Characterization of two 3-hydroxybutyrate dehydrogenases in poly(3-hydroxybutyrate)-degradable bacterium, Ralstonia pickettii T1

Two D-(-)-3-hydroxybutyrate (3HB) dehydrogenases, BDH1 and BDH2, were isolated and purified from a poly(3-hydroxybutyrate) (PHB)-degradable bacterium, Ralstonia pickettii T1. BDH1 activity increased in R. pickettii T1 cells grown on several organic acids as a carbon source but not on 3HB, whereas BDH2 activity markedly increased in the same cells grown on 3HB or PHB. To examine their biochemical properties, bdh1 and bdh2 were cloned and overexpressed in Escherichia coli, and their purified products were characterized. The kinetic parameters indicate that BDH1 is more suitable for converting acetoacetate to 3HB than BDH2, whereas BDH2 is more efficient for the reverse reaction than BDH1. Thus, R. pickettii T1 contains two BDHs with different biochemical properties and physiological roles: BDH1 for cell growth on organic acids other than 3HB and BDH2 for cell growth on 3HB or PHB.     

Fermentative production of (R)-(-)-3-hydroxybutyrate using 3-hydroxybutyrate dehydrogenase null mutant of Ralstonia eutropha and recombinant Escherichia coli

Two systems, one using an (R)-(-)-3-hydroxybutyrate dehydrogenase (BDH) null mutant of Ralstonia eutropha and the other using a recombinant Escherichia coli strain containing a synthetic poly[(R)-(-)-3-hydroxybutyrate] (PHB) operon and an extracellular PHB depolymerase gene, were used for the fermentative production of (R)-(-)-3-hydroxybutyrate (3HB). The concentration of 3HB in the culture supernatant of the mutant R. eutropha system reached about 30 mM after 5 d under anaerobic conditions, although it was about 4-10 mM under aerobic conditions. On the other hand, the 3HB concentration in the culture supernatant of the recombinant E. coli system reached about 70 mM after 4 d, indicating that about 70% of the glucose added was converted to 3HB.     

Taxonomic characterization and metabolic analysis of the Halomonas sp. KM-1, a highly bioplastic poly(3-hydroxybutyrate)-producing bacterium

In a brief previous report, the gram-negative moderately halophilic bacterium, Halomonas sp. KM-1, that was isolated in our laboratory was shown to produce the bioplastic, poly(3-hydroxybutyrate) (PHB), using biodiesel waste glycerol (Kawata and Aiba, Biosci. Biotechnol. Biochem., 74, 175-177, 2010). Here, we further characterized this KM-1 strain and compared it to other Halomonas strains. Strain KM-1 was subjected to a polyphasic taxonomic study. Strain KM-1 was rod-shaped and formed colonies on a plate that were cream-beige in color, smooth, opaque, and circular with entire edges. KM-1 grew under environmental conditions of 0.1%-10% (w/v) NaCl, pH 6.5-10.5 and at temperatures between 10°C and 45°C. The G+C content of strain KM-1 was 63.9 mol%. Of the 16 Halomonas strains examined in this study, the strain KM-1 exhibited the highest production of PHB (63.6%, w/v) in SOT medium supplemented with 10% glycerol, 10.0 g/L sodium nitrate and 2.0 g/L dipotassium hydrogen phosphate. The intracellular structures within which PHB accumulated had the appearance of intracellular granules with a diameter of approximately 0.5 μm, as assessed by electron microscopy. The intra- and extra-cellular metabolites of strain KM-1 were analyzed by capillary electrophoresis mass spectrometry. In spite of the high amount of PHB stored intra-cellularly, as possible precursors for PHB only a small quantity of 3-hydroxybutyric acid and acetyl CoA, and no quantity of 3-hydroxybutyl CoA, acetoacetyl CoA and acetoacetate were detected either intra- or extra-cellularly, suggesting highly efficient conversion of these precursors to PHB.     

