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Applied Microbiology and Biotechnology (v.73, #2)
Well-defined protein–polymer conjugates—synthesis and potential applications by Pall Thordarson; Benjamin Le Droumaguet; Kelly Velonia (pp. 243-254).
During the last decades, numerous studies have focused on combining the unique catalytic/functional properties and structural characteristics of proteins and enzymes with those of synthetic molecules and macromolecules. The aim of such multidisciplinary studies is to improve the properties of the natural component, combine them with those of the synthetic, and create novel biomaterials in the nanometer scale. The specific coupling of polymers onto the protein structures has proved to be one of the most straightforward and applicable approaches in that sense. In this article, we focus on the synthetic pathways that have or can be utilized to specifically couple proteins to polymers. The different categories of well-defined protein–polymer conjugates and the effect of the polymer on the protein function are discussed. Studies have shown that the specific conjugation of a synthetic polymer to a protein conveys its physico-chemical properties and, therefore, modifies the biodistribution and solubility of the protein, making it in certain cases soluble and active in organic solvents. An overview of the applications derived from such bioconjugates in the pharmaceutical industry, biocatalysis, and supramolecular nanobiotechnology is presented at the final part of the article.
Keywords: Biohybrids; Protein–polymer conjugates; Nanotechnology
DNA microarray technology for the microbiologist: an overview by Armin Ehrenreich (pp. 255-273).
DNA microarrays have found widespread use as a flexible tool to investigate bacterial metabolism. Their main advantage is the comprehensive data they produce on the transcriptional response of the whole genome to an environmental or genetic stimulus. This allows the microbiologist to monitor metabolism and to define stimulons and regulons. Other fields of application are the identification of microorganisms or the comparison of genomes. The importance of this technology increases with the number of sequenced genomes and the falling prices for equipment and oligonucleotides. Knowledge of DNA microarrays is of rising relevance for many areas in microbiological research. Much literature has been published on various specific aspects of this technique that can be daunting to the casual user and beginner. This article offers a comprehensive outline of microarray technology for transcription analysis in microbiology. It shortly discusses the types of DNA microarrays available, the printing of custom arrays, common labeling strategies for targets, hybridization, scanning, normalization, and clustering of expression data.
Biodegradation of the cyclic nitramine explosives RDX, HMX, and CL-20 by Fiona H. Crocker; Karl J. Indest; Herbert L. Fredrickson (pp. 274-290).
Cyclic nitramine explosives are synthesized globally mainly as military munitions, and their use has resulted in environmental contamination. Several biodegradation pathways have been proposed, and these are based mainly on end-product characterization because many of the metabolic intermediates are hypothetical and unstable in water. Biodegradation mechanisms for cyclic nitramines include (a) formation of a nitramine free radical and loss of nitro functional groups, (b) reduction of nitro functional groups, (c) direct enzymatic cleavage, (d) α-hydroxylation, or (e) hydride ion transfer. Pathway intermediates spontaneously decompose in water producing nitrite, nitrous oxide, formaldehyde, or formic acid as common end-products. In vitro enzyme and functional gene expression studies have implicated a limited number of enzymes/genes involved in cyclic nitramine catabolism. Advances in molecular biology methods such as high-throughput DNA sequencing, microarray analysis, and nucleic acid sample preparation are providing access to biochemical and genetic information on cultivable and uncultivable microorganisms. This information can provide the knowledge base for rational engineering of bioremediation strategies, biosensor development, environmental monitoring, and green biosynthesis of explosives. This paper reviews recent developments on the biodegradation of cyclic nitramines and the potential of genomics to identify novel functional genes of explosive metabolism.
Applied microbiology and biotechnology in the conservation of stone cultural heritage materials by P. Fernandes (pp. 291-296).
The contribution of applied microbiology and biotechnology for the preservation and restoration of culturally relevant stoneworks has been used only to a minor extent. Until recently it only involved the identification of the living organisms accountable for the deterioration of those materials by classic phenotypic identification methods. This seems to be changing, given the amount of work recently published that focuses in the introduction of molecular-based techniques for the detection of microorganisms in historic stone. Such techniques complement and expand the information up till now gathered by conventional identification methods. Along with this, efforts are being made to develop and implement bio-based methodologies that may actively contribute to the bioremediation of weathered historic stoneworks. The present mini-review aims to provide an overview of recent findings on these matters.
