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Applied Microbiology and Biotechnology (v.97, #6)

Biotechnologies for greenhouse gases (CH₄, N₂O, and CO₂) abatement: state of the art and challenges by Juan C. López; Guillermo Quijano; Theo S. O. Souza; José M. Estrada; Raquel Lebrero; Raúl Muñoz (pp. 2277-2303).

Today, methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂) emissions represent approximately 98 % of the total greenhouse gas (GHG) inventory worldwide, and their share is expected to increase significantly in this twenty-first century. CO₂ represents the most important GHG with approximately 77 % of the total GHG emissions (considering its global warming potential) worldwide, while CH₄ and N₂O are emitted to a lesser extent (14 and 8 %, respectively) but exhibit global warming potentials 23 and 298 times higher than that of CO₂, respectively. Most members of the United Nations, based on the urgent need to maintain the global average temperature 2 °C above preindustrial levels, have committed themselves to significantly reduce their GHG emissions. In this context, an active abatement of these emissions will help to achieve these target emission cuts without compromising industrial growth. Nowadays, there are sufficient empirical evidence to support that biological technologies can become, if properly tailored, a low-cost and environmentally friendly alternative to physical/chemical methods for the abatement of GHGs. This study constitutes a state-of-the-art review of the microbiology (biochemistry, kinetics, and waste-to-value processes) and bioreactor technology of CH₄, N₂O, and CO₂ abatement. The potential and limitations of biological GHG degradation processes are critically discussed, and the current knowledge gaps and technology niches in the field are identified.

Keywords: Biological treatment; Carbon dioxide; Greenhouse gases; Methane; Nitrous oxide

Cell aggregations in yeasts and their applications by J. A. Vallejo; A. Sánchez-Pérez; José P. Martínez; T. G. Villa (pp. 2305-2318).

Yeasts can display four types of cellular aggregation: sexual, flocculation, biofilm formation, and filamentous growth. These cell aggregations arise, in some yeast strains, as a response to environmental or physiological changes. Sexual aggregation is part of the yeast mating process, representing the first step of meiotic recombination. The flocculation phenomenon is a calcium-dependent asexual reversible cellular aggregation that allows the yeast to withstand adverse conditions. Biofilm formation consists of multicellular aggregates that adhere to solid surfaces and are embedded in a protein matrix; this gives the yeast strain either the ability to colonize new environments or to survive harsh environmental conditions. Finally, the filamentous growth is the ability of some yeast strains to grow in filament forms. Filamentous growth can be attained by two different means, with the formation of either hyphae or pseudohyphae. Both hyphae and pseudohyphae arise when the yeast strain is under nutrient starvation conditions and they represent a means for the microbial strain to spread over a wide area to survey for food sources, without increasing its biomass. Additionally, this filamentous growth is also responsible for the invasive growth of some yeast.

Keywords: Yeast aggregation; Sexual aggregation; Flocculation; Biofilms; Filamentous growth

Systems metabolic engineering in an industrial setting by Cees M. J. Sagt (pp. 2319-2326).

Systems metabolic engineering is based on systems biology, synthetic biology, and evolutionary engineering and is now also applied in industry. Industrial use of systems metabolic engineering focuses on strain and process optimization. Since ambitious yields, titers, productivities, and low costs are key in an industrial setting, the use of effective and robust methods in systems metabolic engineering is becoming very important. Major improvements in the field of proteomics and metabolomics have been crucial in the development of genome-wide approaches in strain and process development. This is accompanied by a rapid increase in DNA sequencing and synthesis capacity. These developments enable the use of systems metabolic engineering in an industrial setting. Industrial systems metabolic engineering can be defined as the combined use of genome-wide genomics, transcriptomics, proteomics, and metabolomics to modify strains or processes. This approach has become very common since the technology for generating large data sets of all levels of the cellular processes has developed quite fast into robust, reliable, and affordable methods. The main challenge and scope of this mini review is how to translate these large data sets in relevant biological leads which can be tested for strain or process improvements. Experimental setup, heterogeneity of the culture, and sample pretreatment are important issues which are easily underrated. In addition, the process of structuring, filtering, and visualization of data is important, but also, the availability of a genetic toolbox and equipment for medium/high-throughput fermentation is a key success factor. For an efficient bioprocess, all the different components in this process have to work together. Therefore, mutual tuning of these components is an important strategy.

Keywords: Genomics; Strain; Process; Optimization; Industrial; Biotechnology; Systems biology

Contributions of biosurfactants to natural or induced bioremediation by Łukasz Ławniczak; Roman Marecik; Łukasz Chrzanowski (pp. 2327-2339).

The number of studies dedicated to evaluating the influence of biosurfactants on bioremediation efficiency is constantly growing. Although significant progress regarding the explanation of mechanisms behind biosurfactant-induced effects could be observed, there are still many factors which are not sufficiently elucidated. This corresponds to the fact that although positive influence of biosurfactants is often reported, there are also numerous cases where no or negative effect was observed. This review summarizes the recent finding in the field of biosurfactant-amended bioremediation, focusing mainly on a critical approach towards potential limitations and causes of failure while investigating the effects of biosurfactants on the efficiency of biodegradation and phytoextraction processes. It also provides a summary of successive steps, which should be taken into consideration when designing biosurfactant-related treatment processes.

Keywords: Bioaugmentation; Biodegradation; Bioremediation; Biosurfactants; Phytoextraction

Cephalosporin C acylase: dream and(/or) reality by Loredano Pollegioni; Elena Rosini; Gianluca Molla (pp. 2341-2355).

Cephalosporins currently constitute the most widely prescribed class of antibiotics and are used to treat diseases caused by both Gram-positive and Gram-negative bacteria. Cephalosporins contain a 7-aminocephalosporanic acid (7-ACA) nucleus which is derived from cephalosporin C (CephC). The 7-ACA nucleus is not sufficiently potent for clinical use; however, a series of highly effective antibiotic agents could be produced by modifying the side chains linked to the 7-ACA nucleus. The industrial production of higher-generation semi-synthetic cephalosporins starts from 7-ACA, which is obtained by deacylation of the naturally occurring antibiotic CephC. CephC can be converted to 7-ACA either chemically or enzymatically using d-amino acid oxidase and glutaryl-7-aminocephalosporanic acid acylase. Both these methods show limitation, including the production of toxic waste products (chemical process) and the expense (the enzymatic one). In order to circumvent these problems, attempts have been undertaken to design a single-step means of enzymatically converting CephC to 7-ACA in the course of the past 10 years. The most suitable approach is represented by engineering the activity of a known glutaryl-7-aminocephalosporanic acid acylase such that it will bind and deacylate CephC more preferentially over glutaryl-7-aminocephalosporanic acid. Here, we describe the state of the art in the production of an effective and specific CephC acylase.

Keywords: Cephalosporin C; Protein engineering; Biocatalysis; Acylase

Significantly enhanced production of isoprene by ordered coexpression of genes dxs, dxr, and idi in Escherichia coli by Xiaomei Lv; Haoming Xu; Hongwei Yu (pp. 2357-2365).

We constructed a biosynthetic pathway of isoprene production in Escherichia coli by introducing isoprene synthase (ispS) from Populus alba. 1-deoxy-d-xylulose 5-phosphate synthase (dxs), 1-deoxy-d-xylulose 5-phosphate reductoisomerase (dxr) and isopentenyl diphosphate (IPP) isomerase (idi) were overexpressed to enhance the isoprene production. The isoprene production was improved 0.65, 0.16, and 1.22 fold over the recombinant BL21 (pET-30a-ispS), respectively, and idi was found to be a key regulating point for isoprene production. In order to optimize the production of isoprene in E. coli, we attempted to construct polycistronic operons based on pET-30a with genes dxs, dxr, and idi in various orders. The highest isoprene production yield of 2.727 mg g⁻¹ h⁻¹ (per dry weight) was achieved by E. coli transformed with pET-30a-dxs/dxr/idi. Interestingly, the gene order was found to be consistent with that of the metabolic pathway. This indicates that order of genes is a significant concern in metabolic engineering and a sequential expression pattern can be optimized according to the biosynthetic pathway for efficient product synthesis.

Keywords: Isoprene; Escherichia coli ; Biosynthesis; Ordered coexpression

Immunological features and efficacy of the reconstructed epitope vaccine CtUBE against Helicobacter pylori infection in BALB/c mice model by Le Guo; Kunmei Liu; Wenfeng Zhao; Xiaokang Li; Tong Li; Feng Tang; Rui Zhang; Wutong Wu; Tao Xi (pp. 2367-2378).

