Identification of two pathways mediating protein targeting from ER to lipid droplets.
Journal
Nature cell biology
ISSN: 1476-4679
Titre abrégé: Nat Cell Biol
Pays: England
ID NLM: 100890575
Informations de publication
Date de publication:
09 2022
09 2022
Historique:
received:
28
09
2021
accepted:
05
07
2022
pubmed:
2
9
2022
medline:
21
9
2022
entrez:
1
9
2022
Statut:
ppublish
Résumé
Pathways localizing proteins to their sites of action are essential for eukaryotic cell organization and function. Although mechanisms of protein targeting to many organelles have been defined, how proteins, such as metabolic enzymes, target from the endoplasmic reticulum (ER) to cellular lipid droplets (LDs) is poorly understood. Here we identify two distinct pathways for ER-to-LD protein targeting: early targeting at LD formation sites during formation, and late targeting to mature LDs after their formation. Using systematic, unbiased approaches in Drosophila cells, we identified specific membrane-fusion machinery, including regulators, a tether and SNARE proteins, that are required for the late targeting pathway. Components of this fusion machinery localize to LD-ER interfaces and organize at ER exit sites. We identified multiple cargoes for early and late ER-to-LD targeting pathways. Our findings provide a model for how proteins target to LDs from the ER either during LD formation or by protein-catalysed formation of membrane bridges.
Identifiants
pubmed: 36050470
doi: 10.1038/s41556-022-00974-0
pii: 10.1038/s41556-022-00974-0
pmc: PMC9481466
doi:
Substances chimiques
SNARE Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
1364-1377Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM097194
Pays : United States
Organisme : NCATS NIH HHS
ID : TL1 TR001101
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM132087
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007753
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Informations de copyright
© 2022. The Author(s).
Références
Thiam, A. R., Farese, R. V. & Walther, T. C. The biophysics and cell biology of lipid droplets. Nat. Rev. Mol. Cell Biol. 14, 775–786 (2013).
pubmed: 24220094
pmcid: 4526153
doi: 10.1038/nrm3699
Olzmann, J. A. & Carvalho, P. Dynamics and functions of lipid droplets. Nat. Rev. Mol. Cell Biol. 20, 137–155 (2019).
pubmed: 30523332
pmcid: 6746329
doi: 10.1038/s41580-018-0085-z
Walther, T. C. & Farese, R. V. Lipid droplets and cellular lipid metabolism. Annu. Rev. Biochem. 81, 687–714 (2012).
pubmed: 22524315
pmcid: 3767414
doi: 10.1146/annurev-biochem-061009-102430
Welte, M. A. Expanding roles for lipid droplets. Curr. Biol. 25, R470–R481 (2015).
pubmed: 26035793
pmcid: 4452895
doi: 10.1016/j.cub.2015.04.004
Romeo, S. et al. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat. Genet. 40, 1461–1465 (2008).
pubmed: 18820647
pmcid: 2597056
doi: 10.1038/ng.257
BasuRay, S., Wang, Y., Smagris, E., Cohen, J. C. & Hobbs, H. H. Accumulation of PNPLA3 on lipid droplets is the basis of associated hepatic steatosis. Proc. Natl Acad. Sci. USA 116, 9521–9526 (2019).
pubmed: 31019090
pmcid: 6511016
doi: 10.1073/pnas.1901974116
Abul-Husn, N. S. et al. A protein-truncating HSD17B13 variant and protection from chronic liver disease. N. Engl. J. Med. 378, 1096–1106 (2018).
pubmed: 29562163
pmcid: 6668033
doi: 10.1056/NEJMoa1712191
Gandotra, S. et al. Perilipin deficiency and autosomal dominant partial lipodystrophy. N. Engl. J. Med. 364, 740–748 (2011).
pubmed: 21345103
pmcid: 3773916
doi: 10.1056/NEJMoa1007487
Payne, F. et al. Mutations disrupting the Kennedy phosphatidylcholine pathway in humans with congenital lipodystrophy and fatty liver disease. Proc. Natl Acad. Sci. USA 111, 8901–8906 (2014).
pubmed: 24889630
pmcid: 4066527
doi: 10.1073/pnas.1408523111
Kory, N., Farese, R. V. & Walther, T. C. Targeting fat: mechanisms of protein localization to lipid droplets. Trends Cell Biol. 26, 535–546 (2016).
pubmed: 26995697
pmcid: 4976449
doi: 10.1016/j.tcb.2016.02.007
Dhiman, R., Caesar, S., Thiam, A. R. & Schrul, B. Mechanisms of protein targeting to lipid droplets: a unified cell biological and biophysical perspective. Semin. Cell Dev. Biol. 108, 4–13 (2020).