Production of triacylglycerol and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by the toluene-degrading bacterium Rhodococcus aetherivorans IAR1

Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) produced by various bacteria has been intensively investigated as a promising biodegradable plastic, but required a supply of an expensive precursor as a secondary carbon source for its production. In a previous study, we identified a new bacterial strain, Rhodococcus aetherivorans IAR1, which synthesizes PHBV from toluene without the supply of a precursor. Toluene is the volatile organic compound most abundantly emitted to the environment. In the present paper, we show that R. aetherivorans IAR1 produces triacylglycerols (TAGs) simultaneously with PHBV. Both PHBV and TAGs were synthesized before the nitrogen source is completely exhausted. The cellular content of PHBV reached 10% of cell dry weight (CDW) and its synthesis ceased even during intermittent supply of toluene. However, accumulation of TAGs continued during cultivation and their cellular content reached 24% of CDW at the end of cultivation. Cerulenin inhibited TAG production and increased PHBV cellular content up to 30% of CDW. The mole fraction of 3-hydroxyvalerate (3HV) in PHBV produced from toluene increased from 60% to 80% during its accumulation. Fatty acid compositions of TAGs produced from acetate and toluene were different. At the end of cultivation, the mole fraction of C17:0, one of odd-carbon number fatty acids, was 5% on toluene or 10% on acetate while the mole fraction of 3HV in PHBV from toluene was as high as that in PHBV from acetate, suggesting that a C5 intermediate of toluene degradation might directly become a precursor of 3HV whereas propionyl-CoA is required for the incorporation of C17:0 into TAGs.     

Improved polyhydroxybutyrate (PHB) production in transgenic tobacco by enhancing translation efficiency of bacterial PHB biosynthetic genes

Polyhydroxybutyrate [P(3HB)] was produced in the transgenic tobacco harboring the genes encoding acetoacetyl-CoA reductase (PhaB) and polyhydroxyalkanoate synthase (PhaC) from Ralstonia eutropha (Cupriavidus necator) with optimized codon usage for expression in tobacco. P(3HB) contents in the transformants (0.2mg/g dry cell weight in average) harboring the codon-optimized phaB gene was twofold higher than the control transformants harboring the wild-type phaB gene. The immunodetection revealed an increased production of PhaB in leaves, indicating that the enhanced expression of PhaB was effective to increase P(3HB) production in tobacco. In contrast, codon-optimization of the phaC gene exhibited no apparent effect on P(3HB) production. This result suggests that the efficiency of PhaB-catalyzed reaction contributed to the flux toward P(3HB) biosynthesis in tobacco leaves.     

Improvement of exo-polysaccharides production and modeling kinetics by Armillaria luteo-virens Sacc. in submerged cultivation

Armillaria luteo-virens Sacc. is a special medicinal and edible mushroom in China, and its wild type has been investigated that it contains some functional components. The optimization of submerged culture conditions for mycelium growth and exo-polysaccharide (EPS) production in an edible mushroom A. luteo-virens Sacc. was studied in shake flasks and bioreactors with response surface methodology (RSM). A fractional factorial design (FFD) and central composite design (CCD) were applied to optimize the main factors that affect the fungal polysaccharides production in a submerged culture. Glucose is very important for EPS production by A. luteo-virens Sacc., and yeast extract powder also significantly affects fungal EPS production through fractional factorial experiment. The optimized cultivation medium constituents were derived from the predicted model using central composite design as follows: 31.26 g/l glucose, 1.06 g/l yeast extract powder, 1.00 g/l K₂HPO₄, 0.50 g/l KH₂PO₄, and 0.45 g/l MgSO₄·7H₂O, pH unadjusted. The predicted maximal EPS concentration was 5.40 g/l using the optimized culture medium compositions at 23 °C for 5 days. Additionally, the submerged cultivation process was explained using the optimized cultivation medium. The cultivation kinetics model constructed was suitably depicting the culture process in bioreactor cultivation scale.     

