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Madrazo N, Khattar Z, Powers ET, Rosarda JD, Wiseman RL. Mapping stress-responsive signaling pathways induced by mitochondrial proteostasis perturbations. Mol Biol Cell 2024; 35:ar74. [PMID: 38536439 PMCID: PMC11151107 DOI: 10.1091/mbc.e24-01-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
Imbalances in mitochondrial proteostasis are associated with pathologic mitochondrial dysfunction implicated in etiologically diverse diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria in response to mitochondrial stress. Numerous stress-responsive signaling pathways have been suggested to regulate mitochondria in response to proteotoxic stress. These include the integrated stress response (ISR), the heat shock response (HSR), and the oxidative stress response (OSR). Here, we define the stress signaling pathways activated in response to chronic mitochondrial proteostasis perturbations by monitoring the expression of sets of genes regulated downstream of each of these signaling pathways in published Perturb-seq datasets from K562 cells CRISPRi-depleted of mitochondrial proteostasis factors. Interestingly, we find that the ISR is preferentially activated in response to chronic, genetically-induced mitochondrial proteostasis stress, with no other pathway showing significant activation. Further, we demonstrate that CRISPRi depletion of other mitochondria-localized proteins similarly shows preferential activation of the ISR relative to other stress-responsive signaling pathways. These results both establish our gene set profiling approach as a viable strategy to probe stress responsive signaling pathways induced by perturbations to specific organelles and identify the ISR as the predominant stress-responsive signaling pathway activated in response to chronic disruption of mitochondrial proteostasis.
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Affiliation(s)
- Nicole Madrazo
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
| | - Zinia Khattar
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
- Del Norte High School, San Diego, CA 92127
| | - Evan T. Powers
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
| | - Jessica D. Rosarda
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - R. Luke Wiseman
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
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Goswami MT, Weh E, Subramanya S, Weh KM, Durumutla HB, Hager H, Miller N, Chaudhury S, Andren A, Sajjakulnukit P, Besirli CG, Lyssiotis CA, Wubben TJ. Glutaminase deficiency in rod photoreceptors disrupts nonessential amino acid levels to activate the integrated stress response and induce rapid degeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.582525. [PMID: 38586045 PMCID: PMC10996599 DOI: 10.1101/2024.03.26.582525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The bioenergetic demand of photoreceptors rivals that of cancer cells, and numerous metabolic similarities exist between these cells. Glutamine (Gln) anaplerosis via the tricarboxylic acid (TCA) cycle provides biosynthetic intermediates and is a hallmark of cancer metabolism. In this process, Gln is first converted to glutamate via glutaminase (GLS), which is a crucial pathway in many cancer cells. To date, no study has been undertaken to examine the role of Gln metabolism in vivo in photoreceptors. Here, mice lacking GLS in rod photoreceptors were generated. Animals lacking GLS experienced rapid photoreceptor degeneration with concomitant functional loss. Gln has multiple roles in metabolism including redox balance, biosynthesis of nucleotides and amino acids, and supplementing the TCA cycle. Few alterations were noted in redox balance. Unlabeled targeted metabolomics demonstrated few changes in glycolytic and TCA cycle intermediates, which corresponded with a lack of significant changes in mitochondrial function. GLS deficiency in rod photoreceptors did decrease the fractional labelling of TCA cycle intermediates when provided uniformly labeled 13C-Gln in vivo. However, supplementation with alpha-ketoglutarate provided only marginal rescue of photoreceptor degeneration. Nonessential amino acids, glutamate and aspartate, were decreased in the retina of mice lacking GLS in rod photoreceptors. In accordance with this amino acid deprivation, the integrated stress response (ISR) was found to be activated with decreased global protein synthesis. Importantly, supplementation with asparagine delayed photoreceptor degeneration to a greater degree than alpha-ketoglutarate. These data show that GLS-mediated Gln catabolism is essential for rod photoreceptor amino acid biosynthesis, function, and survival.
