This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Taylor, R. Articles by Atkin, A. L. Search for Related Content PubMed PubMed Citation Articles by Taylor, R. Articles by Atkin, A. L.

Gene Set Coregulated by the Saccharomyces cerevisiae Nonsense-Mediated mRNA Decay Pathway

Rachel Taylor, Bessie Wanja Kebaara, Tara Nazarenus, Ashley Jones, Rena Yamanaka, Rachel Uhrenholdt, Jason P. Wendler, and Audrey L. Atkin^*

School of Biological Sciences, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0666

Received 11 April 2005/ Accepted 27 September 2005

The nonsense-mediated mRNA decay (NMD) pathway has historically been thought of as an RNA surveillance system that degrades mRNAs with premature translation termination codons, but the NMD pathway of Saccharomyces cerevisiae has a second role regulating the decay of some wild-type mRNAs. In S. cerevisiae, a significant number of wild-type mRNAs are affected when NMD is inactivated. These mRNAs are either wild-type NMD substrates or mRNAs whose abundance increases as an indirect consequence of NMD. A current challenge is to sort the mRNAs that accumulate when NMD is inactivated into direct and indirect targets. We have developed a bioinformatics-based approach to address this challenge. Our approach involves using existing genomic and function databases to identify transcription factors whose mRNAs are elevated in NMD-deficient cells and the genes that they regulate. Using this strategy, we have investigated a coregulated set of genes. We have shown that NMD regulates accumulation of ADR1 and GAL4 mRNAs, which encode transcription activators, and that Adr1 is probably a transcription activator of ATS1. This regulation is physiologically significant because overexpression of ADR1 causes a respiratory defect that mimics the defect seen in strains with an inactive NMD pathway. This strategy is significant because it allows us to classify the genes regulated by NMD into functionally related sets, an important step toward understanding the role NMD plays in the normal functioning of yeast cells.

R.T. and B.W.K. contributed equally to this work.

This article has been cited by other articles:

• Kebaara, B. W., Langford, M. L., Navarathna, D. H. M. L. P., Dumitru, R., Nickerson, K. W., Atkin, A. L. (2008). Candida albicans Tup1 Is Involved in Farnesol-Mediated Inhibition of Filamentous-Growth Induction. Eukaryot Cell 7: 980-987 [Abstract] [Full Text]  
• Ulbricht, R. J., Olivas, W. M. (2008). Puf1p acts in combination with other yeast Puf proteins to control mRNA stability. RNA 14: 246-262 [Abstract] [Full Text]  
• Jacobs, J. L., Belew, A. T., Rakauskaite, R., Dinman, J. D. (2007). Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae. Nucleic Acids Res 35: 165-174 [Abstract] [Full Text]  
• Morozov, I. Y., Negrete-Urtasun, S., Tilburn, J., Jansen, C. A., Caddick, M. X., Arst, H. N. Jr. (2006). Nonsense-Mediated mRNA Decay Mutation in Aspergillus nidulans. Eukaryot Cell 5: 1838-1846 [Abstract] [Full Text]  
• Rodriguez-Gabriel, M. A., Watt, S., Bahler, J., Russell, P. (2006). Upf1, an RNA Helicase Required for Nonsense-Mediated mRNA Decay, Modulates the Transcriptional Response to Oxidative Stress in Fission Yeast.. Mol. Cell. Biol. 26: 6347-6356 [Abstract] [Full Text]