[1] Kapp, L.D. and Lorsch, J.R. (2004) The Molecular Mechanics of Eukaryotic Translation. Annual Reviews of Biochemistry, 73, 657-704.
http://dx.doi.org/10.1146/annurev.biochem.73.030403.080419
[2] Koga, H., Kaushik, S. and Cuervo, A.M. (2011) Protein Homeostasis and Aging: The Importance of Exquisite Quality Control. Ageing Research Review, 10, 205-215.
http://dx.doi.org/10.1016/j.arr.2010.02.001
[3] Walter, P. and Ron, D. (2011) The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation. Science, 334, 1081-1086.
http://dx.doi.org/10.1126/science.1209038
[4] Vincenz, L. and Hartl, U. (2014) Sugarcoating ER Stress. Cell, 156, 1125-1127.
http://dx.doi.org/10.1016/j.cell.2014.02.035
[5] Jung, H., Gkogkas, C.G., Sonenberg, N. and Holt, C.H. (2014) Remote Control of Gene Function by Local Translation. Cell, 157, 26-40.
http://dx.doi.org/10.1016/j.cell.2014.03.005
[6] Lusk, C.P., Blobel, G. and King, M.C. (2007) Highway to the Inner Nuclear Membrane: Rules for the Road. National Review of the Molecular Biology, 8, 414-420.
http://dx.doi.org/10.1038/nrm2165
[7] Siniossoglou, S. (2009) Lipins, Lipids and Nuclear Envelope Structure. Traffic, 10, 1181-1187.
http://dx.doi.org/10.1111/j.1600-0854.2009.00923.x
[8] Adams, R.L. and Wente, S.R. (2013) Uncovering Nuclear Pore Complexity with Innovation. Cell, 152, 1218-1221.
http://dx.doi.org/10.1016/j.cell.2013.02.042
[9] Rothman, J.E. (1994) Mechanisms of Intracellular Protein Transport. Nature, 372, 55-63.
http://dx.doi.org/10.1038/372055a0
[10] Bilder, D., Schober, M. and Perrimon, N. (2003) Integrated Activity of PDZ Complexes Regulates Epithelial Polarity. Nature Cell Biology, 5, 53-58.
http://dx.doi.org/10.1038/ncb897
[11] Sharma, N., Low, S.H., Misra, S., Pallavi, B. and Weimbs, T. (2006) Apical Targeting of Synthaxin 3 Is Essential for Epithelial Cell Polarity. Journal of Cell Biology, 173, 937-948.
http://dx.doi.org/10.1083/jcb.200603132
[12] Kawano, M., Kumagai, K., Nishijima, M. and Handa, K. (2006) Efficient Trafficking of Ceramide from Endoplasmic Reticulum to the Golgi Apparatus Requires VAMP-Associated Protein-Interacting FFAT Motif of CERT. The Journal of Biological Chemistry, 281, 30279-30288.
http://dx.doi.org/10.1074/jbc.M605032200
[13] van Meer, G., Halter, D., Sprong, H., Somerharju, P. and Egmond, M.R. (2006) ABC Lipid Transporters: Extruders, Flippases, or Flopless Activators? FEBS Letters, 580, 1171-1177.
http://dx.doi.org/10.1016/j.febslet.2005.12.019
[14] Fölch, H. (2008) Regulation of Membrane Traf-ficking in Polarized Epithelial Cells. Current Opinions in Cell Biology, 20, 208-213.
http://dx.doi.org/10.1016/j.ceb.2008.01.003
[15] Pfeffer, S.R. (2007) Unsolved Mysteries of Membrane Traffic. Annual Review of Biochemistry, 76, 629-645.
http://dx.doi.org/10.1146/annurev.biochem.76.061705.130002
[16] Gohil, V.M. and Greenberg, M.L. (2009) Mitochondrial Membrane Biogenesis: Phospholipids and Proteins Go Hand in Hand. Journal of Cell Biology, 184, 469-472.
