Skip to Main Content
 

Global Search Box

 
 
 
 

Files

File List


A. Axhemi ETD.pdf (5.91 MB)

ETD Abstract Container

Abstract Header

Synergy Between the Exoribonucleases Rrp6p and Rrp44p in the Nuclear Exosome Complex

Axhemi, Armend
http://rave.ohiolink.edu/etdc/view?acc_num=case1586282591705441

Abstract Details

2020, Doctor of Philosophy, Case Western Reserve University, Biochemistry.
The 11-component nuclear exosome (Exo11) plays an essential role in eukaryotic RNA metabolism by degrading or processing nearly all classes of RNA in a 3’ to 5’ direction. Exo11 contains two exonucleases, Rrp6p and Rrp44p, which are located at opposite ends of a nine-component inactive core (Exo9). To perform their biological roles, the nucleases target a large number of substrates, but they do not indiscriminately degrade all RNAs. How they accomplish this selectivity was not understood. It was also unclear how Exo9 impacts the activities of nucleases, and how it integrates their activities in the 11-component complex. We measured RNA binding and degradation kinetics of exosome components in vitro at single nucleotide resolution across a diverse array of substrates. We find that Rrp6p is inherently selective. RNA length and the four 3'-terminal nucleotides contribute most to substrate selectivity of Rrp6p and enable it to discriminate between different RNAs by several orders of magnitude. The most pronounced discrimination is seen against RNAs ending with CCA-3' which correspond to 3'-termini of uncharged tRNAs. Rrp6p is processive for longer substrates but becomes distributive for shorter ones. The data also show that in contrast to many other enzymes that use substrate selectivity to preferentially interact with specific RNAs, Rrp6p uses its selectivity to discriminate against specific RNAs. Rrp44p degrades RNA in two phases. Phase one is rate limiting while phase two is fast and processive. Upstream RNA length, sequence and the four 3’-terminal nucleotides contribute to substrate selectivity of Rrp44p. These features enable Rrp44p to discriminate at binding and forward rate constants for both phases of degradation. Exo9 diminishes the activity of Rrp6p for all substrates while its impact on Rrp44p is substrate dependent. Substrate selectivity of both nucleases is left intact in the 10-component complexes. The 11-component complex (Exo11) integrates optimal features of Rrp6p and Rrp44p to create synergy. The affinity of Exo11 for certain RNAs is roughly two orders of magnitude greater than that of its constituent components for same substrates. Our findings indicate that Exo9 plays a critical role in integrating and coordinating activities to create synergy between the two exonucleases.
Eckhard Jankowsky, Ph.D. (Advisor)
Jeff Coller, Ph.D. (Committee Chair)
Blanton Tolbert, Ph.D. (Committee Member)
Derek Taylor, Ph.D. (Committee Member)
174 p.
Biochemistry
Rrp6p, Rrp44p, nuclear exosome, degradation, kinetics

Recommended Citations

Citations

  • Axhemi, A. (2020). Synergy Between the Exoribonucleases Rrp6p and Rrp44p in the Nuclear Exosome Complex [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1586282591705441

    APA Style (7th edition)

  • Axhemi, Armend. Synergy Between the Exoribonucleases Rrp6p and Rrp44p in the Nuclear Exosome Complex. 2020. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1586282591705441.

    MLA Style (8th edition)

  • Axhemi, Armend. "Synergy Between the Exoribonucleases Rrp6p and Rrp44p in the Nuclear Exosome Complex." Doctoral dissertation, Case Western Reserve University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1586282591705441

    Chicago Manual of Style (17th edition)

case1586282591705441
63
© 2020, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.