Improved triacylglycerol production in Acinetobacter baylyi ADP1 by metabolic engineering

Background

Triacylglycerols are used in various purposes including food applications, cosmetics, oleochemicals and biofuels. Currently the main sources for triacylglycerol are vegetable oils, and microbial triacylglycerol has been suggested as an alternative for these. Due to the low production rates and yields of microbial processes, the role of metabolic engineering has become more significant. As a robust model organism for genetic and metabolic studies, and for the natural capability to produce triacylglycerol, Acinetobacter baylyi ADP1 serves as an excellent organism for modelling the effects of metabolic engineering for energy molecule biosynthesis.

Results

Beneficial gene deletions regarding triacylglycerol production were screened by computational means exploiting the metabolic model of ADP1. Four deletions, acr1, poxB, dgkA, and a triacylglycerol lipase were chosen to be studied experimentally both separately and concurrently by constructing a knock-out strain (MT) with three of the deletions. Improvements in triacylglycerol production were observed: the strain MT produced 5.6 fold more triacylglycerol (mg/g cell dry weight) compared to the wild type strain, and the proportion of triacylglycerol in total lipids was increased by 8-fold.

Conclusions

In silico predictions of beneficial gene deletions were verified experimentally. The chosen single and multiple gene deletions affected beneficially the natural triacylglycerol metabolism of A. baylyi ADP1. This study demonstrates the importance of single gene deletions in triacylglycerol metabolism, and proposes Acinetobacter sp. ADP1 as a model system for bioenergetic studies regarding metabolic engineering.

Alkalizing reactions streamline cellular metabolism in acidogenic microorganisms

An understanding of the integrated relationships among the principal cellular functions that govern the bioenergetic reactions of an organism is necessary to determine how cells remain viable and optimise their fitness in the environment. Urease is a complex enzyme that catalyzes the hydrolysis of urea to ammonia and carbonic acid. While the induction of urease activity by several microorganisms has been predominantly considered a stress-response that is initiated to generate a nitrogen source in response to a low environmental pH, here we demonstrate a new role of urease in the optimisation of cellular bioenergetics. We show that urea hydrolysis increases the catabolic efficiency of Streptococcus thermophilus, a lactic acid bacterium that is widely used in the industrial manufacture of dairy products. By modulating the intracellular pH and thereby increasing the activity of β-galactosidase, glycolytic enzymes and lactate dehydrogenase, urease increases the overall change in enthalpy generated by the bioenergetic reactions. A cooperative altruistic behaviour of urease-positive microorganisms on the urease-negative microorganisms within the same environment was also observed. The physiological role of a single enzymatic activity demonstrates a novel and unexpected view of the non-transcriptional regulatory mechanisms that govern the bioenergetics of a bacterial cell, highlighting a new role for cytosol-alkalizing biochemical pathways in acidogenic microorganisms.

A dairy bacterium displays in vitro probiotic properties for the pharyngeal mucosa by antagonizing group A streptococci and modulating the immune response

The probiotic approach represents an alternative strategy in the prevention and treatment of infectious diseases, not only at the intestinal level but also at other sites of the body where the microbiota plays a role in the maintenance of physiological homeostasis. In this context, we evaluated in vitro the potential abilities of probiotic and dairy bacteria in controlling Streptococcus pyogenes infections at the pharyngeal level. Initially, we analyzed bacterial adhesion to FaDu hypopharyngeal carcinoma cells and the ability to antagonize S. pyogenes on FaDu cell layers and HaCat keratinocytes. Due to its promising adhesive and antagonistic features, we studied the dairy strain Lactobacillus helveticus MIMLh5, also through in vitro immunological experiments. First, we performed quantification of several cytokines and measurement of NF-κB activation in FaDu cells. MIMLh5 efficiently reduced the induction of interleukin-6 (IL-6), IL-8, and tumor necrosis factor alpha (TNF-α), in a dose-dependent manner. After stimulation of cells with IL-1β, active NF-κB was still markedly lowered. Nevertheless, we observed an increased secretion of IL-6, gamma interferon (IFN-γ), and granulocyte-macrophage colony-stimulating factor (GM-CSF) under these conditions. These effects were associated with the ability of MIMLh5 to enhance the expression of the heat shock protein coding gene hsp70. In addition, MIMLh5 increased the GM-CSF/G-CSF ratio. This is compatible with a switch of the immune response toward a TH1 pathway, as supported by our observation that MIMLh5, once in contact with bone marrow-derived dendritic cells, triggered the secretion of TNF-α and IL-2. In conclusion, we propose MIMLh5 as a potential probiotic bacterium for the human pharynx, with promising antagonistic and immunomodulatory properties.