Keywords: Historic stoneworks; Preservation and restoration; Biodeterioration; Bioremediation
Production of red mold rice using a modified Nagata type koji maker by Chiu-Hsia Chiu; Kuang-Huei Ni; Yuan-Kuang Guu; Tzu-Ming Pan (pp. 297-304).
In this research, a commercial koji maker with a rotary perforated bed of 5-m diameter was modified for red mold rice production. Monascus purpureus BCRC 31499 was selected for its high production capacities of monacolin K and red pigment. The selected strain was first cultivated in a 120-l submerged type fermentor at 34°C and 2 vvm aeration rate with 60 rpm agitation for 5 days using 20% liquefied rice porridge as carbon source. The high concentration red mold rice broth (>3.5 g/ml) was harvested for inocula and well mixed with cooked rice to an initial concentration of 2% v/w. The inoculated cooked rice then was directed into the modified koji maker, in which temperature and humidity profiles were kept at varied levels at different stages, respectively. Air was circulated to remove fermentation heat while the perforated bed rotated slowly for providing mild agitation. Lag phase of the Monascus sp. in the modified koji maker was determined to be 16 h by the time the koji temperature raised rapidly. Water was added into the koji bed by a water curtain at the 36th hour to keep the moisture content of the rice koji at 50% or above. At the final stage, temperature was adjusted to 34°C to direct red pigment production. After 7 days, 1,200-kg high quality red mold rice was harvested per batch. Labor costs, space, and fermentation time were reduced tremendously compared with those made by traditional methods.
Discovery of Pseudozyma rugulosa NBRC 10877 as a novel producer of the glycolipid biosurfactants, mannosylerythritol lipids, based on rDNA sequence by Tomotake Morita; Masaaki Konishi; Tokuma Fukuoka; Tomohiro Imura; Dai Kitamoto (pp. 305-313).
The search for a novel producer of glycolipid biosurfactants, mannosylerythritol lipids (MEL) was undertaken based on the analysis of ribosomal DNA sequences on the yeast strains of the genus Pseudozyma. Pseudozyma rugulosa NBRC 10877 was found to produce a large amount of glycolipids from soybean oil. Fluorescence microscopic observation also demonstrated that the strain significantly accumulates polar lipids in the cells. The structure of the glycolipids produced by the strain was analyzed by 1H and 13C nuclear magnetic resonance and gas chromatography–mass spectrometry methods, and was determined to be the same as MEL produced by Pseudozyma antarctica, a well-known MEL producer. The major fatty acids of the present MEL consisted of C8 and C10 acids. Based on high performance liquid chromatography, the composition of the produced MEL was as follows: MEL-A (68%), MEL-B (12%), and MEL-C (20%). To enhance the production of MEL by the novel strain, factors affecting the production, such as carbon and nitrogen sources, were further examined. Soybean oil and sodium nitrate were the best carbon and nitrogen sources, respectively. The supplementation of a MEL precursor, such as erythritol, drastically enhanced the production yield from soybean oil at a rate of 70 to 90%. Under the optimal conditions in a shake culture, a maximum yield, productivity, and yield coefficient (on a weight basis to soybean oil supplied) of 142 g l−1, 5.0 g l−1 day−1, and 0.5 g g−1 were achieved by intermittent feeding of soybean oil and erythritol using the yeast.
Hydrolysis of black soybean isoflavone glycosides by Bacillus subtilis natto by Lun-Cheng Kuo; Wei-Yi Cheng; Ren-Yu Wu; Ching-Jang Huang; Kung-Ta Lee (pp. 314-320).
Hydrolysis of isoflavone glycosides by Bacillus subtilis natto NTU-18 in black soymilk is reported. At the concentration of 3–5% (w/v), black soymilk in flask cultures, the isoflavones, daidzin, and genistin were highly deglycosylated within 24 h. Deglycosylation of isoflavones was further carried out in a 7-l fermenter with 5% black soymilk. During the fermentation, viable cells increased from 103 to 109 CFU ml−1 in 15 h, and the activity of β-glucosidase appeared at 8 h after inoculation and reached a maximum (3.3 U/ml) at 12 h, then decreased rapidly. Deglycosylation of isoflavone glycosides was observed at the same period, the deglycosylation rate of daidzin and genistin at 24 h was 100 and 75%, respectively. It is significantly higher than the previous reports of fermentation with lactic acid bacteria. In accordance with the deglycosylation of isoflavone glycosides, the estrogenic activity of the 24 h fermented black soymilk for ERβ estrogen receptor increased to threefold; meanwhile, the fermented broth activated ERα estrogen receptor to a less extent than ERβ. These results suggest that this fermentation effectively hydrolyzed the glycosides from isoflavone in black soymilk and the fermented black soymilk has the potential to be applied to selective estrogen receptor modulator products.
