Energy supply for active transport in anaerobically grown Escherichia coli

Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation

Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ~100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase-LacI expression system was used to replace the σ(54)-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ~42% of the nitrogenase activity of the σ(54)-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology.

Thermodynamic evaluation of energy metabolism in mixed substrate catabolism: modeling studies of stationary and oscillatory states

Thermodynamic and kinetic calculations were performed in a model of mixed substrate metabolism. The model simulates the catabolic breakdown of a first substrate, glucose (S(1)), in the presence of a second substrate, formate (S(2)), which acts as an additional source of free energy. The principal results obtained with different relative rates of uptake of S(2) allow to predict and interpret the following experimental observations: (1) the existence of increased ATP yields by mixed substrate utilization with a maximum ATP yield and optimum input (or molar) ratio for both substrates; (2) a greater assimilation of S(1) which may be interpreted as a decreasing fraction of energy required for assimilation; (3) a decrease in ATP yields due to increasing energy demand for transport; (4) an increased assimilation of the carbon source (S(1)) as a function of increasing inputs of the additional energy source; (5) thermodynamic efficiency (eta) defined as the ratio between the output power of ATP synthesis and the input catabolic power, increases for S(2)/S(1) ratios ranging between 0.08 and 2 while for ratios higher than two a slight decrease of eta was noticed; and (6) the observed maximum in ATP yield for optimum molar ratio of the two substrates corresponds to high eta predicting that higher biomass yields may be obtained through a variable, high, eta by chanelling fluxes through catabolic pathways with different ATP yields. During oscillatory behavior, maxima in fluxes were almost coincident with maxima in forces. Thus, the pattern of dissipation was not so advantageous as in the single substrate model under starvation conditions.

Analysis of the Actinobacillus pleuropneumoniae ArcA regulon identifies fumarate reductase as a determinant of virulence

The ability of the bacterial pathogen Actinobacillus pleuropneumoniae to grow anaerobically allows the bacterium to persist in the lung. The ArcAB two-component system is crucial for metabolic adaptation in response to anaerobic conditions, and we recently showed that an A. pleuropneumoniae arcA mutant had reduced virulence compared to the wild type (F. F. Buettner, A. Maas, and G.-F. Gerlach, Vet. Microbiol. 127:106-115, 2008). In order to understand the attenuated phenotype, we investigated the ArcA regulon of A. pleuropneumoniae by using a combination of transcriptome (microarray) and proteome (two-dimensional difference gel electrophoresis and subsequent mass spectrometry) analyses. We show that ArcA negatively regulates the expression of many genes, including those encoding enzymes which consume intermediates during fumarate synthesis. Simultaneously, the expression of glycerol-3-phosphate dehydrogenase, a component of the respiratory chain serving as a direct reduction equivalent for fumarate reductase, was upregulated. This result, together with the in silico analysis finding that A. pleuropneumoniae has no oxidative branch of the citric acid cycle, led to the hypothesis that fumarate reductase might be crucial for virulence by providing (i) energy via fumarate respiration and (ii) succinate and other essential metabolic intermediates via the reductive branch of the citric acid cycle. To test this hypothesis, an isogenic A. pleuropneumoniae fumarate reductase deletion mutant was constructed and studied by using a pig aerosol infection model. The mutant was shown to be significantly attenuated, thereby strongly supporting a crucial role for fumarate reductase in the pathogenesis of A. pleuropneumoniae infection.

Use of phi(glp-lac) in studies of respiratory regulation of the Escherichia coli anaerobic sn-glycerol-3-phosphate dehydrogenase genes (glpAB)

Expression of the glpA operon encoding the extrinsic membrane anaerobic sn-glycerol-3-phosphate dehydrogenase complex of Escherichia coli K-12 was studied in five strains carrying independent glpA-lac operon fusions. The location of the fusions was confirmed by transduction. Two of the strains produced an enzymatically active anaerobic sn-glycerol-3-phosphate dehydrogenase that accumulated in the cytoplasmic fraction of the cells. This suggests the loss of a specific membrane anchor subunit encoded by a distal gene, glpB, which was disrupted by the insertion. beta-Galactosidase in all five strains carrying phi(glpA-lac) was highly inducible by glycerol only anaerobically. A mutation in fnr, a pleiotropic activator gene, prevented full induction of the phi(glpA-lac), demonstrating that the Fnr protein is a positive regulator of the primary dehydrogenase as well as of the terminal reductases of anaerobic respiratory chains. Low concentrations of the respiratory poison KCN had a permissive effect on aerobic expression of phi(glpA-lac). Aerobic expression of the hybrid operon was also enhanced in isogenic derivatives of the fusion strains deficient in protoporphyrin biosynthesis (hemA). Thus, heme proteins may play a role in mediating aerobic repression of the anaerobic respiratory chain.

