Vps Factors Are Required for Efficient Transcription Elongation in Budding Yeast

Genetics. 2013 Mar;193(3):829-51. doi: 10.1534/genetics.112.146308. Epub 2013 Jan 18.

Abstract

There is increasing evidence that certain Vacuolar protein sorting (Vps) proteins, factors that mediate vesicular protein trafficking, have additional roles in regulating transcription factors at the endosome. We found that yeast mutants lacking the phosphatidylinositol 3-phosphate [PI(3)P] kinase Vps34 or its associated protein kinase Vps15 display multiple phenotypes indicating impaired transcription elongation. These phenotypes include reduced mRNA production from long or G+C-rich coding sequences (CDS) without affecting the associated GAL1 promoter activity, and a reduced rate of RNA polymerase II (Pol II) progression through lacZ CDS in vivo. Consistent with reported genetic interactions with mutations affecting the histone acetyltransferase complex NuA4, vps15Δ and vps34Δ mutations reduce NuA4 occupancy in certain transcribed CDS. vps15Δ and vps34Δ mutants also exhibit impaired localization of the induced GAL1 gene to the nuclear periphery. We found unexpectedly that, similar to known transcription elongation factors, these and several other Vps factors can be cross-linked to the CDS of genes induced by Gcn4 or Gal4 in a manner dependent on transcriptional induction and stimulated by Cdk7/Kin28-dependent phosphorylation of the Pol II C-terminal domain (CTD). We also observed colocalization of a fraction of Vps15-GFP and Vps34-GFP with nuclear pores at nucleus-vacuole (NV) junctions in live cells. These findings suggest that Vps factors enhance the efficiency of transcription elongation in a manner involving their physical proximity to nuclear pores and transcribed chromatin.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basic-Leucine Zipper Transcription Factors / genetics
  • Basic-Leucine Zipper Transcription Factors / metabolism
  • Cell Nucleus / metabolism
  • Class III Phosphatidylinositol 3-Kinases / genetics
  • Class III Phosphatidylinositol 3-Kinases / metabolism*
  • Cyclin-Dependent Kinases / genetics
  • Cyclin-Dependent Kinases / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • GC Rich Sequence
  • Galactokinase / genetics
  • Galactokinase / metabolism
  • Gene Deletion
  • Histone Acetyltransferases / metabolism
  • Nuclear Pore / metabolism
  • Phenotype
  • Phosphorylation
  • Promoter Regions, Genetic
  • Protein Transport
  • RNA Polymerase II / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription Elongation, Genetic*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Vacuolar Sorting Protein VPS15 / genetics
  • Vacuolar Sorting Protein VPS15 / metabolism*
  • Vacuoles / metabolism

Substances

  • Basic-Leucine Zipper Transcription Factors
  • DNA-Binding Proteins
  • GAL4 protein, S cerevisiae
  • GCN4 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Histone Acetyltransferases
  • NuA4 protein, S cerevisiae
  • Class III Phosphatidylinositol 3-Kinases
  • GAL1 protein, S cerevisiae
  • Galactokinase
  • VPS15 protein, S cerevisiae
  • Vacuolar Sorting Protein VPS15
  • Cyclin-Dependent Kinases
  • Kin28 protein kinase, S cerevisiae
  • RNA Polymerase II