Quantitative aspects of glucose metabolism by Escherichia coli B/r, grown in the presence of pyrroloquinoline quinone

Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals

Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.

Nitrate- and nitrite-dependent anaerobic oxidation of methane

Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N₂ and O₂ for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.

Characterization of a thermostable glucose dehydrogenase with strict substrate specificity from a hyperthermophilic archaeon Thermoproteus sp. GDH-1

A hyperthermophilic archaeon was isolated from a terrestrial hot spring on Kodakara Island, Japan and designated as Thermoproteus sp. glucose dehydrogenase (GDH-1). Cell extracts from cells grown in medium supplemented with glucose exhibited NAD(P)-dependent glucose dehydrogenase activity. The enzyme (TgGDH) was purified and found to display a strict preference for d-glucose. The gene was cloned and expressed in Escherichia coli, resulting in the production of a soluble and active protein. Recombinant TgGDH displayed extremely high thermostability and an optimal temperature higher than 85 °C, in addition to its strict specificity for d-glucose. Despite its thermophilic nature, TgGDH still exhibited activity at 25 °C. We confirmed that the enzyme could be applied for glucose measurements at ambient temperatures, suggesting a potential of the enzyme for use in measurements in blood samples.

Changes in the redox state and composition of the quinone pool of Escherichia coli during aerobic batch-culture growth

Ubiquinones (UQs) and menaquinones (MKs) perform distinct functions in Escherichia coli. Whereas, in general, UQs are primarily involved in aerobic respiration, the MKs serve as electron carriers in anaerobic respiration. Both UQs and MKs can accept electrons from various dehydrogenases, and may donate electrons to different oxidases. Hence, they play a role in maintaining metabolic flexibility in E. coli whenever this organism has to adapt to conditions with changing redox characteristics, such as oxygen availability. Here, the authors report on the changes in both the size and the redox state of the quinone pool when the environment changes from being well aerated to one with low oxygen availability. It is shown that such transitions are accompanied by a rapid increase in the demethylmenaquinone pool, and a slow increase in the MK pool. Moreover, in exponentially growing cultures in a well-shaken Erlenmeyer flask, it is observed that the assumption of a pseudo-steady state does not hold with respect to the redox state of the quinone pool.

Shikimic acid production by a modified strain of E. coli (W3110.shik1) under phosphate-limited and carbon-limited conditions

Shikimic acid is one of several industrially interesting chiral starting materials formed in the aromatic amino acid pathway of plants and microorganisms. In this study, the physiology of a shikimic acid producing strain of Escherichia coli (derived from W3110) deleted in aroL (shikimic acid kinase II gene), was compared to that of a corresponding control strain (W3110) under carbon- and phosphate-limited conditions. For the shikimic acid producing strain (referred to as W3110.shik1), phosphate limitation resulted in a higher yield of shikimic acid (0.059 +/- 0.012 vs. 0.024 +/- 0.005 c-mol/c-mol) and a lower yield of by-products from the shikimate pathway, when compared to carbon-limited condition. The yield of the by-product 3-dehydroshikimic acid (DHS) decreased from 0.076 +/- 0.028 to 0.022 +/- 0.001 c-mol/c-mol. Several other by-products were only detected under carbon-limited conditions. The latter group included 3-dehydroquinic acid (0.021 +/- 0.021 c-mol/c-mol), quinic acid (0.012 +/- 0.005 c-mol/c-mol), and gallic acid (0.002 +/- 0.001 c-mol/c-mol). For both strains, more acetate was produced under phosphate than the carbon-limited case. Considerable cell lysis was found for both strains but was higher for W3110.shik1, and increased for both strains under phosphate limitation. The advantages of the latter condition in terms of an increased shikimic acid yield was thus counteracted by an increased cell lysis, which may make downstream processing more difficult.

Glycolysis and Flux Control

Central metabolism of carbohydrates uses the Embden-Meyerhof-Parnas (EMP), pentose phosphate (PP), and Entner-Doudoroff (ED) pathways. This review reviews the biological roles of the enzymes and genes of these three pathways of E. coli. Glucose, pentoses, and gluconate are primarily discussed as the initial substrates of the three pathways, respectively. The genetic and allosteric regulatory mechanisms of glycolysis and the factors that affect metabolic flux through the pathways are considered here. Despite the fact that a lot of information on each of the reaction steps has been accumulated over the years for E. coli, surprisingly little quantitative information has been integrated to analyze glycolysis as a system. Therefore, the review presents a detailed description of each of the catalytic steps by a systemic approach. It considers both structural and kinetic aspects. Models that include kinetic information of the reaction steps will always contain the reaction stoichiometry and therefore follow the structural constraints, but in addition to these also kinetic rate laws must be fulfilled. The kinetic information obtained on isolated enzymes can be integrated using computer models to simulate behavior of the reaction network formed by these enzymes. Successful examples of such approaches are the modeling of glycolysis in S. cerevisiae, the parasite Trypanosoma brucei, and the red blood cell. With the rapid developments in the field of Systems Biology many new methods have been and will be developed, for experimental and theoretical approaches, and the authors expect that these will be applied to E. coli glycolysis in the near future.

