Stay in touch with the endoplasmic reticulum.

AhYoung, A.P., Jiang, J., Zhang, J., Khoi Dang, X., Loo, J.A., Zhou, Z.H., and Egea, P.F. (2015). Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly. Proc Natl Acad Sci USA 112, E3179–3188.

pubmed: 26056272 pmcid: 4485115 doi: 10.1073/pnas.1422363112

Allison, R., Edgar, J.R., Pearson, G., Rizo, T., Newton, T., Günther, S., Berner, F., Hague, J., Connell, J.W., Winkler, J., et al. (2017). Defects in ER-endosome contacts impact lysosome function in hereditary spastic paraplegia. J Cell Biol 216, 1337–1355.

pubmed: 28389476 pmcid: 5412567 doi: 10.1083/jcb.201609033

Allison, R., Lumb, J.H., Fassier, C., Connell, J.W., Ten Martin, D., Seaman, M.N.J., Hazan, J., and Reid, E. (2013). An ESCRT-spastin interaction promotes fission of recycling tubules from the endosome. J Cell Biol 202, 527–543.

pubmed: 23897888 pmcid: 3734076 doi: 10.1083/jcb.201211045

Alpy, F., Rousseau, A., Schwab, Y., Legueux, F., Stoll, I., Wendling, C., Spiegelhalter, C., Kessler, P., Mathelin, C., Rio, M.C., et al. (2013). STARD3/STARD3NL and VAP make a novel molecular tether between late endosomes and the ER. J Cell Sci 126, jcs.139295.

doi: 10.1242/jcs.139295

Alpy, F., and Tomasetto, C. (2014). START ships lipids across interorganelle space. Biochimie 96, 85–95.

pubmed: 24076129 doi: 10.1016/j.biochi.2013.09.015

Alva, V., and Lupas, A.N. (2016). The TULIP superfamily of eukaryotic lipid-binding proteins as a mediator of lipid sensing and transport. Biochim Biophys Acta 1861, 913–923.

pubmed: 26825693 doi: 10.1016/j.bbalip.2016.01.016

Antonny, B., Bigay, J., and Mesmin, B. (2018). The oxysterol-binding protein cycle: burning off PI(4)P to transport cholesterol. Annu Rev Biochem 87, 809–837.

pubmed: 29596003 doi: 10.1146/annurev-biochem-061516-044924

Appenzeller-Herzog, C., and Hauri, H.P. (2006). The ER-Golgi intermediate compartment (ERGIC): in search of its identity and function. J Cell Sci 119, 2173–2183.

pubmed: 16723730 doi: 10.1242/jcs.03019

Arruda, A.P., Pers, B.M., Parlakgül, G., Güney, E., Inouye, K., and Hotamisligil, G.S. (2014). Chronic enrichment of hepatic endoplasmic reticulum-mitochondria contact leads to mitochondrial dysfunction in obesity. Nat Med 20, 1427–1435.

pubmed: 25419710 pmcid: 4412031 doi: 10.1038/nm.3735

Atakpa, P., Thillaiappan, N.B., Mataragka, S., Prole, D.L., and Taylor, C.W. (2018). IP

pubmed: 30540949 pmcid: 6302550 doi: 10.1016/j.celrep.2018.11.064

Axe, E.L., Walker, S.A., Manifava, M., Chandra, P., Roderick, H.L., Habermann, A., Griffiths, G., and Ktistakis, N.T. (2008). Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 182, 685–701.

pubmed: 18725538 pmcid: 2518708 doi: 10.1083/jcb.200803137

Ba, Q., Raghavan, G., Kiselyov, K., and Yang, G. (2018). Whole-cell scale dynamic organization of lysosomes revealed by spatial statistical analysis. Cell Rep 23, 3591 -3606.

Ballabio, A., and Bonifacino, J.S. (2020). Lysosomes as dynamic regulators of cell and organismal homeostasis. Nat Rev Mol Cell Biol 21, 101–118.

pubmed: 31768005 doi: 10.1038/s41580-019-0185-4

Ban, T., Ishihara, T., Kohno, H., Saita, S., Ichimura, A., Maenaka, K., Oka, T., Mihara, K., and Ishihara, N. (2017). Molecular basis of selective mitochondrial fusion by heterotypic action between OPA1 and cardiolipin. Nat Cell Biol 19, 856–863.

pubmed: 28628083 doi: 10.1038/ncb3560

Bannykh, S.I., Rowe, T., and Balch, W.E. (1996). The organization of endoplasmic reticulum export complexes. J Cell Biol 135, 19–35.

pubmed: 8858160 doi: 10.1083/jcb.135.1.19

Bard, F., Casano, L., Mallabiabarrena, A., Wallace, E., Saito, K., Kitayama, H., Guizzunti, G., Hu, Y., Wendler, F., Dasgupta, R., et al. (2006). Functional genomics reveals genes involved in protein secretion and Golgi organization. Nature 439, 604–607.

pubmed: 16452979 doi: 10.1038/nature04377

Barlowe, C., Orci, L., Yeung, T., Hosobuchi, M., Hamamoto, S., Salama, N., Rexach, M.F., Ravazzola, M., Amherdt, M., et al. (1994). COPII: a membrane coat formed by Sec proteins that drive vesicle budding from the endoplasmic reticulum. Cell 77, 895–907.

pubmed: 8004676 doi: 10.1016/0092-8674(94)90138-4

Barlowe, C.K., and Miller, E.A. (2013). Secretory protein biogenesis and traffic in the early secretory pathway. Genetics 193, 383–410.

pubmed: 23396477 pmcid: 3567731 doi: 10.1534/genetics.112.142810

Baughman, J.M., Perocchi, F., Girgis, H.S., Plovanich, M., Belcher-Timme, C.A., Sancak, Y., Bao, X.R., Strittmatter, L., Goldberger, O., Bogorad, R.L., et al. (2011). Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter. Nature 476, 341–345.

pubmed: 21685886 pmcid: 3486726 doi: 10.1038/nature10234

Baumann, O., and Walz, B. (2001). Endoplasmic reticulum of animal cells and its organization into structural and functional domains. Int Rev Cytol 205, 149–214.

pubmed: 11336391 doi: 10.1016/S0074-7696(01)05004-5

Bean, B.D.M., Dziurdzik, S.K., Kolehmainen, K.L., Fowler, C.M.S., Kwong, W.K., Grad, L.I., Davey, M., Schluter, C., and Conibear, E. (2018). Competitive organelle-specific adaptors recruit Vps13 to membrane contact sites. J Cell Biol 217, 3593–3607.

pubmed: 30018089 pmcid: 6168272 doi: 10.1083/jcb.201804111

Berridge, M.J., and Irvine, R.F. (1989). Inositol phosphates and cell signalling. Nature 341, 197–205.

pubmed: 2550825 doi: 10.1038/341197a0

Berridge, M.J., Lipp, P., and Bootman, M.D. (2000). The versatility and universality of calcium signalling. Nat Rev Mol Cell Biol 1, 11–21.

pubmed: 11413485 doi: 10.1038/35036035

Besprozvannaya, M., Dickson, E., Li, H., Ginburg, K.S., Bers, D.M., Auwerx, J., and Nunnari, J. (2018). GRAM domain proteins specialize functionally distinct ER-PM contact sites in human cells. eLife 7, e31019.

pubmed: 29469807 pmcid: 5823543 doi: 10.7554/eLife.31019

Bian, X., and De Camilli, P. (2019). In vitro assays to measure the membrane tethering and lipid transport activities of the extended synaptotagmins. Methods Mol Biol 1949, 201–212.

pubmed: 30790258 pmcid: 6481592 doi: 10.1007/978-1-4939-9136-5_15

Bian, X., Zhang, Z., Xiong, Q., De Camilli, P., and Lin, C. (2019). A programmable DNA-origami platform for studying lipid transfer between bilayers. Nat Chem Biol 15, 830–837.

pubmed: 31320758 pmcid: 6650167 doi: 10.1038/s41589-019-0325-3

Bockler, S., and Westermann, B. (2014). Mitochondrial ER contacts are crucial for mitophagy in yeast. Dev Cell 28, 450–458.

pubmed: 24530295 doi: 10.1016/j.devcel.2014.01.012

Brandizzi, F., and Barlowe, C. (2013). Organization of the ER-Golgi interface for membrane traffic control. Nat Rev Mol Cell Biol 14, 382–392.

pubmed: 23698585 pmcid: 4064004 doi: 10.1038/nrm3588

Burkhardt, J.K., Echeverri, C.J., Nilsson, T., and Vallee, R.B. (1997). Overexpression of the dynamitin (p50) subunit of the dynactin complex disrupts dynein-dependent maintenance of membrane organelle distribution. J Cell Biol 139, 469–484.

pubmed: 9334349 pmcid: 2139801 doi: 10.1083/jcb.139.2.469

Bykov, Y.S., Schaffer, M., Dodonova, S.O., Albert, S., Plitzko, J.M., Baumeister, W., Engel, B.D., and Briggs, J.A. (2017). The structure of the COPI coat determined within the cell. eLife 6, e32493.

pubmed: 29148969 pmcid: 5716667 doi: 10.7554/eLife.32493

Cabukusta, B., and Neefjes, J. (2018). Mechanisms of lysosomal positioning and movement. Traffic 19, 761–769.

pubmed: 29900632 pmcid: 6175085 doi: 10.1111/tra.12587

Cancela, J.M., Churchill, G.C., and Galione, A. (1999). Coordination of agonist-induced Ca

pubmed: 10078532 doi: 10.1038/18032

Carlton, J.G., Jones, H., and Eggert, U.S. (2020). Membrane and organelle dynamics during cell division. Nat Rev Mol Cell Biol 21, 151–166.

pubmed: 32034394 doi: 10.1038/s41580-019-0208-1

Castellano Brian, M., Thelen, A.M., Moldavski, O., Feltes, M.K., van der Welle, R.E.N., Mydock-McGrane, L., Jiang, X., van Eijkeren, R.J., Davis, O.B., et al. (2017). Lysosomal cholesterol activates mTORC1 via an SLC38A9-Niemann Pick C1 signaling complex. Science 355, 1306–1311.

pubmed: 28336668 pmcid: 5823611 doi: 10.1126/science.aag1417

Champion, L., Linder, M.I., and Kutay, U. (2017). Cellular reorganization during mitotic entry. Trends Cell Biol 27, 26–41.

pubmed: 27528558 doi: 10.1016/j.tcb.2016.07.004

Chang, C.L., Chen, Y.J., and Liou, J. (2017). ER-plasma membrane junctions: why and how do we study them? Biochim Biophys Acta 1864, 1494–1506.

pmcid: 5542405 doi: 10.1016/j.bbamcr.2017.05.018

Chang, C.L., Chen, Y.J., Quintanilla, C.G., Hsieh, T.S., and Liou, J. (2018). EB1 binding restricts STIM1 translocation to ER-PM junctions and regulates store-operated Ca

pubmed: 29563214 pmcid: 5987725 doi: 10.1083/jcb.201711151

Chang, C.L., Hsieh, T.S., Yang, T.T., Rothberg, K.G., Azizoglu, D.B., Volk, E., Liao, J.C., and Liou, J. (2013). Feedback regulation of receptor-induced Ca

pubmed: 24183667 doi: 10.1016/j.celrep.2013.09.038

Chang, C.L., and Liou, J. (2015). Phosphatidylinositol 4,5-Bisphosphate homeostasis regulated by Nir2 and nir3 proteins at endoplasmic reticulum-plasma membrane junctions. J Biol Chem 290, 14289–14301.

pubmed: 25887399 pmcid: 4505499 doi: 10.1074/jbc.M114.621375

Chauhan, S., Kumar, S., Jain, A., Ponpuak, M., Mudd, M.H., Kimura, T., Choi, S.W., Peters, R., Mandell, M., et al. (2016). TRIMs and galectins globally cooperate and TRIM16 and Galectin-3 co-direct autophagy in endomembrane damage homeostasis. Dev Cell 39, 13–27.

pubmed: 27693506 pmcid: 5104201 doi: 10.1016/j.devcel.2016.08.003

Chio, U.S., Cho, H., and Shan, S. (2017). Mechanisms of tail-anchored membrane protein targeting and insertion. Annu Rev Cell Dev Biol 33, 417–438.

pubmed: 28992441 pmcid: 6343671 doi: 10.1146/annurev-cellbio-100616-060839

Chowdhury, S., Otomo, C., Leitner, A., Ohashi, K., Aebersold, R., Lander, G.C., and Otomo, T. (2018). Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. Proc Natl Acad Sci USA 115, E9792–E9801.

pubmed: 30185561 pmcid: 6196511 doi: 10.1073/pnas.1811874115

Chung, J., Torta, F., Masai, K., Lucast, L., Czapla, H., Tanner, L.B., Narayanaswamy, P., Wenk, M.R., Nakatsu, F., and De Camilli, P. (2015). PI4P/phosphatidylserine countertransport at ORP5- and ORP8-mediated ER-plasma membrane contacts. Science 349, 428–432.

pubmed: 26206935 pmcid: 4638224 doi: 10.1126/science.aab1370

Clark, B.J. (2012). The mammalian START domain protein family in lipid transport in health and disease. J Endocrinol 212, 257–275.

pubmed: 21965545 doi: 10.1530/JOE-11-0313

Cockcroft, S., Garner, K., Yadav, S., Gomez-Espinoza, E., and Raghu, P. (2016). RdgBa reciprocally transfers PA and PI at ER-PM contact sites to maintain PI(4,5)P

pubmed: 26862217 doi: 10.1042/BST20150228

Cohen, S., Valm, A.M., and Lippincott-Schwartz, J. (2018). Interacting organelles. Curr Opin Cell Biol 53, 84–91.

pubmed: 30006038 pmcid: 6241252 doi: 10.1016/j.ceb.2018.06.003

Collado, J., Kalemanov, M., Campelo, F., Bourgoint, C., Thomas, F., Loewith, R., Martínez-Sánchez, A., Baumeister, W., Stefan, C.J., and Fernández-Busnadiego, R. (2019). Tricalbin-mediated contact sites control ER curvature to maintain plasma membrane integrity. Dev Cell 51, 476–487.e7.

pubmed: 31743662 pmcid: 6863395 doi: 10.1016/j.devcel.2019.10.018

Connelly, S.V., Manzella-Lapeira, J., Levine, Z.C., Brzostowski, J., Krymskaya, L., Rahman, R.S., Ellis, A.C., Amin, S.N., Sa, J.M., Wellems, T.E., et al. (2021). Restructured mitochondrial-nuclear interaction in Plasmodium falciparum dormancy and persister survival after artemisinin exposure. mBio 12, e0075321.

pubmed: 34044591 doi: 10.1128/mBio.00753-21

Csordas, G., Weaver, D., and Hajnoczky, G. (2018). Endoplasmic reticulum-mitochondrial contactology: structure and signaling functions. Trends Cell Biol 28, 523–540.

pubmed: 29588129 pmcid: 6005738 doi: 10.1016/j.tcb.2018.02.009

Datta, S., Liu, Y., Hariri, H., Bowerman, J., and Henne, W.M. (2019). Cerebellar ataxia disease-associated Snx14 promotes lipid droplet growth at ER-droplet contacts. J Cell Biol 218, 1335–1351.

pubmed: 30765438 pmcid: 6446855 doi: 10.1083/jcb.201808133

de Brito, O.M., and Scorrano, L. (2008). Mitofusin 2 tethers endoplasmic reticulum to mitochondria. Nature 456, 605–610.

pubmed: 19052620 doi: 10.1038/nature07534

De Matteis, M.A., and Rega, L.R. (2015). Endoplasmic reticulum-Golgi complex membrane contact sites. Curr Opin Cell Biol 35, 43–50.

pubmed: 25950841 doi: 10.1016/j.ceb.2015.04.001

De Vos, K.J., Mórotz, G.M., Stoica, R., Tudor, E.L., Lau, K.F., Ackerley, S., Warley, A., Shaw, C.E., and Miller, C.C.J. (2012). VAPB interacts with the mitochondrial protein PTPIP51 to regulate calcium homeostasis. Hum Mol Genet 21, 1299–1311.

pubmed: 22131369 doi: 10.1093/hmg/ddr559

Desai, R., East, D.A., Hardy, L., Faccenda, D., Rigon, M., Crosby, J., Alvarez, M.S., Singh, A., Mainenti, M., Hussey, L.K., et al. (2020). Mitochondria form contact sites with the nucleus to couple prosurvival retrograde response. Sci Adv 6, eabc9955.

pubmed: 33355129 doi: 10.1126/sciadv.abc9955

Di Mattia, T., Wilhelm, L.P., Ikhlef, S., Wendling, C., Spehner, D., Nomine, Y., Giordano, F., Mathelin, C., Drin, G., Tomasetto, C., et al. (2020). Faraway, so close! Functions of Endoplasmic reticulum-Endosome contacts. Biochim Biophys Acta Mol Cell Biol Lipids 1865, 158490.

pubmed: 31252175 doi: 10.1016/j.bbalip.2019.06.016

Di Mattia, T., Wilhelm, L.P., Ikhlef, S., Wendling, C., Spehner, D., Nomine, Y., Giordano, F., Mathelin, C., Drin, G., Tomasetto, C., et al. (2018). Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites. EMBO Rep 19, e45453.

