F O C U S O N O r g a n e l l e b i o g e n e s i s a n d h o m e os ta s i s
FOREWORD Size and position matter Graham Warren
Abstract | The 2013 Nobel Prize in Physiology or Medicine emphasizes the progress made in understanding the molecular mechanisms that underpin the vesicular movement of cargo through the exocytic and endocytic pathways. Attention now focuses on those mechanisms that govern the relative size and position of the many different membranebound compartments. These homeostatic mechanisms are discussed in this issue of Nature Reviews Molecular Cell Biology and must be integrated so as to satisfy the needs of the cell and the organism. The evolution of membrane-bound compartments in the eukaryotic cytoplasm gave unprecedented opportunities to optimize cellular processes and segregate incompatible ones. This came at a price, as the output of some of these processes (such as proteins and lipids) act in a different compartment; they thus have to be moved from the place where they are generated to the place where they function.
Max F. Perutz Laboratories, University and Medical University of Vienna, Doktor-Bohr-Gasse 9, 1030 Vienna, Austria. e‑mail: [email protected]
Sorting at the ER This sorting problem occupied researchers for decades and is best exemplified by the endoplasmic reticulum (ER), through which a subset of proteins being synthesized on cytoplasmic ribosomes is sorted to its final destination. The ER also synthesizes lipids that are needed as components of downstream compartments and beyond. The best characterized compartments downstream of the ER are the Golgi, endosomes and lysosomes, as well as, in some cells, regulated secretory granules. However, there are other compartments, reviewed in this issue, including autophagosomes1, peroxisomes2, lipid droplets3 and plastids4. The ER has to satisfy the needs of all these downstream compartments. It must provide them with the proteins and lipids that are required to carry out their particular cellular functions. To do this, the ER has to populate itself with the translocation machinery and chaperones that have a role in the production and assembly of the cargoes destined for these downstream compartments. It must also populate itself with lipid‑synthesizing enzymes. The surface area of the ER is determined by the need to satisfy these supply demands. To a first approximation it is set by the number of protein-translocating units that are required to populate the downstream compartments. This number will depend on whether the cell is actively growing, in which case the ER also has to drive duplication of all the compartments that it services, including itself. The trafficking capacity required will also
depend on whether the cell is a professional secretory cell. The pancreatic acinar cell is one such example, secreting more than 70% of the total proteins that are synthesized in the cytoplasm. As such, it has an extensive set of flattened ER cisternae that are mostly stacked and located at the base of the cell beneath and partly around the nucleus. Antibody-secreting plasma cells are another example; they have a sparse ER that proliferates by several orders of magnitude upon stimulation, to the extent that each cell can eventually secrete its own weight in immunoglobulin G (IgG) molecules every day. How is this expansion regulated? The details are still being worked out, but it seems that a process first identified as a stress response may have more general applicability. This unfolded protein response (UPR) detects excess unfolded proteins in the ER and initiates a transcriptional programme to mitigate their effects5: more chaperones are synthesized; aggregated proteins are translocated to the cytoplasm for degradation by glycosidases and proteasomes; and bulk protein trans location is temporarily halted. All this increases the size of the ER. The UPR can also, it seems, be used by plasma cells to expand their ER6, but this is not a stress response and the initiating signals still need to be determined. Perhaps the UPR is even involved during the cell cycle when the ER doubles in size and then partitions between each daughter cell. Furthermore, cells not only need a mechanism to grow the ER but also to limit this growth, and it seems that autophagy might be important for this7. How these growth and degradation processes are coordinated to ensure ER homeostasis needs further work.
Cargo modification by the Golgi What about organelles downstream of the ER, such as the Golgi? How the size of the Golgi is determined has long been debated8.
