NDLI: DEAD-box proteins can completely separate an RNA duplex using a single ATP

Content Provider	PubMed Central
Author	Chen, Yingfeng Potratz, Jeffrey P. Tijerina, Pilar Campo, Mark Del Lambowitz, Alan M. Russell, Rick
Abstract	DEAD-box proteins are ubiquitous in RNA metabolism and use ATP to mediate RNA conformational changes. These proteins have been suggested to use a fundamentally different mechanism from the related DNA and RNA helicases, generating local strand separation while remaining tethered through additional interactions with structured RNAs and RNA-protein (RNP) complexes. Here, we provide a critical test of this model by measuring the number of ATP molecules hydrolyzed by DEAD-box proteins as they separate short RNA helices characteristic of structured RNAs (6–11 bp). We show that the DEAD-box protein CYT-19 can achieve complete strand separation using a single ATP, and that 2 related proteins, Mss116p and Ded1p, display similar behavior. Under some conditions, considerably <1 ATP is hydrolyzed per separation event, even though strand separation is strongly dependent on ATP and is not supported by the nucleotide analog AMP-PNP. Thus, ATP strongly enhances strand separation activity even without being hydrolyzed, most likely by eliciting or stabilizing a protein conformation that promotes strand separation, and AMP-PNP does not mimic ATP in this regard. Together, our results show that DEAD-box proteins can disrupt short duplexes by using a single cycle of ATP-dependent conformational changes, strongly supporting and extending models in which DEAD-box proteins perform local rearrangements while remaining tethered to their target RNAs or RNP complexes. This mechanism may underlie the functions of DEAD-box proteins by allowing them to generate local rearrangements without disrupting the global structures of their targets.
Related Links	http://dx.doi.org/10.1073/pnas.0811075106
Ending Page	20208
Page Count	6
Starting Page	20203
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	51
Volume Number	105
Language	English
Publisher	National Academy of Sciences
Publisher Date	2008-12-23
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy

Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase

Structural basis for RNA duplex recognition and unwinding by the DEAD-box helicase Mss116p

Correction for Henn et al., Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA

Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy.

Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity.

Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone

DEAD-box proteins can completely separate an RNA duplex using a single ATP

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