Hydrogen production from glycerol using halophilic fermentative bacteria

Glycerol-based hydrogen production by the halophilic bacteria Halanaerobium saccharolyticum subspecies saccharolyticum and senegalensis was studied as batch experiments. The main metabolites of glycerol fermentation of both strains were hydrogen, carbon dioxide, and acetate. Subspecies saccharolyticum also produced 1,3-propanediol (1,3-PD), butyrate, and ethanol. The highest hydrogen yields were achieved with 2.5g/l glycerol and 150g/l salt at pH 7.4 (subsp. saccharolyticum, yield 0.6mol/mol glycerol) and at pH 7.0 (subsp. senegalensis, yield 1.6mol/mol glycerol). The hydrogen yield of subsp. senegalensis has potential for practical applications after scale-up and bioprocess optimizations and metabolic engineering after genome-wide sequencing could be applied to improve the yield of subsp. saccharolyticum.

Oral bacteria as potential probiotics for the pharyngeal mucosa

The research described here was aimed at the selection of oral bacteria that displayed properties compatible with their potential use as probiotics for the pharyngeal mucosa. We included in the study 56 bacteria newly isolated from the pharynges of healthy donors, which were identified at the intraspecies level and characterized in vitro for their probiotic potential. The experiments led us to select two potential probiotic bacterial strains (Streptococcus salivarius RS1 and ST3) and to compare them with the prototype oral probiotic S. salivarius strain K12. All three strains efficiently bound to FaDu human epithelial pharyngeal cells and thereby antagonized Streptococcus pyogenes adhesion and growth. All were sensitive to a variety of antibiotics routinely used for the control of upper respiratory tract infections. Immunological in vitro testing on a FaDu layer revealed different responses to RS1, ST3, and K12. RS1 and ST3 modulated NF-kappaB activation and biased proinflammatory cytokines at baseline and after interleukin-1beta (IL-1beta) induction. In conclusion, we suggest that the selected commensal streptococci represent potential pharyngeal probiotic candidates. They could display a good degree of adaptation to the host and possess potential immunomodulatory and anti-inflammatory properties.

Implication of an outer surface lipoprotein in adhesion of Bifidobacterium bifidum to Caco-2 cells

We found that the human intestinal isolate Bifidobacterium bifidum MIMBb75 strongly adhered to Caco-2 cells. Proteinase K and lithium chloride treatments showed that proteins play a key role in MIMBb75 adhesion to Caco-2 cells. By studying the cell wall-associated proteins, we identified a surface protein, which we labeled BopA. We purified the protein chromatographically and found that it functioned as an adhesion promoter on Caco-2 cells. In silico analysis of the gene coding for this protein and globomycin experiments showed that BopA is a cysteine-anchored lipoprotein expressed as a precursor polypeptide. A database search indicated that BopA appears to function biologically as an oligopeptide/tripeptide-solute-binding protein in the ABC transport system. We discovered a protein corresponding to BopA and its gene in eight other highly adherent B. bifidum strains. Finally, we found that B. bifidum MIMBb75 and BopA affected the production of interleukin-8 in Caco-2 epithelial cells. BopA is the first protein described to date to be directly involved in the adhesion of bifidobacteria to Caco-2 cells and to show immunomodulatory activity.

