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Applied Microbiology and Biotechnology (v.70, #3)
Pathways and regulation of bacterial arginine metabolism and perspectives for obtaining arginine overproducing strains by Chung-Dar Lu (pp. 261-272).
l-Arginine is produced by bacterial fermentation and is consumed in food flavoring and pharmaceutical industries. A better understanding of arginine metabolism in bacteria could be beneficial for a rational design of recombinant l-arginine producers by genetic engineering. This mini-review illustrated the current status of genes and enzymes for arginine metabolism, including biosynthetic pathways, catabolic pathways, uptake and excretion systems, and regulation. The linkage of polyamine and glutamate metabolism to the arginine network was also discussed, followed by a perspective view on how to construct arginine overproducing strains of bacteria with increasing biosynthesis and excretion and decreasing catabolism and uptake.
Whole-cell living biosensors—are they ready for environmental application? by Hauke Harms; Mona C. Wells; Jan Roelof van der Meer (pp. 273-280).
Since the development of the first whole-cell living biosensor or bioreporter about 15 years ago, construction and testing of new genetically modified microorganisms for environmental sensing and reporting has proceeded at an ever increasing rate. One and a half decades appear as a reasonable time span for a new technology to reach the maturity needed for application and commercial success. It seems, however, that the research into cellular biosensors is still mostly in a proof-of-principle or demonstration phase and not close to extensive or commercial use outside of academia. In this review, we consider the motivations for bioreporter developments and discuss the suitability of extant bioreporters for the proposed applications to stimulate complementary research and to help researchers to develop realistic objectives. This includes the identification of some popular misconceptions about the qualities and shortcomings of bioreporters.
Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples by Tong Zhang; Herbert H. P. Fang (pp. 281-289).
Due to the advanced development of fluorogenic chemistry, quantitative real-time polymerase chain reaction (qRT-PCR) has become an emerging technique for the detection and quantification of microorganisms in the environment. Compared with the conventional hybridization- and PCR-based techniques, qRT-PCR not only has better sensitivity and reproducibility, but it is also quicker to perform and has a minimum risk of amplicon carryover contamination. This article reviews the principle of this emerging technique, its detection reagents, target DNAs, quantification procedures, and affecting factors. The applications of qRT-PCR for the quantification of microorganisms in the environment are also summarized.
Copolymeric polythioesters by lipase-catalyzed thioesterification and transthioesterification of α,ω-alkanedithiols by N. Weber; K. Bergander; E. Fehling; E. Klein; K. Vosmann; K. D. Mukherjee (pp. 290-297).
Linear copolymeric polythioesters [PTE; poly(α,ω-alkanedioic acid-co-α,ω-alkanedithiols)] were formed in good yield (∼69%) by thioesterification of 1,12-dodecanedioic acid with 1,6-hexanedithiol and 1,8-octanedithiol, respectively, catalyzed by immobilized lipase from Rhizomucor miehei (Lipozyme RM IM) in vacuo without a solvent. Similarly, transthioesterification (thiolysis) of diethyl 1,12-dodecanedioate with 1,6-hexanedithiol led to the formation of ∼66% PTE. Poly (1,12-dodecanedioic acid-co-1,6-hexanedithiol) and poly (1,12-dodecanedioic acid-co-1,8-octanedithiol) were extracted from the reaction mixture using methyl-t-butylether, precipitated at −20°C and the precipitates extracted with boiling i-hexane to yield two fractions of PTE. The i-hexane-insoluble fraction of poly (1,12-dodecanedioic acid-co-1,6-hexanedithiol) shows an average molecular mass (Mw) of 1,212 Da, corresponding to a molecular weight range of up to 13,200 Da and a degree of polymerization of up to 38 monomer units. The i-hexane-insoluble fraction of poly (1,12-dodecanedioic acid-co-1,8-octanedithiol) shows a Mw of 2,360 Da, corresponding to a molecular weight range of up to 19,500 Da and a maximum degree of polymerization of up to 52 monomer units. The low-molecular weight (<800 Da) reaction products of thioesterification of 1,12-dodecanedioic acid with 1,6-hexanedithiol, elucidated by gas chromatography–mass spectroscopy, show the following intermediates: (1) 9,20-dioxo-1,8-dithiacycloeicosane; (2) 17,28-dioxo-1,8,9,16-tetrathiacyclooctacosane; (3) 1,12-dodecanedioic acid methyl(O)ester 6′-S-mercaptohexyl thio(S)ester; and (4) oligomeric linear thioester, formed by thioesterification of two molecules of 1,12-dodecanedioic acid with one molecule of 1,6-hexanedithiol.
