The essential RNA helicase, Mtr4, performs a critical role in RNA processing and degradation as an activator of the nuclear exosome. The molecular basis for this vital function is not understood and detailed analysis is significantly limited by the lack of structural data. In this study, we present the crystal structure of Mtr4. The structure reveals a new arch-like domain that is specific to Mtr4 and Ski2 (the cytosolic homologue of Mtr4). In vivo and in vitro analyses demonstrate that the Mtr4 arch domain is required for proper 5.8S rRNA processing, and suggest that the arch functions independently of canonical helicase activity. In addition, extensive conservation along the face of the putative RNA exit site highlights a potential interface with the exosome. These studies provide a molecular framework for understanding fundamental aspects of helicase function in exosome activation, and more broadly define the molecular architecture of Ski2-like helicases.

Nonstop decay is the mechanism of identifying and disposing aberrant transcripts that lack in‐frame stop codons. It is hypothesized that these transcripts are identified during translation when the ribosome arrives at the 3′ end of the mRNA and stalls. Presumably, the ribosome stalling recruits additional cofactors, Ski7 and the exosome complex. The exosome degrades the transcript using either one of its ribonucleolytic activities, and the ribosome and the peptide are both released. Additional precautionary measures by the nonstop decay pathway may include translational repression of the nonstop transcript after translation, and proteolysis of the released peptide by the proteasome. This surveillance mechanism protects the cells from potentially harmful truncated proteins, but it may also be involved in mediating critical cellular functions of transcripts that are prone to stop codon read‐through. Important advances have been made in the past decade as we learn that nonstop decay may have implications in human disease. WIREs RNA 2012 doi: 10.1002/wrna.1124 This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms

The exosome consists of a core of ten essential proteins that includes the ribonuclease Rrp44p and is present in both the cytoplasm and nucleus of eukaryotic cells. The cytoplasmic exosome has been extensively characterized in the budding yeast Saccharomyces cerevisiae and some characterization of its metazoan counterpart indicates that most functional aspects are conserved. These studies have implicated the cytoplasmic exosome in the turnover of normal cellular mRNAs, as well as several mRNA surveillance pathways. For this, the exosome needs a set of four proteins that do not partake in nuclear exosome functions. These cofactors presumably direct the exosome to specific cytoplasmic RNA substrates. Here, we review cofactors and functions of the cytoplasmic exosome and provide unanswered questions on the mechanisms of cytoplasmic exosome function.

The RNA exosome is responsible for a wide variety of RNA processing and degradation reactions. The activity and specificity of the RNA exosome is thought to be controlled by a number of cofactors. Mtr4 is an essential RNA-dependent adenosine triphosphatase that is required for all of the nuclear functions of the RNA exosome. The crystal structure of Mtr4 uncovered a domain that is conserved in the RNA exosome cofactors Mtr4 and Ski2 but not in other helicases, suggesting it has an important role related to exosome activation. Rrp6 provides the nuclear exosome with one of its three nuclease activities, and previous findings suggested that the arch domain is specifically required for Rrp6 functions. Here, we report that the genetic interactions between the arch domain of Mtr4 and Rrp6 cannot be explained by the arch domain solely acting in Rrp6-dependent processing reactions. Specifically, we show that the arch domain is not required for all Rrp6 functions, and that the arch domain also functions independently of Rrp6. Finally, we show that the arch domain of Ski2, the cytoplasmic counterpart of Mtr4, is required for Ski2’s function, thereby confirming that the arch domains of these cofactors function independently of Rrp6.