Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium

When the soil bacterium Pseudomonas putida grows in a complete medium, it prioritizes the assimilation of preferred carbon sources, optimizing its metabolism and growth. This regulatory process is orchestrated by the Crc and Hfq proteins. The present work examines the changes that occur in metabolic fluxes when the crc gene is inactivated and cells grow exponentially in LB complete medium. Analyses were performed at three different moments during exponential growth, examining the assimilation rates for the compounds present in LB, changes in the proteome, and the changes in metabolic fluxes predicted by the iJN1411 metabolic model for P. putida KT2440. During the early exponential phase, consumption rates for sugars, many organic acids and most amino acids were higher in a Crc-null strain than in the wild type, leading to an overflow of the metabolic pathways and the leakage of pyruvate and acetate. These accelerated consumption rates decreased during the mid-exponential phase, when cells mostly used sugars and alanine. At later times, pyruvate was recovered from the medium and utilized. The higher consumption rates of the Crc-null strain reduced the growth rate. The lack of the Crc/Hfq regulatory system thus led to unbalanced metabolism with poorly optimized metabolic fluxes.     

The acetoin assimilation pathway of Pseudomonas putida KT2440 is regulated by overlapping global regulatory elements that respond to nutritional cues

Many microorganisms produce and excrete acetoin (3-hydroxy-2-butanone) when growing in environments that contain glucose or other fermentable carbon sources. This excreted compound can then be assimilated by other bacterial species such as pseudomonads. This work shows that acetoin is not a preferred carbon source of Pseudomonas putida, and that the induction of genes required for its assimilation is down-modulated by different, independent, global regulatory systems when succinate, glucose or components of the LB medium are also present. The expression of the acetoin degradation genes was found to rely on the RpoN alternative sigma factor and to be modulated by the Crc/Hfq, Cyo and PTS^Ntr regulatory elements, with the impact of the latter three varying according to the carbon source present in addition to acetoin. Pyruvate, a poor carbon source for P. putida, did not repress acetoin assimilation. Indeed, the presence of acetoin significantly improved growth on pyruvate, revealing these compounds to have a synergistic effect. This would provide a clear competitive advantage to P. putida when growing in environments in which all the preferred carbon sources have been depleted and pyruvate and acetoin remain as leftovers from the fermentation of sugars by other microorganisms.     

Light-Dependent Assimilation of <Emphasis Type="Italic">trans</Emphasis>-Cinnamate by <Emphasis Type="Italic">Rhodobacter sphaeroides</Emphasis> OU5

We present a novel light-dependent metabolism of an aromatic compound (trans-cinnamate) that is assimilatory rather than dissimilatory. Light-dependent assimilation of trans-cinnamate was observed by both growing and resting cells of Rhodobacter sphaeroides OU5. Trans-cinnamate assimilation could be correlated with simultaneous formation of both phenylalanine and tyrosine at near-stoichiometric ratios. Trans-cinnamate assimilation was promoted by carbon source and electron donors, such as glucose, pyruvate, or α-ketoglutarate, whereas malate, succinate, fumarate, and acetate were inhibitory.     

Role of the ptsN Gene Product in Catabolite Repression of the Pseudomonas putida TOL Toluene Degradation Pathway in Chemostat Cultures▿

The Pseudomonas putida KT2440 TOL upper pathway is repressed under nonlimiting conditions in cells growing in chemostat with succinate as a carbon source. We show that the ptsN gene product IIA^Ntr participates in this repression. Crc, involved in yeast extract-dependent repression in batch cultures, did not influence expression when cells were growing in a chemostat with succinate at maximum rate.     

Metabolic pathway to propionate of Pectinatus frisingensis,a strictly anaerobic beer-spoilage bacterium

      Pectinatus frisingensis, a recently described species of anaerobic mesophilic beer-spoilage bacteria, grows by fermenting various organic compounds, and produces mainly propionate, acetate, and succinate. Although acrylate and succinate were both dismutated by dense resting-cell suspensions, propionate production proceeded through the succinate pathway: [3-¹³C]pyruvate consumption led to equal ¹³C-labeling of propionate on methyl and methylene groups. Growth on glucose or glycerol led to a similar propionate to acetate ratio, suggesting dihydroxyacetone phosphate as being a common metabolic intermediate. Diacetyl, 1,3-propanediol, and 2,3-butanediol were not growth substrates or fermentation products, but they were all dismutated by dense resting-cell suspensions to acetate and propionate. Acetoin was a minor fermentation product. The consumption of [2-¹³C] or [3-¹³C]pyruvate by dense resting-cell suspensions demonstrated the involvement of two equivalent pyruvate molecules during acetoin production. Key enzymes involved in this metabolism were measured in anoxic cell-free extracts. A tentative metabolic pathway to the main fermentation products was proposed from the above results. Received: 17 February 1994 / Accepted: 30 August 1994     

Regulation of the utilization of glucose and aromatic substrates in four strains of Pseudomonas putida