Molecular characterization of Bifidobacterium longum biovar longum NAL8 plasmids and construction of a novel replicon screening system

In this study, we performed molecular characterization and sequence analysis of three plasmids from the human intestinal isolate Bifidobacterium longum biovar longum NAL8 and developed a novel vector screening system. Plasmids pNAL8H (10 kb) and pNAL8M (4.9 kb) show close sequence similarity to and the same gene organization as the already characterized B. longum plasmids. The B. longum plasmid pNAC1 was identified as being most closely related to pNAL8L (3.5 kb). However, DNA sequence analysis suggested that direct repeat-rich sites could have promoted several recombination events to diversify the two plasmid molecules. We verified the likely rolling circle replication of plasmid pNAL8L and studied the phylogenetic relationship in all the Bifidobacterium plasmids fully sequenced to date based on in silico comparative sequence analysis of their replication proteins and iteron regions. Our transformation experiments confirmed that the ColE1 replication origin from high-copy-number pUC vectors could interfere with the replication apparatus of Bifidobacterium plasmids and give rise to false positive clones. As a result, we developed a system suitable for avoiding possible interference by other functional replication modules on the vector and for screening functional replicons from wild-type plasmids.

Intracellular redox equilibrium and growth phase affect the performance of luciferase-based biosensors

Light emission from the bacterial luciferase operon has been variously exploited during last two decades. The use of convenient inducible promoters has granted significant degrees of specificity to whole cell-based assays for high-throughput screening and environmental monitoring. Nevertheless, unexplained unspecific responses have been repeatedly reported. Here, we show that the impairment of the intracellular biochemical equilibrium interferes with the luminescence produced by Escherichia coli and Staphylococcus aureus strains carrying the lux operon under constitutive or inducible control. Compounds as trimethoprim and methotrexate, by indirectly inducing NADPH accumulation, enhance light emission. Conversely, molecules driving the cell toward an oxidized state, as dimethyl sulfoxide, inhibit luminescence. These findings fit into the accepted biochemical pathway for bioluminescence, where NADPH and reducing equivalents are necessary for the production of luciferase substrates, although they do not directly take part into the light-emitting reaction. Moreover, we investigated the influence of induction timing upon the bioluminescence response from inducible reporter systems and demonstrated a correlation between the emitted light and the growth phase at which induction is performed. Our results provide explanations for some unspecific responses recorded so far in whole cell-based luminescent biosensors and emphasize the intrinsic limitations of this kind of reporting system.

Bioluminescence-based bioassays for rapid detection of nisin in food

We have developed a method for determining ultralow amounts of nisin in food samples that is based on luminescent biosensor bacteria. Modified bacterial luciferase operon luxABCDE was placed under control of the nisin-inducible nisA promoter in plasmid pNZ8048, and the construct was transformed into Lactococcus lactis strains NZ9800 and NZ9000. The nisRK genes of these strains allow them to sense nisin and relay the signal to initiate transcription from nisA promoter. The resulting luminescence can be directly measured from living bacteria without the addition of exogenous substrates. Induction leads to detectable luminescence within ten minutes. Lyophilization of the biosensor cells produced viable and inducible sensor elements that can be utilized as freshly cultivated cells for rapid detection of nisin. The linear dose-response relationship perceived in the assay facilitates quantification of nisin in samples. The sensitivity of the nisin bioassay was 0.1 pg/ml in pure solution and 3 pg/ml in milk, exceeding the performance of all previously reported methods.

Staphylococcus aureus adheres to human intestinal mucus but can be displaced by certain lactic acid bacteria

There is increasing evidence that Staphylococcus aureus may colonize the intestinal tract, especially among hospitalized patients. As Staph. aureus has been found to be associated with certain gastrointestinal diseases, it has become important to study whether this bacterium can colonize the intestinal tract and if so, whether it is possible to prevent colonization. Adhesion is the first step in colonization; this study shows that Staph. aureus adheres to mucus from resected human intestinal tissue. Certain lactic acid bacteria (LAB), mainly commercial probiotics, were able to reduce adhesion and viability of adherent Staph. aureus. In displacement assays the amount of adherent Staph. aureus in human intestinal mucus was reduced 39-44% by Lactobacillus rhamnosus GG, Lactococcus lactis subsp. lactis and Propionibacterium freudenreichii subsp. shermanii. Moreover, adherent Lactobacillus reuteri, Lc. lactis and P. freudenreichii reduced viability of adherent Staph. aureus by 27-36%, depending on the strain, after 2 h incubation. This was probably due to the production of organic acids and hydrogen peroxide and possibly in the case of L. reuteri to the production of reuterin. This study shows for the first time that Staph. aureus can adhere to human intestinal mucus and adherent bacteria can be displaced and killed by certain LAB strains via in situ production of antimicrobial substances.