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
VOLUME 14 | DECEMBER 2013 | 755 © 2013 Macmillan Publishers Limited. All rights reserved
F O RE W O RD A key function of the Golgi is the modification of the oligosaccharides on the transiting cargo, and a sufficient amount of enzymes is required to complete these modifications. Therefore, the flux of cargo must be linked to the levels of Golgi-associated enzymes, and this will in turn determine the size of this organelle. At the ER, cargoes are channelled through exit sites, where they are selectively incorporated into budding coat protein complex II (COPII) vesicles. Golgi enzymes are also synthesized in the ER and also seem to be transported to the Golgi in these vesicles; but, how this is coordinated so that the Golgi reaches the right size is unclear. Furthermore, any mechanism at play has to accommodate the very different needs of cargo proteins for oligosaccharide modification. In most cells, there are thousands of different types of cargo protein, each of which may require distinct oligosaccharide modifications. The core patterns of O-linked and N-linked glycosylation can be modified in various ways 9, and such bespoke glycosylation places huge demands on the Golgi; it must provide the necessary enzymes, in the right order, to properly modify the many different cargo molecules. This may explain why the surface area of the Golgi in mammalian cells is roughly the same size as the plasma membrane (and about 10% of the ER). By contrast, in much simpler organisms, the need for cargo modification may not be so great. As an example, in the protozoan parasite Trypanosoma brucei, at any one time almost all the transiting cargo is a single species of glycosylphosphatidylinositol (GPI)-anchored cell surface protein, and therefore the glycosylation machinery can be much simpler. In fact, the surface area of the Golgi in T. brucei is only about 5% of that of the plasma membrane, which is 20‑fold less than in mammalian cells10. Hence, any mechanism for regulating the size of the Golgi must also account for the very different requirements of the transiting cargo. Golgi homeostasis during the cell cycle also remains unexplained. Unlike the ER, the Golgi has a modular structure, and this structural feature is best revealed (at least in mammalian cells) by the addition of the microtubule-disrupting agent nocodazole, which breaks down the Golgi ribbon into its constituent stacks. Whereas the ER doubles its size during the cell cycle, the Golgi stacks must double their number. The mechanism of this duplication is still being debated. For example, is the new Golgi assembled de novo, from the ER or is it constructed, at least in part, from components that originate from the old Golgi11.
Organelle packing and remodelling To date, the studies on organelle biogenesis and homeostasis have focused almost exclusively on single organelles. Studies on the ER, for example, rarely include the Golgi, and vice versa. 1.
2.
Lamb, C. A., Yoshimori, T. & Tooze S. A. The autophagosome: origins unknown, biogenesis complex. Nature Rev. Mol. Cell Biol. 14, 759–774 (2013). Smith, J. J. & Aitchison J. D. Peroxisomes take shape. Nature Rev. Mol. Cell Biol. 14, 803–817 (2013).
3. 4.
However, changes in any one of these organelles could have dramatic implications for others, not only with regard to their size but also their position within the cell. Upon stimulation of plasma cells, for example, the cytoplasm rapidly fills with stacks of ER cisternae, but where this process is initiated remains elusive. Does it occur throughout the cell or at a place initially devoid of other organelles? Are other organelles pushed out of the way by the expanding ER? Conversely, these other organelles might occupy space that cannot be invaded by the proliferating ER. For example, in pancreatic acinar cells the Golgi is located atop the nucleus where it surrounds the centrosome, the emanating microtubules of which provide a mechanism for keeping the Golgi in place. Perhaps this precludes any invasion by the ER, which can then only occupy the space around and beneath the nucleus. Such cellular anatomy echoes the anatomy of multi cellular organisms, but whereas the rules governing the assembly (development) of organisms are wellstudied, those governing intracellular form are at the very early stages of investigation12. Furthermore, the cellular anatomy is not fixed (perhaps analogous to those organisms that undergo metamorphosis). In a classic study, chick corneal epithelial cells were analysed during development 13. As with pancreatic acinar cells, the Golgi is found atop the nucleus, but during chick development it migrates beneath the nucleus and then translocates back. This process is repeated, again coinciding with the deposition of a collagenous matrix beneath the epithelium. This therefore suggests that the anatomy of this cell can predict organelle function. The underlying mechanism is unclear, although these movements are reminiscent of those that have been observed when cells reorient their Golgi towards a wound14. In this case, it seems that the Golgi ribbon and even the stacks are dismantled, at least in part, perhaps to facilitate a coordinated move with the centrosome towards the wound. Dismantling the Golgi may be partly triggered by the MAPK pathway, which operates through Golgi reassembly-stacking proteins (GRASPs), which link Golgi membranes to each other8. Such remodelling of organelles is probably a general feature of cells that permits changes in function through changes in cellular anatomy. Studying the development, maintenance and remodelling of cellular anatomy will be key to our understanding of organelle biogenesis and homeostasis. Progress, however, will only be possible once we can manipulate the process, moving organelles at will to different parts of the cell to study the effects on their function as well as on other organelles. Intracellular ‘embryology’ promises to be an exciting new field.
Thiam, A. R., Farese, R. V. Jr & Walther, T. C. The biophysics and cell biology of lipid droplets. Nature Rev. Mol. Cell Biol. 14, 775–786 (2013). Jarvis, P. & López-Juez, E. Biogenesis and homeostasis of chloroplasts and other plastids. Nature Rev. Mol. Cell Biol. 14, 787–802 (2013).
