DDX3X and DDX3Y constitutively form nano-sized RNA-protein clusters that foster enzymatic activity

Yanas, A.; Him, S.; Owens, M. C.; Liu, K. F.; Goldman, Y. E.

doi:10.1101/2023.11.29.569239

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bioRxiv · 10.1101/2023.11.29.569239

DDX3X and DDX3Y constitutively form nano-sized RNA-protein clusters that foster enzymatic activity

Yanas, A.·Him, S.·Owens, M. C.·Liu, K. F.·Goldman, Y. E.

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Abstract

DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous RNA helicases, DDX3X and DDX3Y, form nano-sized RNA-protein clusters (RPCs) that foster their catalytic activities in vitro and in cells. The IDRs are critical for the formation of these RPCs. A thorough analysis of the catalytic cycle of DDX3X and DDX3Y by ensemble biochemistry and single molecule photon bursts in the confocal microscope showed that RNA release is a major step that differentiates the unwinding activities of DDX3X and DDX3Y. Our findings provide new insights that the nano-sized helicase RPCs may be the normal state of these helicases under non-stressed conditions that promote their RNA unwinding and act as nucleation points for liquid-liquid phase separation under stress. This mechanism may apply broadly among other members of the DEAD-box helicase family.

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Yanas, A., Him, S., Owens, M. C., Liu, K. F., Goldman, Y. E.. 2023-11-29. DDX3X and DDX3Y constitutively form nano-sized RNA-protein clusters that foster enzymatic activity. https://doi.org/10.1101/2023.11.29.569239

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