Urease is an essential virulence factor and colonization factor for Helicobacter pylori, of which the urease B subunit (UreB) is considered as an excellent vaccine candidate antigen. In previous study, an epitope vaccine with cholera toxin B subunit (CTB) and an epitope (UreB_321–339) named CtUBE was constructed and the mice were protected significantly after intragastric vaccination with the CtUBE liposome vaccine. However, the fusion protein CtUBE was expressed as inclusion bodies and was difficultly purified. Besides, the immunogenicity and specificity of the CtUBE vaccine was not investigated in a fairly wide and detailed way. In this study, the fusion peptide CtUBE was reconstructed and expressed as a soluble protein with pectinase signal peptide at the N terminus and the 6-his tag at its C-terminal, and then the immunogenicity, specificity, prophylactic, and therapeutic efficacy of the reconstructed CtUBE (rCtUBE) vaccine were evaluated in BALB/c mice model after purification. The experimental results indicated that mice immunized with rCtUBE could produce comparatively high level of specific antibodies which could respond to natural H. pylori urease, UreB, or the minimal epitope UreB_327–334 involved with the active site of urease, and showed effectively inhibitory effect on the enzymatic activity of urease. Besides, oral prophylactic or therapeutic immunization with rCtUBE significantly decreased H. pylori colonization compared with oral immunization with rCTB or PBS, and the protection was correlated with antigen-specific IgG, IgA, and mucosal sIgA antibody responses, and a Th2 cells response. This rCtUBE vaccine may be a promising vaccine candidate for the control of H. pylori infection.

Keywords: Helicobacter pylori ; Epitope vaccine; Cholera toxin B subunit; Urease B subunit; Neutralizing antibody

In vitro propagation and production of cardiotonic glycosides in shoot cultures of Digitalis purpurea L. by elicitation and precursor feeding by Jitendra Gopichand Patil; Mahendra Laxman Ahire; Kirti Manik Nitnaware; Sayantan Panda; Vijay P. Bhatt; Polavarapu B. Kavi Kishor; Tukaram Dayaram Nikam (pp. 2379-2393).

Digitalis purpurea L. (Scrophulariaceae; Foxglove) is a source of cardiotonic glycosides such as digitoxin and digoxin which are commercially applied in the treatment to strengthen cardiac diffusion and to regulate heart rhythm. This investigation deals with in vitro propagation and elicited production of cardiotonic glycosides digitoxin and digoxin in shoot cultures of D. purpurea L. In vitro germinated seedlings were used as a primary source of explants. Multiple shoot formation was achieved for three explant types (nodal, internodal, and leaf) cultured on Murashige and Skoog (MS) medium with several treatments of cytokinins (6-benzyladenine—BA; kinetin—Kin; and thidiazuron—TDZ) and auxins (indole-3-acetic acid—IAA; α-naphthaleneacetic acid—NAA; and 2,4-dichlorophenoxy acetic acid—2,4-D). Maximum multiple shoots (12.7 ± 0.6) were produced from nodal explants on MS + 7.5 μM BA. Shoots were rooted in vitro on MS containing 15 μM IAA. Rooted plantlets were successfully acclimatized. To further maintain the multiple shoot induction, mother tissue was cut into four equal parts and repeatedly sub-cultured on fresh shoot induction liquid medium after each harvest. On adaptation of this strategy, an average of 18 shoots per explant could be produced. This strategy was applied for the production of biomass and glycosides digitoxin and digoxin in shoot cultures on MS medium supplemented with 7.5 μM BA and several treatments with plant growth regulators, incubation period, abiotic (salicylic acid, mannitol, sorbitol, PEG-6000, NaCl, and KCl), biotic (Aspergillus niger, Helminthosporium sp., Alternaria sp., chitin, and yeast extract) elicitors, and precursors (progesterone, cholesterol, and squalene). The treatment of KCl, mycelial mass of Helminthosporium sp., and progesterone were highly effective for the production of cardenolides. In the presence of progesterone (200 to 300 mg/l), digitoxin and digoxin accumulation was enhanced by 9.1- and 11.9-folds respectively.

Keywords: Cardiotonic glycosides; Digitalis purpurea ; Digitoxin; Digoxin; Shoot cultures

Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution by Weiqi Fu; Ólafur Guðmundsson; Giuseppe Paglia; Gísli Herjólfsson; Ólafur S. Andrésson; Bernhard Ø. Palsson; Sigurður Brynjólfsson (pp. 2395-2403).

There is a particularly high interest to derive carotenoids such as β-carotene and lutein from higher plants and algae for the global market. It is well known that β-carotene can be overproduced in the green microalga Dunaliella salina in response to stressful light conditions. However, little is known about the effects of light quality on carotenoid metabolism, e.g., narrow spectrum red light. In this study, we present UPLC-UV-MS data from D. salina consistent with the pathway proposed for carotenoid metabolism in the green microalga Chlamydomonas reinhardtii. We have studied the effect of red light-emitting diode (LED) lighting on growth rate and biomass yield and identified the optimal photon flux for D. salina growth. We found that the major carotenoids changed in parallel to the chlorophyll b content and that red light photon stress alone at high level was not capable of upregulating carotenoid accumulation presumably due to serious photodamage. We have found that combining red LED (75 %) with blue LED (25 %) allowed growth at a higher total photon flux. Additional blue light instead of red light led to increased β-carotene and lutein accumulation, and the application of long-term iterative stress (adaptive laboratory evolution) yielded strains of D. salina with increased accumulation of carotenoids under combined blue and red light.

Keywords: Dunaliella salina ; Adaptive laboratory evolution; β-carotene and lutein; Carotenoid metabolism; LED-based photobioreactor

A new polysialic acid production process based on dual-stage pH control and fed-batch fermentation for higher yield and resulting high molecular weight product by Zhi-Yong Zheng; Shun-Zhi Wang; Guo-Shun Li; Xiao-Bei Zhan; Chi-Chung Lin; Jian-Rong Wu; Li Zhu (pp. 2405-2412).

To determine the factors influencing the resulting molecular weight of polysialic acid (PSA), batch fermentations by using Escherichia coli were conducted. It was found that temperature and pH were significant factors affecting the PSA production and its resulting molecular weight. When pH was set at 6.4, temperature of 37 °C was suitable for cell growth and PSA production while 33 °C facilitated production of higher molecular weight of PSA. pH 6.4 was favorable for PSA production while pH 7.4 was good for higher molecular weight of PSA at 37 °C. Intramolecular self-cleavage of PSA might lead to relatively low molecular weight under mild acidic condition. Our data suggest that the PSA molecular weight is significantly affected by the pH condition rather than the temperature. It is concluded that the resulting PSA molecular weight not only depends on fermentation conditions but also relates to cell growth rate and PSA production rate. Higher PSA molecular weight was made when its production rate was faster than degradation rate. A novel two-stage pH control fermentation process for production of high molecular weight PSA was developed. At the first stage, pH was set at 6.4 to encourage cell growth and PSA production, whereas pH was set at 7.4 at the second stage to promote the formation of higher molecular weight PSA. PSA yield up to 5.65 g/L and its resulting molecular weight of 260 kDa was attained, the highest level ever reported.

Keywords: Polysialic acid; Escherichia coli ; Molecular weight; Biopolymer

Strict control of auricin production in Streptomyces aureofaciens CCM 3239 involves a feedback mechanism by Peter Kutas; Lubomira Feckova; Alena Rehakova; Renata Novakova; Dagmar Homerova; Erik Mingyar; Bronislava Rezuchova; Beatrica Sevcikova; Jan Kormanec (pp. 2413-2421).

The polyketide gene cluster aur1 is responsible for the production of the angucycline antibiotic auricin in Streptomyces aureofaciens CCM 3239. Auricin production is regulated in a complex manner involving several regulators, including a key pathway-specific positive regulator Aur1P that belongs to the family of ‘atypical’ response regulators. Production of auricin is induced after entry into stationary phase. However, auricin was produced in only a short time interval of several hours. We found that the decrease of auricin production was due to a strict regulation of auricin biosynthetic genes at the transcriptional level by a feedback mechanism; auricin and/or its intermediate(s) inhibited binding of Aur1P to its cognate biosynthetic promoter aur1Ap and consequently stopped its activation. In addition, we also determined that synthesised auricin is unstable during growth of S. aureofaciens CCM3239 in the production medium even though purified auricin is stable for days in various organic solvents. The critical parameter affecting its stability was pH. Auricin is stable at acid pH and unstable at neutral and alkaline pH. The drop in auricin concentration was due to an increase of pH shortly after induction of auricin production during cultivation of S. aureofaciens CCM3239.

Keywords: Antibiotics; Auricin; Polyketide; Regulation; Secondary metabolite; Streptomyces

Biochemical analysis of a highly specific, pH stable xylanase gene identified from a bovine rumen-derived metagenomic library by X. Gong; R. J. Gruniniger; R. J. Forster; R. M. Teather; T. A. McAllister (pp. 2423-2431).