756 | DECEMBER 2013 | VOLUME 14
5.
6.
Gardner, B. M., Pincus, D., Gotthardt, K., Gallagher, C. M. & Walter, P. Endoplasmic reticulum stress sensing in the unfolded protein response. Cold Spring Harb. Perspect. Biol. 5, a013169 (2013). Moore, K. A. & Hollien, J. The unfolded protein response in secretory cell function. Annu. Rev. Genet. 46, 165–183 (2012).
www.nature.com/reviews/molcellbio © 2013 Macmillan Publishers Limited. All rights reserved
F O C U S O N O r g a n e l l e b i o g e n e s i s a n d h oFmOeRE osWta is OsRD 7. Pengo, N. et al. Plasma cells require autophagy for sustainable immunoglobulin production. Nature Immunol. 14, 298–305 (2013). 8. Sengupta, D. & Linstedt, A. D. Control of organelle size: the Golgi complex. Annu. Rev. Cell Dev. Biol. 27, 5.1–5.21 (2011). 9. Varki, A., Freeze, H. H. & Gagneux, P. i n Essentials of Glycobiology (eds. Varki, A. et al.) 2nd edn (Cold Spring Harbour Laboratory Press, 2009). 10. Coppens, I., Opperdoes, F. R., Courtoy, P. J. & Baudhuin, P. Receptor-mediated endocytosis in the bloodstream form of Trypanosoma brucei. Protozool. 34, 465–473 (1987).
11. Lowe, M. & Barr, F. A. Inheritance and biogenesis of organelles in the secretory pathway. Nature Rev. Mol. Cell Biol. 8, 429–439 (2007). 12. Marshall, W. F. Origins of cellular geometry. BMC Biology 9, 57–66 (2011). 13. Trelstad, R. L. The Golgi apparatus in chick corneal epithelium: changes in intracellular position during development. J. Cell Biol. 45, 34–42 (1970). 14. Bisel, B. et al. ERK regulates Golgi and centrosome orientation towards the leading edge through GRASP65. J. Cell Biol. 182, 837–843 (2013).
Competing interests statement
The author declares no competing interests.
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
VOLUME 14 | DECEMBER 2013 | 757 © 2013 Macmillan Publishers Limited. All rights reserved
FOREWORD Size and position matter Graham Warren
Abstract | The 2013 Nobel Prize in Physiology or Medicine emphasizes the progress made in understanding the molecular mechanisms that underpin the vesicular movement of cargo through the exocytic and endocytic pathways. Attention now focuses on those mechanisms that govern the relative size and position of the many different membranebound compartments. These homeostatic mechanisms are discussed in this issue of Nature Reviews Molecular Cell Biology and must be integrated so as to satisfy the needs of the cell and the organism. The evolution of membrane-bound compartments in the eukaryotic cytoplasm gave unprecedented opportunities to optimize cellular processes and segregate incompatible ones. This came at a price, as the output of some of these processes (such as proteins and lipids) act in a different compartment; they thus have to be moved from the place where they are generated to the place where they function.
Max F. Perutz Laboratories, University and Medical University of Vienna, Doktor-Bohr-Gasse 9, 1030 Vienna, Austria. e‑mail: [email protected]
Sorting at the ER This sorting problem occupied researchers for decades and is best exemplified by the endoplasmic reticulum (ER), through which a subset of proteins being synthesized on cytoplasmic ribosomes is sorted to its final destination. The ER also synthesizes lipids that are needed as components of downstream compartments and beyond. The best characterized compartments downstream of the ER are the Golgi, endosomes and lysosomes, as well as, in some cells, regulated secretory granules. However, there are other compartments, reviewed in this issue, including autophagosomes1, peroxisomes2, lipid droplets3 and plastids4. The ER has to satisfy the needs of all these downstream compartments. It must provide them with the proteins and lipids that are required to carry out their particular cellular functions. To do this, the ER has to populate itself with the translocation machinery and chaperones that have a role in the production and assembly of the cargoes destined for these downstream compartments. It must also populate itself with lipid‑synthesizing enzymes. The surface area of the ER is determined by the need to satisfy these supply demands. To a first approximation it is set by the number of protein-translocating units that are required to populate the downstream compartments. This number will depend on whether the cell is actively growing, in which case the ER also has to drive duplication of all the compartments that it services, including itself. The trafficking capacity required will also
depend on whether the cell is a professional secretory cell. The pancreatic acinar cell is one such example, secreting more than 70% of the total proteins that are synthesized in the cytoplasm. As such, it has an extensive set of flattened ER cisternae that are mostly stacked and located at the base of the cell beneath and partly around the nucleus. Antibody-secreting plasma cells are another example; they have a sparse ER that proliferates by several orders of magnitude upon stimulation, to the extent that each cell can eventually secrete its own weight in immunoglobulin G (IgG) molecules every day. How is this expansion regulated? The details are still being worked out, but it seems that a process first identified as a stress response may have more general applicability. This unfolded protein response (UPR) detects excess unfolded proteins in the ER and initiates a transcriptional programme to mitigate their effects5: more chaperones are synthesized; aggregated proteins are translocated to the cytoplasm for degradation by glycosidases and proteasomes; and bulk protein trans location is temporarily halted. All this increases the size of the ER. The UPR can also, it seems, be used by plasma cells to expand their ER6, but this is not a stress response and the initiating signals still need to be determined. Perhaps the UPR is even involved during the cell cycle when the ER doubles in size and then partitions between each daughter cell. Furthermore, cells not only need a mechanism to grow the ER but also to limit this growth, and it seems that autophagy might be important for this7. How these growth and degradation processes are coordinated to ensure ER homeostasis needs further work.
