Biology subjects

Ohtake, F.

Publications and source records attributed to Ohtake, F..

2 recordsLinked to original sources

bioRxiv2026

UFD1 Recognition of Initiator and Proximal Ubiquitin Drives p97-Mediated Substrate Unfolding enhanced by FAF1, FAF2, and UBXD7

The AAA-ATPase p97 and its primary adaptor UFD1-NPL4 (UN) unfold ubiquitinated substrates for their proteasomal degradation. Although cryo-EM has shown that substrate processing begins with unfolding of the initiator ubiquitin and its capture by NPL4, the specific contribution of UFD1 to K48-linked ubiquitin chain engagement has not been fully defined. Here we report a 1.31 [A] crystal structure of the human UFD1-UT3 bound to a K48-linked di-ubiquitin mimic, revealing that UFD1-UT3 engages the unfolded initiator ubiquitin via its Nc subdomain and the proximal ubiquitin via its Nn subdomain. AlphaFold3-guided analyses further demonstrate that accessory adaptors FAF1, FAF2, and UBXD7 enhance p97-UN activity through divergent strategies. FAF1 and FAF2 scaffold UFD1-UT3 near the NPL4-tower, whereas UBXD7 stabilizes transient interactions between UFD1 and the ubiquitin chain. Our results provide a comprehensive molecular model for the initiation of p97-mediated substrate unfolding.

biochemistry↗

bioRxiv2025

Editing of the polyubiquitin architecture on the collided ribosome maintains persistent RQC activity

In Ribosome-associated Quality Control (RQC), K63-linked polyubiquitination of uS10 on the stalled ribosome is crucial for recruiting the RQC-trigger (RQT) complex. However, the mechanisms governing the maintenance and recycling of polyubiquitin architecture on colliding ribosomes remain unclear. Here we demonstrate that two deubiquitinating enzymes (DUBs), Ubp2 and Ubp3, play key roles in editing and recycling polyubiquitin chains on uS10, thereby contributing to the promotion of RQC activity. Specifically, Ubp2 eliminates the K63-linked polyubiquitin chain from uS10 on the free 40S subunit for recycling, while Ubp3 predominantly cleaves the K48-linked di-ubiquitin and the K48/K63-mixed-linkage poly-ubiquitin chain from uS10 on the translating ribosomes. Notably, we further demonstrate that the ubiquitin chains containing K48-linkage of the uS10 on the colliding ribosome act as a negative signal for the RQT-mediated ribosome dissociation process. Collectively, our findings clarify the ubiquitin code in RQC and define the positive functions of these two DUBs in maintaining the persistent RQC activity.

molecular biology↗