A metagenomic library was generated using microbial DNA extracted from the rumen contents of a grass hay-fed dairy cow using a bacterial artificial chromosome-based vector system. Functional screening of the library identified a gene encoding a potent glycoside hydrolase, xyn10N18, localised within a xylanolytic gene cluster consisting of four open-reading frames (ORFs). The ORF, xyn10N18, encodes an endo-β-1,4-xylanase with a glycosyl hydrolase family 10 (GH10) catalytic domain, adopts a canonical α8/ß8-fold and possesses conserved catalytic glutamate residues typical of GH10 xylanases. Xyn10N18 exhibits optimal catalytic activity at 35 °C and pH 6.5 and was highly stable to pH changes retaining at least 85 % relative catalytic activity over a broad pH range (4.0–12.0). It retained 25 % of its relative activity at both low (4 °C) and high (55 °C) temperatures, however the stability of the enzyme rapidly decreased at temperatures of >40 °C. The specific activity of Xyn10N18 is enhanced by the divalent cations Mn²⁺ and Co²⁺ and is dramatically reduced by Hg²⁺ and Cu²⁺. Interestingly, EDTA had little effect on specific activity indicating that divalent cations do not function mechanistically. The enzyme was highly specific for xylan containing substrates and showed no catalytic activity against cellulose. Analysis of the hydrolysis products indicated that Xyn10N18 was an endoxylanase. Through a combination of structural modelling and in vitro enzyme characterisation this study provides an understanding of the mechanism and the substrate specificity of this enzyme serving as a starting point for directed evolution of Xyn10N18 and subsequent downstream use in industry.

Keywords: Xylanase; Cow ruminal microorganisms; BAC library; Glycosyl hydrolase (GH) 10; Biobleaching

Purification and characterization of a cis-epoxysuccinic acid hydrolase from Nocardia tartaricans CAS-52, and expression in Escherichia coli by Ziqiang Wang; Yunshan Wang; Zhiguo Su (pp. 2433-2441).

A highly enantioselective cis-epoxysuccinic acid hydrolase from Nocardia tartaricans was purified to electrophoretic homogeneity. The enzyme was purified 184-fold with a yield of 18.8 %. The purified cis-epoxysuccinic acid hydrolase had a monomeric molecular weight of 28 kDa, and its optimum conditions were 37 °C and pH 7–9. With sodium cis-epoxysuccinate as the substrate, Michaelis–Menten enzyme kinetics analysis gave a Km value of 35.71 mM and a Vmax of 2.65 mM min⁻¹. The enzyme was activated by Ni²⁺ and Al³⁺, while strongly inhibited by Fe³⁺, Fe²⁺, Cu²⁺, and Ag⁺. The cis-epoxysuccinic acid hydrolase gene was cloned, and its open reading frame sequence predicted a protein composed of 253 amino acids. A pET11a expression plasmid carrying the gene under the control of the T7 promoter was introduced into Escherichia coli, and the cis-epoxysuccinic acid hydrolase gene was successfully expressed in the recombinant strains.

Keywords: Cis-epoxysuccinic acid hydrolase; Nocardia tartaricans ; Prokaryotic expression; Enantioselectivity

Characterization of an extracellular lipase and its chaperone from Ralstonia eutropha H16 by Jingnan Lu; Christopher J. Brigham; ChoKyun Rha; Anthony J. Sinskey (pp. 2443-2454).

Lipase enzymes catalyze the reversible hydrolysis of triacylglycerol to fatty acids and glycerol at the lipid–water interface. The metabolically versatile Ralstonia eutropha strain H16 is capable of utilizing various molecules containing long carbon chains such as plant oil, organic acids, or Tween as its sole carbon source for growth. Global gene expression analysis revealed an upregulation of two putative lipase genes during growth on trioleate. Through analysis of growth and activity using strains with gene deletions and complementations, the extracellular lipase (encoded by the lipA gene, locus tag H16_A1322) and lipase-specific chaperone (encoded by the lipB gene, locus tag H16_A1323) produced by R. eutropha H16 was identified. Increase in gene dosage of lipA not only resulted in an increase of the extracellular lipase activity, but also reduced the lag phase during growth on palm oil. LipA is a non-specific lipase that can completely hydrolyze triacylglycerol into its corresponding free fatty acids and glycerol. Although LipA is active over a temperature range from 10 °C to 70 °C, it exhibited optimal activity at 50 °C. While R. eutropha H16 prefers a growth pH of 6.8, its extracellular lipase LipA is most active between pH 7 and 8. Cofactors are not required for lipase activity; however, EDTA and EGTA inhibited LipA activity by 83 %. Metal ions Mg²⁺, Ca²⁺, and Mn²⁺ were found to stimulate LipA activity and relieve chelator inhibition. Certain detergents are found to improve solubility of the lipid substrate or increase lipase-lipid aggregation, as a result SDS and Triton X-100 were able to increase lipase activity by 20 % to 500 %. R. eutropha extracellular LipA activity can be hyper-increased, making the overexpression strain a potential candidate for commercial lipase production or in fermentations using plant oils as the sole carbon source.

Keywords: Ralstonia eutropha ; Lipase; Chaperone; Triacylglycerol; Palm oil; Emulsification

In vitro rapid evolution of fungal immunomodulatory proteins by DNA family shuffling by Xue-Fei Wang; Qi-Zhang Li; Ting-Wen Bao; Wei-Ran Cong; Wen-Xia Song; Xuan-Wei Zhou (pp. 2455-2465).

Fungal immunomodulatory proteins (FIPs) found in a wide variety of mushrooms hold significant therapeutic potential. Despite much research, the structural determinants for their immunomodulatory functions remain unknown. In this study, a DNA shuffling technique was used to create two shuffled FIP protein libraries: an intrageneric group containing products of shuffling between FIP-glu (FIP gene isolated from Ganoderma lucidum) and FIP-gsi (FIP gene isolated from Ganoderma sinense) genes and an intergeneric group containing the products of shuffling between FIP-glu, FIP-fve (FIP gene isolated from Flammulina velutipes), and FIP-vvo (FIP gene isolated from Volvariella volvacea) genes. The gene shuffling generated 426 and 412 recombinant clones, respectively. Using colony blot analysis, we selected clones that expressed relatively high levels of shuffled gene products recognized by specific polyclonal antibodies. We analyzed the DNA sequences of the selected shuffled genes, and testing of their protein products revealed that they maintained functional abilities to agglutinate blood cells and induce cytokine production by splenocytes from Kunming mice in vitro. Meanwhile, the relationships between protein structure and the hemagglutination activity and between the changed nucleotide sites and expression levels were explored by bioinformatic analysis. These combined analyses identified the nucleotide changes involved in regulating the expression levels and hemagglutination activities of the FIPs. Therefore, we were able to generate recombinant FIPs with improved biological activities and expression levels by using DNA shuffling, a powerful tool for the generation of novel therapeutic proteins and for their structural and functional studies.

Keywords: Shuffling; Screen; Colony blot; Hemagglutination; Cytokine

l-Leucine 5-hydroxylase of Nostoc punctiforme is a novel type of Fe(II)/α-ketoglutarate-dependent dioxygenase that is useful as a biocatalyst by Makoto Hibi; Takashi Kawashima; Pavel M. Sokolov; Sergey V. Smirnov; Tomohiro Kodera; Masakazu Sugiyama; Sakayu Shimizu; Kenzo Yokozeki; Jun Ogawa (pp. 2467-2472).

l-Leucine 5-hydroxylase (LdoA) previously found in Nostoc punctiforme PCC 73102 is a novel type of Fe(II)/α-ketoglutarate-dependent dioxygenase. LdoA catalyzed regio- and stereoselective hydroxylation of l-leucine and l-norleucine into (2S,4S)-5-hydroxyleucine and (2S)-5-hydroxynorleucine, respectively. Moreover, LdoA catalyzed sulfoxidation of l-methionine and l-ethionine in the same manner as previously described l-isoleucine 4-hydroxylase. Therefore LdoA should be a promising biocatalyst for effective production of industrially useful amino acids.

Keywords: l-Leucine 5-hydroxylase; Fe(II)/α-ketoglutarate-dependent dioxygenase; (2S,4S)-5-Hydroxyleucine; (2S)-5-Hydroxynorleucine; Nostocyclopeptide

Engineering of formate dehydrogenase: synergistic effect of mutations affecting cofactor specificity and chemical stability by Kathrin Hoelsch; Ilka Sührer; Moritz Heusel; Dirk Weuster-Botz (pp. 2473-2481).

