A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes.
Hundreds of RNA-binding proteins (RBPs) control diverse aspects of post-transcriptional gene regulation. To identify novel and unconventional RBPs, we probed high-density protein microarrays with fluorescently labeled RNA and selected 200 proteins that reproducibly interacted with different types of RNA from budding yeast Saccharomyces cerevisiae. Surprisingly, more than half of these proteins represent previously known enzymes, many of them acting in metabolism, providing opportunities to directly connect intermediary metabolism with posttranscriptional gene regulation. We mapped the RNA targets for 13 proteins identified in this screen and found that they were associated with distinct groups of mRNAs, some of them coding for functionally related proteins. We also found that overexpression of the enzyme Map1 negatively affects the expression of experimentally defined mRNA targets. Our results suggest that many proteins may associate with mRNAs and possibly control their fates, providing dense connections between different layers of cellular regulation.
Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
Tanja
T
Scherrer
Nitish
N
Mittal
Sarath Chandra
SC
Janga
André P
AP
Gerber
D000626:Aminopeptidases / Q000235:genetics / Q000378:metabolism*; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D063208:Methionyl Aminopeptidases; D020411:Oligonucleotide Array Sequence Analysis; D040081:Protein Array Analysis; D011485:Protein Binding; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*
D004798:Enzymes; D020543:Proteome; D012331:RNA, Fungal; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D000626:Aminopeptidases; D063208:Methionyl Aminopeptidases