Precise control of repeating unit composition in biodegradable poly(3-hydroxyalkanoate) polymers synthesized by Escherichia coli

The composition of medium-chain-length (MCL) poly(3-hydroxyalkanoate) (PHA) biopolymers is normally an uncontrollable random mixture of repeating units with differing side chain lengths. Attempts to generate MCL PHA homopolymers and control repeating unit composition have been published in native PHA-producing organisms but have limited ranges for the different sizes of repeating units that can be synthesized. In this study, a new Escherichia coli-based system that exhibits control over repeating unit composition for both MCL PHAs and short-chain-length (SCL) PHAs has been developed, covering an unprecedented range of repeating units. The fadB and fadJ genes from the β-oxidation pathway were eliminated from the chromosome of E. coli LS5218. The subsequent blockage in β-oxidation caused a buildup of enoyl-CoA intermediates, which were converted to PHAs by an (R)-specific enoyl-CoA hydratase (PhaJ4) and PHA synthase [PhaC1(STQK)] expressed from a plasmid DNA construct. Fatty acid substrates were converted to PHAs with repeating units equal in the number of carbon atoms to the fatty acid substrate. The broad substrate specificities of the PhaJ4 and PhaC1(STQK) enzymes allowed for the production of homopolymers with strict control over the repeating unit composition from substrates of four to twelve carbons in length. Polymers were purified and analyzed by GC, GC-MS, and NMR for structural composition and by DSC, TGA, and GPC for thermal and physical characteristics. This study marks the development of the first single biological system to achieve consistent repeating unit control over such a broad range of repeating units in PHAs.     

Effect of an additionally introduced degQ gene on di-d-fructofuranosyl 2,6′:2′,6 anhydride (DFA IV) production by recombinant Bacillus subtilis in a single culture production system

Di-d-fructofuranosyl 2,6′:2′,6 anhydride (DFA IV) was produced directly from sucrose using a single culture of recombinant Bacillus subtilis 168 carrying the levan fructotransferase (lft) gene. In this study, three plasmids carrying the degQ36 gene, which is a degQ allele of B. subtilis (degQ36) with a degQ36 mutation on its promoter, were constructed to overproduce intact DegQ in B. subtilis 168. The transformant B. subtilis/pHT-D36 (with the degQ36 gene) consumed sucrose and produced levan at a higher rate than B. subtilis/pHT43 (without the degQ36 gene). The transformant B. subtilis/pLFT-GD36, carrying the lft and degQ36 genes, also consumed sucrose at a higher rate and produced more DFA IV than B. subtilis/pLFT-G, carrying the lft but without the degQ36 gene. B. subtilis/pLFT-GD36 produced 43.5 g/l of DFA IV and consumed 240 g/l of sucrose (96% of added sucrose) by 72 h of cultivation, whereas B. subtilis/pLFT-G produced 23.4 g/l of DFA IV with 76.9 g/l of sucrose still remaining in the system. Sucrose-inducible expression vectors were also constructed, which made it possible to produce DFA IV without IPTG induction. Using these vectors, sucrose consumption rates were enhanced and DFA IV production was increased upon introduction of the degQ36 gene. From these results, it can be concluded that the additionally introduced regulatory gene, degQ, was able to stimulate sucrose conversion to levan, and therefore increased DFA IV production in this system.     

Effects of nutrient supply methods and illumination with blue light emitting diodes (LEDs) on astaxanthin production by Haematococcus pluvialis

In order to increase the cell concentration and the accumulation of astaxanthin, the effects of nutrient concentration, pH, illumination and methods of supplying nutrients were studied for the cultivation of Haematococcus pluvialis. The replacement of media to avoid the deficiency of nutrients increased the cell concentration above 1 mg-dry cell cm(-3) without induction of astaxanthin accumulation. Illumination with blue light emitting diode lamps and nutrient starvation induced accumulation of astaxanthin, and the interactive effects of these two increased the astaxanthin concentration to 76 mug cm(-3).     

Cloning and Sequence Analysis of the estA gene encoding enzyme for producing (R)-β-acetylmercaptoisobutyric acid from Pseudomonas aeruginosa 1001

The estA gene encoding the enzyme that catalyzes the production of (R)-β-acetylmercaptoisobutyric acid from (R,S)-ester from Pseudomonas aeruginosa 1001, was cloned in Escherichia coli and its nucleotide sequence was determined, revealing the presumed open reading frame encoding a polypeptide of 316 amino acid residues (948 nucleotides). The overall A+T and C+G compositions were 32.59% and 67.41%, respectively. The amino acid sequence of the estA gene product showed a significant similarity with that of the triacylglycerol lipase from Psychrobacter immobilis (38% identity), triacylglycerol lipase from Moraxella sp. (36% identity), and two forms of carboxyl esterases from Acinetobacter calcoaceticus (17% and 17% identities). The deduced amino acid sequences have a pentapeptide consensus sequence, G-X-S-X-G, having an active serine residue, and another active site, dipeptides H-G, located at 70–100 amino acids upstream of the G-X-S-X-G consensus sequence.     