Formate dehydrogenases (FDHs) are frequently used for the regeneration of cofactors in biotransformations employing NAD(P)H-dependent oxidoreductases. Major drawbacks of most native FDHs are their strong preference for NAD⁺ and their low operational stability in the presence of reactive organic compounds such as α-haloketones. In this study, the FDH from Mycobacterium vaccae N10 (MycFDH) was engineered in order to obtain an enzyme that is not only capable of regenerating NADPH but also stable toward the α-haloketone ethyl 4-chloroacetoacetate (ECAA). To change the cofactor specificity, amino acids in the conserved NAD⁺ binding motif were mutated. Among these mutants, MycFDH A198G/D221Q had the highest catalytic efficiency (k _cat/K _m) with NADP⁺. The additional replacement of two cysteines (C145S/C255V) not only conferred a high resistance to ECAA but also enhanced the catalytic efficiency 6-fold. The resulting quadruple mutant MycFDH C145S/A198G/D221Q/C255V had a specific activity of 4.00 ± 0.13 U mg⁻¹ and a K _{m, NADP} ⁺ of 0.147 ± 0.020 mM at 30 °C, pH 7. The A198G replacement had a major impact on the kinetic constants of the enzyme. The corresponding triple mutant, MycFDH C145S/D221Q/C255V, showed the highest specific activity reported to date for a NADP⁺-accepting FDH (v _max, 10.25 ± 1.63 U mg⁻¹). However, the half-saturation constant for NADP⁺ (K _{m, NADP} ⁺ , 0.92 ± 0.10 mM) was about one order of magnitude higher than the one of the quadruple mutant. Depending on the reaction setup, both novel MycFDH variants could be useful for the production of the chiral synthon ethyl (S)-4-chloro-3-hydroxybutyrate [(S)-ECHB] by asymmetric reduction of ECAA with NADPH-dependent ketoreductases.

Keywords: Asymmetric synthesis; Biocatalysis; Cofactor regeneration; Formate dehydrogenase; Protein engineering

Cloning of a dibutyl phthalate hydrolase gene from Acinetobacter sp. strain M673 and functional analysis of its expression product in Escherichia coli by Jun Wu; Xuewei Liao; Fangbo Yu; Zhongbo Wei; Liuyan Yang (pp. 2483-2491).

A dibutyl phthalate (DBP) transforming bacterium, strain M673, was isolated and identified as Acinetobacter sp. This strain could not grow on dialkyl phthalates, including dimethyl, diethyl, dipropyl, dibutyl, dipentyl, dihexyl, di(2-ethylhexyl), di-n-octyl, and dinonyl phthalate, but suspensions of cells could transform these compounds to phthalate via corresponding monoalkyl phthalates. During growth in Luria–Bertani medium, M673 produced the high amounts of non-DBP-induced intracellular hydrolase in the stationary phase. One DBP hydrolase gene containing an open reading frame of 1,095 bp was screened from a genomic library, and its expression product hydrolyzed various dialkyl phthalates to the corresponding monoalkyl phthalates.

Keywords: Dibutyl phthalate (DBP); Transformation; Acinetobacter sp.; DBP hydrolase gene

Exploration of two epimerase homologs in Streptomyces peucetius ATCC 27952 by Bijay Singh; Tae Jin Oh; Jae Kyung Sohng (pp. 2493-2502).

Streptomyces peucetius ATCC 27952 is a potent producer of the therapeutically important antitumor drug, doxorubicin. S. peucetius contains two deoxythymidine diphospho (dTDP)-4-keto-6-deoxyglucose 3,5-epimerase-encoding genes, dnmU and rmbC, in its genome. While dnmU from the doxorubicin biosynthesis gene cluster is involved in the biosynthesis of dTDP-l-daunosamine, rmbC is involved in the biosynthesis of dTDP-l-rhamnose, a precursor of cell wall biosynthesis. The proteins encoded by dnmU and rmbC share 47 % identity and 64 % similarity with each other. Both enzymes converted the same substrate, dTDP-4-keto-6-deoxy-d-glucose, into dTDP-4-keto-l-rhamnose in vitro. However, when disruption of dnmU or rmbC was carried out, neither gene in S. peucetius compensated for each other’s loss of function in vivo. These results demonstrated that although dnmU and rmbC encode for similar functional proteins, their native roles in their respective biosynthetic pathways in vivo are specific and independent of one other. Moreover, the disruption of rmbC resulted in fragmented mycelia that quickly converted into gray pigmented spores. Additionally, the production of doxorubicin, a major product of S. peucetius, appeared to be abolished after the disruption of rmbC, demonstrating its pleiotropic effect. This adverse effect might have switched on the genes encoding for spore formation, arresting the expression of many genes and, thereby, preventing the production of other metabolites.

Keywords: Streptomyces peucetius ; dTDP-4-keto-6-deoxyglucose 3,5-epimerase gene; Sporulation; Doxorubicin

Alginate synthesis in Azotobacter vinelandii is increased by reducing the intracellular production of ubiquinone by Cinthia Núñez; Carlos Peña; Wolf Kloeckner; Alberto Hernández-Eligio; Alexander V. Bogachev; Soledad Moreno; Josefina Guzmán; Jochen Büchs; Guadalupe Espín (pp. 2503-2512).

Azotobacter vinelandii, a soil nitrogen fixing bacterium, produces alginate a polysaccharide with industrial and medical relevant applications. In this work, we characterized a miniTn5 mutant, named GG101, that showed a 14-fold increase in the specific production of alginate when grown diazotrophically on solid minimal medium comparing to the parental E strain (also named AEIV). Quantitative real-time reverse transcription PCR analysis indicated that this increased alginate production was due to higher expression levels of several biosynthetic alg genes such as algD. Sequencing of the locus interrupted in GG101 indicated that the miniTn5 was inserted in the positive strand, and 10 bp upstream the start codon of the gene ubiA, encoding the enzyme for the second step in the biosynthesis of ubiquinone (Q₈). Both the transcription of ubiA and the content of Q₈ are decreased in the mutant GG101 when compared to the wild-type strain E. Genetic complementation of mutant GG101 with a wild-type copy of the ubiCA genes restored the content of Q₈ and reduced the production of alginate to levels similar to those of the parental E strain. Furthermore, respirometric analysis showed a reproducible decrease of about 8 % in the respiratory capacity of mutant GG101, at exponential phase of growth in liquid minimal medium. Collectively, our data show that a decreased content in Q₈ results in higher levels of alginate in A. vinelandii.

Keywords: Azotobacter vinelandii ; Alginate; Ubiquinone; algD expression; Gene regulation; Respirometric analysis

Recruiting alternative glucose utilization pathways for improving succinate production by Jinlei Tang; Xinna Zhu; Jiao Lu; Pingping Liu; Hongtao Xu; Zaigao Tan; Xueli Zhang (pp. 2513-2520).

The phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) of Escherichia coli was usually inactivated to increase PEP supply for succinate production. However, cell growth and glucose utilization rate decreased significantly with PTS inactivation. In this work, two glucose transport proteins and two glucokinases (Glk) from E. coli and Zymomonas mobilis were recruited in PTS⁻ strains, and their impacts on glucose utilization and succinate production were compared. All PTS⁻ strains recruiting Z. mobilis glucose facilitator Glf had higher glucose utilization rates than PTS⁻ strains using E. coli galactose permease (GalP), which was suggested to be caused by higher glucose transport velocity and lower energetic cost of Glf. The highest rate obtained by combinatorial modulation of glf and glk E. coli (2.13 g/L•h) was 81 % higher than the wild-type E. coli and 30 % higher than the highest rate obtained by combinatorial modulation of galP and glk E. coli. On the other hand, although glucokinase activities increased after replacing E. coli Glk with isoenzyme of Z. mobilis, glucose utilization rate decreased to 0.58 g/L•h, which was assumed due to tight regulation of Z. mobilis Glk by energy status of the cells. For succinate production, using GalP led to a 20 % increase in succinate productivity, while recruiting Glf led to a 41 % increase. These efficient alternative glucose utilization pathways obtained in this work can also be used for production of many other PEP-derived chemicals, such as malate, fumarate, and aromatic compounds.

Keywords: Glucose utilization; PTS; Succinate; Galactose permease; Glucose facilitator; Escherichia coli

Deletion of pyruvate decarboxylase by a new method for efficient markerless gene deletions in Gluconobacter oxydans by Björn Peters; Anja Junker; Katharina Brauer; Bernadette Mühlthaler; David Kostner; Markus Mientus; Wolfgang Liebl; Armin Ehrenreich (pp. 2521-2530).

Gluconobacter oxydans, a biotechnologically relevant species which incompletely oxidizes a large variety of carbohydrates, alcohols, and related compounds, contains a gene for pyruvate decarboxylase (PDC). This enzyme is found only in very few species of bacteria where it is normally involved in anaerobic ethanol formation via acetaldehyde. In order to clarify the role of PDC in the strictly oxidative metabolism of acetic acid bacteria, we developed a markerless in-frame deletion system for strain G. oxydans 621H which uses 5-fluorouracil together with a plasmid-encoded uracil phosphoribosyltransferase as counter selection method and used this technique to delete the PDC gene (GOX1081) of G. oxydans 621H. The PDC deletion mutant accumulated large amounts of pyruvate but almost no acetate during growth on d-mannitol, d-fructose or in the presence of l-lactate. This suggested that in G. oxydans acetate formation occurs by decarboxylation of pyruvate and subsequent oxidation of acetaldehyde to acetate. This observation and the efficiency of the markerless deletion system were confirmed by constructing deletion mutants of two acetaldehyde dehydrogenases (GOX1122 and GOX2018) and of the acetyl-CoA-synthetase (GOX0412). Acetate formation during growth of these mutants on mannitol did not differ significantly from the wild-type strain.

