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Sedaghatmehr M, Balazadeh S. Autophagy: a key player in the recovery of plants from heat stress. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2246-2255. [PMID: 38236036 PMCID: PMC11016841 DOI: 10.1093/jxb/erae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/15/2024] [Indexed: 01/19/2024]
Abstract
Plants can be primed to withstand otherwise lethal heat stress (HS) through exposure to a preceding temporary and mild HS, commonly known as the 'thermopriming stimulus'. Plants have also evolved mechanisms to establish 'memories' of a previous stress encounter, or to reset their physiology to the original cellular state once the stress has ended. The priming stimulus triggers a widespread change of transcripts, proteins, and metabolites, which is crucial for maintaining the memory state but may not be required for growth and development under optimal conditions or may even be harmful. In such a scenario, recycling mechanisms such as autophagy are crucial for re-establishing cellular homeostasis and optimizing resource use for post-stress growth. While pivotal for eliminating heat-induced protein aggregates and protecting plants from the harmful impact of HS, recent evidence implies that autophagy also breaks down heat-induced protective macromolecules, including heat shock proteins, functioning as a resetting mechanism during the recovery from mild HS. This review provides an overview of the latest advances in understanding the multifaceted functions of autophagy in HS responses, with a specific emphasis on its roles in recovery from mild HS, and the modulation of HS memory.
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Affiliation(s)
- Mastoureh Sedaghatmehr
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Salma Balazadeh
- Leiden University, PO Box 9500, 2300 RA, Leiden, The Netherlands
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2
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Liu K, Huang H, Xiong M, Wang Q, Chen X, Feng Y, Ma H, Chen W, Li X, Ye X. IL-33 Accelerates Chronic Atrophic Gastritis through AMPK-ULK1 Axis Mediated Autolysosomal Degradation of GKN1. Int J Biol Sci 2024; 20:2323-2338. [PMID: 38617533 PMCID: PMC11008276 DOI: 10.7150/ijbs.93573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Chronic atrophic gastritis (CAG) is a complex disease characterized by atrophy and inflammation in gastric mucosal tissue, especially with high expression of interleukins. However, the interaction and mechanisms between interleukins and gastric mucosal epithelial cells in CAG remain largely elusive. Here, we elucidate that IL-33 stands out as the predominant inflammatory factor in CAG, and its expression is induced by H. pylori and MNNG through the ROS-STAT3 signaling pathway. Furthermore, our findings reveal that the IL-33/ST2 axis is intricately involved in the progression of CAG. Utilizing phosphoproteomics mass spectrometry, we demonstrate that IL-33 enhances autophagy in gastric epithelial cells through the phosphorylation of AMPK-ULK1 axis. Notably, inhibiting autophagy alleviates CAG severity, while augmentation of autophagy exacerbates the disease. Additionally, ROS scavenging emerges as a promising strategy to ameliorate CAG by reducing IL-33 expression and inhibiting autophagy. Intriguingly, IL-33 stimulation promotes GKN1 degradation through the autolysosomal pathway. Clinically, the combined measurement of IL-33 and GKN1 in serum shows potential as diagnostic markers. Our findings unveil an IL-33-AMPK-ULK1 regulatory mechanism governing GKN1 protein stability in CAG, presenting potential therapeutic targets for its treatment.
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Affiliation(s)
- Kewei Liu
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Hongxia Huang
- Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, China
| | - Mengyuan Xiong
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiaojiao Wang
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiantao Chen
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yinqiong Feng
- Department of Gastroenterology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400000, China
| | - Hang Ma
- School of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400038, China
| | - Wanqun Chen
- Department of Gastroenterology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400000, China
| | - Xuegang Li
- School of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400038, China
| | - Xiaoli Ye
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
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Zheng C, Zhou J, Yuan X, Zheng E, Liu X, Cui W, Yan C, Wu Y, Ruan W, Yi K, Chen J, Wang X. Elevating plant immunity by translational regulation of a rice WRKY transcription factor. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1033-1048. [PMID: 37997501 PMCID: PMC10955491 DOI: 10.1111/pbi.14243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/20/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023]
Abstract
Plants have intricate mechanisms that tailor their defence responses to pathogens. WRKY transcription factors play a pivotal role in plant immunity by regulating various defence signalling pathways. Many WRKY genes are transcriptionally activated upon pathogen attack, but how their functions are regulated after transcription remains elusive. Here, we show that OsWRKY7 functions as a crucial positive regulator of rice basal immunity against Xanthomonas oryzae pv. oryzae (Xoo). The activity of OsWRKY7 was regulated at both translational and post-translational levels. Two translational products of OsWRKY7 were generated by alternative initiation. The full-length OsWRKY7 protein is normally degraded by the ubiquitin-proteasome system but was accumulated following elicitor or pathogen treatment, whereas the alternate product initiated from the downstream in-frame start codon was stable. Both the full and alternate OsWRKY7 proteins have transcriptional activities in yeast and rice cells, and overexpression of each form enhanced resistance to Xoo infection. Furthermore, disruption of the main AUG in rice increased the endogenous translation of the alternate stabilized form of OsWRKY7 and enhanced bacterial blight resistance. This study provides insights into the coordination of alternative translation and protein stability in the regulation of plant growth and basal defence mediated by the OsWRKY7 transcription factor, and also suggests a promising strategy to breed disease-resistant rice by translation initiation control.
