Copper tolerance of Saccharomyces cerevisiae nonsense-mediated mRNA decay mutants

Abstract

The eukaryotic nonsense-mediated mRNA (NMD) is a specialized pathway that leads to the recognition and rapid degradation of mRNAs with premature termination codons, and importantly some natural mRNAs as well. Natural mRNAs with atypically long 3′-untranslated regions (UTRs) are degraded by NMD in Saccharomyces cerevisiae. A number of S. cerevisiae mRNAs undergo alternative 3′-end processing producing mRNA isoforms that differ in their 3′-UTR lengths. Some of these alternatively 3′-end processed mRNA isoforms have atypically long 3′-UTRs and would be likely targets for NMD-mediated degradation. Here, we investigated the role NMD plays in the regulation of expression of CTR2, which encodes a vacuolar membrane copper transporter. CTR2 pre-mRNA undergoes alternative 3′-end processing to produce two mRNA isoforms with 300-nt and 2-kb 3′-UTRs. We show that both CTR2 mRNA isoforms are differentially regulated by NMD. The regulation of CTR2 mRNA by NMD has physiological consequences, since nmd mutants are more tolerant to toxic levels of copper relative to wild-type yeast cells and the copper tolerance of nmd mutants is dependent on the presence of CTR2.

mRNAs involved in copper homeostasis are regulated by the nonsense-mediated mRNA decay pathway depending on environmental conditions

“…Transcripts that vary in the 3 0 -UTR length can be produced as a result of alternative 3 0 -end processing (Deliz-Aguirre et al, 2011;Guisbert et al, 2007;Kebaara and Atkin, 2009;Pelechano et al, 2013). Additionally, mRNA 3 0 -end processing is sometimes sensitive to growth conditions, and differing conditions can produce mRNA isoforms of different lengths (Kim Guisbert et al, 2007).…”

“…PTCs can arise as a result of improper pre-mRNA processing or random mutations. NMD also has other roles and has been shown to degrade many natural transcripts (Deliz-Aguirre et al, 2011;Guan et al, 2006;He et al, 2003;Johansson et al, 2007;Kebaara and Atkin, 2009;Lelivelt and Culbertson, 1999). The extent and reason for the targeting of most of these natural mRNAs is generally unknown.…”

“…In S. cerevisiae, mRNA 3 0 -UTRs are fairly short and typically range in size from 50 to 200 nts with a median size of $121 nts (Graber et al, 2002). In general, mRNAs with 3 0 -UTRs that are 350 nt or longer are considered atypically long and are likely to be regulated by NMD (Deliz-Aguirre et al, 2011;Kebaara and Atkin, 2009).…”

“…These features include mRNAs subject to leaky ribosomal scanning (Welch and Jacobson, 1999), a translated upstream open reading frame (uORF) (Gaba et al, 2005), À1 ribosomal frameshifts (into an alternative reading frame) (Belew et al, 2011(Belew et al, , 2014, inefficiently spliced pre-mRNAs (He et al, 1993), and mRNAs with atypically long 3 0 -untranslated regions (UTRs) (Deliz-Aguirre et al, 2011;Kebaara and Atkin, 2009;Parker, 2012;Peccarelli and Kebaara, 2014b;Rebbapragada and Lykke-Andersen, 2009;Schweingruber et al, 2013). One specific targeting mechanism of interest is the presence of a long 3 0 -UTR on an mRNA (Deliz-Aguirre et al, 2011;Kebaara and Atkin, 2009;Rebbapragada and Lykke-Andersen, 2009). In S. cerevisiae, mRNA 3 0 -UTRs are fairly short and typically range in size from 50 to 200 nts with a median size of $121 nts (Graber et al, 2002).…”

Regulation of Natural mRNAs by the Nonsense-Mediated mRNA Decay Pathway

“…In S. cerevisiae, mRNA 3= UTRs range in size from 50 to 200 nt in length, with a median length of 121 nt (69). The majority of the examined transcripts with 3= UTRs of 350 nt or longer are degraded by the NMD pathway (4,70). Interestingly, some mRNAs produce different isoforms of the same transcript that vary in their 3= UTR lengths.…”