The dharma of nonsense-mediated mRNA decay in mammalian cells

Abstract

Mammalian-cell messenger RNAs (mRNAs) are generated in the nucleus from precursor RNAs (pre-mRNAs, which often contain one or more introns) that are complexed with an array of incompletely inventoried proteins. During their biogenesis, pre-mRNAs and their derivative mRNAs are subject to extensive cis-modifications. These modifications promote the binding of distinct polypeptides that mediate a diverse array of functions needed for mRNA metabolism, including nuclear export, inspection by the nonsense-mediated mRNA decay (NMD) quality-control machinery, and synthesis of the encoded protein product. Ribonucleoprotein complex (RNP) remodeling through the loss and gain of protein constituents before and after pre-mRNA splicing, during mRNA export, and within the cytoplasm facilitates NMD, ensuring integrity of the transcriptome. Here we review the mRNP rearrangements that culminate in detection and elimination of faulty transcripts by mammalian-cell NMD.

Fig. 1.

Cis-modifications and Select Proteins Bound to mRNAs in the Nucleus versus the Cytoplasm. During transcription in the nucleus, pre-mRNAs are subject to 5′ capping with a 7-methylguanylate residue in 5′-to-5′ linkage to the nascent transcript. This facilitates binding by the cap-binding complex (CBC), which is composed of cap-binding protein 80 (CBP80) and CBP20. Co- and post-transcriptionally, introns are removed and exons are joined together in a process called pre-mRNA splicing. A consequence of splicing is deposition of an exon-junction complex (EJC) ∼24 nucleotides upstream of exon-exon borders. At their 3′ end, transcripts undergo cleavage and polyadenylation, which allows poly(A)-binding protein nuclear 1 (PABPN1) and poly(A)-binding protein cytoplasmic 1 (PABPC1) to bind. This assembled mRNP is exported through the nuclear pore complex into the cytoplasm. Immediately after export, the mRNP is subject to pioneer translation and, during this process, inspection by NMD. The mRNP is further remodeled in processes that either are or are not augmented by translation. Select events include replacement of CBC by eIF4E, which is the cap-binding component of the eIF4F complex; removal of EJCs via ribosome-associated PYM and early rounds of translation; and replacement of PABPN1 by PABPC1, which is likewise augmented by early rounds of translation. NMD takes place during these dynamic events (see Fig. 2). Successful negotiation of NMD spares the remodeled mRNA from degradation and allows it to template protein production. Horizontal red lines, 5′- and 3′- untranslated regions; horizontal red bar, coding region; vertical purple bar, exon-exon junction.

Fig. 2.

Protein rearrangements during mammalian-cell, EJC-mediated NMD. Immediately after nuclear export, CBC-bound templates are subject to pioneer round(s) of translation. If a premature termination codon (PTC) resides ≥ 50–55 nucleotides (nt) upstream of an exon-exon junction that is bound by an EJC, then CBC escorts UPF1–SMG1 to the eRF3 constituent of the eRF1–eRF3 heterodimer in the context of the terminating ribosome, forming the SURF complex (first, top). CBC also escorts UPF1–SMG1 to the EJC, to which UPF2 is bound via UPF3 or UPF3X (second) to form the DECID complex (which may also include eRF1 and eRF3; Kashima et al., 2006). In this configuration, SMG1 phosphorylates various serines and threonines near the N- and C-termini of UPF1 (third), producing hyperphosphorylated UPF1. UPF1 activation via phosphorylation has several functions (fourth, bottom). It induces translational repression, recruits SMG6 (which endonucleolytically cleaves PTC-bearing mRNAs between the PTC and EJC), and recruits SMG5–SMG7 or SMG5–PNRC2, which further recruit decapping and/or deadenylating enzymes, facilitating exonucleolytic degradation of the mRNA. See text for further details.