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Applied Microbiology and Biotechnology (v.97, #7)

Engineering of NADPH regenerators in Escherichia coli for enhanced biotransformation by Won-Heong Lee; Myoung-Dong Kim; Yong-Su Jin; Jin-Ho Seo (pp. 2761-2772).

Efficient regeneration of NADPH is one of the limiting factors that constrain the productivity of biotransformation processes. In order to increase the availability of NADPH for enhanced biotransformation by engineered Escherichia coli, modulation of the pentose phosphate pathway and amplification of the transhydrogenases system have been conventionally attempted as primary solutions. Recently, other approaches for stimulating NADPH regeneration during glycolysis, such as replacement of native glyceradehdye-3-phosphate dehydrogenase (GAPDH) with NADP-dependent GAPDH from Clostridium acetobutylicum and introduction of NADH kinase catalyzing direct phosphorylation of NADH to NADPH from Saccharomyces cerevisiae, were attempted and resulted in remarkable impacts on NADPH-dependent bioprocesses. This review summarizes several metabolic engineering approaches used for improving the NADPH regenerating capacity in engineered E. coli for whole-cell-based bioprocesses and discusses the key features and progress of those attempts.

Keywords: Biotransformation process; Engineered Escherichia coli ; NADPH regeneration; Pentose phosphate pathway; Transhydrogenase; NADP-dependent glyceradehdye-3-phosphate dehydrogenase; NAD(H) kinase

Total synthesis of antibiotics: recent achievements, limitations, and perspectives by Evgeny V. Prusov (pp. 2773-2795).

Several recently accomplished total syntheses of antibiotic natural products were summarized in this review in order to present current trends in this area of research. Compounds from different substance classes, including polyketide, depsipeptide, polyketide–polypeptide hybrid, and saccharide, were chosen to demonstrate the advancement in both chemical methodology and corresponding synthetic strategy.

Keywords: Natural products; Total synthesis; Microbial antibiotics; Synthetic methodologies

Genetics of Cordyceps and related fungi by Peng Zheng; Yongliang Xia; Siwei Zhang; Chengshu Wang (pp. 2797-2804).

Ascomycete Cordyceps sensu lato consists of hundreds of species of fungi capable of infecting different insects. Species of these fungi are either valued traditional Chinese medicines or used for biocontrol of insect pests. Phylogenomic analysis indicated that fungal entomopathogenicity has evolved for multiple times, and the species of Cordyceps were diverged from the mycoparasite or plant endophyte. Relative to plant pathogens and saprophytes, Cordyceps species demonstrate characteristic genome expansions of proteases and chitinases that are used by the fungi to target insect cuticles. Only a single mating-type gene identified in the sequenced species of Cordyceps sensu lato indicates that these fungi are sexually heterothallic, but the gene structure of the mating-type loci and frequency in performing sexual cycle are considerably different between different species. Similar to the model fungus Neurospora crassa, Cordyceps and related fungi contain the full components for RNA interference pathways. However, the mechanism of repeat-induced point mutation varies between different fungi. Epigenetic rather than genetic alterations are majorly responsible for the frequent occurrence of culture degeneration in Cordyceps-related species. Future genetic and epigenetic studies of fungal sexuality controls and culture degeneration mechanisms will benefit the cost-effective applications of Cordyceps and related fungi in pharmaceuticals and agriculture.

Keywords: Cordyceps; Phylogenomics; Comparative genomics; Sexuality; Genome structure; Culture degeneration; Epigenetic control

Extrachromosomal, extraordinary and essential—the plasmids of the Roseobacter clade by Jörn Petersen; Oliver Frank; Markus Göker; Silke Pradella (pp. 2805-2815).

The alphaproteobacterial Roseobacter clade (Rhodobacterales) is one of the most important global players in carbon and sulfur cycles of marine ecosystems. The remarkable metabolic versatility of this bacterial lineage provides access to diverse habitats and correlates with a multitude of extrachromosomal elements. Four non-homologous replication systems and additional subsets of individual compatibility groups ensure the stable maintenance of up to a dozen replicons representing up to one third of the bacterial genome. This complexity presents the challenge of successful partitioning of all low copy number replicons. Based on the phenomenon of plasmid incompatibility, we developed molecular tools for target-oriented plasmid curing and could generate customized mutants lacking hundreds of genes. This approach allows one to analyze the relevance of specific replicons including so-called chromids that are known as lifestyle determinants of bacteria. Chromids are extrachromosomal elements with a chromosome-like genetic imprint (codon usage, GC content) that are essential for competitive survival in the natural habitat, whereas classical dispensable plasmids exhibit a deviating codon usage and typically contain type IV secretion systems for conjugation. The impact of horizontal plasmid transfer is exemplified by the scattered occurrence of the characteristic aerobic anoxygenic photosynthesis among the Roseobacter clade and the recently reported transfer of the 45-kb photosynthesis gene cluster to extrachromosomal elements. Conjugative transmission may be the crucial driving force for rapid adaptations and hence the ecological prosperousness of this lineage of pink bacteria.

Keywords: Plasmid classification; Compatibility; Chromid concept; Plasmid curing; Conjugation; Rhodobacterales

Recent advances and safety issues of transgenic plant-derived vaccines by Zheng-jun Guan; Bin Guo; Yan-lin Huo; Zheng-ping Guan; Jia-kun Dai; Ya-hui Wei (pp. 2817-2840).

Transgenic plant-derived vaccines comprise a new type of bioreactor that combines plant genetic engineering technology with an organism's immunological response. This combination can be considered as a bioreactor that is produced by introducing foreign genes into plants that elicit special immunogenicity when introduced into animals or human beings. In comparison with traditional vaccines, plant vaccines have some significant advantages, such as low cost, greater safety, and greater effectiveness. In a number of recent studies, antigen-specific proteins have been successfully expressed in various plant tissues and have even been tested in animals and human beings. Therefore, edible vaccines of transgenic plants have a bright future. This review begins with a discussion of the immune mechanism and expression systems for transgenic plant vaccines. Then, current advances in different transgenic plant vaccines will be analyzed, including vaccines against pathogenic viruses, bacteria, and eukaryotic parasites. In view of the low expression levels for antigens in plants, high-level expression strategies of foreign protein in transgenic plants are recommended. Finally, the existing safety problems in transgenic plant vaccines were put forward will be discussed along with a number of appropriate solutions that will hopefully lead to future clinical application of edible plant vaccines.

Keywords: Transgenic; Plant; Vaccine; Safety

Culture medium optimization of a new bacterial extracellular polysaccharide with excellent moisture retention activity by Li Zhao; Fang Fan; Peng Wang; Xiaolu Jiang (pp. 2841-2850).

A new kind of extracellular polysaccharide (EPS) from Pseudomonas fluorescens PGM37 was obtained and culture media was optimized using the statistical methods single factor experiments and response surface methodology (RSM) design. As a result, the optimum cultivation conditions initial pH value, medium volume, inoculum size, temperature, and rotation speed were 7.5, 100 mL/250 mL, 5 %, 28 °C, and 180 rpm, respectively. The optimized media: sucrose 36.23 g L⁻¹, yeast extract 3.32 g L⁻¹, sodium chloride 1.13 g L⁻¹, and calcium chloride 0.20 g L⁻¹. The maximum predicted yield of EPS was 10.1163 g L⁻¹ under these conditions. The validation data was 10.012 g L⁻¹, which could strongly confirm the correlation between the experimental and theoretical values. Gas Chromatography analysis revealed that the polymer was made up of mannose and glucose in the ratio of 1:1. Infrared spectroscopy showed that the polysaccharide had β-D-pyranoid configuration and contained no other substituent. Graded by different multiples of alcohol after specific degradation by enzyme and then detected by LC-ESI-MS, the EPS structure was β-D-Glcp-(1, 4)-β-D-Manp-(1, 4)-β-D-Glcp-(1, 4)-β-D-Manp. The moisture retention ability of the EPS was found to be superior to glycerol and only a little inferior to hyaluronic acid (HA), which presented potential application value in cosmetics and clinical medicine fields.

Keywords: Pseudomonas fluorescens PGM37; Extracellular polysaccharides (EPS); Response surface methodology (RSM); Structure; Moisture retention ability

Antrodia camphorata ATCC 200183 sporulates asexually in submerged culture by Yan Geng; Zhe He; Zhen-Ming Lu; Hong-Yu Xu; Guo-Hua Xu; Jin-Song Shi; Zheng-Hong Xu (pp. 2851-2858).