Biosynthesis of poly(ɛ- l-lysine)s in two newly isolated strains of Streptomyces sp. by Hideo Hirohara; Munenori Takehara; Masayuki Saimura; Atsushi Masayuki; Masahiro Miyamoto (pp. 321-331).
The biosynthesis of poly(ɛ-l-lysine) (ɛ-PL) in the two newly isolated strains of Streptomyces lydicus USE-11 (USE-11) and Streptomyces sp. USE-51 (USE-51) was studied by a newly developed two-stage culture method of cell growth at pH 6.8 and ɛ-PL production at pH 4.5. USE-11 synthesized ɛ-PL consisting of about 28 residues at a high production level, whereas USE-51 did the polymer with 15 ones at a low level. The secreted ɛ-PLs in culture media were digested in a neutral pH range with a peptide hydrolase(s) produced by the ɛ-PL producers. The optimum production levels were presumed to be dependent upon the inherent ɛ-PL synthesis machinery of each producer. The production in USE-51 was sharply dependent upon cell density as was often observed in the production of antibiotics, whereas that in USE-11 was scarcely affected by the density. The % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX!% MathType!MTEF!2!1!+-% feaaeaart1ev0aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbbjxAHX% garmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy0Hgip5wz% aebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbbf9v8qqaq% Fr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq-He9q8qq% Q8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaeaaakeaaca% qGtbGaae4tamaaDaaaleaacaqG0aaabaGaaeOmaiaab2caaaaaaa!3B81! $${ ext{SO}}^{{{ ext{2 - }}}}_{{ ext{4}}}$$ was found to be essential for the ɛ-PL production in both strains. This might suggest the involvement of a thiol group in the polymerization reactions including the activation of l-lysine. This study indicates that USE-11 is a most suitable strain for the exploration of the ɛ-PL biosynthesis at the molecular level as well as for the technical applications.
Whole-cell arsenite biosensor using photosynthetic bacterium Rhodovulum sulfidophilum by Hiroyuki Fujimoto; Masato Wakabayashi; Hidenori Yamashiro; Isamu Maeda; Katsuhiro Isoda; Masuo Kondoh; Masaya Kawase; Hitoshi Miyasaka; Kiyohito Yagi (pp. 332-338).
An arsenite biosensor plasmid was constructed in Escherichia coli by inserting the operator/promoter region of the ars operon and the arsR gene from E. coli and the crtA gene, which is responsible for carotenoid synthesis in the photosynthetic bacterium, Rhodovulum sulfidophilum, into the broad-host-range plasmid vector, pRK415. The biosensor plasmid, pSENSE-As, was introduced into a crtA-deleted mutant strain of R. sulfidophilum (CDM2), which is yellow in culture due to its content of spheroiden (SE) and demethylspheroidene (DMSE). CDM2 containing pSENSE-As changed from yellow to red by the addition of arsenite, which caused enzymatic transformation of SE and DMSE to spheroidenone (SO) and demethylspheroidenone (DMSO). Reverse transcriptase PCR analysis showed that the color change depended on transcription of the crtA gene in pSENSE-As. The color change could be clearly recognized with the naked eye at 5 μg/l arsenite. The biosensor strain did not respond to other metals except for bismuth and antimony, which caused significant accumulation of SO and DMSO in the cells at 60 and 600 μg/l, respectively. This biosensor indicates the presence of arsenite with a bacterial color change without the need to add a special reagent or substrate for color development, enabling this pollutant to be monitored in samples by the naked eye in sunlight, even where electricity is not available.
Molecular cloning of the aspartate 4-decarboxylase gene from Pseudomonas sp. ATCC 19121 and characterization of the bifunctional recombinant enzyme by Nai-Chen Wang; Chia-Yin Lee (pp. 339-348).
