Quantitative analysis of flux regulation through hierarchical regulation analysis

Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation

Saccharomyces cerevisiae is a widely used cell factory; therefore, it is important to understand how it organizes key functional parts when cultured under different conditions. Here, we perform a multiomics analysis of S. cerevisiae by culturing the strain with a wide range of specific growth rates using glucose as the sole limiting nutrient. Under these different conditions, we measure the absolute transcriptome, the absolute proteome, the phosphoproteome, and the metabolome. Most functional protein groups show a linear dependence on the specific growth rate. Proteins engaged in translation show a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins show a linear decrease under respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates; at the same time, an overall increased flux through these pathways is observed. Further analysis show that even though mRNA levels do not correlate with protein levels for all individual genes, the transcriptome level of functional groups correlates very well with its corresponding proteome. Finally, using enzyme-constrained genome-scale modeling, we find that enzyme usage plays an important role in controlling flux in amino acid biosynthesis.

Understanding how yeast organizes its functional proteome is a fundamental task in systems biology. Here, the authors conduct a multiomics analysis on yeast cells cultured with different growth rates, identifying a linear dependence of the functional proteome on the growth rate.

Running-wheel activity delays mitochondrial respiratory flux decline in aging mouse muscle via a post-transcriptional mechanism

Loss of mitochondrial respiratory flux is a hallmark of skeletal muscle aging, contributing to a progressive decline of muscle strength. Endurance exercise alleviates the decrease in respiratory flux, both in humans and in rodents. Here, we dissect the underlying mechanism of mitochondrial flux decline by integrated analysis of the molecular network. Mice were given a lifelong ad libitum low-fat or high-fat sucrose diet and were further divided into sedentary and running-wheel groups. At 6, 12, 18 and 24 months, muscle weight, triglyceride content and mitochondrial respiratory flux were analysed. Subsequently, transcriptome was measured by RNA-Seq and proteome by targeted LC-MS/MS analysis with ¹³ C-labelled standards. In the sedentary groups, mitochondrial respiratory flux declined with age. Voluntary running protected the mitochondrial respiratory flux until 18 months of age. Beyond this time point, all groups converged. Regulation Analysis of flux, proteome and transcriptome showed that the decline of flux was equally regulated at the proteomic and at the metabolic level, while regulation at the transcriptional level was marginal. Proteomic regulation was most prominent at the beginning and at the end of the pathway, namely at the pyruvate dehydrogenase complex and at the synthesis and transport of ATP. Further proteomic regulation was scattered across the entire pathway, revealing an effective multisite regulation. Finally, reactions regulated at the protein level were highly overlapping between the four experimental groups, suggesting a common, post-transcriptional mechanism of muscle aging.

Mitoenergetic Dysfunction Triggers a Rapid Compensatory Increase in Steady-State Glucose Flux

ATP can be produced in the cytosol by glycolytic conversion of glucose (GLC) into pyruvate. The latter can be metabolized into lactate, which is released by the cell, or taken up by mitochondria to fuel ATP production by the tricarboxylic acid cycle and oxidative phosphorylation (OXPHOS) system. Altering the balance between glycolytic and mitochondrial ATP generation is crucial for cell survival during mitoenergetic dysfunction, which is observed in a large variety of human disorders including cancer. To gain insight into the kinetic properties of this adaptive mechanism we determined here how acute (30 min) inhibition of OXPHOS affected cytosolic GLC homeostasis. GLC dynamics were analyzed in single living C2C12 myoblasts expressing the fluorescent biosensor FLII(12)Pglu-700μδ6 (FLII). Following in situ FLII calibration, the kinetic properties of GLC uptake (V1) and GLC consumption (V2) were determined independently and used to construct a minimal mathematical model of cytosolic GLC dynamics. After validating the model, it was applied to quantitatively predict V1 and V2 at steady-state (i.e., when V1 = V2 = Vsteady-state) in the absence and presence of OXPHOS inhibitors. Integrating model predictions with experimental data on lactate production, cell volume, and O2 consumption revealed that glycolysis and mitochondria equally contribute to cellular ATP production in control myoblasts. Inhibition of OXPHOS induced a twofold increase in Vsteady-state and glycolytic ATP production flux. Both in the absence and presence of OXPHOS inhibitors, GLC was consumed at near maximal rates, meaning that GLC consumption is rate-limiting under steady-state conditions. Taken together, we demonstrate here that OXPHOS inhibition increases steady-state GLC uptake and consumption in C2C12 myoblasts. This activation fully compensates for the reduction in mitochondrial ATP production, thereby maintaining the balance between cellular ATP supply and demand.

Elucidating the regulation of complex signalling systems in plant cells

The pollen tube represents a model system for the study of tip growth, and the root provides a valuable system to study gene and signalling networks in plants. In the present article, using the two systems as examples, we discuss how to elucidate the regulation of complex signalling systems in plant cells. First, we discuss how hormones and related genes in plant root development form a complex interacting network, and their activities are interdependent. Therefore their roles in root development must be analysed as an integrated system, and elucidation of the regulation of each component requires the adaptation of a novel modelling methodology: regulation analysis. Secondly, hydrodynamics, cell wall and ion dynamics are all important properties that regulate plant cell growth. We discuss how regulation analysis can be applied to study the regulation of hydrodynamics, cell wall and ion dynamics, using pollen tube growth as a model system. Finally, we discuss future prospects for elucidating the regulation of complex signalling systems in plant cells.

