Plasmid expression level heterogeneity monitoring via heterologous eGFP production at the single-cell level in Cupriavidus necator.

A methodology for plasmid expression level monitoring of eGFP expression suitable for dynamic processes was assessed during fermentation. This technique was based on the expression of a fluorescent biosensor (eGFP) encoded on a recombinant plasmid coupled to single-cell analysis. Fluorescence intensity at single-cell level was measured by flow cytometry. We demonstrated that promoter evaluation based on single-cell analysis versus classic global analysis brings valuable insights. Single-cell analysis pointed out the fact that intrinsic fluorescence increased with the strength of the promoter up to a threshold. Beyond that, cell permeability increases to excrete the fluorescent protein in the medium. The metabolic load due to the increase in the eGFP production in the case of strong constitutive promoters leads to slower growth kinetics compared with plasmid-free cells. With the strain Cupriavidus necator Re2133, growth rate losses were measured from 3% with the weak constitutive promoter Plac to 56% with the strong constitutive promoter Pj5. Through this work, it seems crucial to find a compromise between the fluorescence intensity in single cells and the metabolic load; in our conditions, the best compromise found was the weak promoter Plac. The plasmid expression level monitoring method was tested in the presence of a heterogeneous population induced by plasmid-curing methods. For all the identified subpopulations, the plasmid expression level heterogeneity was significantly detected at the level of fluorescence intensity in single cells. After cell sorting, growth rate and cultivability were assessed for each subpopulation. In conclusion, this eGFP biosensor makes it possible to follow the variations in the level of plasmid expression under conditions of population heterogeneity.Key Points•Development of a plasmid expression level monitoring method at the single-cell level by flow cytometry.•Promoter evaluation by single-cell analysis: cell heterogeneity and strain robustness.•Reporter system optimization for efficient subpopulation detection in pure cultures.

Discriminating changes in intracellular NADH/NAD+ levels due to anoxicity and H2 supply in R. eutropha cells using the Frex fluorescence sensor.

The hydrogen-oxidizing "Knallgas" bacterium Ralstonia eutropha can thrive in aerobic and anaerobic environments and readily switches between heterotrophic and autotrophic metabolism, making it an attractive host for biotechnological applications including the sustainable H2-driven production of hydrocarbons. The soluble hydrogenase (SH), one out of four different [NiFe]-hydrogenases in R. eutropha, mediates H2 oxidation even in the presence of O2, thus providing an ideal model system for biological hydrogen production and utilization. The SH reversibly couples H2 oxidation with the reduction of NAD+ to NADH, thereby enabling the sustainable regeneration of this biotechnologically important nicotinamide cofactor. Thus, understanding the interaction of the SH with the cellular NADH/NAD+ pool is of high interest. Here, we applied the fluorescent biosensor Frex to measure changes in cytoplasmic [NADH] in R. eutropha cells under different gas supply conditions. The results show that Frex is well-suited to distinguish SH-mediated changes in the cytoplasmic redox status from effects of general anaerobiosis of the respiratory chain. Upon H2 supply, the Frex reporter reveals a robust fluorescence response and allows for monitoring rapid changes in cellular [NADH]. Compared to the Peredox fluorescence reporter, Frex displays a diminished NADH affinity, which prevents the saturation of the sensor under typical bacterial [NADH] levels. Thus, Frex is a valuable reporter for on-line monitoring of the [NADH]/[NAD+] redox state in living cells of R. eutropha and other proteobacteria. Based on these results, strategies for a rational optimization of fluorescent NADH sensors are discussed.

PHA granules help bacterial cells to preserve cell integrity when exposed to sudden osmotic imbalances.