pubmed: 29858488 pmcid: 6030701 doi: 10.15252/embr.201745453

Dimitrov, L., Lam, S.K., and Schekman, R. (2013). The role of the endoplasmic reticulum in peroxisome biogenesis. Cold Spring Harb Perspect Biol 5, a013243.

pubmed: 23637287 pmcid: 3632059 doi: 10.1101/cshperspect.a013243

Ding, L., Yang, X., Tian, H., Liang, J.J., Zhang, F.X., Wang, G.D., Wang, Y.C., Ding, M., Shui, G.H., and Huang, X. (2018). Seipin regulates lipid homeostasis by ensuring calcium-dependent mitochondrial metabolism. EMBO J 37, e97572.

pubmed: 30049710 pmcid: 6120665 doi: 10.15252/embj.201797572

Doghman-Bouguerra, M., Granatiero, V., Sbiera, S., Sbiera, I., Lacas-Gervais, S., Brau, F., Fassnacht, M., Rizzuto, R., and Lalli, E. (2016). FATE1 antagonizes calcium- and drug-induced apoptosis by uncoupling ER and mitochondria. EMBO Rep 17, 1264–1280.

pubmed: 27402544 pmcid: 5007562 doi: 10.15252/embr.201541504

Dong, J., Du, X., Wang, H., Wang, J., Lu, C., Chen, X., Zhu, Z., Luo, Z., Yu, L., Brown, A.J., et al. (2019). Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P

pubmed: 30783101 pmcid: 6381110 doi: 10.1038/s41467-019-08791-0

Dong, R., Saheki, Y., Swarup, S., Lucast, L., Harper, J.W., and De Camilli, P. (2016). Endosome-ER contacts control actin nucleation and retromer function through VAP-dependent regulation of PI4P. Cell 166, 408–423.

pubmed: 27419871 pmcid: 4963242 doi: 10.1016/j.cell.2016.06.037

Du, X., Kumar, J., Ferguson, C., Schulz, T.A., Ong, Y.S., Hong, W., Prinz, W.A., Parton, R.G., Brown, A.J., and Yang, H. (2011). A role for oxysterol-binding protein-related protein 5 in endosomal cholesterol trafficking. J Cell Biol 192, 121–135.

pubmed: 21220512 pmcid: 3019559 doi: 10.1083/jcb.201004142

Du, X., Zhou, L., Aw, Y.C., Mak, H.Y., Xu, Y., Rae, J., Wang, W., Zadoorian, A., Hancock, S.E., Osborne, B., et al. (2020). ORP5 localizes to ER-lipid droplet contacts and regulates the level of PI(4)P on lipid droplets. J Cell Biol 219, e201905162.

pubmed: 31653673 doi: 10.1083/jcb.201905162

Eapen, V.V., Swarup, S., Hoyer, M.J., Paulo, J.A., and Harper, J.W. (2021). Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy. eLife 10, e72328.

pubmed: 34585663 pmcid: 8523161 doi: 10.7554/eLife.72328

Eden, E.R., Sanchez-Heras, E., Tsapara, A., Sobota, A., Levine, T.P., and Futter, C.E. (2016). Annexin A1 tethers membrane contact sites that mediate ER to endosome cholesterol transport. Dev Cell 37, 473–483.

pubmed: 27270042 pmcid: 4906250 doi: 10.1016/j.devcel.2016.05.005

Eden, E.R., White, I.J., Tsapara, A., and Futter, C.E. (2010). Membrane contacts between endosomes and ER provide sites for PTP1B-epidermal growth factor receptor interaction. Nat Cell Biol 12, 267–272.

pubmed: 20118922 doi: 10.1038/ncb2026

Eisenberg-Bord, M., Zung, N., Collado, J., Drwesh, L., Fenech, E.J., Fadel, A., Dezorella, N., Bykov, Y.S., Rapaport, D., Fernandez-Busnadiego, R., et al. (2021). Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels. J Cell Biol 220, e202104100.

pubmed: 34694322 pmcid: 8548916 doi: 10.1083/jcb.202104100

Encinar Del Dedo, J., Fernandez-Golbano, I.M., Pastor, L., Meler, P., Ferrer-Orta, C., Rebollo, E., and Geli, M.I. (2021). Coupled sterol synthesis and transport machineries at ER-endocytic contact sites. J Cell Biol 220, e202010016.

pubmed: 34283201 pmcid: 8294947 doi: 10.1083/jcb.202010016

Endo, M. (2009). Calcium-induced calcium release in skeletal muscle. Physiol Rev 89, 1153–1176.

pubmed: 19789379 doi: 10.1152/physrev.00040.2008

Ercan, B., Naito, T., Koh, D.H.Z., Dharmawan, D., and Saheki, Y. (2021). Molecular basis of accessible plasma membrane cholesterol recognition by the GRAM domain of GRAMD1b. EMBOJ40, e106524.

Faelber, K., Dietrich, L., Noel, J.K., Wollweber, F., Pfitzner, A.K., Mühleip, A., Sanchez, R., Kudryashev, M., Chiaruttini, N., Lilie, H., et al. (2019). Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1. Nature 571, 429–433.

pubmed: 31292547 pmcid: 7116848 doi: 10.1038/s41586-019-1372-3

Farias, G.G., Freal, A., Tortosa, E., Stucchi, R., Pan, X., Portegies, S., Will, L., Altelaar, M., and Hoogenraad, C.C. (2019). Feedback-driven mechanisms between microtubules and the endoplasmic reticulum instruct neuronal polarity. Neuron 102, 184–201.e8.

Fei, W.H., Shui, G.H., Gaeta, B., Du, X.M., Kuerschner, L., Li, P., Brown, A.J., Wenk, M.R., Parton, R.G., and Yang, H. (2008). Fld1p, a functional homologue of human seipin, regulates the size of lipid droplets in yeast. J Cell Biol 180, 473–482.

pubmed: 18250201 pmcid: 2234226 doi: 10.1083/jcb.200711136

Feng, Y., He, D., Yao, Z., and Klionsky, D.J. (2014). The machinery of macroautophagy. Cell Res 24, 24–41.

pubmed: 24366339 doi: 10.1038/cr.2013.168

Feng, Z., Yang, K., and Pastor-Pareja, J.C. (2021). Tales of the ER-Golgi Frontier: Drosophila-centric considerations on Tango1 function. Front Cell Dev Biol 8, 619022.

pubmed: 33505971 pmcid: 7829582 doi: 10.3389/fcell.2020.619022

Fernandez-Busnadiego, R., Saheki, Y., and De Camilli, P. (2015). Three-dimensional architecture of extended synaptotagmin-mediated endoplasmic reticulum-plasma membrane contact sites. Proc Natl Acad Sci USA 112, E2004-2013.

Ferrari, A., He, C., Kennelly, J.P., Sandhu, J., Xiao, X., Chi, X., Jiang, H., Young, S.G., and Tontonoz, P. (2020). Aster proteins regulate the accessible cholesterol pool in the plasma membrane. Mol Cell Biol 40, e00255–20.

pubmed: 32719109 pmcid: 7491948 doi: 10.1128/MCB.00255-20

Feske, S., Gwack, Y., Prakriya, M., Srikanth, S., Puppel, S.H., Tanasa, B., Hogan, P.G., Lewis, R.S., Daly, M., and Rao, A. (2006). A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function. Nature 441, 179–185.

pubmed: 16582901 doi: 10.1038/nature04702

Filadi, R., Greotti, E., Turacchio, G., Luini, A., Pozzan, T., and Pizzo, P. (2015). Mitofusin 2 ablation increases endoplasmic reticulum-mitochondria coupling. Proc Natl Acad Sci USA 112, E2174–2181.

pubmed: 25870285 pmcid: 4418914 doi: 10.1073/pnas.1504880112

Fischer, M.A., Temmerman, K., Ercan, E., Nickel, W., and Seedorf, M. (2009). Binding of plasma membrane lipids recruits the yeast integral membrane protein Ist2 to the cortical ER. Traffic 10, 1084–1097.

pubmed: 19453974 doi: 10.1111/j.1600-0854.2009.00926.x

Fox, P.D., Haberkorn, C.J., Akin, E.J., Seel, P.J., Krapf, D., and Tamkun, M.M. (2015). Induction of stable ER-plasma-membrane junctions by Kv2.1 potassium channels. J Cell Sci 128, 2096–2105.

pubmed: 25908859 pmcid: 4457025 doi: 10.1242/jcs.166009

Friedman, J.R., DiBenedetto, J.R., West, M., Rowland, A.A., and Voeltz, G.K. (2013). Endoplasmic reticulum-endosome contact increases as endosomes traffic and mature. Mol Biol Cell 24, 1030–1040.

pubmed: 23389631 pmcid: 3608491 doi: 10.1091/mbc.e12-10-0733

Friedman, J.R., Lackner, L.L., West, M., DiBenedetto, J.R., Nunnari, J., and Voeltz, G.K. (2011). ER tubules mark sites of mitochondrial division. Science 334, 358–362.

pubmed: 21885730 pmcid: 3366560 doi: 10.1126/science.1207385

Fromme, J.C., and Schekman, R. (2005). COPII-coated vesicles: flexible enough for large cargo? Curr Opin Cell Biol 17, 345–352.

pubmed: 15975775 doi: 10.1016/j.ceb.2005.06.004

Fukasawa, M., Nishijima, M., and Hanada, K. (1999). Genetic evidence for ATP-dependent endoplasmic reticulum-to-Golgi apparatus trafficking of ceramide for sphingomyelin synthesis in Chinese hamster ovary cells. J Cell Biol 144, 673–685.

pubmed: 10037789 pmcid: 2132924 doi: 10.1083/jcb.144.4.673

Galione, A., Morgan, A.J., Arredouani, A., Davis, L.C., Rietdorf, K., Ruas, M., and Parrington, J. (2010). NAADP as an intracellular messenger regulating lysosomal calcium-release channels. Biochem Soc Trans 38, 1424–1431.

pubmed: 21118101 doi: 10.1042/BST0381424

Galmes, R., Houcine, A., van Vliet, A.R., Agostinis, P., Jackson, C.L., and Giordano, F. (2016). ORP5/ORP8 localize to endoplasmic reticulum-mitochondria contacts and are involved in mitochondrial function. EMBO Rep 17, 800–810.

pubmed: 27113756 pmcid: 5278607 doi: 10.15252/embr.201541108

Gao, G., Sheng, Y., Yang, H., Chua, B.T., and Xu, L. (2019a). DFCP1 associates with lipid droplets. Cell Biol Int 43, 1492–1504.

pubmed: 31293035 doi: 10.1002/cbin.11199

Gao, M., Huang, X., Song, B.L., and Yang, H. (2019b). The biogenesis of lipid droplets: lipids take center stage. Prog Lipid Res 75, 100989.

pubmed: 31351098 doi: 10.1016/j.plipres.2019.100989

Gatta, A.T., Wong, L.H., Sere, Y.Y., Calderon-Norena, D.M., Cockcroft, S., Menon, A. K., and Levine, T.P. (2015). A new family of StART domain proteins at membrane contact sites has a role in ER-PM sterol transport. eLife 4, e07253.

pubmed: 26001273 pmcid: 4463742 doi: 10.7554/eLife.07253

Ge, J., Bian, X., Ma, L., Cai, Y., Li, Y., Yang, J., Karatekin, E., De Camilli, P., and Zhang, Y. (2022). Stepwise membrane binding of extended synaptotagmins revealed by optical tweezers. Nat Chem Biol 18, 313–320.

pubmed: 34916620 doi: 10.1038/s41589-021-00914-3

Ge, L., Melville, D., Zhang, M., and Schekman, R. (2013). The ER-Golgi intermediate compartment is a key membrane source for the LC3 lipidation step of autophagosome biogenesis. eLife 2, e00947.

pubmed: 23930225 pmcid: 3736544 doi: 10.7554/eLife.00947

Ge, L., Zhang, M., Kenny, S.J., Liu, D., Maeda, M., Saito, K., Mathur, A., Xu, K., and Schekman, R. (2017). Remodeling of ER-exit sites initiates a membrane supply pathway for autophagosome biogenesis. EMBO Rep 18, 1586–1603.

pubmed: 28754694 pmcid: 5579361 doi: 10.15252/embr.201744559

Ge, L., Zhang, M., and Schekman, R. (2014). Phosphatidylinositol 3-kinase and COPII generate LC3 lipidation vesicles from the ER-Golgi intermediate compartment. eLife 3, e04135.

pubmed: 25432021 pmcid: 4270069 doi: 10.7554/eLife.04135

Gelmetti, V., De Rosa, P., Torosantucci, L., Marini, E.S., Romagnoli, A., Di Rienzo, M., Arena, G., Vignone, D., Fimia, G.M., and Valente, E.M. (2017). PINK1 and BECN1 relocalize at mitochondria-associated membranes during mitophagy and promote ER-mitochondria tethering and autophagosome formation. Autophagy 13, 654–669.

pubmed: 28368777 pmcid: 5388214 doi: 10.1080/15548627.2016.1277309

Gerasimenko, J.V., Charlesworth, R.M., Sherwood, M.W., Ferdek, P.E., Mikoshiba, K., Parrington, J., Petersen, O.H., and Gerasimenko, O.V. (2015). Both RyRs and TPCs are required for NAADP-induced intracellular Ca

pubmed: 26100948 pmcid: 4539342 doi: 10.1016/j.ceca.2015.05.005

Ghai, R., Du, X., Wang, H., Dong, J., Ferguson, C., Brown, A.J., Parton, R.G., Wu, J. W., and Yang, H. (2017). ORP5 and ORP8 bind phosphatidylinositol-4,5-biphosphate (PtdIns(4,5)P

pubmed: 28970484 pmcid: 5624964 doi: 10.1038/s41467-017-00861-5

Ghanbarpour, A., Valverde, D.P., Melia, T.J., and Reinisch, K.M. (2021). A model for a partnership of lipid transfer proteins and scramblases in membrane expansion and organelle biogenesis. Proc Natl Acad Sci USA 118, e2101562118.

pubmed: 33850023 pmcid: 8072408 doi: 10.1073/pnas.2101562118

Giordano, F., Saheki, Y., Idevall-Hagren, O., Colombo, S.F., Pirruccello, M., Milosevic, I., Gracheva, E.O., Bagriantsev, S.N., Borgese, N., and De Camilli, P. (2013). PI(4,5) P

pubmed: 23791178 pmcid: 3716012 doi: 10.1016/j.cell.2013.05.026

Golini, L., Chouabe, C., Berthier, C., Cusimano, V., Fornaro, M., Bonvallet, R., Formoso, L., Giacomello, E., Jacquemond, V., and Sorrentino, V. (2011). Junctophilin 1 and 2 proteins interact with the L-type Ca

pubmed: 22020936 pmcid: 3243543 doi: 10.1074/jbc.M111.292755

Gomez-Navarro, N., and Miller, E. (2016). Protein sorting at the ER-Golgi interface. J Cell Biol 215, 769–778.

pubmed: 27903609 pmcid: 5166505 doi: 10.1083/jcb.201610031

Gomez-Sanchez, R., Rose, J., Guimaraes, R., Mari, M., Papinski, D., Rieter, E., Geerts, W.J., Hardenberg, R., Kraft, C., Ungermann, C., et al. (2018). Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores. J Cell Biol 217, 2743–2763.

pubmed: 29848619 pmcid: 6080931 doi: 10.1083/jcb.201710116

Gomez-Sanchez, R., Tooze, S.A., and Reggiori, F. (2021). Membrane supply and remodeling during autophagosome biogenesis. Curr Opin Cell Biol 71, 112–119.

pubmed: 33930785 doi: 10.1016/j.ceb.2021.02.001

Gómez-Suaga, P., Bravo-San Pedro, J.M., González-Polo, R.A., Fuentes, J.M., and Niso-Santano, M. (2018). ER-mitochondria signaling in Parkinson’s disease. Cell Death Dis 9, 337.

pubmed: 29497039 pmcid: 5832754 doi: 10.1038/s41419-017-0079-3

Gomez-Suaga, P., Paillusson, S., and Miller, C.C.J. (2017). ER-mitochondria signaling regulates autophagy. Autophagy 13, 1250–1251.

pubmed: 28548902 pmcid: 5529068 doi: 10.1080/15548627.2017.1317913

Graef, M., Friedman, J.R., Graham, C., Babu, M., and Nunnari, J. (2013). ER exit sites are physical and functional core autophagosome biogenesis components. Mol Biol Cell 24, 2918–2931.

pubmed: 23904270 pmcid: 3771953 doi: 10.1091/mbc.e13-07-0381

Grippa, A., Buxó, L., Mora, G., Funaya, C., Idrissi, F.Z., Mancuso, F., Gomez, R., Muntanyà, J., Sabidó, E., and Carvalho, P. (2015). The seipin complex Fld1/Ldb16 stabilizes ER-lipid droplet contact sites. J Cell Biol 211, 829–844.

pubmed: 26572621 pmcid: 4657162 doi: 10.1083/jcb.201502070

Guardia, C.M., Farias, G.G., Jia, R., Pu, J., and Bonifacino, J.S. (2016). BORC functions upstream of Kinesins 1 and 3 to coordinate regional movement of lysosomes along different microtubule tracks. Cell Rep 17, 1950–1961.

pubmed: 27851960 pmcid: 5136296 doi: 10.1016/j.celrep.2016.10.062

Guillén-Samander, A., Bian, X., and De Camilli, P. (2019). PDZD8 mediates a Rab7-dependent interaction of the ER with late endosomes and lysosomes. Proc Natl Acad Sci USA 116, 22619–22623.

pubmed: 31636202 pmcid: 6842579 doi: 10.1073/pnas.1913509116

Guillén-Samander, A., and De Camilli, P. (2023). Endoplasmic reticulum membrane contact sites, lipid transport, and neurodegeneration. Cold Spring Harb Perspect Biol 15, a041257.

pubmed: 36123033 doi: 10.1101/cshperspect.a041257

Guna, A., Stevens, T.A., Inglis, A.J., Replogle, J.M., Esantsi, T.K., Muthukumar, G., Shaffer, K.C.L., Wang, M.L., Pogson, A.N., Jones, J.J., et al. (2022). MTCH2 is a mitochondrial outer membrane protein insertase. Science 378, 317–322.

pubmed: 36264797 pmcid: 9674023 doi: 10.1126/science.add1856

Guo, Y., Li, D., Zhang, S., Yang, Y., Liu, J.J., Wang, X., Liu, C., Milkie, D.E., Moore, R. P., Tulu, U.S., et al. (2018). Visualizing intracellular organelle and cytoskeletal interactions at nanoscale resolution on millisecond timescales. Cell 175, 1430–1442.e17.

