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Applied Microbiology and Biotechnology (v.93, #6)

Immobilized redox mediators for electrochemical NAD(P)⁺ regeneration by Svenja Kochius; Anders O. Magnusson; Frank Hollmann; Jens Schrader; Dirk Holtmann (pp. 2251-2264).

The applicability of dissolved redox mediators for NAD(P)⁺ regeneration has been demonstrated several times. Nevertheless, the use of mediators in solutions for sensor applications is not a very convenient strategy since the analysis is not reagentless and long stabilization times occur. The most important drawbacks of dissolved mediators in biocatalytic applications are interferences during product purification, limited reusability of the mediators, and their cost-intensive elimination from wastewater. Therefore, the use of immobilized mediators has both economic and ecological advantages. This work critically reviews the current state-of-art of immobilized redox mediators for electrochemical NAD(P)⁺ regeneration. Various surface modification techniques, such as adsorption polymerization and covalent linkage, as well as the corresponding NAD(P)⁺ regeneration rates and the operational stability of the immobilized mediator films, will be discussed. By comparison with other existing regeneration systems, the technical potential and future perspectives of biocatalytic redox reactions based on electrochemically fed immobilized mediators will be assessed.

Keywords: Cofactor; Immobilized mediator; NADH oxidation; Electropolymerization

Degradation of chlorinated nitroaromatic compounds by Pankaj Kumar Arora; Ch. Sasikala; Ch. Venkata Ramana (pp. 2265-2277).

Chlorinated nitroaromatic compounds (CNAs) are persistent environmental pollutants that have been introduced into the environment due to the anthropogenic activities. Bacteria that utilize CNAs as the sole sources of carbon and energy have been isolated from different contaminated and non-contaminated sites. Microbial metabolism of CNAs has been studied, and several metabolic pathways for degradation of CNAs have been proposed. Detoxification and biotransformation of CNAs have also been studied in various fungi, actinomycetes and bacteria. Several physicochemical methods have been used for treatment of wastewater containing CNAs; however, these methods are not suitable for in situ bioremediation. This review describes the current scenario of the degradation of CNAs.

Keywords: Chloronitrophenol; Chloronitrobenzene; Biodegradation; Microbial metabolism

Industrial biotechnology of Pseudomonas putida and related species by Ignacio Poblete-Castro; Judith Becker; Katrin Dohnt; Vitor Martins dos Santos; Christoph Wittmann (pp. 2279-2290).

Since their discovery many decades ago, Pseudomonas putida and related subspecies have been intensively studied with regard to their potential application in industrial biotechnology. Today, these Gram-negative soil bacteria, traditionally known as well-performing xenobiotic degraders, are becoming efficient cell factories for various products of industrial relevance including a full range of unnatural chemicals. This development is strongly driven by systems biotechnology, integrating systems metabolic engineering approaches with novel concepts from bioprocess engineering, including novel reactor designs and renewable feedstocks.

Keywords: Pseudomonas putida ; Cell factory; Bio-catalysis; Biofilm; Systems metabolic engineering; Synthetic biology; Bioeconomy

Strategies to overexpress enterotoxigenic Escherichia coli (ETEC) colonization factors for the construction of oral whole-cell inactivated ETEC vaccine candidates by Joshua Tobias; Ann-Mari Svennerholm (pp. 2291-2300).

Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrheal disease and deaths among children in developing countries and the major cause of traveler's diarrhea (TD). Since surface protein colonization factors (CFs) of ETEC are important for pathogenicity and immune protection is mainly mediated by locally produced IgA antibodies in the gut, much effort has focused on the development of an oral CF-based vaccine. The most extensively studied ETEC candidate vaccine is the rCTB-CF ETEC vaccine, containing recombinantly produced cholera B subunit and the most commonly encountered ETEC CFs on the surface of whole inactivated bacteria. Initial clinical trials with this vaccine showed significant immune responses against the key antigens in different age groups in Bangladesh and Egypt and protection against more severe TD in Western travelers. However, when tested in a phase-III trial in Egyptian infants, the protective efficacy of the vaccine was found to be low, indicating the need to improve the immunogenicity of the vaccine, e.g., by increasing the levels of the protective antigens. This review describes different strategies for the construction of recombinant nontoxigenic E. coli and Vibrio cholerae candidate vaccine strains over-expressing higher amounts of ETEC CFs than clinical ETEC isolates selected to produce high levels of the respective CF, e.g., those ETEC strains which have been used in the rCTB-CF ETEC vaccine. Several different expression vectors containing the genes responsible for the expression and assembly of the examined CFs, all downstream of the powerful tac promoter, which could be maintained either with or without antibiotic selection, were constructed. Expression from the tac promoter was under the control of the lacI ^q repressor present on the plasmids. Following induction with isopropyl-β-d-thiogalactopyranoside, candidate vaccine strains over-expressing single CFs, unnatural combinations of two CFs, and also hybrid forms of ETEC CFs were produced. Specific monoclonal antibodies against the major subunits of the examined CF were used to quantify the amount of the surface-expressed CF by a dot-blot assay and inhibition ELISA. Oral immunization with formalin- or phenol-inactivated recombinant bacteria over-expressing the CFs was found to induce significantly higher antibody responses compared to immunization with the previously used vaccine strains. We therefore conclude that our constructs may be useful as candidate strains in an oral whole-cell inactivated CF ETEC vaccine.

Keywords: Diarrhea; ETEC; Colonization factors; Recombinant over-expression; Nontoxigenic strains; Nonantibiotic selection marker; Oral vaccine

Identification of suitable ionic liquids for application in the enzymatic hydrolysis of rutin by an automated screening by H. Temme; O. Dethloff; W.-R. Pitner; S. Fischer; R. Scheurich; M. Schulte; B. Niemeyer (pp. 2301-2308).

An automated method in milliliter scale was developed for the screening of process parameters concerning the hydrolysis of the flavonoid rutin catalyzed by the rhamnosidase activity of naringinase from Penicillium decumbens. Besides the effect of additives such as ionic liquids and low molecular salts, the productivity in a multiple phase system as well as the recyclability of the enzyme in repetitive batches were studied. The hydrophobic ionic liquid (IL) trihexyl(tetradecyl)phosphonium bis(trifluormethylsulfonyl)imide [P(h₃)t][Tf₂N] was identified to combine the most favorable characteristics out of 23 investigated ILs with regard to enzyme compatibility, substrate solubility and enzyme partition coefficient. Also, for the corresponding cations 1-ethyl-3-methylimidazolium [EMIM], 1-butyl-3-methylimidazolium [BMIM], 1-butyl-1-methylpyrrolidinium [BMPL] and 1-octyl-3-methylimidazolium [OMIM], the entity with the [Tf₂N] anion was best tolerated by the naringinase. With increasing IL content, higher space time yields with up to 1.5 g/(L h) for 80% (v/v) [P(h₃)t][Tf₂N] were achieved. Enhanced specific enzyme activity was observed in the presence of Ca²⁺ ions. By addition of [P(h₃)t][Tf₂N] and calcium chloride, the reactive aqueous phase was successfully used in three repetitive batches with full conversion.

Keywords: Ionic liquids; Flavonoids; Naringinase; Reactive extraction; Robotic platform

Continuous bio-catalytic conversion of sugar mixture to acetone–butanol–ethanol by immobilized Clostridium acetobutylicum DSM 792 by Shrikant A. Survase; Adriaan van Heiningen; Tom Granström (pp. 2309-2316).

Continuous production of acetone, n-butanol, and ethanol (ABE) was carried out using immobilized cells of Clostridium acetobutylicum DSM 792 using glucose and sugar mixture as a substrate. Among various lignocellulosic materials screened as a support matrix, coconut fibers and wood pulp fibers were found to be promising in batch experiments. With a motive of promoting wood-based bio-refinery concept, wood pulp was used as a cell holding material. Glucose and sugar mixture (glucose, mannose, galactose, arabinose, and xylose) comparable to lignocellulose hydrolysate was used as a substrate for continuous production of ABE. We report the best solvent productivity among wild-type strains using column reactor. The maximum total solvent concentration of 14.32 g L⁻¹ was obtained at a dilution rate of 0.22 h⁻¹ with glucose as a substrate compared to 12.64 g L⁻¹ at 0.5 h⁻¹ dilution rate with sugar mixture. The maximum solvent productivity (13.66 g L⁻¹ h⁻¹) was obtained at a dilution rate of 1.9 h⁻¹ with glucose as a substrate whereas solvent productivity (12.14 g L⁻¹ h⁻¹) was obtained at a dilution rate of 1.5 h⁻¹ with sugar mixture. The immobilized column reactor with wood pulp can become an efficient technology to be integrated with existing pulp mills to convert them into wood-based bio-refineries.