l-Aspartate 4-decarboxylase (Asd) is a major enzyme used in the industrial production of l-alanine. Its gene was cloned from Pseudomonas sp. ATCC 19121 and characterized in the present study. The 1,593-bp asd encodes a protein with a molecular mass of 59,243 Da. The Asd from this Pseudomonas strain was considerably homologous to other Asds and aminotransferases, and has evolved independently of these enzymes from gram-positive microbes. Productivity rate of the C-terminal His-tagged fusion Asd was at 33 mg/l of Escherichia coli transformant culture. The kinetic parameters K m and V max of the fusion protein were 11.50 mM and 0.11 mM/min, respectively. Gel filtration analysis demonstrated that Asd is a dodecamer at pH 5.0 while 4.4 % of the recombinant protein dissociated into dimer when the pH was increased to 7.0. Asd exhibited its maximum activity at pH 5.0 and specific activity of 280 U/mg, and remained stable over a broad range of pH. The optimum temperature for Asd reaction was 45 °C, and 92 % of the activity remained when the enzyme was incubated at 40 °C for 40 min. This enzyme did not have any preferred divalent cation for catalysis. The recombinant Asd also exhibited aminotransferase activity when d,l-Asp, l-Glu, l-Gln, and l-Ala were utilized as substrates. However, the decarboxylation activity of l-aspartate was 2,477 times higher than its aminotransferase activity. The present study is the first investigation on the important biochemical properties of the purified recombinant Asd.
A novel psychrophilic lipase from Pseudomonas fluorescens with unique property in chiral resolution and biodiesel production via transesterification by Yu Luo; Yitao Zheng; Zhengbing Jiang; Yushu Ma; Dongzhi Wei (pp. 349-355).
A lipase-producing bacterium strain B68 screened from soil samples of China was identified as Pseudomonas fluorescens. With GenomeWalker, the open reading frame of lipase gene lipB68, encoding 476 amino acids, was cloned and expressed in Escherichia coli BL21 (DE3). By affinity chromatography, the recombinant LipB68 protein was purified to the purity of 95%. As a member of lipase subfamily I.3, LipB68 has a unique optimum temperature of 20 °C, which was the lowest in this subfamily. In chiral resolution, LipB68 effectively catalyzed the transesterification of both α-phenylethanol and α-phenylpropanol at 20 °C, achieving E values greater than 100 and 60 after 120 h, respectively. Among all the known catalysts in biodiesel production, LipB68 produced biodiesel with a yield of 92% after 12 h, at the lowest temperature of 20 °C, and is the first one of the I.3 lipase subfamily reported to be capable of catalyzing the transesterification reaction of biodiesel production. Since lipase-mediated biodiesel production is normally carried out at 35–50 °C, the availability of a highly active lipase with a low optimal temperature can provide substantial savings in energy consumption. Thus, this novel psychrophilic lipase (LipB68) may represent a highly competitive energy-saving biocatalyst.
Genetic characterization and expression of the novel fungal protease, EPg222 active in dry-cured meat products by María J. Benito; Ian F. Connerton; Juan J. Córdoba (pp. 356-365).
EPg222 protease is a novel extracellular enzyme produced by Penicillium chrysogenum (Pg222) isolated from dry-cured hams that has the potential for use over a broad range of applications in industries that produce dry-cured meat products. The gene encoding EPg222 protease has been identified. Peptide sequences of EPg222 were obtained by de novo sequencing of tryptic peptides using mass spectrometry. The corresponding gene was amplified by PCR using degenerated primers based on a combination of conserved serine protease-encoding sequences and reverse translation of the peptide sequences. EPg222 is encoded as a gene of 1,361 bp interrupted by two introns. The deduced amino acid sequence indicated that the enzyme is synthesized as a preproenzyme with a putative signal sequence of 19 amino acids (aa), a prosequence of 96 aa and a mature protein of 283 aa. A cDNA encoding EPg222 has been cloned and expressed as a functionally active enzyme in Pichia pastoris. The recombinant enzyme exhibits similar activities to the native enzyme against a wide range of protein substrates including muscle myofibrillar protein. The mature sequence contains conserved aa residues characteristic of those forming the catalytic triad of serine proteases (Asp42, His76 and Ser228) but notably the food enzyme exhibits specific aa substitutions in the immunoglobulin-E recognition regions that have been identified in protein homologues that are allergenic.
Keywords: Penicillium chrysogenum ; Protease; Proteolysis; Dry-cured meat products
Improvement of protein production in lactic acid bacteria using 5′-untranslated leader sequence of slpA from Lactobacillus acidophilus by Junya Narita; Saori Ishida; Kenji Okano; Sakurako Kimura; Hideki Fukuda; Akihiko Kondo (pp. 366-373).