Whole Cell Strategies Based on lux Genes for High Throughput Applications Toward New Antimicrobials

The discovery/development of novel drug candidates has witnessed dramatic changes over the last two decades. Old methods to identify lead compounds are not suitable to screen wide libraries generated by combinatorial chemistry techniques. High throughput screening (HTS) has become irreplaceable and hundreds of different approaches have been described. Assays based on purified components are flanked by whole cell-based assays, in which reporter genes are used to monitor, directly or indirectly, the influence of a chemical over the metabolism of living cells. The most convenient and widely used reporters for real-time measurements are luciferases, light emitting enzymes from evolutionarily distant organisms. Autofluorescent proteins have been also extensively employed, but proved to be more suitable for end-point measurements, in situ applications - such as the localization of fusion proteins in specific subcellular compartments - or environmental studies on microbial populations. The trend toward miniaturization and the technical advances in detection and liquid handling systems will allow to reach an ultra high throughput screening (uHTS), with 100,000 of compounds routinely screened each day. Here we show how similar approaches may be applied also to the search for new and potent antimicrobial agents.

Bioluminescent yeast assays for detecting estrogenic and androgenic activity in different matrices

In this paper we describe the construction and use of a set of bioluminescent yeast strains for the detection of compounds that can affect androgen or estrogen receptor mediated hormonal signalling. The set includes Saccharomyces cerevisiae strains expressing human androgen receptor (AR), estrogen receptor alpha (ERalpha) or estrogen receptor beta (ERbeta), along with firefly luciferase controlled by a respective hormone responsive promoter. A constitutively luminescent strain was included in the set for determining the cytotoxicity of the sample. Yeast cells were incubated with pure chemicals or complex samples for 2.5 h, after which the signal could be detected from the cell-sample mixture after simply adding the D-luciferin substrate. The assays could be completed in one day and they required no cell lysis or centrifugation steps, which makes them suitable for high-throughput analysis of samples. Due to a short incubation time the assays are directly applicable to different sample matrices, requiring no pretreatment of the samples. The assays were used to assess the hormonal activity in moisturizing lotions as an example of a complex sample matrix known to contain endocrine disrupting chemicals. Six out of eight tested moisturisers showed high estrogenic activity, whereas no androgenic activity was observed in the samples.

A new recombinant cell-based bioluminescent assay for sensitive androgen-like compound detection

A public concern is continuously arising about the presence of natural and anthropogenic compounds which affect human health by modulating normal endocrine functions. These substances, defined as endocrine disrupting compounds (EDC) represent an heterogeneous class of molecules either steroidal or not, sharing the ability of interfering with the endocrine system via nuclear receptor signaling pathways. Therefore there is an urgent need for high throughput screening systems able to detect EDCs and evaluate their biological activity. However, little attention has been dedicated to the development of assays for androgen-like compounds. The present work describes the development and optimization of a new rapid and sensitive bioluminescent yeast-based bioassay for androgen-like compounds in a 96-well microplate format. The bioassay is based on recombinant Saccharomyces cerevisiae cells modified to express human androgen receptor (hAR) and containing the sequence androgen response element (ARE) which drives the expression of Photinus pyralis luciferase, used as reporter gene. A recombinant yeast strain constitutively expressing luciferase was used as external control to correct the light signal accordingly to cell viability and sample matrix aspecific effects. The bioassay responds to testosterone as reference androgen in a concentration-dependent manner from 0.05 to 1000 nM allowing an accurate and precise quantitative evaluation in aqueous environmental samples down to 10(-11)mol/L. Other known androgen-like compounds exhibit similar dose-response behavior, thus permitting the use of the bioassay for an overall detection of androgen-like effect in environmental samples.

