Quantitative analysis of the change of metabolite fluxes along the pentose phosphate and glycolytic pathways in Tetrahymena in response to carbohydrates

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

BACKGROUND

The study of cell metabolism is becoming central in several fields such as biotechnology, evolution/adaptation and human disease investigations. Here we present CiliateGEM, the first metabolic network reconstruction draft of the freshwater ciliate Tetrahymena thermophila. We also provide the tools and resources to simulate different growth conditions and to predict metabolic variations. CiliateGEM can be extended to other ciliates in order to set up a meta-model, i.e. a metabolic network reconstruction valid for all ciliates. Ciliates are complex unicellular eukaryotes of presumably monophyletic origin, with a phylogenetic position that is equal from plants and animals. These cells represent a new concept of unicellular system with a high degree of species, population biodiversity and cell complexity. Ciliates perform in a single cell all the functions of a pluricellular organism, including locomotion, feeding, digestion, and sexual processes.

RESULTS

After generating the model, we performed an in-silico simulation with the presence and absence of glucose. The lack of this nutrient caused a 32.1% reduction rate in biomass synthesis. Despite the glucose starvation, the growth did not stop due to the use of alternative carbon sources such as amino acids.

CONCLUSIONS

The future models obtained from CiliateGEM may represent a new approach to describe the metabolism of ciliates. This tool will be a useful resource for the ciliate research community in order to extend these species as model organisms in different research fields. An improved understanding of ciliate metabolism could be relevant to elucidate the basis of biological phenomena like genotype-phenotype relationships, population genetics, and cilia-related disease mechanisms.

Analysis of metabolic flux using dynamic labelling and metabolic modelling

Metabolic fluxes and the capacity to modulate them are a crucial component of the ability of the plant cell to react to environmental perturbations. Our ability to quantify them and to attain information concerning the regulatory mechanisms that control them is therefore essential to understand and influence metabolic networks. For all but the simplest of flux measurements labelling methods have proven to be the most informative. Both steady-state and dynamic labelling approaches have been adopted in the study of plant metabolism. Here the conceptual basis of these complementary approaches, as well as their historical application in microbial, mammalian and plant sciences, is reviewed, and an update on technical developments in label distribution analyses is provided. This is supported by illustrative cases studies involving the kinetic modelling of secondary metabolism. One issue that is particularly complex in the analysis of plant fluxes is the extensive compartmentation of the plant cell. This problem is discussed from both theoretical and experimental perspectives, and the current approaches used to address it are assessed. Finally, current limitations and future perspectives of kinetic modelling of plant metabolism are discussed.

Parallel labeling experiments and metabolic flux analysis: Past, present and future methodologies

Radioactive and stable isotopes have been applied for decades to elucidate metabolic pathways and quantify carbon flow in cellular systems using mass and isotope balancing approaches. Isotope-labeling experiments can be conducted as a single tracer experiment, or as parallel labeling experiments. In the latter case, several experiments are performed under identical conditions except for the choice of substrate labeling. In this review, we highlight robust approaches for probing metabolism and addressing metabolically related questions though parallel labeling experiments. In the first part, we provide a brief historical perspective on parallel labeling experiments, from the early metabolic studies when radioisotopes were predominant to present-day applications based on stable-isotopes. We also elaborate on important technical and theoretical advances that have facilitated the transition from radioisotopes to stable-isotopes. In the second part of the review, we focus on parallel labeling experiments for (13)C-metabolic flux analysis ((13)C-MFA). Parallel experiments offer several advantages that include: tailoring experiments to resolve specific fluxes with high precision; reducing the length of labeling experiments by introducing multiple entry-points of isotopes; validating biochemical network models; and improving the performance of (13)C-MFA in systems where the number of measurements is limited. We conclude by discussing some challenges facing the use of parallel labeling experiments for (13)C-MFA and highlight the need to address issues related to biological variability, data integration, and rational tracer selection.

