Characterization of a novel 3-hydroxybutyrate dehydrogenase from <Emphasis Type="Italic">Ralstonia pickettii</Emphasis> T1

We previously reported that the activities of two 3-hydroxybutyrate dehydrogenases (BDH1 and BDH2) were greatly influenced by culture conditions when Ralstonia pickettii T1, a strain growing on extracellular poly-3-hydroxybutyrate (PHB), was grown on different carbon sources such as 3HB and succinate. In this study, knockout mutants of bdh1 or bdh2 were constructed and characterized under different culture conditions. In addition, a novel BDH (BDH3) was found in bdh2 mutants, and bdh3 was cloned. Apparent kinetic parameters for the substrates of BDH3 indicated that the enzyme is suitable for the oxidation reaction of 3-hydroxybutyrate (3HB) to acetoacetate. In Western blotting, it was clear that BDH3 is produced only in cells grown on 3HB or PHB as a carbon source, while BDH1 and BDH2 are produced in cells grown on various carbon sources such as sugars, amino acids, organic acids, 3HB, and PHB. Both the bdh1 and bdh2 mutants lagged behind the wild type in growth rates when the cells were cultured with 3HB, citrate, succinate, or nutrient broth. A test of sensitivity to diamide as an oxidative stress revealed that the lack of BDH1 or BDH2 caused a decline in the capacity to neutralize the stress. These results suggested that BDH1 and BDH2 are needed to regulate the cytoplasmic redox state as well as to utilize 3HB, while BDH3 is specialized to utilize 3HB. The expression of bdh3 may be coordinately regulated with a gene encoding putative 3HB permease.     

Production of Short Side Chain-Poly[Hydroxyalkanoate] by a Newly Isolated Ralstonia Pickettii Strain

In order to obtain better bacterial species or strains for production of short side chain-poly[hydroxyalkanoate](ssc-PHA) from cheap carbon sources, a bioprospecting programme was performed in a subtropical rainforest soil. From 398 bacterial isolates, one produced high amounts of ssc-PHA when grown on sugarcane molasses or sucrose as detected by spectrophotometric scanning and gas chromatography coupled to mass spectrometry. Also, the GC—MS analysis indicated that the polymer was composed basically of poly[3-hydroxybutyrate](PHB). Phylogenetic studies using 16S rDNA analysis showed that the isolated bacterium belonged to the Ralstonia pickettii species and had a high identity/similarity with 16S rDNA obtained from total DNA of uncultured strains of soils and with unidentified bacteria at species level. The new strain was named R. pickettii 61A6. Spectrofluorometric analysis showed that the best rates of ssc-PHA accumulation within the cells occurred in 10%(w/v) sucrose and in 5%(w/v) sugarcane molasses at the stationary phase, with a yield of 231 and 357 mg/l of ssc-PHA per g dry cell weight, respectively.     

Biosynthesis of short-chain-length-polyhydroxyalkanoates during the dual-nutrient-limited zone by Ralstonia eutropha

Biosynthesis of PHAs by Raltonia eutropha during the dual nutrient-limitation-zone was investigated with mixed organic acids as carbon sources and (NH₄)₂SO₄ as nitrogen source. Two different methods of maintaining the dual-nutrient-limitation zone were adopted by feeding mixed acids and (NH₄)₂SO₄ at determined rates into the fermentation cultures which were initially free of carbon sources (method A) or nitrogen sources (method B). The results indicate that, firstly, with the increase of the width of the dual-nutrient-limitation zone, the yield of short-chain-length-polyhydroxyalkanoates also increases and it suggests that most of the short-chain-length-polyhydroxyalkanoates were biosynthesized during the dual-nutrient-limitation zone. Secondly, in contrast with the dual-nutrient-limitation method of limiting the nitrogen source first (method B), the dual-nutrient-limitation method of limiting the carbon source first (method A) was more favourable for the production of short-chain-length-polyhydroxyalkanoates, and the maximum production of short-chain-length-polyhydroxyalkanoates of these two methods are 3.72 and 2.55 g/l, respectively.     