Polyhydroxyalkanoates (PHA) are microbial polyesters which accumulate as intracellular granules in numerous prokaryotes and mainly serve as storage materials; beyond this primary function, PHA also enhance the robustness of bacteria against various stress factors. We have observed that the presence of PHA in bacterial cells substantially enhances their ability to maintain cell integrity when suddenly exposed to osmotic imbalances. In the case of the non-halophilic bacterium Cupriavidus necator, the presence of PHA decreased plasmolysis-induced cytoplasmic membrane damage during osmotic up-shock, which subsequently enabled the cells to withstand subsequent osmotic downshock. In contrast, sudden induction of osmotic up- and subsequent down-shock resulted in massive hypotonic lysis of non-PHA containing cells as determined by Transmission Electron Microscopy and Thermogravimetrical Analysis. Furthermore, a protective effect of PHA against hypotonic lysis was also observed in the case of the halophilic bacterium Halomonas halophila; here, challenged PHA-rich cells were capable of retaining cell integrity more effectively than their PHA-poor counterparts. Hence, it appears that the fact that PHA granules, as an added value to their primary storage function, protect halophiles from the harmful effect of osmotic down-shock might explain why PHA accumulation is such a common feature among halophilic prokaryotes. The results of this study, apart from their fundamental importance, are also of practical biotechnological significance: because PHA-rich bacterial cells are resistant to osmotic imbalances, they could be utilized in in-situ bioremediation technologies or during enrichment of mixed microbial consortia in PHA producers under conditions of fluctuating salinity.

The presence of PHB granules in cytoplasm protects non-halophilic bacterial cells against the harmful impact of hypertonic environments.

Numerous prokaryotes accumulate polyhydroxybutyrate (PHB) intracellularly as a storage material. It has also been proposed that PHB accumulation improves bacterial stress resistance. Cupriavidus necator and its PHB non-accumulating mutant were employed to investigate the protective role of PHB under hypertonic conditions. The presence of PHB granules enhanced survival of the bacteria after exposure to hypertonic conditions. Surprisingly, when coping with such conditions, the bacteria did not utilize PHB to harvest carbon or energy, suggesting that, in the osmotic upshock of C. necator, the protective mechanism of PHB granules is not associated with their hydrolysis. The presence of PHB granules influenced the overall properties of the cells, since challenged PHB-free cells underwent massive plasmolysis accompanied by damage to the cell membrane and the leakage of cytoplasm content, while no such effects were observed in PHB containing bacteria. Moreover, PHB granules demonstrated "liquid-like" properties indicating that they can partially repair and stabilize cell membranes by plugging small gaps formed during plasmolysis. In addition, the level of dehydration and changes in intracellular pH in osmotically challenged cells were less pronounced for PHB-containing cultures, demonstrating the important role of PHB for bacterial survival under hyperosmotic conditions.

Poly(3-hydroxybutyrate) anabolism in Cupriavidus necator cultivated at various carbon-to-nitrogen ratios: insights from single-cell Raman spectroscopy.

Cupriavidus necator accumulates large amounts of poly(3-hydroxybutyrate) (PHB), a biodegradable substitute for petroleum-based plastics, under certain nutrient conditions. Conventional solvent-extraction-based methods for PHB quantification only obtain average information from cell populations and, thus, mask the heterogeneity among individual cells. Laser tweezers Raman spectroscopy (LTRS) was used to monitor dynamic changes in the contents of PHB, nucleic acids, and proteins in

Development of a rapid method to isolate polyhydroxyalkanoates from bacteria for screening studies.

We describe a novel method of Polyhydroxyalkanoate (PHA) extraction using dimethyl sulphoxide (DMSO) for use in screening studies. Compared to conventional chloroform extraction, the DMSO method was shown to release comparable quantities of PHA from Cupriavidus necator cells, with comparable properties as determined using Fourier transform infrared spectroscopy and differential scanning calorimetry.

Efficient biological conversion of carbon monoxide (CO) to carbon dioxide (CO2) and for utilization in bioplastic production by Ralstonia eutropha through the display of an enzyme complex on the cell surface.

An enzyme complex for biological conversion of CO to CO2 was anchored on the cell surface of the CO2-utilizing Ralstonia eutropha and successfully resulted in a 3.3-fold increase in conversion efficiency. These results suggest that this complexed system may be a promising strategy for CO2 utilization as a biological tool for the production of bioplastics.

Rapid and direct compositional analysis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in whole bacterial cells by thermally assisted hydrolysis and methylation-gas chromatography.

