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Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. Several previous transcript-profiling experiments have compared separate anaerobic and aerobic cultures. Here the process of adaptation was investigated by determining changes in transcript profiles when anaerobic steady-state cultures were perturbed by the introduction of air. Within 5 min of culture aeration the abundances of transcripts associated with anaerobic metabolism were decreased, whereas transcripts associated with aerobic metabolism were increased. In addition to the rapid switch to aerobic central metabolism, transcript profiling, supported by experiments with relevant mutants, revealed transient changes suggesting that the peroxide stress response, methionine biosynthesis, and degradation of putrescine play important roles during the adaptation to aerobic conditions. Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. As an inhabitant of the lower intestine, E. coli often occupies an oxygen-starved niche only to be excreted from the host into an aerobic external environment. The ability to adapt to such changes is rooted in altered patterns of gene expression in response to key cues, such as O 2 availability.Depending on the availabilities of electron donors and acceptors, E. coli uses one of three metabolic modes to support growth (1). In the presence of O 2 , aerobic respiration allows the complete oxidation of a growth substrate and therefore is the most productive and hence the preferred metabolic mode (1). During aerobic metabolism, the glycolytic conversion of glucose to pyruvate and the oxidative decarboxylation of pyruvate by the pyruvate dehydrogenase complex leads to the formation of acetyl-CoA, which feeds the citric acid cycle (CAC).2 Oxidation of the acetyl units generates reducing equivalents that are transferred to O 2 via aerobic electron transport chains, creating proton gradients that can be used to generate ATP and drive other essential activities (2). In the absence of O 2 , two alternative metabolic modes are available. If a terminal electron acceptor, such as NO 3 Ϫ , is present, then anaerobic respiration is possible. During anaerobic respiration the role of the pyruvate dehydrogenase complex is assumed by pyruvate formate-lyase; the CAC is repressed, and the metabolic flow in the C 4 section of the CAC is reversed. Anaerobic respiration yields less energy than aerobic respiration because the substrate is only partially oxidized (1). However, anaerobic respiration is more productive than fermentation, where energy is conserved by substrate level phosphorylation, and redox balance is achieved by the formation of acetate, ethanol, H 2 , CO 2 , formate, succinate, and lactate (3). Thus, enormous changes in E. coli physiology are provoked by changes in O 2 availability.Previous reports of the effects of O 2 on the transcript profile of E. coli have compared separate aerobic and anaerobic cultures, usua...

Section: Transcripts Encoding a Putrescine Degradation Pathway Are Enmentioning

confidence: 99%

Escherichia coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions

Partridge

Scott

Tang

et al. 2006

“…The biogenic polyamines putrescine [NH 2 (CH 2 ) 4 3 NH 2 ] (Structure 1) are the most prevalent polyamines in mammalian cells. They are small aliphatic polycations involved in numerous diverse biological processes, such as the ability to modulate gene expression and enzyme activities, activation of DNA synthesis, cell proliferation and differentiation, and others (1)(2)(3)(4)(5)(6)(7)(8).…”

mentioning

confidence: 99%

“…They are small aliphatic polycations involved in numerous diverse biological processes, such as the ability to modulate gene expression and enzyme activities, activation of DNA synthesis, cell proliferation and differentiation, and others (1)(2)(3)(4)(5)(6)(7)(8). Other functions of polyamines have been related to DNA protection from external agents (9,10) and against radiation damage (11,12).…”

