-410).

The ammonia-oxidizing bacterial community (AOB) was investigated in two types of laboratory-scale bioreactors performing partial oxidation of ammonia to nitrite or nitrate at high (80 mM) to extremely high (428 mM) concentrations of ammonium bicarbonate. At all conditions, the dominant AOB was affiliated to the Nitrosomonas europaea lineage as was determined by fluorescence in situ hybridization and polymerase chain reaction in combination with denaturing gradient gel electrophoresis. Molecular analysis of the mixed populations, based on the 16S rRNA and cbbL genes, demonstrated the presence of two different phylotypes of Nitrosomonas, while microbiological analysis produced a single phylotype, represented by three different morphotypes. One of the most striking features of the AOB populations encountered in the bioreactors was the domination of highly aggregated obligate microaerophilic Nitrosomonas, with unusual cellular and colony morphology, commonly observed in nitrifying bioreactors but rarely investigated by cultural methods. The latter is probably not an adaptation to stressful conditions created by high ammonia or nitrite concentrations, but oxygen seems to be a stressful factor in these bioreactors.

Keywords: Ammonia-oxidizing bacteria (AOB); DGGE; FISH; Nitrosomonas ; Partial nitrification

Molecular phylogenetic diversity of Bacillus community and its temporal–spatial distribution during the swine manure of composting by Jing Yi; Hua-Yu Wu; Jian Wu; Chang-Yan Deng; Rong Zheng; Zhe Chao (pp. 411-421).

In order to obtain the diversity and temporal–spatial distribution of Bacillus community during the swine manure composting, we utilized traditional culture methods and the modern molecular biology techniques of polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and –denaturing gradient gel electrophoresis (PCR-DGGE). Bacillus species were firstly isolated from the composting. Based on temperature changes, the temporal–spatial characteristics of total culturable Bacillus were remarkable that the number of the culturable Bacillus detected at the high-temperature stage was the highest in each layer of the pile and that detected in the middle layer was the lowest at each stage of composting respectively. The diversity of cultivated Bacillus species isolated from different composting stages was low. A total of 540 isolates were classified by the RFLP method and partial 16S rDNA sequences. They affiliated to eight species including Bacillus subtilis, Bacillus cereus, Bacillus thuringiensis, Bacillus anthracis, Bacillus megaterium, Bacillus licheniformis, Bacillus pumilus, and Bacillus circulans. The predominant species was B. subtilis, and the diversity of culturable Bacillus isolated in the middle-level samples at temperature rising and cooling stages was the highest. The DGGE profile and clone library analysis revealed that the temporal–spatial distribution of Bacillus community was not obvious, species belonging to the Bacillus were dominant (67%) with unculturable bacteria and B. cereus was the second major culturable Bacillus species. This study indicated that a combination of culture and culture-independent approaches could be very useful for monitoring the diversity and temporal–spatial distribution of Bacillus community during the composting process.

Keywords: Composting; Bacillus ; Diversity; Temporal–spatial distribution; RFLP; DGGE

Dynamic changes in the microbial community composition in microbial fuel cells fed with sucrose by Nelli J. Beecroft; Feng Zhao; John R. Varcoe; Robert C. T. Slade; Alfred E. Thumser; Claudio Avignone-Rossa (pp. 423-437).

The performance and dynamics of the bacterial communities in the biofilm and suspended culture in the anode chamber of sucrose-fed microbial fuel cells (MFCs) were studied by using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes followed by species identification by sequencing. The power density of MFCs was correlated to the relative proportions of species obtained from DGGE analysis in order to detect bacterial species or taxonomic classes with important functional role in electricity production. Although replicate MFCs showed similarity in performance, cluster analysis of DGGE profiles revealed differences in the evolution of bacterial communities between replicate MFCs. No correlation was found between the proportion trends of specific species and the enhancement of power output. However, in all MFCs, putative exoelectrogenic denitrifiers and sulphate-reducers accounted for approximately 24% of the bacterial biofilm community at the end of the study. Pareto–Lorenz evenness distribution curves extracted from the DGGE patterns obtained from time course samples indicated community structures where shifts between functionally similar species occur, as observed within the predominant fermentative bacteria. These results suggest the presence of functional redundancy within the anodic communities, a probable indication that stable MFC performance can be maintained in changing environmental conditions. The capability of bacteria to adapt to electricity generation might be present among a wide range of bacteria.

Keywords: Microbial fuel cell (MFC); Electricity generation; PCR-DGGE; Microbial community dynamics

Stability and inhibition of anaerobic processes caused by insufficiency or excess of ammonia nitrogen by Jindřich Procházka; Petr Dolejš; Josef Máca; Michal Dohányos (pp. 439-447).

Ammonia increases buffer capacity of methanogenic medium in mesophilic anaerobic reactor thus increasing the stability of anaerobic digestion process. Optimal ammonia concentration ensures sufficient buffer capacity while not inhibiting the process. It was found out in this paper that this optimum depends on the quality of anaerobic sludge under investigation. The optimal concentrations for methanogens were 2.1, 2.6 and 3.1 g/L of ammonia nitrogen in dependence on inoculum origin. High ammonia nitrogen concentration (4.0 g/L) inhibited methane production, while low ammonia nitrogen concentration (0.5 g/L) caused low methane yield, loss of biomass (as VSS) and loss of the aceticlastic methanogenic activity. It was found out that negative effect of low ammonia nitrogen concentration on biomass is caused not only by low buffer capacity but also by insufficiency of nitrogen as nutrient. It was also found out that anaerobic sludge with higher ammonia nitrogen concentration (4.2 g/L) tolerates even concentration of volatile fatty acids (160 mmol/L) which causes inhibition of the process with low ammonia nitrogen concentration (0.2 g/L).

Keywords: Ammonia inhibition; Anaerobic digestion; Buffer capacity; Process stability; Volatile fatty acids

Erratum to: Highly sensitive field test lateral flow immunodiagnostics of PVX infection by Yuri F. Drygin; Anatoly N. Blintsov; Vitaly G. Grigorenko; Irina P. Andreeva; Alexander P. Osipov; Yuri A. Varitzev; Alexander I. Uskov; Dmitry V. Kravchenko; Joseph G. Atabekov (pp. 449-449).

Erratum to: Corynebacterium glutamicum as a potent biocatalyst for the bioconversion of pentose sugars to value-added products by Vipin Gopinath; Anusree Murali; Kiran S. Dhar; K. Madhavan Nampoothiri (pp. 451-453).

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Applied Microbiology and Biotechnology (v.93, #1)

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Applied Microbiology and Biotechnology (v.93, #1)