Thermally assisted hydrolysis and methylation-gas chromatography (THM-GC) in the presence of an organic alkali was applied to the direct analysis of copolymer composition for poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] accumulated in whole bacterial cells. Cupriavidus necator was grown on a liquid medium with different molar ratios of valeric acid (V) to glucose (G) in order to control the compositions of P(3HB-co-3HV) produced in the cells. Trace amounts (0.03 mg) of dried Cupriavidus necator cells were directly subjected to THM-GC in the presence of tetramethylammonium hydroxide (TMAH) at 400°C. The obtained chromatograms clearly showed nine characteristic peaks, attributed to the THM products from 3HB and 3HV units in the polymer chains, without any appreciable interference by the bacterial matrix components. Based on these peak intensities, the copolymer compositions were determined rapidly without using any cumbersome sample pretreatment. Moreover, the compositions thus obtained were in good agreement with those obtained by the conventional technique.

Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system.

Photovoltaic cells have considerable potential to satisfy future renewable-energy needs, but efficient and scalable methods of storing the intermittent electricity they produce are required for the large-scale implementation of solar energy. Current solar-to-fuels storage cycles based on water splitting produce hydrogen and oxygen, which are attractive fuels in principle but confront practical limitations from the current energy infrastructure that is based on liquid fuels. In this work, we report the development of a scalable, integrated bioelectrochemical system in which the bacterium Ralstonia eutropha is used to efficiently convert CO2, along with H2 and O2 produced from water splitting, into biomass and fusel alcohols. Water-splitting catalysis was performed using catalysts that are made of earth-abundant metals and enable low overpotential water splitting. In this integrated setup, equivalent solar-to-biomass yields of up to 3.2% of the thermodynamic maximum exceed that of most terrestrial plants. Moreover, engineering of R. eutropha enabled production of the fusel alcohol isopropanol at up to 216 mg/L, the highest bioelectrochemical fuel yield yet reported by >300%. This work demonstrates that catalysts of biotic and abiotic origin can be interfaced to achieve challenging chemical energy-to-fuels transformations.

[Engineering of a D-xylose metabolic pathway in eutropha W50].

OBJECTIVE: This study aimed to broaden the substrate spectrum of Ralstonia eutropha W50 to use D-xylose, which can produce poly-beta-hydroxybutyrates (PHB) at a high level. METHODS: The D-xylose transporter gene xylE from Escherichia coli K-12 W3110 was cloned by PCR technique and integrated into the R. eutropha W50 chromosome. The recombinant strain W50-E was obtained. The D-xylose catabolic genes xylAB from E. coli K-12 W3110 and the promotor of PHA synthase gene phaC1 from R. eutropha H16 were cloned into pBBR1MCS to construct a recombinant plasmid. The plasmid was transformed into R. eutropha W50 and W50-E to generate the recombinant strains W50-AB and W50-EAB respectively. The characteristics of D-xylose utilization by W50-AB and W50-EAB were investigated. RESULTS: The expression of xylA and xylB genes in R. eutropha W50 was confirmed by enzyme assay. The recombinant strain W50-AB could grow on 0.1 mol/L D-xylose with the maximum specific growth rate of 0.025 h(-1), but no growth and D-xylose consumption were observed when cultivated on 0.01 mol/L D-xylose. The recombinant strain W50-EAB exhibited a faster growth than W50-AB on 0.1 mol/L D-xylose, with the maximum specific growth rate of 0.035 h(-1). Furthermore, it exhibited a slow but defined growth and D-xylose consumption on 0.01 mol/L D-xylose. The PHB content assay showed that both recombinant strains accumulated a small amount of PHB, with a proportion of 15.07 +/- 1.01% and 15.07 +/- 1.64% on the basis of dry cell weight respectively, by using D-xylose (0.1 mol/L) as substrate. And their final D-xylose-PHB conversion rates were 0.0920 g x g(-1) and 0.0838 g x g(-1) respectively, which were much lower than their glucose-PHB conversion rates( > 0.22 g x g(-1)). However, the recombinant strains W50-AB and W50-EAB exhibited better fermentation performance and more PHB accumulation when using glucose(0.01 mol/L) and D-xylose (0.09 mol/L) mixed sugars as fermentative substrate. CONCLUSION: The recombinant strain W50-AB can metabolize D-xylose by the expression of xylAB genes, and the further expression of xylE gene is able to improve its D-xylose consumption rate. Meanwhile, the two recombinant strains can accumulate a small amount of PHB by using D-xylose as the sole carbon source.

