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MECHANISM OF RNA REMODELING BY DEAD-BOX HELICASES

Yang, Quansheng
http://rave.ohiolink.edu/etdc/view?acc_num=case1173812791

Abstract Details

2007, Doctor of Philosophy, Case Western Reserve University, Biochemistry.
DEAD-box proteins remodel RNA duplexes and displace proteins from RNA in an ATP-dependent fashion. To understand how DEAD-box proteins remodel duplex RNA, I studied the mechanism of RNA remodeling by the DEAD-box protein Ded1 from S.cerevisiae. I found that Ded1 promotes not only RNA unwinding but also strand annealing. Ded1 establishes an ATP-dependent steady state between unwinding and annealing, which allows the enzyme to modulate the balance between the two opposing activities through ATP and ADP. By coordinating its unwinding and annealing activities, Ded1 can convert RNA structures via two distinct pathways. One pathway depends on ATP hydrolysis and represents a kinetically controlled steady state between the RNA structures that involves the complete disassembly of the RNA structures. This pathway allows the formation of less stable RNA structures from more stable ones and thus facilitates the distribution of RNA structures against thermodynamic equilibrium values. The other pathway is ATP independent and involves stabilization of a multipartite intermediate by Ded1. These results provide a basic mechanistic framework for a protein-assisted RNA conversion that illuminates the role of ATP hydrolysis and an unexpected diversity of pathways. I also discovered that Ded1 unwinds duplex RNA with a mechanism distinct from “traditional” DNA helicases and some viral RNA helicases. These “traditional” helicases unwind duplexes by first loading them to one of the two nucleic acid strands, mostly at a single stranded region, and then by translocating on this strand in a unidirectional fashion, thereby removing complementary strand. Ded1 does not unwind duplexes by translocating on a single stranded. Instead, a single stranded RNA loads Ded1 to the duplex region, where strand separation is initiated directly. I also showed that the DEAD-box proteins Ded1 and Mss116 from S.cerevisiae can initiate duplex unwinding from internal positions of the duplex region. This new type of helicase activity explains puzzling observations with many other DEAD-box proteins and may be the prototype for duplex-unwinding reactions in RNA metabolism.
Eckhard Jankowsky (Advisor)
Biology, Molecular
RNA helicases; DEAD-box proteins; Unwinding; Annealing; Structure conversion

Recommended Citations

Citations

  • Yang, Q. (2007). MECHANISM OF RNA REMODELING BY DEAD-BOX HELICASES [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1173812791

    APA Style (7th edition)

  • Yang, Quansheng. MECHANISM OF RNA REMODELING BY DEAD-BOX HELICASES. 2007. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1173812791.

    MLA Style (8th edition)

  • Yang, Quansheng. "MECHANISM OF RNA REMODELING BY DEAD-BOX HELICASES." Doctoral dissertation, Case Western Reserve University, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=case1173812791

    Chicago Manual of Style (17th edition)

case1173812791
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© 2007, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.