Methionine coordinates a hierarchically organized anabolic program enabling proliferation

Abstract

Methionine availability during overall amino acid limitation metabolically reprograms cells to support proliferation, the underlying basis for which remains unclear. Here we construct the organization of this methionine-mediated anabolic program using yeast. Combining comparative transcriptome analysis and biochemical and metabolic flux-based approaches, we discover that methionine rewires overall metabolic outputs by increasing the activity of a key regulatory node. This comprises the pentose phosphate pathway (PPP) coupled with reductive biosynthesis, the glutamate dehydrogenase (GDH)-dependent synthesis of glutamate/glutamine, and pyridoxal-5-phosphate (PLP)-dependent transamination capacity. This PPP-GDH-PLP node provides the required cofactors and/or substrates for subsequent rate-limiting reactions in the synthesis of amino acids and therefore nucleotides. These rate-limiting steps in amino acid biosynthesis are also induced in a methionine-dependent manner. This thereby results in a biochemical cascade establishing a hierarchically organized anabolic program. For this methionine-mediated anabolic program to be sustained, cells co-opt a “starvation stress response” regulator, Gcn4p. Collectively, our data suggest a hierarchical metabolic framework explaining how methionine mediates an anabolic switch.

Life span extension by glucose restriction is abrogated by methionine supplementation: Cross-talk between glucose and methionine and implication of methionine as a key regulator of life span

“…The cross-talk from methionine to carbon metabolism has been observed previously. For example, Walvekar et al found that adding methionine to minimum media induces pentose phosphate pathway (PPP) and nucleotide synthesis, coordinating a global anabolic program to promote cell proliferation (36). This finding is consistent with the earlier genetic analysis that found a PPP mutant to be methionine auxotrophic (37).…”

“…Besides the direct control of translation, methionine likely influences life span by altering the metabolic program of the cell. As mentioned above, methionine can cross-talk with carbon metabolism by inducing the PPP and a hierarchically organized anabolic program to support cell growth and proliferation (36) and consequently affect life span. One of the derivatives of methionine, S-adenosyl methionine (SAM), is a cofactor that serves as a methyl donor.…”

Metabolic excretion associated with nutrient–growth dysregulation promotes the rapid evolution of an overt metabolic defect

“…This is because in the wild, yeast strains are diploid and thus remain prototrophic (capable of synthesizing a metabolite) even if one of the 2 gene copies for metabolite synthesis is impaired. In special cases, auxotrophic limitation might mimic natural limitation; e.g., intracellular glutamine level may reflect nitrogen availability [15], whereas intracellular methionine level may reflect sulfur or general amino acid availability [16,17]. Leucine, whose biosynthesis occurs in both cytoplasm and mitochondria, may monitor the tricarboxylic acid (TCA) cycle and the ADP/ATP ratio [18].…”

A versatile LC-MS/MS approach for comprehensive, quantitative analysis of central metabolic pathways

“…Combining information from other “omics” (such as transcriptomics, genomics) with metabolomics can be a very powerful approach in determining how different aspects (such as signaling pathways, genes) are connected to metabolism 10 , 11 , 14 , 15 . Although various LC-MS/MS based methods are available for quantitation of metabolites, they rarely cover multiple pathways.…”

“…In recent studies, we have measured stable-isotope label incorporation into amino acids and nucleotides, under different growth conditions and genetic backgrounds 10 , 11 . Here we summarize the methodology for analyzing steady-state amounts of these and central carbon metabolism pathway metabolites by LC-MS/MS, using multiple-reaction monitoring (MRM) methods.…”