Biochemical and molecular characterization of a succinate semialdehyde dehydrogenase involved in the catabolism of 4-hydroxybutyric acid in Ralstonia eutropha

A succinate semialdehyde dehydrogenase gene (gabD) was identified to be disrupted in a transposon-induced mutant of Ralstonia eutropha exhibiting the phenotype 4-hydroxybutyric acid-leaky. The native gabD gene was cloned by colony hybridization using a homologous gabD-specific DNA probe. DNA sequencing revealed an 1452-bp open reading frame, and the deduced amino acid sequence showed strong similarities to NADP(+)-dependent succinate semialdehyde dehydrogenases from Escherichia coli, Rhizobium sp., Homo sapiens and Rattus norvegicus. The gabD gene was heterologously expressed in a recombinant E. coli strain harboring plasmid pSK::EE6.8. Similar to the molecular organization of the gab cluster in E. coli, additional genes encoding enzymes for the degradation of gamma-aminobutyrate are closely related to gabD in R. eutropha. Enzymatic studies indicated the existence of a second NAD(+)-dependent succinate semialdehyde dehydrogenase in R. eutropha.     

Production of succinate and polyhydroxyalkanoate from substrate mixture by metabolically engineered Escherichia coli

The strategic design of this study aimed at producing succinate and polyhydroxyalkanoate (PHA) from substrate mixture of glycerol/glucose and fatty acid in Escherichia coli. To accomplish this, an E. coli KNSP1 strain derived from E. coli LR1110 was constructed by deletions of ptsG, sdhA and pta genes and overexpression of phaC1 from Pseudomonas aeruginosa. Cultivation of E. coli KNSP1 showed that this strain was able to produce 21.07 g/L succinate and 0.54 g/L PHA (5.62 wt.% of cell dry weight) from glycerol and fatty acid mixture. The generated PHA composed of 58.7 mol% 3-hydroxyoctanoate (3HO) and 41.3 mol% 3-hydroxydecanoate (3HD). This strain would be useful for complete utilization of byproducts glycerol and fatty acid of biodiesel production process.     

Short communication: Benzene metabolism via the intradiol cleavage in a Rhodococcus sp.

Benzene was metabolized by Rhodococcus sp. 33 through the intradiol cleavage (ortho-) pathway producing cis-benzene glycol, catechol and cis, cis-muconic acid as the intermediates. This is the first elucidation of the pathway by which benzene is degraded by a gram-positive organism. The enzyme assays have also suggested that Rhodococcus 33 does not have a fully functional tricarboxylic acid cycle but may have an operational glyoxylate bypass.     

Menaquinone is an obligatory component of the chain catalyzing succinate respiration in Bacillus subtilis

The question was investigated as to whether the bacterial menaquinone (MK) is a component of the electron transport chain catalyzing succinate respiration in Bacillus subtilis. Three different methods were applied, and the following consistent results were obtained. (i) Solvent extraction of MK from the bacterial membrane caused total inhibition of the respiratory activities with succinate and NADH, while the activity of succinate dehydrogenase remained unaffected. The respiratory activities were restored onincorporation of vitamin K₁ into the membrane preparation. (ii) The membrane fraction of a B. subtilis mutant containing 15% of the wild-type amount of MK, respired succinate and NADH at reduced activities. Wild-type activities were restored on fusion of the preparation to liposomes containing vitamin K₁. (iii) The membrane fraction of B. subtilis catalyzed succinate oxidation by various water-soluble naphtho- or benzoquinones at specific activities exceeding to that of succinate respiration. The results suggest that MK is involved in succinate respiration, although its redox potential is unfavorable.Abbreviations MK menaquinone - MKH₂ reduced menaquinone - E₀' standard redox potential at pH 7 - PMS phenazine methosulfate - DCPIP 2,6-Dichlorophenol-indophenol - Q ubiquinone - Q₀ 2,3-dimethoxy-5-methyl-1,4-bezoquinone - DMN, 2,3 dimethyl-1,4-naphthoquinone - DMK demethylmenaquinone     

Regulation of glucose catabolism in Thiobacillus A2 grown in the chemostat under dual limitation by succinate and glucose