[17] Südhof, T.C. and Rothman, J.E. (2009) Membrane Fusion: Grappling with SNARE and SM Proteins. Science, 323, 474-477.
http://dx.doi.org/10.1126/science.1161748
[18] Beck, R., Prinz, S., Distellköter-Bechart, P., Röhling, S., Adolf, F., Hoehner, K., et al. (2011) Coatomer and Dimeric ADP Ribosylation Factor 1 Promote Distinct Steps in Membrane Scission. Journal of Cell Biology, 194, 765-777.
[19] Brodsky, J.L. (2012) Cleaning Up: ER-Associated Degradation to the Rescue. Cell, 151, 1163-1167.
http://dx.doi.org/10.1016/j.cell.2012.11.012
[20] Keiser, M., Alfalah, M., Propsting, M.J., Castelletti, D. and Naim, H.Y. (2006) Altered Folding, Turnover, and Polarized Sorting Act in Concert to Define a Novel Pathomechanism of Congenital Sucrose-Isomaltase Deficiency. Journal of Biological Chemistry, 281, 14393-14399.
http://dx.doi.org/10.1074/jbc.M513631200
[21] Smith, M.H., Ploegh, H.L. and Weissman, J.S. (2011) Road to Ruin: Targeting Proteins for Degradation in the Endoplasmic Reticulum. Science, 334, 1086-1090.
http://dx.doi.org/10.1126/science.1209235
[22] Marion, G., Madeo, F. and Kroemer, G. (2011) Autophagy for Tissue Homeostasis and Neuroprotection. Current Opinions in Cell Biology, 23, 198-206.
http://dx.doi.org/10.1016/j.ceb.2010.10.001
[23] Lukacs, G.L. and Verkman, A.S. (2012) CFTR: Folding, Mis-folding and Correcting the ΔF508 Conformational Defect. Trends in Molecular Medicine, 18, 81-91.
http://dx.doi.org/10.1016/j.molmed.2011.10.003
[24] Ron, E., Shenkman, M., Groisman, B., Izenshtein, Y B., Leitman, J. and Lederkremer, G.Z. (2011) Bypyss of Glycan-Dependent Glycoprotein Delivery to ERAD by Up-Regulated EDEM1. Molecular Biology of the Cell, 22, 3945-3954.
http://dx.doi.org/10.1091/mbc.E10-12-0944
[25] Rodriguez-Boulan, E. and Müsch, A. (2005) Protein Sorting in Golgi Complex: Shifting Paradigms. Biochimica et Biophysica Acta (BBA), Molecular Cell Research, 1744, 455-464.
http://dx.doi.org/10.1016/j.bbamcr.2005.04.007
[26] De Matteis, M.A. and Luini, A. (2008) Exiting the Golgi Complex. Nature Reviews of Molecular Cell Biology, 9, 273-284.
http://dx.doi.org/10.1038/nrm2378
[27] Mertins, P., Qiao, J.W., Patel, J., Udeshi, N.D., Clauser, K.R., Mani, D.R., Burgess, M.W., Gillette M.A., Jaffe, J.D. and Carr, S.A. (2013) Integrated Proteomic Analysis of Post-Translational Modifications by Serial Enrichment. Nature Methods, 10, 634-637.
http://dx.doi.org/10.1038/nmeth.2518
[28] Swaney, D.L., Beltrao, P., Starita, L., Guo, A., Rush, J., Fields, S., Krogan, N.J. and Villén, J. (2013) Global Analysis of Phosphorylation and Ubiquitylation Cross-Talk in Protein Degradation. Nature Methods, 10, 676-682.
http://dx.doi.org/10.1038/nmeth.2519
[29] Toulmay, A. and Prinz, W.A. (2011) Lipid Transfer and Signaling at Organelle Contact Sites: The Tip of the Iceberg. Current Opinions in Cell Biology, 23, 458-463.