Optimization of polyhydroxyalkanoates fermentations with on-line capacitance measurement.

The aim of this work was to provide an effective methodology for optimization of the polyhydroxyalkanoates (PHAs) fermentation with Ralstonia eutropha by the on-line capacitance measurement. The present study found the capacitance values could reflect variations of microbial morphology and viability. Furthermore, oxygen uptake rate, specific oxygen uptake rate and specific growth rate were measured in real-time and compared with the capacitance value. In addition, a fed-batch control strategy based on the on-line capacitance measurement was proposed to improve the PHAs production by 22%.

Novel approach for productivity enhancement of polyhydroxyalkanoates (PHA) production by Cupriavidus necator DSM 545.

In the global context of increased concerns for our environment, the use of bioplastics as a replacement for existing petroleum-based polymers is an important challenge. Indeed, bioplastics hardly meet economical and technical constraints. One, of the most promising among currently studied bioplastics, is the polyhydroxyalkanoate (PHA). To circumvent the economical issue for this particular biopolymer one solution can be the enhancement of the overall productivity by the improvement of the nutritional medium of the microorganism producing the biopolymer. Thus, several nutrition media, supplemented or not with sodium glutamate, were tested for the growth and the PHA production by Cupriavidus necator DSM 545 strain. The most efficient for the biomass and the PHA production improvement were found to be the Luria broth (LB) and the Bonnarme's media, both supplemented with 10 g/L sodium glutamate. Hence the overall productivity was 33 times enhanced comparing to traditional cultivation methods. These results open a new route for the PHA production by C. necator which appears to be more suitable on a rich, or enriched, medium with no limiting factors.

Enhanced recovery and purification of P(3HB-co-3HHx) from recombinant Cupriavidus necator using alkaline digestion method.

A simple, efficient and economical method for the recovery of P(3HB-co-3HHx) was developed using various chemicals and parameters. The initial content of P(3HB-co-3HHx) in bacterial cells was 50-60 wt%, whereas the monomer composition of 3HHx used in this experiments was 3-5 mol%. It was found that sodium hydroxide (NaOH) was the most effective chemical for the recovery of biodegradable polymer. High polyhydroxyalkanoate purity and recovery yield both in the range of 80-90 wt% were obtained when 10-30 mg/ml of cells were incubated in NaOH at the concentration of 0.1 M for 60-180 min at 30 °C and polished using 20 % (v/v) of ethanol.

Adaptation of Cupriavidus necator to conditions favoring polyhydroxyalkanoate production.

The fatty acid (FA) composition of the bacterial membrane of Cupriavidus necator DSM 545 was assessed during the time course of two-stage fed-batch cultivations for the production of short-chain polyhydroxyalkanoates (PHA). Changes in the relative proportion of straight, methyl and cyclopropyl saturated, unsaturated, hydroxy substituted and polyunsaturated FA were observed, depending on the C sources and cultivation conditions used to favor the synthesis of poly(3-hydroxybutyrate) (P(3HB)), poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB)) or poly(3-hydroxybutyrate-4-hydroxybutyrate-3-hydroxyvalerate) (P(3HB-4HB-3HV)), under N limiting conditions. The relative percentage of each FA class was studied using glucose or waste glycerol (GRP), as main C source for P(3HB) production. The FA profile was also assessed when GRP was used together with i) γ-butyrolactone (GBL) (precursor of 4HB monomers) for P(3HB-4HB) synthesis and ii) GBL and propionic acid (PA) (3HV precursor) to yield P(3HB-4HB-3HV). The effect of GBL and PA utilization as PHA monomer precursors on the FA profile of the cell membrane was studied under two different dissolved oxygen concentrations (DOC).

Production of polyhydroxyalkanoates (PHAs) with canola oil as carbon source.