Biotransformation of (R)-(+)- and (S)-(−)-limonene to α-terpineol by Penicillium digitatum— investigation of the culture conditions

The biotransformation of (R)-(+)- and (S)-(−)-limonene by Penicillium digitatum was investigated. One strain of P. digitatum was able to convert (R)-(+)-limonene to pure (R)-(+)-α-terpineol in 8 h with a yield of up to 93%. It was found that (R)-(+)-limonene was converted much better into α-terpineol than (S)-(−)-limonene, and that no significant chemical conversion of the substrate occurred in control flasks at pH 3.5. The culture conditions involved such as the type and concentration of co-solvent applied and the sequential addition of substrate were investigated, taking into account some findings on the physical behaviour of the system. The highest bioconversion yields were obtained when the substrate was applied as a diluted solution in EtOH.     

Induction of electrophile-responsive element (EpRE)-mediated gene expression by tomato extracts in vitro

The market for food products with additional health benefits is increasing rapidly and tools for identification of bio-functional characteristics of food items are essential. To facilitate the detection of beneficial effects of tomato on gene expression, methods to prepare tomato extracts suitable to test in the EpRE LUX assay and other cell-based reporter gene assays for health-related bioactivity mechanisms, were developed. An isoprenoid-containing chloroform extract of tomato fruit and most individual isoprenoids did not induce electrophile-responsive element (EpRE)-mediated gene expression. A semi-polar extract of tomato fruits, enzymatically hydrolysed to remove the glycosyl residues from the phenolic ingredients was able to induce EpRE-mediated luciferase expression at both mRNA and protein level, which might be partly due to the presence of quercetin, kaempferol, naringenin and naringenin chalcone. It was concluded that induction of EpRE-regulated genes, such as detoxifying phase II and antioxidant enzymes, may contribute to the beneficial health effects of tomato.     

The porcine tribbles homolog 3 (TRIB3) gene: Identification of a missense mutation and association analysis with meat quality and production traits in Italian heavy pigs

TRIB3 plays an important role in energy metabolism. This work aimed to study the porcine tribbles homolog 3 (TRIB3) gene and to evaluate its association with meat quality and carcass traits in pigs. By sequencing a portion of the porcine TRIB3 gene two single nucleotide polymorphisms (SNPs) in the first coding exon (one synonymous SNP: c.132 T > C; and one missense mutation: c.146C > T, p.P49L) were identified. The two polymorphisms were in complete linkage disequilibrium. In silico analysis of the p.P49L mutation suggested that it could have functional effects. Association studies in four groups of pigs (651 animals in total) indicated that this gene marker was associated with back fat thickness in Italian Large White and Italian Duroc pigs in two different experimental designs (P < 0.1 and P < 0.05). This polymorphism tended to be associated with lactate content of the semimembranosus muscle (P < 0.1). Among several other tissues, TRIB3 is expressed in fat and skeletal muscle.     

Triggering mechanism of L-glutamate overproduction by DtsR1 in coryneform bacteria

The mechanism of L-glutamate-overproduction by Corynebacterium glutamicum, a biotin auxotroph, is very unique and interesting. L-Glutamate overproduction by this bacterium is induced by biotin-limitation and suppressed by an excess of biotin. Addition of a surfactant or penicillin is also induces L-glutamate overproduction even under excess biotin. After the development of general molecular biological tools such as cloning vectors and DNA transfer techniques, genes encoding biosynthetic enzymes were isolated. With those genes and tools, recombinant DNA technology can be applied to the analysis of biosynthetic pathways and the construction of C. glutamicum strains. In this review, recent studies on the triggering mechanism of L-glutamate overproduction by C. glutamicum are discussed. Disruption of the dtsR1 gene, which encodes a putative component of a biotin-containing enzyme complex that is involved in fatty acid synthesis, causes constitutive overproduction of L-glutamate. As in the case of biotin-limitation, i.e., addition of a surfactant or penicillin, dtsR1-disruption also reduces the activity of the 2-oxoglutarate dehydrogense complex (ODHC). These results indicate that the DtsR1 level affects the activity of ODHC. In our recent studies, a novel regulatory factor that suppresses the expression of DtsR1 was determined. Based on these findings, the triggering mechanism of L-glutamate overproduction is expected to be clarified in more detail.     