pubmed: 32201131
doi: 10.1016/j.semcdb.2020.03.004
Rowe, E. R. et al. Conserved amphipathic helices mediate lipid droplet targeting of perilipins 1–3. J. Biol. Chem. 291, 6664–6678 (2016).
pubmed: 26742848
pmcid: 4807253
doi: 10.1074/jbc.M115.691048
Prévost, C. et al. Mechanism and determinants of amphipathic helix- containing protein targeting to lipid droplets. Dev. Cell 44, 73–86 (2018).
pubmed: 29316443
pmcid: 5764114
doi: 10.1016/j.devcel.2017.12.011
Pataki, C. I. et al. Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors. Proc. Natl Acad. Sci. USA 115, E8172–E8180 (2018).
pubmed: 30104359
pmcid: 6126764
doi: 10.1073/pnas.1807981115
Schrul, B. & Kopito, R. R. Peroxin-dependent targeting of a lipid-droplet-destined membrane protein to ER subdomains. Nat. Cell Biol. 18, 740–751 (2016).
pubmed: 27295553
pmcid: 4925261
doi: 10.1038/ncb3373
Kassan, A. et al. Acyl-CoA synthetase 3 promotes lipid droplet biogenesis in ER microdomains. J. Cell Biol. 203, 985–1001 (2013).
pubmed: 24368806
pmcid: 3871434
doi: 10.1083/jcb.201305142
Wilfling, F. et al. Triacylglycerol synthesis enzymes mediate lipid droplet growth by relocalizing from the ER to lipid droplets. Dev. Cell 24, 384–399 (2013).
pubmed: 23415954
pmcid: 3727400
doi: 10.1016/j.devcel.2013.01.013
Wang, H. et al. Seipin is required for converting nascent to mature lipid droplets. eLife 5, e16582 (2016).
pubmed: 27564575
pmcid: 5035145
doi: 10.7554/eLife.16582
Chung, J. et al. LDAF1 and seipin form a lipid droplet assembly complex. Dev. Cell 51, 551–563 (2019).
pubmed: 31708432
pmcid: 7235935
doi: 10.1016/j.devcel.2019.10.006
Jacquier, N. et al. Lipid droplets are functionally connected to the endoplasmic reticulum in Saccharomyces cerevisiae. J. Cell Sci. 124, 2424–2437 (2011).
pubmed: 21693588
doi: 10.1242/jcs.076836
Cottier, S. & Schneiter, R. Lipid droplets form a network interconnected by the endoplasmic reticulum through which their proteins equilibrate. J. Cell Sci. 135, jcs258819 (2022).
pubmed: 34373922
doi: 10.1242/jcs.258819
Beck, R., Ravet, M., Wieland, F. T. & Cassel, D. The COPI system: molecular mechanisms and function. FEBS Lett. 583, 2701–2709 (2009).
pubmed: 19631211
doi: 10.1016/j.febslet.2009.07.032
Wilfling, F. et al. Arf1/COPI machinery acts directly on lipid droplets and enables their connection to the ER for protein targeting. eLife 3, e01607 (2014).
pubmed: 24497546
pmcid: 3913038
doi: 10.7554/eLife.01607
Beller, M. et al. COPI complex is a regulator of lipid homeostasis. PLoS Biol. 6, 2530–2549 (2008).
doi: 10.1371/journal.pbio.0060292
Soni, K. G. et al. Coatomer-dependent protein delivery to lipid droplets. J. Cell Sci. 122, 1834–1841 (2009).
pubmed: 19461073
pmcid: 2684835
doi: 10.1242/jcs.045849
Ellong, E. N. et al. Interaction between the triglyceride lipase ATGL and the arf1 activator GBF1. PLoS ONE 6, e21889 (2011).
pubmed: 21789191
pmcid: 3138737
doi: 10.1371/journal.pone.0021889
Thiam, A. R. et al. COPI buds 60-nm lipid droplets from reconstituted water–phospholipid–triacylglyceride interfaces, suggesting a tension clamp function. Proc. Natl Acad. Sci. USA 110, 13244–13249 (2013).
pubmed: 23901109
pmcid: 3746913
doi: 10.1073/pnas.1307685110
Thiel, K. et al. The evolutionarily conserved protein CG9186 is associated with lipid droplets, required for their positioning and for fat storage. J. Cell Sci. 126, 2198–2212 (2013).