Antrodia camphorata is a well-known Chinese medicinal mushroom that protects against diverse health-related conditions. Submerged fermentation of A. camphorata is an alternative choice for the effective production of bioactive metabolites, but the effects of nutrition and environment on mycelial morphology are largely unknown. In this study, we show that A. camphorata American Type Culture Collection 200183 can form arthrospores in the end of liquid fermentation. Different morphologies of A. camphorata in submerged culture were analyzed using scanning electron microscopy. The optimal carbon and nitrogen sources for sporulation were soluble starch and yeast extract. We found that a carbon-to-nitrogen ratio (C/N) of 40:1, MgSO₄ (0.5 g/l), KH₂PO₄ (3.0 g/l), an initial pH 5.0, and an inoculum size of 1.5 × 10⁵ spores/ml led to maximum production of arthroconidia. Our results will be useful in the regulation and optimization of A. camphorata cultures for efficient production of arthroconidia in submerged culture, which can be used as inocula in subsequent fermentation processes.

Keywords: Antrodia camphorata ; Arthroconidia; Sporulation; Submerged culture

Growth condition optimization for docosahexaenoic acid (DHA) production by Moritella marina MP-1 by Kumar B. Kautharapu; John Rathmacher; Laura R. Jarboe (pp. 2859-2866).

The marine organism Moritella marina MP-1 produces the polyunsaturated fatty acid docosahexaenoic acid (DHA). While the basic metabolic pathway for DHA production in this organism has been identified, the impact of growth conditions on DHA production is largely unknown. This study examines the effect of supplemental carbon, nitrogen and salts, growth temperature and media composition and pH on DHA and biomass production and the fatty acid profile. The addition of supplemental nitrogen significantly increased the overall DHA titer via an increase in biomass production. Supplemental glucose or glycerol increased biomass production, but decreased the amount of DHA per biomass, resulting in no net change in the DHA titer. Acidification of the baseline media pH to 6.0 increased DHA per biomass. Changes in growth temperature or provision of supplemental sodium or magnesium chloride did not increase DHA titer. This organism was also shown to grow on defined minimal media. For both media types, glycerol enabled more DHA production per biomass than glucose. Combination of these growth findings into marine broth supplemented with glycerol, yeast extract, and tryptone at pH 6.0 resulted in a final titer of 82 ± 5 mg/L, a nearly eightfold increase relative to the titer of 11 ± 1 mg/L seen in the unsupplemented marine broth. The relative distribution of other fatty acids was relatively robust to growth condition, but the presence of glycerol resulted in a significant increase in myristic acid (C14:0) and decrease in palmitic acid (C16:0). In summary, DHA production by M. marina MP-1 can be increased more than fivefold by changing the growth media. Metabolic engineering of this organism to increase the amount of DHA produced per biomass could result in additional increases in titer.

Keywords: Moritella marina MP-1; Polyunsaturated fatty acids; Membrane fluidity; Polyketide; Marine broth

High-level expression and immunogenicity of a porcine circovirus type 2 capsid protein through codon optimization in Pichia pastoris by Yabin Tu; Yanqun Wang; Gang Wang; Jianan Wu; Yonggang Liu; Shujie Wang; Chenggang Jiang; Xuehui Cai (pp. 2867-2875).

The porcine circovirus type 2 (PCV2) capsid protein (Cap) is an important antigen for the development of vaccines. To achieve high-level expression of recombinant PCV2 Cap in Pichia pastoris, the wild-type Cap (wt-Cap) and optimized Cap (opti-Cap) gene fragments encoding the same amino acid sequence of PCV2 were amplified by PCR using DNA from lymph nodes of postweaning multisystemic wasting syndrome-suffered pigs and synthesized based on the codon bias of the methylotrophic yeast P. pastoris, respectively. The wt-Cap and opti-Cap gene fragments were inserted into the site between EcoRI and NotI sites in pPIC9K, which was under the control of the alcohol oxidase 1 (AOX1) promoter and α-mating factor signal sequence from Saccharomyces cerevisiae. The recombinant plasmids, designated as pPIC9K-wt-Cap and pPIC9K-opti-Cap, were linearized using SacI and transformed into P. pastoris GS115 by electroporation. The expressed intracellular soluble opti-Cap reached 174 μg/mL without concentration in a shake flask and kept good reactivity to PCV2-specific positive sera, whereas the wt-Cap could not be detectable throughout three times electroporation. Strong specific PCV2-Cap antibodies were elicited from piglets immunized with vaccine based on opti-Cap. To the best of our knowledge, the achieved opti-Cap yield is the highest ever reported. Our results demonstrated that codon optimization play an important role on the high-level expression of a codon-optimized PCV2-Cap gene in P. pastoris, and the vaccine based on opti-Cap may be a potential subunit vaccine candidate.

Keywords: Porcine circovirus type 2; Capsid protein; Pichia pastoris ; Expression; Immunogenicity

Construction and expression of sTRAIL–melittin combining enhanced anticancer activity with antibacterial activity in Escherichia coli by Hongyan Liu; Yangyang Han; Haiyan Fu; Meng Liu; Jing Wu; Xiaonan Chen; Shuangquan Zhang; Yuqing Chen (pp. 2877-2884).

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), as an anticancer protein with tumor-selective apoptotic activity, has been examined for use in clinical application. Melittin, an antibacterial peptide isolated from the bee Apis mellifera, has shown strong cytotoxicity to both tumor and normal cells. To ameliorate the cytotoxicity of melittin on cells and enhance the activity of TRAIL on cancer cells, we constructed a novel fusion protein, sTRAIL–melittin, containing a small ubiquitin-related modifier (SUMO) tag and expressed this fusion protein in Escherichia coli. Data showed that expression of the soluble fusion protein with the SUMO tag was approximately 85 % of total target protein which was much higher than that without the SUMO tag (approximately 10 %); sTRAIL–melittin was easily purified using Ni-NTA affinity chromatography and the tag was removed easily using SUMO-specific protease. To assay anticancer activity and side effects, methyl thiazolyl tetrazolium, hemolytic, and apoptosis assays were employed. Results demonstrated that sTRAIL–melittin had cytotoxic and apoptotic activity in K562 leukemia cells and HepG2 liver carcinoma cells, while it had only a minimal effect on erythrocytes and normal HEK293 cells. This indicates that the cytotoxicity of sTRAIL–melittin in normal cells was low and the anticancer activity of the fusion protein in tumor cells was significantly enhanced compared with sTRAIL (P < 0.01). Furthermore, we found that sTRAIL–melittin also showed antibacterial activity to Staphylococcus aureus due to the presence of the melittin domain. Therefore, TRAIL fused with an antibacterial peptide may be a promising novel TRAIL-based anticancer treatment strategy.

Keywords: SUMO; sTRAIL; Melittin; Anticancer; Escherichia coli

Rational and efficient preparation of a chimeric protein containing a tandem dimer of thrombopoietin mimetic peptide fused to human growth hormone in Escherichia coli by Song Wang; Mingqiang Shen; Yang Xu; Fang Chen; Mo Chen; Shilei Chen; Aiping Wang; Zhou Zhang; Xinze Ran; Tianmin Cheng; Yongping Su; Junping Wang (pp. 2885-2894).

The 14-mer thrombopoietin mimetic peptide (TMP), especially in the form of dimer, displayed potent megakaryocytopoiesis activity in vitro. However, it is difficult to prepare such short peptide with high bioactivity through gene-engineering approaches. In this study, a chimeric protein containing a tandem dimer of TMP (dTMP) fused to human growth hormone (hGH), a kind of hematopoietic growth factor that activates the same signal pathways as thrombopoietin, was produced in Escherichia coli by soluble expression. By rational utilization of the XmnI and EcoRV restriction sites, a PCR fragment encoding dTMP-GH was inserted into the plasmid vector pMAL-p2X at the position right after Xa factor cleavage site, in frame with maltose-binding protein (MBP) gene. Under optimized conditions, a high-level expression of soluble MBP-dTMP-GH fusion protein was obtained. By application of amylose resin chromatography, Xa factor digestion, hydrophobic chromatography followed by gel filtration, the dTMP-GH fusion protein was separated. Finally, a relatively high yield of dTMP-GH fusion protein with high purity (>98 %) and without redundant amino acid was achieved, as identified by high-performance liquid chromatography, mass spectrometry, and amino acid sequencing. The functional assays showed that dTMP-GH could promote the proliferation of megakaryoblast cells and maturation of murine megakaryocytes derived from bone marrow, in a dose-dependent manner. Moreover, an enhanced effect of dTMP-GH on megakaryocytopoiesis was found as compared with equimolar concentration of dTMP and rhGH. This work provides a new avenue to generate thrombopoietic agents based on TMP.

Keywords: Thrombopoietin mimetic peptide; Human growth hormone; Fusion protein; Escherichia coli ; Preparation

Biochemical characterization of a GH53 endo-β-1,4-galactanase and a GH35 exo-β-1,4-galactanase from Penicillium chrysogenum by Tatsuji Sakamoto; Yuichi Nishimura; Yosuke Makino; Yoichi Sunagawa; Naoki Harada (pp. 2895-2906).

