Date of Award:

5-2014

Document Type:

Thesis

Degree Name:

Master of Science (MS)

Department:

Chemistry and Biochemistry

Advisor/Chair:

Sean J. Johnson

Abstract

There are numerous RNAs transcribed in the cell that are not directly involved in protein translation. Maintaining proper levels of RNA is crucial for cell viability, making RNA surveillance an essential process (equivalent to regulating protein levels). Mtr4 is an essential RNA helicase that activates exosome-mediated 3'-5' turnover in RNA processing mechanisms. Mtr4 has several binding partners, with the most prominent one being the complex Trf4/5-Air1/2-Mtr4 polyadenylating (TRAMP) complex. The polyadenylation and unwinding activity of TRAMP is modulated by a sensing mechanism in Mtr4 that detects both length and identity of 3'-end poly(A) tails. While it has been known that Mtr4 has an unwinding preference for substrates with a 3' poly(A) tail and a length of approximately 5 nucleotides, the mechanistic detail is unclear. It is also unclear what structural features of Mtr4 contribute to this sensing function. By using x-ray crystal structures of Mtr4, a ratchet helix was identified to interact with RNA substrates. Significant conservation of this ratchet helix along the RNA binding path was observed, similar to conservation patterns throughout Ski2-like and DEAH/RHA-box helicases. Structural characterization revealed a novel arch domain shown to bind structured RNAs, which may aid in cooperative RNA recognition in conjunction with the ratchet helix. In this thesis we demonstrate that the conserved residues at the third (R1030) and fourth (E1033) turns of the Mtr4 ratchet helix uniquely influence RNA unwinding rates. Furthermore, when mutated, ratchet helix positions confer slow growth phenotypes to Saccharomyces cerevisiae and are synthetically lethal in an Mtr4-archless background. The unwinding activity of these mutants when in the TRAMP complex alters the unwinding rates of Mtr4, and in some instances recovers substrate specificity. Our findings demonstrate the importance of R1030 and E1033 for helicase activity, and additionally link the arch domain of Mtr4 in essential unwinding events.

Available for download on Sunday, May 01, 2016

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