Keywords: Gluconobacter oxydans ; Acetic acid bacteria; Uracil phosphoribosyltransferase; Markerless deletion; Pyruvate decarboxylase; Acetate metabolism

Overexpression of CHOP alone and in combination with chaperones is effective in improving antibody production in mammalian cells by Daisuke Nishimiya; Takashi Mano; Kenji Miyadai; Hiroko Yoshida; Tohru Takahashi (pp. 2531-2539).

Secretory capacities including folding and assembly are believed to be limiting factors in the establishment of mammalian cell lines producing high levels of recombinant therapeutic proteins. To achieve industrial success, it is also important to improve protein folding, assembly, and secretory processes in combination with increasing transcription and translation. Here, we identified the expression of CHOP/Gadd153 and GRP78, which are unfolded protein response (UPR)-related genes, correlated with recombinant antibody production in stable CHO cells. Subsequently, CHOP overexpression resulted in increasing recombinant antibody production in some mammalian cell lines, and in addition a threefold further enhancement was obtained by combining expression with UPR-related genes or ER chaperones in transient assays. Overexpression of CHOP had no effect on the biochemical characteristics of the product. These results suggest overexpression of CHOP and its combinations may be an effective method to efficiently select a single cell line with a high level of antibody production in the development of cell lines for manufacturing.

Keywords: Antibody production; UPR; ER chaperone; CHOP

Characterization of the diatomite binding domain in the ribosomal protein L2 from E. coli and functions as an affinity tag by Junhua Li; Yang Zhang; Yanjun Yang (pp. 2541-2549).

The ribosomal protein L2, a constituent protein of the 50S large ribosomal subunit, can be used as Si-tag using silica particles for the immobilization and purification of recombinant proteins (Ikeda et al. (Protein Expr Purif 71:91–95, 2010); Taniguchi et al. (Biotechnol Bioeng 96:1023–1029, 2007)). We applied a diatomite powder, a sedimentary rock mainly composed with diatoms silica, as an affinity solid phase and small ubiquitin-like modifier (SUMO) technology to release a target protein from the solid phase. The L2 (203–273) was the sufficient region for the adsorption of ribosomal protein L2 on diatomite. We comparatively analyzed the different adsorption properties of the two deleted proteins of L2 (L2 (1–60, 203–273) and L2 (203–273)) on diatomite. The time required to reach adsorption equilibrium of L2 (203–273) fusion protein on diatomite was shorter than that of L2 (1–60, 203–273) fusion protein. The maximum adsorption capacity of L2 (203–273) fusion protein was larger than that of L2 (1–60, 203–273) fusion protein. In order to study whether the L2 (203–273) can function as an affinity purification tag, SUMO was introduced as one specific protease cleavage site between the target protein and the purification tags. The L2 (203–273) and SUMO fusion protein purification method was tested using enhanced green fluorescent protein as a model protein; the result shows that the purification performance of this affinity purification method was good. The strong adsorption characteristic of L2 (203–273) on diatomite also provides a potential protein fusion tag for the immobilization of enzyme.

Keywords: Affinity adsorption; Diatomite; Ribosomal protein L2; Small ubiquitin-related modifier; Enhanced green fluorescence protein

The thioredoxin reductase-encoding gene ActrxR1 is involved in the cephalosporin C production of Acremonium chrysogenum in methionine-supplemented medium by Li Liu; Liang-Kun Long; Yang An; Jing Yang; Xinxin Xu; Chang-hua Hu; Gang Liu (pp. 2551-2562).

The thioredoxin system including thioredoxin and thioredoxin reductase (TrxR) is used for oxidative stress defenses in fungi. Based on the genomic sequence, a thioredoxin reductase-encoding gene (ActrxR1) was isolated from Acremonium chrysogenum CGMCC3.3795. Like other TrxRs, AcTrxR1 contains FAD binding domain, Redox domain, and NADPH binding domain. Disruption of ActrxR1 in A. chrysogenum led to the formation of smaller colonies and hyphal swelling in Tryptic soy agar (TSA). In chemically defined medium, the spore germination of ActrxR1 disruption mutant was strongly inhibited, which was recovered by the addition of dl-methionine. The disruption mutant grew slowly on TSA compared with the wild-type strain, but it did not show to be more sensitive to exogenous hydrogen peroxide or menadione. In defined medium of fermentation supplemented with dl-methionine, the ActrxR1 disruption mutant grew normally, and its cephalosporin C production increased by about onefold compared with the wild type (73 μg/ml for wild-type strain and 136 μg/ml for the mutant at 5 days of fermentation). Real-time polymerase chain reaction (RT-PCR) showed that the transcriptional levels of pcbC, cefEF, and cefG were obviously enhanced in the ActrxR1 mutant at the early stage of fermentation. These results indicate that ActrxR1 is required for the normal growth of A. chrysogenum and related with cephalosporin C production in methionine-supplemented medium.

Keywords: Acremonium chrysogenum ; Thioredoxin reductase gene; Morphological differentiation; Cephalosporin C production; Methionine

Effect of combined oxidative and nitrosative stresses on Staphylococcus aureus transcriptome by Lígia S. Nobre; Lígia M. Saraiva (pp. 2563-2573).

Staphylococcus aureus is a pathogen responsible for severe community- and nosocomially acquired infections. To fight pathogen intrusion, the innate immune system uses a plethora of weapons, with the generation of oxidative and nitrosative stresses among the most efficient. In this work, the S. aureus genome-wide transcriptional responses to oxidative stress generated by hydrogen peroxide, to nitrosative stress imposed by S-nitrosoglutathione (GSNO), and to the combination of the two were investigated using microarray analysis. The results showed that these stresses have a significant impact on the transcriptome of S. aureus. Hydrogen peroxide modified mainly the mRNA abundance of genes involved in oxidative detoxification and DNA metabolism, which together represent 14 % of the total number of upregulated genes. GSNO caused significant alteration of the expression of gene products with regulatory function. However, the simultaneous addition of GSNO and hydrogen peroxide was found to cause the more significant transcriptomic alteration, affecting ∼10 % of the total transcriptome. In particular, exposure of S. aureus to GSNO plus hydrogen peroxide modified the transcription of genes associated with cell envelope and iron metabolism, including induction of ftnA and dps genes that encode iron-storage and oxidative-protecting proteins. Further studies revealed that when exposed to combined GSNO–hydrogen peroxide stresses, S. aureus has decreased viability, which is enhanced in the presence of iron, and low siderophore activity. Altogether, this study revealed, for the first time, how the combined oxidative and nitrosative stresses inflicted during phagocytosis interfere at the transcriptional level with the S. aureus cellular metabolism.

Keywords: Staphylococcus aureus ; Transcriptome; Oxidative stress; Nitrosative stress

Role of alternative sigma factor 54 (RpoN) from Vibrio anguillarum M3 in protease secretion, exopolysaccharide production, biofilm formation, and virulence by Bin Hao; Zhao-Lan Mo; Peng Xiao; Hai-Jian Pan; Xin Lan; Gui-Yang Li (pp. 2575-2585).

The sigma factor σ⁵⁴ (RpoN) is an important regulator of bacterial response to environmental stresses. Here, we demonstrate the roles of RpoN in Vibrio anguillarum M3 by comparative investigation of physiological phenotypes and virulence of the wild-type, an rpoN mutant, and an rpoN complemented strain. Disruption of rpoN was found to decrease biofilm formation, production of exopolysaccharides, and production of the metalloproteases EmpA and PrtV. Injection experiments in fish showed that the M3 ΔrpoN mutant was attenuated in virulence when administrated either by intramuscular injection or by immersion challenge. Slower proliferation of the mutant in fish was also observed. Complementation of the mutant strain with rpoN restored some of the phenotypes to wild-type levels. RpoN was involved in regulation of some virulence-associated genes, as shown by real-time quantitative reverse PCR analysis. These results revealed a pleiotropic regulatory role of RpoN in biofilm formation, production of proteases and exopolysaccharides, and virulence in V. anguillarum M3.

Keywords: Vibrio anguillarum ; RpoN (σ⁵⁴); Biofilm; Exopolysaccharides; Metalloproteases; Virulence

The EmhABC efflux pump in Pseudomonas fluorescens LP6a is involved in naphthalene tolerance but not efflux by Abigail A. Adebusuyi; Julia M. Foght (pp. 2587-2596).