Keywords: n-Butanol; Wood pulp; Immobilization; Clostridium acetobutylicum

Enzymatic synthesis of S-adenosylhomocysteine: immobilization of recombinant S-adenosylhomocysteine hydrolase from Corynebacterium glutamicum (ATCC 13032) by J. D. Lozada-Ramírez; A. Sánchez-Ferrer; F. García-Carmona (pp. 2317-2325).

Recombinant S-adenosylhomocysteine hydrolase from Corynebacterium glutamicum (CgSAHase) was covalently bound to Eupergit® C. The maximum yield of bound protein was 91% and the catalytic efficiency was 96.9%. When the kinetic results for the immobilized enzyme were compared with those for the soluble enzyme, no decrease in the catalytic efficiency of the former was detected. Both soluble and immobilized enzymes showed similar optimum pH and temperature ranges. The reuse of immobilized CgSAHase caused a loss of synthetic activity due to NAD⁺ release, although the binding to the support was sufficiently strong for up to 5 cycles with 95% conversion efficiency. The immobilized enzyme was incubated every 3 cycles with 100 μM NAD⁺ to recover the loss of activity after 5 cycles. This maintained the activity for another 50 cycles. The purification of S-adenosylhomocysteine (SAH) provided an overall yield of 76% and 98% purity as determined by HPLC and NMR analyses. The results indicate the suitability of immobilized CgSAHase for synthesizing SAH and other important S-nucleosidylhomocysteine.

Keywords: S-Adenosylhomocysteine; S-Adenosylhomocysteine hydrolase; Corynebacterium glutamicum ; Immobilization; Synthesis

Modulation of guanosine nucleotides biosynthetic pathways enhanced GDP-l-fucose production in recombinant Escherichia coli by Won-Heong Lee; So-Yeon Shin; Myoung-Dong Kim; Nam Soo Han; Jin-Ho Seo (pp. 2327-2334).

Guanosine 5′-triphosphate (GTP) is the key substrate for biosynthesis of guanosine 5′-diphosphate (GDP)-l-fucose. In this study, improvement of GDP-l-fucose production was attempted by manipulating the biosynthetic pathway for guanosine nucleotides in recombinant Escherichia coli-producing GDP-l-fucose. The effects of overexpression of inosine 5′-monophosphate (IMP) dehydrogenase, guanosine 5′-monophosphate (GMP) synthetase (GuaB and GuaA), GMP reductase (GuaC) and guanosine–inosine kinase (Gsk) on GDP-l-fucose production were investigated in a series of fed-batch fermentations. Among the enzymes tested, overexpression of Gsk led to a significant improvement of GDP-l-fucose production. Maximum GDP-l-fucose concentration of 305.5 ± 5.3 mg l⁻¹ was obtained in the pH-stat fed-batch fermentation of recombinant E. coli-overexpressing Gsk, which corresponds to a 58% enhancement in the GDP-l-fucose production compared with the control strain overexpressing GDP-l-fucose biosynthetic enzymes. Such an enhancement of GDP-l-fucose production could be due to the increase in the intracellular level of GMP.

Keywords: Recombinant Escherichia coli ; GDP-l-fucose; Guanosine nucleotides; Guanosine–inosine kinase; pH-stat fed-batch fermentation

Enhancement of transglutaminase production in Streptomyces mobaraensis as achieved by treatment with excessive MgCl₂ by Lili Zhang; Lanwei Zhang; Xue Han; Ming Du; Yingchun Zhang; Zhen Feng; Huaxi Yi; Yanhe Zhang (pp. 2335-2343).

In this study, we first tested the capacity for eight different salts as stress-mediated bioprocesses in the production of transglutaminase (TGase). A significant effect on the cell growth and TGase production was obtained with the highest yield of TGase being observed at 96 h of incubation (4.3 U/ml) when the basic medium was supplemented 0.10 M MgCl₂, as opposed to that observed with the basic medium control (2.1 U/ml at 120 h). Data from Western blot assays showed that transformation of pro-TGase to its mature enzyme occurred more rapidly in MgCl₂ medium. Furthermore, total protease, metalloprotease, and serine protease were also synthesized at a faster rate in the medium containing MgCl₂. The results demonstrate that MgCl₂ enhanced the production of key proteases involved in the activation of TGase biosynthesis. To explore the mechanism, viability assay was performed. The results show that MgCl₂ induced the mycelia differentiation, decreased cell growth rate, and stimulated cell death. We argue that TGase production was promoted by the stimulation of mycelium differentiation induced by MgCl₂ stress.

Keywords: Streptomyces mobaraensis; Transglutaminase; Production; MgCl₂ ; Protease; Biosynthesize

Production of bioactive, SUMO-modified, and native-like TNF-α of the rhesus monkey, Macaca mulatta, in Escherichia coli by Dianlong Jia; Hao Yang; Lin Wan; Jingqiu Cheng; Xiaofeng Lu (pp. 2345-2355).

Biotechnologically produced tumor necrosis factor alpha (TNF-α) neutralizing agents have proven efficient in patients suffering from disparate autoimmune diseases. The rhesus monkey (Macaca mulatta) could be developed as a model for human autoimmune disease. Consequently, a large amount of M. mulatta TNF-α (mmTNFα) is required to further understand TNF-α-related pathogenesis and evaluate novel human TNF-α (hTNFα) neutralizing agents. We therefore attempted to express mmTNFα by using a small ubiquitin-like modifier (SUMO) fusion system. The synthetic gene, encoding the fusion protein SUMO-mmTNFα, was inserted into a pQE30 plasmid and was transformed into Escherichia coli M15. The fusion protein was expressed as both soluble and insoluble protein in E. coli. Approximately 10–12 mg of SUMO–mmTNFα was obtained from the soluble fraction of 1 L of bacterial culture. Cleavage of the fusion protein with SUMO protease produced native-like mmTNFα. Both native-like and SUMO-modified mmTNFα formed functional trimers and showed excellent cytotoxicity (ED₅₀, 0.05–0.1 ng/ml) in standard L929 cells. In addition, SUMO–mmTNFα and mmTNFα also exhibited cytotoxicity in human cancer cell types, such as, breast, lung, and liver cancer cells. The hTNFα neutralizing agents, including soluble receptors of hTNFα and antibodies against hTNFα, interacted with the mmTNFα. These results demonstrate that the bioactive mmTNFα produced with the SUMO fusion system is useful for further research, especially for the in vitro preclinical evaluation of biological hTNFα neutralizing agents.

Keywords: Tumor necrosis factor; Autoimmune disease; Rhesus monkey; Small ubiquitin-like modifier

Regio- and enantio-selective glycosylation of tetrahydroprotoberberines by Gliocladium deliquescens NRRL1086 resulting in unique alkaloidal glycosides by Hai-Xia Ge; Jian Zhang; Cui Kai; Ji-Hua Liu; Bo-Yang Yu (pp. 2357-2364).

The microbial transformation of a series of tetrahydroprotoberberines (THPBs, 1–5) by Gliocladium deliquescens NRRL1086 was investigated. In this research, the novel glycosylation of tetrahydroberberrubine (1) was observed with fast rate and high regio- and enantio-selectivity. One pair of unique enantiomorphic alkaloidal glycosides T-1 and T-2 was isolated and their structures were elucidated unambiguously by HR-MS, CD, 1D and 2D NMR spectrum. It is interesting that different amounts of glucose in the potato broth medium could influence the ratio of T-1 and T-2; in the 1.5% glucose medium, the ratio was about 15:1 and the yield of the S-form product T-1 may reach the theoretical maximum yield of about 50% which could provide one practical method to prepare the enantiomerically pure product and one alternative resolution method of tetrahydroberberrubine. The preliminary enzymatic research by using sodium dodecyl sulfate (SDS) and imidazole as glycosyltransferase and glycosidase inhibitors revealed that glycosyltransferase may contribute to glycosylation process. This is the first successful approach to glycosylation of tetrahydroprotoberberines.

Keywords: Microbial glycosylation; Tetrahydroprotoberberines; Biotransformation; Gliocladium deliquescens NRRL1086; Tetrahydroberberrubine

Compatibility of garlic (Allium sativum L.) leaf agglutinin and Cry1Ac δ-endotoxin for gene pyramiding by Santosh Kumar Upadhyay; Seema Singh; Krishnappa Chandrashekar; Rakesh Tuli; Pradhyumna Kumar Singh (pp. 2365-2375).