[30] Mellman, I. and Nelson, W.J. (2008) Coordinated Protein Sorting, Targeting and Distribution in Polarized Cells. Nature Reviews Molecular Cell Biology, 9, 833-855.
http://dx.doi.org/10.1038/nrm2525
[31] Lee, M.C., Miller, E.A., Goldberg, J., Orci, L. and Schekman, R. (2004) Bi-Directional Protein Transport between the ER and Golgi. Annual Reviews of Cell Development and Biology, 20, 87-123.
http://dx.doi.org/10.1146/annurev.cellbio.20.010403.105307
[32] Glick, B.S. and Nakano, A. (2009) Membrane Traffic within the Golgi Apparatus. Annual Review of Cell Development Biology, 25, 113-132.
http://dx.doi.org/10.1146/annurev.cellbio.24.110707.175421
[33] Houtkooper, R.H. and Vaz, F.M. (2008) Cardiolipin, the Heart of Mitochondrial Metabolism. Cellular and Molecular Life Sciences, 65, 2493-2206.
http://dx.doi.org/10.1007/s00018-008-8030-5
[34] Lemmon, M.A. (2008) Membrane Recognition by Phospholipids Binding Proteins. Nature Reviews of Molecular Cell Biology, 9, 99-111.
http://dx.doi.org/10.1038/nrm2328
[35] Whitelegge, J. (2011) Up Close with Membrane Lipid-Protein Complexes. Science, 334, 320-321.
http://dx.doi.org/10.1126/science.1214084
[36] Osman, C., Voelker, D.R. and Langer, T. (2011) Making Heads or Tails of Phospholipids in Mitochondria. Journal of Cell Biology, 192, 7-16.
[37] Rusinova, R., Hobart, E.A, Koeppe II, R.E. and Andersen, O.S. (2013) Phosphoinositides Alter Lipid Bilayer Properties. Journal of General Physiology, 141, 673-690.
http://dx.doi.org/10.1085/jgp.201310960
[38] Park, S.H., Das, B.B., Casagrande, F., Tian, Y., Nothnagel, H.J., Chu, M., Kiefer, H., Maier, K., De Angelis, A.A., Marassi, F.M. and Opella, S.J. (2012) Structure of the Chemokine Receptor CXCR1 in Phospholipid Bilayers. Nature, 491, 779-783.
[39] Slomiany, A., Grzelinska, E., Kasinathan, C., Yamaki, K., Palecz, D., Slomiany, B.A., et al. (1992) Biogenesis of Endoplasmic Reticulum Transport Vesicles Transferring Gastric Apomucin from ER to Golgi. Experimental Cell Research, 201, 1669-1682.
http://dx.doi.org/10.1016/0014-4827(92)90280-L
[40] Slomiany, A. and Slomiany, B.L. (2011) Transformations of Phosphatidylinositol Phosphates in the Outer and Inner Nuclear Membrane Are Linked to Synthesis and Restitution of Cellular Membranes. Health, 3, 187-199.
http://dx.doi.org/10.4236/health.2011.34035
[41] Slomiany, A., Grabska, M. and Slomiany, B.L. (2006) Homeostatic Restitution of Cell Membranes. Nuclear Membrane Lipid Biogenesis and Transport of Protein from Cytosol to Intranuclear Spaces. International Journal of Biological Sciences, 2, 216-226.
http://dx.doi.org/10.7150/ijbs.2.216
[42] Slomiany, A. and Slomiany, B.L. (2013) Homeostatic Cell Cycle and the Origin of Autophagosomal Vesicles. Advances in Biological Chemistry, 3, 275-287.
http://dx.doi.org/10.4236/abc.2013.33031
[43] Slomiany, A. and Slomiany, B.L. (2012) Phosphatidylglycerol-Containing ER-Transport Vesicles Built and Restore Outer Mitochondrial Membrane and Deliver Nuclear DNA Translation Products to Generate Cardiolipin in the Inner Mitochondrial Membrane. Advances in Biological Chemistry, 2, 132-145.
http://dx.doi.org/10.4236/abc.2012.22016
[44] Sano, S., Slomiany, B.L. and Slomiany, A. (1995) Isolation and Characterization of the First Enzyme in the Pathway of Sphingolipids Synthesis. FASEB Journal, 9, A2719.