The 5′-untranslated leader sequence (UTLS) of the slpA gene from Lactobacillus acidophilus contributes to mRNA stabilization by producing a 5′ stem and loop structure, and a high-level expression system for the lactic acid bacteria was developed using the UTLS in this study. A plasmid, which expresses α-amylase under the control of the ldh promoter, was constructed by integrating the core promoter sequence with the UTLS. The role of the UTLS in increasing the copies of the α-amylase mRNA was proved by measuring α-amylase activity in the culture supernatant and the relative expression of α-amylase mRNA was determined by the quantitative real-time PCR analysis. Moreover, several expression systems were constructed by combining the core promoter sequence with the UTLS or with the partially deleted UTLS and the expression level was evaluated. The use of the UTLS led to the success in improving α-amylase expression in the two strains of Lactobacillus casei and Lactococcus lactis. The current study showed that the improvement in protein production using the UTLS could be applied to the expression system in the lactic acid bacteria.
Redirection electron flow to high coupling efficiency of terminal oxidase to enhance riboflavin biosynthesis by Xiao-Jing Li; Tao Chen; Xun Chen; Xue-Ming Zhao (pp. 374-383).
The metabolic impact of redirection electron flow to high coupling efficiency of terminal oxidases on riboflavin biosynthetic ability was quantitatively assessed during batch culture in this paper. While disruption of the low coupling bd oxidase of the riboflavin overproducing B. subtilis PK, the apparent phenotype with more rapid specific growth rate and higher biomass yield was achieved. Compared to by-products formation, a discernible shift to less acetate and more acetoin in cyd mutant was observed. As the overflow metabolism was decreased in B. subtilis PK cyd, more carbon source was directed to biomass and riboflavin biosynthetic pathway, which resulted in higher biomass and about 30% improvement of riboflavin biosynthetic ability. The higher product-corrected biomass yield in mutant showed that the efficient energy generation is an important factor for exponential growth of riboflavin overproducing B. subtilis strain in batch culture.
Outer membrane mutation effects on UDP-glucose permeability and whole-cell catalysis rate by Ye Ni; Zichao Mao; Rachel R. Chen (pp. 384-393).
In whole-cell biocatalysis, cell envelopes represent a formidable barrier for substrates to permeate. The present research addresses this critical issue by investigating the effects of outer membrane mutation on uridine diphosphate (UDP)-glucose-utilizing enzymes in whole-cell systems. Owing to the severe limitation in substrate permeability, the wild-type Escherichia coli cells only exhibited as low as 4% of available enzyme activities. The reduction of the barriers of the outer membrane permeability (by mutations in its structure) led to a striking acceleration (up to 14-fold) of the reaction rate in cells expressing UDP-glucose dehydrogenase. Mutations in the lipopolysaccharide synthesis pathway or Braun’s lipoprotein are both effective. The acceleration was dependent upon the substrate concentrations as well as the enzyme expression level. In addition, the mutation has been demonstrated to be much more effective than the freeze–thaw permeabilizing method. An application of outer membrane mutants was illustrated with the synthesis of a disaccharide (N-acetyllactosamine) from UDP-glucose. Both reaction rate and product yield were enhanced significantly (more than twofold) in the lipoprotein mutant, demonstrating the importance of the outer membrane permeability barrier and the advantages of using outer membrane mutants in synthesis. This research and the results outlined in this paper point to a valid strategy in addressing permeability issues in whole-cell biocatalysis. It also highlights a need for an assessment of substrate permeability in biocatalysis research and development.
Keywords: Whole-cell biocatalysis; Substrate permeability; Permeabilization; E. coli ; Outer membrane
Intraspecific diversity of Oenococcus oeni strains determined by sequence analysis of target genes by Arnaud Delaherche; Elisabeth Bon; Aurelien Dupé; Megumi Lucas; Benoit Arveiler; Antoine De Daruvar; Aline Lonvaud-Funel (pp. 394-403).
Using molecular techniques and sequencing, we studied the intraspecific diversity of Oenococcus oeni, a lactic acid bacterium involved in red winemaking. A relationship between the phenotypic and genotypic characterization of 16 O. oeni strains isolated from wine with different levels of enological potential was shown. The study was based on the comparative genomic analysis by subtractive hybridization between two strains of O. oeni with opposite enological potential. The genomic sequences obtained from subtractive hybridization were amplified by polymerase chain reaction and sequenced for the 16 strains. A considerable diversity among strains of O. oeni was observed.
Keywords: O. oeni species; Variability; Genes
Enhanced productivity of protease-sensitive heterologous proteins by disruption of multiple protease genes in the fission yeast Schizosaccharomyces pombe by Alimjan Idiris; Hideki Tohda; Ke-wei Bi; Atsushi Isoai; Hiromichi Kumagai; Yuko Giga-Hama (pp. 404-420).