In contrast to its diauxic behaviour in batch culture, Thiobacillus A2 grew in chemostat culture using glucose and succinate as dual limiting substrates. Biomass production under dual limitations was the sum of that on single substrates with each substrate being oxidized and assimilated to similar extents in single and dual substrate-limited cultures. In glucose and glucose + succinate-limited cultures glucose was oxidized largely by the Entner-Doudoroff and pentose phosphate pathways, but other mechanisms also contributed and the ratios of pathways depended on substrate ratios and the previous substrate-history of the culture. Variations in specific activities of enzymes of carbohydrate metabolism following switches from single to mixed substrates were considerable, ranging from fourfold for fructose diphosphate aldolase to more than 200-fold for hexokinase, fructose diphosphatase, glucose 6-phosphate and 6-phosphogluconate dehydrogenases. Changes in specific activities occurred only over prolonged time periods in the chemostat, probably reflecting low concentrations of free substrates in carbon-limited cultures and consequent low levels of catabolite repression.     

Improvement of succinate production by overexpression of a cyanobacterial carbonic anhydrase in Escherichia coli

Succinate fermentation was investigated in Escherichia coli strains overexpressing cyanobacterium Anabaena sp. 7120 ecaA gene encoding carbonic anhydrase (CA). In strain BL21 (DE3) bearing ecaA, the activity of CA was 21.8 U mg⁻¹ protein, whereas non-detectable CA activity was observed in the control strain. Meanwhile, the activity of phosphoenolpyruvate carboxylase (PEPC) increased from 0.2 U mg⁻¹ protein to 1.13 U mg⁻¹ protein. The recombinant bearing ecaA reached a succinate yield of 0.39 mol mol⁻¹ glucose at the end of the fermentation. It was 2.1-fold higher than that of control strain which was just 0.19 mol mol⁻¹ glucose. EcaA gene was also introduced into E. coli DC1515, which was deficient in glucose phosphotransferase, lactate dehydrogenase and pyruvate:formate lyase. Succinate yield can be further increased to 1.26 mol mol⁻¹ glucose. It could be concluded that the enhancement of the supply of HCO₃⁻ in vivo by ecaA overexpression is an effective strategy for the improvement of succinate production in E. coli.     

An Escherichia coli mutant defective in the NAD-dependent succinate semialdehyde dehydrogenase

Escherichia coli mutants, unable to grown on 4-hydroxyphenylacetate, have been isolated and found to be defective in the NAD-dependent succinate semialdehyde dehydrogenase. When the mutants are grown with 4-aminobutyrate as sole nitrogen source an NAD-dependent succinate semialdehyde dehydrogenase seen in the parental strain is absent but, as in the parental strain, an NADP-dependent enzyme is induced. Growth of the mutants is inhibited by 4-hydroxyphenylacetate due to the accumulation of succinate semialdehyde. The mutants are more sensitive to inhibition by exogenous succinate semialdehyde than is the parental strain. Secondary mutants able to grow in the presence of 4-hydroxyphenylacetate but still unable to use it as sole carbon source were defective in early steps of 4-hydroxyphenylacetate catabolism and so did not form succinate semialdehyde from 4-hydroxyphenylacetate. The gene encoding the NAD-dependent succinate semialdehyde dehydrogenase of Escherichia coli K-12 was located at min 34.1 on the genetic map.     

Incorporation of 8 succinate per mol nickel into factors F430 by Methanobacterium thermoautotrophicum

Factors F₄₃₀ from methanogenic bacteria have recently been shown to contain nickel and it has been speculated that they may have a nickel tetrapyrrole structure. This assumption was tested by determining whether succinate is incorporated by growing Methanobacterium thermoautotrophicum into three factors F₄₃₀. Succinate is assimilated by Methanobacterium thermoautotrophicum into the amino acids glutamate, arginine and proline and into tetrapyrroles rather than other cell components. It was found that per mol nickel 8–9 mol of succinate were incorporated into the three factors F₄₃₀ which is the amount predicted for a tetrapyrrole structure. Since the three factors F₄₃₀ only contained significant amounts of glutamate rather than arginine or proline, the incorporation data suggest that factors F₄₃₀ are nickel tetrapyrrole compounds. Spectral properties of the three factors F₄₃₀, apparent molecular weights, and the absence of phosphor in these compounds are also described.     