Wautersia eutropha was able to synthesize medium chain length polyhydroxyalkanoates (PHAs) when canola oil was used as carbon source. W. eutropha was cultivated using fructose and ammonium sulphate as carbon and nitrogen sources, respectively, for growth and inoculum development. The experiments were done in a laboratory scale bioreactor in three stages. Initially, the biomass was adapted in a batch culture. Secondly, a fed-batch was used to increase the cell dry weight and PHA concentration to 4.36 g L(-1) and 0.36 g L(-1), respectively. Finally, after the addition of canola oil as carbon source a final concentration of 18.27 g L(-1) PHA was obtained after 40 h of fermentation. With canola oil as carbon source, the polymer content of the cell dry matter was 90%. The polymer was purified from dried cells and analyzed by FTIR, NMR and DSC using PHB as reference. The polymer produced by W. eutropha from canola oil had four carbon monomers in the structure of the PHA and identified by 1H and 13C NMR analysis as 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), 3-hydroxyoctanoate (3HO), and 3-hydroxydodecanoate (3HDD).

Modeling of p-nitrophenol biodegradation by Ralstonia eutropha via application of the substrate inhibition concept.

In this study, the capability of Ralstonia eutropha H16 to degrade p-nitrophenol with or without a supplementary substrate (glucose or yeast extract) was investigated. Using PNP as the sole energy and carbon source, the biodegradation behavior of the bacterium was modeled by applying a modified form of the Monod equation that considers substrate inhibition, as suggested in the literature (mu=(mu(m)S/k(s) +S)(1-(S/S(m)(n)). PNP at a 6 mg/L initial level was degraded within 20h under the defined incubation conditions (shaking at the reciprocal mode, pH 7 and temperature of 30 degrees C) however the biodegradation was enhanced when yeast extract included in the test medium (50% reduction in the time for complete degradation). When glucose was used instead of yeast extract in the test medium R. eutropha growth was not supported by this carbohydrate and PNP was degraded in about 14h indicating degradation time reduced by 1/3. Comparison of R. eutropha growth pattern showed that biomass formation was insignificant when the bacterium grew in the test medium containing only PNP or PNP plus glucose. But by use of yeast extract considerable biomass formation was observed (OD(546)=0.35 versus 0.1). The presence of organic pollutants in natural ecosystems at low levels frequently occurs in form of mixture with other compounds. The findings of the present work were discussed in terms of secondary substrate utilization for R. eutropha at low PNP level.

On-line characterization of physiological state in poly(beta-hydroxybutyrate) production by Wautersia eutropha.

Culture fluorescence measurement technique has the potential for on-line characterization of metabolic status of fermentation processes. Many fluorophores present inside the living cells such as NADH + H+, tryptophan, pyridoxine, and riboflavin fluoresce at specific excitation and emission wavelength combinations. Since these key intracellular metabolites are involved in cell growth and metabolism, their concentration change at any time inside the cell could reflect the changes in cell metabolic activity. NADH + H+ spectrofluorometry was used for on-line characterization of physiological state during batch cultivation of poly-beta-hydroxybutyric acid (PHB) production by Wautersia eutropha. The culture fluorescence increased with an increase in the biomass concentration with time. A linear correlation between cell mass concentration and net NADH + H+ fluorescence was established during active growth phase (13 to 38 h) of batch cultivation. The rate of change of culture fluorescence (dF/dt) exhibited a gradual increase during the predominantly growth phase of batch cultivation (till 20 h). Thereafter, a sudden drop in the dF/dt rate and its leveling was recorded indicating major changes in culture metabolism status which synchronized with the start-up of accumulation of PHB. After 48 h, yet another decrease in the rate of change of fluorescence (dF/dt) was observed primarily due to severe substrate limitation in the reactor. On-line NADH + H+ fluorescence signal and its rate (dF/dt) could therefore be used to distinguish the growth, product formation, and nutrient depletion stage (the metabolic state marker) during the batch cultivation of W. eutropha.

Isolated poly(3-hydroxybutyrate) (PHB) granules are complex bacterial organelles catalyzing formation of PHB from acetyl coenzyme A (CoA) and degradation of PHB to acetyl-CoA.