mentioning

confidence: 99%

Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

Ouameur

Tajmir-Riahi

2004

286

234

Biogenic polyamines, such as putrescine, spermidine, and spermine are small organic polycations involved in numerous diverse biological processes. These compounds play an important role in nucleic acid function due to their binding to DNA and RNA. It has been shown that biogenic polyamines cause DNA condensation and aggregation similar to that of inorganic cobalt(III)hexamine cation, which has the ability to induce DNA conformational changes. However, the nature of the polyamine⅐DNA binding at the molecular level is not clearly established and is the subject of much controversy. In the present study the effects of spermine, spermidine, putrescine, and cobalt(III)hexamine on the solution structure of calf-thymus DNA were investigated using affinity capillary electrophoresis, Fourier transform infrared, and circular dichroism spectroscopic methods. At low polycation concentrations, putrescine binds preferentially through the minor and major grooves of double strand DNA, whereas spermine, spermidine, and cobalt(III)hexamine bind to the major groove. At high polycation concentrations, putrescine interaction with the bases is weak, whereas strong base binding occurred for spermidine in the major and minor grooves of DNA duplex. However, major groove binding is preferred by spermine and cobalt(III)hexamine cations. Electrostatic attractions between polycation and the backbone phosphate group were also observed. No major alterations of B-DNA were observed for biogenic polyamines, whereas cobalt(III)hexamine induced a partial B 3 A transition. DNA condensation was also observed for cobalt(III)hexamine cation, whereas organic polyamines induced duplex stabilization. The binding constants calculated for biogenic polyamines are K Spm ‫؍‬ 2.3 ؋ 10 5 M ؊1 , K Spd ‫؍‬ 1.4 ؋ 10 5 M ؊1 , and K Put ‫؍‬ 1.02 ؋ 10 5 M ؊1 . Two binding constants have been found for cobalt(III)hexamine with K 1 ‫؍‬ 1.8 ؋ 10 5 M ؊1 and K 2 ‫؍‬ 9.2 ؋ 10 4 M ؊1 . The Hill coefficients indicate a positive cooperativity binding for biogenic polyamines and a negative cooperativity for cobalt(III)hexamine.The biogenic polyamines putrescine [NH 2 (CH 2 ) 4 NH 2 ], spermidine [NH 2 (CH 2 ) 4 NH(CH 2 ) 3 NH 2 ], and spermine [NH 2 (C-H 2 ) 3 NH(CH 2 ) 4 NH(CH 2 ) 3 NH 2 ] (Structure 1) are the most prevalent polyamines in mammalian cells. They are small aliphatic polycations involved in numerous diverse biological processes, such as the ability to modulate gene expression and enzyme activities, activation of DNA synthesis, cell proliferation and differentiation, and others (1-8). Other functions of polyamines have been related to DNA protection from external agents (9, 10) and against radiation damage (11, 12). In general, spermidine and spermine are present in millimolar concentrations in vivo, whereas putrescine levels are slightly lower (13-15). However, the most important characteristic of polyamines within the cells is to bind nucleic acids and DNA in particular (1, 6).Polyamines also have the ability to induce DNA conformational transitions. Their bindi...

“…They participate in many cellular processes including modulation of gene expression, signal transduction, protein synthesis, regulation of cell growth and differentiation, and an oxidative defense mechanism (13,16,18,22,25,31). Despite their biological importance, the participation of polyamines in acid resistance has been rarely studied to date.…”

mentioning

confidence: 99%

Polyamines and Glutamate Decarboxylase-based Acid Resistance in Escherichia coli

Jung

Kim

2003

The expression of gadA and gadB, which encode two glutamate decarboxylases (GADs) of Escherichia coli, is induced by an acidic environment and participate in acid resistance. In this study, we constructed a polyamine-deficient mutant and investigated the role of polyamines in acid resistance. The expression of gadA and gadB was shown to be dependent on polyamines. For that reason, the polyamine-deficient mutant was completely devoid of GAD activity and was very susceptible to low pH if large amounts of polyamines were not provided. We also showed that the polyamine-deficient mutant contained higher cAMP levels than the isogenic polyamine-proficient wild type, and cAMP negatively regulated the expression of gadA and gadB. Therefore, introduction of the cya (encoding adenylate cyclase) mutation allele into the polyamine-deficient mutant resulted in the increment of GAD activity and thus restored the reduced acid resistance of the mutant. The positive regulators, H-NS (histone-like protein, encoded by the hns gene) and RpoS (alternative RNA polymerase subunit, encoded by rpoS gene), also significantly governed the expression of gadA and gadB, respectively. However, polyamines did not regulate either the intracellular H-NS level or rpoS expression under these culture conditions. These results strongly suggest that there are at least two different regulatory systems in acid resistance, one is positive regulation via a H-NS/ RpoS system and the other is negative regulation via a polyamine/cAMP system.