The EmhABC efflux pump in Pseudomonas fluorescens LP6a effluxes polycyclic aromatic hydrocarbons (PAHs) such as phenanthrene and anthracene but not naphthalene. We previously showed that the presence of EmhABC decreased the efficiency of phenanthrene biodegradation. In this study, we determined whether P. fluorescens LP6a tolerance to naphthalene is a function of the EmhABC efflux pump and how its presence affects the efficiency of naphthalene biodegradation. Growth, membrane fatty acid (FA) composition, and cell morphology showed that 5-mmol L⁻¹ naphthalene is inhibitory to P. fluorescens LP6a strains. The deleterious effect of naphthalene is suppressed in the presence of EmhABC, which suggests that, although naphthalene is not effluxed by EmhABC, this efflux pump is involved in tolerance of naphthalene toxicity. LP6a mutants lacking the EmhB efflux pump were unable to convert cis-unsaturated FAs to cyclopropane FAs, indicating that naphthalene interferes with the formation of cyclopropane FAs and supporting the proposal that EmhABC is involved in FA turnover in P. fluorescens LP6a strains. The EmhABC efflux pump increases the efficiency of naphthalene metabolism in strain LP6a, which may make naphthalene efflux unnecessary. Thus, the activity of hydrocarbon efflux pumps may be an important factor to consider when selecting bacterial strains for bioremediation or biocatalysis of PAHs.

Keywords: RND efflux pump; Membrane modification; Biodegradation; Polycyclic aromatic hydrocarbons; Pseudomonas fluorescens ; Cyclopropane fatty acids

Reduction of furan derivatives by overexpressing NADH-dependent Adh1 improves ethanol fermentation using xylose as sole carbon source with Saccharomyces cerevisiae harboring XR–XDH pathway by Jun Ishii; Kazuya Yoshimura; Tomohisa Hasunuma; Akihiko Kondo (pp. 2597-2607).

Several alcohol dehydrogenase (ADH)-related genes have been identified as enzymes for reducing levels of toxic compounds, such as, furfural and/or 5-hydroxymethylfurfural (5-HMF), in hydrolysates of pretreated lignocelluloses. To date, overexpression of these ADH genes in yeast cells have aided ethanol production from glucose or glucose/xylose mixture in the presence of furfural or 5-HMF. However, the effects of these ADH isozymes on ethanol production from xylose as a sole carbon source remain uncertain. We showed that overexpression of mutant NADH-dependent ADH1 derived from TMB3000 strain in the recombinant Saccharomyces cerevisiae, into which xylose reductase (XR) and xylitol dehydrogenase (XDH) pathway of Pichia stipitis has been introduced, improved ethanol production from xylose as a sole carbon source in the presence of 5-HMF. Enhanced furan-reducing activity is able to regenerate NAD⁺ to relieve redox imbalance, resulting in increased ethanol yield arising from decreased xylitol accumulation. In addition, we found that overexpression of wild-type ADH1 prevented the more severe inhibitory effects of furfural in xylose fermentation as well as overexpression of TMB3000-derived mutant. After 120 h of fermentation, the recombinant strains overexpressing wild-type and mutant ADH1 completely consumed 50 g/L xylose in the presence of 40 mM furfural and most efficiently produced ethanol (15.70 g/L and 15.24 g/L) when compared with any other test conditions. This is the first report describing the improvement of ethanol production from xylose as the sole carbon source in the presence of furan derivatives with xylose-utilizing recombinant yeast strains via the overexpression of ADH-related genes.

Keywords: Ethanol; Xylose fermentation; Furfural; 5-Hydroxymethylfurfural; Redox imbalance; Saccharomyces cerevisiae

Bioresolution of (R)-glycidyl azide by Aspergillus niger ZJUTZQ208: a new and concise synthon for chiral vicinal amino alcohols by Lin Chen; Honglei Shen; Chun Wei; Qing Zhu (pp. 2609-2616).

A newly isolated Aspergillus niger strain containing epoxide hydrolase was used to resolve racemic glycidyl azide and four derivatives to the (R)-enantiomers. After optimization of the biotransformation conditions, (R)-glycidyl azide was produced with good enantioselectivity (e.e._s > 95 %, E > 20). The substrate structure, pH, and reaction time were found to have profound influences on the catalytic property of A. niger ZJUTZQ208. Enantiopure glycidyl azide was further utilized to synthesize linezolid in good yield, indicating it is a new and concise synthon for chiral vicinal amino alcohols. Enzyme–substrate docking studies were carried out with glycidyl azide to study the selectivity of this strain.

Keywords: Aspergillus niger ; Enantioselective; Epoxide hydrolase; Glycidyl azide; Docking study

Impact of dissolved hydrogen partial pressure on mixed culture fermentations by Stefan de Kok; Jasper Meijer; Mark C. M. van Loosdrecht; Robbert Kleerebezem (pp. 2617-2625).

Mixed culture fermentations are of interest for the low-cost production of organic acids from complex agricultural waste streams. Models are developed for these processes in order to predict the product spectrum as a function of the environmental process conditions. An important assumption in many existing models for anaerobic mixed culture fermentations is that the NADH/NAD⁺ ratio is directly coupled to the dissolved hydrogen partial pressure (pH_{2, liquid}). In this study, this assumption was tested experimentally with mixed culture chemostats operated at dilution rates of 0.05 and 0.125 h⁻¹ for a wide range of calculated dissolved hydrogen partial pressures (0.04–6.8 atm). No correlation was found between pH_{2, liquid} and the NADH/NAD⁺ ratio. This result, together with thermodynamic calculations, suggests that additional electron carriers such as ferredoxin and formate should be included in models predicting product formation by mixed cultures.

Keywords: Mixed culture fermentation; Intracellular metabolites; NADH/NAD⁺ ratio; Thermodynamics; Ferredoxin; Formate

AI-2 analogs and antibiotics: a synergistic approach to reduce bacterial biofilms by Varnika Roy; Mariana T. Meyer; Jacqueline A. I. Smith; Sonja Gamby; Herman O. Sintim; Reza Ghodssi; William E. Bentley (pp. 2627-2638).

Quorum sensing (QS), the process of autoinducer-mediated cell–cell signaling among bacteria, facilitates biofilm formation, virulence, and many other multicellular phenotypes. QS inhibitors are being investigated as antimicrobials because of their potential to reduce symptoms of infectious disease while slowing the emergence of resistant strains. Autoinducer-2 (AI-2) analogs have been shown to inhibit genotypic QS responses among many bacteria. We demonstrate for the first time, the ability of C1-alkyl AI-2 analog, isobutyl-DPD, to significantly inhibit the maturation of Escherichia coli biofilms grown in vitro. Using a novel microfluidic device that incorporates dynamic, real-time measurements of biofilm density, we also show that a combinatorial approach wherein isobutyl-DPD ((S)-4,5-dihydroxy-2,3-pentanedione) is used with the antibiotic gentamicin is quite effective in rendering near complete clearance of pre-existing E. coli biofilms. Similarly, another AI-2 analog, phenyl-DPD, also used in combination with near MIC levels of gentamicin, resulted in clearance of preformed Pseudomonas aeruginosa biofilms. Clearance of pre-existing biofilms has remained a significant health care challenge; these results warrant consideration of a new approach based on the combination of “quenching” QS signal transduction processes with traditional antibiotic treatment.

Keywords: AI-2; Biofilms; Quorum quenching; Quorum sensing

Bacillus subtilis and Enterobacter cloacae endophytes from healthy Theobroma cacao L. trees can systemically colonize seedlings and promote growth by Hianna Almeida Câmara Leite; Anderson Barbosa Silva; Fábio Pinto Gomes; Karina Peres Gramacho; José Cláudio Faria; Jorge Teodoro de Souza; Leandro Lopes Loguercio (pp. 2639-2651).

Clonal genotypes resistant to fungal diseases are an important component of the cocoa production system in southeastern Bahia state (Brazil), so that technologies for faster production of stronger and healthier plantlets are highly desirable. In this study, the effects of inoculated bacterial endophytes isolated from healthy adult cacao plants on seedlings, and aspects related to inoculation methods, colonization patterns, and photosynthesis were investigated. Sequencing of 16S rRNA, hsp-60, and rpo-B genes placed the wild-type isolates within the species Enterobacter cloacae (isolates 341 and 344) and Bacillus subtilis (isolate 629). Spontaneous rifampicin-resistant (rif^R) variants for 344 were also produced and tested. Endophytic application was either by immersion of surface sterilized seeds in bacterial suspensions or direct inoculation into soil, 20 days after planting non-inoculated seeds into pots. Results from in vitro recovery of inoculated isolates showed that the wild-type endophytes and rif^R variants systemically colonized the entire cacao seedlings in 15–20 days, regardless of the inoculation method. Some endophytic treatments showed significant increases in seedlings’ height, number of leaves, and dry matter. Inoculation methods affected the combined application of endophytes, which maintained the growth-promotion effects, but not in the same manner as in single applications. Interestingly, the 344-3.2 rif^R variant showed improved performance in relation to both the wild type and another related variant. Photosynthetic rates and stomatal conductance increased significantly for some endophytic treatments, being partially associated with effects on growth and affected by the inoculation method. The results suggest that E. cloacae and B. subtilis endophytes from healthy adult plants (not transmitted by seeds) were able to promote vegetative growth on cacao seedlings. The development of products for large-scale use in seedlings/plantlets production systems was discussed.