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

Regulation levels of the gene expression cascade controlling protein levels and metabolic fluxes for cells to achieve faster growth have not been elaborated in acceptable detail. Furthermore, there is need for specific growth rate (μ) dependent absolute quantitative transcriptome and proteome data to understand the molecular relationships for enabling cells to modify μ. We address these questions, for the first time, by presenting regulatory strategies for more efficient metabolism of Escherichia coli at higher μ by statistical covariance analysis of genome-wide intracellular mRNA and protein concentrations coupled to metabolic flux analysis in the steady state range of μ = 0.11-0.49 h(-1). Our analyses show dominating post-transcriptional control of protein abundances and post-translational control of flux rates. On average, E. coli achieved five-times faster growth through 3.7-fold increase of apparent catalytic rates of enzymes (kapp) and 2.5-fold increased translation rates, demonstrating the relevance of post-translational regulation for increasing flux throughput. Interestingly, pathways carrying the highest flux showed both high protein abundance and kapp values. Furthermore, co-regulation analysis of enzymatic capacities revealed tightly coupled regulatory dependencies of protein synthesis and RNA precursor synthesis, substrate utilization, biosynthetic and energy generation pathways carrying the highest flux. We also observed metabolic pathway and COG specific protein and metabolic flux control levels, protein expression costs and genome-wide principles for translation efficiency and transcription unit polarity. This work contributes to the much needed quantitative understanding of coordinated gene expression regulation and metabolic flux control. Our findings will also advance modeling and metabolic engineering of industrial strains.

Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis

Regulation of enzyme expression is one key mechanism by which cells control their metabolic programs. In this work, a quantitative analysis of metabolism in a model bacterium under different conditions shows that expression alone cannot explain the majority of the observed metabolic changes.

Most enzymes are indeed highly expressed in conditions where they are more active.

Quantitatively, however, the observed changes in expression between conditions do not match the changes in activity for most enzymes.

A good quantitative match is only observed for enzymes involved in the TCA cycle.

Metabolomics reveals that increased substrate availability explains only a few instances of changes in activity.

One of the key ways in which microbes are thought to regulate their metabolism is by modulating the availability of enzymes through transcriptional regulation. However, the limited success of efforts to manipulate metabolic fluxes by rewiring the transcriptional network has cast doubt on the idea that transcript abundance controls metabolic fluxes. In this study, we investigate control of metabolic flux in the model bacterium Bacillus subtilis by quantifying fluxes, transcripts, and metabolites in eight metabolic states enforced by different environmental conditions. We find that most enzymes whose flux switches between on and off states, such as those involved in substrate uptake, exhibit large corresponding transcriptional changes. However, for the majority of enzymes in central metabolism, enzyme concentrations were insufficient to explain the observed fluxes—only for a number of reactions in the tricarboxylic acid cycle were enzyme changes approximately proportional to flux changes. Surprisingly, substrate changes revealed by metabolomics were also insufficient to explain observed fluxes, leaving a large role for allosteric regulation and enzyme modification in the control of metabolic fluxes.

Metabolic host responses to infection by intracellular bacterial pathogens

The interaction of bacterial pathogens with mammalian hosts leads to a variety of physiological responses of the interacting partners aimed at an adaptation to the new situation. These responses include multiple metabolic changes in the affected host cells which are most obvious when the pathogen replicates within host cells as in case of intracellular bacterial pathogens. While the pathogen tries to deprive nutrients from the host cell, the host cell in return takes various metabolic countermeasures against the nutrient theft. During this conflicting interaction, the pathogen triggers metabolic host cell responses by means of common cell envelope components and specific virulence-associated factors. These host reactions generally promote replication of the pathogen. There is growing evidence that pathogen-specific factors may interfere in different ways with the complex regulatory network that controls the carbon and nitrogen metabolism of mammalian cells. The host cell defense answers include general metabolic reactions, like the generation of oxygen- and/or nitrogen-reactive species, and more specific measures aimed to prevent access to essential nutrients for the respective pathogen. Accurate results on metabolic host cell responses are often hampered by the use of cancer cell lines that already exhibit various de-regulated reactions in the primary carbon metabolism. Hence, there is an urgent need for cellular models that more closely reflect the in vivo infection conditions. The exact knowledge of the metabolic host cell responses may provide new interesting concepts for antibacterial therapies.

Somewhat in control--the role of transcription in regulating microbial metabolic fluxes

The most common way for microbes to control their metabolism is by controlling enzyme levels through transcriptional regulation. Yet recent studies have shown that in many cases, perturbations to the transcriptional regulatory network do not result in altered metabolic phenotypes on the level of the flux distribution. We suggest that this may be a consequence of cells protecting their metabolism against stochastic fluctuations in expression as well as enabling a fast response for those fluxes that may need to be changed quickly. Furthermore, it is impossible for a regulatory program to guarantee optimal expression levels in all conditions. Several studies have found examples of demonstrably suboptimal regulation of gene expression, and improvements to the regulatory network have been investigated in laboratory evolution experiments.