Killing the messenger: new insights into nonsense-mediated mRNA decay Peter H. Byers J Clin Invest. 2002;109(1):3-6. https://doi.org/10.1172/JCI14841. Spotlight Nonsense-mediated mRNA decay (NMD) is one of many quality control mechanisms developed by cells to maintain the metabolic status quo. The cell’s objective in this case is to destroy mRNA species that contain premature termination codons (PTCs) so that only full-length proteins are produced. Targeted destruction of proteins that misfold as a result of missense mutations (those that result in substitution for amino acids in the protein) and NMD are ancient and evolutionarily conserved strategies to protect the cell from mutations (or errors in transcription) that could yield truncated, potentially hazardous proteins. Eukaryotes as diverse as yeast, Caenorhabditis elegans, and humans employ a limited and overlapping array of proteins that cooperate to destroy mRNA species harboring PTCs. The site of mRNA destruction and the mechanisms by which the cell recognizes premature, as opposed to the constitutive, termination codons have been the objects of intense scrutiny and continuing debate over the last decade and a half. In that time, seven C. elegans genes have been identified that are essential for NMD (named smg-1 through smg-7). Three of these have yeast homologs and the same three genes have human homologs, although the human repertoire is larger than that in yeast (Table 1) as a result of gene duplication. Some additional genes have been identified in yeast as involved in the NMD pathway, […] Find the latest version: https://jci.me/14841/pdf SPOTLIGHT Critical review Killing the messenger: new insights missense mutations (those that result in substitution into nonsense-mediated mRNA decay for amino acids in the protein) and NMD are ancient and evolutionarily conserved strategies to protect the cell from mutations (or errors in transcription) that Peter H. Byers could yield truncated, potentially hazardous pro- teins. Eukaryotes as diverse as yeast, Caenorhabditis ele- Departments of Pathology and Medicine, University of Washington, gans, and humans employ a limited and overlapping Seattle, Washington, USA array of proteins that cooperate to destroy mRNA Address correspondence to: Peter H. Byers, Department of Pathology, species harboring PTCs. Box 357470, University of Washington, Seattle, The site of mRNA destruction and the mechanisms Washington 98195-7470, USA. by which the cell recognizes premature, as opposed to Phone: (206) 543-4206; Fax: (206) 616-1899; the constitutive, termination codons have been the E-mail: [email protected]. objects of intense scrutiny and continuing debate over J. Clin. Invest. 109:3–6 (2002). DOI:10.1172/JCI200214841. the last decade and a half. In that time, seven C. elegans genes have been identified that are essential for NMD (named smg-1 through smg-7). Three of these have Nonsense-mediated mRNA decay (NMD) is one of yeast homologs and the same three genes have human many quality control mechanisms developed by cells homologs, although the human repertoire is larger to maintain the metabolic status quo. The cell’s than that in yeast (Table 1) as a result of gene dupli- objective in this case is to destroy mRNA species that cation. Some additional genes have been identified in contain premature termination codons (PTCs) so yeast as involved in the NMD pathway, but their that only full-length proteins are produced. Targeted homologs in mammalian cells and C. elegans have not destruction of proteins that misfold as a result of been extensively explored (see Table 1). Table 1 Nonsense-mediated decay genes and their chromosomal location, putative function, and homologies to yeast and worm genes Human gene Putative function S. cerevisiae gene C. elegans gene GenBank accession no.A GenBank accession no. GenBank accession no. SMG-1–like Phosphatidylinositol 3-kinase–like Not identified smg-1 AB061371 AF149821 RENT-1, hUPF1 RNA helicase, RNA-dependent ATPase, upf1 smg-2 XM_051416 RNA-binding protein YSCUPF1 AF074017 RENT-2, hUPF2 Acidic 127-kDa protein that shares homology and upf2/nmd2 smg-3 XM_018031 motifs with eIF4G and a cap-binding protein (CBP80) SCU14974 AF074017 hUPF3AB Basic 45-kDa protein with nuclear localization and upf3 smg-4 XM_058893 nuclear export sequences L41153 CAA94820 No human homolog No structural elements identified in C. elegans sequence No apparent yeast homolog smg-5 identified U64441 No human homolog No apparent yeast homolog smg-6 identified Mapped; sequence not available in WormBaseC No human homolog No apparent yeast homolog smg-7 identified Not identified in WormBase Y14 (RBM8A) mRNA export factor has an RNA-binding domain yralp Not identified in WormBase AF299118 U72633 ALY/REF RNA-binding protein Not identified Not identified in WormBase AF047002 Not identified in Has a “nudix” domain common in many proteins that nmd1 Not identified human ESTs interact with other proteins U31377 CGI-07 No specific protein motifs found nmd3 Hypothetical protein T25G3.3 BC013317 U31376 Shares homology with Nuclear poly-A–binding protein hrp1/nab4 