δ-Endotoxins produced by Bacillus thuringiensis (Bt) have been used as bio-pesticides for the control of lepidopteran insect pests. Garlic (Allium sativum L.) leaf agglutinin (ASAL), being toxic to several sap-sucking pests and some lepidopteran pests, may be a good candidate for pyramiding with δ-endotoxins in transgenic plants for enhancing the range of resistance to insect pests. Since ASAL shares the midgut receptors with Cry1Ac in Helicoverpa armigera, there is possibility of antagonism in their toxicity. Our study demonstrated that ASAL increased the toxicity of Cry1Ac against H. armigera while Cry1Ac did not alter the toxicity of ASAL against cotton aphids. The two toxins interacted and increased binding of each other to brush border membrane vesicle (BBMV) proteins and to the two important receptors, alkaline phosphatase (ALP) and aminopeptidase N (APN). The results indicated that the toxins had different binding sites on the ALP and APN but influenced mutual binding. We conclude that ASAL can be safely employed with Cry1Ac for developing transgenic crops for wider insect resistance.

Keywords: Alkaline phosphatase; Aminopeptidase; Allium sativum leaf agglutinin; Brush border membrane vesicles; Cry1Ac; H. armigera

Active site analysis of cis-epoxysuccinate hydrolase from Nocardia tartaricans using homology modeling and site-directed mutagenesis by Vinayagam Vasu; Jayaraman Kumaresan; Manoharan Ganesh Babu; Sankaranarayanan Meenakshisundaram (pp. 2377-2386).

Cis-epoxysuccinate hydrolase (CESH, EC 3.3.2.3) from Nocardia tartaricans is known to catalyze the opening of an epoxide ring of cis-epoxysuccinate (CES), thereby converting it to corresponding vicinal diol, l(+)-tartaric acid. An attempt has been made to build a 3D homology model of CESH to investigate the structure–function relationship, and also to understand the mechanism of the enzymatic reaction. Using a combination of molecular-docking simulation and multiple sequence alignment, a set of putative residues that are involved in the CESH catalysis has been identified. Functional roles of these putative active-site residues were further evaluated by site-directed mutagenesis. Interestingly, the mutants D18A, D18E, Q20E, T22A, R55E, N134D, K164A, H190A, H190N, H190Q, D193A, and D193E resulted in complete loss of activity, whereas the mutants Y58F, T133A, S189A, and Y192D retained partial enzyme activity. Furthermore, the active-site residues responsible for the opening of CES were analyzed, and the mechanism underlying the catalytic triad involved in l(+)-tartaric acid biosynthesis was proposed.

Keywords: Cis-epoxysuccinate hydrolase; Active site; Nocardia tartaricans ; Site-directed mutagenesis; Homology modeling

Cloning, expression, and characterization of an insoluble glucan-producing glucansucrase from Leuconostoc mesenteroides NRRL B-1118 by Gregory L. Côté; Christopher D. Skory (pp. 2387-2394).

We have cloned a glucansucrase from the type strain of Leuconostoc mesenteroides (NRRL B-1118; ATCC 8293) and successfully expressed the enzyme in Escherichia coli. The recombinant processed enzyme has a putative sequence identical to the predicted secreted native enzyme (1,473 amino acids; 161,468 Da). This enzyme catalyzed the synthesis of a water-insoluble α-D-glucan from sucrose (K _M 12 mM) with a broad pH optimum between 5.0 and 5.7 in the presence of calcium. Removal of calcium with dialysis resulted in lower activity in the acidic pH range, effectively shifting the pH optimum to 6.0–6.2. The enzyme was quickly inactivated at temperatures above approximately 45°C. The presence of dextran offered some protection from thermal inactivation between room temperature and 40°C but had little effect above 45°C. NMR and methylation analysis of the water-insoluble α-d-glucan revealed that it had approximately equal amounts of α(1 → 3)-linked and α(1 → 6)-linked d-glucopyranosyl units and a low degree of branching.

Keywords: Leuconostoc mesenteroides ; Dextransucrase; Glucansucrase; Glucosyltransferase

New strategy of site-directed mutagenesis identifies new sites to improve Streptomyces clavuligerus deacetoxycephalosporin C synthase activity toward penicillin G by Junjie Ji; Xiuyun Tian; Keqiang Fan; Keqian Yang (pp. 2395-2401).

Based on multiple sequence alignment of different deacetoxycephalosporin C synthase (DAOCSs) and the crystal structure of Streptomyces clavuligerus DAOCS, 2-oxoglutarate, and penicillin G triple complex, ten residues (Y184, V245, S261, C37, T42, V51, S59, A61, Q126, and T213) not directly involved in substrate recognition were selected as mutational targets. Twenty one mutants were generated and characterized, and five (Q126M, T213V, S261M, S261A, and Y184A) showed improved activity toward penicillin G, with 1.45- to 4.50-fold increment in the k _cat/K _m. Q126, T213, and S261 are identified for the first time, as sites with significant effect on enzyme activity.

Keywords: DAOCS; Site-directed mutagenesis; Streptomyces clavuligerus ; Kinetics

A thermostable recombinant transaldolase with high activity over a broad pH range by Song-Yan Huang; Y.-H. Percival Zhang; Jian-Jiang Zhong (pp. 2403-2410).

Thermophilic enzymes are in high demand for various applications due to their prolonged lifetimes and high reaction rates at elevated temperatures. In this work, an open reading frame TM0295, which encodes a putative transaldolase (TAL) from a hyper-thermophilic microorganism, Thermotoga maritima, was cloned and expressed in Escherichia coli. The enzyme activity of transaldolase at high temperatures (e.g., at 80 °C) was reported here for the first time. The recombinant T. maritima transaldolase was extremely thermostable, with a half-life time of 198 and 13.0 h at 60 °C and 80 °C, respectively. The estimated total turn-over number was 1.5 × 10⁶ mol of product per mol of enzyme at 80 °C. This enzyme also exhibited high activities within a broad pH range of 6.0–9.0. This ultra-thermostable TAL with high activity shows great potential for use in such applications as the production of enzymatic biofuels production and the synthesis of high-value carbohydrates by cell-free synthetic pathway biotransformation.

Keywords: Building block; Cell-free synthetic biology; Transaldolase activity; Thermotoga maritima ; Thermostability

Pasteurella multocida CMP-sialic acid synthetase and mutants of Neisseria meningitidis CMP-sialic acid synthetase with improved substrate promiscuity by Yanhong Li; Hai Yu; Hongzhi Cao; Saddam Muthana; Xi Chen (pp. 2411-2423).

Cytidine 5′-monophosphate (CMP)-sialic acid synthetases (CSSs) catalyze the formation of CMP-sialic acid from CTP and sialic acid, a key step for sialyltransferase-catalyzed biosynthesis of sialic acid-containing oligosaccharides and glycoconjugates. More than 50 different sialic acid forms have been identified in nature. To facilitate the enzymatic synthesis of sialosides with diverse naturally occurring sialic acid forms and their non-natural derivatives, CMP-sialic acid synthetases with promiscuous substrate specificity are needed. Herein we report the cloning, characterization, and substrate specificity studies of a new CSS from Pasteurella multocida strain P-1059 (PmCSS) and a CSS from Haemophillus ducreyi (HdCSS). Based on protein sequence alignment and substrate specificity studies of these two CSSs and a Neisseria meningitidis CSS (NmCSS), as well as crystal structure modeling and analysis of NmCSS, NmCSS mutants (NmCSS_S81R and NmCSS_Q163A) with improved substrate promiscuity were generated. The strategy of combining substrate specificity studies of enzymes from different sources and protein crystal structure studies can be a general approach for designing enzyme mutants with improved activity and substrate promiscuity.

Keywords: Carbohydrate synthesis; CMP-sialic acid; CMP-sialic acid synthetase; Mutagenesis; Sialic acid; Substrate specificity

Molecular determinants for substrate selectivity of ω-transaminases by Eul-Soo Park; Minji Kim; Jong-Shik Shin (pp. 2425-2435).

