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Kettel P, Karagöz GE. Endoplasmic reticulum: Monitoring and maintaining protein and membrane homeostasis in the endoplasmic reticulum by the unfolded protein response. Int J Biochem Cell Biol 2024; 172:106598. [PMID: 38768891 DOI: 10.1016/j.biocel.2024.106598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
The endoplasmic reticulum (ER) regulates essential cellular processes, including protein folding, lipid synthesis, and calcium homeostasis. The ER homeostasis is maintained by a conserved set of signaling cascades called the Unfolded Protein Response (UPR). How the UPR senses perturbations in ER homeostasis has been the subject of active research for decades. In metazoans, the UPR consists of three ER-membrane embedded sensors: IRE1, PERK and ATF6. These sensors detect the accumulation of misfolded proteins in the ER lumen and adjust protein folding capacity according to cellular needs. Early work revealed that the ER-resident chaperone BiP binds to all three UPR sensors in higher eukaryotes and BiP binding was suggested to regulate their activity. More recent data have shown that in higher eukaryotes the interaction of the UPR sensors with a complex network of chaperones and misfolded proteins modulates their activation and deactivation dynamics. Furthermore, emerging evidence suggests that the UPR monitors ER membrane integrity beyond protein folding defects. However, the mechanistic and structural basis of UPR activation by proteotoxic and lipid bilayer stress in higher eukaryotes remains only partially understood. Here, we review the current understanding of novel protein interaction networks and the contribution of the lipid membrane environment to UPR activation.
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Affiliation(s)
- Paulina Kettel
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Medical University of Vienna, Vienna, Austria.
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Kischuck LT, Brown AI. Tube geometry controls protein cluster conformation and stability on the endoplasmic reticulum surface. SOFT MATTER 2023; 19:6771-6783. [PMID: 37642520 DOI: 10.1039/d3sm00694h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The endoplasmic reticulum (ER), a cellular organelle that forms a cell-spanning network of tubes and sheets, is an important location of protein synthesis and folding. When the ER experiences sustained unfolded protein stress, IRE1 proteins embedded in the ER membrane activate and assemble into clusters as part of the unfolded protein response (UPR). We use kinetic Monte Carlo simulations to explore IRE1 clustering dynamics on the surface of ER tubes. While initially growing clusters are approximately round, once a cluster is sufficiently large a shorter interface length can be achieved by 'wrapping' around the ER tube. A wrapped cluster can grow without further interface length increases. Relative to wide tubes, narrower tubes enable cluster wrapping at smaller cluster sizes. Our simulations show that wrapped clusters on narrower tubes grow more rapidly, evaporate more slowly, and require a lower protein concentration to grow compared to equal-area round clusters on wider tubes. These results suggest that cluster wrapping, facilitated by narrower tubes, could be an important factor in the growth and stability of IRE1 clusters and thus impact the persistence of the UPR, connecting geometry to signaling behavior. This work is consistent with recent experimental observations of IRE1 clusters wrapped around narrow tubes in the ER network.
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Affiliation(s)
- Liam T Kischuck
- Department of Physics, Toronto Metropolitan University, Toronto, Ontario, M5B 2K3, Canada.
| | - Aidan I Brown
- Department of Physics, Toronto Metropolitan University, Toronto, Ontario, M5B 2K3, Canada.
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Garcia G, Zhang H, Moreno S, Tsui CK, Webster BM, Higuchi-Sanabria R, Dillin A. Lipid homeostasis is essential for a maximal ER stress response. eLife 2023; 12:e83884. [PMID: 37489956 PMCID: PMC10368420 DOI: 10.7554/elife.83884] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 05/08/2023] [Indexed: 07/26/2023] Open
Abstract
Changes in lipid metabolism are associated with aging and age-related diseases, including proteopathies. The endoplasmic reticulum (ER) is uniquely a major hub for protein and lipid synthesis, making its function essential for both protein and lipid homeostasis. However, it is less clear how lipid metabolism and protein quality may impact each other. Here, we identified let-767, a putative hydroxysteroid dehydrogenase in Caenorhabditis elegans, as an essential gene for both lipid and ER protein homeostasis. Knockdown of let-767 reduces lipid stores, alters ER morphology in a lipid-dependent manner, and blocks induction of the Unfolded Protein Response of the ER (UPRER). Interestingly, a global reduction in lipogenic pathways restores UPRER induction in animals with reduced let-767. Specifically, we find that supplementation of 3-oxoacyl, the predicted metabolite directly upstream of let-767, is sufficient to block induction of the UPRER. This study highlights a novel interaction through which changes in lipid metabolism can alter a cell's response to protein-induced stress.
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Affiliation(s)
- Gilberto Garcia
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Hanlin Zhang
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Sophia Moreno
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - C Kimberly Tsui
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Brant Michael Webster
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Ryo Higuchi-Sanabria
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Andrew Dillin
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
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Li W, Maekiniemi A, Sato H, Osman C, Singer RH. An improved imaging system that corrects MS2-induced RNA destabilization. Nat Methods 2022; 19:1558-1562. [PMID: 36357695 PMCID: PMC7613886 DOI: 10.1038/s41592-022-01658-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/21/2022] [Indexed: 11/12/2022]
Abstract
The MS2 and MS2-coat protein (MS2-MCP) imaging system is widely used to study messenger RNA (mRNA) spatial distribution in living cells. Here, we report that the MS2-MCP system destabilizes some tagged mRNAs by activating the nonsense-mediated mRNA decay pathway. We introduce an improved version, which counteracts this effect by increasing the efficiency of translation termination of the tagged mRNAs. Improved versions were developed for both yeast and mammalian systems.
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Affiliation(s)
- Weihan Li
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
| | - Anna Maekiniemi
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
| | - Hanae Sato
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Robert H. Singer
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
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