An endo-β-1,4-galactanase (PcGAL1) and an exo-β-1,4-galactanase (PcGALX35C) were purified from the culture filtrate of Penicillium chrysogenum 31B. Pcgal1 and Pcgalx35C cDNAs encoding PcGAL1 and PcGALX35C were isolated by in vitro cloning. The deduced amino acid sequences of PcGAL1 and PcGALX35C are highly similar to a putative endo-β-1,4-galactanase of Aspergillus terreus (70 % amino acid identity) and a putative β-galactosidase of Neosartorya fischeri (72 %), respectively. Pfam analysis revealed a “Glyco_hydro_53” domain in PcGAL1. PcGALX35C is composed of five distinct domains including “Glyco_hydro_35,” “BetaGal_dom2,” “BetaGal_dom3,” and two “BetaGal_dom4_5” domains. Recombinant enzymes (rPcGAL1 and rPcGALX35C) expressed in Escherichia coli and Pichia pastoris, respectively, were active against lupin galactan. The reaction products of lupin galactan revealed that rPcGAL1 cleaved the substrate in an endo manner. The enzyme accumulated galactose and galactobiose as the main products. The smallest substrate for rPcGAL1 was β-1,4-galactotriose. On the other hand, rPcGALX35C released only galactose from lupin galactan throughout the reaction, indicating that it is an exo-β-1,4-galactanase. rPcGALX35C was active on both β-1,4-galactobiose and triose, but not on lactose, β-1,3- or β-1,6-galactooligosaccharides even after 24 h of incubation. To our knowledge, this is the first report of a gene encoding a microbial exo-β-1,4-galactanase. rPcGAL1 and rPcGALX35C acted synergistically in the degradation of lupin galactan and soybean arabinogalactan. Lupin galactan was almost completely degraded to galactose by the combined actions of rPcGAL1 and rPcGALX35C. Surprisingly, neither rPcGAL1 nor rPcGALX35C released any galactose from sugar beet pectin.

Keywords: Penicillium chrysogenum ; Endo-β-1,4-galactanase; Exo-β-1,4-galactanase; Glycoside hydrolase family 35; Glycoside hydrolase family 53

Combination of site-directed mutagenesis and calcium ion addition for enhanced production of thermostable MBP-fused heparinase I in recombinant Escherichia coli by Shuo Chen; Ziliang Huang; Jingjun Wu; Yin Chen; Fengchun Ye; Chong Zhang; Rie Yatsunami; Satoshi Nakamura; Xin-Hui Xing (pp. 2907-2916).

Heparinase I (HepI), which specifically cleaves heparin and heparan sulfate, is one of the most extensively studied glycosaminoglycan lyases. Low productivity of HepI has largely hindered its industrial and pharmaceutical applications. Loss of bacterial HepI enzyme activity through poor thermostability during its expression and purification process in production can be an important issue. In this study, using a thermostabilization strategy combining site-directed mutagenesis and calcium ion addition during its production markedly improved the yield of maltose-binding protein-fused HepI (MBP–HepI) from recombinant Escherichia coli. Substitution of Cys297 to serine in MBP–HepI offered a 30.6 % increase in the recovered total enzyme activity due to a mutation-induced thermostabilizing effect. Furthermore, upon addition of Ca²⁺ as a stabilizer at optimized concentrations throughout its expression, extraction, and purification process, purified mutant MBP–HepI showed a specific activity of 56.3 IU/mg, 206 % higher than that of the wild type obtained without Ca²⁺ addition, along with a 177 % increase in the recovered total enzyme activity. The enzyme obtained through this novel approach also exhibited significantly enhanced thermostability, as indicated by both experimental data and the kinetic modeling. High-yield production of thermostable MBP–HepI using the present system will facilitate its applications in laboratory-scale heparin analysis as well as industrial-scale production of low molecular weight heparin as an improved anticoagulant substitute.

Keywords: Heparinase; Maltose-binding protein; Site-directed mutagenesis; Calcium; Thermal stability; Protein expression; Purification

The stability of almond β-glucosidase during combined high pressure–thermal processing: a kinetic study by Netsanet Shiferaw Terefe; Paul Sheean; Susil Fernando; Cornelis Versteeg (pp. 2917-2928).

The thermal and the combined high pressure–thermal inactivation kinetics of almond β-glucosidase (β-d-glucoside glucohydrolase, EC 3.2.1.21) were investigated at pressures from 0.1 to 600 MPa and temperatures ranging from 30 to 80 °C. Thermal treatments at temperatures higher than 50 °C resulted in significant inactivation with complete inactivation after 2 min of treatment at 80 °C. Both the thermal and high pressure inactivation kinetics were described well by first-order model. Application of pressure increased the inactivation kinetics of the enzyme except at moderate temperatures (50 to 70 °C) and pressures between 0.1 and 100 MPa where slight pressure stabilisation of the enzyme against thermal denaturation was observed. The activation energy for the inactivation of the enzyme at atmospheric pressure was estimated to be 216.2 ± 8.6 kJ/mol decreasing to 55.2 ± 3.9 kJ/mol at 600 MPa. The activation volumes were negative at all temperature conditions excluding the temperature–pressure range where slight pressure stabilisation was observed. The values of the activation volumes were estimated to be −29.6 ± 0.6, −29.8 ± 1.7, −20.6 ± 3.2, −41.2 ± 4.8, −36.5 ± 1.8, −39.6 ± 4.3, −31.0 ± 4.5 and −33.8 ± 3.9 cm³/mol at 30, 35, 40, 45, 50, 60, 65 and 70 °C, respectively, with no clear trend with temperature. The pressure–temperature dependence of the inactivation rate constants was well described by an empirical third-order polynomial model.

Keywords: β-Glucosidase; High pressure processing; Thermal inactivation kinetics; High pressure inactivation kinetics; Almond; Kinetic modelling

Genome mining and motif modifications of glycoside hydrolase family 1 members encoded by Geobacillus kaustophilus HTA426 provide thermostable 6-phospho-β-glycosidase and β-fucosidase by Hirokazu Suzuki; Fumiyoshi Okazaki; Akihiko Kondo; Ken-ichi Yoshida (pp. 2929-2938).

Members of glycoside hydrolase family 1 (GH1) hydrolyze various glycosides and are widely distributed in organisms. With the aim of producing thermostable GH1 catalysts with potential applications in biotechnology, three GH1 members encoded by the thermophile Geobacillus kaustophilus HTA426 (GK1856, GK2337, and GK3214) were characterized using 24 p-nitrophenyl glycosides as substrates. GK1856 and GK3214 exhibited 6-phospho-β-glycosidase activity, while GK2337 did not. GK3214 was extremely thermostable and retained most of its activity during 7 days of incubation at 60 °C. GK3214 was found to have transglycosylation activity, a dimeric structure, and a possible motif that governed its substrate specificity. Substitution of the GK3214 motif with that of a β-glucosidase resulted in the unexpected generation of a thermostable, highly specific β-fucosidase, concomitant with large increases in β-glucosidase, β-cellobiosidase, α-arabinofuranosidase, β-mannosidase, β-glucuronidase, β-xylopyranosidase, and β-fucosidase activities and a dramatic decline in 6-phospho-β-glycosidase activity. This is the first report to identify a gene encoding thermostable 6-phospho-β-glycosidase and to generate a thermostable β-fucosidase. These results provided thermostable enzyme catalysts and also suggested a promising approach to develop novel GH1 biocatalysts.

Keywords: β-Fucosidase; 6-Phospho-β-glycosidase; Thermostable; Glycoside hydrolase family 1; Geobacillus

Study and reengineering of the binding sites and allosteric regulation of biosynthetic threonine deaminase by isoleucine and valine in Escherichia coli by Lin Chen; Zhen Chen; Ping Zheng; Jibin Sun; An-Ping Zeng (pp. 2939-2949).

Biosynthetic threonine deaminase (TD) is a key enzyme for the synthesis of isoleucine which is allosterically inhibited and activated by Ile and Val, respectively. The binding sites of Ile and Val and the mechanism of their regulations in TD are not clear, but essential for a rational design of efficient productive strain(s) for Ile and related amino acids. In this study, structure-based computational approach and site-directed mutagenesis were combined to identify the potential binding sites of Ile and Val in Escherichia coli TD. Our results demonstrated that each regulatory domain of the TD monomer possesses two nonequivalent effector-binding sites. The residues R362, E442, G445, A446, Y369, I460, and S461 only interact with Ile while E347, G350, and F352 are involved not only in the Ile binding but also in the Val binding. By further considering enzyme kinetic data, we propose a concentration-dependent mechanism of the allosteric regulation of TD by Ile and Val. For the construction of Ile overproducing strain, a novel TD mutant with double mutation of F352A/R362F was also created, which showed both higher activity and much stronger resistance to Ile inhibition comparing to those of wild-type enzyme. Overexpression of this mutant TD in E. coli JW3591 significantly increased the production of ketobutyrate and Ile in comparison to the reference strains overexpressing wild-type TD or the catabolic threonine deaminase (TdcB). This work builds a solid basis for the reengineering of TD and related microorganisms for Ile production.

