The RNA : Terminator K. Arnold, J. David, J Diez, S. Franczak, A. Griffith-Topps, C. Kuehn, C. Lois,, M. Pitts, C. Sargent, L. Schraufnagel, T. Siy, S. Strandberg, C. Strother, J. Strother, S. Urban Teachers: S Strandberg, S Fleischmann Mentor: Mark T. McNally, PhD, Medical College of Wisconsin

The Exosome and RNA Degradation Exosome Molecular Structure Evolutionary Significance

In addition to transcription, the steady state levels of RNA within a cell Figure 2. RNA Exosome based on 41FD.pdb. Since this machine is found are also determined by RNA degradation. RNA degradation also serves in all living organisms on earth, it to remove defective that might be toxic or lead to production of must be of great importance, which toxic . The RNA exosome is a multicomponent molecular is reflected in similar structure and machine with many functions in trimming and degradation of mRNA. function. The machine has RNA degradation is a natural process in all branches of life and plays a maintained a generally similar prominent role in regulating protein abundance. structure over time with minor The Rrp4 cap (pink) contains an modifications as organisms have The minimal exosome is made up of eleven proteins that form three active site consisting of Arg 110, Arg become more complex. The overall domains. The cap protein, Rrp4, contains an active site that 123, Phe 177, and Asp 179 that prokaryotic exosomes have the unwinds the RNA (yellow). unfolds RNA into single strands. The cap pulls in a single strand of RNA barrel, which has RNase activity, and feeds it into a six-protein core, which directs the strand into the The core consists of six and may have a cap-like structure Rrp44 protein (also called DIS3) at the bottom where the RNA is proteins (blue) that the (a,b). Archaeal exosomes degraded by RNB RNase domain from the 3’-to-5’ direction. A host of RNA travels through. resemble bacterial complexes (c). ‘add-on’ proteins give unique activities to the exosome in the nucleus display the basic and . Structures from , archea, and eukaryotes exosome structure, including the reveal evolutionary conservation of this important machine. The Rrp44 protein (purple), cap and barrel, but the barrel includes an RNase active proteins are inactive; additional In humans, exosome variants may also site containing the amino proteins (e.g., Rrp44) act as the acids Arg 847 and Tyr 595. predispose people to like RNase. Therefore, the multiple myeloma, as exosome mutations preservation of the basic exosome are recurrent in these patients. Thus, the structure over time reveals the understanding of how these mutations essential function of the exosome influence exosome structure and function Figure 3. At right, an illustration of the RNA complex. would be beneficial and may lead to path through the exosome and the protein– Figure 4. The RNA exosome RNA interactions within the structure. Polar exists in all organisms with slight treatments for these cancers. interactions are illustrated by dotted lines, and evolutionary differences. stacking interactions with thick black lines. From Januszyk and Lima, 2014. Figure 1. An illustration of the structure of the From Makino et al., 2013 RNA exosome. From Robinson et al., 2015 Conclusion

RNA Must Traverse the Entire Exosome to be Degraded The RNA exosome degrades mRNA as a means of regulating protein production and preventing potentially Figure 5. A. Experiment from Makino et al. 2013 that shows B fatal results. Further research may find a link between the RNA must be unwound and travel to the RNase domain A exosome mutational malfunctions and excessive production at the bottom of the exosome to be efficiently degraded. The of proteins such as human growth hormones, which may indicated RNAs were added to purified exosomes for various times, and RNA was visualized by gel electrophoresis. B. cause uncontrolled cell division and consequent cancers. Cartoon summarizing the data in A. Single stranded (ss)27 is long enough to reach the RNase and is efficiently degraded, whereas short RNAs (A10, 15) are not. A20, which is just References long enough to traverse the exosome, is modestly degraded, Primary Citation: but longer RNAs (A26 and A35) are pulled out of the dsRNA Makino, Baumgartner, and Conti. Crystal Structure of an RNA-bound 11-subunit Eukaryotic Exosome Complex. and degraded. If the exosome could not unwind (or ‘reel in’) 2013. Nature 495:70-75. the RNA, the RNA would not degrade since the dsRNA part Januszyk and Lima. The Eukaryotic RNA Exosome. 2014. Current Opinion in Structural 24:132-40. at the top would prevent ‘reeling in’. Because A26 is Robinson, Oliver, Chevassut, and Newbury. The 3' to 5' DIS3: From Structure and degraded, it must be pulled out of the double strand. Mechanisms to Biological Functions and Role in Human Disease. 2015. Biomolecules 5:1515-1539.

The MSOE Center for BioMolecular Modeling would like to acknowledge and thank the National Institutes of Health Science Education Partnership Award (NIH-SEPA 1R25OD010505-01) and the National Institutes of Health Clinical and Translational Science Award (NIH-CTSA UL1TR001436) for their support in funding the 2016-2017 SMART Team program.