Structural basis of phosphatidylinositol 3-kinase C2α function.
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
03 2022
03 2022
Historique:
received:
13
07
2021
accepted:
21
01
2022
pubmed:
9
3
2022
medline:
20
4
2022
entrez:
8
3
2022
Statut:
ppublish
Résumé
Phosphatidylinositol 3-kinase type 2α (PI3KC2α) is an essential member of the structurally unresolved class II PI3K family with crucial functions in lipid signaling, endocytosis, angiogenesis, viral replication, platelet formation and a role in mitosis. The molecular basis of these activities of PI3KC2α is poorly understood. Here, we report high-resolution crystal structures as well as a 4.4-Å cryogenic-electron microscopic (cryo-EM) structure of PI3KC2α in active and inactive conformations. We unravel a coincident mechanism of lipid-induced activation of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C-C2 domains, and can serve as a model for the entire class II PI3K family. Moreover, we describe a PI3KC2α-specific helical bundle domain that underlies its scaffolding function at the mitotic spindle. Our results advance our understanding of PI3K biology and pave the way for the development of specific inhibitors of class II PI3K function with wide applications in biomedicine.
Identifiants
pubmed: 35256802
doi: 10.1038/s41594-022-00730-w
pii: 10.1038/s41594-022-00730-w
pmc: PMC8930771
doi:
Substances chimiques
Lipids
0
Phosphatidylinositol 3-Kinase
EC 2.7.1.137
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
218-228Informations de copyright
© 2022. The Author(s).
Références
Bilanges, B., Posor, Y. & Vanhaesebroeck, B. PI3K isoforms in cell signalling and vesicle trafficking. Nat. Rev. Mol. Cell Biol. 20, 515–534 (2019).
pubmed: 31110302
doi: 10.1038/s41580-019-0129-z
Toker, A. & Cantley, L. C. Signalling through the lipid products of phosphoinositide-3-OH kinase. Nature 387, 673–676 (1997).
pubmed: 9192891
doi: 10.1038/42648
Wymann, M. P. & Schneiter, R. Lipid signalling in disease. Nat. Rev. Mol. Cell Biol. 9, 162–176 (2008).
pubmed: 18216772
doi: 10.1038/nrm2335
Burke, J. E. Structural basis for regulation of phosphoinositide kinases and their involvement in human disease. Mol. Cell 71, 653–673 (2018).
pubmed: 30193094
doi: 10.1016/j.molcel.2018.08.005
Pacold, M. E. et al. Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase gamma. Cell 103, 931–943 (2000).
pubmed: 11136978
doi: 10.1016/S0092-8674(00)00196-3
Walker, E. H., Perisic, O., Ried, C., Stephens, L. & Williams, R. L. Structural insights into phosphoinositide 3-kinase catalysis and signalling. Nature 402, 313–320 (1999).
pubmed: 10580505
doi: 10.1038/46319
Rostislavleva, K. et al. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science 350, aac7365 (2015).
pubmed: 26450213
pmcid: 4601532
doi: 10.1126/science.aac7365
Stjepanovic, G., Baskaran, S., Lin, M. G. & Hurley, J. H. Vps34 kinase domain dynamics regulate the autophagic PI 3-kinase complex. Mol. Cell 67, 528–534 e3 (2017).
pubmed: 28757208
pmcid: 5573195
doi: 10.1016/j.molcel.2017.07.003
Braccini, L. et al. PI3K-C2gamma is a Rab5 effector selectively controlling endosomal Akt2 activation downstream of insulin signalling. Nat. Commun. 6, 7400 (2015).
pubmed: 26100075
doi: 10.1038/ncomms8400
Marat, A. L. et al. mTORC1 activity repression by late endosomal phosphatidylinositol 3,4-bisphosphate. Science 356, 968–972 (2017).
pubmed: 28572395
doi: 10.1126/science.aaf8310
Boukhalfa, A. et al. PI3KC2alpha-dependent and VPS34-independent generation of PI3P controls primary cilium-mediated autophagy in response to shear stress. Nat. Commun. 11, 294 (2020).
pubmed: 31941925
pmcid: 6962367
doi: 10.1038/s41467-019-14086-1
Campa, C. C. et al. Rab11 activity and PtdIns(3)P turnover removes recycling cargo from endosomes. Nat. Chem. Biol. 14, 801–810 (2018).
pubmed: 29915378
doi: 10.1038/s41589-018-0086-4
Franco, I. et al. PI3K class II alpha controls spatially restricted endosomal PtdIns3P and Rab11 activation to promote primary cilium function. Dev. Cell 28, 647–658 (2014).