ω-Transaminase (ω-TA) is an industrially important enzyme for production of chiral amines. About 20 (S)-specific ω-TAs known to date show remarkably similar substrate selectivity characterized by stringent steric constraint precluding entry of a substituent larger than an ethyl group in the small binding pocket (S) and dual recognition of an aromatic substituent as well as a carboxylate group in the large pocket (L). The strictly defined substrate selectivity of the available ω-TAs remains a limiting factor in the production of structurally diverse chiral amines. In this work, we cloned, purified, and characterized three new ω-TAs from Ochrobactrum anthropi, Acinetobacter baumannii, and Acetobacter pasteurianus that were identified by a BLASTP search using the previously studied ω-TA from Paracoccus denitrificans. All the new ω-TAs exhibited similar substrate specificity, which led us to explore whether the molecular determinants for the substrate specificity are conserved among the ω-TAs. To this end, key active site residues were identified by docking simulation using the X-ray structure of the ω-TA from Pseudomonas putida. We found that the dual recognition in the L pocket is ascribed to Tyr23, Phe88*, and Tyr152 for hydrophobic interaction and Arg414 for recognition of a carboxylate group. In addition, the docking simulation indicates that Trp60 and Ile262 form the S pocket where the substituent size up to an ethyl group turns out to be sterically allowed. The six key residues were found to be essentially conserved among nine ω-TA sequences, underlying the molecular basis for the high similarity in the substrate selectivity.

Keywords: Transaminase; Active site; Substrate specificity; Docking simulation; Chiral amine

High-level mucosal and systemic immune responses induced by oral administration with Lactobacillus-expressed porcine epidemic diarrhea virus (PEDV) S1 region combined with Lactobacillus-expressed N protein by Liu Di-qiu; Ge Jun-wei; Qiao Xin-yuan; Jiang Yan-ping; Liu Song-mei; Li Yi-jing (pp. 2437-2446).

To develop effective mucosal vaccine formulation against porcine epidemic diarrhea virus (PEDV) infection, the DNA fragments encoding spike protein immunodominant region S1 and nucleocapsid N of PEDV were inserted into pPG1 (surface-displayed) or pPG2 (secretory) plasmids followed by electrotransformation into Lactobacillus casei (Lc) to yield four recombinant strains: PG1-S1, PG2-S1, PG1-N, and PG2-N. After intragastric administration, it was observed that live Lc-expressing S1 protein combined with Lc-expressing N protein could elicit much more potent mucosal and systemic immune responses than the former alone (P < 0.001), however slightly inferior to the latter alone (P > 0.05). Furthermore, the surface-displayed mixture (PG1-S1+ PG1-N) revealed stronger immunogenicity than the secretory mixture (PG2-S1+ PG2-N) as well as PEDV-neutralizing potency in vitro (P < 0.001). On 49th day after the last immunization, splenocytes were prepared from mice immunized with surface-displayed mixture, secretory mixture and negative control to be stimulated by purified N and S protein, respectively. The results of ELISA analysis showed that N protein was capable of inducing a higher level of IL-4 (P < 0.001) and IFN-γ (P < 0.001) than S1 protein in the immunized mice. Taken together, Lc-expressed N protein as molecular adjuvant or immunoenhancer was able to effectively facilitate the induction of mucosal and systemic immune responses by Lc-expressing S1 region.

Keywords: Combined intragastric immunization; Porcine epidemic diarrhea virus; Lactobacillus casei ; N protein and S1 region

Biological synthesis of quercetin 3-O-N-acetylglucosamine conjugate using engineered Escherichia coli expressing UGT78D2 by Bong-Gyu Kim; Su Hyun Sung; Joong-Hoon Ahn (pp. 2447-2453).

Biotransformation of flavonoids using Escherichia coli harboring nucleotide sugar-dependent uridine diphosphate-dependent glycosyltransferases (UGTs) commonly results in the production of a glucose conjugate because most UGTs are specific for UDP-glucose. The Arabidopsis enzyme AtUGT78D2 prefers UDP-glucose as a sugar donor and quercetin as a sugar acceptor. However, in vitro, AtUGT78D2 could use UDP-N-acetylglucosamine as a sugar donor, and whole cell biotransformation of quercetin using E. coli harboring AtUGT78D2 produced quercetin 3-O-N-acetylglucosamine. In order to increase the production of quercetin 3-O-N-acetylglucosamine via biotransformation, two E. coli mutant strains deleted in phosphoglucomutase (pgm) or glucose-1-phosphate uridylyltransferase (galU) were created. The galU mutant produced up to threefold more quercetin 3-O-N-acetylglucosamine than wild type, resulting in the production of 380-mg/l quercetin 3-O-N-acetylglucosamine and a negligible amount of quercetin 3-O-glucoside. These results show that construction of bacterial strains for the synthesis of unnatural flavonoid glycosides is possible through rational selection of the nucleotide sugar-dependent glycosyltransferase and engineering of the nucleotide sugar metabolic pathway in the host strain.

Keywords: Flavonoid glycones; Uridine diphosphate-dependent glycosyltransferase (UGT); N-acetylglucosamine

Combinatorial modulation of galP and glk gene expression for improved alternative glucose utilization by Jiao Lu; Jinlei Tang; Yi Liu; Xinna Zhu; Tongcun Zhang; Xueli Zhang (pp. 2455-2462).

Phosphoenolpyruvate (PEP) is an important precursor for anaerobic production of succinate and malate. Although inactivating PEP/carbohydrate phosphotransferase systems (PTS) could increase PEP supply, the resulting strain had a low glucose utilization rate. In order to improve anaerobic glucose utilization rate for efficient production of succinate and malate, combinatorial modulation of galactose permease (galP) and glucokinase (glk) gene expression was carried out in chromosome of an Escherichia coli strain with inactivated PTS. Libraries of artificial regulatory parts, including promoter and messenger RNA stabilizing region (mRS), were firstly constructed in front of β-galactosidase gene (lacZ) in E. coli chromosome through λ-Red recombination. Most regulatory parts selected from mRS library had constitutive strengths under different cultivation conditions. A convenient one-step recombination method was then used to modulate galP and glk gene expression with different regulatory parts. Glucose utilization rates of strains modulated with either galP or glk all increased, and the rates had a positive relation with expression strength of both genes. Combinatorial modulation had a synergistic effect on glucose utilization rate. The highest rate (1.64 g/L h) was tenfold higher than PTS⁻ strain and 39% higher than the wild-type E. coli. These modulated strains could be used for efficient anaerobic production of succinate and malate.

Keywords: Regulatory parts; Modulation of gene expression; Glucose utilization; PTS; Escherichia coli

Polyclonal antibody against conserved sequences of mce1A protein blocks MTB infection in macrophages by Sasikala Sivagnanam; Nalini Namasivayam; Rajamanickam Chellam (pp. 2463-2473).

The pathogenesis of Mycobacterium tuberculosis is largely due to its ability to enter and survive within human macrophages. It is suggested that a specific protein namely mammalian cell entry protein is involved in the pathogenesis and the specific gene for this protein mce1A has been identified in several pathogenic organisms such as Rickettsia, Shigella, Escherichia coli, Helicobacter, Streptomyces, Klebsiella, Vibrio, Neisseria, Rhodococcus, Nocardioides, Saccharopolyspora erthyrae, and Pseudomonas. Analysis of mce1 operons in the above mentioned organisms through bioinformatics tools has revealed the presence of unique sequences (conserved regions) suggesting that these sequences may be involved in the process of infection. Presently, the mce1A full-length (1,365 bp) region from Mycobacterium bovis and its conserved regions (303 bp) were cloned in to an expression vector and the purified expressed proteins of molecular weight ∼47 and ∼11 kDa, respectively, were injected to rabbits to raise the polyclonal antibodies. The purified polyclonal antibodies were checked for their ability to inhibit the Mycobacterium infection in cultured human macrophages. In macrophage invasion assay, when antibody added at high concentration, decrease in viable counts was observed in all cell cultures within the first 5 days after infection, where the intracellular bacterial CFU obtained from the infected MTB increased by the 3rd day at low concentration of antibody. The macrophage invasion assay has indicated that the purified antibodies of mce1A conserved region can inhibit the infection of Mycobacterium.

Keywords: mce1Aconserved (303 bp) domain; Macrophage studies; M. bovis genomic DNA-PCR/RT-PCR; Polyclonal antibodies; TEM analysis

A novel single-chain Fv antibody for connective tissue growth factor against the differentiation of fibroblast into myofibroblast by Guoqiu Wu; Xiyong Wang; Xuepeng Deng; Pengpeng Wu; Xiulei Xue; Xuejiao Yan; Xihua Wang (pp. 2475-2482).

