Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins.
eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes. However the extent to which specific mRNA targets are regulated by 4E-BPs remains unknown. We performed translational profiling by microarray analysis of polysome and monosome associated mRNAs in wild-type and mutant cells to identify mRNAs in yeast regulated by the 4E-BPs Caf20p and Eap1p; the first-global comparison of 4E-BP target mRNAs. We find that yeast 4E-BPs modulate the translation of >1000 genes. Most target mRNAs differ between the 4E-BPs revealing mRNA specificity for translational control by each 4E-BP. This is supported by observations that eap1Δ and caf20Δ cells have different nitrogen source utilization defects, implying different mRNA targets. To account for the mRNA specificity shown by each 4E-BP, we found correlations between our data sets and previously determined targets of yeast mRNA-binding proteins. We used affinity chromatography experiments to uncover specific RNA-stabilized complexes formed between Caf20p and Puf4p/Puf5p and between Eap1p and Puf1p/Puf2p. Thus the combined action of each 4E-BP with specific 3'-UTR-binding proteins mediates mRNA-specific translational control in yeast, showing that this form of translational control is more widely employed than previously thought.
Cridge
Andrew G
AG
The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK.
Castelli
Lydia M
LM
Smirnova
Julia B
JB
Selley
Julian N
JN
Rowe
William
W
Hubbard
Simon J
SJ
McCarthy
John E G
JE
Ashe
Mark P
MP
Grant
Christopher M
CM
Pavitt
Graham D
GD
D000596:Amino Acids / Q000378:metabolism; D016213:Cyclins / Q000235:genetics; D039642:Eukaryotic Initiation Factors / Q000235:genetics / Q000502:physiology*; D017353:Gene Deletion; D015966:Gene Expression Regulation, Fungal; D009584:Nitrogen / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology*; D014158:Transcription, Genetic
D000596:Amino Acids; C555411:Caf20 protein, S cerevisiae; D016213:Cyclins; C555412:Eap1 protein, S cerevisiae; D039642:Eukaryotic Initiation Factors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D009584:Nitrogen