Gutierrez, T., and Simmen, T. (2018). Endoplasmic reticulum chaperones tweak the mitochondrial calcium rheostat to control metabolism and cell death. Cell Calcium 70, 64–75.

pubmed: 28619231 doi: 10.1016/j.ceca.2017.05.015

Güttinger, S., Laurell, E., and Kutay, U. (2009). Orchestrating nuclear envelope disassembly and reassembly during mitosis. Nat Rev Mol Cell Biol 10, 178–191.

pubmed: 19234477 doi: 10.1038/nrm2641

Haj, F.G., Verveer, P.J., Squire, A., Neel, B.G., and Bastiaens, P.I.H. (2002). Imaging sites of receptor dephosphorylation by PTP1B on the surface of the endoplasmic reticulum. Science 295, 1708–1711.

pubmed: 11872838 doi: 10.1126/science.1067566

Hamasaki, M., Furuta, N., Matsuda, A., Nezu, A., Yamamoto, A., Fujita, N., Oomori, H., Noda, T., Haraguchi, T., Hiraoka, Y., et al. (2013). Autophagosomes form at ER-mitochondria contact sites. Nature 495, 389–393.

pubmed: 23455425 doi: 10.1038/nature11910

Hanada, K., Kumagai, K., Yasuda, S., Miura, Y., Kawano, M., Fukasawa, M., and Nishijima, M. (2003). Molecular machinery for non-vesicular trafficking of ceramide. Nature 426, 803–809.

pubmed: 14685229 doi: 10.1038/nature02188

Hancock-Cerutti, W., Wu, Z., Xu, P., Yadavalli, N., Leonzino, M., Tharkeshwar, A.K., Ferguson, S.M., Shadel, G.S., and De Camilli, P. (2022). ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling. J Cell Biol 221, e202106046.

pubmed: 35657605 pmcid: 9170524 doi: 10.1083/jcb.202106046

Hanna, M.G., Block, S., Frankel, E.B., Hou, F., Johnson, A., Yuan, L., Knight, G., Moresco, J.J., Yates, J.R., Ashton, R., et al. (2017). TFG facilitates outer coat disassembly on COPII transport carriers to promote tethering and fusion with ER-Golgi intermediate compartments. Proc Natl Acad Sci USA 114, E7707–E7716.

pubmed: 28851831 pmcid: 5604033 doi: 10.1073/pnas.1709120114

Harada, A., Takei, Y., Kanai, Y., Tanaka, Y., Nonaka, S., and Hirokawa, N. (1998). Golgi vesiculation and Lysosome dispersion in cells lacking cytoplasmic dynein. J Cell Biol 141, 51–59.

pubmed: 9531547 pmcid: 2132725 doi: 10.1083/jcb.141.1.51

Hariri, H., Speer, N., Bowerman, J., Rogers, S., Fu, G., Reetz, E., Datta, S., Feathers, J. R., Ugrankar, R., Nicastro, D., et al. (2019). Mdm1 maintains endoplasmic reticulum homeostasis by spatially regulating lipid droplet biogenesis. J Cell Biol 218, 1319–1334.

pubmed: 30808705 pmcid: 6446837 doi: 10.1083/jcb.201808119

Hayashi, T., Rizzuto, R., Hajnoczky, G., and Su, T.P. (2009). MAM: more than just a housekeeper. Trends Cell Biol 19, 81–88.

pubmed: 19144519 pmcid: 2750097 doi: 10.1016/j.tcb.2008.12.002

Hayashi-Nishino, M., Fujita, N., Noda, T., Yamaguchi, A., Yoshimori, T., and Yamamoto, A. (2009). A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Nat Cell Biol 11, 1433–1437.

pubmed: 19898463 doi: 10.1038/ncb1991

Helle, S.C.J., Kanfer, G., Kolar, K., Lang, A., Michel, A.H., and Kornmann, B. (2013). Organization and function ofmembrane contact sites. Biochim Biophys Acta 1833, 2526–2541.

pubmed: 23380708 doi: 10.1016/j.bbamcr.2013.01.028

Henkart, M., Landis, D.M., and Reese, T.S. (1976). Similarity of junctions between plasma membranes and endoplasmic reticulum in muscle and neurons. J Cell Biol 70, 338–347.

pubmed: 939781 doi: 10.1083/jcb.70.2.338

Hirabayashi, Y., Kwon, S.K., Paek, H., Pernice, W.M., Paul, M.A., Lee, J., Erfani, P., Raczkowski, A., Petrey, D.S., Pon, L.A., et al. (2017). ER-mitochondria tethering by PDZD8 regulates Ca

pubmed: 29097544 pmcid: 5818999 doi: 10.1126/science.aan6009

Hoffmann, P.C., Bharat, T.A.M., Wozny, M.R., Boulanger, J., Miller, E.A., and Kukulski, W. (2019). Tricalbins contribute to cellular lipid flux and form curved ER-PM contacts that are bridged by rod-shaped structures. Dev Cell 51, 488–502. e8.

pubmed: 31743663 pmcid: 6863393 doi: 10.1016/j.devcel.2019.09.019

Hoglinger, D., Burgoyne, T., Sanchez-Heras, E., Hartwig, P., Colaco, A., Newton, J., Futter, C.E., Spiegel, S., Platt, F.M., and Eden, E.R. (2019). NPC1 regulates ER contacts with endocytic organelles to mediate cholesterol egress. Nat Commun 10, 4276.

pubmed: 31537798 pmcid: 6753064 doi: 10.1038/s41467-019-12152-2

Holmes, S.E., O’Hearn, E., Rosenblatt, A., Callahan, C., Hwang, H.S., Ingersoll-Ashworth, R.G., Fleisher, A., Stevanin, G., Brice, A., Potter, N.T., et al. (2001). A repeat expansion in the gene encoding junctophilin-3 is associated with Huntington disease-like 2. Nat Genet 29, 377–378.

pubmed: 11694876 doi: 10.1038/ng760

Hong, Z., Adlakha, J., Wan, N., Guinn, E., Giska, F., Gupta, K., Melia, T.J., and Reinisch, K.M. (2022). Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation. J Cell Biol 221, e202207022.

pubmed: 36282247 pmcid: 9597353 doi: 10.1083/jcb.202207022

Horenkamp, F.A., Valverde, D.P., Nunnari, J., and Reinisch, K.M. (2018). Molecular basis for sterol transport by StART-like lipid transfer domains. EMBO J 37, e98002.

pubmed: 29467216 pmcid: 5852651 doi: 10.15252/embj.201798002

Hoth, M., and Penner, R. (1992). Depletion of intracellular calcium stores activates a calcium current in mast cells. Nature 355, 353–356.

pubmed: 1309940 doi: 10.1038/355353a0

Hoyer, M.J., Chitwood, P.J., Ebmeier, C.C., Striepen, J.F., Qi, R.Z., Old, W.M., and Voeltz, G.K. (2018). A novel class of ER membrane proteins regulates ER-associated endosome fission. Cell 175, 254–265.e14.

pubmed: 30220460 pmcid: 6195207 doi: 10.1016/j.cell.2018.08.030

Hugenroth, M., and Bohnert, M. (2020). Come a little bit closer! Lipid droplet-ER contact sites are getting crowded. Biochim Biophys Acta 1867, 118603.

doi: 10.1016/j.bbamcr.2019.118603

Hughes, H., Budnik, A., Schmidt, K., Palmer, K.J., Mantell, J., Noakes, C., Johnson, A., Carter, D.A., Verkade, P., Watson, P., et al. (2009). Organisation ofhuman ER-exit sites: requirements for the localisation of Sec16 to transitional ER. J Cell Sci 122, 2924–2934.

pubmed: 19638414 pmcid: 2724609 doi: 10.1242/jcs.044032

Hung, V., Lam, S.S., Udeshi, N.D., Svinkina, T., Guzman, G., Mootha, V.K., Carr, S.A., and Ting, A.Y. (2017). Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. eLife 6, e24463.

pubmed: 28441135 pmcid: 5404927 doi: 10.7554/eLife.24463

Huotari, J., and Helenius, A. (2011). Endosome maturation. EMBO J 30, 3481–3500.

pubmed: 21878991 pmcid: 3181477 doi: 10.1038/emboj.2011.286

Iaea, D.B., Mao, S., Lund, F.W., and Maxfield, F.R. (2017). Role of STARD4 in sterol transport between the endocytic recycling compartment and the plasma membrane. Mol Biol Cell 28, 1111–1122.

pubmed: 28209730 pmcid: 5391187 doi: 10.1091/mbc.e16-07-0499

Iaea, D.B., Spahr, Z.R., Singh, R.K., Chan, R.B., Zhou, B., Bareja, R., Elemento, O., Di Paolo, G., Zhang, X., and Maxfield, F.R. (2020). Stable reduction of STARD4 alters cholesterol regulation and lipid homeostasis. Biochim Biophys Acta 1865, 158609.

doi: 10.1016/j.bbalip.2020.158609

Idevall-Hagren, O., Lu, A., Xie, B., and De Camilli, P. (2015). Triggered Ca

pubmed: 26202220 pmcid: 4585464 doi: 10.15252/embj.201591565

Jacquemyn, J., Cascalho, A., and Goodchild, R.E. (2017). The ins and outs of endoplasmic reticulum-controlled lipid biosynthesis. EMBO Rep 18, 1905–1921.

pubmed: 29074503 pmcid: 5666603 doi: 10.15252/embr.201643426

Jansen, M., Ohsaki, Y., Rita Rega, L., Bittman, R., Olkkonen, V.M., and Ikonen, E. (2011). Role of ORPs in sterol transport from plasma membrane to ER and lipid droplets in mammalian cells. Traffic 12, 218–231.

pubmed: 21062391 doi: 10.1111/j.1600-0854.2010.01142.x

Jensen, D., and Schekman, R. (2011). COPII-mediated vesicle formation at a glance. J Cell Sci 124, 1–4.

pubmed: 21172817 doi: 10.1242/jcs.069773

Jentsch, J.A., Kiburu, I., Pandey, K., Timme, M., Ramlall, T., Levkau, B., Wu, J., Eliezer, D., Boudker, O., and Menon, A.K. (2018). Structural basis of sterol binding and transport by a yeast StARkin domain. J Biol Chem 293, 5522–5531.

pubmed: 29463678 pmcid: 5900764 doi: 10.1074/jbc.RA118.001881

Jeyasimman, D., and Saheki, Y. (2020). SMP domain proteins in membrane lipid dynamics. Biochim Biophys Acta 1865, 158447.

doi: 10.1016/j.bbalip.2019.04.007

Jha, A., Ahuja, M., Patel, S., Brailoiu, E., and Muallem, S. (2014). Convergent regulation of the lysosomal two-pore channel-2 by Mg

pubmed: 24502975 pmcid: 3989630 doi: 10.1002/embj.201387035

Jha, A., Chung, W.Y., Vachel, L., Maleth, J., Lake, S., Zhang, G., Ahuja, M., and Muallem, S. (2019). Anoctamin 8 tethers endoplasmic reticulum and plasma membrane for assembly of Ca

pubmed: 31061173 pmcid: 6576175 doi: 10.15252/embj.2018101452

Ji, C., Zhao, H., Chen, D., Zhang, H., and Zhao, Y.G. (2021). β-propeller proteins WDR45 and WDR45B regulate autophagosome maturation into autolysosomes in neural cells. Curr Biol 31, 1666–1677.e6.

pubmed: 33636118 doi: 10.1016/j.cub.2021.01.081

Jing, J., He, L., Sun, A., Quintana, A., Ding, Y., Ma, G., Tan, P., Liang, X., Zheng, X., Chen, L., et al. (2015). Proteomic mapping of ER-PM junctions identifies STIMATE as a regulator of Ca

pubmed: 26322679 pmcid: 4589512 doi: 10.1038/ncb3234

Johannes, L., Jacob, R., and Leffler, H. (2018). Galectins at a glance. J Cell Sci 131, jcs208884.

pubmed: 29717004 doi: 10.1242/jcs.208884

Johansson, M., Rocha, N., Zwart, W., Jordens, I., Janssen, L., Kuijl, C., Olkkonen, V.M., and Neefjes, J. (2007). Activation of endosomal dynein motors by stepwise assembly of Rab7-RILP-p150

pubmed: 17283181 pmcid: 2063981 doi: 10.1083/jcb.200606077

John Peter, A.T., Petrungaro, C., Peter, M., and Kornmann, B. (2022). METALIC reveals interorganelle lipid flux in live cells by enzymatic mass tagging. Nat Cell Biol 24, 996–1004.

pubmed: 35654841 pmcid: 9203272 doi: 10.1038/s41556-022-00917-9

Johnson, A., Bhattacharya, N., Hanna, M., Pennington, J.G., Schuh, A.L., Wang, L., Otegui, M.S., Stagg, S.M., and Audhya, A. (2015). TFG clusters COPII-coated transport carriers and promotes early secretory pathway organization. EMBO J 34, 811–827.

pubmed: 25586378 pmcid: 4369316 doi: 10.15252/embj.201489032

Johnson, B., Leek, A.N., Solé, L., Maverick, E.E., Levine, T.P., and Tamkun, M.M. (2018). Kv2 potassium channels form endoplasmic reticulum/plasma membrane junctions via interaction with VAPA and VAPB. Proc Natl Acad Sci USA 115, E7331–E7340.

pubmed: 29941597 pmcid: 6077746 doi: 10.1073/pnas.1805757115

Jongsma, M.L.M., Berlin, I., Wijdeven, R.H.M., Janssen, L., Janssen, G.M.C., Garstka, M.A., Janssen, H., Mensink, M., van Veelen, P.A., Spaapen, R.M., et al. (2016). An ER-associated pathway defines endosomal architecture for controlled cargo transport. Cell 166, 152–166.

pubmed: 27368102 pmcid: 4930482 doi: 10.1016/j.cell.2016.05.078

Kaiser, S.E., Brickner, J.H., Reilein, A.R., Fenn, T.D., Walter, P., and Brunger, A.T. (2005). Structural basis of FFAT motif-mediated ER targeting. Structure 13, 1035–1045.

pubmed: 16004875 doi: 10.1016/j.str.2005.04.010

Kameoka, S., Adachi, Y., Okamoto, K., Iijima, M., and Sesaki, H. (2018). Phosphatidic acid and cardiolipin coordinate mitochondrial dynamics. Trends Cell Biol 28, 67–76.

pubmed: 28911913 doi: 10.1016/j.tcb.2017.08.011

Kang, F., Zhou, M., Huang, X., Fan, J., Wei, L., Boulanger, J., Liu, Z., Salamero, J., Liu, Y., and Chen, L. (2019). E-syt1 re-arranges STIM1 clusters to stabilize ring-shaped ER-PM contact sites and accelerate Ca

pubmed: 30850711 pmcid: 6408583 doi: 10.1038/s41598-019-40331-0

Kawasaki, A., Sakai, A., Nakanishi, H., Hasegawa, J., Taguchi, T., Sasaki, J., Arai, H., Sasaki, T., Igarashi, M., and Nakatsu, F. (2022). PI4P/PS countertransport by ORP10 at ER-endosome membrane contact sites regulates endosome fission. J Cell Biol 221, e202103141.

pubmed: 34817532 doi: 10.1083/jcb.202103141

Kawasaki, T., Lange, I., and Feske, S. (2009). A minimal regulatory domain in the C terminus of STIM1 binds to and activates ORAI1 CRAC channels. Biochem Biophys Res Commun 385, 49–54.

pubmed: 19433061 pmcid: 2821023 doi: 10.1016/j.bbrc.2009.05.020

Kelu, J.J., Webb, S.E., Parrington, J., Galione, A., and Miller, A.L. (2017). Ca

pubmed: 28390800 pmcid: 6677577 doi: 10.1016/j.ydbio.2017.03.031

Kilpatrick, B.S., Eden, E.R., Hockey, L.N., Yates, E., Futter, C.E., and Patel, S. (2017). An endosomal NAADP-sensitive two-pore Ca

pubmed: 28199837 pmcid: 5318655 doi: 10.1016/j.celrep.2017.01.052

Kilpatrick, B.S., Eden, E.R., Schapira, A.H., Futter, C.E., and Patel, S. (2013). Direct mobilisation of lysosomal Ca

pubmed: 23108667 doi: 10.1242/jcs.118836

Kim, S., Coukos, R., Gao, F., and Krainc, D. (2022). Dysregulation of organelle membrane contact sites in neurological diseases. Neuron 110, 2386–2408.