Efficient induction of ginsenoside biosynthesis and alteration of ginsenoside heterogeneity in cell cultures of Panax notoginseng by using chemically synthesized 2-hydroxyethyl jasmonate by Wei Wang; Zhen-Jiang Zhao; Yufang Xu; Xuhong Qian; Jian-Jiang Zhong (pp. 298-307).
Chemically synthesized 2-hydroxyethyl jasmonate (HEJA) was for the first time employed to induce the ginsenoside biosynthesis and to manipulate the product heterogeneity in plant cell cultures. The dose response and timing of HEJA elicitation were investigated in cell suspension cultures of Panax notoginseng. The optimal concentration and timing of HEJA addition for both cell growth and ginsenoside accumulation was identified to be 200 μM added on day 4. It was interestingly found that HEJA could stimulate ginsenosides biosynthesis and change their heterogeneity more efficiently than methyl jasmonate (MJA), i.e., the total ginsenoside content and the Rb/Rg ratio increased about 60 and 30% with HEJA elicitation than that by MJA, respectively. The activity of Rb1 biosynthetic enzyme, i.e., UDPG-ginsenoside Rd glucosyltransferase (UGRdGT), was also higher in the former case. A maximal production titer of ginsenoside Rg1, Re, Rb1, and Rd was 47.4±4.8, 52.3±4.4, 190±18, and 12.1±2.5 mg/l with HEJA elicitation, which was about 1.3-, 1.3-, 1.7-, and 2.1-fold than that using MJA, respectively. Early signal events in plant defense response, including oxidative burst and jasmonic acid (JA) biosynthesis, were also examined. Levels of H2O2 and NO in medium and l-phenylalanine ammonia lyase activity in cells were not affected by addition of MJA and HEJA. On the other hand, the JA content in cells was increased with external jasmonates elicitation, and it was inhibited with the addition of JA biosynthesis inhibitors. The results suggest that oxidative burst might not be involved in the jasmonates-elicited signal transduction pathway, and MJA and HEJA may induce the ginsenoside biosynthesis via induction of endogenous JA biosynthesis and key enzymes (such as UGRdGT) in the ginsenoside biosynthetic pathway of P. notoginseng cells. The information is useful for hyperproduction of plant-specific heterogeneous products.
Recovery of pyruvic acid from biotransformation solutions by C. Q. Ma; J. C. Li; J. H. Qiu; M. Wang; P. Xu (pp. 308-314).
The aim of this investigation was to separate pyruvic acid of biotransformation solutions from lactic acid through complex extraction. For this purpose, complex extraction was investigated from model solutions. Tri-n-octanylamine (TOA) was used as the extractant. The effects of various diluents, the stoichiometry of pyruvic acid to TOA, and the initial pH of the aqueous phase on the extraction process were investigated in this study. The effects of sodium hydroxide (NaOH) and trimethylamine (TMA) on the back extraction process were also studied, respectively. The optimal conditions attained from the model solutions proved efficient on the biotransformation solutions of different concentrations. A total recovery of 71–82% of pyruvic acid was obtained, whereas 89–92% of lactic acid was removed. The purity of pyruvic acid reached 97% after the removal of TMA by a simple distillation.
Catalytic activity of lignin peroxidase and partition of veratryl alcohol in AOT/isooctane/toluene/water reverse micelles by Wenjuan Zhang; Xirong Huang; Yuezhong Li; Yinbo Qu; Peiji Gao (pp. 315-320).