Adhesion of bacteria to resected human colonic tissue: quantitative analysis of bacterial adhesion and viability

Adhesion to the intestinal mucosa is considered to be one of the main selection criteria of lactic acid bacteria for probiotic use. Adhesive probiotics are, for example, considered to provide better antagonism against pathogenic bacteria when compared to non-adhesive strains. Here a new model is described for studying adhesion and interaction of probiotic and pathogenic bacteria in the intestinal mucus in which the intestinal microbiota is present. The model is based on the use of human intestinal tissue, fluorescent-tagged bacteria and confocal laser scanning microscopy (CLSM) in adhesion measurements as well as human intestinal mucus and bioluminescent-tagged bacteria in viability measurements. Use of CLSM enabled, for the first time, real-time three-dimensional observations of live probiotic bacteria in their natural environment, the intestinal mucosa. When the real-time measurement of bacterial adhesion was combined with the real-time sensitive measurement of bacterial viability, it could be studied whether or not the adherent pathogens were alive. The model was used to study the interaction between Lactobacillus rhamnosus GG and Salmonella enterica serovar Typhimurium. We show that L. rhamnosus GG did not affect the adhesion or the viability of S. enterica serovar Typhimurium. Instead S. enterica serovar Typhimurium was shown to decrease the adhesion of L. rhamnosus GG in displacement assays. Moreover, the method is suitable for studies in which the interaction of two or more bacteria is examined in an environment in which other bacteria are present.

Quantification of streptavidin adsorption in microtitration wells

Streptavidin-coated microtitration plates have an important role as a solid phase in clinical diagnostics. We have designed techniques for evaluating quantitative and functional aspects of streptavidin adsorbed in microtitration wells. The theoretical monolayer adsorption capacity was modeled based on the molecular dimensions of the protein. Adsorbed streptavidin was quantified by direct labeling of protein with terbium chelate and with a sensitive bicinchoninic acid-based protein assay. A new small molecular weight (1037Da) reporter molecule, a europium-labeled biotin (Eu-biotin), was synthesized and used for monitoring adsorption and for determination of biotin-binding capacities of the streptavidin-coated wells. The theoretical monolayer adsorption of streptavidin yielded 6.20 pmol/cm(2) (370 ng) and consequently the theoretical adsorption capacity of a C12-format microtitration well (200 microl liquid, coated area 1.54 cm(2)) was 9.55 pmol/well (570 ng). Adsorption properties of streptavidin from two suppliers were tested, one of which yielded 350-380 ng/well while the other yielded over 500 ng/well. The biotin binding capacities were about 11 and 14 pmol/well, respectively. We managed to quantify surface-adsorbed streptavidin with sensitive fluorescence and protein measurement methods in the microtitration well. The new Eu-biotin reporter molecule enabled an exact and convenient determination of the biotin-binding capacities of streptavidin surfaces.

Measurement of bacterial adhesion—in vitro evaluation of different methods

The adhesion of bacteria to host tissue is the first step in pathogenesis. Similarly, bacterial adhesion to inanimate surfaces is the first step in formation of biofilms-a real problem in industrial processes and medical devices. Various agents capable of blocking the adhesion of bacteria to surfaces have been identified, such as probiotics, which are supposed to prevent the adhesion of pathogenic bacteria to the intestinal mucosa. Although measurement of bacterial adhesion is important itself, especially when agents used to prevent adhesion are developed, a relative small number of techniques can be used in the measurement of adhesion. These techniques are not well validated and there is lack of studies where those methods are compared to each other. Here we have compared different commonly used methods to measure adhesion of bacteria; radioactive labelling, fluorescence tagging, and staining of bacteria. The methods were used to measure the adhesion of Escherichia coli and Salmonella enterica serovar Typhimurium to intestinal mucus. Moreover, selected probiotic strains were used to study whether probiotics or the adhesion method used affected the results. As a result, we show that the best reproducibility and sensitivity were obtained using radioactive labelling. With other methods, the sensitivity was too low due to poorly adhering bacteria and low signal-to-background ratio.