No specific transcript identified many human sequences U38535/U35737 in WormBase AWhen the accession numbers are entered at the National Center for Biotechnology Information home site (http://www.ncbi.nlm.nih.gov/) they will provide direct links to nucleotide and protein sequences as well as references to the identification of these genes. BUPF3B (XM_016123) and UPF3X (NM_023010) appear to represent two additional copies of the UPF3 gene. How they differ in function from the UPF3A gene and transcript is not understood. CThe web address for WormBase, the database for C. elegans genome information, is http://www.wormbase.org/. EST, expressed sequence tag. The Journal of Clinical Investigation | January 2002 | Volume 109 | Number 1 3 Cellular recognition of PTCs difference in mechanism between yeast NMD and the Termination codons can arise by mutations within a process in mammalian cells is the relation to splicing. In coding sequence in several different ways. The first and the yeast S. cerevisiae, which has few intron-containing simplest is the introduction of a nonsense mutation, in genes, the presence of a downstream element in the 3′- which a sense codon undergoes a single base pair sub- untranslated region is used to “mark” the correct termi- stitution to yield a TAG, TAA, or TGA termination nation codon. This led to models in which a “mark” codon. Second, insertion or deletion of a number of appears within the processed spliced mRNA in mam- nucleotides not divisible by 3 will create a frame shift in malian cells, presumably in the aftermath of splicing. the coding sequence and, on average, yield a new stop codon within 20 downstream codons. Such frame shifts A molecular model for cytoplasmic NMD can arise by insertion or deletion during replication, The emerging picture by which these PTC-containing often in regions of repetitive nucleotides. Alternatively, transcripts are recognized is proving increasingly com- mutations that lead either to the use of cryptic splice plex and interesting. Although textbooks often depict sites or to exon-skipping will result in frame shifts in precursor mRNA molecules and mRNA molecules as many instances. Finally, intron inclusion, depending on lonely travelers in a complex nucleus, this image could the size of the intron, is very likely to result in either a hardly be farther from the truth. From the moment of frame shift or the introduction of a PTC. transcriptional initiation, the mRNAs in the nucleus In Saccharomyces cerevisiae, NMD appears to occur are in the company of numerous proteins. Soon after exclusively in the cytoplasm. The site of NMD in mam- transcription is completed, the 5′ end of the nascent malian cells remains an open question, with evidence mRNA is modified (“capped”), and a protein complex that supports both a nuclear and a cytoplasmic loca- associates with the newly capped end of the molecule. tion. Indeed, it may well be that recognition and In the cytoplasm, translational initiation and decap- destruction occur in both locales. But the enduring ping reactions compete for the site, to determine question remains: How are the interloper PTCs recog- whether protein synthesis or mRNA degradation car- nized by the cell so that the mRNA can be targeted for ries the day. Mature mRNA species in the nucleus are destruction? For a long time it has been argued that the also protected from decapping, although the mecha- cell really has only a single system capable of sensing in- nism for this protection is likely to be distinct from frame stop codons — translation. So, the argument con- that which occurs in the cytoplasm. If, as is generally tinues, recognition of the abnormal mRNA species assumed, translational initiation occurs solely in the must occur in the context of translation and, thus, cytoplasm, or even if a single round of pioneer transla- ought to be localized to the cytoplasm, the universally tion occurs within this compartment, it is unlikely that acknowledged site of translation. As a compromise posi- initiation complexes would be sufficiently abundant to tion, the nuclear pore — the site of exit of the mRNA protect the 5′ end of mRNAs from degradation. from the nucleus — might allow recognition and The next set of events for most transcripts involves destruction by anchoring ribosomes in the local region splicing, the removal of intervening sequences (introns) and subjecting mRNA to degradation as it leaves the from between the coding domains (exons). Intron nucleus. Yet, there is clear evidence that at least some removal is orderly but not processive; introns are mRNA species that house PTCs do not exit the nucleus removed from a given pre-mRNA species in a charac- (1). Two recently published papers that propose that teristic but not invariant order, which, in large genes, translation of some mRNA species occurs in the nucle- does not correspond to simple progression from 5′ to us (2, 3) provide one interesting resolution to this dilem- 3′ (although, in general the 5′-end introns are processed ma by allowing a “pioneer” round of translation (that is, prior to those at the 3′ end).