The activity of lignin peroxidase (LiP) and the partition of its optimum substrate veratryl alcohol (VA) in sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/isooctane/toluene/water reverse micelles were studied in this paper to understand the microheterogeneous effect of the medium on the catalytic properties of LiP hosted in the reverse micelle. Results showed that LiP from Phanerochaete chrysosporium could express its activity in the reverse micelles, but its activity depended, to a great extent, on the composition of the reverse micelles. Optimum activity occurred at a molar ratio of water to AOT (ω0) of 11, a pH value of 3.6, and a volume ratio of isooctane to toluene of 7–9. Under optimum conditions, the half-life of LiP was circa 12 h. The dependence of LiP activity on the volume fraction of water in the medium (θ), at a constant ω0 value of 11, indicated that VA was mainly solubilized in the pseudophase of the reverse micelle. Based on the pseudobiphasic model and the corresponding kinetic method, a linear line can be obtained in a plot of apparent Michaelis constant of VA vs θ, and the partition coefficient of VA between the pseudophase and the organic solvent phase was determined to be 35.8, which was higher than that (22.3) between bulk water and the corresponding mixed organic solvent. H2O2 inhibited LiP at concentrations higher than 80 μM; this concentration value seems to be different from that in aqueous solution (about 3 mM). The differences mentioned above should be ascribed to the microheterogeneity and the interface of the AOT reverse micelle.
New cold-adapted lipase from Photobacterium lipolyticum sp. nov. that is closely related to filamentous fungal lipases by H. S. Ryu; H. K. Kim; W. C. Choi; M. H. Kim; S. Y. Park; N. S. Han; T. K. Oh; J. K. Lee (pp. 321-326).
A Photobacterium strain, M37, showing lipolytic activity, was previously isolated from an intertidal flat of the Yellow Sea in Korea and identified as Photobacterium lipolyticum sp. nov. In the present study, the corresponding gene was cloned using the shotgun method. The amino acid sequence deduced from the nucleotide sequence (1,023 bp) corresponded to a protein of 340 amino acid residues with a molecular weight of 38,026. No sequence similarity was found with any known bacterial lipases/esterases; instead, the most similar enzymes were several filamentous fungal lipases. Although the similarity was very low (less than 16%), there were many conserved regions over the entire sequence and N-terminal oxyanion hole (RG) region, a signature sequence of filamentous fungal lipases. The novel protein M37 was produced in both a soluble and insoluble form when the Escherichia coli cells harboring the gene were cultured at 18°C. The soluble protein exhibited lipase activity in a pH-stat assay using an olive oil emulsion. The M37 lipase also displayed a maximum activity at 25°C and maintained its activity at a low temperature range (5–25°C) with an activation energy (E a) of 2.07 kcal/mol. Accordingly, these results indicate that the M37 lipase from P. lipolyticum sp. nov. is a new cold-adapted enzyme.
Characterization of two novel lipase genes isolated directly from environmental sample by Zhengbing Jiang; Hongping Wang; Yushu Ma; Dongzhi Wei (pp. 327-332).
Two novel lipase genes (lipJ02, lipJ03) were isolated directly from environmental DNA via genome-walking method. Lipase gene lipJ02 contained an open reading frame (ORF) of 1,425 bp and encoded a 474-amino acids lipase protein, while lipase gene lipJ03 contained an ORF of 1,413 bp and encoded a 470-amino acids lipase protein. The lipase genes were cloned into expression vector pPIC9K and successfully integrated into a heterologous fungal host, Pichia pastoris KM71, and the recombinant P. pastoris were screened via a high-throughput method. The recombinants were induced by methanol to secrete active lipases into cultural medium. The recombinant lipases were also purified and characterized. The optimum temperature for the purified lipase LipJ02 and LipJ03 was 30 and 35°C, respectively, at pH 8.0. They exhibited similar thermostability, but LipJ02 exhibited better pH stability than LipJ03.