pubmed: 23525007
Olzmann, J. A., Richter, C. M. & Kopito, R. R. Spatial regulation of UBXD8 and p97/VCP controls ATGL-mediated lipid droplet turnover. Proc. Natl Acad. Sci. USA 110, 1345–1350 (2013).
pubmed: 23297223
pmcid: 3557085
doi: 10.1073/pnas.1213738110
Thul, P. J. et al. Targeting of the Drosophila protein CG2254/Ldsdh1 to a subset of lipid droplets. J. Cell Sci. 130, 3141–3157 (2017).
pubmed: 28775149
Liu, Y. et al. Hydroxysteroid dehydrogenase family proteins on lipid droplets through bacteria, C. elegans, and mammals. Biochim. Biophys. Acta Mol. Cell Biol. Lipids https://doi.org/10.1016/j.bbalip.2018.04.018 (2018).
Yu, J. et al. The adrenal lipid droplet is a new site for steroid hormone metabolism. Proteomics 18, e1800136 (2018).
pubmed: 30358111
doi: 10.1002/pmic.201800136
Mejhert, N. et al. The Lipid Droplet Knowledge Portal: a resource for systematic analyses of lipid droplet biology. Dev. Cell 57, 387–397.e4 (2022).
pubmed: 35134345
pmcid: 9129885
doi: 10.1016/j.devcel.2022.01.003
Vinayagam, A. et al. Protein complex-based analysis framework for high-throughput data sets. Sci. Signal. 6, rs5 (2013).
pubmed: 23443684
pmcid: 3756668
doi: 10.1126/scisignal.2003629
Bard, F. et al. Functional genomics reveals genes involved in protein secretion and Golgi organization. Nature 439, 604–607 (2006).
pubmed: 16452979
doi: 10.1038/nature04377
Tan, R. et al. Small GTPase Rab40c associates with lipid droplets and modulates the biogenesis of lipid droplets. PLoS ONE 8, e63213 (2013).
pubmed: 23638186
pmcid: 3640056
doi: 10.1371/journal.pone.0063213
Wang, C., Liu, Z. & Huang, X. Rab32 is important for autophagy and lipid storage in Drosophila. PLoS ONE 7, e32086 (2012).
pubmed: 22348149
pmcid: 3279429
doi: 10.1371/journal.pone.0032086
Schroeder, B. et al. The small GTPase Rab7 as a central regulator of hepatocellular lipophagy. Hepatology 61, 1896–1897 (2015).
pubmed: 25565581
doi: 10.1002/hep.27667
Wu, L. et al. Rab8a–AS160–MSS4 regulatory circuit controls lipid droplet fusion and growth. Dev. Cell 30, 378–393 (2014).
pubmed: 25158853
doi: 10.1016/j.devcel.2014.07.005
Xu, D. et al. Rab18 promotes lipid droplet (LD) growth by tethering the ER to LDs through SNARE and NRZ interactions. J. Cell Biol. 217, 975–995 (2018).
pubmed: 29367353
pmcid: 5839781
doi: 10.1083/jcb.201704184
Satoh, A. K., Tokunaga, F., Kawamura, S. & Ozaki, K. In situ inhibition of vesicle transport and protein processing in the dominant negative Rab1 mutant of Drosophila. J. Cell Sci. 110, 2943–2953 (1997).
pubmed: 9359879
doi: 10.1242/jcs.110.23.2943
Söllner, T. et al. SNAP receptors implicated in vesicle targeting and fusion. Nature 362, 318–324 (1993).
pubmed: 8455717
doi: 10.1038/362318a0
Hong, W. SNAREs and traffic. Biochim. Biophys. Acta 1744, 120–144 (2005).
pubmed: 15893389
doi: 10.1016/j.bbamcr.2005.03.014
Ungar, D. & Hughson, F. M. SNARE protein structure and function. Annu. Rev. Cell Dev. Biol. 19, 493–517 (2003).
pubmed: 14570579
doi: 10.1146/annurev.cellbio.19.110701.155609
Südhof, T. C. & Rothman, J. E. Membrane fusion: grappling with SNARE and SM proteins. Science 323, 474–477 (2009).
pubmed: 19164740
pmcid: 3736821
doi: 10.1126/science.1161748
Zhao, M. et al. Mechanistic insights into the recycling machine of the SNARE complex. Nature 518, 61–67 (2015).
pubmed: 25581794
pmcid: 4320033
doi: 10.1038/nature14148
Whiteheart, S. W. et al. N-ethylmaleimide-sensitive fusion protein: a trimeric ATPase whose hydrolysis of ATP is required for membrane fusion. J. Cell Biol. 126, 945–954 (1994).