[45] Slomiany, A., Grzelinska, E., Grabska, M. and Slomiany, B.L. (1992) Intracelular Processes Associated with Glycoprotein Transport and Processing. Archives of Biochemistry and Biophysics, 298, 167-175.
http://dx.doi.org/10.1016/0003-9861(92)90108-9
[46] Slomiany, A., Grzelinska, E., Yamaki, K. and Slomiany, B.L. (1992) Function of Intracellular Phospholipase A2 in Vectorial Transport of Apoproteins from ER to Golgi. International Journal of Biochemistry, 24, 1397-1406.
http://dx.doi.org/10.1016/0020-711X(92)90065-9
[47] Slomiany, A., Grabska, M., Piotrowski, E. and Slomiany, B.L. (1994) Intracellular Processes Associated with Vesicular Transport from Endoplasmic Reticulum to Golgi and Exocytosis. Archives of Biochemistry and Biophysics, 310, 247-255.
http://dx.doi.org/10.1006/abbi.1994.1164
[48] Slomiany, A. and Slomiany, B.L. (2003) Lipidomic Processes in Homeostatic and LPS-Modified Cell Renewal Cycle. Role of Phosphatidylinositol 3-Kinase Pathway in Biomembrane Synthesis and Restitution of Apical Epithelial Membrane. Journal Physiology and Pharmacology, 54, 533-551.
[49] Slomiany, A., Sano, S., Grabska, M., Yamaki, K. and Slomiany, B.L. (2004) Gastric Mucosal Cell Homeostatic Physiome. Critical Role of ER-Initiated Membrane Restitution in the Fidelity of Cell Function Renewal. Journal of Physiology and Pharmacology, 55, 837-860.
[50] Slomiany, A. and Slomiany, B.L. (2010) Cell Membranes Composition Is Defined in ER and Their Restitution Proceeds by en Bloc Fusion of ER Generated Transport Vesicles. Health, 2, 1444-1454.
http://dx.doi.org/10.4236/health.2010.212214
[51] Obrig, T.G., Culp, W.J., McKeehan, W.L. and Hardesty, B. (1971) The Mechanism by Which Cycloheximide and Related Glutarimide Antibiotics Inhibit Peptide Synthesis on Reticulocyte Ribosomes. Journal of Biological Chemistry, 246, 174-181.
[52] Croze, E.M. and Morré, D.J. (1984) Isolation of Plasma Membrane, Golgi Apparatus, and Endoplasmic Reticulum from Single Homogenates of Mouse Liver. Journal of Cellular Physiology, 119, 46-57.
http://dx.doi.org/10.1002/jcp.1041190109
[53] Slomiany, A., Nowak, P., Piotrowski, E. and Slomiany, B.L. (1998) Effect of Ethanol on Intracellular Vesicular Transport from Golgi to the Apical Membrane. Role of Phosphatidylinositol 3-Kinase and Phospholipase A2 in Golgi Transport Vesicles Association and Fusion with the Apical Membrane. Alcohol, Clinical and Experimental Research, 22, 167-175.
[54] Parsons, D.F., Willims, G.R. and Chance, B. (1966) Characteristics of Isolated and Purified Preparations of the Outer and Inner Membranes of Mitochondria. Annals of the New York Academy of Sciences, 137, 643-666.
http://dx.doi.org/10.1111/j.1749-6632.1966.tb50188.x
[55] Tjelle, T.E., Brech, A., Juvet, L.K., Griffiths, G. and Berg, T. (1996) Isolation and Characterization of Early Endosomes, Late Endosomes, Late Endosomes and Terminal Lysosomes: Their Role in Protein Degradation. Journal of Cell Sciences, 109, 2905-2914.