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Affiliation(s)
- Chao Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- College of Plant ProtectionNorthwest A&F UniversityYanglingP.R. China
| | - Jie Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
| | - Xiaoya Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- College of Plant ProtectionNorthwest A&F UniversityYanglingP.R. China
| | - Ersong Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- College of Plant ProtectionNorthwest A&F UniversityYanglingP.R. China
| | - Xiuli Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
| | - Weijun Cui
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
| | - Chengqi Yan
- Institute of BiotechnologyNingbo Academy of Agricultural SciencesNingboP.R. China
| | - Yueyan Wu
- Zhejiang Wan Li UniversityNingboP.R. China
| | - Wenyuan Ruan
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Keke Yi
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- Institute of Plant VirologyNingbo UniversityNingboP. R. China
| | - Xuming Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
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Ayaz A, Jalal A, Qian Z, Khan KA, Liu L, Hu C, Li Y, Hou X. Investigating the effects of tauroursodeoxycholic acid (TUDCA) in mitigating endoplasmic reticulum stress and cellular responses in Pak choi. PHYSIOLOGIA PLANTARUM 2024; 176:e14246. [PMID: 38467573 DOI: 10.1111/ppl.14246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
The accumulation of misfolded proteins in the endoplasmic reticulum (ER) within plant cells due to unfavourable conditions leads to ER stress. This activates interconnected pathways involving reactive oxygen species (ROS) and unfolded protein response (UPR), which play vital roles in regulating ER stress. The aim of this study is to investigate the underlying mechanisms of tunicamycin (TM) induced ER stress and explore the potential therapeutic applications of tauroursodeoxycholic acid (TUDCA) in mitigating cellular responses to ER stress in Pak choi (Brassica campestris subsp. chinensis). The study revealed that ER stress in Pak choi leads to detrimental effects on plant morphology, ROS levels, cellular membrane integrity, and the antioxidant defence system. However, treatment with TUDCA in TM-induced ER stressed Pak choi improved morphological indices, pigment contents, ROS accumulation, cellular membrane integrity, and antioxidant defence system restoration. Additionally, TUDCA also modulates the transcription levels of ER stress sensors genes, ER chaperone genes, and ER-associated degradation (ERAD) genes during ER stress in Pak choi. Furthermore, TUDCA has demonstrated its ability to alleviate ER stress, stabilize the UPR, reduce oxidative stress, prevent apoptosis, and positively influence plant growth and development. These results collectively comprehend TUDCA as a promising agent for mitigating ER stress-induced damage in Pak choi plants and provide valuable insights for further research and potential applications in crop protection and stress management.
