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The DEAD-box family of RNA helicases is the largest of all known RNA helicase families, where they restructure RNA by binding and unwinding the RNA double helix via an ATP-energy-dependent mechanism. Lacking translocation capability, i.e., the ability to ‘walk’ down the RNA strand, these helicases are known to unwind only a limited amount, < 10-20 RNA bases, locally nearby the site of binding. However, some DEAD-box RNA helicases have recently been shown to unwind efficiently upon oligomerization, i.e., multiple proteins joining forces to work together. The DEAD-box RNA helicase Ded1p has been observed to efficiently unwind RNA possessing a single-stranded RNA (ssRNA) tail as a trimer (i.e., an assembly of three identical Ded1p proteins). The mechanism of Ded1p trimer assembly and unwinding of RNA remains unknown. Using optical tweezers, it is possible to grab and stretch single nucleic acid strand and observe the activity of individual protein molecular machines like Ded1p in real-time. Here, we combined single-molecule fluorescence spectroscopy with high-resolution optical tweezers to directly observe the detailed step-by-step binding and dissociation of Ded1p proteins and subsequent unwinding and rezipping of RNA. The overall trimer activity previously observed in ensemble experiments was recapitulated. A complete general model of unwinding is developed whereby unwinding is initiated by binding of a single Ded1p to the duplex adjacent ssRNA tail. Subsequently, in sequence two additional Ded1p bind and unwind a 5-7 bp portion of the duplex each resulting in the full 16 bp duplex unwinding. The reaction is highly dynamic and stochastic, with unwinding combining with frequent rezipping reversals. Rezipping reversals are suppressed when ATP hydrolysis is suppressed via use of an ATP analog. While unwinding and rezipping are easily captured by high-resolution tweezers, Ded1p binding and dissociation on ssRNA tail was measured via the protein-induced-fluorescence-enhancement (PIFE) signal from the fluorophore-labeled tail. The combined methods allowed us to fully observe the coordinated binding and unwinding of the RNA substrate by individual protomers of the Ded1p trimer.
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