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Affiliation(s)
- Moloy T. Goswami
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Eric Weh
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Shubha Subramanya
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Katherine M. Weh
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Hima Bindu Durumutla
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
- Molecular and Developmental Biology Graduate Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Heather Hager
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Nicholas Miller
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Sraboni Chaudhury
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Anthony Andren
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
| | - Peter Sajjakulnukit
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
| | - Cagri G. Besirli
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
| | - Costas A. Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI 48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109
| | - Thomas J. Wubben
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105
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Madrazo N, Khattar Z, Powers ET, Rosarda JD, Wiseman RL. Mapping Stress-Responsive Signaling Pathways Induced by Mitochondrial Proteostasis Perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577830. [PMID: 38352575 PMCID: PMC10862789 DOI: 10.1101/2024.01.30.577830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Imbalances in mitochondrial proteostasis are associated with pathologic mitochondrial dysfunction implicated in etiologically-diverse diseases. This has led to considerable interest in defining the biological mechanisms responsible for regulating mitochondria in response to mitochondrial stress. Numerous stress responsive signaling pathways have been suggested to regulate mitochondria in response to proteotoxic stress, including the integrated stress response (ISR), the heat shock response (HSR), and the oxidative stress response (OSR). Here, we define the specific stress signaling pathways activated in response to mitochondrial proteostasis stress by monitoring the expression of sets of genes regulated downstream of each of these signaling pathways in published Perturb-seq datasets from K562 cells CRISPRi-depleted of individual mitochondrial proteostasis factors. Interestingly, we find that the ISR is preferentially activated in response to mitochondrial proteostasis stress, with no other pathway showing significant activation. Further expanding this study, we show that broad depletion of mitochondria-localized proteins similarly shows preferential activation of the ISR relative to other stress-responsive signaling pathways. These results both establish our gene set profiling approach as a viable strategy to probe stress responsive signaling pathways induced by perturbations to specific organelles and identify the ISR as the predominant stress-responsive signaling pathway activated in response to mitochondrial proteostasis disruption.
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Affiliation(s)
- Nicole Madrazo
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
- These authors contributed equally
| | - Zinia Khattar
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
- Del Norte High School, San Diego, CA 92127
- These authors contributed equally
| | - Evan T. Powers
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
| | - Jessica D. Rosarda
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - R. Luke Wiseman
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
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Zhang SX, Wang JJ, Starr CR, Lee EJ, Park KS, Zhylkibayev A, Medina A, Lin JH, Gorbatyuk M. The endoplasmic reticulum: Homeostasis and crosstalk in retinal health and disease. Prog Retin Eye Res 2024; 98:101231. [PMID: 38092262 PMCID: PMC11056313 DOI: 10.1016/j.preteyeres.2023.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
The endoplasmic reticulum (ER) is the largest intracellular organelle carrying out a broad range of important cellular functions including protein biosynthesis, folding, and trafficking, lipid and sterol biosynthesis, carbohydrate metabolism, and calcium storage and gated release. In addition, the ER makes close contact with multiple intracellular organelles such as mitochondria and the plasma membrane to actively regulate the biogenesis, remodeling, and function of these organelles. Therefore, maintaining a homeostatic and functional ER is critical for the survival and function of cells. This vital process is implemented through well-orchestrated signaling pathways of the unfolded protein response (UPR). The UPR is activated when misfolded or unfolded proteins accumulate in the ER, a condition known as ER stress, and functions to restore ER homeostasis thus promoting cell survival. However, prolonged activation or dysregulation of the UPR can lead to cell death and other detrimental events such as inflammation and oxidative stress; these processes are implicated in the pathogenesis of many human diseases including retinal disorders. In this review manuscript, we discuss the unique features of the ER and ER stress signaling in the retina and retinal neurons and describe recent advances in the research to uncover the role of ER stress signaling in neurodegenerative retinal diseases including age-related macular degeneration, inherited retinal degeneration, achromatopsia and cone diseases, and diabetic retinopathy. In some chapters, we highlight the complex interactions between the ER and other intracellular organelles focusing on mitochondria and illustrate how ER stress signaling regulates common cellular stress pathways such as autophagy. We also touch upon the integrated stress response in retinal degeneration and diabetic retinopathy. Finally, we provide an update on the current development of pharmacological agents targeting the UPR response and discuss some unresolved questions and knowledge gaps to be addressed by future research.
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Affiliation(s)
- Sarah X Zhang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States.
| | - Josh J Wang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Christopher R Starr
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Eun-Jin Lee
- Department of Ophthalmology and Byers Eye Institute, Stanford University, Stanford, CA, United States; VA Palo Alto Healthcare System, Palo Alto, CA, United States; Department of Pathology, Stanford University, Stanford, CA, United States
| | - Karen Sophia Park
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Assylbek Zhylkibayev
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Andy Medina
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Jonathan H Lin
- Department of Ophthalmology and Byers Eye Institute, Stanford University, Stanford, CA, United States; VA Palo Alto Healthcare System, Palo Alto, CA, United States; Department of Pathology, Stanford University, Stanford, CA, United States
| | - Marina Gorbatyuk
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL, United States
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