pubmed: 35561676 pmcid: 9357093 doi: 10.1016/j.neuron.2022.04.020

Kim, S.H., Kedan, A., Marom, M., Gavert, N., Keinan, O., Selitrennik, M., Laufman, O., and Lev, S. (2013). The phosphatidylinositol-transfer protein Nir2 binds phosphatidic acid and positively regulates phosphoinositide signalling. EMBO Rep 14, 891–899.

pubmed: 23897088 pmcid: 3807235 doi: 10.1038/embor.2013.113

Kim, Y.J., Guzman-Hernandez, M.L., Wisniewski, E., and Balla, T. (2015). Phosphatidylinositol-phosphatidic acid exchange by Nir2 at ER-PM contact sites maintains phosphoinositide signaling competence. Dev Cell 33, 549–561.

pubmed: 26028218 pmcid: 4476625 doi: 10.1016/j.devcel.2015.04.028

Kinnaird, A., Zhao, S., Wellen, K.E., and Michelakis, E.D. (2016). Metabolic control of epigenetics in cancer. Nat Rev Cancer 16, 694–707.

pubmed: 27634449 doi: 10.1038/nrc.2016.82

Kinnear, N.P., Wyatt, C.N., Clark, J.H., Calcraft, P.J., Fleischer, S., Jeyakumar, L.H., Nixon, G.F., and Evans, A.M. (2008). Lysosomes co-localize with ryanodine receptor subtype 3 to form a trigger zone for calcium signalling by NAADP in rat pulmonary arterial smooth muscle. Cell Calcium 44, 190–201.

pubmed: 18191199 pmcid: 3982125 doi: 10.1016/j.ceca.2007.11.003

Kirmiz, M., Vierra, N.C., Palacio, S., and Trimmer, J.S. (2018). Identification of VAPA and VAPB as Kv2 channel-interacting proteins defining endoplasmic reticulum-plasma membrane junctions in mammalian brain neurons. J Neurosci 38, 7562–7584.

pubmed: 30012696 pmcid: 6113906 doi: 10.1523/JNEUROSCI.0893-18.2018

Kleele, T., Rey, T., Winter, J., Zaganelli, S., Mahecic, D., Perreten Lambert, H., Ruberto, F.P., Nemir, M., Wai, T., Pedrazzini, T., et al. (2021). Distinct fission signatures predict mitochondrial degradation or biogenesis. Nature 593, 435–439.

pubmed: 33953403 doi: 10.1038/s41586-021-03510-6

Kopec, K.O., Alva, V., and Lupas, A.N. (2010). Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria. Bioinformatics 26, 1927–1931.

pubmed: 20554689 pmcid: 2916718 doi: 10.1093/bioinformatics/btq326

Kornmann, B., Currie, E., Collins, S.R., Schuldiner, M., Nunnari, J., Weissman, J.S., and Walter, P. (2009). An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science 325, 477–481.

pubmed: 19556461 pmcid: 2933203 doi: 10.1126/science.1175088

Korobova, F., Ramabhadran, V., and Higgs, H.N. (2013). An actin-dependent step in mitochondrial fission mediated by the ER-associated formin INF2. Science 339, 464–467.

pubmed: 23349293 doi: 10.1126/science.1228360

Korzeniowski, M.K., Popovic, M.A., Szentpetery, Z., Varnai, P., Stojilkovic, S.S., and Balla, T. (2009). Dependence of STIM1/Orai1-mediated calcium entry on plasma membrane phosphoinositides. J Biol Chem 284, 21027–21035.

pubmed: 19483082 pmcid: 2742867 doi: 10.1074/jbc.M109.012252

Kotani, T., Kirisako, H., Koizumi, M., Ohsumi, Y., and Nakatogawa, H. (2018). The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation. Proc Natl Acad Sci USA 115, 10363–10368.

pubmed: 30254161 pmcid: 6187169 doi: 10.1073/pnas.1806727115

Kumagai, K., Kawano, M., Shinkai-Ouchi, F., Nishijima, M., and Hanada, K. (2007). Interorganelle trafficking of ceramide is regulated by phosphorylation-dependent cooperativity between the PH and START domains of CERT. J Biol Chem 282, 17758–17766.

pubmed: 17442665 doi: 10.1074/jbc.M702291200

Kumar, N., Leonzino, M., Hancock-Cerutti, W., Horenkamp, F.A., Li, P.Q., Lees, J.A., Wheeler, H., Reinisch, K.M., and De Camilli, P. (2018). VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites. J Cell Biol 217, 3625–3639.

pubmed: 30093493 pmcid: 6168267 doi: 10.1083/jcb.201807019

Kurokawa, K., Okamoto, M., and Nakano, A. (2014). Contact of cis-Golgi with ER exit sites executes cargo capture and delivery from the ER. Nat Commun 5, 3653.

pubmed: 24728174 doi: 10.1038/ncomms4653

Kwak, C., Shin, S., Park, J.S., Jung, M., Nhung, T.T.M., Kang, M.G., Lee, C., Kwon, T. H., Park, S.K., Mun, J.Y., et al. (2020). Contact-ID, a tool for profiling organelle contact sites, reveals regulatory proteins of mitochondrial-associated membrane formation. Proc Natl Acad Sci USA 117, 12109–12120.

pubmed: 32414919 pmcid: 7275737 doi: 10.1073/pnas.1916584117

Labbe, K., Mookerjee, S., Le Vasseur, M., Gibbs, E., Lerner, C., and Nunnari, J. (2021). The modified mitochondrial outer membrane carrier MTCH2 links mitochondrial fusion to lipogenesis. J Cell Biol 220, e202103122.

pubmed: 34586346 pmcid: 8496048 doi: 10.1083/jcb.202103122

Lacruz, R.S., and Feske, S. (2015). Diseases caused by mutations in ORAI1 and STIM1. Ann New York Acad Sci 1356, 45–79.

doi: 10.1111/nyas.12938

Landstrom, A.P., Beavers, D.L., and Wehrens, X.H.T. (2014). The junctophilin family of proteins: from bench to bedside. Trends Mol Med 20, 353–362.

pubmed: 24636942 pmcid: 4041816 doi: 10.1016/j.molmed.2014.02.004

Lang, A.B., Peter, A.T.J., Walter, P., and Kornmann, B. (2015). ER-mitochondrial junctions can be bypassed by dominant mutations in the endosomal protein Vps13. J Cell Biol 210, 883–890.

pubmed: 26370498 pmcid: 4576869 doi: 10.1083/jcb.201502105

Lang, S., Pfeffer, S., Lee, P.H., Cavalié, A., Helms, V., Förster, F., and Zimmermann, R. (2017). An update on Sec61 channel functions, mechanisms, and related diseases. Front Physiol 8, 887.

pubmed: 29163222 pmcid: 5672155 doi: 10.3389/fphys.2017.00887

Laraia, L., Friese, A., Corkery, D.P., Konstantinidis, G., Erwin, N., Hofer, W., Karatas, H., Klewer, L., Brockmeyer, A., Metz, M., et al. (2019). The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis. Nat Chem Biol 15, 710–720.

pubmed: 31222192 doi: 10.1038/s41589-019-0307-5

Lawrence, R.E., and Zoncu, R. (2019). The lysosome as a cellular centre for signalling, metabolism and quality control. Nat Cell Biol 21, 133–142.

pubmed: 30602725 doi: 10.1038/s41556-018-0244-7

Lee, I., and Hong, W. (2006). Diverse membrane-associated proteins contain a novel SMP domain. FASEB Journal 20, 202–206.

pubmed: 16449791 doi: 10.1096/fj.05-4581hyp

Lees, J.A., Messa, M., Sun, E.W., Wheeler, H., Torta, F., Wenk, M.R., De Camilli, P., and Reinisch, K.M. (2017). Lipid transport by TMEM24 at ER-plasma membrane contacts regulates pulsatile insulin secretion. Science 355, eaah6171.

pubmed: 28209843 pmcid: 5414417 doi: 10.1126/science.aah6171

Levin-Konigsberg, R., Montano-Rendón, F., Keren-Kaplan, T., Li, R., Ego, B., Mylvaganam, S., DiCiccio, J.E., Trimble, W.S., Bassik, M.C., Bonifacino, J.S., et al. (2019). Phagolysosome resolution requires contacts with the endoplasmic reticulum and phosphatidylinositol-4-phosphate signalling. Nat Cell Biol 21, 1234–1247.

pubmed: 31570833 pmcid: 8340083 doi: 10.1038/s41556-019-0394-2

Li, G., Su, B., Fu, P., Bai, Y., Ding, G., Li, D., Wang, J., Yang, G., and Chu, B. (2022a). NPC1-regulated dynamic of clathrin-coated pits is essential for viral entry. Sci China Life Sci 65, 341–361.

pubmed: 34047913 doi: 10.1007/s11427-021-1929-y

Li, P., Lees, J.A., Lusk, C.P., and Reinisch, K.M. (2020). Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes. J Cell Biol 219, e202001161.

pubmed: 32182622 pmcid: 7199853 doi: 10.1083/jcb.202001161

Li, S., Yan, R., Xu, J., Zhao, S., Ma, X., Sun, Q., Zhang, M., Li, Y., Liu, J.G., Chen, L., et al. (2022b). A new type of ERGIC-ERES membrane contact mediated by TMED9 and SEC12 is required for autophagosome biogenesis. Cell Res 32, 119–138.

pubmed: 34561617 doi: 10.1038/s41422-021-00563-0

Li, W., Zhang, S., and Yang, G. (2021a). Dynamic organization of intracellular organelle networks. WIREs Mech Dis 13, e1505.

pubmed: 32865347 doi: 10.1002/wsbm.1505

Li, Y.E., Wang, Y., Du, X., Zhang, T., Mak, H.Y., Hancock, S.E., McEwen, H., Pandzic, E., Whan, R.M., Aw, Y.C., et al. (2021b). TMEM41B and VMP1 are scramblases and regulate the distribution of cholesterol and phosphatidylserine. J Cell Biol 220, e202103105.

pubmed: 33929485 pmcid: 8077175 doi: 10.1083/jcb.202103105

Lim, C.Y., Davis, O.B., Shin, H.R., Zhang, J., Berdan, C.A., Jiang, X., Counihan, J.L., Ory, D.S., Nomura, D.K., and Zoncu, R. (2019). ER-lysosome contacts enable cholesterol sensing by mTORC1 and drive aberrant growth signalling in Niemann-Pick type C. Nat Cell Biol 21, 1206–1218.

pubmed: 31548609 pmcid: 6936960 doi: 10.1038/s41556-019-0391-5

Liou, J., Fivaz, M., Inoue, T., and Meyer, T. (2007). Live-cell imaging reveals sequential oligomerization and local plasma membrane targeting of stromal interaction molecule 1 after Ca

pubmed: 17517596 pmcid: 1890489 doi: 10.1073/pnas.0702866104

Liou, J., Kim, M.L., Do Heo, W., Jones, J.T., Myers, J.W., Ferrell, J.E. Jr., and Meyer, T. (2005). STIM is a Ca

pubmed: 16005298 pmcid: 3186072 doi: 10.1016/j.cub.2005.05.055

Litvak, V., Dahan, N., Ramachandran, S., Sabanay, H., and Lev, S. (2005). Maintenance of the diacylglycerol level in the Golgi apparatus by the Nir2 protein is critical for Golgi secretory function. Nat Cell Biol 7, 225–234.

pubmed: 15723057 doi: 10.1038/ncb1221

Liu, L., Yang, S., Liu, Y., Li, X., Hu, J., Xiao, L., and Xu, T. (2022). DeepContact: high-throughput quantification of membrane contact sites based on electron microscopy imaging. J Cell Biol 221, e202106190.

pubmed: 35929833 pmcid: 9361564 doi: 10.1083/jcb.202106190

Liu, M., Feng, Z., Ke, H., Liu, Y., Sun, T., Dai, J., Cui, W., and Pastor-Pareja, J.C. (2017). Tango1 spatially organizes ER exit sites to control ER export. J Cell Biol 216, 1035–1049.

pubmed: 28280122 pmcid: 5379956 doi: 10.1083/jcb.201611088

Liu, N., Zhao, H., Zhao, Y.G., Hu, J., and Zhang, H. (2021). Atlastin 2/3 regulate ER targeting of the ULK1 complex to initiate autophagy. J Cell Biol 220, e202012091.

pubmed: 33988678 pmcid: 8129792 doi: 10.1083/jcb.202012091

Liu, X., Guo, X., Niu, L., Li, X., Sun, F., Hu, J., Wang, X., and Shen, K. (2019a). Atlastin-1 regulates morphology and function of endoplasmic reticulum in dendrites. Nat Commun 10, 568.

pubmed: 30718476 pmcid: 6362286 doi: 10.1038/s41467-019-08478-6

Liu, Y., Ma, X., Fujioka, H., Liu, J., Chen, S., and Zhu, X. (2019b). DJ-1 regulates the integrity and function of ER-mitochondria association through interaction with IP3R3-Grp75-VDAC1. Proc Natl Acad Sci USA 116, 25322–25328.

pubmed: 31767755 pmcid: 6911199 doi: 10.1073/pnas.1906565116

Loewen, C.J., Roy, A., and Levine, T.P. (2003). A conserved ER targeting motif in three families of lipid binding proteins and in Opi1p binds VAP. EMBO J 22, 2025–2035.

pubmed: 12727870 pmcid: 156073 doi: 10.1093/emboj/cdg201

Lopez-Sanjurjo, C.I., Tovey, S.C., Prole, D.L., and Taylor, C.W. (2013). Lysosomes shape ins(1,4,5)P

pubmed: 23097044 pmcid: 3603520 doi: 10.1242/jcs.116103

Lu, M., van Tartwijk, F.W., Lin, J.Q., Nijenhuis, W., Parutto, P., Fantham, M., Christensen, C.N., Avezov, E., Holt, C.E., Tunnacliffe, A., et al. (2020). The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes. Sci Adv 6, eabc7209.

pubmed: 33328230 pmcid: 7744115 doi: 10.1126/sciadv.abc7209

Lu, Q., Yang, P., Huang, X., Hu, W., Guo, B., Wu, F., Lin, L., Kovacs, A.L., Yu, L., and Zhang, H. (2011). The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes. Dev Cell 21, 343–357.

pubmed: 21802374 doi: 10.1016/j.devcel.2011.06.024

Luo, J., Jiang, L., Yang, H., and Song, B. (2017). Routes and mechanisms of postendosomal cholesterol trafficking: a story that never ends. Traffic 18, 209–217.

pubmed: 28191915 doi: 10.1111/tra.12471

Luo, J., Jiang, L.Y., Yang, H., and Song, B.L. (2019). Intracellular cholesterol transport by sterol transfer proteins at membrane contact sites. Trends Biochem Sci 44, 273–292.

pubmed: 30415968 doi: 10.1016/j.tibs.2018.10.001

Luzio, J.P., Pryor, P.R., and Bright, N.A. (2007). Lysosomes: fusion and function. Nat Rev Mol Cell Biol 8, 622–632.

pubmed: 17637737 doi: 10.1038/nrm2217

Maeda, K., Anand, K., Chiapparino, A., Kumar, A., Poletto, M., Kaksonen, M., and Gavin, A.C. (2013). Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins. Nature 501, 257–261.

pubmed: 23934110 doi: 10.1038/nature12430

Maeda, M., Katada, T., and Saito, K. (2017). TANGO1 recruits Sec16 to coordinately organize ER exit sites for efficient secretion. J Cell Biol 216, 1731–1743.

pubmed: 28442536 pmcid: 5461033 doi: 10.1083/jcb.201703084

Maeda, S., Otomo, C., and Otomo, T. (2019). The autophagic membrane tether ATG2A transfers lipids between membranes. eLife 8, e45777.

pubmed: 31271352 pmcid: 6625793 doi: 10.7554/eLife.45777

Maejima, I., Takahashi, A., Omori, H., Kimura, T., Takabatake, Y., Saitoh, T., Yamamoto, A., Hamasaki, M., Noda, T., Isaka, Y., et al. (2013). Autophagy sequesters damaged lysosomes to control lysosomal biogenesis and kidney injury. EMBO J 32, 2336–2347.

pubmed: 23921551 pmcid: 3770333 doi: 10.1038/emboj.2013.171

Magré, J., Delépine, M., Khallouf, E., Gedde-Dahl Jr, T., Van Maldergem, L., Sobel, E., Papp, J., Meier, M., Mégarbané, A., BSCL Working Group, et al. (2001). Identification of the gene altered in Berardinelli-Seip congenital lipodystrophy on chromosome 11q13. Nat Genet 28, 365–370.

pubmed: 11479539 doi: 10.1038/ng585

Malhotra, V., and Erlmann, P. (2015). The pathway of collagen secretion. Annu Rev Cell Dev Biol 31, 109–124.

