Cis and trans interactions between genes encoding PAF1 complex and ESCRT machinery components in yeast

Joana Rodrigues,David Lydall

doi:10.1007/s00294-018-0828-6

Abstract

Saccharomyces cerevisiae is a commonly used model organism for understanding eukaryotic gene function. However, the close proximity between yeast genes can complicate the interpretation of yeast genetic data, particularly high-throughput data. In this study, we examined the interplay between genes encoding components of the PAF1 complex and VPS36, the gene located next to CDC73 on chromosome XII. The PAF1 complex (Cdc73, Paf1, Ctr9, Leo1, and Rtf1, in yeast) affects RNA levels by affecting transcription, histone modifications, and post-transcriptional RNA processing. The human PAF1 complex is linked to cancer, and in yeast, it has been reported to play a role in telomere biology. Vps36, part of the ESCRT-II complex, is involved in sorting proteins for vacuolar/lysosomal degradation. We document a complex set of genetic interactions, which include an adjacent gene effect between CDC73 and VPS36 and synthetic sickness between vps36Δ and cdc73Δ, paf1Δ, or ctr9Δ. Importantly, paf1Δ and ctr9Δ are synthetically lethal with deletions of other components of the ESCRT-II (SNF8 and VPS25), ESCRT-I (STP22), or ESCRT-III (SNF7) complexes. We found that RNA levels of VPS36, but not other ESCRT components, are positively regulated by all components of the PAF1 complex. Finally, we show that deletion of ESCRT components decreases the telomere length in the S288C yeast genetic background, but not in the W303 background. Together, our results outline complex interactions, in cis and in trans, between genes encoding PAF1 and ESCRT-II complex components that affect telomere function and cell viability in yeast.

Highlights

The budding yeast Saccharomyces cerevisiae is the best understood eukaryotic model organism
CDC73 and VPS36 point towards each other, with the stop codons separated by 204 bp (Fig. 2a), and vps36Δ and cdc73Δ have been suggested to demonstrate an adjacent gene effect (Ben-Shitrit et al 2012)
We report a synthetic fitness defect in cells simultaneously depleted of Vps36 and Cdc73, which is likely independent of the telomere length of these cells

Summary

Introduction

The budding yeast Saccharomyces cerevisiae is the best understood eukaryotic model organism. It is interesting to note that the five proteins of the PAF1 complex associate with RNA pol II, deletion of individual PAF1 complex components in yeast leads to distinct phenotypes (Betz et al 2002; Rodrigues and Lydall 2018). Data from numerous experimental systems support the idea that the different PAF1 complex components perform different functions and the more severe defects of cells lacking Paf or Ctr have been attributed to the scaffolding properties of these components (Nordick et al 2008; Tomson and Arndt 2013; Xu et al 2017; Rodrigues and Lydall 2018). We show that VPS36 RNA levels are controlled by the PAF1 complex

Materials and methods

Results

Discussion