The CTLH ubiquitin ligase substrates ZMYND19 and MKLN1 negatively regulate mTORC1 at the lysosomal membrane
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Abstract
Most Epstein–Barr virus-associated gastric carcinoma (EBVaGC) harbor non-silent mutations that activate phosphoinositide 3 kinase (PI3K) to drive downstream metabolic signaling. To gain insights into PI3K/mTOR pathway dysregulation in this context, we perform a human genome-wide CRISPR/Cas9 screen for hits that synergistically blocked EBVaGC proliferation together with the PI3K antagonist alpelisib. Multiple subunits of carboxy terminal to LisH (CTLH) E3 ligase, including the catalytic MAEA subunit, are among top screen hits. CTLH negatively regulates gluconeogenesis in yeast, but not in higher organisms. The CTLH substrates MKLN1 and ZMYND19, which highly accumulated upon MAEA knockout, associate with one another and with lysosome outer membranes to inhibit mTORC1. Rather than perturbing mTORC1 lysosomal recruitment, ZMYND19 and MKLN1 block the interaction between mTORC1 and Rheb and also with mTORC1 substrates S6 and 4E-BP1. Thus, CTLH enables cells to rapidly tune mTORC1 activity at the lysosomal membrane via the ubiquitin/proteasome pathway.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Role of GPX4 in ferroptosis and its pharmacological implication
Seibt, T. M., Proneth, B., & Conrad, M. (2019) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2018.09.014 · Cited by 1,520 · see citing works
Sestrin2 is a leucine sensor for the mTORC1 pathway
Wolfson, R. L., Chantranupong, L., Saxton, R. A., Shen, K., Scaria, S. M., Cantor, J. R., & Sabatini, D. M. (2016) · Science · doi:10.1126/science.aab2674 · Cited by 1,306 · see citing works
The TSC1–TSC2 complex: a molecular switchboard controlling cell growth
Huang, J., & Manning, B. D. (2008) · Biochemical Journal · doi:10.1042/bj20080281 · Cited by 1,237 · cited 3× · see citing works
“Together with TSC2 and TBC1D7, TSC1 negatively regulatesmTORC1activationthroughGTPase-activatingprotein(GAP) activity towards the small GTPase Rheb 48 , whereas GATOR1 GAP activity negatively regulates mTORC1 lysosomal recruitment by the Ragulator-Rag complex in response to amino acid depletion 8,49 – 51 .”
InfluentialBar-Peled, L., Chantranupong, L., Cherniack, A. D., Chen, W. W., Ottina, K. A., Grabiner, B. C., Spear, E. D., Carter, S. L., Meyerson, M., & Sabatini, D. M. (2013) · Science · doi:10.1126/science.1232044 · Cited by 1,080 · see citing works
Tee, A. R., Fingar, D. C., Manning, B. D., Kwiatkowski, D. J., Cantley, L. C., & Blenis, J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202476899 · Cited by 827 · see citing works
mTORC1 induces purine synthesis through control of the mitochondrial tetrahydrofolate cycle
Ben-Sahra, I., Hoxhaj, G., Ricoult, S. J. H., Asara, J. M., & Manning, B. D. (2016) · Science · doi:10.1126/science.aad0489 · Cited by 795 · see citing works
Self-citationMechanisms of mTORC1 activation by RHEB and inhibition by PRAS40
Yang, H., Jiang, X., Li, B., Yang, H. J., Miller, M., Yang, A., Dhar, A., & Pavletich, N. P. (2017) · Nature · doi:10.1038/nature25023 · Cited by 548 · see citing works
The deubiquitinylation and localization of PTEN are regulated by a HAUSP-PML network
Song, M. S., Salmena, L., Carracedo, A., Egia, A., Lo-Coco, F., Teruya-Feldstein, J., & Pandolfi, P. P. (2008) · Nature · doi:10.1038/nature07290 · Cited by 548 · see citing works
Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition
Wong, G. S., Zhou, J., Liu, J. B., Wu, Z., Xu, X., Li, T., Xu, D., Schumacher, S. E., Puschhof, J., McFarland, J., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0022-x · Cited by 266 · see citing works
Liu, Q., Chang, J. W., Wang, J., Kang, S. A., Thoreen, C. C., Markhard, A., Hur, W., Zhang, J., Sim, T., Sabatini, D. M., et al. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm101144f · Cited by 257 · see citing works
Architecture of the human GATOR1 and GATOR1–Rag GTPases complexes
Shen, K., Huang, R. K., Brignole, E. J., Condon, K. J., Valenstein, M. L., Chantranupong, L., Bomaliyamu, A., Choe, A., Hong, C., Yu, Z., et al. (2018) · Nature · doi:10.1038/nature26158 · Cited by 192 · see citing works
Regulation of TOR by small GTPases
Durán, R. V., & Hall, M. N. (2012) · The EMBO Reports · doi:10.1038/embor.2011.257 · Cited by 102 · cited 1× · see citing works
“Taken together, these data suggest that the ZMYND19 zinc fi nger supports association with MKLN1, Raptor and CTLH. mTORC1activityistightlyregulatedbyRagproteinsandRheb 75 – 77 .”
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- Authors
- Wang, Y., Liao, Y., Sun, Y., Mitra, B., Guo, R., Piedras, B. I., White, S., Tang, H.-Y., Asara, J. M., Tempera, I., Lieberman, P. M., & Gewurz, B. E.
- Affiliations
- Broad Institute (US)
- The Wistar Institute (US)
- Beth Israel Deaconess Medical Center (US)
- Corresponding author
- Gewurz, Benjamin E.
- ORCID
- Venue
- Nature Communications
- Published
- 2025-11-28
- Volume
- 16
- Issue
- 1
- Pages
- 10731-10731
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC12663577
- OpenAlex
- W4416794512
- Cited by
- 7
- References
- 13
- Citations by year
- 2026: 4 · 2025: 3
- FWCI
- 2.09
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (P01CA269043)
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (R01AI164709)
- Burroughs Wellcome Fund
- American Cancer Society (PF-24-1194768-01-TBE, PF-23-1144614-01-IBCD, PF-24-1250090-01-IBCD, PF-24-1308318-01-TBE)
- U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (R00 DE031016)
- Lymphoma Research Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › PI3K/AKT/mTOR signaling in cancer
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolism, Diabetes, and Cancer
- Keywords
- mTORC1, lysosomal membrane, PI3K/mTOR signaling, alpelisib, ubiquitin-proteasome system, Rheb, ribosomal protein S6, 4E-BP1, CRISPR-Cas9 screen, gluconeogenesis
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