The creation of protease-deficient mutants to avoid product degradation is one of the current strategies employed to improve productivity and secretion efficiency of heterologous protein expression. We previously constructed a set of single protease-deficient mutants of the fission yeast Schizosaccharomyces pombe by respective disruption of 52 protease genes, and we succeeded in confirming useful disruptants (Idiris et al., Yeast 23:83–99, 2006). In the present study, we attempted multiple deletions of 13 protease genes, single deletions of which were previously confirmed as being beneficial for reducing extracellular product degradation. Using PCR-based gene replacement, a series of multiple deletion strains was constructed by multiple disruption of a maximum of seven protease genes. Effects of the resultant multiple deletion strains on heterologous expression were then measured by practical expression of a proteolytically sensitive model protein, the human growth hormone (hGH). Time profiles of hGH secretion from each resultant mutant demonstrated significantly enhanced hGH productivity with processing of the multiple protease deletions. The data clearly indicated that disruption of multiple protease genes in the fission yeast is an effective method for controlling proteolytic degradation of heterologous proteins particularly susceptible to proteases.
Chloroform degradation by butane-grown cells of Rhodococcus aetherovorans BCP1 by Dario Frascari; Davide Pinelli; Massimo Nocentini; Stefano Fedi; Youri Pii; Davide Zannoni (pp. 421-428).
The ability of a Rhodococcus aetherovorans strain, BCP1, to grow on butane and to degrade chloroform in the 0–633 μM range (0–75.5 mg l−1) via aerobic cometabolism was investigated by means of resting-cell assays. BCP1 degraded chloroform with a complete mineralization of the organic Cl. The resulting butane and chloroform maximum specific degradation rates were equal to 118 and 22 μmol % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! % MathType!MTEF!2!1!+- % feaaeaart1ev0aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbbjxAHX % garmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy0Hgip5wz % aebbnrfifHhDYfgasaacH8qrps0lbbf9q8WrFfeuY-Hhbbf9v8qqaq % Fr0xc9pk0xbba9q8WqFfea0-yr0RYxir-Jbba9q8aq0-yq-He9q8qq % Q8frFve9Fve9Ff0dmeaabaqaciGacaGaaeqabaWaaeWaeaaakeaaca % qGTbGaae4zamaaDaaaleaacaqGWbGaaeOCaiaab+gacaqG0bGaaeyz % aiaabMgacaqGUbaabaGaaeylaiaabgdaaaGccaqGKbGaaeyyaiaabM % hadaahaaWcbeqaaiaab2cacaqGXaaaaaaa!45F3! $${{mg}}^{{{{ - 1}}}}_{{{{protein}}}} {{day}}^{{{{ - 1}}}}$$ , respectively. Butane inhibition on chloroform degradation was satisfactorily interpreted by means of a model of competitive inhibition, with an inhibition constant equal to 38 % of the estimated butane half-saturation constant, whereas chloroform (at 11 μM) did not inhibit butane utilization. Acetylene (1,720 μM) induced an almost complete inactivation of the degradation of both butane and chloroform, indicating that the studied cometabolic process is mediated by a monooxygenase enzyme. BCP1 proved capable of degrading vinyl chloride and 1,1,2-trichloroethane, but not 1,2-trans-dichloroethylene. BCP1 could grow on the intermediates of the most common butane metabolic pathways and on the aliphatic hydrocarbons from ethane to n-heptane. After growth on n-hexane, it was able to deplete chloroform (13 μM) with a degradation rate higher than that obtained, at the same chloroform concentration, after growth on butane.
Physiological–biochemical properties and the ability to synthesize polyhydroxyalkanoates of the glucose-utilizing strain of the hydrogen bacterium Ralstonia eutropha B8562 by T. G. Volova; M. Y. Trusova; G. S. Kalacheva; I. V. Kozhevnicov (pp. 429-433).
Physiological–biochemical, genetic, and cultural properties of the glucose-utilizing mutant strain Ralstonia eutropha B8562 have been compared with those of its parent strain R. eutropha B5786. It has been shown that growth characteristics of the strain cultured on glucose as the sole carbon and energy source are comparable with those of the parent strain. Strain B8562 is characterized by high polyhydroxyalkanoate (PHA) yields on different carbon sources (CO2, fructose, and glucose). PHA accumulation in the strain batch cultured on glucose under nitrogen deficiency reaches 90 %. The major monomer in the PHA is β-hydroxybutyric acid (more than 99 mol %); the identified minor components are β-hydroxyvaleric acid (0.25–0.72 mol %) and β-hydroxyhexanoic acid (0.08–1.5 mol %). The strain is a promising PHA producer on available sugar-containing media with glucose.