Specific dynamic action in two body size groups of the southern catfish (Silurus meridionalis) fed diets differing in carbohydrate and lipid contents

Specific dynamic action (SDA), the energy costs associated with meal digestion and assimilation, is generally affected by body size and food composition. We assessed the postprandial metabolic response and calculated SDA in two size groups of the southern catfish (Silurus meridionalis), each fed one of two diets, high lipid or high carbohydrate, at a meal size of 4% the body mass. Using a continuous-flow respirometer, we determined the oxygen consumption rate at 2-h intervals until the postprandial oxygen consumption rate returned to the prefeeding level. None of the parameters (resting metabolic rate, Rpeak, factorial ratio, time-to-peak, duration, energy expended on SDA, or SDA coefficient) were significantly affected by diet nor was there an interaction between diet and body mass. Rpeak and energy expended on SDA for the whole fish body were significantly higher in the larger fish than the smaller one in both dietary treatments, whereas no significant effect of body size was found in mass specific values. Factorial ratio (range 3.41 to 3.60), peak time (range 9.6 to 12.7 h), SDA coefficient (range 9.36 to 10.36%), and SDA duration (range 62.0 to 71.0 h) did not significantly differ between body size groups. These results suggest that in S. meridionalis the percentage of assimilated energy allocated to SDA may be independent of the body mass.

Measuring multiple fluxes through plant metabolic networks

Fluxes through metabolic networks are crucial for cell function, and a knowledge of these fluxes is essential for understanding and manipulating metabolic phenotypes. Labeling provides the key to flux measurement, and in network flux analysis the measurement of multiple fluxes allows a flux map to be superimposed on the metabolic network. The principles and practice of two complementary methods, dynamic and steady-state labeling, are described, emphasizing best practice and illustrating their contribution to network flux analysis with examples taken from the plant and microbial literature. The principal analytical methods for the detection of stable isotopes are also described, as well as the procedures for obtaining flux maps from labeling data. A series of boxes summarizing the key concepts of network flux analysis is provided for convenience.

Effects of culture age and hexoses on fatty acid oxidation by Leishmania major

The effect of culture age on the rate of oxidation of short-, medium, and long-chain fatty acids by Leishmania major promastigotes was investigated. Promastigotes from 5-day stationary phase cultures oxidized several saturated fatty acids about 3-to-4-fold faster than cells from late log phase cultures, but [10-14C]oleate was oxidized 9-fold faster. The increase in rate of oxidation was partially reversed within 5 h and almost completely reversed within 30 h after resuspending cells from a 5-day stationary culture in fresh medium. Addition of acetate, leucine, or alanine caused moderate inhibitions of [1-14C]palmitate oxidation, while glycerol had little effect. Glucose, however, was a powerful inhibitor of the oxidation of [1-14C]palmitate and of [1-14C]octanoate. Mannose and fructose were also strong inhibitors of palmitate oxidation, but neither galactose, 2-deoxyglucose or 6-deoxyglucose caused appreciable inhibition. The extent of inhibition by acetate increased with increasing culture age, whereas inhibition by glucose decreased. In addition to demonstrating a reversible rise in beta-oxidation capacity with culture age, these data also demonstrate a hitherto unrecognized strong and culture age-dependent inhibition of fatty acid oxidation by glucose.

On the analysis of substrate cycles in large metabolic systems

The simultaneous operation of paired, opposing reactions (substrate cycles) or parallel reactions (dual pathways) with seeming wastage of ATP is widespread in cellular metabolism. Analysis of such "futile" pathways has hitherto been limited to loci with only two or three interconnecting fluxes. We introduce here a method that allows straightforward analysis of more complex systems. The method involves the linear superposition of "fundamental" modes, one or more of which may be energetically wasteful. Decomposition of a flux pattern into such modes allows computation of the amount of free energy "wasted" at any locus. Appropriate normalizations of energy wastage yield a number of indices useful for assessing the energetic impact of futile pathways on the cell and for comparing the degree of regulation of substrate cycles or dual pathways under different metabolic conditions. This approach is applied to steady-state flux data obtained in the protozoan Tetrahymena pyriformis and in isolated rat hepatocytes under a variety of conditions.