Identification of a Novel One-carbon Metabolism Regulon in Saccharomyces cerevisiae

Abstract

Glycine specifically induces genes encoding subunits of the glycine decarboxylase complex (GCV1, GCV2, and GCV3), and this is mediated by a fall in cytoplasmic levels of 5,10-methylenetetrahydrofolate caused by inhibition of cytoplasmic serine hydroxymethyltransferase. Here it is shown that this control system extends to genes for other enzymes of one-carbon metabolism and de novo purine biosynthesis. Northern analysis of the response to glycine demonstrated that the induction of the GCV genes and the induction of other amino acid metabolism genes are temporally distinct. The genomewide response to glycine revealed that several other genes are rapidly co-induced with the GCV genes, including SHM2, which encodes cytoplasmic serine hydroxymethyltransferase. These results were refined by examining transcript levels in an shm2⌬ strain (in which cytoplasmic 5,10-methylenetetrahydrofolate levels are reduced) and a met13⌬ strain, which lacks the main methylenetetrahydrofolate reductase activity of yeast and is effectively blocked at consumption of 5,10-methylene tetrahydrofolate for methionine synthesis. Glycine addition also caused a substantial transient disturbance to metabolism, including a sequence of changes in induction of amino acid biosynthesis and respiratory chain genes. Analysis of the glycine response in the shm2⌬ strain demonstrated that apart from the one-carbon regulon, most of these transient responses were not contingent on a disturbance to onecarbon metabolism. The one-carbon response is distinct from the Bas1p purine biosynthesis regulon and thus represents the first example of transcriptional regulation in response to activated one-carbon status.

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

“…Significant gene ontology enrichments were identified for enzymes primarily involved in mitochondrial-associated reactions (P ¼ 0.01), including TCA metabolic processes (P ¼ 0.02) and oxidative phosphorylation (P ¼ 0.005). These results are generally consistent with glycine-induced transcriptional changes observed for C1 metabolic enzymes (Gelling et al 2004).…”

“…Under conditions of glycine induction Gelling et al (2004) noticed a similar pattern of C1 enzyme differential expression; however, Bas1 was not required for the observed effect in this case. In both of these studies the intact cytosolic serine hydroxymethyltransferase Shm2 (EC 2.1.2.1) was necessary for glycine-dependent changes in C1 enzyme expression (Gelling et al 2004;Subramanian et al 2005). Although contradicting evidence exists, results reported thus far demonstrate the dynamic control of C1 metabolism in eukaryotes.…”

“…Upon glycine withdrawal many enzymes involved in C1 metabolism are strongly repressed, a regulatory event that requires the transcription factor Bas1 (Subramanian et al 2005). Under conditions of glycine induction Gelling et al (2004) noticed a similar pattern of C1 enzyme differential expression; however, Bas1 was not required for the observed effect in this case. In both of these studies the intact cytosolic serine hydroxymethyltransferase Shm2 (EC 2.1.2.1) was necessary for glycine-dependent changes in C1 enzyme expression (Gelling et al 2004;Subramanian et al 2005).…”

“…However, loss of Fum1 alone does not account for retrograde signaling in PSY3642, as transcriptional changes in fum1 single mutants are limited; only $20 genes are affected, none of which encode typical retrograde responsive TCA cycle enzymes (McCammon et al 2003). Furthermore, although Gelling et al (2004) showed that C1 metabolic flux changes significantly affect the expression status of respiratory chain components, mitochondrial deficiency and retrograde signaling were not reported as a consequence. From these results we conclude that enzyme deletions predicted by our model cause systemic metabolic changes that modulate C1 flux and activate retrograde signaling in PSY3642.…”

High-Resolution Global Analysis of the Influences of Bas1 and Ino4 Transcription Factors on Meiotic DNA Break Distributions in Saccharomyces cerevisiae

“…It has been proposed that formation of a complex between Bas1 and Bas2 unmasks an activator function of Bas1, but there may be other partners that can bind Bas1 as well . Bas1 and Bas2 also regulate several genes involved in one-carbon metabolism, such as GLN1, SHM2, and MTD1 (Denis and Gelling et al 2004). Meiotic DSBs were previously mapped genome-wide in a bas1 mutant by microarray hybridization of Spo11-attached DNA from a rad50S mutant (Mieczkowski et al 2006).…”