Recovery of poly(3-hydroxybutyrate) from high cell density culture of Ralstonia eutropha by direct addition of sodium dodecyl sulfate

A simple and effective method for the recovery poly(3-hydroxybutyrate) [P(3HB)] directly from high cell density culture broth with no pretreatment steps has been developed. This method consists of direct addition of sodium dodecyl sulfate (SDS) to the culture broth, shaking, heat treatment, and washing steps. When the SDS/biomass ratio was higher than 0.4, the purity of recovered P(3HB) was over 95% for various cell concentrations of 50–300 g dry cell l^–1, with the highest value of 97%. The recovery of P(3HB) was over 90% regardless of cell concentration and SDS dosage (SDS/biomass ratios, 0.1–0.7). One g SDS digests 0.72 g non-P(3HB) cell materials. The reduction in molecular weight, due to degradation of P(3HB) by SDS, was negligible.     

Control of succinate oxidation by cucumber (Cucumis sativus L.) cotyledon mitochondria

The aim of this work was to assess the extent to which mitochondria control the gluconeogenic flux in cucumber (Cucumis sativus L.) cotyledons, by quantifying the distribution of control of succinate oxidation by cotyledon mitochondria. The methods of metabolic control analysis were applied under state 3 and state 4 conditions and in the presence of cell-free extracts in order to simulate in-vivo conditions. Oxygen uptake by isolated cotyledon mitochondria oxidising succinate under state 3 conditions was examined using inhibitor titrations. During lipid mobilisation in light-grown cotyledons (3-4 d post-imbibition), control was shared between the adenine-nucleotide translocator (flux-control coefficient, C = 0.25–0.28) and the dicarboxylate-uptake system (C = 0.69–0.72). The dicarboxylate-uptake system was also important in dark-grown cotyledons at this stage (C = 0.55–0.57). In the photosynthetic phase of development (more than 5 d post-imbibition) control rested with the respiratory chain. Application of an external ATP demand provided either by cell-free extracts of cucumber cotyledons or a glucose/hexokinase ADP-regenerating system showed that the reactions outside the mitochondria exert control (C = 0.45–0.54 and C = 0.24–0.38, for cytosolic extract and glucose/hexokinase, respectively). The adenine-nucleotide translocator was a controlling step of both oxygen uptake (C = 0.11–0.32) and the flux between succinate and hexose phosphates (C = 0.28). Other mitochondrial steps made a significant contribution to control. Control of oxygen uptake was dependent on both the nature of the external load and on the rate of phosphorylation. A potential role for mitochondrial membrane-transport processes, including the adenine-nucleotide translocator, is proposed for the integration of lipid breakdown and gluconeogenesis in vivo.Abbreviations AdNT adenine-nucleotide translocator - C flux-control coefficient - F1,6BP fructose-1,6-biphosphate - F1,6BPase fructose-1,6-biphosphatase - F2,6BP fructose-2,6-bi-phosphate - F6P fructose-6-phosphate - OAA oxaloacetate - PEP phospho(enol)pyruvate - PFK phosphofructokinase - PFP pyrophosphate fructose-6-phosphate 1-phosphotransferase This work was supported by the Gatsby Charitable Foundation (Sainsbury Research Studentship to S.A.H.) and the Agricultural and Food Research Council (grant No. PG43/516 to C.J.L.).     

Evaluation of two alternative metabolic pathways for creatinine degradation in microorganisms

The microbial decomposition of creatinine was found to proceed mainly via N-methylhydantoin or creatine as the first degradation product. Either N-methylhydantoin or urea or both were detected as metabolites derived from creatinine in various microorganisms, and creatinine deiminase and creatinine amidohydrolase activities were detected concomitantly. N-Methylhydantoin hydrolase and N-carbamoylsarcosine amidohydrolase were found to be formed inducibly in the presence of creatinine or N-methylhydantoin. Three microorganisms which decompose creatinine in different ways were screened from soil. Pseudomonas putida 77 rapidly metabolized creatinine solely via N-methylhydantoin. Degradation of creatinine proceeded with both creatine and N-methylhydantoin as the first degradation products at the same time in Pseudomonas sp. H21. Pseudomonas sp. 0114 was found to metabolize creatinine mainly via creatine and to also metabolize N-methylhydantoin. Changes in the metabolites of creatinine during a cultivation or enzyme reaction were found to be closely related to the enzyme activities of interest which are regulated by creatinine or N-methylhydantoin in different ways depending on the microbial strain.     