Keywords: Threonine deaminase; Feedback inhibition; L-isoleucine; L-valine

Biodegradable plastic-degrading enzyme from Pseudozyma antarctica: cloning, sequencing, and characterization by Yukiko Shinozaki; Tomotake Morita; Xiao-hong Cao; Shigenobu Yoshida; Motoo Koitabashi; Takashi Watanabe; Ken Suzuki; Yuka Sameshima-Yamashita; Toshiaki Nakajima-Kambe; Takeshi Fujii; Hiroko K. Kitamoto (pp. 2951-2959).

Pseudozyma antarctica JCM 10317 exhibits a strong degradation activity for biodegradable plastics (BPs) such as agricultural mulch films composed of poly(butylene succinate) (PBS) and poly(butylene succinate-co-adipate) (PBSA). An enzyme named PaE was isolated and the gene encoding PaE was cloned from the strain by functional complementation in Saccharomyces cerevisiae. The deduced amino acid sequence of PaE contains 198 amino acids with a predicted molecular weight of 20,362.41. High identity was observed between this sequence and that of cutinase-like enzymes (CLEs) (61–68 %); therefore, the gene encoding PaE was named PaCLE1. The specific activity of PaE against emulsified PBSA was 54.8 ± 6.3 U/mg. In addition to emulsified BPs, PaE degraded solid films of PBS, PBSA, poly(ε-caprolactone), and poly(lactic acid).

Keywords: Biodegradable plastic; Pseudozyma antarctica ; Cutinase; Poly(butylene succinate); Poly(ε-caprolactone); Poly(lactic acid)

Enzymatic production of 3,6-anhydro-l-galactose from agarose and its purification and in vitro skin whitening and anti-inflammatory activities by Eun Ju Yun; Saeyoung Lee; Ji Hye Kim; Bo Bae Kim; Hee Taek Kim; Sun Hee Lee; Jeffrey G. Pelton; Nam Joo Kang; In-Geol Choi; Kyoung Heon Kim (pp. 2961-2970).

3,6-Anhydro-l-galactose (L-AHG) constitutes 50 % of agarose, which is the main component of red macroalgae. No information is currently available on the mass production, metabolic fate, or physiological effects of L-AHG. Here, agarose was converted to L-AHG in the following three steps: pre-hydrolysis of agarose into agaro-oligosaccharides by using acetic acid, hydrolysis of the agaro-oligosaccharides into neoagarobiose by an exo-agarase, and hydrolysis of neoagarobiose into L-AHG and galactose by a neoagarobiose hydrolase. After these three steps, L-AHG was purified by adsorption and gel permeation chromatographies. The final product obtained was 95.6 % pure L-AHG at a final yield of 4.0 % based on the initial agarose. In a cell proliferation assay, L-AHG at a concentration of 100 or 200 μg/ mL did not exhibit any significant cytotoxicity. In a skin whitening assay, 100 μg/ mL of L-AHG showed significantly lower melanin production compared to arbutin. L-AHG at 100 and 200 μg/ mL showed strong anti-inflammatory activity, indicating the significant suppression of nitrite production. This is the first report on the production of high-purity L-AHG and its physiological activities.

Keywords: 3,6-Anhydro-l-galactose; Agar; Red macroalgae; Skin whitening; Anti-inflammation

A highly thermoactive and salt-tolerant α-amylase isolated from a pilot-plant biogas reactor by Dina Jabbour; Anneke Sorger; Kerstin Sahm; Garabed Antranikian (pp. 2971-2978).

Aiming at the isolation of novel enzymes from previously uncultured thermophilic microorganisms, a metagenome library was constructed from DNA isolated from a pilot-plant biogas reactor operating at 55 °C. The library was screened for starch-degrading enzymes, and one active clone was found. An open reading frame of 1,461 bp encoding an α-amylase from an uncultured organism was identified. The amy13A gene was cloned in Escherichia coli, resulting in high-level expression of the recombinant amylase. The novel enzyme Amy13A showed the highest sequence identity (75 %) to α-amylases from Petrotoga mobilis and Halothermothrix orenii. Amy13A is highly thermoactive, exhibiting optimal activity at 80 °C, and it is also highly salt-tolerant, being active in 25 % (w/v) NaCl. Amy13A is one of the few enzymes that tolerate high concentrations of salt and elevated temperatures, making it a potential candidate for starch processing under extreme conditions.

Keywords: α-Amylase; Glycoside hydrolase family 13; Petrotoga ; Thermophile; Halophile; Calcium-dependent; Metagenome

Strategies for strain improvement in Fusarium fujikuroi: overexpression and localization of key enzymes of the isoprenoid pathway and their impact on gibberellin biosynthesis by Sabine Albermann; Pia Linnemannstöns; Bettina Tudzynski (pp. 2979-2995).

The rice pathogen Fusarium fujikuroi is known to produce a wide range of secondary metabolites, such as the pigments bikaverin and fusarubins, the mycotoxins fusarins and fusaric acid, and the phytohormones gibberellic acids (GAs), which are applied as plant growth regulators in agri- and horticulture. The development of high-producing strains is a prerequisite for the efficient biotechnological production of GAs. In this work, we used different molecular approaches for strain improvement to directly affect expression of early isoprenoid genes as well as GA biosynthetic genes. Overexpression of the first GA pathway gene ggs2, encoding geranylgeranyl diphosphate synthase 2, or additional integration of ggs2 and cps/ks, the latter encoding the bifunctional ent-copalyldiphosphate synthase/ent-kaurene synthase, revealed an enhanced production level of 150 %. However, overexpression of hmgR and fppS, encoding the key enzymes of the mevalonate pathway, hydroxymethylglutaryl coenzyme A reductase, and farnesyldiphosphate synthase, resulted in a reduced production level probably due to a negative feedback regulation of HmgR. Subsequent deletion of the transmembrane domains of HmgR and overexpression of the remaining catalytic domain led to an increased GA content (250 %). Using green fluorescent protein and mCherry fusion constructs, we localized Cps/Ks in the cytosol, Ggs2 in small point-like structures, which are not the peroxisomes, and HmgR at the endoplasmatic reticulum. In summary, it was shown for the first time that amplification or truncation of key enzymes of the isoprenoid and GA pathway results in elevated production levels (2.5-fold). Fluorescence microscopy revealed localization of the key enzymes in different compartments.

Keywords: Fusarium fujikuroi ; Gibberellic acid; Hydroxymethylglutaryl coenzyme A reductase; Geranylgeryanyldiphosphate synthase; ent-copalyldiphosphate synthase/ent-kaurene synthase

Improving the thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 using a computationally aided method by Jian Tian; Ping Wang; Lu Huang; Xiaoyu Chu; Ningfeng Wu; Yunliu Fan (pp. 2997-3006).

Good protein thermostability is very important for the protein application. In this report, we propose a strategy which contained a prediction method to select residues related to protein thermal stability, but not related to protein function, and an experiment method to screen the mutants with enhanced thermostability. The prediction strategy was based on the calculated site evolutionary entropy and unfolding free energy difference between the mutant and wild-type (WT) methyl parathion hydrolase enzyme from Ochrobactrum sp. M231 [Ochr-methyl parathion hydrolase (MPH)]. As a result, seven amino acid sites within Ochr-MPH were selected and used to construct seven saturation mutagenesis libraries. The results of screening these libraries indicated that six sites could result in mutated enzymes exhibiting better thermal stability than the WT enzyme. A stepwise evolutionary approach was designed to combine these selected mutants and a mutant with four point mutations (S274Q/T183E/K197L/S192M) was selected. The T _m and T ₅₀ of the mutant enzyme were 11.7 and 10.2 °C higher, respectively, than that of the WT enzyme. The success of this design methodology for Ochr-MPH suggests that it was an efficient strategy for enhancing protein thermostability and suitable for protein engineering.

Keywords: Methyl parathion hydrolase; Site evolutionary entropy; Thermostability; Prethermut; Unfolding free energy

Improving the safety of viral DNA vaccines: development of vectors containing both 5′ and 3′ homologous regulatory sequences from non-viral origin by A. Martinez-Lopez; P. Encinas; P. García-Valtanen; E. Gomez-Casado; J. M. Coll; A. Estepa (pp. 3007-3016).

Although some DNA vaccines have proved to be very efficient in field trials, their authorisation still remains limited to a few countries. This is in part due to safety issues because most of them contain viral regulatory sequences to driving the expression of the encoded antigen. This is the case of the only DNA vaccine against a fish rhabdovirus (a negative ssRNA virus), authorised in Canada, despite the important economic losses that these viruses cause to aquaculture all over the world. In an attempt to solve this problem and using as a model a non-authorised, but efficient DNA vaccine against the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV), we developed a plasmid construction containing regulatory sequences exclusively from fish origin. The result was an “all-fish vector”, named pJAC-G, containing 5′ and 3′ regulatory sequences of β-acting genes from carp and zebrafish, respectively. In vitro and in vivo, pJAC-G drove a successful expression of the VHSV glycoprotein G (G), the only antigen of the virus conferring in vivo protection. Furthermore, and by means of in vitro fusion assays, it was confirmed that G protein expressed from pJAC-G was fully functional. Altogether, these results suggest that DNA vaccines containing host-homologous gene regulatory sequences might be useful for developing safer DNA vaccines, while they also might be useful for basic studies.