This study was aimed to investigate the effect of a single-chain fragment variable antibody of connective tissue growth factor (anti-CTGF scFv) against the differentiation of fibroblast into myofibroblast. The scFv antibody was firstly expressed in Escherichia coli cells and was then purified by affinity chromatography. The yield scFv protein reached a purity over 95% after purification. Immunoreactivity assay demonstrated that scFv possessed a special affinity toward CTGF. RT-PCR, western blot, and immunofluorescence experiments showed that increased expression of α-smooth muscle actin induced by TGF-β1 could be suppressed by this scFv antibody through inhibiting the phosphorylation of Akt.

Keywords: Single-chain Fv antibody (scFv); Connective tissue growth factor (CTGF); Fibroblast; α-Smooth muscle actin (α-SMA); Transforming growth factor-β1 (TGF-β1)

Construction of new Pichia pastoris X-33 strains for production of lycopene and β-carotene by J. M. Araya-Garay; L. Feijoo-Siota; F. Rosa-dos-Santos; P. Veiga-Crespo; T. G. Villa (pp. 2483-2492).

In this study, we used the non-carotenogenic yeast Pichia pastoris X33 as a receptor for β-carotene-encoding genes, in order to obtain new recombinant strains capable of producing different carotenoidic compounds. We designed and constructed two plasmids, pGAPZA-EBI* and pGAPZA-EBI*L*, containing the genes encoding lycopene and β-carotene, respectively. Plasmid pGAPZA-EBI*, expresses three genes, crtE, crtB, and crtI*, that encode three carotenogenic enzymes, geranylgeranyl diphosphate synthase, phytoene synthase, and phytoene desaturase, respectively. The other plasmid, pGAPZA-EBI*L*, carried not only the three genes above mentioned, but also the crtL* gene, that encodes lycopene β-cyclase. The genes crtE, crtB, and crtI were obtained from Erwinia uredovora, whereas crtL* was cloned from Ficus carica (JF279547). The plasmids were integrated into P. pastoris genomic DNA, and the resulting clones Pp-EBI and Pp-EBIL were selected for either lycopene or β-carotene production and purification, respectively. Cells of these strains were investigated for their carotenoid contents in YPD media. These carotenoids produced by the recombinant P. pastoris clones were qualitatively and quantitatively analyzed by high-resolution liquid chromatography, coupled to photodiode array detector. These analyses confirmed that the recombinant P. pastoris clones indeed produced either lycopene or β-carotene, according to the integrated vector, and productions of 1.141 μg of lycopene and 339 μg of β-carotene per gram of cells (dry weight) were achieved. To the best of our knowledge, this is the first time that P. pastoris has been genetically manipulated to produce β-carotene, thus providing an alternative source for large-scale biosynthesis of carotenoids.

Keywords: Pichia pastoris X-33; Carotenoids; Lycopene; β-carotene

Biotin protein ligase from Corynebacterium glutamicum: role for growth and l-lysine production by P. Peters-Wendisch; K. C. Stansen; S. Götker; V. F. Wendisch (pp. 2493-2502).

Corynebacterium glutamicum is a biotin auxotrophic Gram-positive bacterium that is used for large-scale production of amino acids, especially of l-glutamate and l-lysine. It is known that biotin limitation triggers l-glutamate production and that l-lysine production can be increased by enhancing the activity of pyruvate carboxylase, one of two biotin-dependent proteins of C. glutamicum. The gene cg0814 (accession number YP_225000) has been annotated to code for putative biotin protein ligase BirA, but the protein has not yet been characterized. A discontinuous enzyme assay of biotin protein ligase activity was established using a 105aa peptide corresponding to the carboxyterminus of the biotin carboxylase/biotin carboxyl carrier protein subunit AccBC of the acetyl CoA carboxylase from C. glutamicum as acceptor substrate. Biotinylation of this biotin acceptor peptide was revealed with crude extracts of a strain overexpressing the birA gene and was shown to be ATP dependent. Thus, birA from C. glutamicum codes for a functional biotin protein ligase (EC 6.3.4.15). The gene birA from C. glutamicum was overexpressed and the transcriptome was compared with the control strain revealing no significant gene expression changes of the bio-genes. However, biotin protein ligase overproduction increased the level of the biotin-containing protein pyruvate carboxylase and entailed a significant growth advantage in glucose minimal medium. Moreover, birA overexpression resulted in a twofold higher l-lysine yield on glucose as compared with the control strain.

Keywords: Biotin protein ligase; BirA; Corynebacterium glutamicum ; Amino acid production; l-lysine

Intracellular interactome of secreted antibody Fab fragment in Pichia pastoris reveals its routes of secretion and degradation by Martin Pfeffer; Michael Maurer; Johannes Stadlmann; Josephine Grass; Marizela Delic; Friedrich Altmann; Diethard Mattanovich (pp. 2503-2512).

Protein translation, translocation, folding, processing, and secretion in eukaryotic cells are complex and not always straightforward processes, e.g., different routes of secretion and degradation exist. Formation of malfolded proteins in the endoplasmic reticulum (ER) can be one of the major bottlenecks for recombinant protein production. In this regard, an in-depth analysis of the interactions of a secreted protein during its pathway through the cell may be beneficial, as realized in this study for the methylotrophic yeast Pichia pastoris. The antibody fragment Fab3H6 used here is the anti-idiotype to the HIV neutralizing antibody 2F5 and is known to be intracellularly degraded in significant amounts when expressed in P. pastoris. The interactome of Fab3H6 was analyzed by using a pull-down mass spectrometry approach, and 23 proteins were found to bind specifically to the antibody fragment. Those allowed concluding that Fab3H6 is post-translationally translocated into the ER and degraded via the proteasome as well as the vacuole. In line with this, the expression of Fab3H6 increased the proteasomal activities by over 20%. Partial inhibition of the proteasome resulted in a significant increase of extracellular Fab3H6. Thus, it seems that ER quality control overshoots its requirements for the recombinant protein expressed and that more than just terminally malfolded protein is degraded by ER-associated degradation. This work will further facilitate our understanding how recombinant proteins behave in the secretory pathway.

Keywords: Interactome; Heterologous protein; Antibody fragment; Secretion; Proteasome; Pichia pastoris

Genome-wide transcriptomic analysis of a flocculent strain of Zymomonas mobilis by Young Jae Jeon; Zhao Xun; Ping Su; Peter L. Rogers (pp. 2513-2518).

ZM401, a flocculent mutant strain of Zymomonas mobilis ZM4 was studied using genome-wide transcriptomic analysis for evidence related to phenotypic changes associated with its cell–cell attachment behaviour. Batch fermentation studies with ZM401 and its parent strain ZM4 demonstrated that similar ethanol yields and productivities could be achieved with both strains indicating the potential of the flocculent strains for cost-effective cell biomass recycling with resultant high ethanol volumetric productivities. The results showed that twofold or greater differential expression occurred for 26 genes of ZM401 when compared to those of ZM4. Among these, significant over-expression was evident for the genes ZMO1083 and ZMO1084 which are associated with bacterial cellulose synthesis, while reduced expression was found for ZMO0614, ZMO0613, and ZMO0635 which are all associated with synthesis of flagella-related proteins. Both enhanced cellulose production and reduced flagella activity are likely to facilitate more stable flocculent behaviour in ZM401. From comparative DNA sequence analysis of these 26 genes, only one single point mutation was identified. This occurred at the amino acid position A525V of ZMO1055 which encodes for diguanyl cyclase/phosphoesterase which may be related to cell motility and cellulose synthesis in Z. mobilis.

Keywords: Zymomonas mobilis ; High productivity fermentation; Cell flocculation; Transcriptomic analysis

Mannitol production by heterofermentative Lactobacillus reuteri CRL 1101 and Lactobacillus fermentum CRL 573 in free and controlled pH batch fermentations by Cecilia Rodríguez; Tom Rimaux; María José Fornaguera; Gino Vrancken; Graciela Font de Valdez; Luc De Vuyst; Fernanda Mozzi (pp. 2519-2527).

Certain lactic acid bacteria, especially heterofermentative strains, are capable to produce mannitol under adequate culture conditions. In this study, mannitol production by Lactobacillus reuteri CRL 1101 and Lactobacillus fermentum CRL 573 in modified MRS medium containing a mixture of fructose and glucose in a 6.5:1.0 ratio was investigated during batch fermentations with free pH and constant pH 6.0 and 5.0. Mannitol production and yields were higher under constant pH conditions compared with fermentations with free pH, the increase being more pronounced in the case of the L. fermentum strain. Maximum mannitol production and yields from fructose for L. reuteri CRL 1101 (122 mM and 75.7 mol%, respectively) and L. fermentum CRL 573 (312 mM and 93.5 mol%, respectively) were found at pH 5.0. Interestingly, depending on the pH conditions, fructose was used only as an alternative external electron acceptor or as both electron acceptor and energy source in the case of the L. reuteri strain. In contrast, L. fermentum CRL 573 used fructose both as electron acceptor and carbon source simultaneously, independently of the pH value, which strongly affected mannitol production by this strain. Studies on the metabolism of these relevant mannitol-producing lactobacilli provide important knowledge to either produce mannitol to be used as food additive or to produce it in situ during fermented food production.

