Academic journal article Genetics

Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors through 3'UTR Introns

Academic journal article Genetics

Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors through 3'UTR Introns

Article excerpt

THE nonsense-mediated mRNA decay (NMD) pathway targets mRNA for degradation through the recognition of translated termination codons determined to be premature (Nicholson et al. 2009; Kervestin and Jacobson 2012; Popp and Maquat 2013). The NMD pathway can degrade mRNAs that contain upstream open reading frames (uORFs) or long 39-UTRs. The termination-related processes that trigger uORFmediated or long 39-UTR-mediatedNMDareconsideredtobe similar (Amrani et al. 2004, 2006; Nicholson et al. 2009) in that termination events occurring far from the context created by the mRNA poly(A) tail can result in mRNA degradation (the "faux-UTR" model). In higher eukaryotes, NMD can also act on mRNAs that contain an intron downstream of a termination codon, such as aberrantly spliced transcripts or 39-UTR introncontaining transcripts (Sauliere et al. 2010; Bicknell et al. 2012). When a spliced intron is positioned at least 50-55 nt downstream of a termination codon, the exon junction complex (EJC) positioned near the exon-exon junction is not displaced by translating ribosomes and its continued association with mRNA targets the mRNA for degradation by NMD (Isken and Maquat 2007). While there are some shared factors, such as the UPF factors, this branch of NMD appears distinct from the faux-UTR branch in that, for NMD to occur, it requires an EJC to remain on the mRNA downstream from the termination event that triggers NMD.

In mammals, the nuclear cap-binding complex (CBC), which is composed of CBP80 and CBP20, is preferentially associated with mRNAs undergoing EJC-targeted NMD (Ishigaki et al. 2001). This has led to a model in which EJC-mediated targeting of mRNAs for NMD occurs during pioneer rounds of translation. During these pioneer rounds, CBC has not yet been replaced by eIF4E, the cytoplasmic cap-binding protein (Maquat et al. 2010). The implication of these studies was that the CBC must also be associated with the mRNA for EJC-mediated NMD to occur. However, more recent data show that EJC-mediated NMD can occur on mRNAs associated with the cytoplasmic cap-binding factor eIF4E (Durand and Lykke-Andersen 2013; Rufener and Muhlemann 2013; Popp and Maquat 2014), and the role of the CBC in NMD, and even whether it is essential for this process (Hosoda et al. 2005; Dzikiewicz-Krawczyk et al. 2008), is not fully understood.

EJC-mediated NMD has been observed in animals and plants, but in the budding yeast Saccharomyces cerevisiae, multiple components of the EJC, and EJC-mediated NMD, are lacking, and in fission yeast Schizosaccharomyces pombe, while EJC components are present, a role for them in determining mRNA stability via NMD-related pathways has not been demonstrated (Wen and Brogna 2010). Thus a comprehensive understanding of the evolutionary significance of EJC and CBC factors in NMD and the means to dissect the functions of the EJC and CBC factors that contribute to NMD in highly tractable model fungal systems remain lacking.

The filamentous fungi generally encode NMD and EJC machinery (Feldbrugge et al. 2008). In Aspergillus nidulans,arolefornmdA,theupf2 homolog, has been identified in the control of mRNA stability (Morozov et al. 2006) and the recognition of premature stop codons through upf1 is associated with additional processes affecting mRNA degradation (Morozov et al. 2012). The genome of the model filamentous fungus Neurospora crassa contains homologs of the NMD components UPF1, UPF2, and UPF3, the core EJC components eIF4A3, Mago, and Y14, and CBC components CBP20 and CBP80. A role for upf1 in N. crassa biology is indicated by identification of alleles causing a circadian rhythm defect (Compton 2003). The molecular basis for this circadian defect-a short period-is not known.

Measurement of mRNA stability is critical for determining whether NMD, EJC, or CBC mutations directly or indirectly affect mRNA levels. Metabolic labeling with 4-thiouracil (4TU) can be used to examine mRNA half-life (Cleary et al. …

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