Keywords: Terminators; Vector regulatory sequences; Fish; DNA; Vaccines; Plasmid; VHSV; Rhabdovirus

Use of uridine auxotrophy (ura3) for markerless transformation of the mycoinsecticide Beauveria bassiana by Sheng-Hua Ying; Ming-Guang Feng; Nemat O. Keyhani (pp. 3017-3025).

Genetic engineering offers a practical route for enhancing the insect biological control potential of entomopathogenic fungi such as Beauveria bassiana. To date, however, such efforts have relied upon transformation protocols that utilize antibiotic or herbicidal resistance markers as selection agents for the introduction of genes into the fungus. In order to avoid the use of such markers for the development of field-usable fungal strains, a markerless transformation system based upon complementation of uridine auxotrophy was developed. A targeted gene deletion knockout of orotidine 5′-phosphate decarboxylase (ura3) was isolated using a positive screening protocol with 5′-fluoro-orotate. Although growth was restored when the mutant, ΔBbura3, was grown in the presence of exogenous uridine, conidiation remained impaired and conidial yield was reduced. Insect bioassays revealed that the ΔBbura3 strain was essentially avirulent using both topical and intrahemocoel injection assays, indicating that the deletion mutant was unable to scavenge uridine from the host during infection. A series of plasmid constructs were developed for complementation of the ura3 mutant, and complemented strains were restored to wild-type growth and virulence. These data indicate that the ura3 mutant and corresponding complementation vectors can be used to construct markerless strains for the bioengineering of desired traits in B. bassiana.

Keywords: Beauveria bassiana ; Insect biological control; Uridine auxotrophy; Markerless transformation

Improving polyhydroxyalkanoate production by knocking out the genes involved in exopolysaccharide biosynthesis in Haloferax mediterranei by Dahe Zhao; Lei Cai; Jinhua Wu; Ming Li; Hailong Liu; Jing Han; Jian Zhou; Hua Xiang (pp. 3027-3036).

Haloferax mediterranei is capable of producing large amounts of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from many kinds of carbon sources, with exopolysaccharide (EPS) as a by-product. In this study, we identified a gene cluster involved in EPS biosynthesis in H. mediterranei. Knocking out the genes in this cluster encoding the putative UDP-N-acetylglucosamine 6-dehydrogenase (HFX_2145), glycosyltransferases (HFX_2146 and HFX_2147) and polysaccharide transporter (HFX_2148) eliminated EPS synthesis. The deficiency in EPS biosynthesis in the mutant strain remarkably decreased the viscosity of culture broth, and hence increased the dissolved oxygen content and decreased the foaming propensity. Compared with the wild-type (WT) strain, the PHBV production of the EPS-mutant strain was significantly enhanced (approximately 20 %), whereas the cell growth rate remained similar under the same culture conditions. These results indicated that the carbon sources used for synthesizing EPS were shifted to PHBV production. Thus, a novel engineered H. mediterranei strain was developed, which would be favorable for future industrial production of PHBV.

Keywords: Haloarchaea; Haloferax mediterranei ; Exopolysaccharide; Viscosity; Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)

Generalizing a hybrid synthetic promoter approach in Yarrowia lipolytica by John Blazeck; Ben Reed; Rishi Garg; Rachelle Gerstner; Annie Pan; Vaibhav Agarwala; Hal S. Alper (pp. 3037-3052).

Both varied and strong promoters are essential for metabolic and pathway engineering applications in any host organism. To enable this capacity, here we demonstrate a generalizable method for the de novo construction of strong, synthetic hybrid promoter libraries. Specifically, we demonstrate how promoter truncation and fragment dissection analysis can be utilized to identify both novel upstream activating sequences (UAS) and core promoters—the two components required to generate hybrid promoters. As a base case, the native TEF promoter in Yarrowia lipolytica was examined to identify putative UAS elements that serve as modular synthetic transcriptional activators. Resulting synthetic promoters containing a core promoter region activated by between one and twelve tandem repeats of the newly isolated, 230 nucleotide UAS_TEF#2 element showed promoter strengths 3- to 4.5-fold times the native TEF promoter. Further analysis through transcription factor binding site abrogation revealed the GCR1p binding site to be necessary for complete UAS_TEF#2 function. These various promoters were tested for function in a variety of carbon sources. Finally, by combining disparate UAS elements (in this case, UAS_TEF and UAS1B), we developed a high-strength promoter with for Y. lipolytica with an expression level of nearly sevenfold higher than that of the strong, constitutive TEF promoter. Thus, the general strategy described here enables the efficient, de novo construction of synthetic promoters to both increase native expression capacity and to produce libraries for tunable gene expression.

Keywords: Hybrid promoter; Promoter engineering; Yarrowia lipolytica ; TEF

Application of a combined approach involving classical random mutagenesis and metabolic engineering to enhance FK506 production in Streptomyces sp. RM7011 by SangJoon Mo; Sung-Kwon Lee; Ying-Yu Jin; Chung-Hun Oh; Joo-Won Suh (pp. 3053-3062).

FK506 production by a mutant strain (Streptomyces sp. RM7011) induced by N-methyl-N′-nitro-N-nitrosoguanidine and ultraviolet mutagenesis was improved by 11.63-fold (94.24 mg/l) compared to that of the wild-type strain. Among three different metabolic pathways involved in the biosynthesis of methylmalonyl-CoA, only expression of propionyl-CoA carboxylase (PCC) pathway led to a 1.75-fold and 2.5-fold increase in FK506 production and the methylmalonyl-CoA pool, respectively, compared to those of the RM7011 strain. Lipase activity of the high FK506 producer mutant increased in direct proportion to the increase in FK506 yield, from low detection level up to 43.1 U/ml (12.6-fold). The level of specific FK506 production and lipase activity was improved by enhancing the supply of lipase inducers. This improvement was approximately 1.88-fold (71.5 mg/g) with the supplementation of 5 mM Tween 80, which is the probable effective stimulator in lipase production, to the R2YE medium. When 5 mM vinyl propionate was added as a precursor for PCC pathway to R2YE medium, the specific production of FK506 increased approximately 1.9-fold (71.61 mg/g) compared to that under the non-supplemented condition. Moreover, in the presence of 5 mM Tween 80, the specific FK506 production was approximately 2.2-fold (157.44 mg/g) higher than that when only vinyl propionate was added to the R2YE medium. In particular, PCC expression in Streptomyces sp. RM7011 (RM7011/pSJ1003) together with vinyl propionate feeding resulted in an increase in the FK506 titer to as much as 1.6-fold (251.9 mg/g) compared with that in RM7011/pSE34 in R2YE medium with 5 mM Tween 80 supplementation, indicating that the vinyl propionate is more catabolized to propionate by stimulated lipase activity on Tween 80, that propionyl-CoA yielded from propionate generates methylmalonyl-CoA, and that the PCC pathway plays a key role in increasing the methylmalonyl-CoA pool for FK506 biosynthesis in RM7011 strain. Overall, these results show that a combined approach involving classical random mutation and metabolic engineering can be applied to supply the limiting factor for FK506 biosynthesis, and vinyl propionate could be successfully used as a precursor of important methylmalonyl-CoA building blocks.

Keywords: FK506; Methylmalonyl-CoA; Metabolic engineering; Propionyl-CoA carboxylase; Lipase activity; Vinyl propionate

Malic enzyme activity is not the only bottleneck for lipid accumulation in the oleaginous fungus Mucor circinelloides by Rosa Amarilis Rodríguez-Frómeta; Adrián Gutiérrez; Santiago Torres-Martínez; Victoriano Garre (pp. 3063-3072).

Commercial interest in microbial lipids is increasing due to their potential use as feedstock for biodiesel production. The supply of NADPH generated by malic enzyme (ME; NADP⁺-dependent; EC 1.1.1.40) has been postulated as being the rate-limiting step for fatty acid biosynthesis in oleaginous fungi, based mainly on data from the zygomycete Mucor circinelloides studies. This fungus contains five genes that code for six different ME isoforms. One of these genes, malA, codes for the isoforms III and IV, which have previously been associated with lipid accumulation. Following a strategy of targeted integration of an engineered malA gene, a stable strain overexpressing malA and showing high ME activity has been obtained, demonstrating the feasibility of this strategy to overexpress genes of biotechnological interest in M. circinelloides. This is the first report showing the integration and overexpression of a gene in Zygomycetes. Unexpectedly, the genetically modified strain showed a lipid content similar to that of a prototrophic non-overexpressing control strain, suggesting that another limiting step in the fatty acid synthesis pathway may have been revealed as a consequence of the elimination of malic enzyme-based bottleneck. Otherwise, the fact that prototrophic strains showed at least a 2.5-fold increase in lipid accumulation in comparison with leucine auxotrophic strains suggests that a wild-type leucine biosynthetic pathway is required for lipid accumulation. Moreover, increasing concentrations of leucine in culture medium increased growth of auxotrophs but failed to increase lipid content, suggesting that the leucine synthesized by the fungus is the only leucine available for lipid biosynthesis. These results support previous data postulating leucine metabolism as one of the pathways involved in the generation of the acetyl-CoA required for fatty acid biosynthesis.