Keywords: Mannitol; Polyol; Fermentation; Lactic acid bacteria

Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures by Timothy J. Hanly; Morgan Urello; Michael A. Henson (pp. 2529-2541).

Current researches into the production of biochemicals from lignocellulosic feedstocks are focused on the identification and engineering of individual microbes that utilize complex sugar mixtures. Microbial consortia represent an alternative approach that has the potential to better exploit individual species capabilities for substrate uptake and biochemical production. In this work, we construct and experimentally validate a dynamic flux balance model of a Saccharomyces cerevisiae and Escherichia coli co-culture designed for efficient aerobic consumption of glucose/xylose mixtures. Each microbe is a substrate specialist, with wild-type S. cerevisiae consuming only glucose and engineered E. coli strain ZSC113 consuming only xylose, to avoid diauxic growth commonly observed in individual microbes. Following experimental identification of a common pH and temperature for optimal co-culture batch growth, we demonstrate that pure culture models developed for optimal growth conditions can be adapted to the suboptimal, common growth condition by adjustment of the non-growth associated ATP maintenance of each microbe. By comparing pure culture model predictions to co-culture experimental data, the inhibitory effect of ethanol produced by S. cerevisiae on E. coli growth was found to be the only interaction necessary to include in the co-culture model to generate accurate batch profile predictions. Co-culture model utility was demonstrated by predicting initial cell concentrations that yield simultaneous glucose and xylose exhaustion for different sugar mixtures. Successful experimental validation of the model predictions demonstrated that steady-state metabolic reconstructions developed for individual microbes can be adapted to develop dynamic flux balance models of microbial consortia for the production of renewable chemicals.

Keywords: Co-culture; Escherichia coli ; In silico; Metabolic flux analysis; Saccharomyces cerevisiae

Effect of substrate and IPTG concentrations on the burden to growth of Escherichia coli on glycerol due to the expression of Lac proteins by Pushkar Malakar; K. V. Venkatesh (pp. 2543-2549).

Expression of proteins unneeded for growth diverts cellular resources from making necessary protein and leads to a reduction in the growth rate of an organism. This reduction in growth rate is termed as cost. Cost plays an important role in determining the selected expression of a protein in a particular environment. Characterization of cost is important in biotechnology industries where microorganisms are used to produce foreign proteins. We have used the lactose system in Escherichia coli to quantify the cost of growth on glycerol in the presence of isopropyl-β-d-thiogalactopyranoside (IPTG), an inducer of the lactose system. The effect of the concentration of the carbon source, glycerol, and the inducer of Lac enzymes, IPTG, is studied. The results show that the cost is dependent on the glycerol concentration with a decreasing trend with increasing concentration of glycerol. Also as expected, the cost increases and saturates at a higher concentration of IPTG. The studies also demonstrate that the cost is higher in early exponential phase relative to late exponential phase during the growth as has been reported in the literature. Hill equation fit yielded a typical Monod-type expression for growth on glycerol with and without IPTG. An apparent half-saturation constant was defined which was used to characterize the burden on growth due to protein expression.

Keywords: Cost due to protein expression; Burden on growth; Early exponential phase; Late exponential phase; Glycerol; Escherichia coli ; IPTG

Hydroxy-fatty acid production in a Pseudomonas aeruginosa 42A2 PHA synthase mutant generated by directed mutagenesis by Noelia Torrego-Solana; Ignacio Martin-Arjol; Mònica Bassas-Galia; Pilar Diaz; Angeles Manresa (pp. 2551-2561).

Pseudomonas aeruginosa 42A2 growing on waste frying oils is capable to synthesize polyhydroxyalkanoic acids (PHAs) and hydroxy-fatty acids as a result of several enzymatic conversions. In order to study the physiological role of PHA biosynthesis in P. aeruginosa with respect to the synthesis of hydroxy-fatty acids, an unmarked deletion mutant deficient for PHA biosynthesis was generated in P. aeruginosa 42A2. A combination of the sacB-based negative selection system with a cre-lox antibiotic marker recycling method was used for mutant isolation. Electron microscopy, nuclear magnetic resonance analysis, and transmission electron microscopy confirmed that PHA accumulation was completely abolished in the mutant strain. Interestingly, the new mutant strain showed higher carbon and oxygen uptake rate than the wild-type strain and higher efficiency in the conversion of oleic acid into (E)-10-hydroxy-8-octadecenic acid-octadecenoic acid.

Keywords: Pseudomonas aeruginosa ; PHA-negative mutant; sacB-based negative selection; cre-lox antibiotic recycling; Hydroxy-fatty acids

Gas discharge plasmas are effective in inactivating Bacillus and Clostridium spores by Shawn Tseng; Nina Abramzon; James O. Jackson; Wei-Jen Lin (pp. 2563-2570).

Bacterial spores are the most resistant form of life and have been a major threat to public health and food safety. Nonthermal atmospheric gas discharge plasma is a novel sterilization method that leaves no chemical residue. In our study, a helium radio-frequency cold plasma jet was used to examine its sporicidal effect on selected strains of Bacillus and Clostridium. The species tested included Bacillus subtilis, Bacillus stearothermophilus, Clostridium sporogenes, Clostridium perfringens, Clostridium difficile, and Clostridium botulinum type A and type E. The plasmas were effective in inactivating selected Bacillus and Clostridia spores with D values (decimal reduction time) ranging from 2 to 8 min. Among all spores tested, C. botulinum type A and C. sporogenes were significantly more resistant to plasma inactivation than other species. Observations by phase contrast microscopy showed that B. subtilis spores were severely damaged by plasmas and the majority of the treated spores were unable to initiate the germination process. There was no detectable fragmentation of the DNA when the spores were treated for up to 20 min. The release of dipicolinic acid was observed almost immediately after the plasma treatment, indicating the spore envelope damage could occur quickly resulting in dipicolinic acid release and the reduction of spore resistance.

Keywords: Plasma; Sporicidal; Sterilization; Spores; Clostridium ; Bacillus

Plasmid DNA fermentation strategies: influence on plasmid stability and cell physiology by Filomena Silva; João A. Queiroz; Fernanda C. Domingues (pp. 2571-2580).

In order to provide sufficient pharmaceutical-grade plasmid DNA material, it is essential to gain a comprehensive knowledge of the bioprocesses involved; so, the development of protocols and techniques that allow a fast monitoring of process performance is a valuable tool for bioprocess design. Regarding plasmid DNA production, the metabolic stress of the host strain as well as plasmid stability have been identified as two of the key parameters that greatly influence plasmid DNA yields. The present work describes the impact of batch and fed-batch fermentations using different C/N ratios and different feeding profiles on cell physiology and plasmid stability, investigating the potential of these two monitoring techniques as valuable tools for bioprocess development and design. The results obtained in batch fermentations showed that plasmid copy number values suffered a pronounced increase at the end of almost all fermentation conditions tested. Regarding fed-batch fermentations, the strategies with exponential feeding profiles, in contrast with those with constant feeding, showed higher biomass and plasmid yields, the maximum values obtained for these two parameters being 95.64 OD₆₀₀ and 344.3 mg plasmid DNA (pDNA)/L, respectively, when using an exponential feed rate of 0.2 h⁻¹. Despite the results obtained, cell physiology and plasmid stability monitoring revealed that, although higher pDNA overall yields were obtained, this fermentation exhibited lower plasmid stability and percentage of viable cells. In conclusion, this study allowed clarifying the bioprocess performance based on cell physiology and plasmid stability assessment, allowing improvement of the overall process and not only plasmid DNA yield and cell growth.

Keywords: Plasmid DNA; Batch; Fed-batch; Cell physiology; Segregational stability

Biodegradation of Leonardite by an Alkali-producing bacterial community and characterization of the degraded products by Tong-Guo Gao; Feng Jiang; Jin-Shui Yang; Bao-Zhen Li; Hong-Li Yuan (pp. 2581-2590).

