Date of Award:

5-2014

Document Type:

Thesis

Degree Name:

Master of Science (MS)

Department:

Chemistry and Biochemistry

Committee Chair(s)

Sean J. Johnson

Committee

Sean J. Johnson

Committee

Lance C. Seefeldt

Committee

Joan M. Hevel

Abstract

The central dogma states that DNA is transcribed into RNA, which is then translated into protein. This concept conveys a minimal view of the role of RNA, portraying it simply as an intermediary between DNA and protein. However, it is now known that the role of RNA in the cell is critical in regulating protein expression both directly and indirectly. RNA in the cell typically goes through modifications to become active (on) and inactive (off) to eventually become targeted for degradation and start the cycle all over again. The protein complex that regulates the proper maturation and degradation of RNA in the cell is the 3’-5’ RNA degrading exosome complex, composed of 9 subunits and several other associating proteins. One such associating protein that helps activate the exosome is the RNA helicase Mtr4.

Mtr4 unwinds structured RNA to then feed the single-stranded RNA through the exosome for proper trimming or degradation. Mtr4 is an essential protein for cell viability, and if functioning improperly, can result in certain neurological and immune disorders. Understanding how Mtr4 works is important to regulating RNA surveillance and treating the diseases and disorders caused by the presence of improperly functioning protein. In this thesis, a detailed analysis of Mtr4 unwinding and substrate recognition is explored. Additionally, our data show an interesting result in which we have discovered a potential role for the novel arch domain of Mtr4.

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