pubmed: 26422332 doi: 10.1146/annurev-cellbio-100913-013002

Manford, A.G., Stefan, C.J., Yuan, H.L., MacGurn, J.A., and Emr, S.D. (2012). ER-to-plasma membrane tethering proteins regulate cell signaling and ER morphology. Dev Cell 23, 1129–1140.

pubmed: 23237950 doi: 10.1016/j.devcel.2012.11.004

Manik, M.K., Yang, H., Tong, J., and Im, Y.J. (2017). Structure of yeast OSBP-related protein Osh1 reveals key determinants for lipid transport and protein targeting at the nucleus-vacuole junction. Structure 25, 617–629.e3.

pubmed: 28319008 doi: 10.1016/j.str.2017.02.010

Manor, U., Bartholomew, S., Golani, G., Christenson, E., Kozlov, M., Higgs, H., Spudich, J., and Lippincott-Schwartz, J. (2015). A mitochondria-anchored isoform of the actin-nucleating spire protein regulates mitochondrial division. eLife 4, e08828.

pubmed: 26305500 pmcid: 4574297 doi: 10.7554/eLife.08828

Marek, M., Vincenzetti, V., and Martin, S.G. (2020). Sterol biosensor reveals LAM-family Ltc1-dependent sterol flow to endosomes upon Arp2/3 inhibition. J Cell Biol 219, e202001147.

pubmed: 32320462 pmcid: 7265315 doi: 10.1083/jcb.202001147

Markgraf, D.F., Klemm, R.W., Junker, M., Hannibal-Bach, H.K., Ejsing, C.S., and Rapoport, T.A. (2014). An ER protein functionally couples neutral lipid metabolism on lipid droplets to membrane lipid synthesis in the ER. Cell Rep 6, 44–55.

pubmed: 24373967 doi: 10.1016/j.celrep.2013.11.046

Masone, M.C., Morra, V., and Venditti, R. (2019). Illuminating the membrane contact sites between the endoplasmic reticulum and the trans-Golgi network. FEBS Lett 593, 3135–3148.

pubmed: 31610025 doi: 10.1002/1873-3468.13639

Matsunaga, K., Morita, E., Saitoh, T., Akira, S., Ktistakis, N.T., Izumi, T., Noda, T., and Yoshimori, T. (2010). Autophagy requires endoplasmic reticulum targeting of the PI3-kinase complex via Atg14L. J Cell Biol 190, 511–521.

pubmed: 20713597 pmcid: 2928018 doi: 10.1083/jcb.200911141

Matsushita, M., Tanaka, S., Nakamura, N., Inoue, H., and Kanazawa, H. (2004). A novel kinesin-like protein, KIF1Bβ3 is involved in the movement of lysosomes to the cell periphery in non-neuronal cells. Traffic 5, 140–151.

pubmed: 15086790 doi: 10.1111/j.1600-0854.2003.00165.x

Mattiazzi Ušaj, M., Brložnik, M., Kaferle, P., Žitnik, M., Wolinski, H., Leitner, F., Kohlwein, S.D., Zupan, B., and Petrovic, U. (2015). Genome-wide localization study of yeast Pex11 identifies peroxisome-mitochondria interactions through the ERMES complex. J Mol Biol 427, 2072–2087.

pubmed: 25769804 pmcid: 4429955 doi: 10.1016/j.jmb.2015.03.004

McCaughey, J., Miller, V.J., Stevenson, N.L., Brown, A.K., Budnik, A., Heesom, K.J., Alibhai, D., and Stephens, D.J. (2016). TFG promotes organization of transitional ER and efficient collagen secretion. Cell Rep 15, 1648–1659.

pubmed: 27184855 pmcid: 4885023 doi: 10.1016/j.celrep.2016.04.062

Medina, D.L., Di Paola, S., Peluso, I., Armani, A., De Stefani, D., Venditti, R., Montefusco, S., Scotto-Rosato, A., Prezioso, C., Forrester, A., et al. (2015). Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. Nat Cell Biol 17, 288–299.

pubmed: 25720963 pmcid: 4801004 doi: 10.1038/ncb3114

Mesmin, B., Bigay, J., Moser von Filseck, J., Lacas-Gervais, S., Drin, G., and Antonny, B. (2013). A four-step cycle driven by PI(4)P hydrolysis directs sterol/PI(4)P exchange by the ER-Golgi tether OSBP. Cell 155, 830–843.

pubmed: 24209621 doi: 10.1016/j.cell.2013.09.056

Mesmin, B., Bigay, J., Polidori, J., Jamecna, D., Lacas-Gervais, S., and Antonny, B. (2017). Sterol transfer, PI4P consumption, and control of membrane lipid order by endogenous OSBP. EMBO J 36, 3156–3174.

pubmed: 28978670 pmcid: 5666618 doi: 10.15252/embj.201796687

Mesmin, B., Pipalia, N.H., Lund, F.W., Ramlall, T.F., Sokolov, A., Eliezer, D., and Maxfield, F.R. (2011). STARD4 abundance regulates sterol transport and sensing. Mol Biol Cell 22, 4004–4015.

pubmed: 21900492 pmcid: 3204063 doi: 10.1091/mbc.e11-04-0372

Mikoshiba, K. (1997). The InsP3 receptor and intracellular Ca

pubmed: 9232803 doi: 10.1016/S0959-4388(97)80061-X

Milligan, S.C., Alb, J.G. Jr., Elagina, R.B., Bankaitis, V.A., and Hyde, D.R. (1997). The phosphatidylinositol transfer protein domain of Drosophila retinal degeneration B protein is essential for photoreceptor cell survival and recovery from light stimulation. J Cell Biol 139, 351–363.

pubmed: 9334340 pmcid: 2139788 doi: 10.1083/jcb.139.2.351

Min, S.W., Chang, W.P., and Südhof, T.C. (2007). E-Syts, a family of membranous Ca

pubmed: 17360437 pmcid: 1820668 doi: 10.1073/pnas.0611725104

Mizushima, N. (2018). A brief history of autophagy from cell biology to physiology and disease. Nat Cell Biol 20, 521–527.

pubmed: 29686264 doi: 10.1038/s41556-018-0092-5

Mizushima, N., Yoshimori, T., and Ohsumi, Y. (2011). The role of atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 27, 107–132.

pubmed: 21801009 doi: 10.1146/annurev-cellbio-092910-154005

Mochizuki, S., Miki, H., Zhou, R., Kido, Y., Nishimura, W., Kikuchi, M., and Noda, Y. (2018). Oxysterol-binding protein-related protein (ORP) 6 localizes to the ER and ER-plasma membrane contact sites and is involved in the turnover of PI4P in cerebellar granule neurons. Exp Cell Res 370, 601–612.

pubmed: 30028970 doi: 10.1016/j.yexcr.2018.07.025

Morgan, A.J., Davis, L.C., Wagner, S.K.T.Y., Lewis, A.M., Parrington, J., Churchill, G. C., and Galione, A. (2013). Bidirectional Ca

pubmed: 23479744 pmcid: 3601362 doi: 10.1083/jcb.201204078

Morgan, A.J., Platt, F.M., Lloyd-Evans, E., and Galione, A. (2011). Molecular mechanisms of endolysosomal Ca

pubmed: 21992097 doi: 10.1042/BJ20110949

Moriguchi, S., Nishi, M., Komazaki, S., Sakagami, H., Miyazaki, T., Masumiya, H., Saito, S., Watanabe, M., Kondo, H., Yawo, H., et al. (2006). Functional uncoupling between Ca

pubmed: 16809425 pmcid: 1502313 doi: 10.1073/pnas.0509863103

Morishita, H., and Mizushima, N. (2019). Diverse cellular roles of autophagy. Annu Rev Cell Dev Biol 35, 453–475.

pubmed: 31283377 doi: 10.1146/annurev-cellbio-100818-125300

Moser von Filseck, J., Copie, A., Delfosse, V., Vanni, S., Jackson, C.L., Bourguet, W., and Drin, G. (2015a). Phosphatidylserine transport by ORP/Osh proteins is driven by phosphatidylinositol 4-phosphate. Science 349, 432–436.

pubmed: 26206936 doi: 10.1126/science.aab1346

Moser von Filseck, J, Vanni, S., Mesmin, B., Antonny, B., and Drin, G. (2015b). A phosphatidylinositol-4-phosphate powered exchange mechanism to create a lipid gradient between membranes. Nat Commun 6, 6671.

pubmed: 25849868 doi: 10.1038/ncomms7671

Munoz-Braceras, S., Tornero-Ecija, A.R., Vincent, O., and Escalante, R. (2019). VPS13A, a closely associated mitochondrial protein, is required for efficient lysosomal degradation. Dis Model Mech 12, dmm.036681.

Murley, A., Lackner, L.L., Osman, C., West, M., Voeltz, G.K., Walter, P., and Nunnari, J. (2013). ER-associated mitochondrial division links the distribution of mitochondria and mitochondrial DNA in yeast. eLife 2, e00422.

pubmed: 23682313 pmcid: 3654481 doi: 10.7554/eLife.00422

Naito, T., Ercan, B., Krshnan, L., Triebl, A., Koh, D.H.Z., Wei, F.Y., Tomizawa, K., Torta, F.T., Wenk, M.R., and Saheki, Y. (2019). Movement of accessible plasma membrane cholesterol by the GRAMD1 lipid transfer protein complex. eLife 8, e51401.

pubmed: 31724953 pmcid: 6905856 doi: 10.7554/eLife.51401

Nakata, T., and Hirokawa, N. (1995). Point mutation of adenosine triphosphate-binding motif generated rigor kinesin that selectively blocks anterograde lysosome membrane transport. J Cell Biol 131, 1039–1053.

pubmed: 7490281 doi: 10.1083/jcb.131.4.1039

Nakatogawa, H. (2020). Mechanisms governing autophagosome biogenesis. Nat Rev Mol Cell Biol 21, 439–458.

pubmed: 32372019 doi: 10.1038/s41580-020-0241-0

Nakatsu, F., Baskin, J.M., Chung, J., Tanner, L.B., Shui, G., Lee, S.Y., Pirruccello, M., Hao, M., Ingolia, N.T., Wenk, M.R., et al. (2012). PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity. J Cell Biol 199, 1003–1016.

pubmed: 23229899 pmcid: 3518224 doi: 10.1083/jcb.201206095

Nath, V.R., Mishra, S., Basak, B., Trivedi, D., and Raghu, P. (2020). Extended synaptotagmin regulates membrane contact site structure and lipid transfer function in vivo. EMBO Rep 21, e50264.

pubmed: 32716137 pmcid: 7507014 doi: 10.15252/embr.202050264

Ngo, M., and Ridgway, N.D. (2009). Oxysterol binding protein-related Protein 9 (ORP9) is a cholesterol transfer protein that regulates Golgi structure and function. Mol Biol Cell 20, 1388–1399.

pubmed: 19129476 pmcid: 2649274 doi: 10.1091/mbc.e08-09-0905

Nemani, N., Dong, Z., Daw, C.C., Madaris, T.R., Ramachandran, K., Enslow, B.T., Rubannelsonkumar, C.S., Shanmughapriya, S., Mallireddigari, V., Maity, S., et al. (2020). Mitochondrial pyruvate and fatty acid flux modulate MICU1-dependent control of MCU activity. Sci Signal 13, eaaz6206.

pubmed: 32317369 pmcid: 7667998 doi: 10.1126/scisignal.aaz6206

Nishimura, T., Tamura, N., Kono, N., Shimanaka, Y., Arai, H., Yamamoto, H., and Mizushima, N. (2017). Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains. EMBO J 36, 1719–1735.

pubmed: 28495679 pmcid: 5470044 doi: 10.15252/embj.201695189

Olarte, M.J., Kim, S., Sharp, M.E., Swanson, J.M.J., Farese Jr., R.V., and Walther, T.C. (2020). Determinants of endoplasmic reticulum-to-lipid droplet protein targeting. Dev Cell 54, 471–487.e7.

pubmed: 32730754 pmcid: 7696655 doi: 10.1016/j.devcel.2020.07.001

Orci, L., Ravazzola, M., Le Coadic, M., Shen, W., Demaurex, N., and Cosson, P. (2009). STTM1-induced precortical and cortical subdomains of the endoplasmic reticulum. Proc Natl Acad Sci USA 106, 19358–19362.

pubmed: 19906989 pmcid: 2775999 doi: 10.1073/pnas.0911280106

Orci, L., Stamnes, M., Ravazzola, M., Amherdt, M., Perrelet, A., Söllner, T.H., and Rothman, J.E. (1997). Bidirectional transport by distinct populations of COPI-coated vesicles. Cell 90, 335–349.

pubmed: 9244307 doi: 10.1016/S0092-8674(00)80341-4

Orrenius, S., Zhivotovsky, B., and Nicotera, P. (2003). Regulation of cell death: the calcium-apoptosis link. Nat Rev Mol Cell Biol 4, 552–565.

pubmed: 12838338 doi: 10.1038/nrm1150

Osawa, T., Ishii, Y., and Noda, N.N. (2020). Human ATG2B possesses a lipid transfer activity which is accelerated by negatively charged lipids and WIPI4. Genes Cells 25, 65–70.

pubmed: 31721365 doi: 10.1111/gtc.12733

Osawa, T., Kotani, T., Kawaoka, T., Hirata, E., Suzuki, K., Nakatogawa, H., Ohsumi, Y., and Noda, N.N. (2019). Atg2 mediates direct lipid transfer between membranes for autophagosome formation. Nat Struct Mol Biol 26, 281–288.

pubmed: 30911189 doi: 10.1038/s41594-019-0203-4

Özkan, N., Koppers, M., van Soest, I., van Harten, A., Jurriens, D., Liv, N., Klumperman, J., Kapitein, L.C., Hoogenraad, C.C., and Farías, G.G. (2021). ER-lysosome contacts at a pre-axonal region regulate axonal lysosome availability. Nat Commun 12, 4493.

pubmed: 34301956 pmcid: 8302662 doi: 10.1038/s41467-021-24713-5

Palade, G. (1975). Intracellular aspects of the process of protein synthesis. Science 189, 347–358.

pubmed: 1096303 doi: 10.1126/science.1096303

Palande, K., Roovers, O., Gits, J., Verwijmeren, C., Iuchi, Y., Fujii, J., Neel, B.G., Karisch, R., Tavernier, J., and Touw, I.P. (2011). Peroxiredoxin-controlled G-CSF signalling at the endoplasmic reticulum-early endosome interface. J Cell Sci 124, 3695–3705.

pubmed: 22045733 pmcid: 3215578 doi: 10.1242/jcs.089656

Pallafacchina, G., Zanin, S., and Rizzuto, R. (2021). From the identification to the dissection of the physiological role of the mitochondrial calcium uniporter: an ongoing story. Biomolecules 11, 786.

pubmed: 34071006 pmcid: 8224590 doi: 10.3390/biom11060786

Palty, R., Raveh, A., Kaminsky, I., Meller, R., and Reuveny, E. (2012). SARAF inactivates the store operated calcium entry machinery to prevent excess calcium refilling. Cell 149, 425–438.

pubmed: 22464749 doi: 10.1016/j.cell.2012.01.055

Pang, Q., Liu, C., Qiao, Y., Zhao, J., Lam, S.M., Mei, M., Shui, G., Bao, S., and Li, Q. (2022). GM130 regulates pulmonary surfactant protein secretion in alveolar type II cells. Sci China Life Sci 65, 193–205.

pubmed: 33740186 doi: 10.1007/s11427-020-1875-x

Pankiv, S., Alemu, E.A., Brech, A., Bruun, J.A., Lamark, T., Øvervatn, A., Bjørkøy, G., and Johansen, T. (2010). FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport. J Cell Biol 188, 253–269.

pubmed: 20100911 pmcid: 2812517 doi: 10.1083/jcb.200907015

Parenti, G., Andria, G., and Ballabio, A. (2015). Lysosomal storage diseases: from pathophysiology to therapy. Annu Rev Med 66, 471–486.

pubmed: 25587658 doi: 10.1146/annurev-med-122313-085916

Park, C.Y., Hoover, P.J., Mullins, F.M., Bachhawat, P., Covington, E.D., Raunser, S., Walz, T., Garcia, K.C., Dolmetsch, R.E., and Lewis, R.S. (2009). STTM1 clusters and activates CRAC channels via direct binding of a cytosolic domain to Orai1. Cell 136, 876–890.

pubmed: 19249086 pmcid: 2670439 doi: 10.1016/j.cell.2009.02.014

Park, J.S., and Neiman, A.M. (2012). VPS13 regulates membrane morphogenesis during sporulation in Sflcchflromyces cerevisifle. J Cell Sci 125, jcs.105114.

doi: 10.1242/jcs.105114

Park, J.S., Thorsness, M.K., Policastro, R., McGoldrick, L.L., Hollingsworth, N.M., Thorsness, P.E., and Neiman, A.M. (2016). Yeast Vps13 promotes mitochondrial function and is localized at membrane contact sites. Mol Biol Cell 27, 2435–2449.

pubmed: 27280386 pmcid: 4966984 doi: 10.1091/mbc.e16-02-0112

Park, M.K., Petersen, O.H., and Tepikin, A.V. (2000). The endoplasmic reticulum as one continuous Ca

pubmed: 11060024 pmcid: 305795 doi: 10.1093/emboj/19.21.5729

Pedersen, N.M., Wenzel, E.M., Wang, L., Antoine, S., Chavrier, P., Stenmark, H., and Raiborg, C. (2020). Protrudin-mediated ER-endosome contact sites promote MT1MMP exocytosis and cell invasion. J Cell Biol 219, e202003063.