pubmed: 24697898
pmcid: 4042153
doi: 10.1016/j.devcel.2014.01.022
Gulluni, F., De Santis, M. C., Margaria, J. P., Martini, M. & Hirsch, E. Class II PI3K functions in cell biology and disease. Trends Cell Biol. 29, 339–359 (2019).
pubmed: 30691999
doi: 10.1016/j.tcb.2019.01.001
Posor, Y. et al. Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature 499, 233–237 (2013).
pubmed: 23823722
doi: 10.1038/nature12360
Wang, H. et al. Phosphatidylinositol 3,4-bisphosphate synthesis and turnover are spatially segregated in the endocytic pathway. J. Biol. Chem. 295, 1091–1104 (2020).
pubmed: 31831620
doi: 10.1016/S0021-9258(17)49918-2
Aki, S., Yoshioka, K., Takuwa, N. & Takuwa, Y. TGFbeta receptor endocytosis and Smad signaling require synaptojanin1, PI3K-C2alpha-, and INPP4B-mediated phosphoinositide conversions. Mol. Biol. Cell 31, 360–372 (2020).
pubmed: 31913757
pmcid: 7183790
doi: 10.1091/mbc.E19-11-0662
Biswas, K. et al. Essential role of class II phosphatidylinositol-3-kinase-C2alpha in sphingosine 1-phosphate receptor-1-mediated signaling and migration in endothelial cells. J. Biol. Chem. 288, 2325–2339 (2013).
pubmed: 23192342
doi: 10.1074/jbc.M112.409656
Yoshioka, K. et al. Endothelial PI3K-C2alpha, a class II PI3K, has an essential role in angiogenesis and vascular barrier function. Nat. Med. 18, 1560–1569 (2012).
pubmed: 22983395
doi: 10.1038/nm.2928
Islam, S. et al. Class II phosphatidylinositol 3-kinase alpha and beta isoforms are required for vascular smooth muscle Rho activation, contraction and blood pressure regulation in mice. J. Physiol. Sci. 70, 18 (2020).
pubmed: 32192434
pmcid: 7082390
doi: 10.1186/s12576-020-00745-2
Abere, B. et al. Kaposi’s sarcoma-associated herpesvirus nonstructural membrane protein pK15 recruits the class II phosphatidylinositol 3-kinase PI3K-C2alpha to activate productive viral replication. J. Virol. 92, e00544 (2018).
Polachek, W. S. et al. High-throughput small interfering RNA screening identifies phosphatidylinositol 3-kinase class ii alpha as important for production of human cytomegalovirus virions. J. Virol. 90, 8360–8371 (2016).
pubmed: 27412598
pmcid: 5008103
doi: 10.1128/JVI.01134-16
Mountford, J. K. et al. The class II PI 3-kinase, PI3KC2alpha, links platelet internal membrane structure to shear-dependent adhesive function. Nat. Commun. 6, 6535 (2015).
pubmed: 25779105
doi: 10.1038/ncomms7535
Valet, C. et al. Essential role of class II PI3K-C2alpha in platelet membrane morphology. Blood 126, 1128–1137 (2015).
pubmed: 26109204
doi: 10.1182/blood-2015-03-636670
Tiosano, D. et al. Mutations in PIK3C2A cause syndromic short stature, skeletal abnormalities, and cataracts associated with ciliary dysfunction. PLoS Genet. 15, e1008088 (2019).
pubmed: 31034465
pmcid: 6508738
doi: 10.1371/journal.pgen.1008088
Gulluni, F. et al. Mitotic spindle assembly and genomic stability in breast cancer require PI3K-C2alpha scaffolding function. Cancer Cell 32, 444–459 e7 (2017).
pubmed: 29017056
doi: 10.1016/j.ccell.2017.09.002
Young, L. N., Goerdeler, F. & Hurley, J. H. Structural pathway for allosteric activation of the autophagic PI 3-kinase complex I. Proc. Natl Acad. Sci. USA 116, 21508–21513 (2019).
pubmed: 31591221
pmcid: 6815113
doi: 10.1073/pnas.1911612116
Selvadurai, M. V. et al. Disrupting the platelet internal membrane via PI3KC2alpha inhibition impairs thrombosis independently of canonical platelet activation. Sci. Transl. Med. 12, eaar8430 (2020).