Cargo modification by the Golgi What about organelles downstream of the ER, such as the Golgi? How the size of the Golgi is determined has long been debated8.
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
VOLUME 14 | DECEMBER 2013 | 755 © 2013 Macmillan Publishers Limited. All rights reserved
F O RE W O RD A key function of the Golgi is the modification of the oligosaccharides on the transiting cargo, and a sufficient amount of enzymes is required to complete these modifications. Therefore, the flux of cargo must be linked to the levels of Golgi-associated enzymes, and this will in turn determine the size of this organelle. At the ER, cargoes are channelled through exit sites, where they are selectively incorporated into budding coat protein complex II (COPII) vesicles. Golgi enzymes are also synthesized in the ER and also seem to be transported to the Golgi in these vesicles; but, how this is coordinated so that the Golgi reaches the right size is unclear. Furthermore, any mechanism at play has to accommodate the very different needs of cargo proteins for oligosaccharide modification. In most cells, there are thousands of different types of cargo protein, each of which may require distinct oligosaccharide modifications. The core patterns of O-linked and N-linked glycosylation can be modified in various ways 9, and such bespoke glycosylation places huge demands on the Golgi; it must provide the necessary enzymes, in the right order, to properly modify the many different cargo molecules. This may explain why the surface area of the Golgi in mammalian cells is roughly the same size as the plasma membrane (and about 10% of the ER). By contrast, in much simpler organisms, the need for cargo modification may not be so great. As an example, in the protozoan parasite Trypanosoma brucei, at any one time almost all the transiting cargo is a single species of glycosylphosphatidylinositol (GPI)-anchored cell surface protein, and therefore the glycosylation machinery can be much simpler. In fact, the surface area of the Golgi in T. brucei is only about 5% of that of the plasma membrane, which is 20‑fold less than in mammalian cells10. Hence, any mechanism for regulating the size of the Golgi must also account for the very different requirements of the transiting cargo. Golgi homeostasis during the cell cycle also remains unexplained. Unlike the ER, the Golgi has a modular structure, and this structural feature is best revealed (at least in mammalian cells) by the addition of the microtubule-disrupting agent nocodazole, which breaks down the Golgi ribbon into its constituent stacks. Whereas the ER doubles its size during the cell cycle, the Golgi stacks must double their number. The mechanism of this duplication is still being debated. For example, is the new Golgi assembled de novo, from the ER or is it constructed, at least in part, from components that originate from the old Golgi11.
Organelle packing and remodelling To date, the studies on organelle biogenesis and homeostasis have focused almost exclusively on single organelles. Studies on the ER, for example, rarely include the Golgi, and vice versa. 1.
2.
Lamb, C. A., Yoshimori, T. & Tooze S. A. The autophagosome: origins unknown, biogenesis complex. Nature Rev. Mol. Cell Biol. 14, 759–774 (2013). Smith, J. J. & Aitchison J. D. Peroxisomes take shape. Nature Rev. Mol. Cell Biol. 14, 803–817 (2013).
3. 4.