The biochemistry, physiology and genetics of PQQ and PQQ-containing enzymes

Pyrrolo-quinoline quinone (PQQ) is the non-covalently bound prosthetic group of many quinoproteins catalysing reactions in the periplasm of Gram-negative bacteria. Most of these involve the oxidation of alcohols or aldose sugars. PQQ is formed by fusion of glutamate and tyrosine, but details of the biosynthetic pathway are not known; a polypeptide precursor in the cytoplasm is probably involved, the completed PQQ being transported into the periplasm. In addition to the soluble methanol dehydrogenase of methylotrophs, there are three classes of alcohol dehydrogenases; type I is similar to methanol dehydrogenase; type II is a soluble quinohaemoprotein, having a C-terminal extension containing haem C; type III is similar but it has two additional subunits (one of which is a multihaem cytochrome c), bound in an unusual way to the periplasmic membrane. There are two types of glucose dehydrogenase; one is an atypical soluble quinoprotein which is probably not involved in energy transduction. The more widely distributed glucose dehydrogenases are integral membrane proteins, bound to the membrane by transmembrane helices at the N-terminus. The structures of the catalytic domains of type III alcohol dehydrogenase and membrane glucose dehydrogenase have been modelled successfully on the methanol dehydrogenase structure (determined by X-ray crystallography). Their mechanisms are likely to be similar in many ways and probably always involve a calcium ion (or other divalent cation) at the active site. The electron transport chains involving the soluble alcohol dehydrogenases usually consist only of soluble c-type cytochromes and the appropriate terminal oxidases. The membrane-bound quinohaemoprotein alcohol dehydrogenases pass electrons to membrane ubiquinone which is then oxidized directly by ubiquinol oxidases. The electron acceptor for membrane glucose dehydrogenase is ubiquinone which is subsequently oxidized directly by ubiquinol oxidases or by electron transfer chains involving cytochrome bc1, cytochrome c and cytochrome c oxidases. The function of most of these systems is to produce energy for growth on alcohol or aldose substrates, but there is some debate about the function of glucose dehydrogenases in those bacteria which contain one or more alternative pathways for glucose utilization. Synthesis of the quinoprotein respiratory systems requires production of PQQ, haem and the dehydrogenase subunits, transport of these into the periplasm, and incorporation together with divalent cations, into active quinoproteins and quinohaemoproteins. Six genes required for regulation of synthesis of methanol dehydrogenase have been identified in Methylobacterium, and there is evidence that two, two-component regulatory systems are involved.

Pyrroloquinoline quinone, a chemotactic attractant for Escherichia coli

Escherichia coli is attracted by pyrroloquinoline quinone (PQQ), and chemotaxis toward glucose is enhanced by the presence of PQQ. A ptsI mutant showed no chemotactic response to either glucose or PQQ alone but did show a chemotactic response to a mixture of glucose and PQQ. A strain lacking the methylated chemotaxis receptor protein Tar showed no response to PQQ.

Effect of PQQ glucose dehydrogenase overexpression in Escherichia coli on sugar-dependent respiration

Pyrroloquinoline quinone glucose dehydrogenase (PQQGDH) was overexpressed in Escherichia coli, and its impact on sugar-dependent respiration was investigated. Sugar-dependent respiration patterns under PQQGDH overexpression can be devided into two types. The first type involves D-glucose and D-mannose, which are utilized by the phosphotransferase system (PTS) and are also the substrates of PQQGDH. As a result of PQQGDH overexpression, the apparent Km value of sugar-dependent respiration shifted to higher concentration compared with E. coli parental cells. The second type included D-xylose and D-galactose, which are the substrates of PQQGDH, but not the PTS sugars. PQQGDH overexpressing cells showed much higher respiration than parental cells. These results suggested that PQQGDH overexpression may alter sugar utilization preferences in E. coli, suggesting further possible applications in metabolic engineering for carbon source utilization.

Reconstruction of glucose uptake and phosphorylation in a glucose-negative mutant of Escherichia coli by using Zymomonas mobilis genes encoding the glucose facilitator protein and glucokinase

Expression of the Zymomonas mobilis glf (glucose facilitator protein) and glk (glucokinase) genes in Escherichia coli ZSC113 (glucose negative) provided a new functional pathway for glucose uptake and phosphorylation. Both genes were essential for the restoration of growth in glucose minimal medium and for acid production on glucose-MacConkey agar plates.