Comparison of phbC genes cloned from Ralstonia eutropha and Alcaligenes latus for utilization in metabolic engineering of polyhydroxyalkanoate biosynthesis

Two cloned phbC genes, encoding polyhydroxybutyrate (PHB) synthase from Ralstonia eutropha and from Alcaligenes latus, were transformed into a PHB-negative mutant of R. eutropha. The expression characteristics of both genes were compared for the biosyntheses of PHB and its copolymers. Each phbC gene had different characteristics not only in the biosyntheses of PHB, poly(3-hydroxybutyrate-3-hydroxy-valerate), and poly(3-hydroxybutyrate-4-hydroxybutyrate) but also in the resulting morphology of PHB granules.     

Quantifying the surface characteristics and flocculability of Ralstonia eutropha

The microbial surface and flocculability were qualitatively characterized through the combination of the surface thermodynamic and the extended DLVO approaches, with Ralstonia eutropha, a polyhydroxybutyrate-producing bacterium, as an example. The negativity of the ζ potential of R. eutropha decreased from the initial −19.5 to −11 mV in its cultivation with the consumption of glucose. The total interfacial free energy (ΔG _adh) was changed from −80 to 28.5 mJ m⁻² in its entire growth process. This suggests that the bacterial surface changed from hydrophobic into hydrophilic, resulting in an alteration of its surface characteristics and flocculability in its different growth phases. As a result, the stability ratio of suspensions increased with the increasing cultivation time, indicating that the cell particles became more repulsive with each other and led to a more stable suspension of R. eutropha in its cultivation. The obtained information in this work might be useful for better understanding the surface characteristics and the flocculability and even manipulating its flocculability in the microbial growth process.     

Isolation of Endophytic Actinomycetes from Different Cultivars of Tomato and their Activities Against Ralstonia solanacearum in Vitro

The populations of endophytic actinomycetes from healthy and wilting tomato plants (tomato cultivars resistant and susceptible to Ralstonia solanacearum) grown in three different sites from Guangzhou, Guangdong Province, South China were investigated by cultivation methods. Most of the isolates belonged to streptomycetes. The Aureus group of Streptomyces was the most frequently isolated group. The population composition of Streptomyces varied according to tomato cultivars, physiological status and soil types. The proportions of antagonistic Streptomyces strains from healthy plants were higher than that from wilting plants (P < 0.05), although the difference among the proportions of antagonistic Streptomyces strains from different cultivars of healthy tomato was not significant, the similar result was found from wilting plants. No significant difference was found in the proportions of siderophere-producing Streptomyces strains from the same site (P > 0.05), but the difference was found from the different sampling sites (P < 0.05). The percentage of bacterial cell wall-degrading streptomycetes from wilting tomato was higher than that from healthy plants (P < 0.05). These results indicated that the cultivar of the host plant, physiological status and sampling sites would influence the proportion of endophytic streptomycetes with different physiological traits. Diversity of endophytic Streptomyces and their physiological diversity should be involved in developing potential biocontrol agents.     

Oleic acid improves poly(3-hydroxybutyrate-co-3-hydroxyvalerate) production by Ralstonia eutropha in inverted sugar and propionic acid

With the objective of verifying the influence of oleic acid as a nutritional supplement in the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by Ralstonia eutropha, cultures were established with 0.3 g oleic acid l^–1 and without this supplement, in 30 g inverted sugar l^–1 and 1 g propionic acid l^–1. The use of this supplement increased the accumulation of polymer from 18.3% to 28.3% (w/w) although the mass of 3-hydroxyvalerate in the polymer remained constant for both cultures.