Alliouachene, S. et al. Inactivation of class II PI3K-C2alpha induces leptin resistance, age-dependent insulin resistance and obesity in male mice. Diabetologia 59, 1503–1512 (2016).
pubmed: 27138914
pmcid: 4901096
doi: 10.1007/s00125-016-3963-y
Wang, H. et al. Autoregulation of class ii alpha PI3K activity by its lipid-binding PX-C2 domain module. Mol. Cell 71, 343–351 e4 (2018).
pubmed: 30029007
doi: 10.1016/j.molcel.2018.06.042
Miller, S. et al. Shaping development of autophagy inhibitors with the structure of the Lipid Kinase Vps34. Science 327, 1638–1642 (2010).
pubmed: 20339072
pmcid: 2860105
doi: 10.1126/science.1184429
Siempelkamp, B. D., Rathinaswamy, M. K., Jenkins, M. L. & Burke, J. E. Molecular mechanism of activation of class IA phosphoinositide 3-kinases (PI3Ks) by membrane-localized HRas. J. Biol. Chem. 292, 12256–12266 (2017).
pubmed: 28515318
pmcid: 5519374
doi: 10.1074/jbc.M117.789263
Schoneberg, J. et al. Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Commun. 8, 15873 (2017).
Miller, M. S. et al. Structural basis of nSH2 regulation and lipid binding in PI3Kalpha. Oncotarget 5, 5198–5208 (2014).
pubmed: 25105564
pmcid: 4170646
doi: 10.18632/oncotarget.2263
Wymann, M. P. & Schultz, C. The chemical biology of phosphoinositide 3-kinases. Chem. Bio. Chem. 13, 2022–2035 (2012).
pubmed: 22965647
doi: 10.1002/cbic.201200089
Yang, H. et al. mTOR kinase structure, mechanism and regulation. Nature 497, 217–223 (2013).
pubmed: 23636326
pmcid: 4512754
doi: 10.1038/nature12122
Chen, K. E., Tillu, V. A., Chandra, M. & Collins, B. M. Molecular basis for membrane recruitment by the PX and C2 domains of class II phosphoinositide 3-kinase-C2alpha. Structure 26, 1612–1625 e4 (2018).
pubmed: 30293811
doi: 10.1016/j.str.2018.08.010
Karaca, E., Melquiond, A. S., de Vries, S. J., Kastritis, P. L. & Bonvin, A. M. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Mol. Cell Proteom. 9, 1784–1794 (2010).
doi: 10.1074/mcp.M000051-MCP201
Gaidarov, I., Smith, M. E., Domin, J. & Keen, J. H. The class II phosphoinositide 3-kinase C2alpha is activated by clathrin and regulates clathrin-mediated membrane trafficking. Mol. Cell 7, 443–449 (2001).
pubmed: 11239472
doi: 10.1016/S1097-2765(01)00191-5
Hon, W. C., Berndt, A. & Williams, R. L. Regulation of lipid binding underlies the activation mechanism of class IA PI3-kinases. Oncogene 31, 3655–3666 (2012).
pubmed: 22120714
doi: 10.1038/onc.2011.532
He, K. et al. Dynamics of phosphoinositide conversion in clathrin-mediated endocytic traffic. Nature 552, 410–414 (2017).
pubmed: 29236694
pmcid: 6263037
doi: 10.1038/nature25146
Phua, S. C. et al. Dynamic remodeling of membrane composition drives cell cycle through primary cilia excision. Cell 168, 264-+ (2017).
pubmed: 28086093
pmcid: 5660509
doi: 10.1016/j.cell.2016.12.032
Sparta, K. M., Krug, M., Heinemann, U., Mueller, U. & Weiss, M. S. Xdsapp20. J. Appl. Crystallogr. 49, 1085–1092 (2016).
doi: 10.1107/S1600576716004416
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D. Struct. Biol. 75, 861–877 (2019).
pubmed: 31588918
pmcid: 6778852
doi: 10.1107/S2059798319011471
Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D. Biol. Crystallogr. 67, 355–367 (2011).
pubmed: 21460454
pmcid: 3069751
doi: 10.1107/S0907444911001314
Bricogne, G. Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. Acta Crystallogr. D. Biol. Crystallogr. 49, 37–60 (1993).
pubmed: 15299544
doi: 10.1107/S0907444992010400
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
doi: 10.1107/S0907444910007493
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
pubmed: 26278980
pmcid: 6760662
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
pubmed: 23000701
pmcid: 3690530
doi: 10.1016/j.jsb.2012.09.006
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
doi: 10.1038/nmeth.4169
pubmed: 28165473
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
pubmed: 28671674
pmcid: 5533649
doi: 10.1038/nmeth.4347
Liu, F., Lossl, P., Scheltema, R., Viner, R. & Heck, A. J. R. Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nat. Commun. 8, 15473 (2017).
pubmed: 28524877
pmcid: 5454533
doi: 10.1038/ncomms15473