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Affiliation(s)
- Aliya Ayaz
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/ National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Abdul Jalal
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Zhou Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/ National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Khalid Ali Khan
- Applied College, Mahala Campus and the Unit of Bee Research and Honey Production/Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
| | - Liwang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/ National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Chunmei Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/ National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/ National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/ National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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5
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Mota MN, Matos M, Bahri N, Sá-Correia I. Shared and more specific genetic determinants and pathways underlying yeast tolerance to acetic, butyric, and octanoic acids. Microb Cell Fact 2024; 23:71. [PMID: 38419072 PMCID: PMC10903034 DOI: 10.1186/s12934-024-02309-0] [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: 10/12/2023] [Accepted: 01/17/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The improvement of yeast tolerance to acetic, butyric, and octanoic acids is an important step for the implementation of economically and technologically sustainable bioprocesses for the bioconversion of renewable biomass resources and wastes. To guide genome engineering of promising yeast cell factories toward highly robust superior strains, it is instrumental to identify molecular targets and understand the mechanisms underlying tolerance to those monocarboxylic fatty acids. A chemogenomic analysis was performed, complemented with physiological studies, to unveil genetic tolerance determinants in the model yeast and cell factory Saccharomyces cerevisiae exposed to equivalent moderate inhibitory concentrations of acetic, butyric, or octanoic acids. RESULTS Results indicate the existence of multiple shared genetic determinants and pathways underlying tolerance to these short- and medium-chain fatty acids, such as vacuolar acidification, intracellular trafficking, autophagy, and protein synthesis. The number of tolerance genes identified increased with the linear chain length and the datasets for butyric and octanoic acids include the highest number of genes in common suggesting the existence of more similar toxicity and tolerance mechanisms. Results of this analysis, at the systems level, point to a more marked deleterious effect of an equivalent inhibitory concentration of the more lipophilic octanoic acid, followed by butyric acid, on the cell envelope and on cellular membranes function and lipid remodeling. The importance of mitochondrial genome maintenance and functional mitochondria to obtain ATP for energy-dependent detoxification processes also emerged from this chemogenomic analysis, especially for octanoic acid. CONCLUSIONS This study provides new biological knowledge of interest to gain further mechanistic insights into toxicity and tolerance to linear-chain monocarboxylic acids of increasing liposolubility and reports the first lists of tolerance genes, at the genome scale, for butyric and octanoic acids. These genes and biological functions are potential targets for synthetic biology approaches applied to promising yeast cell factories, toward more robust superior strains, a highly desirable phenotype to increase the economic viability of bioprocesses based on mixtures of volatiles/medium-chain fatty acids derived from low-cost biodegradable substrates or lignocellulose hydrolysates.
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Affiliation(s)
- Marta N Mota
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
| | - Madalena Matos
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
| | - Nada Bahri
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal.
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal.
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Song MS, Lee DK, Lee CY, Park SC, Yang J. Host Subcellular Organelles: Targets of Viral Manipulation. Int J Mol Sci 2024; 25:1638. [PMID: 38338917 PMCID: PMC10855258 DOI: 10.3390/ijms25031638] [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: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Viruses have evolved sophisticated mechanisms to manipulate host cell processes and utilize intracellular organelles to facilitate their replication. These complex interactions between viruses and cellular organelles allow them to hijack the cellular machinery and impair homeostasis. Moreover, viral infection alters the cell membrane's structure and composition and induces vesicle formation to facilitate intracellular trafficking of viral components. However, the research focus has predominantly been on the immune response elicited by viruses, often overlooking the significant alterations that viruses induce in cellular organelles. Gaining a deeper understanding of these virus-induced cellular changes is crucial for elucidating the full life cycle of viruses and developing potent antiviral therapies. Exploring virus-induced cellular changes could substantially improve our understanding of viral infection mechanisms.
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Affiliation(s)
- Min Seok Song
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Dong-Kun Lee
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Sang-Cheol Park
- Artificial Intelligence and Robotics Laboratory, Myongji Hospital, Goyang 10475, Republic of Korea
| | - Jinsung Yang
- Department of Biochemistry and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
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Zhai H, Wang T, Liu D, Pan L, Sun Y, Qiu HJ. Autophagy as a dual-faced host response to viral infections. Front Cell Infect Microbiol 2023; 13:1289170. [PMID: 38125906 PMCID: PMC10731275 DOI: 10.3389/fcimb.2023.1289170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Autophagy selectively degrades viral particles or cellular components, either facilitating or inhibiting viral replication. Conversely, most viruses have evolved strategies to escape or exploit autophagy. Moreover, autophagy collaborates with the pattern recognition receptor signaling, influencing the expression of adaptor molecules involved in the innate immune response and regulating the expression of interferons (IFNs). The intricate relationship between autophagy and IFNs plays a critical role in the host cell defense against microbial invasion. Therefore, it is important to summarize the interactions between viral infections, autophagy, and the host defense mechanisms against viruses. This review specifically focuses on the interactions between autophagy and IFN pathways during viral infections, providing a comprehensive summary of the molecular mechanisms utilized or evaded by different viruses.