pubmed: 32479595 pmcid: 7401796 doi: 10.1083/jcb.202003063

Penner, R., Matthews, G., and Neher, E. (1988). Regulation of calcium influx by second messengers in rat mast cells. Nature 334, 499–504.

pubmed: 2457169 doi: 10.1038/334499a0

Peotter, J., Kasberg, W., Pustova, I., and Audhya, A. (2019). COPII-mediated trafficking at the ER/ERGIC interface. Traffic 20, 491–503.

pubmed: 31059169 pmcid: 6640837 doi: 10.1111/tra.12654

Perera, R.M., and Zoncu, R. (2016). The lysosome as a regulatory hub. Annu Rev Cell Dev Biol 32, 223–253.

pubmed: 27501449 pmcid: 9345128 doi: 10.1146/annurev-cellbio-111315-125125

Petkovic, M., Jemaiel, A., Daste, F., Specht, C.G., Izeddin, I., Vorkel, D., Verbavatz, J.M., Darzacq, X., Triller, A., Pfenninger, K.H., et al. (2014). The SNARE Sec22b has a non-fusogenic function in plasma membrane expansion. Nat Cell Biol 16, 434–444.

pubmed: 24705552 doi: 10.1038/ncb2937

Picard, C., McCarl, C.A., Papolos, A., Khalil, S., Lüthy, K., Hivroz, C., LeDeist, F., Rieux-Laucat, F., Rechavi, G., Rao, A., et al. (2009). STIM1 mutation associated with a syndrome of immunodeficiency and autoimmunity. N Engl J Med 360, 1971–1980.

pubmed: 19420366 pmcid: 2851618 doi: 10.1056/NEJMoa0900082

Pietrangelo, A., and Ridgway, N.D. (2018). Golgi-localization of oxysterol binding protein-related protein 4L (ORP4L) is regulated by ligand binding. J Cell Sci 131, jcs.215335.

doi: 10.1242/jcs.215335

Porter, K.R., and Palade, G.E. (1957). Studies on the endoplasmic reticulum. J Cell Biol 3, 269–300.

doi: 10.1083/jcb.3.2.269

Pottekat, A., Becker, S., Spencer, K.R., Yates, J.R. III, Manning, G., Itkin-Ansari, P., and Balch, W.E. (2013). Insulin biosynthetic interaction network component, TMEM24, facilitates insulin reserve pool release. Cell Rep 4, 921–930.

pubmed: 24012759 doi: 10.1016/j.celrep.2013.07.050

Prinz, W.A., Toulmay, A., and Balla, T. (2020). The functional universe of membrane contact sites. Nat Rev Mol Cell Biol 21, 7–24.

pubmed: 31732717 doi: 10.1038/s41580-019-0180-9

Protasi, F. (2002). Structural interaction between RYRs and DHPRs in calcium release units of cardiac and skeletal muscle cells. Front Biosci 7, d650-658.

Pu, J., Guardia, C.M., Keren-Kaplan, T., and Bonifacino, J.S. (2016). Mechanisms and functions of lysosome positioning. J Cell Sci 129, jcs.196287.

doi: 10.1242/jcs.196287

Putney, J.W. Jr. (1986). A model for receptor-regulated calcium entry. Cell Calcium 7, 1–12.

pubmed: 2420465 doi: 10.1016/0143-4160(86)90026-6

Putney, J.W Jr. (1990). Capacitative calcium entry revisited. Cell Calcium 11, 611–624.

pubmed: 1965707 doi: 10.1016/0143-4160(90)90016-N

Qi, H., Li, L., and Shuai, J. (2015). Optimal microdomain crosstalk between endoplasmic reticulum and mitochondria for Ca

pubmed: 25614067 pmcid: 4303883 doi: 10.1038/srep07984

Qian, K., Tol, M.J., Wu, J., Uchiyama, L.F., Xiao, X., Cui, L., Bedard, A.H., Weston, T. A., Rajendran, P.S., Vergnes, L., et al. (2023). CLSTN3β enforces adipocyte multilocularity to facilitate lipid utilization. Nature 613, 160–168.

pubmed: 36477540 doi: 10.1038/s41586-022-05507-1

Qian, T., Li, C., He, R., Wan, C., Liu, Y., and Yu, H. (2021). Calcium-dependent and -independent lipid transfer mediated by tricalbins in yeast. J Biol Chem 296, 100729.

pubmed: 33933446 pmcid: 8163979 doi: 10.1016/j.jbc.2021.100729

Quintana, A., Rajanikanth, V., Farber-Katz, S., Gudlur, A., Zhang, C., Jing, J., Zhou, Y., Rao, A., and Hogan, P.G. (2015). TMEM110 regulates the maintenance and remodeling of mammalian ER-plasma membrane junctions competent for STIMORAI signaling. Proc Natl Acad Sci USA 112, E7083–7092.

pubmed: 26644574 pmcid: 4697383 doi: 10.1073/pnas.1521924112

Quintanilla, C.G., Lee, W.R., and Liou, J. (2022). Nir1 constitutively localizes at ERPM junctions and promotes Nir2 recruitment for PIP2 homeostasis. Mol Biol Cell 33, br2.

pubmed: 35020418 pmcid: 9250379 doi: 10.1091/mbc.E21-07-0356

Quon, E., Sere, Y.Y., Chauhan, N., Johansen, J., Sullivan, D.P., Dittman, J.S., Rice, W. J., Chan, R.B., Di Paolo, G., Beh, C.T., et al. (2018). Endoplasmic reticulum-plasma membrane contact sites integrate sterol and phospholipid regulation. PLoS Biol 16, e2003864.

pubmed: 29782498 pmcid: 5983861 doi: 10.1371/journal.pbio.2003864

Radulovic, M., Schink, K.O., Wenzel, E.M., Nähse, V., Bongiovanni, A., Lafont, F., and Stenmark, H. (2018). ESCRT-mediated lysosome repair precedes lysophagy and promotes cell survival. EMBO J 37, e99753.

pubmed: 30314966 pmcid: 6213280 doi: 10.15252/embj.201899753

Raiborg, C., Wenzel, E.M., Pedersen, N.M., Olsvik, H., Schink, K.O., Schultz, S.W., Vietri, M., Nisi, V., Bucci, C., Brech, A., et al. (2015). Repeated ER-endosome contacts promote endosome translocation and neurite outgrowth. Nature 520, 234–238.

pubmed: 25855459 doi: 10.1038/nature14359

Rampoldi, L., Dobson-Stone, C., Rubio, J.P., Danek, A., Chalmers, R.M., Wood, N.W., Verellen, C., Ferrer, X., Malandrini, A., Fabrizi, G.M., et al. (2001). A conserved sorting-associated protein is mutant in chorea-acanthocytosis. Nat Genet 28, 119–120.

pubmed: 11381253 doi: 10.1038/88821

Raote, I., and Malhotra, V. (2021). Tunnels for protein export from the endoplasmic reticulum. Annu Rev Biochem 90, 605–630.

pubmed: 33503381 doi: 10.1146/annurev-biochem-080120-022017

Raychaudhuri, S., Im, Y.J., Hurley, J.H., and Prinz, W.A. (2006). Nonvesicular sterol movement from plasma membrane to ER requires oxysterol-binding protein-related proteins and phosphoinositides. J Cell Biol 173, 107–119.

pubmed: 16585271 pmcid: 2063795 doi: 10.1083/jcb.200510084

Reinisch, K.M., and De Camilli, P. (2016). SMP-domain proteins at membrane contact sites: structure and function. Biochim Biophys Acta-Mol Cell Biol Lipids 1861, 924–927.

doi: 10.1016/j.bbalip.2015.12.003

Riegelhaupt, J.J., Waase, M.P., Garbarino, J., Cruz, D.E., and Breslow, J.L. (2010). Targeted disruption of steroidogenic acute regulatory protein D4 leads to modest weight reduction and minor alterations in lipid metabolism. J Lipid Res 51, 1134–1143.

pubmed: 19965609 pmcid: 2853440 doi: 10.1194/jlr.M003095

Rizzuto, R., Brini, M., Murgia, M., and Pozzan, T. (1993). Microdomains with high Ca

pubmed: 8235595 doi: 10.1126/science.8235595

Rocha, N., Kuijl, C., van der Kant, R., Janssen, L., Houben, D., Janssen, H., Zwart, W., and Neefjes, J. (2009). Cholesterol sensor ORP1L contacts the ER protein VAP to control Rab7-RILP-p150Glued and late endosome positioning. J Cell Biol 185, 1209–1225.

pubmed: 19564404 pmcid: 2712958 doi: 10.1083/jcb.200811005

Rodriguez-Agudo, D., Calderon-Dominguez, M., Ren, S., Marques, D., Redford, K., Medina-Torres, M.A., Hylemon, P., Gil, G., and Pandak, W.M. (2011). Subcellular localization and regulation of StarD4 protein in macrophages and fibroblasts. Biochim Biophys Acta 1811, 597–606.

pubmed: 21767660 pmcid: 3156897 doi: 10.1016/j.bbalip.2011.06.028

Rodriguez-Agudo, D., Malacrida, L., Kakiyama, G., Sparrer, T., Fortes, C., Maceyka, M., Subler, M.A., Windle, J.J., Gratton, E., Pandak, W.M., et al. (2019). StarD5: an ER stress protein regulates plasma membrane and intracellular cholesterol homeostasis. J Lipid Res 60, 1087–1098.

pubmed: 31015253 pmcid: 6547630 doi: 10.1194/jlr.M091967

Roos, J., DiGregorio, P.J., Yeromin, A.V., Ohlsen, K., Lioudyno, M., Zhang, S., Safrina, O., Kozak, J.A., Wagner, S.L., Cahalan, M.D., et al. (2005). STM1, an essential and conserved component of store-operated Ca

pubmed: 15866891 pmcid: 2171946 doi: 10.1083/jcb.200502019

Rosenbluth, J. (1962). Subsurface cisterns and their relationship to the neuronal plasma membrane. J Cell Biol 13, 405–421.

pubmed: 14493991 pmcid: 2106078 doi: 10.1083/jcb.13.3.405

Rowland, A.A., Chitwood, P.J., Phillips, M.J., and Voeltz, G.K. (2014). ER contact sites define the position and timing of endosome fission. Cell 159, 1027–1041.

pubmed: 25416943 pmcid: 4634643 doi: 10.1016/j.cell.2014.10.023

Ruas, M., Rietdorf, K., Arredouani, A., Davis, L.C., Lloyd-Evans, E., Koegel, H., Funnell, T.M., Morgan, A.J., Ward, J.A., Watanabe, K., et al. (2010). Purified TPC isoforms form NAADP receptors with distinct roles for Ca

pubmed: 20346675 pmcid: 2861162 doi: 10.1016/j.cub.2010.02.049

Sabatini, D.D. (1999). George E. Palade: charting the secretory pathway. Trends Cell Biol 9, 413–417.

pubmed: 10481180 doi: 10.1016/S0962-8924(99)01633-5

Saheki, Y., Bian, X., Schauder, C.M., Sawaki, Y., Surma, M.A., Klose, C., Pincet, F., Reinisch, K.M., and De Camilli, P. (2016). Control of plasma membrane lipid homeostasis by the extended synaptotagmins. Nat Cell Biol 18, 504–515.

pubmed: 27065097 pmcid: 4848133 doi: 10.1038/ncb3339

Saito, K., Chen, M., Bard, F., Chen, S., Zhou, H., Woodley, D., Polischuk, R., Schekman, R., and Malhotra, V. (2009). TANGO1 facilitates cargo loading at endoplasmic reticulum exit sites. Cell 136, 891–902.

pubmed: 19269366 doi: 10.1016/j.cell.2008.12.025

Salo, V.T., Belevich, I., Li, S., Karhinen, L., Vihinen, H., Vigouroux, C., Magré, J., Thiele, C., Hölttä-Vuori, M., Jokitalo, E., et al. (2016). Seipin regulates ER-lipid droplet contacts and cargo delivery. EMBO J 35, 2699–2716.

pubmed: 27879284 pmcid: 5167346 doi: 10.15252/embj.201695170

Salo, V.T., Li, S., Vihinen, H., Hölttä-Vuori, M., Szkalisity, A., Horvath, P., Belevich, I., Peränen, J., Thiele, C., Somerharju, P., et al. (2019). Seipin facilitates triglyceride flow to lipid droplet and counteracts droplet ripening via endoplasmic reticulum contact. Dev Cell 50, 478–493.e9.

pubmed: 31178403 doi: 10.1016/j.devcel.2019.05.016

Sancak, Y., Bar-Peled, L., Zoncu, R., Markhard, A.L., Nada, S., and Sabatini, D.M. (2010). Ragulator-rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 141, 290–303.

pubmed: 20381137 pmcid: 3024592 doi: 10.1016/j.cell.2010.02.024

Sandhu, J., Li, S., Fairall, L., Pfisterer, S.G., Gurnett, J.E., Xiao, X., Weston, T.A., Vashi, D., Ferrari, A., Orozco, J.L., et al. (2018). Aster proteins facilitate nonvesicular plasma membrane to ER cholesterol transport in mammalian cells. Cell 175, 514–529.e20.

pubmed: 30220461 pmcid: 6469685 doi: 10.1016/j.cell.2018.08.033

Santos, A.J., Raote, I., Scarpa, M., Brouwers, N., and Malhotra, V. (2015). TANGO1 recruits ERGIC membranes to the endoplasmic reticulum for procollagen export. eLife 4, e10982.

pubmed: 26568311 pmcid: 4709264 doi: 10.7554/eLife.10982

Saraste, J., and Marie, M. (2018). Intermediate compartment (IC): from pre-Golgi vacuoles to a semi-autonomous membrane system. Histochem Cell Biol 150, 407–430.

pubmed: 30173361 pmcid: 6182704 doi: 10.1007/s00418-018-1717-2

Schauder, C.M., Wu, X., Saheki, Y., Narayanaswamy, P., Torta, F., Wenk, M.R., de Camilli, P., and Reinisch, K.M. (2014). Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer. Nature 510, 552–555.

pubmed: 24847877 pmcid: 4135724 doi: 10.1038/nature13269

Schneider, M.F., and Chandler, W.K. (1973). Voltage dependent charge movement in skeletal muscle: a possible step in excitation-contraction coupling. Nature 242, 244–246.

pubmed: 4540479 doi: 10.1038/242244a0

Schulz, T.A., Choi, M.G., Raychaudhuri, S., Mears, J.A., Ghirlando, R., Hinshaw, J.E., and Prinz, W.A. (2009). Lipid-regulated sterol transfer between closely apposed membranes by oxysterol-binding protein homologues. J Cell Biol 187, 889–903.

pubmed: 20008566 pmcid: 2806323 doi: 10.1083/jcb.200905007

Schutter, M., Giavalisco, P., Brodesser, S., and Graef, M. (2020). Local fatty acid channeling into phospholipid synthesis drives phagophore expansion during autophagy. Cell 180, 135–149.e14.

pubmed: 31883797 doi: 10.1016/j.cell.2019.12.005

Sclip, A., Bacaj, T., Giam, L.R., and Sudhof, T.C. (2016). Extended synaptotagmin (ESyt) triple knock-out mice are viable and fertile without obvious endoplasmic reticulum dysfunction. PLoS ONE 11, e0158295.

pubmed: 27348751 pmcid: 4922586 doi: 10.1371/journal.pone.0158295

Scorrano, L., De Matteis, M.A., Emr, S., Giordano, F., Hajnóczky, G., Kornmann, B., Lackner, L.L., Levine, T.P., Pellegrini, L., Reinisch, K., et al. (2019). Coming together to define membrane contact sites. Nat Commun 10, 1287.

pubmed: 30894536 pmcid: 6427007 doi: 10.1038/s41467-019-09253-3

Shai, N., Yifrach, E., van Roermund, C.W.T., Cohen, N., Bibi, C., IJlst, L., Cavellini, L., Meurisse, J., Schuster, R., Zada, L., et al. (2018). Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact. Nat Commun 9, 1761.

pubmed: 29720625 pmcid: 5932058 doi: 10.1038/s41467-018-03957-8

Sharma, S., Quintana, A., Findlay, G.M., Mettlen, M., Baust, B., Jain, M., Nilsson, R., Rao, A., and Hogan, P.G. (2013). An siRNA screen for NFAT activation identifies septins as coordinators of store-operated Ca

pubmed: 23792561 doi: 10.1038/nature12229

Shinoda, Y., Fujita, K., Saito, S., Matsui, H., Kanto, Y., Nagaura, Y., Fukunaga, K., Tamura, S., and Kobayashi, T. (2012). Acyl-CoA binding domain containing 3 (ACBD3) recruits the protein phosphatase PPM1L to ER-Golgi membrane contact sites. FEBS Lett 586, 3024–3029.

pubmed: 22796112 doi: 10.1016/j.febslet.2012.06.050

Shirane, M., Wada, M., Morita, K., Hayashi, N., Kunimatsu, R., Matsumoto, Y., Matsuzaki, F., Nakatsumi, H., Ohta, K., Tamura, Y., et al. (2020). Protrudin and PDZD8 contribute to neuronal integrity by promoting lipid extraction required for endosome maturation. Nat Commun 11, 4576.