During the oxidation of various mixtures of glucose and aromatic substrates by four strains of Pseudomonas putida, diauxic growth was not observed. Strain A3.12 grew faster on benzoate than on glucose, whereas three other strains showed faster growth on glucose than on the aromatic test substrates. Growth rates on mixtures of glucose and aromatics were intermediate between those on the single substrates.The presence of glucose in media containing aromatic substrates accelerated in the bacteria the appearance of the ability to oxidize aromatic substrates. During growth of the organisms on binary mixtures of aromatics, simultaneous utilization of these compounds occurred, the utilization ratio depending on the quality of the compounds as carbon and energy sources. Addition of glucose to dual aromatic substrate media greatly increased the utilization ratio in favour of the better aromatic substrate.With decreasing concentration of glucose in relation to that of aromatic substrates, the rate of carbon assimilation from glucose increased. Enzymological and radiochemical studies demonstrated that even in the presence of an excess of aromatic substrates, glucose was exclusively catabolized via the 2-keto-3-deoxy-6-phosphogluconate pathway. In contrast, the rate of carbon assimilation from ¹⁴C-ring-labelled benzoate and anisate was unaffected by the presence of an excess of glucose.Abbreviations KDPG 2-keto-3-deoxy-6-phosphogluconate - PP pentose-phosphate - OD optical density     

Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed

Pseudomonas putida is a soil bacterium with a versatile and robust metabolism. When confronted with mixtures of carbon sources, it prioritizes the utilization of the preferred compounds, optimizing metabolism and growth. This response is particularly strong when growing in a complex medium such as LB. This work examines the changes occurring in P. putida KT2440 metabolic fluxes, while it grows exponentially in LB medium and sequentially consumes the compounds available. Integrating the uptake rates for each compound at three different moments during the exponential growth with the changes observed in the proteome, and with the metabolic fluxes predicted by the iJN1411 metabolic model for this strain, allowed the metabolic rearrangements that occurred to be determined. The results indicate that the bacterium changes significantly the configuration of its metabolism during the early, mid and late exponential phases of growth. Sugars served as an energy source during the early phase and later as energy and carbon source. The configuration of the tricarboxylic acids cycle varied during growth, providing no energy in the early phase, and turning to a reductive mode in the mid phase and to an oxidative mode later on. This work highlights the dynamism and flexibility of P. putida metabolism.     

The Pseudomonas putida Crc global regulator controls the expression of genes from several chromosomal catabolic pathways for aromatic compounds

The Crc protein is involved in the repression of several catabolic pathways for the assimilation of some sugars, nitrogenated compounds, and hydrocarbons in Pseudomonas putida and Pseudomonas aeruginosa when other preferred carbon sources are present in the culture medium (catabolic repression). Crc appears to be a component of a signal transduction pathway modulating carbon metabolism in pseudomonads, although its mode of action is unknown. To better understand the role of Crc, the proteome profile of two otherwise isogenic P. putida strains containing either a wild-type or an inactivated crc allele was compared. The results showed that Crc is involved in the catabolic repression of the hpd and hmgA genes from the homogentisate pathway, one of the central catabolic pathways for aromatic compounds that is used to assimilate intermediates derived from the oxidation of phenylalanine, tyrosine, and several aromatic hydrocarbons. This led us to analyze whether Crc also regulates the expression of the other central catabolic pathways for aromatic compounds present in P. putida. It was found that genes required to assimilate benzoate through the catechol pathway (benA and catBCA) and 4-OH-benzoate through the protocatechuate pathway (pobA and pcaHG) are also negatively modulated by Crc. However, the pathway for phenylacetate appeared to be unaffected by Crc. These results expand the influence of Crc to pathways used to assimilate several aromatic compounds, which highlights its importance as a master regulator of carbon metabolism in P. putida.     

Studies on the mode of action of the antibacterial agent diethyltin dichloride onEscherichia coli

The mode of action of diethyltin dichloride as a representative of the antibacterial dialkyl-substituted tin compounds was studied forEscherichia coli. The oxygen uptake by resting cells ofEicoli with glucose, lactate, pyruvate or glutamate as substrates is strongly inhibited by diethyltin dichloride at a concentration of 0.08mm which is still below the minimum inhibitory concentration for growth on a rich medium. Inhibition of oxygen uptake with glucose or lactate as substrates is accompanied by an increase in the amount of pyruvic acid accumulating. A slight rise in the concentration of -ketoglutaric acid results from the inhibition of succinate and malate oxidation by diethyltin dichloride, while inhibition of -keto acid production is obtained with glutamate as a substrate. Anaerobically, with glucose as a substrate, ethanol formation as well as the production of carbon dioxide and hydrogen are inhibited by diethyltin dichloride. In many respects the effects of diethyltin dichloride on metabolism resemble those of arsenite.The inhibition of pyruvate metabolism probably results in a lack of acetyl-CoA, and this is suggested to be a possible cause of growth inhibition.     

The effect of succinate on respiration, transamination, and pyruvate formation in cells of the yeast Dipodascus magnusii

The effect of succinate on the growth and respiration of the yeast Dipodascus magnusii VKM Y-1072, which is auxotrophic for thiamine and biotin, was studied. The addition of succinate to a culture grown on glucose was found to activate the respiration of cells on various substrates by enhancing the processes related to transamination reactions. In this case, aerobic fermentation (ethanol production) decreased, whereas pyruvate production increased. When succinate was added to the medium as the sole carbon source, it supported yeast growth in the absence of one of the two vitamins, thiamine or biotin, but not both. The yeast metabolism was completely respiratory, without any signs of aerobic fermentation. A drastic rise in pyruvate production in the yeast grown on glucose in the presence of succinate and the absence of biotin are also indicative of metabolic changes.