Synthesis,characterisation and analytical application of Fe3O4@SiO2@polyaminoquinoline magnetic nanocomposite for the extraction and pre-concentration of Cd(II) and Pb(II) in food samples

This work describes a novel Fe₃O₄@SiO₂@polyaminoquinoline magnetic nanocomposite and its application in the pre-concentration of Cd(II) and Pb(II) ions. The parameters affecting the pre-concentration procedure were optimised by a Box–Behnken design through response surface methodology. Three variables (extraction time, magnetic sorbent amount and pH) were selected as the main factors affecting the sorption step, while four variables (type, volume and concentration of the eluent, and elution time) were selected as main factors in the optimisation study of the elution step. Following the sorption and elution of analytes, the ions were quantified by flame atomic absorption spectrometry (FASS). The limits of detection were 0.1 and 0.7 ng ml^?1 for Cd(II) and Pb(II) ions, respectively. All the relative standard deviations were less than 7.6%. The sorption capacities of this new sorbent were 57 mg g^?1 for Cd(II) and 73 mg g^?1 for Pb(II). Ultimately, this nanocomposite was successfully applied to the rapid extraction of trace quantities of these heavy metal ions from seafood and agricultural samples and satisfactory results were obtained.     

Rapid and reliable identification of Staphylococcus aureus harbouring the enterotoxin gene cluster (egc) and quantitative detection in raw milk by real time PCR

A TaqMan and a SYBR Green real time PCR (rt-PCR) were developed for the reliable identification and quantitative detection of Staphylococcus (S.) aureus strains harbouring the enterotoxin gene cluster (egc) regardless of its variants. Both approaches revealed 100% specificity against a panel of 70 reference strains, including 29 clinical and foodborne S. aureus strains harbouring all the egc variants to date known, 4 egc⁻S. aureus strains and 37 strains of phylogenetically closely and distantly related species. Standard curves made by 10 fold dilutions of either genomic DNA or cells from an egc⁺S. aureus log-phase broth culture showed a good linearity of response (R² ≥ 0.993) for six orders of magnitude, with about 100% relative accuracy and a low inter-assay variability (CV ≤ 3.02). The overall limit of quantification (LOQ) for both rt-PCR assays (about 100% PCR efficiency; running time 30 min) was 10 cfu or 10 genome equivalents per reaction mixture although 1 cfu or 1 genome equivalent was detected with a 33.33% probability. These performances were confirmed in raw milk artificially contaminated with log-phase broth cultures of either a single egc⁺S. aureus strain or a mixture of S. aureus strains harbouring all the egc variants to date known. Similar results were also obtained with a raw milk based standard curve of the S. aureus egc⁺ mixture in the presence of 10⁶ cfu/mL of egc⁻S. aureus strains harbouring some of the commonest enterotoxin genes associated to the staphylococcal food poisoning. Nonetheless, the TaqMan based approach resulted in a lower sensitivity (LOQ = 100 cfu equivalents per reaction mixture) than the SYBR Green based assay (LOQ = 10 cfu equivalents per reaction mixture). When applied to real milk samples, both PCR assays provided a good response with 100% diagnostic specificity and 96-107% relative accuracy, as compared to conventional culture-based PCR approaches. Due to the high specificity, the wide dynamic range of detection and the high sensitivity demonstrated even in a complex and potentially highly contaminated raw milk matrix, the SYBR Green rt-PCR assay is a useful diagnostic tool for quick, high throughput and reliable routine screening of egc⁺S. aureus isolates. Moreover, the SYBR Green based quantitative detection of these pathogens in raw milk could remarkably contribute to clarify their actual role in staphylococcal food poisoning and other clinical syndromes associated with the consumption of milk and milk-based products.