Carbon source-dependent alteration of Puf3p activity mediates rapid changes in the stabilities of mRNAs involved in mitochondrial function

Abstract

The Puf family of RNA-binding proteins regulates gene expression primarily by interacting with the 3′ untranslated region (3′ UTR) of targeted mRNAs and inhibiting translation and/or stimulating decay. Physical association and computational analyses of yeast Puf3p identified >150 potential mRNA targets involved in mitochondrial function. However, only COX17 has been established as a target of Puf3p-mediated deadenylation and decapping. We have identified 10 new targets that are rapidly degraded in a Puf3p-dependent manner. We also observed changes in Puf3p activity in response to environmental conditions. Puf3p promotes rapid degradation of mRNA targets in the fermentable carbon source dextrose. However, Puf3p-mediated decay activity is inhibited in carbon sources that require mitochondrial function for efficient cell growth. In addition, the activity of Puf3p is rapidly altered by changing the carbon source. PUF3 expression is not decreased at the RNA or protein level by different carbon sources and localization is not significantly altered, suggesting that Puf3p activity is regulated posttranslationally. Finally, under conditions when Puf3p is unable to stimulate decay, Puf3p can still bind its target mRNAs. Together, these experiments provide insight into the carbon source-specific control of Puf3p activity and how such alterations allow Puf3p to dynamically regulate mitochondrial function.

Glucose-Regulated Phosphorylation of the PUF Protein Puf3 Regulates the Translational Fate of Its Bound mRNAs and Association with RNA Granules

“…We therefore concluded that Puf3p is subject to phosphorylation modifications that correlate with an increase in transcript levels of nuclear-encoded mitochondrial genes, both in the YMC and in batch culture (Figure 1C). Such transcripts harboring a Puf3p binding sequence in their 3'UTR have been shown to have a shorter half-life in the presence of Puf3p and in glucose medium (Foat et al, 2005; Miller et al, 2014), which is consistent with the lower steady-state levels of such mRNAs observed here in glucose medium.…”

Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

“…Puf3 is one such RBP in S. cerevisiae. Puf3 is important for the decay of numerous nuclear transcripts encoding mitochondrial proteins involved in respiration (15). How its activity, but not binding, is regulated is unknown.…”

“…In the case of nuclear transcripts encoding mitochondrial proteins, the role of the RBP Puf3 is one of the best understood in Saccharomyces cerevisiae. The activity of Puf3, but not its expression, localization, or RNA binding, is regulated by carbon source to ensure that transcripts encoding mitochondrial proteins important for aerobic metabolism have a longer half-life when a fermentable carbon source is absent (15).…”

“…Snf1, together with the cyclic AMP (cAMP)-dependent protein kinase A (PKA) and target of rapamycin (TOR) pathways, coordinates many of the nutrientresponsive metabolic pathways in yeast (10). Despite the preponderance of evidence indicating altered transcription as the major factor determining the increase in mRNA abundance when yeast cells are depleted of glucose, there is considerable evidence indicating that posttranscriptional changes, particularly an increase in mRNA stability, are also important in determining gene expression levels (11)(12)(13)(14)(15). A recent study demonstrated that promoter sequences influence the subcellular location and efficiency of translation of transcripts upregulated by glucose starvation (16).…”

Localized translation near the mitochondrial outer membrane: An update

“…1, denoted as (1) and (2)). Puf3 was also shown to play a role in regulation of translation and mRNA stability, [73][74][75][76] functions that might also be significant for mRNA localization near the mitochondria. In particular, differential stabilization of mRNAs is one of the modes through which localization in Drosophila embryos is achieved.…”