Keywords: Endophytic colonization; Hologenome theory; Holobiont; Enterobacteriaceae; Nurseries production; PGPR; Plant growth promotion; Seedlings; Spore forming

Screening soy hydrolysates for the production of a recombinant therapeutic protein in commercial cell line by combined approach of near-infrared spectroscopy and chemometrics by Guiyang Li; Zai-qing Wen (pp. 2653-2660).

Soy hydrolysates are widely used as the major nutrient sources for cell culture processes for industrial manufacturing of therapeutic recombinant proteins. The primary goal of this study was to develop a spectroscopy based chemometric method, a partial least squares (PLS), to screen soy hydrolysates for better yield of protein production (titers) in cell culture medium. Harvest titer values of 29 soy hydrolysate lots with production yield between 490 and 1,350 mg/L were obtained from shake flask models or from manufacture engineering runs. The soy hydrolysate samples were measured by near-infrared (NIR) in reflectance mode using an infrared fiber optic probe. The fiber optic probe could easily enable in situ measurement of the soy hydrolysates for convenient raw material screening. The best PLS calibration has a determination coefficient of R ² = 0.887 utilizing no spectral preprocessing, the two spectral ranges of 10,000–5,376 cm⁻¹ and 4,980–4,484 cm⁻¹, and a rank of 6 factors. The cross-validation of the model resulted in a determination coefficient of R ² = 0.741 between the predicted and actual titer values with an average standard deviation of 72 mg/L. Compared with the resource demanding shake flask model, the combination of NIR and chemometric modeling provides a convenient method for soy hydrolysate screening with the advantage of fast speed, low cost and non-destructive.

Keywords: Near-infrared spectroscopy; Chemometrics; Soy hydrolysates; Commercial cell line; Harvest titer; Therapeutic protein

Dynamic chromatin remodelling of ciliate macronuclear DNA as determined by an optimized chromatin immunoprecipitation (ChIP) method for Paramecium tetraurelia by Miriam Cheaib; Martin Simon (pp. 2661-2670).

We report the detailed evaluation of crucial parameters for chromatin immunoprecipitation (ChIP) of macronuclear DNA in the unicellular eukaryote Paramecium tetraurelia. Optimized parameters include crosslinking conditions, chromatin sonication and antibody titration thus providing a detailed protocol for successful ChIP in P. tetraurelia. As this ciliate is bacterivorous and RNAi by feeding represents a powerful tool for analysis of gene function, we moreover determined the effects of ingested nucleic acids by food bacteria. Feasibility of our protocol is demonstrated by characterisation of chromatin remodelling at promoters of cytosolic HSP70 isoforms during transcriptional activation under heat shock conditions by analyzing RNA abundance, nucleosome occupancy and levels of H3 lysine 9 acetylation.

Keywords: Post-translational histone modifications; Ciliate; Heat shock protein; HSP70

Kinetics during the redox biotransformation of pollutants mediated by immobilized and soluble humic acids by Francisco J. Cervantes; Claudia M. Martínez; Jorge Gonzalez-Estrella; Arturo Márquez; Sonia Arriaga (pp. 2671-2679).

The aim of this study was to elucidate the kinetic constraints during the redox biotransformation of the azo dye, Reactive Red 2 (RR2), and carbon tetrachloride (CT) mediated by soluble humic acids (HA_s) and immobilized humic acids (HA_i), as well as by the quinoid model compounds, anthraquinone-2,6-disulfonate (AQDS) and 1,2-naphthoquinone-4-sulfonate (NQS). The microbial reduction of both HA_s and HA_i by anaerobic granular sludge (AGS) was the rate-limiting step during decolorization of RR2 since the reduction of RR2 by reduced HA_i proceeded at more than three orders of magnitute faster than the electron-transferring rate observed during the microbial reduction of HA_i by AGS. Similarly, the reduction of RR2 by reduced AQDS proceeded 1.6- and 1.9-fold faster than the microbial reduction of AQDS by AGS when this redox mediator (RM) was supplied in soluble and immobilized form, respectively. In contrast, the reduction of NQS by AGS occurred 1.6- and 19.2-fold faster than the chemical reduction of RR2 by reduced NQS when this RM was supplied in soluble and immobilized form, respectively. The microbial reduction of HA_s and HA_i by a humus-reducing consortium proceeded 1,400- and 790-fold faster than the transfer of electrons from reduced HA_s and HA_i, respectively, to achieve the reductive dechlorination of CT to chloroform. Overall, the present study provides elucidation on the rate-limiting steps involved in the redox biotransformation of priority pollutants mediated by both HA_s and HA_i and offers technical suggestions to overcome the kinetic restrictions identified in the redox reactions evaluated.

Keywords: Humus; Immobilization; Recalcitrant pollutants; Redox mediator; Wastewater

Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing by Lin Ye; Tong Zhang (pp. 2681-2690).

In this study, we successfully demonstrated that 454 pyrosequencing was a powerful approach for investigating the bacterial communities in the activated sludge, digestion sludge, influent, and effluent samples of a full scale wastewater treatment plant treating saline sewage. For each sample, 18,808 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis. In total, 2,455, 794, 1,667, and 1,932 operational taxonomic units were obtained at 3 % distance cutoff in the activated sludge, digestion sludge, influent, and effluent samples, respectively. The corresponding most dominant classes in the four samples are Alphaproteobacteria, Thermotogae, Deltaproteobacteria, and Gammaproteobacteria. About 67 % sequences in the digestion sludge sample were found to be affiliated with the Thermotogales order. Also, these sequences were assigned into a recently proposed genus Kosmotoga by the Ribosomal Database Project classifier. In the effluent sample, we found high abundance of Mycobacterium and Vibrio, which are genera containing pathogenic bacteria. Moreover, in this study, we proposed a method to differentiate the “gene percentage” and “cell percentage” by using Ribosomal RNA Operon Copy Number Database.

Keywords: WWTP influent; WWTP effluent; Activated sludge; Digestion sludge; 454 Pyrosequencing; Bacterial community

Molinate biodegradation in soils: natural attenuation versus bioaugmentation by Ana R. Lopes; Anthony S. Danko; Célia M. Manaia; Olga C. Nunes (pp. 2691-2700).

The aims of the present study were to assess the potential of natural attenuation or bioaugmentation to reduce soil molinate contamination in paddy field soils and the impact of these bioremediation strategies on the composition of soil indigenous microbiota. A molinate mineralizing culture (mixed culture DC) was used as inoculum in the bioaugmentation assays. Significantly higher removal of molinate was observed in bioaugmentation than in natural attenuation microcosms (63 and 39 %, respectively) after 42 days of incubation at 22 °C. In the bioaugmentation assays, the impact of Gulosibacter molinativorax ON4^T on molinate depletion was observed since the gene encoding the enzyme responsible for the initial molinate breakdown (harboured by that actinobacterium) was only detected in inoculated microcosms. Nevertheless, the exogenous mixed culture DC did not overgrow as the heterotrophic counts of the bioaugmentation microcosms were not significantly different from those of natural attenuation and controls. Moreover, the actinobacterial clone libraries generated from the bioaugmentation microcosms did not include any 16S rRNA gene sequences with significant similarity to that of G. molinativorax ON4^T. The multivariate analysis of the 16S rRNA DGGE patterns of the soil microcosm suggested that the activity of mixed culture DC did not affect the soil bacterial community structure since the DGGE patterns of the bioaugmentation microcosms clustered with those of natural attenuation and controls. Although both bioremediation approaches removed molinate without indigenous microbiota perturbation, the results suggested that bioaugmentation with mixed culture DC was more effective to treat soils contaminated with molinate.

Keywords: Natural attenuation; Bioaugmentation; Molinate; Bacterial community; Paddy field soil

Simultaneous nutrient removal and lipid production from pretreated piggery wastewater by Chlorella vulgaris YSW-04 by Min-Kyu Ji; Hyun-Chul Kim; Veer Raghavulu Sapireddy; Hyun-Shik Yun; Reda A. I. Abou-Shanab; Jaeyoung Choi; Wontae Lee; Thomas C. Timmes; Inamuddin; Byong-Hun Jeon (pp. 2701-2710).

The feasibility of using a microalga Chlorella vulgaris YSW-04 was investigated for removal of nutrients from piggery wastewater effluent. The consequent lipid production by the microalga was also identified and quantitatively determined. The wastewater effluent was diluted to different concentrations ranging from 20 to 80 % of the original using either synthetic media or distilled water. The dilution effect on both lipid production and nutrient removal was evaluated, and growth rate of C. vulgaris was also monitored. Dilution of the wastewater effluent improved microalgal growth, lipid productivity, and nutrient removal. The growth rate of C. vulgaris was increased with decreased concentration of piggery wastewater in the culture media regardless of the diluent type. Lipid production was relatively higher when using synthetic media than using distilled water for dilution of wastewater. The composition of fatty acids accumulated in microalgal biomass was dependent upon both dilution ratio and diluent type. The microalga grown on a 20 % concentration of wastewater effluent diluted with distilled water was more promising for generating high-efficient biodiesel compared to the other culture conditions. The highest removal of inorganic nutrients was also achieved at the same dilution condition. Our results revealed the optimal pretreatment condition for the biodegradation of piggery wastewater with microalgae for subsequent production of high-efficient biodiesel.