Kluyveromyces lactis and Saccharomyces cerevisiae, two potent deacidifying and volatile-sulphur-aroma-producing microorganisms of the cheese ecosystem by Dafni-Maria Kagkli; Roselyne Tâche; Timothy M. Cogan; Colin Hill; Serge Casaregola; Pascal Bonnarme (pp. 434-442).
Cheese flavour is the result of complex biochemical transformations attributed to bacteria and yeasts grown on the curd of smear-ripened cheeses. Volatile sulphur compounds (VSCs) are responsible for the characteristic aromatic notes of several cheeses. In the present study, we have assessed the ability of Kluyveromyces lactis, Kluyveromyces marxianus and Saccharomyces cerevisiae strains, which are frequently isolated from smear-ripened cheeses, to grow and deacidify a cheese medium and generate VSCs resulting from l-methionine degradation. The Kluyveromyces strains produced a wider variety and higher amounts of VSCs than the S. cerevisiae ones. We have shown that the pathway is likely to be proceeding differently in these two yeast genera. The VSCs are mainly generated through the degradation of 4-methylthio-oxobutyric acid in the Kluyveromyces strains, in contrast to the S. cerevisiae ones which have higher l-methionine demethiolating activity, resulting in a direct conversion of l-methionine to methanethiol. The deacidification activity which is of major importance in the early stages of cheese-ripening was also compared in S. cerevisiae and Kluyveromyces strains.
Keywords: Volatile sulphur compounds; Methionine catabolism; Deacidification; Kluyveromyces ; Saccharomyces
High-yield 5-keto-d-gluconic acid formation is mediated by soluble and membrane-bound gluconate-5-dehydrogenases of Gluconobacter oxydans by Marcel Merfort; Ute Herrmann; Stephanie Bringer-Meyer; Hermann Sahm (pp. 443-451).
Gluconobacter oxydans DSM 2343 is known to catalyze the oxidation of glucose to gluconic acid, and subsequently, to 2-keto-d-gluconic acid (2-KGA) and 5-keto-d-gluconic acid (5-KGA), by membrane-bound and soluble dehydrogenases. In G. oxydans MF1, in which the membrane-bound gluconate-2-dehydrogenase complex was inactivated, formation of the undesired 2-KGA was absent. This mutant strain uniquely accumulates high amounts of 5-KGA in the culture medium. To increase the production rate of 5-KGA, which can be converted to industrially important l-(+)-tartaric acid, we equipped G. oxydans MF1 with plasmids allowing the overproduction of the soluble and the membrane-bound 5-KGA-forming enzyme. Whereas the overproduction of the soluble gluconate:NADP 5-oxidoreductase resulted in the accumulation of up to 200 mM 5-KGA, the detected 5-KGA accumulation was even higher when the gene coding for the membrane-bound gluconate-5-dehydrogenase was overexpressed (240 to 295 mM 5-KGA). These results provide a basis for designing a biotransformation process for the conversion of glucose to 5-KGA using the membrane-bound as well as the soluble enzyme system.
Keywords: Gluconobacter ; 5-keto-d-gluconic acid; Gluconate-5-dehydrogenase; Tartaric acid
Oxidative stress by biphenyl metabolites induces inhibition of bacterial cell separation by T. Yamada; Y. Shimomura; Y. Hiraoka; K. Kimbara (pp. 452-457).
Cell–cell separation of a polychlorinated biphenyl (PCB)-degrading bacterium Comamonas testosteroni TK102 was monitored by flow cytometry. When monohydroxy metabolites of biphenyl (BP) (2-hydroxybiphenyl and 3-hydroxybiphenyl) were added to the culture, cell–cell separation of strain TK102 was inhibited at stationary phase. This inhibition was reproduced on non-PCB degrading bacteria such as Pseudomonas putida PpY101 and Escherichia coli MV1184, but was not observed on Pseudomonas aeruginosa PAO1. An opportunistic pathogen, P. aeruginosa PAO1, produces exopolysaccharide, which is known to scavenge damaging chemicals such as reactive oxygen species (ROS). The higher level of ROS and lipid peroxidants were detected in the cells treated by monohydroxybiphenyls. Fat-soluble vitamin E, which is a lipid radical scavenger, maintained bacterial cell separation during monohydroxybiphenyls treatment. Our results demonstrated that intracellular oxidative stress played an important role in the inhibition of bacterial cell separation during BP metabolism. This study shows that metabolites of environmental pollutants, such as monohydroxylated BP, inhibit bacterial cell separation by oxidative stress.