Keywords: Leucine metabolism; Fatty acid biosynthesis; Biodiesel; Oleaginous fungi

The transport of phenylacetic acid across the peroxisomal membrane is mediated by the PaaT protein in Penicillium chrysogenum by Marta Fernández-Aguado; Ricardo V. Ullán; Fernando Teijeira; Raquel Rodríguez-Castro; Juan F. Martín (pp. 3073-3084).

Penicillium chrysogenum, an industrial microorganism used worldwide for penicillin production, is an excellent model to study the biochemistry and the cell biology of enzymes involved in the synthesis of secondary metabolites. The well-known peroxisomal location of the last two steps of penicillin biosynthesis (phenylacetyl–CoA ligase and isopenicillin N acyltransferase) requires the import into the peroxisomes of the intermediate isopenicillin N and the precursors phenylacetic acid and coenzyme A. The mechanisms for the molecular transport of these precursors are still poorly understood. In this work, a search was made, in the genome of P. chrysogenum, in order to find a Major Facilitator Superfamily (MFS) membrane protein homologous to CefT of Acremonium chrysogenum, which is known to confer resistance to phenylacetic acid. The paaT gene was found to encode a MFS membrane protein containing 12 transmembrane spanners and one Pex19p-binding domain for Pex19-mediated targeting to peroxisomal membranes. RNA interference-mediated silencing of the paaT gene caused a clear reduction of benzylpenicillin secretion and increased the sensitivity of P. chrysogenum to the penicillin precursor phenylacetic acid. The opposite behavior was found when paaT was overexpressed from the glutamate dehydrogenase promoter that increases phenylacetic acid resistance and penicillin production. Localization studies by fluorescent laser scanning microscopy using PaaT–DsRed and EGFP–SKL fluorescent fusion proteins clearly showed that the protein was located in the peroxisomal membrane. The results suggested that PaaT is involved in penicillin production, most likely through the translocation of side-chain precursors (phenylacetic acid and phenoxyacetic acid) from the cytosol to the peroxisomal lumen across the peroxisomal membrane of P. chrysogenum.

Keywords: Penicillium chrysogenum ; Penicillin biosynthetic pathway; Phenylacetic acid; MFS transporter; Peroxisomal membrane protein

The novel antimicrobial peptide PXL150 in the local treatment of skin and soft tissue infections by Emma Myhrman; Joakim Håkansson; Kerstin Lindgren; Camilla Björn; Veronika Sjöstrand; Margit Mahlapuu (pp. 3085-3096).

Dramatic increase in bacterial resistance towards conventional antibiotics emphasises the importance to identify novel, more potent antimicrobial therapies. Antimicrobial peptides (AMPs) have emerged as a promising new group to be evaluated in therapeutic intervention of infectious diseases. Here we describe a novel AMP, PXL150, which demonstrates in vitro a broad spectrum microbicidal action against both Gram-positive and Gram-negative bacteria, including resistant strains. The potent microbicidal activity and broad antibacterial spectrum of PXL150 were not associated with any hemolytic activity. Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) failed to develop resistance towards PXL150 during continued selection pressure. PXL150 caused a rapid depolarisation of cytoplasmic membrane of S. aureus, and dissipating membrane potential is likely one mechanism for PXL150 to kill its target bacteria. Studies in human cell lines indicated that PXL150 has anti-inflammatory properties, which might be of additional benefit. PXL150 demonstrated pronounced anti-infectious effect in an in vivo model of full thickness wounds infected with MRSA in rats and in an ex vivo model of pig skin infected with S. aureus. Subcutaneous or topical application of the peptide in rats did not lead to any adverse reactions. In conclusion, PXL150 may constitute a new therapeutic alternative for local treatment of infections, and further studies are warranted to evaluate the applicability of this AMP in clinical settings.

Keywords: Antimicrobial peptide; Wound infection; Antibiotic resistance; Staphylococcus aureus ; MRSA

Developmental cycle and pharmaceutically relevant compounds of Salinispora actinobacteria isolated from Great Barrier Reef marine sponges by Yi Kai Ng; Amitha K. Hewavitharana; Richard Webb; P. Nicholas Shaw; John A. Fuerst (pp. 3097-3108).

The developmental cycle of the obligate marine antibiotic producer actinobacterium Salinispora arenicola isolated from a Great Barrier Reef marine sponge was investigated in relation to mycelium and spore ultrastructure, synthesis of rifamycin antibiotic compounds, and expression of genes correlated with spore formation and with rifamycin precursor synthesis. The developmental cycle of S. arenicola M413 on solid agar medium was characterized by substrate mycelium growth, change of colony color, and spore formation; spore formation occurred quite early in colony growth but development of black colonies occurred only at late stages, correlated with a change in spore maturity in relation to cell wall layers. Rifamycins were detected throughout the growth cycle, but changed in relative quantity at particular phases in the cycle, with a marked increase after 32 days. Expression of the spore division gene ssgA and the rifK gene for 3-amino-5-hydroxybenzoate synthase responsible for rifamycin precursor synthesis was seen even at early stages of the growth cycle. ssgA expression significantly increased between days 26 and 31, but rifK expression effectively remained constant throughout the growth cycle, consistent with the early synthesis of rifamycin. Factors other than precursor synthesis may be responsible for an observed late increase in rifamycin production. A useful approach for measuring and exploring the regulation of antibiotic synthesis and gene expression in the marine natural product producer S. arenicola has been established.

Keywords: Salinispora ; Actinobacteria; Marine bacteria; Antibiotics; Electron microscopy; Developmental cycle

Fermentation of xylo-oligosaccharides by Bifidobacterium adolescentis DSMZ 18350: kinetics, metabolism, and β-xylosidase activities by Alberto Amaretti; Tatiana Bernardi; Alan Leonardi; Stefano Raimondi; Simona Zanoni; Maddalena Rossi (pp. 3109-3117).

Xylo-oligosaccharides (XOS) are sugar oligomers of β-1,4-linked xylopyranosyl moieties which exert bifidogenic effect and are increasingly used as prebiotics. The kinetics and the metabolism of Bifidobacterium adolescentis DSMZ 18350 growing on XOS and xylose were investigated. The growth rate was higher on XOS, but greater biomass yield was attained on xylose. Unlike other prebiotics, XOS oligomers were utilized simultaneously, regardless of their chain length. Throughout XOS utilization, xylose concentration slightly increased, being not neatly consumed and remaining unfermented. During growth on XOS, β-xylosidase activity was present in the cytosol, but it occurred in the supernatant as well. A β-1,4-xylolytic enzyme was purified from the supernatant of XOS cultures. The enzyme, a homotetramer of a 39-kDa single protein, was capable of complete XOS hydrolysis and exhibited maximum activity at pH 6.0 and 55 °C. Based on the molecular weight, the protein can be ascribable to the product of the gene BAD_1527, the activity of which has been inferred as an endo-β-1,4-xylanase, but has not been characterized so far. This β-1,4-xylolytic enzyme, found to be active in the cultural supernatant, gives a reason for the never explained accumulation of the monosaccharides in the media of bifidobacterial cultures growing on XOS, without excluding the major role of the intracellular hydrolysis of the imported oligomers.

Keywords: Bifidobacterium adolescentis ; XOS; Xylo-oligosaccharides; Xylose; Xylosidase

Effectiveness of arbuscular mycorrhizal fungi (AMF) for inducing the accumulation of major carotenoids, chlorophylls and tocopherol in green and red leaf lettuces by Marouane Baslam; Raquel Esteban; José I. García-Plazaola; Nieves Goicoechea (pp. 3119-3128).

Previous studies demonstrated that arbuscular mycorrhizal fungi (AMF) can induce the accumulation of carotenoids, phenolics, anthocyanins and some mineral nutrients in leaves of lettuce (Lactuca sativa L.) thus enhancing its nutritional quality. Our objectives were to know which carotenoids were the most accumulated in leaves of mycorrhizal lettuces and to assess the effect of AMF on tocopherols’ levels in leaves of lettuce plants. AMF always enhanced growth and, in most cases, increased the levels of all major carotenoids, chlorophylls and tocopherols in green and red leaf lettuces. Since these molecules are also important nutraceuticals, mycorrhization emerges as reliable technique to enhance the nutritional value of edible vegetables. These results are compared with other methods developed to improve nutritional quality.

