When core competence is not enough: functional interplay of the DEAD-box helicase core with ancillary domains and auxiliary factors in RNA binding and unwinding

Abstract

DEAD-box helicases catalyze RNA duplex unwinding in an ATP-dependent reaction. Members of the DEAD-box helicase family consist of a common helicase core formed by two RecA-like domains. According to the current mechanistic model for DEAD-box mediated RNA unwinding, binding of RNA and ATP triggers a conformational change of the helicase core, and leads to formation of a compact, closed state. In the closed conformation, the two parts of the active site for ATP hydrolysis and of the RNA binding site, residing on the two RecA domains, become aligned. Closing of the helicase core is coupled to a deformation of the RNA backbone and destabilization of the RNA duplex, allowing for dissociation of one of the strands. The second strand remains bound to the helicase core until ATP hydrolysis and product release lead to re-opening of the core. The concomitant disruption of the RNA binding site causes dissociation of the second strand. The activity of the helicase core can be modulated by interaction partners, and by flanking N-and C-terminal domains. A number of C-terminal flanking regions have been implicated in RNA binding: RNA recognition motifs (RRM) typically mediate sequence-specific RNA binding, whereas positively charged, unstructured regions provide binding sites for structured RNA, without sequence-specificity. Interaction partners modulate RNA binding to the core, or bind to RNA regions emanating from the core. The functional interplay of the helicase core and ancillary domains or interaction partners in RNA binding and unwinding is not entirely understood. This review summarizes our current knowledge on RNA binding to the DEAD-box helicase core and the roles of ancillary domains and interaction partners in RNA binding and unwinding by DEAD-box proteins.

Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin

“…ATP promotes high RNA-binding affinity by DEAD-box proteins [38]. The population effects seen in our smFRET studies suggest that Yra1 may decrease the affinity of Dbp2 for RNA, similar to the absence of ATP.…”

The DDX5/Dbp2 subfamily of DEAD‐box RNA helicases

“…DEAD‐box proteins, on the other hand, do not unwind in a translocation‐based fashion, but rather load directly onto the duplex region and separate the two strands (Q. Yang & Jankowsky, ; Yang, Del Campo, Lambowitz, & Jankowsky, ). This is possible because DEAD‐box proteins can disrupt RNA duplexes locally by bending one of the RNA strands (Rudolph & Klostermeier, ).…”

“…Multiple X‐ray crystallographic studies of DEAD‐box helicases have demonstrated that DEAD‐box proteins contain a structurally conserved helicase core that consists of two globular RecA‐like domains (RecA_N and RecA_C) (Andersen et al, ; Del Campo & Lambowitz, ; Rudolph & Klostermeier, ; Sengoku, Nureki, Nakamura, Kobayashi, & Yokoyama, ; von Moeller, Basquin, & Conti, ). The two domains are connected by a flexible linker to form a characteristic “dumbbell‐like” core.…”

Allosteric regulation of helicase core activities of the DEAD-box helicase YxiN by RNA binding to its RNA recognition motif

“…RNA binding domains may anchor helicases on their target RNAs (18). Yet it is unknown if they act as passive anchors or actively present the bound RNA to the helicase core for unwinding (see (23)). Specifically, it has not been studied if these domains move with respect to the helicase core upon RNA binding, and how RNA binding to the ancillary domain may be communicated to the helicase core.…”