Characterization of the function of the DEAD-box RNA helicase Dbp2

Wai Kit Ma, Purdue University

Abstract

In eukaryotes, there are highly coupled mechanisms that require RNA-binding proteins to facilitate gene expression. Proper RNA structure and ribonucleoprotein (RNP) complex formation are critical for gene expression. DEAD-box proteins are the largest class of RNA helicases that play fundamental roles in RNA and RNP structure remodeling. However, the precise biological role of the vast majority of the ~ 40 members in this family has not been completely described. Therefore, my research focused on characterizing the role of the DEAD-box RNA helicase Dbp2 during gene expression in S. cerevisiae. To decipher the biological roles of DEAD-box proteins, I first demonstrated that the S. cerevisiae DEAD-box protein Dbp2 is an active RNA dependent ATPase and RNA helicase that unwinds RNA duplexes in vitro. Furthermore, I found that Dbp2 associates with actively transcribing genes via RNA and functions as a co-transcriptional RNA chaperone to promote efficient assembly of the mRNA binding proteins, Yra1, Nab2, and Mex67, onto poly(A)+RNA. This assembly is critical for 3’ end processing and mRNA export. I also showed that Yra1 interacts directly with Dbp2 and inhibits its unwinding activity by reducing single-stranded RNA-binding activity. This inhibition prevents over-accumulation of Dbp2 on mRNA and stabilization of a subset of RNA Pol II transcripts. Collectively, my work shows that Dbp2 is recruited to nascent RNA to unwind aberrant structures and facilitate assembly of RNA-binding proteins, including Yra1, Nab2, and Mex67, during transcription. Yra1 then prevents further cycles of unwinding by inhibiting the ability of Dbp2 to associate with single-stranded RNA. This sequential order of events involving regulation of a DEAD-box RNA helicase is critical for efficient mRNP assembly and proper gene expression. These findings provide ideas on how DEAD-box proteins are regulated and insights on the role of DDX5, which is the human ortholog of Dbp2 and is often overexpressed in cancer cells.

Degree

Ph.D.

Advisors

Tran, Purdue University.

Subject Area

Biochemistry

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