Remodeling of ribonucleoprotein complexes with DExH/D RNA helicases

Abstract

The DExH/D protein family is the largest group of enzymes in eukaryotic RNA metabolism. DExH/D proteins are mainly known for their ability to unwind RNA duplexes in an ATP-dependent fashion. However, it has become clear in recent years that these DExH/D RNA helicases are also involved in the ATP-dependent remodeling of RNA–protein complexes. Here we review recent studies that highlight physiological roles of DExH/D proteins in the displacement of proteins from RNA. We further discuss work with simple RNA–protein complexes in vitro, which illuminates mechanisms by which DExH/D proteins remove proteins from RNA. Although we are only beginning to understand how DExH/D proteins remodel RNA–protein complexes, these studies have shown that an ‘RNA helicase’ does not per se require cofactors to displace proteins from RNA, that protein displacement does not necessarily involve RNA duplex unwinding, and that not all DExH/D proteins are able to disassemble the same range of ribonucleoproteins.

Involvement of DEAD-box Proteins in Group I and Group II Intron Splicing. Biochemical Characterization of Mss116p, ATP Hydrolysis-dependent and -independent Mechanisms, and General RNA Chaperone Activity

“…These characteristics may include: (i) ability to bind RNA and RNP substrates non-specifically; (ii) high on and off rates for RNA binding by the catalytic domain, enabling multiple cycles of activity on the same RNA; (iii) duplex unwinding without preferred polarity and ability to unwind blunt-end substrates, enabling remodeling of diverse substrates and substrate regions; (iv) limited processivity of duplex unwinding and/or an optimal balance between duplex-unwinding and strand-annealing activities to avoid over disruption of RNA structure; and (v) ability to displace or remodel incorrectly bound proteins from RNP complexes. 43,44 Finally, our findings show that while CYT-19, Mss116p, and Ded1p all have RNA chaperone activity, they differ in their ability to promote the splicing of different group I and group II intron RNAs. These differences likely reflect that the balance of RNA-binding, duplexunwinding, and strand-annealing activities has been tuned by coevolution to function optimally only on specific RNA substrates.…”

From unwinding to clamping — the DEAD box RNA helicase family

“…Moreover, proteins can be displaced from structured and from unstructured RNA, suggesting that duplex unwinding is not required for release 49 . In accordance with a non-processive activit y of DEAD box proteins, protein displacement has been directly observed for proteins with a footprint of fewer than eight nucleotides [49][50][51][52] . Proteins with larger footprints cannot be displaced by DEAD box proteins, whereas other helicases readily remove such proteins 49,53 .…”

“…In addition to ATPdependent RNA unwinding and clamping, DEAD box proteins can remove proteins from RNA in an ATPdriven reaction, as has been suggested for the removal of yeast Mud2 by the DEAD box protein Sub2 during pre-mRNA splicing and for the removal of mRNA export factor 67 (Mex67) during mRNA export by DEAD box protein 5 (Dbp5) [47][48][49][50][51][52] . Moreover, proteins can be displaced from structured and from unstructured RNA, suggesting that duplex unwinding is not required for release 49 .…”

“…Although it is not known whether protein removal and duplex unwinding by DEAD box proteins rely on identical mechanisms, observations are consistent with a displacement mode that is not based on translocation of the DEAD box protein 50 . The inability to displace a certain set of proteins from RNA might be important for limiting RNA remodelling activity of DEAD box helicases in the cell to avoid complete dissociation of RNP complexes 52 .…”

The LOTUS domain is a conserved DEAD-box RNA helicase regulator essential for the recruitment of Vasa to the germ plasm and nuage

“…The core of DEAD-box RNA helicases is formed by two highly conserved RecA-like domains, often flanked by helicase-specific N-terminal and C-terminal extensions (Jankowsky and Fairman 2007). DEAD-box proteins can bind RNA in an ATP-driven manner and have been shown to separate short RNA duplexes and displace proteins from ssRNA (Jankowsky and Bowers 2006;Jankowsky and Putnam 2010). Within cells, most DEADbox proteins do not function in isolation but are part of larger multicomponent assemblies in which they catalyze remodeling of higher-order ribonucleoprotein (RNP) complexes (Linder and Jankowsky 2011;Jarmoskaite and Russell 2014).…”