5′ Untranslated region of the Hsp12 gene contributes to efficient translation in Aspergillus oryzae by Akio Koda; Takayuki Bogaki; Toshitaka Minetoki; Masato Hirotsune (pp. 333-336).
We describe a 5′ untranslated region (5′UTR) that dramatically increases the expression level of an exogenous gene in Aspergillus oryzae. Using a series of 5′UTR::GUS (uidA) fusion constructs, we analyzed the translation efficiency of chimeric mRNAs with different 5′UTRs at different temperatures. We found that the 5′UTR of a heat-shock protein gene, Hsp12, greatly enhanced the translation efficiency of the chimeric GUS mRNA at normal temperature (30°C). Moreover, at high temperature (37°C), the translation efficiency of the mRNA containing the Hsp12 5′UTR was far superior to that of mRNAs containing nonheat-shock 5′UTRs, resulting in much more efficient expression of GUS protein (about 20-fold higher GUS activity compared to the control construct). This 5′UTR can be used in combination with various strong promoters to enhance the expression of foreign proteins in A. oryzae.
Use of Physcomitrella patens actin 5′ regions for high transgene expression: importance of 5′ introns by Andreas Weise; Marta Rodriguez-Franco; Barbara Timm; Matthias Hermann; Sandra Link; Wolfgang Jost; Gilbert Gorr (pp. 337-345).
We have isolated four actin (Act) genes from Physcomitrella patens and used their corresponding 5′ regions for recombinant expression of the human vascular endothelial growth factor (rhVEGF121) in transiently transformed Physcomitrella protoplasts and in stable transformed lines. In the transient system, we found up to 11-fold activity of the corresponding 5′ regions as compared with that of the plant constitutive 35S promoter. Moreover, the use of an optimised expression vector in which the human VEGF signal peptide was exchanged with a plant signal peptide resulted in an additional 7-fold increase in secreted rhVEGF. We found that the 5′ introns of PpAct1, PpAct5 and PpAct7 are essential for high expression. The enhancing mechanisms of the introns, however, seem to be different since in the case of PpAct1, the expression level is stimulated only in the presence of the endogenous promoter, whereas the 5′ introns of PpAct5 and PpAct7 stimulate expression also in combination with the 35S promoter. Beyond this, the isolated 5′ regions are shown to be useful for high expression levels in transgenic moss lines with values of secreted rhVEGF up to 96 μg g-1 dry weight.
Comparative analysis of transcriptional responses to saline stress in the laboratory and brewing strains of Saccharomyces cerevisiae with DNA microarray by T. Hirasawa; Y. Nakakura; K. Yoshikawa; K. Ashitani; K. Nagahisa; C. Furusawa; Y. Katakura; H. Shimizu; S. Shioya (pp. 346-357).
To construct yeast strains showing tolerance to high salt concentration stress, we analyzed the transcriptional response to high NaCl concentration stress in the yeast Saccharomyces cerevisiae using DNA microarray and compared between two yeast strains, a laboratory strain and a brewing one, which is known as a stress-tolerant strain. Gene expression dynamically changed following the addition of NaCl in both yeast strains, but the degree of change in the gene expression level in the laboratory strain was larger than that in the brewing strain. The response of gene expression to the low NaCl concentration stress was faster than that to the high NaCl concentration stress in both strains. Expressions of the genes encoding enzymes involved in carbohydrate metabolism and energy production in both strains or amino acid metabolism in the brewing strain were increased under high NaCl concentration conditions. Moreover, the genes encoding sodium ion efflux pump and copper metallothionein proteins were more highly expressed in the brewing strain than in the laboratory strain. According to the results of transcriptome analysis, candidate genes for the creation of stress-tolerant strain were selected, and the effect of overexpression of candidate genes on the tolerance to high NaCl concentration stress was evaluated. Overexpression of the GPD1 gene encoding glycerol-3-phosphate dehydrogenase, ENA1 encoding sodium ion efflux protein, and CUP1 encoding copper metallothionein conferred high salt stress tolerance to yeast cells, and our selection of candidate genes for the creation of stress-tolerant yeast strains based on the transcriptome data was validated.
