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Glover HL, Mendes M, Gomes-Neto J, Rusilowicz-Jones EV, Rigden DJ, Dittmar G, Urbé S, Clague MJ. Microtubule association of TRIM3 revealed by differential extraction proteomics. J Cell Sci 2024; 137:jcs261522. [PMID: 38149663 PMCID: PMC10917062 DOI: 10.1242/jcs.261522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/15/2023] [Indexed: 12/28/2023] Open
Abstract
The microtubule network is formed from polymerised tubulin subunits and associating proteins, which govern microtubule dynamics and a diverse array of functions. To identify novel microtubule-binding proteins, we have developed an unbiased biochemical assay, which relies on the selective extraction of cytosolic proteins from U2OS cells, while leaving behind the microtubule network. Candidate proteins are linked to microtubules by their sensitivities to the depolymerising drug nocodazole or the microtubule-stabilising drug taxol, which is quantitated by mass spectrometry. Our approach is benchmarked by co-segregation of tubulin and previously established microtubule-binding proteins. We then identify several novel candidate microtubule-binding proteins, from which we have selected the ubiquitin E3 ligase tripartite motif-containing protein 3 (TRIM3) for further characterisation. We map TRIM3 microtubule binding to its C-terminal NHL-repeat region. We show that TRIM3 is required for the accumulation of acetylated tubulin, following treatment with taxol. Furthermore, loss of TRIM3 partially recapitulates the reduction in nocodazole-resistant microtubules characteristic of α-tubulin acetyltransferase 1 (ATAT1) depletion. These results can be explained by a decrease in ATAT1 following depletion of TRIM3 that is independent of transcription.
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Affiliation(s)
- Hannah L. Glover
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Marta Mendes
- Proteomics of Cellular Signalling, Department of Infection and Immunity,Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Joana Gomes-Neto
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Emma V. Rusilowicz-Jones
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Daniel J. Rigden
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Gunnar Dittmar
- Proteomics of Cellular Signalling, Department of Infection and Immunity,Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, 2 Avenue de l'Université, Campus Belval, L-4365 Esch-sur-Alzette, Luxembourg
| | - Sylvie Urbé
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Michael J. Clague
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
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