Characterization of cadmium removal by Rhodotorula sp. Y11 by Zhijian Li; Hongli Yuan (pp. 458-463).
Experiments were conducted studying the removal of Cd2+ from water via biosorption using Rhodotorula sp. Y11. The effects of temperature and initial pH of the solution on biosorption were studied. Caustic and heat treatments showed different influences on the biosorption capacity, and the highest metal uptake value (19.38 mg g−1) was obtained by boiling treated yeast cells. The presence of competing cations, such as Ag+, Cu2+, and Mg2+, except Na+ ions, significantly interfered with the metal uptake. Results indicate that the Langmuir model gave a better fit to the experimental data than the Freundlich equation. The q 10 value was 11.38 mg g−1 for Cd2+ uptake by Y11. Chemical modifications of the biomass demonstrated that carboxyl and amide groups play an important role in Cd2+ biosorption.
RelA1 gene control of Escherichia coli lipid structure and cell performance during glucose limited fed-batch conditions by Atefeh Shokri; Andres Veide; Gen Larsson (pp. 464-473).
At increasing glucose limitation, typical for fed-batch cultivation performance, cultivation of Escherichia coli (relA1) results in development of a lipid structure that radically differs from the wild type and is characterised by accumulation of neutral phospholipids and saturated fatty acids. The mutant can, furthermore, not change the level of cardiolipin, which is generally the hallmark of changes to severe glucose limitation. The result suggests an increased negative control in the mutant with respect to the flux to phosphatidyl glycerol and cardolipin as well as to unsaturated fatty acids. Opposite to the wild type, the cardiolipin-depleted membrane is more fragile with respect to sonication and osmotic chock, at severe limitation, and results in extensive foaming during the process. Protein leakage and cell lysis is, however, lower in the mutant most likely due to the increased amounts of saturated fatty acids, which might be a possible strategy to overcome the reduced amounts of membrane-strengthening cardiolipin. The membrane potential of the outer surface is negative, however less negative for the mutant. This was supported by aqueous two-phase extraction experiments which, furthermore indicated a difference in outer surface hydrofobicity. These findings suggest that the relA1 gene has a defined, but ppGpp-independent, role in cells with a slowly decreasing metabolism of glucose to control the membrane morphology.
Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101 by Nobutada Kimura; Wataru Kitagawa; Toshio Mori; Nobutaka Nakashima; Tomohiro Tamura; Yoichi Kamagata (pp. 474-484).
Rhodococcus opacus strain SAO101 was shown to degrade on various polycyclic aromatic hydrocarbons such as naphthalene, dibenzofuran (DF), and dibenzo-p-dioxin (DD). One of the unique traits of the strain SAO101 is its ability to oxidize DF compounds by lateral dioxygenation. To clone the lateral dioxygenase gene involved in compound degradation in strain SAO101, we identified a cosmid clone that oxidizes aromatic compounds by using SAO101 genomic DNA. Sequencing analysis revealed that isolated cosmid clone contained ring-hydroxylating dioxygenase genes (narAaAb) with homologies to indene dioxygenase genes of Rhodococcus strain I24 and naphthalene dioxygenase genes of Rhodococcus strain NCIMB12038. The NarAaAb-expressing Rhodococcus cells exhibited broad substrate specificity for bicyclic aromatic compounds and had high ability to degrade dibenzofuran and naphthalene. Metabolite analysis revealed that dihydrodiol compounds were detected as metabolites from dibenzofuran by the NarAaAb-expressing Rhodococcus strain, indicating that dibenzofuran was converted by lateral dioxygenase activity of NarA dioxygenase. Based on reverse transcriptase-polymerase chain reaction analysis, it was found that the narAaAb genes were cotranscribed and that their expression was induced in the presence of aromatic hydrocarbon compounds. It is likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by this strain. Strain SAO101 harbors three huge linear plasmids, pWK301 (1,100 kbp), pWK302 (1,000 kbp), and pWK303 (700 kbp), and the nar genes were found to be located on the pWK301 plasmid.