Development of a Bioluminescence Resonance Energy-Transfer Assay for Estrogen-Like Compound in Vivo Monitoring

A new bioluminescence resonance energy transfer (BRET) homogeneous assay to evaluate the presence of estrogen-like compounds has been developed and optimized. The assay is based on the direct evaluation of estrogen alphareceptor (ERalpha) homodimerization as a result of estrogen-like compound binding. ERalpha monomer was genetically fused either to Renilla luciferase (Rluc) or to enhanced yellow fluorescent protein (EYFP). In the presence of estrogens, ERalpha dimerization brings Rluc and EYFP molecules close enough for an energy transfer. An in vitro BRET assay was first developed using purified fusion proteins (ERalpha-Rluc and ERalpha-EYFP) expressed in Escherichia coli to evaluate and optimize the analytical performances of the assay in the presence of 17-beta estradiol. The "in vivo" BRET quantitative assay was then developed by coexpressing the two fusion proteins in live HepG2 cells. The assay can be performed in 96-well microplate format with a 30-min incubation and allows detection with adequate accuracy and precision of as low as 1 nM of 17-beta estradiol. This new "in vivo" BRET assay allows evaluating the estrogen-like activity and synthetic xenoestrogens from biological and environmental samples.

Discarding multidrug resistance inducers, the possible role of a biosensing reporter in antimicrobial discovery

The aim of the present work was to determine whether the luminescence-based reporter plasmid pQacLux could be applied to drug discovery in order to discard compounds with defined properties. Non-pathogenic Staphylococcus aureus RN4220 cells bearing pQacLux were incubated with different concentrations of a disinfectant of common use in hospitals. The in vivo light emission response of the plasmid to the given stimuli was then quantified and compared to a negative control for the construction of dose-response curves. The selected disinfectant provided a convenient model for the activity of quaternary ammonium compounds. In spite of the use of a raw model solution, the system revealed high levels of sensitivity. According to the results obtained, pQacLux could be conveniently used in the first steps of drug development in order to discard all possible multidrug resistance inducers.

A cell-free biosensor for the detection of transcriptional inducers using firefly luciferase as a reporter

A cell-free biosensor for the detection of transcription induction by specific small-molecule ligands is presented. As model systems, tetracycline and mercury-inducible promoters were used containing firefly luciferase as reporter gene. Escherichia coli S30 extract was prepared and used for coupled transcription-translation reactions. By using purified Tet repressor and MerR regulatory proteins, we could study repressor-operator interactions for optimizing the relative concentrations of each component. Previously, detection of tetracycline and mercury using similar transcriptional regulation in whole living cells has been carried out. As compared to whole-cell biosensors, our results showed better sensitivity for the detection of tetracycline and the toxic effect of mercury was avoided in the cell-free system. Also, as the system omits cell cultivation and bacterial membranes as molecule passage inhibitors, it is possible to carry out assays in much shorter times and without the use of genetically modified organisms.

Rapid screening method for the detection of antimicrobial substances

Bioluminescence is phenomenon where living organisms produce light and this production is directly dependent on metabolic activity of the organism. Genes encoding enzymes, luciferases, responsible for light production can be cloned into indicator strains, thus allowing sensitive detection of antimicrobial activity. This study utilized bacterial luciferase genes cloned into Staphylococcus aureus, Escherichia coli and Salmonella enterica serovar Typhimurium indicator strains and showed that the detection of antimicrobial activity can be obtained already in 2 h without laborious plate counting and overnight incubation. Indicator strains used in the study harboured luxAB genes responsible of producing light as well as luxCDE genes for synthesis of long-chain fatty aldehyde as substrate for light production. As a consequence, no exogenous aldehyde addition was needed allowing stable light production. Furthermore, the method was used for the detection of antimicrobial activity from lactic acid bacteria after the effect of organic acids was eliminated.

Monitoring promoter activity in a single bacterial cell by using green and red fluorescent proteins

We investigated the possibility of monitoring promoter activity with flow cytometry by using green fluorescent protein (GFPmut2) and red fluorescent protein (drFP583) in a single bacterial cell. The drFP583 was used as an intrinsic marker of the bacterial cells, because it was expressed constantly in Escherichia coli MC1061 strain. The GFPmut2 expressed under the control of the Hg(2+) ion inducible mer promoter/operator, was used to study promoter activity. Over 75% of the cells were positive for red and green fluorescence in flow cytometric analysis. The average green fluorescence of the whole population increased from 6.7 to 1700 when the mercury concentration was increased from 0 to 1 x 10(-4) M, while the red fluorescence was unaffected by the mercury concentration. These results show that gfpmut2 and drFP583 could be expressed under different promoters in one bacterial cell and measured independently with a flow cytometer.