pubmed: 32917905 pmcid: 7486383 doi: 10.1038/s41467-020-18413-9

Shomron, O., Nevo-Yassaf, I., Aviad, T., Yaffe, Y., Zahavi, E.E., Dukhovny, A., Perlson, E., Brodsky, I., YeheskelA.Pasmanik-Chor, M., Mironov, A., et al. (2021). COPII collar defines the boundary between ER and ER exit site and does not coat cargo containers. J Cell Biol 220, e201907224.

pubmed: 33852719 pmcid: 8054201 doi: 10.1083/jcb.201907224

Simoes, I.C.M., Morciano, G., Lebiedzinska-Arciszewska, M., Aguiari, G., Pinton, P., Potes, Y., and Wieckowski, M.R. (2020). The mystery of mitochondria-ER contact sites in physiology and pathology: a cancer perspective. Biochim Biophys Acta Mol Basis Dis 1866, 165834.

pubmed: 32437958 doi: 10.1016/j.bbadis.2020.165834

Skowyra, M.L., Schlesinger, P.H., Naismith, T.V., and Hanson, P.I. (2018). Triggered recruitment of ESCRT machinery promotes endolysosomal repair. Science 360, eaar5078.

pubmed: 29622626 pmcid: 6195421 doi: 10.1126/science.aar5078

Smirnova, E., Shurland, D.L., Ryazantsev, S.N., and van der Bliek, A.M. (1998). A human dynamin-related protein controls the distribution of mitochondria. J Cell Biol 143, 351–358.

pubmed: 9786947 pmcid: 2132828 doi: 10.1083/jcb.143.2.351

Sohn, M., Korzeniowski, M., Zewe, J.P., Wills, R.C., Hammond, G.R.V., Humpolickova, J., Vrzal, L., Chalupska, D., Veverka, V., Fairn, G.D., et al. (2018). PI(4,5)P

pubmed: 29472386 pmcid: 5940310 doi: 10.1083/jcb.201710095

Song, J., Mizrak, A., Lee, C.W., Cicconet, M., Lai, Z.W., Tang, W.C., Lu, C.H., Mohr, S. E., Farese Jr., R.V., and Walther, T.C. (2022). Identification of two pathways mediating protein targeting from ER to lipid droplets. Nat Cell Biol 24, 1364–1377.

pubmed: 36050470 pmcid: 9481466 doi: 10.1038/s41556-022-00974-0

Sonnichsen, B., De Renzis, S., Nielsen, E., Rietdorf, J., and Zerial, M. (2000). Distinct membrane domains on endosomes in the recycling pathway visualized by multicolor imaging of Rab4, Rab5, and Rab11. J Cell Biol 149, 901–914.

pubmed: 10811830 pmcid: 2174575 doi: 10.1083/jcb.149.4.901

Spits, M., Heesterbeek, I.T., Voortman, L.M., Akkermans, J.J., Wijdeven, R.H., Cabukusta, B., and Neefjes, J. (2021). Mobile late endosomes modulate peripheral endoplasmic reticulum network architecture. EMBO Rep 22, e50815.

pubmed: 33554435 pmcid: 7926257 doi: 10.15252/embr.202050815

Srikanth, S., Jew, M., Kim, K.D., Yee, M.K., Abramson, J., and Gwack, Y. (2012). Junctate is a Ca

pubmed: 22586105 pmcid: 3365170 doi: 10.1073/pnas.1200667109

Srikanth, S., Jung, H.J., Kim, K.D., Souda, P., Whitelegge, J., and Gwack, Y. (2010). A novel EF-hand protein, CRACR2A, is a cytosolic Ca

pubmed: 20418871 pmcid: 2875865 doi: 10.1038/ncb2045

Stathopulos, P.B., Zheng, L., and Ikura, M. (2009). Stromal interaction molecule (STIM) 1 and STIM2 calcium sensing regions exhibit distinct unfolding and oligomerization kinetics. J Biol Chem 284, 728–732.

pubmed: 19019825 doi: 10.1074/jbc.C800178200

Stathopulos, P.B., Zheng, L., Li, G.Y., Plevin, M.J., and Ikura, M. (2008). Structural and mechanistic insights into STIM1-mediated initiation of store-operated calcium entry. Cell 135, 110–122.

pubmed: 18854159 doi: 10.1016/j.cell.2008.08.006

Stefan, C.J., Manford, A.G., Baird, D., Yamada-Hanff, J., Mao, Y., and Emr, S.D. (2011). Osh proteins regulate phosphoinositide metabolism at ER-plasma membrane contact sites. Cell 144, 389–401.

pubmed: 21295699 doi: 10.1016/j.cell.2010.12.034

Stocco, D.M. (2001). StAR protein and the regulation of steroid hormone biosynthesis. Annu Rev Physiol 63, 193–213.

pubmed: 11181954 doi: 10.1146/annurev.physiol.63.1.193

Stoica, R., De Vos, K.J., Paillusson, S., Mueller, S., Sancho, R.M., Lau, K.F., Vizcay-Barrena, G., Lin, W.L., Xu, Y.F., Lewis, J., et al. (2014). ER-mitochondria associations are regulated by the VAPB-PTPIP51 interaction and are disrupted by ALS/FTD-associated TDP-43. Nat Commun 5, 3996.

pubmed: 24893131 doi: 10.1038/ncomms4996

Stuible, M., Abella, J.V., Feldhammer, M., Nossov, M., Sangwan, V., Blagoev, B., Park, M., and Tremblay, M.L. (2010). PTP1B targets the endosomal sorting machinery. J Biol Chem 285, 23899–23907.

pubmed: 20504764 pmcid: 2911340 doi: 10.1074/jbc.M110.115295

Sui, X., Arlt, H., Brock, K.P., Lai, Z.W., DiMaio, F., Marks, D.S., Liao, M., Farese, R.V. Jr., and Walther, T.C. (2018). Cryo-electron microscopy structure of the lipid droplet-formation protein seipin. J Cell Biol 217, 4080–4091.

pubmed: 30327422 pmcid: 6279392 doi: 10.1083/jcb.201809067

Sun, E.W., Guillén-Samander, A., Bian, X., Wu, Y., Cai, Y., Messa, M., and De Camilli, P. (2019). Lipid transporter TMEM24/C2CD2L is a Ca

Sun, S., Tang, X., Guo, Y., and Hu, J. (2021). Endoplasmic reticulum composition and form: Proteins in and out. Curr Opin Cell Biol 71, 1–6.

pubmed: 33611096 doi: 10.1016/j.ceb.2021.01.008

Suzuki, K., Akioka, M., Kondo-Kakuta, C., Yamamoto, H., and Ohsumi, Y. (2013). Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae. J Cell Sci 126, jcs.122960.

doi: 10.1242/jcs.122960

Szabadkai, G., Bianchi, K., Várnai, P., De Stefani, D., Wieckowski, M.R., Cavagna, D., Nagy, A.I., Balla, T., and Rizzuto, R. (2006). Chaperone-mediated coupling of endoplasmic reticulum and mitochondrial Ca

pubmed: 17178908 pmcid: 2064700 doi: 10.1083/jcb.200608073

Szymanski, K.M., Binns, D., Bartz, R., Grishin, N.V., Li, W.P., Agarwal, A.K., Garg, A., Anderson, R.G.W., and Goodman, J.M. (2007). The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology. Proc Natl Acad Sci USA 104, 20890–20895.

pubmed: 18093937 pmcid: 2409237 doi: 10.1073/pnas.0704154104

Takeshima, H., Komazaki, S., Nishi, M., Iino, M., and Kangawa, K. (2000). Junctophilins: a novel family of junctional membrane complex proteins. Mol Cell 6, 11–22.

pubmed: 10949023

Tan, J.X., and Finkel, T. (2022). A phosphoinositide signalling pathway mediates rapid lysosomal repair. Nature 609, 815–821.

pubmed: 36071159 pmcid: 9450835 doi: 10.1038/s41586-022-05164-4

Terasaki, M., Chen, L.B., and Fujiwara, K. (1986). Microtubules and the endoplasmic reticulum are highly interdependent structures. J Cell Biol 103, 1557–1568.

pubmed: 3533956 doi: 10.1083/jcb.103.4.1557

Thyme, S.B., Pieper, L.M., Li, E.H., Pandey, S., Wang, Y., Morris, N.S., Sha, C., Choi, J. W., Herrera, K.J., Soucy, E.R., et al. (2019). Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions. Cell 177, 478–491.e20.

pubmed: 30929901 pmcid: 6494450 doi: 10.1016/j.cell.2019.01.048

Tian, S., Ohta, A., Horiuchi, H., and Fukuda, R. (2018). Oxysterol-binding protein homologs mediate sterol transport from the endoplasmic reticulum to mitochondria in yeast. J Biol Chem 293, 5636–5648.

pubmed: 29487131 pmcid: 5900766 doi: 10.1074/jbc.RA117.000596

Tian, Y., Li, Z., Hu, W., Ren, H., Tian, E., Zhao, Y., Lu, Q., Huang, X., Yang, P., Li, X., et al. (2010). C. elegans screen identifies autophagy genes specific to multicellular organisms. Cell 141, 1042–1055.

doi: 10.1016/j.cell.2010.04.034

Tikhomirova, M.S., Kadosh, A., Saukko-Paavola, A.J., Shemesh, T., and Klemm, R.W. (2022). A role for endoplasmic reticulum dynamics in the cellular distribution of microtubules. Proc Natl Acad Sci USA 119, e2104309119.

pubmed: 35377783 pmcid: 9169640 doi: 10.1073/pnas.2104309119

Tong, J., Manik, M.K., and Im, Y.J. (2018). Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites. Proc Natl Acad Sci USA 115, E856–E865.

pubmed: 29339490 pmcid: 5798383 doi: 10.1073/pnas.1719709115

Toulmay, A., and Prinz, W.A. (2012). A conserved membrane-binding domain targets proteins to organelle contact sites. J Cell Sci 125, 49–58.

pubmed: 22250200 pmcid: 3269022 doi: 10.1242/jcs.085118

Tremblay, M.G., and Moss, T. (2016). Loss of all 3 extended synaptotagmins does not affect normal mouse development, viability or fertility. Cell Cycle 15, 2360–2366.

pubmed: 27399837 pmcid: 5004701 doi: 10.1080/15384101.2016.1203494

Trinh, M.N., Brown, M.S., Goldstein, J.L., Han, J., Vale, G., McDonald, J.G., Seemann, J., Mendell, J.T., and Lu, F. (2020). Last step in the path of LDL cholesterol from lysosome to plasma membrane to ER is governed by phosphatidylserine. Proc Natl Acad Sci USA 117, 18521–18529.

pubmed: 32690708 pmcid: 7414171 doi: 10.1073/pnas.2010682117

Uemura, T., Yamamoto, M., Kametaka, A., Sou, Y., Yabashi, A., Yamada, A., Annoh, H., Kametaka, S., Komatsu, M., and Waguri, S. (2014). A cluster of thin tubular structures mediates transformation of the endoplasmic reticulum to autophagic isolation membrane. Mol Cell Biol 34, 1695–1706.

pubmed: 24591649 pmcid: 3993601 doi: 10.1128/MCB.01327-13

Ueno, S., Maruki, Y., Nakamura, M., Tomemori, Y., Kamae, K., Tanabe, H., Yamashita, Y., Matsuda, S., Kaneko, S., and Sano, A. (2001). The gene encoding a newly discovered protein, chorein, is mutated in chorea-acanthocytosis. Nat Genet 28, 121–122.

pubmed: 11381254 doi: 10.1038/88825

Ugur, B., Hancock-Cerutti, W., Leonzino, M., and De Camilli, P. (2020). Role of VPS13, a protein with similarity to ATG2, in physiology and disease. Curr Opin Genet Dev 65, 61–68.

pubmed: 32563856 pmcid: 7746581 doi: 10.1016/j.gde.2020.05.027

Ungricht, R., and Kutay, U. (2017). Mechanisms and functions of nuclear envelope remodelling. Nat Rev Mol Cell Biol 18, 229–245.

pubmed: 28120913 doi: 10.1038/nrm.2016.153

Valm, A.M., Cohen, S., Legant, W.R., Melunis, J., Hershberg, U., Wait, E., Cohen, A.R., Davidson, M.W., Betzig, E., and Lippincott-Schwartz, J. (2017). Applying systems-level spectral imaging and analysis to reveal the organelle interactome. Nature 546, 162–167.

pubmed: 28538724 pmcid: 5536967 doi: 10.1038/nature22369

Valverde, D.P., Yu, S., Boggavarapu, V., Kumar, N., Lees, J.A., Walz, T., Reinisch, K. M., and Melia, T.J. (2019). ATG2 transports lipids to promote autophagosome biogenesis. J Cell Biol 218, 1787–1798.

pubmed: 30952800 pmcid: 6548141 doi: 10.1083/jcb.201811139

Van Petegem, F. (2012). Ryanodine receptors: structure and function. J Biol Chem 287, 31624–31632.

pubmed: 22822064 pmcid: 3442496 doi: 10.1074/jbc.R112.349068

Venditti, R., Masone, M.C., and De Matteis, M.A. (2020). ER-Golgi membrane contact sites. Biochem Soc Trans 48, 187–197.

pubmed: 32065234 doi: 10.1042/BST20190537

Venditti, R., Masone, M.C., Rega, L.R., Di Tullio, G., Santoro, M., Polishchuk, E., Serrano, I.C., Olkkonen, V.M., Harada, A., Medina, D.L., et al. (2019a). The activity of Sac1 across ER-TGN contact sites requires the four-phosphate-adaptor-protein-1. J Cell Biol 218, 783–797.

pubmed: 30659099 pmcid: 6400556 doi: 10.1083/jcb.201812021

Venditti, R., Rega, L.R., Masone, M.C., Santoro, M., Polishchuk, E., Sarnataro, D., Paladino, S., D’Auria, S., Varriale, A., Olkkonen, V.M., et al. (2019b). Molecular determinants of ER-Golgi contacts identified through a new FRET-FLIM system. J Cell Biol 218, 1055–1065.

pubmed: 30659100 pmcid: 6400564 doi: 10.1083/jcb.201812020

Vietri, M., Radulovic, M., and Stenmark, H. (2020). The many functions of ESCRTs. Nat Rev Mol Cell Biol 21, 25–42.

pubmed: 31705132 doi: 10.1038/s41580-019-0177-4

Vig, M., Peinelt, C., Beck, A., Koomoa, D.L., Rabah, D., Koblan-Huberson, M., Kraft, S., Turner, H., Fleig, A., Penner, R., et al. (2006). CRACM1 is a plasma membrane protein essential for store-operated Ca

pubmed: 16645049 pmcid: 5685805 doi: 10.1126/science.1127883

Vihervaara, T., Uronen, R.L., Wohlfahrt, G., Björkhem, I., Ikonen, E., and Olkkonen, V.M. (2011). Sterol binding by OSBP-related protein 1L regulates late endosome motility and function. Cell Mol Life Sci 68, 537–551.

pubmed: 20690035 doi: 10.1007/s00018-010-0470-z

Voeltz, G.K., Prinz, W.A., Shibata, Y., Rist, J.M., and Rapoport, T.A. (2006). A class of membrane proteins shaping the tubular endoplasmic reticulum. Cell 124, 573–586.

pubmed: 16469703 doi: 10.1016/j.cell.2005.11.047

Wanders, R.J.A., Waterham, H.R., and Ferdinandusse, S. (2016). Metabolic interplay between peroxisomes and other subcellular organelles including mitochondria and the endoplasmic reticulum. Front Cell Dev Biol 3, 83.

pubmed: 26858947 pmcid: 4729952 doi: 10.3389/fcell.2015.00083

Wang, F., Gómez-Sintes, R., and Boya, P. (2018). Lysosomal membrane permeabilization and cell death. Traffic 19, 918–931.

pubmed: 30125440 doi: 10.1111/tra.12613

Wang, H., Becuwe, M., Housden, B.E., Chitraju, C., Porras, A.J., Graham, M.M., Liu, X. N., Thiam, A.R., SavageD.B.Agarwal, A.K., et al. (2016). Seipin is required for converting nascent to mature lipid droplets. eLife 5, e16582.

pubmed: 27564575 pmcid: 5035145 doi: 10.7554/eLife.16582

Wang, H., Ma, Q., Qi, Y., Dong, J., Du, X., Rae, J., Wang, J., Wu, W.F., Brown, A.J., Parton, R.G., et al. (2019). ORP2 Delivers Cholesterol to the Plasma Membrane in Exchange for Phosphatidylinositol 4, 5-Bisphosphate (PI(4,5)P2). Mol Cell 73, 458–473.e7.