[56] Rome, L.H. and Crain, L.R. (1981) Degradation of Mucopolysacharide in Intact Isolated Lysosomes. Journal of Biological Chemistry, 256, 10763-10768.
[57] Schneider-Poetsch, T., Ju, J., Eyler, D.E., Dang, Y., Bhat, S., Merrick, W.C., Green, R., Shen, B. and Liu, J.O. (2010) Inhibition of Eukaryotic Translation Elongation by Cycloheximide and Lactimidomycin. Nature Chemistry and Biology, 6, 209-217.
http://dx.doi.org/10.1038/nchembio.304
[58] Kawashima, A., Sato, A., Kawashima, M., Nitta, K., Yamura, W., Sugino, N., Nihei, H. and Natori, Y. (1998) A Simple Procedure for the Isolation of Rat Kidney Lysosomes. Kidney International, 54, 275-278.
http://dx.doi.org/10.1046/j.1523-1755.1998.00958.x
[59] Liu, P. and Anderson, R.G.W. (1995) Compartmentalized Production of Ceramide at the Cell Surface. Journal of Biological Chemistry, 270, 27179-27185.
http://dx.doi.org/10.1074/jbc.270.45.27179
[60] Slomiany, A., Grabska, M., Slomiany, B.A., Grzelinska, E., Morita, M. and Slomiany, B.L. (1993) Intracellular Transport, Organelle Biogenesis and Establishment of Golgi Identity: Impact of Brefeldin A on the Activity of Lipid Synthesizing Enzymes. International Journal of Biochemistry, 25, 891-901.
http://dx.doi.org/10.1016/0020-711X(93)90245-A
[61] Nunnari, J. and Walter, P. (1996) Regulation of Organelle Biogenesis. Cell, 84, 389-394.
http://dx.doi.org/10.1016/S0092-8674(00)81283-0
[62] Burke, B. and Ellenberg, J. (2002) Remodeling the Walls of the Nucleus. Nature Reviews Molecular Cell Biology, 3, 487-497.
http://dx.doi.org/10.1038/nrm860
[63] Akhtar, A. and Gasser, S.M. (2007) The Nuclear Envelope and Transcriptional Control. National Review Genetics, 8, 507-517. http://dx.doi.org/10.1038/nrg2122
[64] Saftig, P. and Klumperman, J. (2009) Lysosome Biogenesis and Lysosomal Membrane Proteins: Trafficking Meets Function. Nature Reviews Molecular Cell Biology, 10, 623-635.
http://dx.doi.org/10.1038/nrm2745
[65] Slomiany, A. and Slomiany, B.L. (2011) Transformations of Phosphatidylinositol Phosphates in the Outer and Inner Nuclear Membrane Are Linked to Synthesis and Restitution of Cellular Membranes. Health, 4, 187-199.
[66] Lloyd, A.C. (2013) The Regulation of Cell Size. Cell, 154, 1194-1205.
http://dx.doi.org/10.1016/j.cell.2013.08.053
[67] Atilla-Gokcumen, G.E., Muro, E., Relat-Goberna, J., Sasse, S., Bedigian, A., Coughlin, M., Garcia-Manyes S. and Eggert, U.S. (2014) Dividing Cells Regulate Their Lipid Composition and Localization. Cell, 156, 428-439.
http://dx.doi.org/10.1016/j.cell.2013.12.015
[68] Mari, M., Tooze, S.E. and Reggiori, F. (2011) The Puzzling Origin of the Autophagosomal Membrane. F1000 Biology Reports, 3, 25-34.