Keywords: Arbuscular mycorrhizal fungi; β-carotene; Lactuca sativa L.; Tocopherols; Xanthophylls

Fermentation of quinoa and wheat slurries by Lactobacillus plantarum CRL 778: proteolytic activity by Andrea Micaela Dallagnol; Micaela Pescuma; Graciela Font De Valdez; Graciela Rollán (pp. 3129-3140).

Quinoa fermentation by lactic acid bacteria (LAB) is an interesting alternative to produce new bakery products with high nutritional value; furthermore, they are suitable for celiac patients because this pseudo-cereal contains no gluten. Growth and lactic acid production during slurry fermentations by Lactobacillus plantarum CRL 778 were greater in quinoa (9.8 log cfu/mL, 23.1 g/L) than in wheat (8.9 log cfu/mL, 13.9 g/L). Lactic fermentation indirectly stimulated flour protein hydrolysis by endogenous proteases of both slurries. However, quinoa protein hydrolysis was faster, reaching 40–100 % at 8 h of incubation, while wheat protein hydrolysis was only 0–20 %. In addition, higher amounts of peptides (24) and free amino acids (5 g/L) were determined in quinoa compared to wheat. Consequently, greater concentrations (approx. 2.6-fold) of the antifungal compounds (phenyllactic and hydroxyphenyllactic acids) were synthesized from Phe and Tyr in quinoa by L. plantarum CRL 778, an antifungal strain. These promising results suggest that this LAB strain could be used in the formulation of quinoa sourdough to obtain baked goods with improved nutritional quality and shelf life, suitable for celiac patients.

Keywords: Quinoa; Proteolysis; Lactobacillus ; Fermentation

Inhibition of yeast-to-hypha transition in Candida albicans by phorbasin H isolated from Phorbas sp. by So-Hyoung Lee; Ju-eun Jeon; Chan-Hong Ahn; Soon-Chun Chung; Jongheon Shin; Ki-Bong Oh (pp. 3141-3148).

Phorbasin H is a diterpene acid of a bisabolane-related skeletal class isolated from the marine sponge Phorbas sp. In this study, we examined whether phorbasin H acted as a yeast-to-hypha transition inhibitor of Candida albicans. Growth experiments suggest that this compound does not inhibit yeast cell growth but inhibits filamentous growth in C. albicans. Northern blot analysis of signaling pathway components indicated that phorbasin H inhibited the expression of mRNAs related to cAMP–Efg1 pathway. The exogenous addition of db-cAMP to C. albicans cells had no influence on the frequency of hyphal formation. The expression of hypha-specific HWP1 and ALS3 mRNAs, both of which are positively regulated by the important regulator of cell wall dynamics Efg1, was significantly inhibited by the addition of phorbasin H. This compound also reduced the ability of C. albicans cells to adhere in a dose-dependent manner. Our findings suggest that phorbasin H impacts the activity of the cAMP–Efg1 pathway, thus leading to an alteration of C. albicans morphology.

Keywords: Candida albicans ; Morphogenesis; Phorbasin H; cAMP–Efg1 pathway

Cadmium removal and 2,4-dichlorophenol degradation by immobilized Phanerochaete chrysosporium loaded with nitrogen-doped TiO₂ nanoparticles by Guiqiu Chen; Song Guan; Guangming Zeng; Xiaodong Li; Anwei Chen; Cui Shang; Ying Zhou; Huanke Li; Jianmin He (pp. 3149-3157).

Phanerochaete chrysosporium has been identified as an effective bioremediation agent for its biosorption and degradation ability. However, the applications of P. chrysosporium are limited owing to its long degradation time and low resistance to pollutants. In this research, nitrogen-doped TiO₂ nanoparticles were loaded on P. chrysosporium to improve the remediation capacity for pollutants. The removal efficiencies were maintained at a high level: 84.2 % for Cd(II) and 78.9 % for 2,4-dichlorophenol (2,4-DCP) in the wide pH range of 4.0 to 7.0 in 60 h. The removal capacity of immobilized P. chrysosporium loaded with nitrogen-doped TiO₂ nanoparticles (PTNs) was strongly affected by the initial Cd(II) and 2,4-DCP concentrations. The hyphae of PTNs became tight, and a large amount of crystals adhered to them after the reaction. Fourier transform infrared spectroscopy showed that carboxyl, amino, and hydroxyl groups on the surface of PTNs were responsible for the biosorption. In the degradation process, 2,4-DCP was broken down into o-chlorotoluene and 4-hexene-1-ol. These results showed that PTNs is promising for simultaneous removal of Cd(II) and 2,4-DCP from wastewater.

Keywords: Phanerochaete chrysosporium ; Cadmium; 2,4-Dichlorophenol; Biosorption; Degradation

Impact of Phanerochaete chrysosporium inoculation on indigenous bacterial communities during agricultural waste composting by Jiachao Zhang; Guangming Zeng; Yaoning Chen; Man Yu; Hongli Huang; Changzheng Fan; Yi Zhu; Hui Li; Zhifeng Liu; Ming Chen; Min Jiang (pp. 3159-3169).

This research was conducted to distinguish between the separate effects of the Phanerochaete chrysosporium inoculation and sample property heterogeneity induced by different inoculation regimes on the indigenous bacterial communities during agricultural waste composting. P. chrysosporium was inoculated during different phases. The bacterial community abundance and structure were determined by quantitative PCR and denaturing gradient gel electrophoresis analysis, respectively. Results indicated a significant stimulatory effect of P. chrysosporium inoculation on the bacterial community abundance. The bacterial community abundance significantly coincided with pile temperature, ammonium, and nitrate (P < 0.006). Variance partition analysis showed that the P. chrysosporium inoculation directly explained 20.5 % (P = 0.048) of the variation in the bacterial communities, whereas the sample property changes induced by different inoculation regimes indirectly explained up to 35.1 % (P = 0.002). The bacterial community structure was significantly related to pile temperature, water-soluble carbon (WSC), and C/N ratio when P. chrysosporium were inoculated. The C/N ratio solely explained 7.9 % (P = 0.03) of the variation in community structure, whereas pile temperature and WSC explained 7.7 % (P = 0.026) and 7.5 % (P = 0.034) of the variation, respectively. P. chrysosporium inoculation affected the indigenous bacterial communities most probably indirectly through increasing pile temperature, enhancing the substrate utilizability, and changing other physico-chemical factors.

Keywords: Composting; Phanerochaete chrysosporium ; Inoculation; Bacterial community; Redundancy analysis; Variance partition analysis

Comparison of RNA- and DNA-based bacterial communities in a lab-scale methane-degrading biocover by Tae Gwan Kim; Kyung-Eun Moon; Jeonghee Yun; Kyung-Suk Cho (pp. 3171-3181).

Methanotrophs must become established and active in a landfill biocover for successful methane oxidation. A lab-scale biocover with a soil mixture was operated for removal of methane and nonmethane volatile organic compounds, such as dimethyl sulfide (DMS), benzene (B), and toluene (T). The methane elimination capacity was 211 ± 40 g m⁻² d⁻¹ at inlet loads of 330–516 g m⁻² d⁻¹. DMS, B, and T were completely removed at the bottom layer (40–50 cm) with inlet loads of 221.6 ± 92.2, 99.6 ± 19.5, and 23.4 ± 4.9 mg m⁻² d⁻¹, respectively. The bacterial community was examined based on DNA and RNA using ribosomal tag pyrosequencing. Interestingly, methanotrophs comprised 80 % of the active community (RNA) while 29 % of the counterpart (DNA). Types I and II methanotrophs equally contributed to methane oxidation, and Methylobacter, Methylocaldum, and Methylocystis were dominant in both communities. The DNA vs. RNA comparison suggests that DNA-based analysis alone can lead to a significant underestimation of active members.

Keywords: Biocover; Methanotroph; DNA; RNA; Pyrosequencing; Microbial ecology

Successive transformation of benzo[a]pyrene by laccase of Trametes versicolor and pyrene-degrading Mycobacterium strains by Jun Zeng; Xiangui Lin; Jing Zhang; Hong Zhu; Hong Chen; Ming Hung Wong (pp. 3183-3194).

We previously hypothesized that polycyclic aromatic hydrocarbon (PAH)-degrading bacteria that produce laccase may enhance the degree of benzo[a]pyrene mineralization. However, whether the metabolites of benzo[a]pyrene oxidized by laccase can be further transformed by PAH degraders remains unknown. In this study, pyrene-degrading mycobacteria with diverse degradation properties were isolated and employed for investigating the subsequent transformation on the metabolites of benzo[a]pyrene oxidized by fungal laccase of Trametes versicolor. The results confirm the successive transformation of benzo[a]pyrene metabolites, 6-benzo[a]pyrenyl acetate, and quinones by Mycobacterium strains, and report the discovery of the involvement of a O-methylation mediated pathway in the process. In detail, the vast majority of metabolite 6-benzo[a]pyrenyl acetate was transformed into benzo[a]pyrene quinones or methoxybenzo[a]pyrene, via two distinct steps that were controlled by the catechol-O-methyltransferase mediated O-methylation, while quinones were reduced to dihydroxybenzo[a]pyrene and further transformed into dimethoxy derivatives.