However, changes in any one of these organelles could have dramatic implications for others, not only with regard to their size but also their position within the cell. Upon stimulation of plasma cells, for example, the cytoplasm rapidly fills with stacks of ER cisternae, but where this process is initiated remains elusive. Does it occur throughout the cell or at a place initially devoid of other organelles? Are other organelles pushed out of the way by the expanding ER? Conversely, these other organelles might occupy space that cannot be invaded by the proliferating ER. For example, in pancreatic acinar cells the Golgi is located atop the nucleus where it surrounds the centrosome, the emanating microtubules of which provide a mechanism for keeping the Golgi in place. Perhaps this precludes any invasion by the ER, which can then only occupy the space around and beneath the nucleus. Such cellular anatomy echoes the anatomy of multi cellular organisms, but whereas the rules governing the assembly (development) of organisms are wellstudied, those governing intracellular form are at the very early stages of investigation12. Furthermore, the cellular anatomy is not fixed (perhaps analogous to those organisms that undergo metamorphosis). In a classic study, chick corneal epithelial cells were analysed during development 13. As with pancreatic acinar cells, the Golgi is found atop the nucleus, but during chick development it migrates beneath the nucleus and then translocates back. This process is repeated, again coinciding with the deposition of a collagenous matrix beneath the epithelium. This therefore suggests that the anatomy of this cell can predict organelle function. The underlying mechanism is unclear, although these movements are reminiscent of those that have been observed when cells reorient their Golgi towards a wound14. In this case, it seems that the Golgi ribbon and even the stacks are dismantled, at least in part, perhaps to facilitate a coordinated move with the centrosome towards the wound. Dismantling the Golgi may be partly triggered by the MAPK pathway, which operates through Golgi reassembly-stacking proteins (GRASPs), which link Golgi membranes to each other8. Such remodelling of organelles is probably a general feature of cells that permits changes in function through changes in cellular anatomy. Studying the development, maintenance and remodelling of cellular anatomy will be key to our understanding of organelle biogenesis and homeostasis. Progress, however, will only be possible once we can manipulate the process, moving organelles at will to different parts of the cell to study the effects on their function as well as on other organelles. Intracellular ‘embryology’ promises to be an exciting new field.
Thiam, A. R., Farese, R. V. Jr & Walther, T. C. The biophysics and cell biology of lipid droplets. Nature Rev. Mol. Cell Biol. 14, 775–786 (2013). Jarvis, P. & López-Juez, E. Biogenesis and homeostasis of chloroplasts and other plastids. Nature Rev. Mol. Cell Biol. 14, 787–802 (2013).
756 | DECEMBER 2013 | VOLUME 14
5.
6.
Gardner, B. M., Pincus, D., Gotthardt, K., Gallagher, C. M. & Walter, P. Endoplasmic reticulum stress sensing in the unfolded protein response. Cold Spring Harb. Perspect. Biol. 5, a013169 (2013). Moore, K. A. & Hollien, J. The unfolded protein response in secretory cell function. Annu. Rev. Genet. 46, 165–183 (2012).
www.nature.com/reviews/molcellbio © 2013 Macmillan Publishers Limited. All rights reserved
F O C U S O N O r g a n e l l e b i o g e n e s i s a n d h oFmOeRE osWta is OsRD 7. Pengo, N. et al. Plasma cells require autophagy for sustainable immunoglobulin production. Nature Immunol. 14, 298–305 (2013). 8. Sengupta, D. & Linstedt, A. D. Control of organelle size: the Golgi complex. Annu. Rev. Cell Dev. Biol. 27, 5.1–5.21 (2011). 9. Varki, A., Freeze, H. H. & Gagneux, P. i n Essentials of Glycobiology (eds. Varki, A. et al.) 2nd edn (Cold Spring Harbour Laboratory Press, 2009). 10. Coppens, I., Opperdoes, F. R., Courtoy, P. J. & Baudhuin, P. Receptor-mediated endocytosis in the bloodstream form of Trypanosoma brucei. Protozool. 34, 465–473 (1987).
11. Lowe, M. & Barr, F. A. Inheritance and biogenesis of organelles in the secretory pathway. Nature Rev. Mol. Cell Biol. 8, 429–439 (2007). 12. Marshall, W. F. Origins of cellular geometry. BMC Biology 9, 57–66 (2011). 13. Trelstad, R. L. The Golgi apparatus in chick corneal epithelium: changes in intracellular position during development. J. Cell Biol. 45, 34–42 (1970). 14. Bisel, B. et al. ERK regulates Golgi and centrosome orientation towards the leading edge through GRASP65. J. Cell Biol. 182, 837–843 (2013).
Competing interests statement
The author declares no competing interests.
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
VOLUME 14 | DECEMBER 2013 | 757 © 2013 Macmillan Publishers Limited. All rights reserved