pubmed: 8051214
doi: 10.1083/jcb.126.4.945
Dascher, C., Matteson, J. & Balch, W. E. Syntaxin 5 regulates endoplasmic reticulum to Golgi transport. J. Biol. Chem. 269, 29363–29366 (1994).
pubmed: 7961911
doi: 10.1016/S0021-9258(18)43884-7
Krahmer, N. et al. Organellar proteomics and phospho-proteomics reveal subcellular reorganization in diet-induced hepatic steatosis. Dev. Cell 47, 205–221 (2018).
pubmed: 30352176
doi: 10.1016/j.devcel.2018.09.017
Krahmer, N. et al. Protein correlation profiles identify lipid droplet proteins with high confidence. Mol. Cell Proteom. 12, 1115–1126 (2013).
doi: 10.1074/mcp.M112.020230
Bersuker, K. et al. A proximity labeling strategy provides insights into the composition and dynamics of lipid droplet proteomes. Dev. Cell 44, 97–112 (2018).
pubmed: 29275994
doi: 10.1016/j.devcel.2017.11.020
Liu, P. et al. Rab-regulated interaction of early endosomes with lipid droplets. Biochim. Biophys. Acta 1773, 784–793 (2007).
pubmed: 17395284
pmcid: 2676670
doi: 10.1016/j.bbamcr.2007.02.004
Bannykh, S. I., Rowe, T. & Balch, W. E. The organization of endoplasmic reticulum export complexes. J. Cell Biol. 135, 19–35 (1996).
pubmed: 8858160
doi: 10.1083/jcb.135.1.19
Ivan, V. et al. Drosophila Sec16 mediates the biogenesis of tER sites upstream of Sar1 through an arginine-rich motif. Mol. Biol. Cell 19, 4352–4365 (2008).
pubmed: 18614796
pmcid: 2555954
doi: 10.1091/mbc.e08-03-0246
Sui, X. et al. Cryo-electron microscopy structure of the lipid droplet-formation protein seipin. J. Cell Biol. 217, 4080–4091 (2018).
pubmed: 30327422
pmcid: 6279392
doi: 10.1083/jcb.201809067
Yan, R. et al. Human SEIPIN binds anionic phospholipids. Dev. Cell 47, 248–256 (2018).
pubmed: 30293840
doi: 10.1016/j.devcel.2018.09.010
Arlt, H. et al. Seipin forms a flexible cage at lipid droplet formation sites. Nat. Struct. Mol. Biol. 29, 194–194 (2022).
pubmed: 35210614
pmcid: 8930772
doi: 10.1038/s41594-021-00718-y
Salo, V. T. et al. Seipin regulates ER−lipid droplet contacts and cargo delivery. EMBO J. 35, 2699–2716 (2016).
pubmed: 27879284
pmcid: 5167346
doi: 10.15252/embj.201695170
Allan, B. B., Moyer, B. D. & Balch, W. E. Rab1 recruitment of p115 into a cis-SNARE complex: programming budding COPII vesicles for fusion. Science 289, 444–448 (2000).
pubmed: 10903204
doi: 10.1126/science.289.5478.444
Beard, M., Satoh, A., Shorter, J. & Warren, G. A cryptic Rab1-binding site in the p115 tethering protein. J. Biol. Chem. 280, 25840–25848 (2005).
pubmed: 15878873
doi: 10.1074/jbc.M503925200
Moyer, B. D., Allan, B. B. & Balch, W. E. Rab1 interaction with a GM130 effector complex regulates COPII vesicle cis-Golgi tethering. Traffic 2, 268–276 (2001).
pubmed: 11285137
doi: 10.1034/j.1600-0854.2001.1o007.x
Westrate, L. M., Hoyer, M. J., Nash, M. J. & Voeltz, G. K. Vesicular and uncoated Rab1-dependent cargo carriers facilitate ER to Golgi transport. J. Cell Sci. 133, jcs239814 (2020).
pubmed: 32616562
pmcid: 7390636
doi: 10.1242/jcs.239814
Fukasawa, M., Varlamov, O., Eng, W. S., Söllner, T. H. & Rothman, J. E. Localization and activity of the SNARE Ykt6 determined by its regulatory domain and palmitoylation. Proc. Natl Acad. Sci. USA 101, 4815–4820 (2004).