Keywords: Benzo[a]pyrene; Fungal laccase; Mycobacterium ; Successive transformation

Characterisation of microbial floras and functional gene levels in an anaerobic/aerobic bio-reactor for the degradation of carboxymethyl cellulose by Guodong Ji; Chen Wang; Feng Guo (pp. 3195-3206).

The current study determined the carboxymethyl cellulose (CMC) degradation efficiency, dominant microbial flora, eubacteria and archaebacteria characteristics, and expression levels of genes cel5A, cel6B, and bglC in an anaerobic/aerobic bio-reactor consisting of two-stage UASB (U1 and U2) and two-stage BAF (B1 and B2). The results showed that under three CMC loads, the CMC degradation efficiency of the UASB-BAF system was 91.25 %, 80.44 %, and 78.73 %, respectively. At higher CMC loads, the degradation of cellulose and transformation to cellobiose in U1 was higher, while the transformation to glucose was lower. The results of DGGE and real-time PCR indicated that cellulose degradation bacteria are dominant in U1, cellulose degradation bacteria and cellulose degradation symbiosis bacteria are dominant in B1, and non-cellulose degradation symbiosis bacteria are dominant in both U2 and B2. The rate-limiting enzyme gene of cellulose degradation in U1, B1, and B2 is cel6B, but it is cel5A in U2.

Keywords: Anaerobic/aerobic bio-reactor; Carboxymethyl cellulose; Cellulolytic microorganisms; Functional genes

Comparative study of mycelia growth and sporophore yield of Auricularia polytricha (Mont.) Sacc on selected palm oil wastes as fruiting substrate by Dang Lelamurni Abd Razak; Noorlidah Abdullah; Norjuliza Mohd Khir Johari; Vikineswary Sabaratnam (pp. 3207-3213).

The potential for using agricultural and industrial by-products as substrate for the production of the edible mushroom, Auricularia polytricha, was evaluated using several formulations of selected palm oil wastes mixed with sawdust and further supplemented with selected nitrogen sources. The best substrate formulations were sawdust (SD) mixed with oil palm frond (OPF; 90:10) added with 15 % spent grain (SG) and sawdust mixed with empty fruit bunch (EFB; 50:50) added with 10 % spent grain (SG) with mycelia growth rate of 8 mm/day and 7 mm/day respectively. These two substrate formulations were then subjected to different moisture content levels (65 %, 75 % and 85 %). Highest total fresh sporophore yield at 0.43 % was obtained on SD + OPF (90:10) + 15 % SG at 85 % moisture content, followed closely by SD + EFB (50:50) + 10 % SG with 0.40 % total yield, also at 85 % moisture content. Each of the substrate formulations at 85 % moisture content gave the highest biological efficiency (BE) at 288.9 % and 260.7 %, respectively. Both yield and biological efficiency of A. polytricha on these two formulations were almost three times higher when compared to sawdust substrate alone, thus proving the potential of these formulations to improve yield of this mushroom.

Keywords: Agro-residues; Sawdust; Edible mushroom; Mycelia growth; Biological efficiency; Fruiting

Bioreactor studies predict whole microbial population dynamics in oil sands tailings ponds by Ernest Chi Fru; Michael Chen; Gillian Walshe; Tara Penner; Christopher Weisener (pp. 3215-3224).

Microorganisms in oil sands fluid fine tailings (FFT) are critical to biogeochemical elemental cycling as well as to the degradation of residual hydrocarbon constituents and subsequent methane and CO₂ production. Microbial activity enhances particulate matter sedimentation rates and the dewatering of FFT materials, allowing water to be recycled back into bitumen extraction. A bulk of this evidence comes from bioreactor studies and has implications for engineering and environmental management of the FFT ponds. Yet, it is largely uncertain whether such laboratory populations are representative of whole field scale microbial communities. By using population ecology tools, we compared whole microbial communities present in FFT bioreactors to reference populations existing in Syncrude's West In Pit (WIP) tailings pond. Bacteria were found to be persistent in a sulfidic zone in both the oxic and anoxic bioreactors at all occasions tested. In contrast to the WIP, archaea only became predominant in bioreactors after 300 days, at which point analysis of similarity (global R statistic p < 0.5) revealed no significant dissimilarities between the populations present in either system. A whole community succession pattern from bacterial dominated prevalence to a new assemblage predominated by archaea was suggested. These results have implications for the stepwise development of microbial model systems for predictive management of field scale FFT basins.

Keywords: Whole community fingerprinting; Oil sands; Fine fluid tailings; Microbial community succession; Bacteria; Archaea

Activated zeolite—suitable carriers for microorganisms in anaerobic digestion processes? by S. Weiß; M. Lebuhn; D. Andrade; A. Zankel; M. Cardinale; R. Birner-Gruenberger; W. Somitsch; B. J. Ueberbacher; G. M. Guebitz (pp. 3225-3238).

Plant cell wall structures represent a barrier in the biodegradation process to produce biogas for combustion and energy production. Consequently, approaches concerning a more efficient de-polymerisation of cellulose and hemicellulose to monomeric sugars are required. Here, we show that natural activated zeolites (i.e. trace metal activated zeolites) represent eminently suitable mineral microhabitats and potential carriers for immobilisation of microorganisms responsible for anaerobic hydrolysis of biopolymers stabilising related bacterial and methanogenic communities. A strategy for comprehensive analysis of immobilised anaerobic populations was developed that includes the visualisation of biofilm formation via scanning electron microscopy and confocal laser scanning microscopy, community and fingerprint analysis as well as enzyme activity and identification analyses. Using SDS polyacrylamide gel electrophoresis, hydrolytical active protein bands were traced by congo red staining. Liquid chromatography/mass spectroscopy revealed cellulolytical endo- and exoglucanase (exocellobiohydrolase) as well as hemicellulolytical xylanase/mannase after proteolytic digestion. Relations to hydrolytic/fermentative zeolite colonisers were obtained by using single-strand conformation polymorphism analysis (SSCP) based on amplification of bacterial and archaeal 16S rRNA fragments. Thereby, dominant colonisers were affiliated to the genera Clostridium, Pseudomonas and Methanoculleus. The specific immobilisation on natural zeolites with functional microbes already colonising naturally during the fermentation offers a strategy to systematically supply the biogas formation process responsive to population dynamics and process requirements.

Keywords: Biogas; Zeolites; Hemicellulases; Cellulases; Microbial community; Grass silage

Membrane stress caused by octanoic acid in Saccharomyces cerevisiae by Ping Liu; Andriy Chernyshov; Tarek Najdi; Yao Fu; Julie Dickerson; Suzanne Sandmeyer; Laura Jarboe (pp. 3239-3251).

In order to compete with petroleum-based fuel and chemicals, engineering a robust biocatalyst that can convert renewable feedstocks into biorenewable chemicals, such as carboxylic acids, is increasingly important. However, product toxicity is often problematic. In this study, the toxicity of the carboxylic acids hexanoic, octanoic, and decanoic acid on Saccharomyces cerevisiae was investigated, with a focus on octanoic acid. These compounds are completely inhibitory at concentrations of magnitude 1 mM, and the toxicity increases as chain length increases and as media pH decreases. Transciptome analysis, reconstruction of gene regulatory network, and network component analysis suggested decreased membrane integrity during challenge with octanoic acid. This was confirmed by quantification of dose-dependent and chain length-dependent induction of membrane leakage, though membrane fluidity was not affected. This induction of membrane leakage could be significantly decreased by a period of pre-adaptation, and this pre-adaptation was accompanied by increased oleic acid content in the membrane, significantly increased production of saturated lipids relative to unsaturated lipids, and a significant increase in the average lipid chain length in the membrane. However, during adaptation cell surface hydrophobicity was not altered. The supplementation of oleic acid to the medium not only elevated the tolerance of yeast cells to octanoic acid but also attenuated the membrane leakiness. However, while attempts to mimic the oleic acid supplementation effects through expression of the Trichoplusia ni acyl-CoA Δ9 desaturase OLE1(TniNPVE desaturase) were able to increase the oleic acid content, the magnitude of the increase was not sufficient to reproduce the supplementation effect and increase octanoic acid tolerance. Similarly, introduction of cyclopropanated fatty acids through expression of the Escherichia coli cfa gene was not helpful for tolerance. Thus, we have provided quantitative evidence that carboxylic acids damage the yeast membrane and that manipulation of the lipid content of the membrane can increase tolerance, and possibly production, of these valuable products.

Keywords: S. cerevisiae ; Carboxylic acid; Membrane leakage; Membrane lipid composition

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Applied Microbiology and Biotechnology (v.97, #7)

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Applied Microbiology and Biotechnology (v.97, #7)