Enzyme-to-enzyme channelling in the early steps of glycolysis in rat pancreatic islets

Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints

After feeding microbes with a defined (13)C substrate, unique isotopic patterns (isotopic fingerprints) can be formed in their metabolic products. Such labelling information not only can provide novel insights into functional pathways but also can determine absolute carbon fluxes through the metabolic network via metabolic modelling approaches. This technique has been used for finding pathways that may have been mis-annotated in the past, elucidating new enzyme functions, and investigating cell metabolisms in microbial communities. In this review paper, we summarize the applications of (13)C approaches to analyse novel cell metabolisms for the past 3 years. The isotopic fingerprints (defined as unique isotopomers useful for pathway identifications) have revealed the operations of the Entner-Doudoroff pathway, the reverse tricarboxylic acid cycle, new enzymes for biosynthesis of central metabolites, diverse respiration routes in phototrophic metabolism, co-metabolism of carbon nutrients and novel CO(2) fixation pathways. This review also discusses new isotopic methods to map carbon fluxes in global metabolisms, as well as potential factors influencing the metabolic flux quantification (e.g. metabolite channelling, the isotopic purity of (13)C substrates and the isotopic effect). Although (13)C labelling is not applicable to all biological systems (e.g. microbial communities), recent studies have shown that this method has a significant value in functional characterization of poorly understood micro-organisms, including species relevant for biotechnology and human health.

Metabolic pathway determination and flux analysis in nonmodel microorganisms through 13C-isotope labeling

C-isotope labeling is a commonly used technique for determining and quantifying pathways in microorganisms under various growth conditions. The experimental protocol consists of feeding the cell with a composition-defined substrate and measuring isotopic labeling patterns in the synthesized metabolites (often the amino acids). Not only can the labeling information be cross-referenced with genomic information to identify the novel pathways, but it can also be used to decipher absolute carbon fluxes through the metabolic network of interest. This technique can be widely used for functional characterization of nonmodel microbial species, and thus we provide a (13)C-pathway and flux analysis protocol. The five key procedures are: (1) growing cells using labeled substrates, (2) measuring extracellular metabolite and biomass component, (3) analyzing isotopic labeling patterns in amino acids and central metabolites using gas chromatography-mass spectrometry, (4) tracing (13)C carbon transitions in metabolites and discovering new pathways, and (5) estimating flux distributions based on isotopomer constraints. This protocol provides complementary information to the recently published protocol for (13)C-based metabolic flux analysis of the model species Escherichia coli (Nat Protoc 4:878-892, 2009).

Bridging the gap between fluxomics and industrial biotechnology

Metabolic flux analysis is a vital tool used to determine the ultimate output of cellular metabolism and thus detect biotechnologically relevant bottlenecks in productivity. ¹³C-based metabolic flux analysis (¹³C-MFA) and flux balance analysis (FBA) have many potential applications in biotechnology. However, noteworthy hurdles in fluxomics study are still present. First, several technical difficulties in both ¹³C-MFA and FBA severely limit the scope of fluxomics findings and the applicability of obtained metabolic information. Second, the complexity of metabolic regulation poses a great challenge for precise prediction and analysis of metabolic networks, as there are gaps between fluxomics results and other omics studies. Third, despite identified metabolic bottlenecks or sources of host stress from product synthesis, it remains difficult to overcome inherent metabolic robustness or to efficiently import and express nonnative pathways. Fourth, product yields often decrease as the number of enzymatic steps increases. Such decrease in yield may not be caused by rate-limiting enzymes, but rather is accumulated through each enzymatic reaction. Fifth, a high-throughput fluxomics tool hasnot been developed for characterizing nonmodel microorganisms and maximizing their application in industrial biotechnology. Refining fluxomics tools and understanding these obstacles will improve our ability to engineer highlyefficient metabolic pathways in microbial hosts.

Investigation of interaction between enolase and phosphoglycerate mutase using molecular dynamics simulation

Two glycolytic enzymes, phosphoglycerate mutase (PGM) and enolase from Saccharomyces cerevisiae have been chosen to detect complex formation between active centers (a/c), using molecular dynamics simulation. Enzymes have been separated by 10 A distance and placed in a water box of size 173 x 173 x 173 A. Three different orientations where a/c of PGM and enolase were positioned toward each other have been used for investigation. The two initial 3-phosphoglycerate substrates at near active centers of initial structure of PGM have been replaced with final 2-phosphoglycerate products. 150mM of NaCl have been added to the system to observe binding activity in the near physiological conditions. Analysis of interaction energies and conformation changes for 3ns simulation indicates that PGM and enolase do show binding affinity between their near active regions. Moreover the similarity between final conformations of the first two orientations with the initial conformation of the third orientation suggests that complex formation between a/c of enzymes is not confined only by discussed orientations. Clear interaction of enolase with C-terminal tail of PGM has been recorded. These results suggest that substrate direct transfer mechanism may exist between enzymes.

Enzyme-to-enzyme channeling in the early steps of glycolysis in rat pancreatic islets

The enzyme-to-enzyme channeling of metabolic intermediates is not an uncommon process. The present review draws attention to recent experimental work documenting, in rat pancreatic islets, the enzyme-to-enzyme channeling of alpha-D-glucose 6-phosphate between hexokinase isoenzyme(s), mainly glucokinase, and phosphoglucoisomerase. Likewise, the possible enzyme-to-enzyme channeling of beta-D-fructose 6-phosphate between phosphoglucoisomerase and phosphofructokinase is briefly evoked. These considerations are relevant to the anomeric specificity of D-glucose metabolism, even in islets exposed to equilibrated D-glucose, to the perturbation of such an anomeric specificity in the phenomenon of so-called B-cell glucotoxicity, and to the correct interpretation of 3HOH generation from D-[2-(3H)]glucose.