Isolation and characterization of a new Mycobacterium austroafricanum strain, IFP 2015, growing on MTBE by Nicolas Lopes Ferreira; Helena Maciel; Hugues Mathis; Frédéric Monot; Françoise Fayolle-Guichard; Charles W. Greer (pp. 358-365).
A new Mycobacterium austroafricanum strain, IFP 2015, growing on methyl tert-butyl ether (MTBE) as a sole carbon source was isolated from an MTBE-degrading microcosm inoculated with drain water of an MTBE-supplemented gasoline storage tank. M. austroafricanum IFP 2015 was able to grow on tert-butyl formate, tert-butyl alcohol (TBA) and α-hydroxyisobutyrate. 2-Methyl-1,2-propanediol was identified as the TBA oxidation product in M. austroafricanum IFP 2015 and in the previously isolated M. austroafricanum IFP 2012. M. austroafricanum IFP 2015 also degraded ethyl tert-butyl ether more rapidly than M. austroafricanum IFP 2012. Specific primers designed to monitor the presence of M. austroafricanum strains could be used as molecular tools to detect similar strains in MTBE-contaminated environment.
Correlation between acetic acid resistance and characteristics of PQQ-dependent ADH in acetic acid bacteria by Janja Trcek; Hirohide Toyama; Jerzy Czuba; Anna Misiewicz; Kazunobu Matsushita (pp. 366-373).
In this study, we compared the growth properties and molecular characteristics of pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenase (ADH) among highly acetic acid-resistant strains of acetic acid bacteria. Ga. europaeus exhibited the highest resistance to acetic acid (10%), whereas Ga. intermedius and Acetobacter pasteurianus resisted up to 6% of acetic acid. In media with different concentrations of acetic acid, the maximal acetic acid production rate of Ga. europaeus slowly increased, but specific growth rates decreased concomitant with increased concentration of acetic acid in medium. The lag phase of A. pasteurianus was twice and four times longer in comparison to the lag phases of Ga. europaeus and Ga. intermedius, respectively. PQQ-dependent ADH activity was twice as high in Ga. europaeus and Ga. intermedius as in A. pasteurinus. The purified enzymes showed almost the same specific activity to each other, but in the presence of acetic acid, the enzyme activity decreased faster in A. pasteurianus and Ga. intermedius than in Ga. europaeus. These results suggest that high ADH activity in the Ga. europaeus cells and high acetic acid stability of the purified enzyme represent two of the unique features that enable this species to grow and stay metabolically active at extremely high concentrations of acetic acid.
Bioaugmentation and enhanced formation of microbial granules used in aerobic wastewater treatment by Volodymyr Ivanov; Xiao-Hui Wang; Stephen Tiong-Lee Tay; Joo-Hwa Tay (pp. 374-381).
Microbial aggregates of an aerobic granular sludge can be used for the treatment of industrial or municipal wastewater, but their formation from a microbial activated sludge requires several weeks. Therefore, the aim of this research was the selection of microbial cultures to shorten the granule-forming period from several weeks to a few days. An enrichment culture with the ability to accelerate granulation was obtained by repeating the selection and batch cultivation of fast-settling microbial aggregates isolated from the aerobic granular sludge. Bacterial cultures of Klebsiella pneumoniae strain B and Pseudomonas veronii strain F, with self-aggregation indexes of 65 and 51%, respectively, and a coaggregation index of 58%, were isolated from the enrichment culture. A mixture of these strains with the activated sludge was used as an inoculum in an experimental sequencing batch reactor to start up an aerobic granulation process. Aerobic granules with a mean diameter of 446±76 μm were formed in an experiment after 8 days of cultivation, but microbial granules were absent in controls. Considering biosafety issues, K. pneumoniae strain B was excluded from further studies, but P. veronii strain F was selected for larger-scale testing.