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Liu, Qun, Maqbool, Abbas, Mirkin, Federico G., Singh, Yeshveer, Stevenson, Clare E. M., Lawson, David M., Kamoun, Sophien 
ORCID: https://orcid.org/0000-0002-0290-0315, Huang, Weijie and Hogenhout, Saskia A.
(2023)
Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation.
Proceedings of the National Academy of Sciences of the United States of America, 120 (49).
ISSN 0027-8424
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Abstract
In eukaryotes, targeted protein degradation (TPD) typically depends on a series of interactions among ubiquitin ligases that transfer ubiquitin molecules to substrates leading to degradation by the 26S proteasome. We previously identified that the bacterial effector protein SAP05 mediates ubiquitin-independent TPD. SAP05 forms a ternary complex via interactions with the von Willebrand Factor Type A (vWA) domain of the proteasomal ubiquitin receptor Rpn10 and the zinc-finger (ZnF) domains of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) and GATA BINDING FACTOR (GATA) transcription factors (TFs). This leads to direct TPD of the TFs by the 26S proteasome. Here, we report the crystal structures of the SAP05–Rpn10vWA complex at 2.17 Å resolution and of the SAP05–SPL5ZnF complex at 2.20 Å resolution. Structural analyses revealed that SAP05 displays a remarkable bimodular architecture with two distinct nonoverlapping surfaces, a “loop surface” with three protruding loops that form electrostatic interactions with ZnF, and a “sheet surface” featuring two β-sheets, loops, and α-helices that establish polar interactions with vWA. SAP05 binding to ZnF TFs involves single amino acids responsible for multiple contacts, while SAP05 binding to vWA is more stable due to the necessity of multiple mutations to break the interaction. In addition, positioning of the SAP05 complex on the 26S proteasome points to a mechanism of protein degradation. Collectively, our findings demonstrate how a small bacterial bimodular protein can bypass the canonical ubiquitin–proteasome proteolysis pathway, enabling ubiquitin-independent TPD in eukaryotic cells. This knowledge holds significant potential for the creation of TPD technologies.
| Item Type: | Article |
|---|---|
| Additional Information: | Data, Materials, and Software Availability: Two PDB X-ray structures data have been deposited in SAP05-ZnF and SAP05-vWA. Crystal structure data are available in the Protein Data Bank [PDB ID code 8PFC (61) and 8PFD (62)]. All other data are included in the manuscript and/or SI Appendix. Funding Information: This work was supported by the Human Frontier Science Program (grant number: RGP0024/2015), the UK Research and Innovation (UKRI) Engineering and Physical Sciences Research Council (grant number: EP/ X024415/1), start-up funding from the CAS Center for Excellence in Molecular Plant Sciences, the Natural Science Foundation of Shanghai (grant number: 23ZR1470300), and the UKRI BBSRC (grant numbers: BBS/E/J/000PR9797 and BB/X010996/1) with additional support from the John Innes Foundation and the Gatsby Charitable Foundation. Acknowledgements: We acknowledge Diamond Light Source for access to beamline I04 under proposal MX25108. We thank Julia Mundy, Biophysical Analysis and Protein Crystallography platform at the John Innes Centre (JIC) for their support with ITC, protein crystallization, and X-ray data collection. |
| Uncontrolled Keywords: | 26s proteasome,bacterial effector protein,phytoplasma,targeted protein degradation,ubiquitin-independent,general ,/dk/atira/pure/subjectarea/asjc/1000 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Science > Research Groups > Plant Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 31 Oct 2024 12:30 |
| Last Modified: | 01 Nov 2024 12:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97373 |
| DOI: | 10.1073/pnas.2310664120 |
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