Repression of Mitochondrial Translation, Respiration and a Metabolic Cycle-Regulated Gene, SLF1, by the Yeast Pumilio-Family Protein Puf3p

Marc Chatenay-Lapointe,Gerald S Shadel,Janine Santos

doi:10.1371/journal.pone.0020441

Abstract

Synthesis and assembly of the mitochondrial oxidative phosphorylation (OXPHOS) system requires genes located both in the nuclear and mitochondrial genomes, but how gene expression is coordinated between these two compartments is not fully understood. One level of control is through regulated expression mitochondrial ribosomal proteins and other factors required for mitochondrial translation and OXPHOS assembly, which are all products of nuclear genes that are subsequently imported into mitochondria. Interestingly, this cadre of genes in budding yeast has in common a 3′-UTR element that is bound by the Pumilio family protein, Puf3p, and is coordinately regulated under many conditions, including during the yeast metabolic cycle. Multiple functions have been assigned to Puf3p, including promoting mRNA degradation, localizing nucleus-encoded mitochondrial transcripts to the outer mitochondrial membrane, and facilitating mitochondria-cytoskeletal interactions and motility. Here we show that Puf3p has a general repressive effect on mitochondrial OXPHOS abundance, translation, and respiration that does not involve changes in overall mitochondrial biogenesis and largely independent of TORC1-mitochondrial signaling. We also identified the cytoplasmic translation factor Slf1p as yeast metabolic cycle-regulated gene that is repressed by Puf3p at the post-transcriptional level and promotes respiration and extension of yeast chronological life span when over-expressed. Altogether, these results should facilitate future studies on which of the many functions of Puf3p is most relevant for regulating mitochondrial gene expression and the role of nuclear-mitochondrial communication in aging and longevity.

Highlights

The assembly of the mitochondrial oxidative phosphorylation (OXPHOS) system is a remarkably complex process, in part, because expression from two genomes, mtDNA and nuclear DNA, must be coordinated [1]
We observed no significant increases in ‘‘mitochondrial housekeeping’’ markers Coq5p and porin compared to the actin loading control, suggesting that overall mitochondrial biogenesis was not increased in puf3D cells (Figure 1B)
We have examined Puf3p, the member of this family that preferentially binds to nuclear mRNAs that encode proteins involved in mitochondrial translation and OXPHOS assembly [22]

Summary

Introduction

The assembly of the mitochondrial oxidative phosphorylation (OXPHOS) system is a remarkably complex process, in part, because expression from two genomes, mtDNA and nuclear DNA, must be coordinated [1]. This process is more intricate given the fact that all of proteins required for replication of mtDNA, as well as transcription and translation of it mRNA products, are encoded by nuclear DNA and imported into the organelle [2,3]. The repression by the PUF family of proteins is conserved and involves the binding of Pop2p, which in turn recruits CCR4-NOT deadenylase machinery as well as decapping factors, Dcp1p and Dhh1p [16]

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