In this study, three bacterial communities were obtained from 12 Leonardite samples with the aim of identifying a clean, effective, and economic technique for the dissolution of Leonardite, a type of low-grade coal, in the production of humic acid (HA). The biodegradation ability and characteristics of the degraded products of the most effective bacterial community (MCSL-2), which degraded 50% of the Leonardite within 21 days, were further investigated. Analyses of elemental composition, ¹³C NMR, and Fourier transform infrared revealed that the contents of C, O, and aliphatic carbon were similar in biodegraded humic acid (bHA) and chemically (alkali) extracted humic acid (cHA). However, the N and carboxyl carbon contents of bHA was higher than that of cHA. Furthermore, a positive correlation was identified between the degradation efficiency and the increasing pH of the culture medium, while increases of manganese peroxidase and esterase activities were also observed. These data demonstrated that both alkali production and enzyme reactions were involved in Leonardite solubilization by MCSL-2, although the former mechanism predominated. No fungus was observed by microscopy. Only four bacterial phylotypes were recognized, and Bacillus licheniformis-related bacteria were identified as the main group in MCSL-2 by analysis of amplified 16S rRNA genes, thus demonstrating that Leonardite degradation ability has a limited distribution in bacteria. Hormone-like bioactivities of bHA were also detected. In this study, a bacterial community capable of Leonardite degradation was identified and the products characterized. These data implicate the use of such bacteria for the exploitation of Leonardite as a biofertilizer.

Keywords: Leonardite; Biodegradation; Humic acid; Bacterial community

Improved inhibitor tolerance in xylose-fermenting yeast Spathaspora passalidarum by mutagenesis and protoplast fusion by Xiaoru Hou; Shuo Yao (pp. 2591-2601).

The xylose-fermenting yeast Spathaspora passalidarum showed excellent fermentation performance utilizing glucose and xylose under anaerobic conditions. But this yeast is highly sensitive to the inhibitors such as furfural present in the pretreated lignocellulosic biomass. In order to improve the inhibitor tolerance of this yeast, a combination of UV mutagenesis and protoplast fusion was used to construct strains with improved performance. Firstly, UV-induced mutants were screened and selected for improved tolerance towards furfural. The most promised mutant, S. passalidarum M7, produced 50% more final ethanol than the wild-type strain in a synthetic xylose medium containing 2 g/l furfural. However, this mutant was unable to grow in a medium containing 75% liquid fraction of pretreated wheat straw (WSLQ), in which furfural and many other inhibitors were present. Hybrid yeast strains, obtained from fusion of the protoplasts of S. passalidarum M7 and a robust yeast, Saccharomyces cerevisiae ATCC 96581, were able to grow in 75% WSLQ and produce around 0.4 g ethanol/g consumed xylose. Among the selected hybrid strains, the hybrid FS22 showed the best fermentation capacity in 75% WSLQ. Phenotypic and partial molecular analysis indicated that S. passalidarum M7 was the dominant parental contributor to the hybrid. In summary, the hybrids are characterized by desired phenotypes derived from both parents, namely the ability to ferment xylose from S. passalidarum and an increased tolerance to inhibitors from S. cerevisiae ATCC 96581.

Keywords: Spathaspora passalidarum ; Saccharomyces cerevisiae ; UV mutagenesis; Protoplast fusion; Inhibitor tolerance

Ion mobility spectrometry for microbial volatile organic compounds: a new identification tool for human pathogenic bacteria by Melanie Jünger; Wolfgang Vautz; Martin Kuhns; Lena Hofmann; Siobhán Ulbricht; Jörg Ingo Baumbach; Michael Quintel; Thorsten Perl (pp. 2603-2614).

Presently, 2 to 4 days elapse between sampling at infection suspicion and result of microbial diagnostics. This delay for the identification of pathogens causes quite often a late and/or inappropriate initiation of therapy for patients suffering from infections. Bad outcome and high hospitalization costs are the consequences of these currently existing limited pathogen identification possibilities. For this reason, we aimed to apply the innovative method multi-capillary column–ion mobility spectrometry (MCC-IMS) for a fast identification of human pathogenic bacteria by determination of their characteristic volatile metabolomes. We determined volatile organic compound (VOC) patterns in headspace of 15 human pathogenic bacteria, which were grown for 24 h on Columbia blood agar plates. Besides MCC-IMS determination, we also used thermal desorption–gas chromatography–mass spectrometry measurements to confirm and evaluate obtained MCC-IMS data and if possible to assign volatile compounds to unknown MCC-IMS signals. Up to 21 specific signals have been determined by MCC-IMS for Proteus mirabilis possessing the most VOCs of all investigated strains. Of particular importance is the result that all investigated strains showed different VOC patterns by MCC-IMS using positive and negative ion mode for every single strain. Thus, the discrimination of investigated bacteria is possible by detection of their volatile organic compounds in the chosen experimental setup with the fast and cost-effective method MCC-IMS. In a hospital routine, this method could enable the identification of pathogens already after 24 h with the consequence that a specific therapy could be initiated significantly earlier.

Keywords: Pathogen identification; Volatile metabolome; Multi-capillary column (MCC); Ion mobility spectrometry (IMS); Volatile organic compound (VOC)

Effect of Mn²⁺ augmentation on reinforcing aerobic sludge granulation in a sequencing batch reactor by Lihui Huang; Tao Yang; Weiliang Wang; Bo Zhang; Yuanyuan Sun (pp. 2615-2623).

Two sequencing batch reactors were synchronously operated to investigate the effect of manganese (II) (Mn²⁺) augmentation on aerobic granulation. Reactor 1 (R1) was added with 10 mg/L Mn²⁺, while there was no Mn²⁺ augmentation in reactor 2 (R2). Results showed that R1 had a faster granulation process than R2 and R1 performed better in chemical oxygen demand (COD) and ammonium nitrogen (NH ₄ ⁺ –N) removal efficiencies. Moreover, the mature granules augmented with Mn²⁺ behaved better on their physical characteristics and size distributions, and they also had higher production of extracellular polymeric substances (EPS) content. The result of three-dimensional excitation and emission matrix fluorescence showed that Mn²⁺ had the function of causing organic material diversity (especially proteins diversity) in EPS fraction from granules. Polymerase chain reaction and denaturing gradient gel electrophoresis techniques were employed to analyze the microbial and genetic characteristics in mature granules. The results exhibited that Mn²⁺ augmentation was mainly responsible for the higher microbial diversity of granules from R1 compared with that from R2. Uncultured sludge bacterium A16 (AF234726) and Rhodococcus sp. WTZ-R2 (HM004214) were the major species in R1, while only uncultured sludge bacterium A16 (AF234726) in R2. Moreover, there were eight species of organisms found in both two aerobic granules, and three species were found only in aerobic granules from R1. It could be concluded that Mn²⁺ could enhance the sludge granulation process and have a key effect role on the biological properties during the sludge granulation.

Keywords: Mn²⁺ ; Aerobic granulation; Sequencing batch reactor; Microbial diversity

Temporal and spatial distribution of Bacillus and Clostridium histolyticum in swine manure composting by fluorescent in situ hybridization (FISH) by Jing Yi; Rong Zheng; Fenge Li; Zhe Chao; Chang Yan Deng; Jian Wu (pp. 2625-2632).

The temporal and spatial distribution of the genus Bacillus and Clostridium histolyticum group in swine manure composting was determined by fluorescent in situ hybridization using fluorescently labeled 16S rRNA-targeted oligonucleotide probes LGC353b and Chis150, respectively. The temporal distribution of total bacteria, Bacillus and C. histolyticum, detected in each layer of the composting pile was noticeable in that the number of them detected at the high-temperature stage was higher than that of the cooling stage. The number detected at the cooling stage was higher than that of the temperature-rising stage. The number of the total bacteria distributed in three locations achieved balance at the stage of cooling. The spatial distribution of the genus Bacillus cells was that the number and the relative abundance of Bacillus cells detected in the middle layer of composting pile were the lowest at each stage of composting. However, the minimum value of the relative abundance exceeded 8%. Compared with Bacillus spp., the C. histolyticum group displayed higher relative abundance in the same layer at different stages of composting except in the top layer at the stage of high temperature. However, the characteristic of the spatial distribution was not noticeable. The detected limits of the genus Bacillus and C. histolyticum group were both found to be the high cell density of 10⁶ cells g⁻¹ (wet weight). These results indicated that the genus Bacillus and C. histolyticum group were the predominant bacteria in the swine manure composting process and may play important role in this complex environment.

