Isotopomer subspaces as indicators of metabolic-pathway structure

Stable isotopes of fatty acids: current and future perspectives for advancing trophic ecology

To understand consumer dietary requirements and resource use across ecosystems, researchers have employed a variety of methods, including bulk stable isotope and fatty acid composition analyses. Compound-specific stable isotope analysis (CSIA) of fatty acids combines both of these tools into an even more powerful method with the capacity to broaden our understanding of food web ecology and nutritional dynamics. Here, we provide an overview of the potential that CSIA studies hold and their constraints. We first review the use of fatty acid CSIA in ecology at the natural abundance level as well as enriched physiological tracers, and highlight the unique insights that CSIA of fatty acids can provide. Next, we evaluate methodological best practices when generating and interpreting CSIA data. We then introduce three cutting-edge methods: hydrogen CSIA of fatty acids, and fatty acid isotopomer and isotopologue analyses, which are not yet widely used in ecological studies, but hold the potential to address some of the limitations of current techniques. Finally, we address future priorities in the field of CSIA including: generating more data across a wider range of taxa; lowering costs and increasing laboratory availability; working across disciplinary and methodological boundaries; and combining approaches to answer macroevolutionary questions. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.

The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin-Benson-Bassham cycle

The photosynthetic carbon reduction cycle, or Calvin-Benson-Bassham (CBB) cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still the subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about the cycle's structure was fuelled by the findings of Gibbs and Kandler in 1956 and 1957, when they observed that radioactive 14CO2 was dynamically incorporated in hexoses in a very atypical and asymmetrical way, a phenomenon later termed the 'photosynthetic Gibbs effect'. Now, it is widely accepted that the photosynthetic Gibbs effect is not in contradiction to the reaction scheme proposed by CBB, but the arguments given have been largely qualitative and hand-waving. To fully appreciate the controversy and to understand the difficulties in interpreting the Gibbs effect, it is illustrative to illuminate the history of the discovery of the CBB cycle. We here give an account of central scientific advances and discoveries, which were essential prerequisites for the elucidation of the cycle. Placing the historic discoveries in the context of the modern textbook pathway scheme illustrates the complexity of the cycle and demonstrates why especially dynamic labelling experiments are far from easy to interpret. We conclude by arguing that it requires sound theoretical approaches to resolve conflicting interpretations and to provide consistent quantitative explanations.

Metabolomics of ADSOL (AS-1) red blood cell storage

Population-based investigations suggest that red blood cells (RBCs) are therapeutically effective when collected, processed, and stored for up to 42 days under validated conditions before transfusion. However, some retrospective clinical studies have shown worse patient outcomes when transfused RBCs have been stored for the longest times. Furthermore, studies of RBC persistence in the circulation after transfusion have suggested that considerable donor-to-donor variability exists and may affect transfusion efficacy. To understand the limitations of current blood storage technologies and to develop approaches to improve RBC storage and transfusion efficacy, we investigated the global metabolic alterations that occur when RBCs are stored in AS-1 (AS1-RBC). Leukoreduced AS1-RBC units prepared from 9 volunteer research donors (12 total donated units) were serially sampled for metabolomics analysis over 42 days of refrigerated storage. Samples were tested by gas chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry, and specific biochemical compounds were identified by comparison to a library of purified standards. Over 3 experiments, 185 to 264 defined metabolites were quantified in stored RBC samples. Kinetic changes in these biochemicals confirmed known alterations in glycolysis and other pathways previously identified in RBCs stored in saline, adenine, glucose and mannitol solution (SAGM-RBC). Furthermore, we identified additional alterations not previously seen in SAGM-RBCs (eg, stable pentose phosphate pathway flux, progressive decreases in oxidized glutathione), and we delineated changes occurring in other metabolic pathways not previously studied (eg, S-adenosyl methionine cycle). These data are presented in the context of a detailed comparison with previous studies of SAGM-RBCs from human donors and murine AS1-RBCs. Global metabolic profiling of AS1-RBCs revealed a number of biochemical alterations in stored blood that may affect RBC viability during storage as well as therapeutic effectiveness of stored RBCs in transfusion recipients. These results provide future opportunities to more clearly pinpoint the metabolic defects during RBC storage, to identify biomarkers for donor screening and prerelease RBC testing, and to develop improved RBC storage solutions and methodologies.

Alterations of red blood cell metabolome during cold liquid storage of erythrocyte concentrates in CPD-SAGM

Erythrocyte concentrates for transfusion purposes represent a life-saving therapeutics of primary relevance in the clinical setting. However, efforts have been continuously proposed to improve safety and efficacy of long-term stored red blood cells. By means of liquid chromatography coupled with Q-TOF mass spectrometry, we were able to perform an untargeted metabolomics analysis in order to highlight metabolic species (i.e. low molecular biochemicals including sugars, lipids, nucleotides, aminoacids, etc.), both in red blood cells and supernatants, which showed fluctuations against day 0 controls over storage duration on a weekly basis. We could confirm and expand existing literature about the rapid fall of glycolytic rate and accumulation of glycolysis end products. A shift was observed towards the oxidative phase of pentose phosphate pathway, in response to an exacerbation of oxidative stress (altered glutathione homeostasis and accumulation of peroxidation/inflammatory products in the supernatant). The present study provides the first evidence that over storage duration metabolic fluxes in red blood cells proceed from pentose phosphate pathway towards purine salvage pathway, instead of massively re-entering glycolysis via the nonoxidative phase. This article is part of a Special Issue entitled: Integrated omics.

Models of the human metabolic network: aiming to reconcile metabolomics and genomics

The metabolic syndrome, inborn errors of metabolism, and drug-induced changes to metabolic states all bring about a seemingly bewildering array of alterations in metabolite concentrations; these often occur in tissues and cells that are distant from those containing the primary biochemical lesion. How is it possible to collect sufficient biochemical information from a patient to enable us to work backwards and pinpoint the primary lesion, and possibly treat it in this whole human metabolic network? Potential analyses have benefited from modern methods such as ultra-high-pressure liquid chromatography, mass spectrometry, nuclear magnetic resonance spectroscopy, and more. A yet greater challenge is the prediction of outcomes of possible modern therapies using drugs and genetic engineering. This exposes the notion of viewing metabolism from a completely different perspective, with focus on the enzymes, regulators, and structural elements that are encoded by genes that specify the amino acid sequences, and hence encode the various interactions, be they regulatory or catalytic. The mainstream view of metabolism is being challenged, so we discuss here the reconciling of traditionally quantitative chemocentric metabolism with the seemingly 'parameter-free' genomic description, and vice versa.

Genome-scale models of bacterial metabolism: reconstruction and applications

Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities.