Cycles, sources, and sinks: Conceptualizing how phosphate balance modulates carbon flux using yeast metabolic networks

Abstract

Phosphates are ubiquitous molecules that enable critical intracellular biochemical reactions. Therefore, cells have elaborate responses to phosphate limitation. Our understanding of long-term transcriptional responses to phosphate limitation is extensive. Contrastingly, a systems-level perspective presenting unifying biochemical concepts to interpret how phosphate balance is critically coupled to (and controls) metabolic information flow is missing. To conceptualize such processes, utilizing yeast metabolic networks we categorize phosphates utilized in metabolism into cycles, sources and sinks. Through this, we identify metabolic reactions leading to putative phosphate sources or sinks. With this conceptualization, we illustrate how mass action driven flux towards sources and sinks enable cells to manage phosphate availability during transient/immediate phosphate limitations. We thereby identify how intracellular phosphate availability will predictably alter specific nodes in carbon metabolism, and determine signature cellular metabolic states. Finally, we identify a need to understand intracellular phosphate pools, in order to address mechanisms of phosphate regulation and restoration.

Keywords: carbon metabolism; computational biology; gene expression; mass action; metabolic flux; metabolic networks; phosphate; systems biology.

Figure 1.. Biochemical reactions illustrating phosphate cycles in metabolism.

(A) The synthesis and hydrolysis of ATP is depicted in the reactions. One molecule each of AMP and ATP are utilized for the synthesis of two molecules of ADP by adenylate kinase, collectively a phosphate-neutral reaction. In the second reaction, the synthesis and hydrolysis of ATP with the concurrent release or use of a Pi molecule, and a water molecule is shown. Here, the net change in Pi is zero for each cycle. (B) Examples where the hydrolysis of a phosphoanhydride bond drives the synthesis of phosphate-containing products. The conversion of D-glucose to D-glucose-6-phosphate by hexokinases, and D-glucose-1-phosphate to UDP-glucose by UDP-glucose pyrophosphorylase are shown. Here, ATP and UTP act as phosphate group donors, respectively. (C) Examples where the hydrolysis of a phosphoanhydride bond drives the synthesis of products with the release of phosphate. The conversion of pyruvate to oxaloacetate by pyruvate carboxylase, and glutamate to glutamine (by glutamine synthetase is shown). Here, the hydrolysis of a phosphoanhydride bond in ATP provides energy for the catalysis of the reaction.

Figure 2.. Long-term (molecular) and short-term (metabolic) responses in response to phosphate limitation.

(A) A schematic representation of a typical long-term cellular response upon severe phosphate starvation is shown (the S. cerevisiae PHO system is used illustratively). This response is mediated by gene expression changes through activation of phosphate responsive transcription factors (TFs). These transcription factors increase the expression of transcripts, which encode proteins involved in phosphate acquisition and release. These include phosphate transporters, acid- and alkaline-phosphatases (APases), and vacuolar phosphate transporters. These proteins result in both the increased uptake of extracellular phosphate and the release of phosphate from intracellular phosphate pools. (B) A schematic representation of a hypothetical set of biochemical pathways (a toy model) is shown; illustrating how these reactions can release or consume phosphates. In such a short-term metabolic response, which is elicited upon transient fluctuations in phosphate levels, changes in metabolic flux through specific nodes can immediately restore phosphate, either through increased synthesis of molecules that will release phosphate (highlighted in green box), or by decreased synthesis of molecules that will consume phosphate (highlighted in the red box).

Figure 3.. Metabolic sources and sinks of phosphates.

(A) An illustration of a hypothetical set of biochemical reactions, representing metabolic sources and sinks of phosphates. The top reaction shows that during the synthesis of a phosphate source (highlighted in green box), phosphate is released, while the bottom reaction shows that during the synthesis of a phosphate sink (highlighted in the red box), phosphate is utilized. (B) A schematic showing possible outcomes that restore phosphate during transient fluctuations in phosphate availability. Through largely mass action based processes, limitations in phosphate will promote metabolic reactions leading to the synthesis of a phosphate source metabolite, accompanied with the release of Pi. As a result of this, two possible cellular scenarios can occur- first, if phosphate levels are restored through this process, this can result in the subsequent utilization of the metabolic phosphate source and phosphate for the synthesis of metabolic sink. Alternately, if source producing reactions are insufficient to restore phosphate, this can result in continuing synthesis of metabolic sources, and the possible utilization of metabolic sinks, both of which results in phosphate release. (C) A set of key metabolic pathways, derived from glucose metabolism, illustrating the flow of phosphates, and highlighting major reactions that result in the synthesis of metabolic phosphate sources (green boxes) accompanied by Pi release, and few reactions that result in the synthesis of metabolic phosphate sinks (red boxes) accompanied by utilization of Pi.