A quantitative analysis of metabolite fluxes along some of the pathways of intermediary metabolism in Tetrahymena pyriformis

Revealing gene expression heterogeneity in a clonal population of Tetrahymena thermophila through single-cell RNA sequencing

We performed single-cell RNA sequencing (scRNA-seq) on a population of 5,000 Tetrahymena thermophila, using the 10x Genomics 3' gene expression analysis, to investigate gene expression variability within this clonal population. Initially, we estimated the 3'-untranslated regions (3' UTRs), which were absent in existing annotation files but are crucial for the 10x Genomics 3' gene expression analysis, using the peaks2utr method. This allowed us to create a modified annotation file, which was then utilized in our scRNA-seq analysis. Our analysis revealed significant gene expression variability within the population, even after removing the effect of cell phase-related features. This variability predominantly appeared in six distinct clusters. Through gene ontology and KEGG pathway enrichment analyses, we identified that these were primarily associated with ribosomal proteins, proteins specific to mitochondria, proteins involved in peroxisome-specific carbon metabolism, cytoskeletal proteins, motor proteins, and immobilized antigens.

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.

In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum

The C(3)-C(4) metabolite interconversion at the anaplerotic node in many microorganisms involves a complex set of reactions. C(3) carboxylation to oxaloacetate can originate from phosphoenolpyruvate and pyruvate, and at the same time multiple C(4)-decarboxylating enzymes may be present. The functions of such parallel reactions are not yet fully understood. Using a (13)C NMR-based strategy, we here quantify the individual fluxes at the anaplerotic node of Corynebacterium glutamicum, which is an example of a bacterium possessing multiple carboxylation and decarboxylation reactions. C. glutamicum was grown with a (13)C-labeled glucose isotopomer mixture as the main carbon source and (13)C-labeled lactate as a cosubstrate. 58 isotopomers as well as 15 positional labels of biomass compounds were quantified. Applying a generally applicable mathematical model to include metabolite mass and carbon labeling balances, it is shown that pyruvate carboxylase contributed 91 +/- 7% to C(3) carboxylation. The total in vivo carboxylation rate of 1.28 +/- 0.14 mmol/g dry weight/h exceeds the demand of carboxylated metabolites for biosyntheses 3-fold. Excess oxaloacetate was recycled to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase. This shows that the reactions at the anaplerotic node might serve additional purposes other than only providing C(4) metabolites for biosynthesis.

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.

Effect of 4-pentenoic acid on intermediate metabolism of Tetrahymena

The growth of Tetrahymena pyriformis strain HSM was strongly inhibited by 4-pentenoic acid. Supplementing the medium acetate reversed the growth inhibition, but pyruvate was ineffective. Glycogen content was much lower in cells grown with 4-pentenoic acid than in controls; this effect was not reversed by acetate or by pyruvate. There was little effect of 4-penteonic acid on the in incorporation of label from [1-14C]acetate, [2-14C]glycerol, [1-14C]ribose, [U-14C]fructose, or [1-14C]glucose into CO2 but incorporation of label into glycogen was inhibited, the strongest inhibition being on acetate and the weakest approximately 20%) on ribose, fructose, and glucose. A 3-compartment model for quantitation of labeled acetyl CoA fluxes was shown to be applicable to Tetrahymena grown in the presence of 4-pentenoic acid, and experiments were performed to establish the flux of [1-14C]acetyl CoA into glycogen, lipids, CO2, glutamate, and alanine. It was evident from the results of these experiments that 4-pentenoic acid did not appreciably inhibit beta-oxidation or lipogenesis, but markedly decreased the glyconeogenic flux of labeled acetyl-CoA from the peroxismal and outer mitochondrial compartments.

Triacylglycerol turnover in Tetrahymena pyriformis. Relation to phospholipid synthesis

The metabolic function of triaclyglycerol in Tetrahymena pyriformis was investigated by prelabeling endogenous lipid with a 14C-labeled short chain fatty acid, and then following the disappearance of radioactivity from triacylglycerol and its appearance in other products. In 90 min, up to 85% of the label in triacylglycerol turns over, and although some radioactivity appears in CO2 and glycogen, most of the label appears in phospholipid. Starvation of the cells, as well as resuspension in enriched medium or provision of acetate all block triacylglycerol breakdown, while supplementation of the medium with pyruvate does not. Prelabeling lipid with [3H] glycerol shows that some of the transfer of material from triacylglycerol to phospholipid involves transfer of the glycerol backbone, although transfer of triacylglycerol fatty acids directly to phospholipid probably also occurs. In addition, the catabolism of triacylglycerol occurs by a "last-in-first-out" mechanism, indicating some form of compartmentation of triacylglycerol in this cell. The results demonstrate an important metabolic interrelationship between triacylglycerol catabolism and phospholipid synthesis and raise the question, in this cell at least, of the validity of considering triacylglycerol only as a fuel storage form.