Poly(3-hydroxybutyrate) (PHB) granules isolated in native form (nPHB granules) from Ralstonia eutropha catalyzed formation of PHB from (14)C-labeled acetyl coenzyme A (CoA) in the presence of NADPH and concomitantly released CoA, revealing that PHB biosynthetic proteins (acetoacetyl-CoA thiolase, acetoacetyl-CoA reductase, and PHB synthase) are present and active in isolated nPHB granules in vitro. nPHB granules also catalyzed thiolytic cleavage of PHB in the presence of added CoA, resulting in synthesis of 3-hydroxybutyryl-CoA (3HB-CoA) from PHB. Synthesis of 3HB-CoA was also shown by incubation of artificial (protein-free) PHB with CoA and PhaZa1, confirming that PhaZa1 is a PHB depolymerase catalyzing the thiolysis reaction. Acetyl-CoA was the major product detectable after incubation of nPHB granules in the presence of NAD(+), indicating that downstream mobilizing enzyme activities were also present and active in isolated nPHB granules. We propose that intracellular concentrations of key metabolites (CoA, acetyl-CoA, 3HB-CoA, NAD(+)/NADH) determine whether a cell accumulates or degrades PHB. Since the degradation product of PHB is 3HB-CoA, the cells do not waste energy by synthesis and degradation of PHB. Thus, our results explain the frequent finding of simultaneous synthesis and breakdown of PHB.

Studies on the influence of phasins on accumulation and degradation of PHB and nanostructure of PHB granules in ralstonia eutropha H16.

Phasins play an important role in the formation of poly(3-hydroxybutyrate) [PHB] granules and affect their size and number in the cells. Recent studies on the PHB granule proteome and analysis of the complete genomic DNA sequence of Ralstonia eutropha H16 have identified three homologues of the phasin protein PhaP1. In this study, mutants of R. eutropha deficient in the expression of the phasin genes phaP1, phaP2, phaP3, phaP4, phaP12, phaP123, and phaP1234 were examined by gas chromatography. In addition, the nanostructures of the PHB granules of the wild-type and of the mutants were imaged by atomic force microscopy (AFM), and the molecular masses of the accumulated PHB were analyzed by gel permeation chromatography. For this, cells were cultivated under conditions permissive for accumulation of PHB and were then cultivated under conditions permissive for degradation of PHB. Mutants deficient in the expression of phaP2, phaP3, or phaP4 genes mobilized the stored PHB only slowly like the wild-type, whereas degradation occurred much earlier and faster in the phaP1 single mutant as well as in all multiple mutants defective in the phaP1 gene plus one or more other phasin genes. This indicated that the presence of the major phasin PhaP1 on the granule surface is important for PHB degradation and that this phasin is therefore of particular relevance for PHB accumulation. It was also shown that the molecular weights of the accumulated PHB were identical in all examined strains; phasins have therefore no influence on the molecular weight of PHB. The AFM images obtained in this study showed that the PHB granules of R. eutropha H16 form a single interconnected system inside the wild-type cells.

Enzymatic recovery and purification of polyhydroxybutyrate produced by Ralstonia eutropha.

Polyhydroxybutyrate (PHB) is the most studied among a wide variety of polyhydroxyalkanoates, bacterial biodegradable polymers known as potential substitutes for conventional plastics. This work aimed at evaluating the use of enzymes to recover and purify the PHB produced by Ralstonia eutropha DSM545. Screening experiments allowed the selection of trypsin, bromelain and lysozyme among six enzymes, based on their efficiency in lysing cells of a non-PHB producing R. eutropha strain. Then, process conditions for high efficiency in PHB purification from the DSM545 cells were searched for the enzymes previously selected. The best result was achieved with 2.0% of bromelain (enzyme mass per biomass), equivalent to 14.1 U ml(-1), at 50 degrees C and pH 9.0, resulting in 88.8% PHB purity. Aiming at improving the process efficiency and reducing the enzyme cost, experiments were carried out with pancreatin, leading to 90.0% polymer purity and an enzyme cost three times lower than the one obtained with bromelain. The molecular mass analysis of PHB showed no polymer degradation. Therefore, this work demonstrates the potential of using enzymes in order to recover and purify PHB and bacterial biopolymers in general.