Characterization of a nonsense-mediated mRNA decay (NMD) copper regulon.

The nonsense-mediated mRNA decay (NMD) pathway was originally identified as a pathway that degrades mRNAs harboring premature termination codons. NMD is now also recognized as a pathway that degrades natural mRNAs. In Saccharomyces cerevisiae, five features are known to target natural mRNAs to NMD. The extent to which natural mRNAs from the same functional group are regulated by this pathway is not widely known. Here, we invested eight mRNAs involved in copper homeostasis that are predicted to be sensitive to NMD. We found that majority of these mRNAs have atypically long 3'-Untranslated Regions (UTRs) that could potentially target them for NMD-mediated degradation. We investigated the sequence elements that target a subset of these mRNAs to NMD and found that the long CTR2 3'-UTR and the COX23 3'-UTR are sufficient to target an NMD-insensitive mRNA to NMD. We also found that the COX19 and FRE2 3'-UTRs contribute to the degradation of the transcripts by the pathway. Additional studies involving sequence elements demonstrated that lengthening the open reading frame of CTR2 abrogates NMD, preventing degradation of the mRNA. Moreover, we found that transcription of CTR2 mRNAs driven by the GPD promoter causes altered NMD sensitivity when compared to CTR2 driven by the CTR2 promoter. Lastly, we found that low copper growth conditions affect NMD sensitivity of the MAC1 mRNA; demonstrating that NMD can be influenced by environmental conditions. The studies presented here are novel in that they investigate the regulation of functionally related, natural mRNAs by NMD. We show that the regulation of these mRNAs is transcript specific, and that regulation can be influenced by sequence elements as well as the environmental conditions.