Keywords: Composting; FISH; Bacillus ; Clostridium histolyticum ; Distribution

Effect of compost, nitrogen salts, and NPK fertilizers on methane oxidation potential at different temperatures by Louis-B. Jugnia; Yaseen Mottiar; Euphrasie Djuikom; Alexandre R. Cabral; Charles W. Greer (pp. 2633-2643).

The effects of compost, nitrogen salts, and nitrogen–phosphorous–potassium (NPK) fertilizers on the methane oxidation potential (MOP) of landfill cover soil at various temperatures were assessed. For this, we used batch assays conducted at 5°C, 15°C, and 25°C with microcosms containing landfill cover soil slurries amended with these elements. Results indicated variable impacts dependent on the type of amendment and the incubation temperature. For a given incubation temperature, MOP varied from one compost to another and with the amount of compost added, except for the shrimp/peat compost. With this latter compost, independent of the amount, MOP values remained similar and were significantly higher than those obtained with other composts. Amendment with most of the tested nitrogen salts led to similar improvements in methanotrophic activity, except for urea. MOP with NPK fertilizer addition was amongst the highest in this study; the minimum value obtained with NPK (20–0–20) suggested the importance of P for methanotrophs. MOP generally increased with temperature, and nutrient limitation became less important at higher temperatures. Overall, at each of the three temperatures tested, MOP with NPK fertilizer amendments provided the best results and was comparable to those observed with the addition of the shrimp/peat compost. The results of this study provide the first evidence of the following: (1) compost addition to improve methanotrophic activity in a landfill cover soil should consider the amount and type of compost used and (2) the importance of using NPK fertilizers rather than nitrogen salts, in enhancing this activity, primarily at low temperatures. One can also consider the potential beneficial impact of adding these elements to enhance plant growth, which is an advantage for MOP.

Keywords: Methanotrophs; Potential activity; Compost; Nitrogen salts; NPK fertilizers

Essential roles of eDNA and AI-2 in aerobic granulation in sequencing batch reactors operated at different settling times by Yanghui Xiong; Yu Liu (pp. 2645-2651).

Settling time has been considered as one of the most effective selection pressures for aerobic granulation in sequencing batch reactors (SBRs), i.e., poorly settleable bioparticles would be washed out from SBRs, and the heavy and good settling ones would be retained at a shorter setting time. However, its biological implication remains unclear. This study investigated the microbiological mechanisms of aerobic granulation at different settling times. It provided experimental evidence for the first time showing that a shorter settling time could enhance release of extracellular DNA through cell lysis, which in turn initiated microbial aggregation leading to increased biomass size and density, while AI-2-mediated quorum sensing was found not to be involved in initial aggregation. It was further shown that the AI-2-mediated quorum sensing system was activated to regulate the growth and maturation of aerobic granules when the biomass density reached a threshold of 1.025 g ml⁻¹. It appears from this study that a short settling time of SBR would induce microbiological and physiological responses of bacteria which are required at different stages of aerobic granulation and provide new insights into biological mechanisms of settling time-triggered aerobic granulation.

Keywords: Settling time; SBRs; Aerobic granulation; eDNA; AI-2; Quorum sensing

Biological and chemical interaction of oxygen on the reduction of Fe(III)EDTA in a chemical absorption–biological reduction integrated NO x removal system by Shi-Han Zhang; Yao Shi; Wei Li (pp. 2653-2659).

A promising chemical absorption–biological reduction integrated process has been proposed. A major problem of the process is oxidation of the active absorbent, ferrous ethylenediaminetetraacetate (Fe(II)EDTA), to the ferric species, leading to a significant decrease in NO removal efficiency. Thus the biological reduction of Fe(III)EDTA is vitally important for the continuous NO removal. Oxygen, an oxidizing agent and biological inhibitor, is typically present in the flue gas. It can significantly retard the application of the integrated process. This study investigated the influence mechanism of oxygen on the regeneration of Fe(II)EDTA in order to provide insight on how to eliminate or decrease the oxygen influence. The experimental results revealed that the dissolved oxygen and Fe(III)EDTA simultaneously served as electron acceptor for the microorganism. The Fe(III)EDTA reduction activity were directly inhibited by the dissolved oxygen. When the bioreactor was supplied with 3% and 8% oxygen in the gas phase, the concentration of initial dissolved oxygen in the liquid phase was 0.28 and 0.68 mg l⁻¹. Correspondingly, the instinct Fe(III)EDTA reduction activity of the microorganism determined under anoxic condition in a rotation shaker decreased from 1.09 to 0.84 and 0.49 mM h⁻¹. The oxidation of Fe(II)EDTA with dissolved oxygen prevented more dissolved oxygen access to the microorganism and eased the inhibition of dissolved oxygen on the microorganisms.

Keywords: Fe(III)EDTA; Biological reduction; Oxygen; Inhibition; NO x

Humic analog AQDS and AQS as an electron mediator can enhance chromate reduction by Bacillus sp. strain 3C₃ by Yiguo Hong; Peng Wu; Wenru Li; Jiguang Gu; Shunshan Duan (pp. 2661-2668).

Humus as an electron mediator is recognized as an effective strategy to improve the biological transformation and degradation of toxic substances, yet the action of humus in microbial detoxification of chromate is still unknown. In this study, a humus-reducing strain 3C₃ was isolated from mangrove sediment. Based on the analyses of morphology, physiobiochemical characteristics, and 16S rRNA gene sequence, this strain was identified Bacillus sp. Strain 3C₃ can effectively reduce humic analog anthraquinone-2,6-disulfonate (AQDS) and anthraquinone-2-sulfonate (AQS) with lactate, formate, or glucose as electron donors. When the cells were killed by incubation at 95°C for 30 min or an electron donor was absent, the humic reduction did not occur, showing that the humic reduction was a biochemical process. However, strain 3C₃ had low capability of chromate reduction under anaerobic conditions, despite of having strong tolerance of the toxic metal. But in the presence of humic substances AQDS or AQS, we found that chromate reduction by strain 3C₃ was enhanced greatly. Because strain 3C₃ is an effective humus-reducing bacterium, it is proposed that humic substances could serve as electron mediator to interact with chromate and accelerate chromate reduction. Our results suggest that chromate contaminations can be detoxified by adding humic analog (low to 0.1 mM) as an electron mediator in the microbial incubation.

Keywords: Humic reduction; Electron mediator; Chromate reduction; Bacillus sp. strain 3C₃

Alginate beads provide a beneficial physical barrier against native microorganisms in wastewater treated with immobilized bacteria and microalgae by Sergio A. Covarrubias; Luz E. de-Bashan; Manuel Moreno; Yoav Bashan (pp. 2669-2680).

When the freshwater microalga Chlorella sorokiniana and the plant growth-promoting bacterium Azospirillum brasilense were deployed as free suspensions in unsterile, municipal wastewater for tertiary wastewater treatment, their population was significantly lower compared with their populations in sterile wastewater. At the same time, the numbers of natural microfauna and wastewater bacteria increased. Immobilization of C. sorokiniana and A. brasilense in small (2–4 mm in diameter), polymer Ca-alginate beads significantly enhanced their populations when these beads were suspended in normal wastewater. All microbial populations within and on the surface of the beads were evaluated by quantitative fluorescence in situ hybridization combined with scanning electron microscopy and direct measurements. Submerging immobilizing beads in wastewater created the following sequence of events: (a) a biofilm composed of wastewater bacteria and A. brasilense was created on the surface of the beads, (b) the bead inhibited penetration of outside organisms into the beads, (c) the bead inhibited liberation of the immobilized microorganisms into the wastewater, and (d) permitted an uninterrupted reduction of ammonium and phosphorus from the wastewater. This study demonstrated that wastewater microbial populations are responsible for decreasing populations of biological agents used for wastewater treatment and immobilization in alginate beads provided a protective environment for these agents to carry out uninterrupted tertiary wastewater treatment.

Keywords: Alginate; Azospirillum ; Chlorella ; Microalgae; Plant growth-promoting bacteria; Protection; Wastewater treatment

Erratum to: Efficient synthesis of optically pure alcohols by asymmetric hydrogen-transfer biocatalysis: application of engineered enzymes in a 2-propanol–water medium by Nobuya Itoh; Kentaro Isotani; Masatoshi Nakamura; Kousuke Inoue; Yasuhiro Isogai; Yoshihide Makino (pp. 2681-2682).

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Applied Microbiology and Biotechnology (v.93, #6)

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Applied Microbiology and Biotechnology (v.93, #6)