[69] Maiuri, M.C., Zalckvar, E., Kimchi, A. and Kroemer, G. (2007) Self-Eating and Self-Killing: Cross Talk between Autophagy and Apoptosis. Nature Reviews Molecular Cell Biology, 8, 741-752.
http://dx.doi.org/10.1038/nrm2239
[70] Karunakaren, V. and Wickner, W. (2013) Fusion Proteins and Select Lipids Cooperate as Membrane Receptors for the soluble N-Methylmaleimide-Sensitive Factor Attachment Protein Receptor (SNARE) Vam7p. The Journal of Biological Chemistry, 288, 28557-28566.
http://dx.doi.org/10.1074/jbc.M113.484410
[71] Hetz, C. (2012) The Unfolded Protein Response: Controlling Cell Fate Decision under ER Stress and Beyond. National Reviews Molecular Cell Biology, 13, 89-102.
[72] Idone, V., Tam, C. and Andrews, N.W. (2008) Two-Way Traffic on the Road to Plasma Membrane Repair. Trends in Cellular Biology, 18, 552-559.
http://dx.doi.org/10.1016/j.tcb.2008.09.001
[73] Neupert, H. and Herrmann, J.M. (2007) Translocation of Proteins into Mitochondria. Annual Review of Biochemistry, 76, 723-749.
http://dx.doi.org/10.1146/annurev.biochem.76.052705.163409
[74] Kobayashi, T., Beuchat, M.H., Chevallier, J., Makino, A., Mayran, N., Escola, J.M., Lebrand, C., Cosson, P., Kobayashi, T. and Gruenberg, J. (2002) Separation and Characterization of Late Endosomal Membrane Domains. Journal of Biological Chemistry, 277, 32157-32164.
http://dx.doi.org/10.1074/jbc.M202838200
[75] Hammond, G.R.V., Machner, M.P. and Balla, T. (2014) A Novel Probe for Phosphatidylinositol 4-Phosphate Reveals Multiple Pools beyond the Golgi. Journal of Cell Biology, 205, 113-126.
http://dx.doi.org/10.1083/jcb.201312072
[76] Yoshimori, T. and Noda, T. (2008) Toward Unraveling Membrane Biogenesis in Mammalian Autophagy. Current Opinions in Cell Biology, 20, 401-407.
http://dx.doi.org/10.1016/j.ceb.2008.03.010
[77] Hayashi-Nishino, M., Fujita, M., Noda, T., Yamaguchi, A., Yoshimori, T. and Yamamoto, A. (2009) A Subdomain of the Endoplasmic Reticulum Forms a Cradle for Autophagosome Formation. National Cell Biology, 5, 1180-1185.
[78] Tooze, S.E. and Yoshimuri, T. (2010) The Origin of the Autophagosomal Membrane. National Cell Biology, 12, 831-835.
http://dx.doi.org/10.1038/ncb0910-831
[79] Hailey, D.W., Rambold, A.S., Satpute-Krishnan, P., Mitra, K., Sougrat, R., Kim, P.K. and Lippincott-Schwartz, J. (2010) Mitochondra Supply Membranes for Autophagosomal Biogenesis during Starvation. Cell, 141, 656-667.
http://dx.doi.org/10.1016/j.cell.2010.04.009
[80] van der Vaart, A. and Reggiori, F. (2010) The Golgi Complex as a Source for Yeast Autophagosomal Membranes. Autophagy, 6, 800-801.
http://dx.doi.org/10.4161/auto.6.6.12575
[81] Ravikumar, B., Moreau, K., Jahreiss, L., Puri, C. and Rubinsztein, D.C. (2010) Plasma Membrane Contributes to the Formation of Pre-Autophagosomal Structures. National Cell Biology, 12, 747-757.
http://dx.doi.org/10.1038/ncb2078
[82] Hurley, J.H. and Schulman, B.A. (2014) Atomistic Autophagy: The Structures of Cellular Self-Digestion. Cell, 157, 300-311.
http://dx.doi.org/10.1016/j.cell.2014.01.070