Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

PLoS Biol. 2004 Mar;2(3):E79. doi: 10.1371/journal.pbio.0020079. Epub 2004 Mar 16.


Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of RNA-binding proteins in Saccharomyces cerevisiae and DNA microarrays to comprehensively identify the associated mRNAs. Distinct groups of 40-220 different mRNAs with striking common themes in the functions and subcellular localization of the proteins they encode are associated with each of the five Puf proteins: Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. We identified distinct sequence motifs in the 3'-untranslated regions of the mRNAs bound by Puf3p, Puf4p, and Puf5p. Three-hybrid assays confirmed the role of these motifs in specific RNA-protein interactions in vivo. The results suggest that combinatorial tagging of transcripts by specific RNA-binding proteins may be a general mechanism for coordinated control of the localization, translation, and decay of mRNAs and thus an integral part of the global gene expression program.

Publication types

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

MeSH terms

  • 3' Untranslated Regions
  • Amino Acid Motifs
  • Animals
  • Cell Cycle Proteins / genetics
  • Chromatin / chemistry
  • Chromatin / metabolism
  • Cytoplasm / metabolism
  • DNA Primers / chemistry
  • Fungal Proteins / chemistry
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal
  • Genes, Fungal
  • Membrane Proteins / genetics
  • Microscopy, Fluorescence
  • Mitochondria / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis
  • Phenotype
  • Plasmids / metabolism
  • RNA / chemistry
  • RNA Processing, Post-Transcriptional
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • Repressor Proteins / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Two-Hybrid System Techniques


  • 3' Untranslated Regions
  • Cell Cycle Proteins
  • Chromatin
  • DNA Primers
  • Fungal Proteins
  • JSN1 protein, S cerevisiae
  • MPT5 protein, S cerevisiae
  • Membrane Proteins
  • PUF2 protein, S cerevisiae
  • PUF3 protein, S cerevisiae
  • PUF4 protein, S cerevisiae
  • RNA, Messenger
  • RNA-Binding Proteins
  • Repressor Proteins
  • Saccharomyces cerevisiae Proteins
  • RNA

Associated data

  • GENBANK/P34691
  • SWISSPROT/P21399
  • SWISSPROT/P25724
  • SWISSPROT/P25822
  • SWISSPROT/P97330
  • SWISSPROT/Q14671
  • SWISSPROT/Q17339
  • SWISSPROT/Q18317
  • SWISSPROT/Q92904