Wang, X., Zhang, X., Dong, X., Samie, M., Li, X., Cheng, X., Goschka, A., Shen, D., Zhou, Y., Harlow, J., et al. (2012). TPC proteins are phosphoinositide-activated sodium-selective ion channels in endosomes and lysosomes. Cell 151, 372–383.

pubmed: 23063126 pmcid: 3475186 doi: 10.1016/j.cell.2012.08.036

Wang, Y., Li, Z., Wang, X., Zhao, Z., Jiao, L., Liu, R., Wang, K., Ma, R., Yang, Y., Chen, G., et al. (2023). Insights into membrane association of the SMP domain of extended synaptotagmin. Nat Commun 14, 1504.

pubmed: 36932127 pmcid: 10023780 doi: 10.1038/s41467-023-37202-8

Waterman-Storer, C.M., and Salmon, E.D. (1998). Endoplasmic reticulum membrane tubules are distributed by microtubules in living cells using three distinct mechanisms. Curr Biol 8, 798–807.

pubmed: 9663388 doi: 10.1016/S0960-9822(98)70321-5

Weigel, A.V., Chang, C.L., Shtengel, G., Xu, C.S., Hoffman, D.P., Freeman, M., Iyer, N., Aaron, J., Khuon, S., Bogovic, J., et al. (2021). ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER. Cell 184, 2412–2429.e16.

Wenzel, E.M., Elfmark, L.A., Stenmark, H., and Raiborg, C. (2022). ER as master regulator of membrane trafficking and organelle function. J Cell Biol 221, e202205135.

pubmed: 36108241 pmcid: 9481738 doi: 10.1083/jcb.202205135

West, M., Zurek, N., Hoenger, A., and Voeltz, G.K. (2011). A 3D analysis of yeast ER structure reveals how ER domains are organized by membrane curvature. J Cell Biol 193, 333–346.

pubmed: 21502358 pmcid: 3080256 doi: 10.1083/jcb.201011039

Westrate, L.M., Hoyer, M.J., Nash, M.J., and Voeltz, G.K. (2020). Vesicular and uncoated Rab1-dependent cargo carriers facilitate ER to Golgi transport. J Cell Sci 133, jcs239814.

pubmed: 32616562 pmcid: 7390636 doi: 10.1242/jcs.239814

Westrate, L.M., Lee, J.E., Prinz, W.A., and Voeltz, G.K. (2015). Form follows function: the importance of endoplasmic reticulum shape. Annu Rev Biochem 84, 791–811.

pubmed: 25580528 doi: 10.1146/annurev-biochem-072711-163501

Wilfling, F., Thiam, A.R., Olarte, M.J., Wang, J., Beck, R., Gould, T.J., Allgeyer, E.S., Pincet, F., Bewersdorf, J., Farese, R.V., et al. (2014). Arf1/COPI machinery acts directly on lipid droplets and enables their connection to the ER for protein targeting. eLife 3, e01607.

pubmed: 24497546 pmcid: 3913038 doi: 10.7554/eLife.01607

Wilhelm, L.P., Wendling, C., Vedie, B., Kobayashi, T., Chenard, M.P., Tomasetto, C., Drin, G., and Alpy, F. (2017). STARD3 mediates endoplasmic reticulum-to-endosome cholesterol transport at membrane contact sites. EMBO J 36, 1412–1433.

pubmed: 28377464 pmcid: 5430228 doi: 10.15252/embj.201695917

Witte, K., Schuh, A.L., Hegermann, J., Sarkeshik, A., Mayers, J.R., Schwarze, K., Yates III, J.R., Eimer, S., and Audhya, A. (2011). TFG-1 function in protein secretion and oncogenesis. Nat Cell Biol 13, 550–558.

pubmed: 21478858 pmcid: 3311221 doi: 10.1038/ncb2225

Wong, L.H., Gatta, A.T., and Levine, T.P. (2019). Lipid transfer proteins: the lipid commute via shuttles, bridges and tubes. Nat Rev Mol Cell Biol 20, 85–101.

pubmed: 30337668 doi: 10.1038/s41580-018-0071-5

Wong, L.H., and Levine, T.P. (2017). Tubular lipid binding proteins (TULIPs) growing everywhere. Biochim Biophys Acta 1864, 1439–1449.

pmcid: 5507252 doi: 10.1016/j.bbamcr.2017.05.019

Woo, J.S., Srikanth, S., Nishi, M., Ping, P., Takeshima, H., and Gwack, Y. (2016). Junctophilin-4, a component of the endoplasmic reticulum-plasma membrane junctions, regulates Ca

pubmed: 26929330 pmcid: 4790987 doi: 10.1073/pnas.1524229113

Wu, H., Carvalho, P., and Voeltz, G.K. (2018). Here, there, and everywhere: the importance of ER membrane contact sites. Science 361, eaan5835.

pubmed: 30072511 pmcid: 6568312 doi: 10.1126/science.aan5835

Wu, H., and Voeltz, G.K. (2021). Reticulon-3 promotes endosome maturation at ER membrane contact sites. Dev Cell 56, 52–66.e7.

Xiao, J., Luo, J., Hu, A., Xiao, T., Li, M., Kong, Z., Jiang, L., Zhou, Z., Liao, Y., Xie, C., et al. (2019). Cholesterol transport through the peroxisome-ER membrane contacts tethered by PI(4,5)P2 and extended synaptotagmins. Sci China Life Sci 62, 1117–1135.

pubmed: 31144242 doi: 10.1007/s11427-019-9569-9

Xiao, X., Kim, Y., Romartinez-Alonso, B., Sirvydis, K., OryD.S.Schwabe, J.W.R., Jung, M.E., and Tontonoz, P. (2021). Selective aster inhibitors distinguish vesicular and nonvesicular sterol transport mechanisms. Proc Natl Acad Sci USA 118, e2024149118.

pubmed: 33376205 doi: 10.1073/pnas.2024149118

Xie, B., Nguyen, P.M., and Idevall-Hagren, O. (2019). Feedback regulation of insulin secretion by extended synaptotagmin-1. FASEB J 33, 4716–4728.

pubmed: 30589572 doi: 10.1096/fj.201801878R

Xie, B., Nguyen, P.M., and Idevall-Hagren, O. (2022). The endoplasmic reticulum-plasma membrane tethering protein TMEM24 is a regulator of cellular Ca

pubmed: 34821358 doi: 10.1242/jcs.259073

Xu, D., Li, Y., Wu, L., Li, Y., Zhao, D., Yu, J., Huang, T., Ferguson, C., Parton, R.G., Yang, H., et al. (2018). Rab18 promotes lipid droplet (LD) growth by tethering the ER to LDs through SNARE and NRZ interactions. J Cell Biol 217, 975–995.

pubmed: 29367353 pmcid: 5839781 doi: 10.1083/jcb.201704184

Xu, H., and Ren, D. (2015). Lysosomal physiology. Annu Rev Physiol 77, 57–80.

pubmed: 25668017 pmcid: 4524569 doi: 10.1146/annurev-physiol-021014-071649

Xu, L., Wang, X., and Tong, C. (2020). Endoplasmic reticulum-mitochondria contact sites and neurodegeneration. Front Cell Dev Biol 8, 428.

pubmed: 32626703 pmcid: 7314981 doi: 10.3389/fcell.2020.00428

Xu, N., Zhang, S.O., Cole, R.A., McKinney, S.A., Guo, F., Haas, J.T., Bobba, S., Farese, R.V. Jr., and Mak, H.Y. (2012). The FATP1-DGAT2 complex facilitates lipid droplet expansion at the ER-lipid droplet interface. J Cell Biol 198, 895–911.

pubmed: 22927462 pmcid: 3432760 doi: 10.1083/jcb.201201139

Yadav, S., Cockcroft, S., and Raghu, P. (2016). The Drosophila photoreceptor as a model system for studying signalling at membrane contact sites. Biochem Soc Trans 44, 447–451.

pubmed: 27068953 doi: 10.1042/BST20150256

Yan, R., Qian, H., Lukmantara, I., Gao, M., Du, X., Yan, N., and Yang, H. (2018). Human seipin binds anionic phospholipids. Dev Cell 47, 248–256.e4.

Yang, K., Liu, M., Feng, Z., Rojas, M., Zhou, L., Ke, H., and Pastor-Pareja, J.C. (2021). ER exit sites in Drosophila display abundant ER-Golgi vesicles and pearled tubes but no megacarriers. Cell Rep 36, 109707.

pubmed: 34525362 doi: 10.1016/j.celrep.2021.109707

Yao, Y., Xu, M., Qiao, L., Nie, H., Lu, F., and Huang, X. (2022). BAP60 plays an opposite role to the MRT-NURF complex in regulating lipid droplet size. J Genet Genomics 49, 377–379.

pubmed: 35196573 doi: 10.1016/j.jgg.2022.02.003

Yeshaw, W.M., van der Zwaag, M., Pinto, F., Lahaye, L.L., Faber, A.I., Gómez-Sánchez, R., Dolga, A.M., Poland, C., Monaco, A.P., van IJzendoorn, S.C., et al. (2019). Human VPS13A is associated with multiple organelles and influences mitochondrial morphology and lipid droplet motility. eLife 8, e43561.

pubmed: 30741634 pmcid: 6389287 doi: 10.7554/eLife.43561

Yla-Anttila, P., Vihinen, H., Jokitalo, E., and Eskelinen, E.L. (2009). 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 5, 1180–1185.

pubmed: 19855179 doi: 10.4161/auto.5.8.10274

Yoboue, E.D., Sitia, R., and Simmen, T. (2018). Redox crosstalk at endoplasmic reticulum (ER) membrane contact sites (MCS) uses toxic waste to deliver messages. Cell Death Dis 9, 331.

pubmed: 29491367 pmcid: 5832433 doi: 10.1038/s41419-017-0033-4

Yu, H., Liu, Y., Gulbranson, D.R., Paine, A., Rathore, S.S., and Shen, J. (2016). Extended synaptotagmins are Ca

pubmed: 27044075 pmcid: 4843466 doi: 10.1073/pnas.1517259113

Yuan, J.P., Zeng, W., Dorwart, M.R., Choi, Y.J., Worley, P.F., and Muallem, S. (2009). SOAR and the polybasic STIM1 domains gate and regulate Orai channels. Nat Cell Biol 11, 337–343.

pubmed: 19182790 pmcid: 2663385 doi: 10.1038/ncb1842

Zacharogianni, M., Aguilera-Gomez, A., Veenendaal, T., Smout, J., and Rabouille, C. (2014). A stress assembly that confers cell viability by preserving ERES components during amino-acid starvation. eLife 3, e04132.

pubmed: 25386913 pmcid: 4270098 doi: 10.7554/eLife.04132

Zanetti, G., Pahuja, K.B., Studer, S., Shim, S., and Schekman, R. (2011). COPII and the regulation of protein sorting in mammals. Nat Cell Biol 14, 20–28.

pubmed: 22193160 doi: 10.1038/ncb2390

Zervopoulos, S.D., Boukouris, A.E., Saleme, B., Haromy, A., Tejay, S., Sutendra, G., and Michelakis, E.D. (2022). MFN2-driven mitochondria-to-nucleus tethering allows a non-canonical nuclear entry pathway of the mitochondrial pyruvate dehydrogenase complex. Mol Cell 82, 1066–1077.e7.

Zeuschner, D., Geerts, W.J.C., van Donselaar, E., Humbel, B.M., Slot, J.W., Koster, A.J., and Klumperman, J. (2006). Immuno-electron tomography of ER exit sites reveals the existence of free COPII-coated transport carriers. Nat Cell Biol 8, 377–383.

pubmed: 16531996 doi: 10.1038/ncb1371

Zhang, D., Bidone, T.C., and Vavylonis, D. (2016). ER-PM contacts define actomyosin kinetics for proper contractile ring assembly. Curr Biol 26, 647–653.

pubmed: 26877082 pmcid: 4783277 doi: 10.1016/j.cub.2015.12.070

Zhang, D., Vjestica, A., and Oliferenko, S. (2010). The cortical ER network limits the permissive zone for actomyosin ring assembly. Curr Biol 20, 1029–1034.

pubmed: 20434336 doi: 10.1016/j.cub.2010.04.017

Zhang, D., Vjestica, A., and Oliferenko, S. (2012). Plasma membrane tethering of the cortical er necessitates its finely reticulated architecture. Curr Biol 22, 2048–2052.

pubmed: 23041194 doi: 10.1016/j.cub.2012.08.047

Zhang, H., and Hu, J. (2016). Shaping the endoplasmic reticulum into a social network. Trends Cell Biol 26, 934–943.

pubmed: 27339937 doi: 10.1016/j.tcb.2016.06.002

Zhang, S.L., Yeromin, A.V., Zhang, X.H.F., Yu, Y., Safrina, O., Penna, A., Roos, J., Stauderman, K.A., and Cahalan, M.D. (2006). Genome-wide RNAi screen of Ca

pubmed: 16751269 pmcid: 1482614 doi: 10.1073/pnas.0603161103

Zhang, S.L., Yu, Y., Roos, J., Kozak, J.A., Deerinck, T.J., Ellisman, M.H., Stauderman, K.A., and Cahalan, M.D. (2005). STM1 is a Ca

pubmed: 16208375 pmcid: 1618826 doi: 10.1038/nature04147

Zhang, X., Gibhardt, C.S., Will, T., Stanisz, H., Körbel, C., Mitkovski, M., Stejerean, I., Cappello, S., Pacheu-Grau, D., Dudek, J., et al. (2019). Redox signals at the ER-mitochondria interface control melanoma progression. EMBO J 38, e100871.

pubmed: 31304984 pmcid: 6669928 doi: 10.15252/embj.2018100871

Zhang, Y., Guan, Y., Pan, S., Yan, L., Wang, P., Chen, Z., Shen, Q., Zhao, F., Zhang, X., Li, J., et al. (2020a). Hypothalamic extended synaptotagmin-3 contributes to the development of dietary obesity and related metabolic disorders. Proc Natl Acad Sci USA 117, 20149–20158.

pubmed: 32747560 pmcid: 7443966 doi: 10.1073/pnas.2004392117

Zhang, Y., Schroeder, L.K., Lessard, M.D., Kidd, P., Chung, J., Song, Y., Benedetti, L., Li, Y., Ries, J., Grimm, J.B., et al. (2020b). Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging. Nat Methods 17, 225–231.

pubmed: 31907447 pmcid: 7028321 doi: 10.1038/s41592-019-0676-4

Zhao, H., Li, T., Wang, K., Zhao, F., Chen, J., Xu, G., Zhao, J., Li, T., Chen, L., Li, L., et al. (2019). AMPK-mediated activation of MCU stimulates mitochondrial Ca

pubmed: 30858581 doi: 10.1038/s41556-019-0296-3

Zhao, K., Foster, J., and Ridgway, N.D. (2020). Oxysterol-binding protein-related protein 1 variants have opposing cholesterol transport activities from the endolysosomes. Mol Biol Cell 31, 793–802.

pubmed: 32023146 pmcid: 7185962 doi: 10.1091/mbc.E19-12-0697

Zhao, K., and Ridgway, N.D. (2017). Oxysterol-binding protein-related protein 1L regulates cholesterol egress from the endo-lysosomal system. Cell Rep 19, 1807–1818.

pubmed: 28564600 doi: 10.1016/j.celrep.2017.05.028

Zhao, Y.G., Chen, Y., Miao, G., Zhao, H., Qu, W., Li, D., Wang, Z., Liu, N., Li, L., Chen, S., et al. (2017). The ER-localized transmembrane protein EPG-3/VMP1 regulates SERCA activity to control ER-isolation membrane contacts for autophagosome formation. Mol Cell 67, 974–989.e6.

pubmed: 28890335 doi: 10.1016/j.molcel.2017.08.005

Zhao, Y.G., Liu, N., Miao, G., Chen, Y., Zhao, H., and Zhang, H. (2018). The ER contact proteins VAPA/B interact with multiple autophagy proteins to modulate autophagosome biogenesis. Curr Biol 28, 1234–1245.e4.

pubmed: 29628370 doi: 10.1016/j.cub.2018.03.002

Zhao, Y.G., and Zhang, H. (2019). Core autophagy genes and human diseases. Curr Opin Cell Biol 61, 117–125.

pubmed: 31480011 doi: 10.1016/j.ceb.2019.08.003

Zheng, P., Obara, C.J., Szczesna, E., Nixon-Abell, J., Mahalingan, K.K., Roll-Mecak, A., Lippincott-Schwartz, J., and Blackstone, C. (2022). ER proteins decipher the tubulin code to regulate organelle distribution. Nature 601, 132–138.

pubmed: 34912111 doi: 10.1038/s41586-021-04204-9

Zoncu, R., Bar-Peled, L., Efeyan, A., Wang, S., Sancak, Y., and Sabatini, D.M. (2011). mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H

pubmed: 22053050 pmcid: 3211112 doi: 10.1126/science.1207056

Zoncu, R., and Perera, R.M. (2022). Built to last: lysosome remodeling and repair in health and disease. Trends Cell Biol 32, 597–610.

pubmed: 35123838 pmcid: 9189017 doi: 10.1016/j.tcb.2021.12.009

Stay in touch with the endoplasmic reticulum.

Journal

Informations de publication

Résumé

Identifiants

Types de publication

Langues

Sous-ensembles de citation

Informations de copyright

Références

Auteurs

Sha Sun (S)

Gan Zhao (G)

Mingkang Jia (M)

Qing Jiang (Q)

Shulin Li (S)

Haibin Wang (H)

Wenjing Li (W)

Yunyun Wang (Y)

Xin Bian (X)

Yan G Zhao (YG)

Xun Huang (X)

Ge Yang (G)

Huaqing Cai (H)

Jose C Pastor-Pareja (JC)

Liang Ge (L)

Chuanmao Zhang (C)

Junjie Hu (J)

Classifications MeSH