Keywords: Piggery effluent; Microalgae; Nitrogen species; Phosphorus; Lipids; Fatty acids

Influence of the surface speciation on biofilm attachment to chalcopyrite by Acidithiobacillus thiooxidans by René H. Lara; J. Viridiana García-Meza; Ignacio González; Roel Cruz (pp. 2711-2724).

Surfaces of massive chalcopyrite (CuFeS₂) electrodes were modified by applying variable oxidation potential pulses under growth media in order to induce the formation of different secondary phases (e.g., copper-rich polysulfides, S n ²⁻; elemental sulfur, S⁰; and covellite, CuS). The evolution of reactivity (oxidation capacity) of the resulting chalcopyrite surfaces considers a transition from passive or inactive (containing CuS and S n ²⁻) to active (containing increasing amounts of S⁰) phases. Modified surfaces were incubated with cells of sulfur-oxidizing bacteria (Acidithiobacillus thiooxidans) for 24 h in a specific culture medium (pH 2). Abiotic control experiments were also performed to compare chemical and biological oxidation. After incubation, the density of cells attached to chalcopyrite surfaces, the structure of the formed biofilm, and their exopolysaccharides and nucleic acids were analyzed by confocal laser scanning microscopy (CLSM) and scanning electron microscopy coupled to dispersive X-ray analysis (SEM-EDS). Additionally, CuS and S n ²⁻/S⁰ speciation, as well as secondary phase evolution, was carried out on biooxidized and abiotic chalcopyrite surfaces using Raman spectroscopy and SEM-EDS. Our results indicate that oxidized chalcopyrite surfaces initially containing inactive S n ²⁻ and S n ²⁻/CuS phases were less colonized by A. thiooxidans as compared with surfaces containing active phases (mainly S⁰). Furthermore, it was observed that cells were partially covered by CuS and S⁰ phases during biooxidation, especially at highly oxidized chalcopyrite surfaces, suggesting the innocuous effect of CuS phases during A. thiooxidans performance. These results may contribute to understanding the effect of the concomitant formation of refractory secondary phases (as CuS and inactive S n ²⁻) during the biooxidation of chalcopyrite by sulfur-oxidizing microorganisms in bioleaching systems.

Keywords: Acidithiobacillus thiooxidans ; Electrooxidation; Reactivity; Chalcopyrite; Active and inactive sulfur; Biofilms

Denitrification performance and microbial diversity in a packed-bed bioreactor using PCL as carbon source and biofilm carrier by Weizhong Wu; Luhua Yang; Jianlong Wang (pp. 2725-2733).

Polycaprolactone (PCL) was used as both carbon source and biofilm support for denitrifying bacteria in a packed-bed bioreactor. The denitrification performance and microbial diversity were investigated. The microbial community of biofilm developed on the surface of PCL in the reactor was analyzed by pyrosequencing method. The experimental results showed the average nitrate removal efficiency reached 93 % at stable operation. ESEM observation and FTIR analysis were conducted to characterize the PCL structure before and after microbial utilization. For the microbial community, Betaproteobacteria predominated, and most of the PCL-degrading denitrifying bacteria assigned to the family of Comamonadacea. Denitrifying bacteria accounted for more than 20 % in the total population, indicating that PCL is a good carrier and carbon source for biological denitrification.

Keywords: Nitrate; Denitrification; PCL; Solid carbon source; Pyrosequencing; Betaproteobacteria

Reactive oxygen species generated in the presence of fine pyrite particles and its implication in thermophilic mineral bioleaching by G. C. Jones; R. P. van Hille; S. T. L. Harrison (pp. 2735-2742).

In the tank bioleaching process, maximising solid loading and mineral availability, the latter through decreasing particle size, are key to maximising metal extraction. In this study, the effect of particle size distribution on bioleaching performance and microbial growth was studied through applying knowledge based on medical geology research to understand the adverse effects of suspended fine pyrite particles. Small-scale leaching studies, using pyrite concentrate fractions (106–75, 75–25, −25 μm fines), were used to confirm decreasing performance with decreasing particle size (D ₅₀ <40 μm). Under equivalent experimental conditions, the generation of the reactive oxygen species (ROS), hydrogen peroxide and hydroxyl radicals from pyrite was illustrated. ROS generation measured from the different pyrite fractions was found to increase with increasing pyrite surface area loading (1.79–74.01 m² L⁻¹) and Fe²⁺ concentration (0.1–2.8 g L⁻¹) in solution. The highest concentration of ROS was measured from the finest fraction of pyrite (0.85 mM) and from the largest concentration of Fe²⁺ (0.78 mM). No ROS was detected from solutions containing only Fe³⁺ under the same conditions tested. The potential of ROS to inhibit microbial performance under bioleaching conditions was demonstrated. Pyrite-free Sulfolobus metallicus cultures challenged with hydrogen peroxide (0.5–2.5 mM) showed significant decrease in both cell growth and Fe²⁺ oxidation rates within the concentration range 1.5–2.5 mM. In combination, the results from this study suggest that conditions of large pyrite surface area loading, coupled with high concentrations of dissolved Fe²⁺, can lead to the generation of ROS, resulting in oxidative stress of the microorganisms.

Keywords: Mineral bioleaching; Reactive oxygen species; Particle size; Mineral sulphide; Pyrite

Determining the impacts of fermentative bacteria on wollastonite dissolution kinetics by S. S. Salek; R. Kleerebezem; H. M. Jonkers; J. H. L. Voncken; M. C. M. van Loosdrecht (pp. 2743-2752).

Silicate minerals can be a source of calcium and alkalinity, enabling CO₂ sequestration in the form of carbonates. For this to occur, the mineral needs to be first dissolved in an acidifying process such as the biological process of anaerobic fermentation. In the present study, the main factors which govern the dissolution process of an alkaline silicate mineral (wollastonite, CaSiO₃) in an anaerobic fermentation process were determined. Wollastonite dissolution kinetics was measured in a series of chemical batch experiments in order to be able to estimate the required amount of alkaline silicate that can neutralize the acidifying fermentation process. An anaerobic fermentation of glucose with wollastonite as the neutralizing agent was consequently performed in a fed-batch reactor. Results of this experiment were compared with an abiotic (control) fed-batch reactor in which the fermentation products (i.e. organic acids and alcohols) were externally supplied to the system at comparable rates and proportions, in order to provide chemical conditions similar to those during the biotic (fermentation) experiment. This procedure enabled us to determine whether dissolution of wollastonite was solely enhanced by production of organic acids or whether there were other impacts that fermentative bacteria could have on the mineral dissolution rate. The established pH profiles, which were the direct indicator of the dissolution rate, were comparable in both experiments suggesting that the mineral dissolution rate was mostly influenced by the quantity of the organic acids produced.

Keywords: Alkaline silicate minerals; Anaerobic fermentation; Wollastonite; Mineral dissolution; Carbon dioxide sequestration; Mineral carbonation

Engineering E. coli for triglyceride accumulation through native and heterologous metabolic reactions by Joanna Rucker; Julie Paul; Blaine A. Pfeifer; Kyongbum Lee (pp. 2753-2759).

Triglycerides, traditionally sourced from plant oils, are heavily used in both industrial and healthcare applications. Commercially significant products produced from triglycerides include biodiesel, lubricants, moisturizers, and oils for cooking and dietary supplements. The need to rely upon plant-based production, however, raises concerns of increasing demand and sustainability. The reliance on crop yields and a strong demand for triglycerides provides motivation to engineer production from a robust microbial platform. In this study, Escherichia coli was engineered to synthesize and accumulate triglycerides. Triglycerides were produced from cell wall phospholipid precursors through engineered expression of two enzymes, phosphatidic acid phosphatase (PAP) and diacylglycerol acyltransferase (DGAT). A liquid chromatography–mass spectrometry (LC–MS) method was developed to analyze the production of triglycerides by the engineered E. coli strains. This proof-of-concept study demonstrated a yield of 1.1 mg/L triglycerides (2 g/L dry cell weight) in lysogeny broth medium containing 5 g/L glucose at 8 h following induction of PAP and DGAT expression. LC–MS results also demonstrated that the intracellular triglyceride composition of E. coli was highly conserved. Triglycerides containing the fatty acid distributions 16:0/16:0/16:1, 16:0/16:0/18:1, and 18:1/16:0/16:1 were found in highest concentrations and represent ∼70 % of triglycerides observed.

Keywords: Triglycerides; Phosphatidic acid; Escherichia coli ; LC–MS/MS

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Applied Microbiology and Biotechnology (v.97, #6)

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Applied Microbiology and Biotechnology (v.97, #6)