pubmed: 15044687
pmcid: 387331
doi: 10.1073/pnas.0401183101
Budnik, A. & Stephens, D. J. ER exit sites—localization and control of COPII vesicle formation. FEBS Lett. 583, 3796–3803 (2009).
pubmed: 19850039
doi: 10.1016/j.febslet.2009.10.038
Liu, M. et al. Tango1 spatially organizes ER exit sites to control ER export. J. Cell Biol. 216, 1035–1049 (2017).
pubmed: 28280122
pmcid: 5379956
doi: 10.1083/jcb.201611088
Raote, I. et al. TANGO1 builds a machine for collagen export by recruiting and spatially organizing COPII, tethers and membranes. eLife 7, e32723 (2018).
pubmed: 29513218
pmcid: 5851698
doi: 10.7554/eLife.32723
Raote, I. et al. TANGO1 assembles into rings around COPII coats at ER exit sites. J. Cell Biol. 216, 901–909 (2017).
pubmed: 28280121
pmcid: 5379947
doi: 10.1083/jcb.201608080
Weigel, A. V. et al. ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER. Cell 184, 2412–2429 (2021).
pubmed: 33852913
doi: 10.1016/j.cell.2021.03.035
Santos, A. J. M., Nogueira, C., Ortega-Bellido, M. & Malhotra, V. TANGO1 and Mia2/cTAGE5 (TALI) cooperate to export bulky pre-chylomicrons/VLDLs from the endoplasmic reticulum. J. Cell Biol. 213, 343–354 (2016).
pubmed: 27138255
pmcid: 4862334
doi: 10.1083/jcb.201603072
Olarte, M. J. et al. Determinants of endoplasmic reticulum-to-lipid droplet protein targeting. Dev. Cell 54, 471–487 (2020).
pubmed: 32730754
pmcid: 7696655
doi: 10.1016/j.devcel.2020.07.001
Kory, N., Thiam, A. R., Farese, R. V. & Walther, T. C. Protein crowding is a determinant of lipid droplet protein composition. Dev. Cell 34, 351–363 (2015).
pubmed: 26212136
pmcid: 4536137
doi: 10.1016/j.devcel.2015.06.007
Grippa, A. et al. The seipin complex Fld1/Ldb16 stabilizes ER–lipid droplet contact sites. J. Cell Biol. 211, 829–844 (2015).
pubmed: 26572621
pmcid: 4657162
doi: 10.1083/jcb.201502070
Lerner, D. W. et al. A Rab10-dependent mechanism for polarized basement membrane secretion during organ morphogenesis. Dev. Cell 24, 159–168 (2013).
pubmed: 23369713
pmcid: 3562474
doi: 10.1016/j.devcel.2012.12.005
Housden, B. E., Hu, Y. & Perrimon, N. Design and generation of Drosophila single guide RNA expression constructs. Cold Spring Harb. Protoc. 2016, 782–788 (2016).
Housden, B. E. & Perrimon, N. Design and generation of donor constructs for genome engineering in Drosophila. Cold Spring Harb. Protoc. 2016, 789–793 (2016).
Krahmer, N. et al. Phosphatidylcholine synthesis for lipid droplet expansion is mediated by localized activation of CTP:phosphocholine cytidylyltransferase. Cell Metab. 14, 504–515 (2011).
pubmed: 21982710
pmcid: 3735358
doi: 10.1016/j.cmet.2011.07.013
Riedel, F., Gillingham, A. K., Rosa-Ferreira, C., Galindo, A. & Munro, S. An antibody toolkit for the study of membrane traffic in Drosophila melanogaster. Biol. Open 5, 987–992 (2016).
pubmed: 27256406
pmcid: 4958275
doi: 10.1242/bio.018937
Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663–670 (2003).
pubmed: 12585499
doi: 10.1021/ac026117i
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
doi: 10.1038/nmeth.2019
Bolte, S. & Cordelieres, F. P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006).
pubmed: 17210054
doi: 10.1111/j.1365-2818.2006.01706.x
Gilles, J. F., Dos Santos, M., Boudier, T., Bolte, S. & Heck, N. DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis. Methods 115, 55–64 (2017).
pubmed: 27890650
doi: 10.1016/j.ymeth.2016.11.016
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).
pubmed: 19029910
doi: 10.1038/nbt.1511
Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794–1805 (2011).
pubmed: 21254760
doi: 10.1021/pr101065j
Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).
pubmed: 27348712
doi: 10.1038/nmeth.3901
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).
pubmed: 27207943
doi: 10.1093/bioinformatics/btw313
Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: Improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019).
pubmed: 30395289
doi: 10.1093/nar/gky1106