Proteins induced by anaerobiosis in Escherichia coli

The contribution of protein induction and repression to the adaptation of cells to changes in oxygen supply is only poorly understood. We assessed this contribution by measuring the levels of 170 individual polypeptides produced by Escherichia coli K-12 in cells growing aerobically or anaerobically with and without nitrate. Eighteen reached their highest levels during anaerobic growth. These 18 polypeptides include at least 4 glycolytic enzymes and pyruvate formate-lyase (beta-subunit). Most of these proteins were found at significant levels during aerobic growth and appeared to undergo metabolic regulation by stimuli other than anaerobiosis. Anaerobic induction ratios ranged from 1.8- to 11-fold, and nitrate antagonized the anaerobic induction of all of the proteins except one. The time course of synthesis of the proteins after shifts in oxygen supply revealed at least three distinct temporal patterns. These results are discussed in light of known physiological alterations associated with changes in oxygen availability.

The electrochemical proton gradient generated by the fumarate-reductase system in Escherichia coli and its bioenergetic implications

Proton translocation, coupled to electron transfer in the fumarate reductase system, generates and electrochemical potential gradient for protons (delta approximately mu H+). The magnitude of this free energy gradient has been determined in the Escherichia coli strains ML 208-225 and AN 283. The measurements were performed in (inverted) membrane particles, right-side out membrane vesicles and EDTA-treated intact cells in external media of various ionic compositions and pH. The maximal values of delta approximately mu H+ in these three systems were +103, -101 and -105 mV, respectively. This implicates that in E. coli, upon transition from oxygen to fumarate as electron acceptor, the magnitude of the delta approximately mu H+ decreases considerably. This change of delta approximately mu H+ has substantial consequences for the cellular metabolism.

Generation of an electrochemical proton gradient by lactate efflux in membrane vesicles of Escherichia coli

The 'energy-recycling model' [Michels et al. (1979) FEMS Microbiol. Lett. 5, 357-364] postulates the generation of an electrochemical gradient across the bacterial cytoplasmic membrane by carrier-mediated efflux of metabolic endproducts in symport with protons. Experimental evidence for this model is presented. In membrane vesicles from Escherichia coli ML 308-255 L-lactate translocation (both uptake and efflux) is carrier-mediated. The H+/L-lactate stoichiometry varies, depending on the external pH, between 1 and 2. This change in stoichiometry is most likely the result of a protonation of the lactate carrier protein. This process has a pK of 6.75. L-Lactate efflux from membrane vesicles, loaded with 50 mM potassium L-lactate, results at an external pH of 6.6 in an 11-fold accumulation of proline inside the vesicles. This accumulation is completely inhibited by the uncoupler carbonyl cyanide p-trifluoromethoxyphenylhydrazone. The uptake of proline is not the result of a potassium or an osmotic gradient. At an external pH of 6.6 efflux of L-lactate from the vesicles leads to the generation of an electrical potential across the membrane of -55 mV, as is demonstrated from the accumulation of the lipophilic cation tetraphenylphosphonium.

Genetic and physical characterization of lambda transducing phages (lambda frdA) containing the fumarate reductase gene of Escherichia coli K12

Two types of fumarate reductase transducing phages, lambda frdA, carrying the wild-type frdA gene but differing in the orientation of a R.HindIII fragment of bacterial DNA were isolated from populations of recombinant transducing phages by their ability to complement the lesions of frdA mutants of E. coli. In lysogens, the cloned frdA gene was controlled by its own promoter and was fully responsive to normal regulatory stimuli. The lambda frdA phages would not complement the defects of succinate dehydrogenase (sdh) mutants. Genetic studies showed that the R.HindIII fragment contains ampA, the cis-acting regulatory locus for the chromosomal beta-lactamase gene ampC. No evidence for the presence of other markers was detected but the bacterial segment could be extended to produce plaque-forming phage derivatives containing the amp operon and a gene concerned with bacteriophage morphogenesis, groE(mop). A physical map of the 4.9 kb R.HindIII fragment was constructed by restriction analysis and flanking fragments were identified by DNA:DNA hybridization analysis. The frdA region contained a single asymmetric R.EcoRI target 3.33 kb from one end and the orientation of the physical map with respect to the E.coli linkage map was established.

Stimulatory effect of low ATP pools on transport of purine nucleosides in cells of Escherichia coli

Cells of Escherichia coli contain two nucleoside-transport systems. Energy-starved cells of a strain containing only one of these systems and, in addition, carrying a mutation in the Ca2+- and Mg2+-dependent ATPase (ATP phosphohydrolase 3.6.1.3) are still able to transport nucleosides. The rate is only slightly lower than the rate measured in unstarved cells. Freshly harvested uncA cells transport purine nucleosides at a higher rate than cells from the isogenic strain containing a functional ATPase. If cells from the latter strain are treated with arsenate, transport rates increase to the same levels as found in uncA cells. The presence of an uncA mutation has no effect on the transport rates for cytidine, deoxycytidine, and uridine, nor has arsenate treatment. These findings indicate that ATP is not required as energy donor for nucleoside transport. The enhanced transport rate for purine nucleosides after treatment with arsenate seems to suggest a regulatory relationship between the transport of these nucleosides and the cellular levels of ATP or a closely related metabolite.