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Affiliation(s)
| | | | | | | | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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8
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Chandran A, Oliver HJ, Rochet JC. Role of NFE2L1 in the Regulation of Proteostasis: Implications for Aging and Neurodegenerative Diseases. BIOLOGY 2023; 12:1169. [PMID: 37759569 PMCID: PMC10525699 DOI: 10.3390/biology12091169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
A hallmark of aging and neurodegenerative diseases is a disruption of proteome homeostasis ("proteostasis") that is caused to a considerable extent by a decrease in the efficiency of protein degradation systems. The ubiquitin proteasome system (UPS) is the major cellular pathway involved in the clearance of small, short-lived proteins, including amyloidogenic proteins that form aggregates in neurodegenerative diseases. Age-dependent decreases in proteasome subunit expression coupled with the inhibition of proteasome function by aggregated UPS substrates result in a feedforward loop that accelerates disease progression. Nuclear factor erythroid 2- like 1 (NFE2L1) is a transcription factor primarily responsible for the proteasome inhibitor-induced "bounce-back effect" regulating the expression of proteasome subunits. NFE2L1 is localized to the endoplasmic reticulum (ER), where it is rapidly degraded under basal conditions by the ER-associated degradation (ERAD) pathway. Under conditions leading to proteasome impairment, NFE2L1 is cleaved and transported to the nucleus, where it binds to antioxidant response elements (AREs) in the promoter region of proteasome subunit genes, thereby stimulating their transcription. In this review, we summarize the role of UPS impairment in aging and neurodegenerative disease etiology and consider the potential benefit of enhancing NFE2L1 function as a strategy to upregulate proteasome function and alleviate pathology in neurodegenerative diseases.
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Affiliation(s)
- Aswathy Chandran
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Haley Jane Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
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9
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Guzman UH, Aksnes H, Ree R, Krogh N, Jakobsson ME, Jensen LJ, Arnesen T, Olsen JV. Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae. Nat Commun 2023; 14:4517. [PMID: 37500638 PMCID: PMC10374663 DOI: 10.1038/s41467-023-40224-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Protein N-terminal (Nt) acetylation is one of the most abundant modifications in eukaryotes, covering ~50-80 % of the proteome, depending on species. Cells with defective Nt-acetylation display a wide array of phenotypes such as impaired growth, mating defects and increased stress sensitivity. However, the pleiotropic nature of these effects has hampered our understanding of the functional impact of protein Nt-acetylation. The main enzyme responsible for Nt-acetylation throughout the eukaryotic kingdom is the N-terminal acetyltransferase NatA. Here we employ a multi-dimensional proteomics approach to analyze Saccharomyces cerevisiae lacking NatA activity, which causes global proteome remodeling. Pulsed-SILAC experiments reveals that NatA-deficient strains consistently increase degradation of ribosomal proteins compared to wild type. Explaining this phenomenon, thermal proteome profiling uncovers decreased thermostability of ribosomes in NatA-knockouts. Our data are in agreement with a role for Nt-acetylation in promoting stability for parts of the proteome by enhancing the avidity of protein-protein interactions and folding.
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Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Magnus E Jakobsson
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Biosciences, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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10
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Alula KM, Theiss AL. Autophagy in Crohn's Disease: Converging on Dysfunctional Innate Immunity. Cells 2023; 12:1779. [PMID: 37443813 PMCID: PMC10341259 DOI: 10.3390/cells12131779] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease marked by relapsing, transmural intestinal inflammation driven by innate and adaptive immune responses. Autophagy is a multi-step process that plays a critical role in maintaining cellular homeostasis by degrading intracellular components, such as damaged organelles and invading bacteria. Dysregulation of autophagy in CD is revealed by the identification of several susceptibility genes, including ATG16L1, IRGM, NOD2, LRRK2, ULK1, ATG4, and TCF4, that are involved in autophagy. In this review, the role of altered autophagy in the mucosal innate immune response in the context of CD is discussed, with a specific focus on dendritic cells, macrophages, Paneth cells, and goblet cells. Selective autophagy, such as xenophagy, ERphagy, and mitophagy, that play crucial roles in maintaining intestinal homeostasis in these innate immune cells, are discussed. As our understanding of autophagy in CD pathogenesis evolves, the development of autophagy-targeted therapeutics may benefit subsets of patients harboring impaired autophagy.
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Affiliation(s)
| | - Arianne L. Theiss
- Division of Gastroenterology & Hepatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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11
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Kallergi E, Siva Sankar D, Matera A, Kolaxi A, Paolicelli RC, Dengjel J, Nikoletopoulou V. Profiling of purified autophagic vesicle degradome in the maturing and aging brain. Neuron 2023:S0896-6273(23)00384-7. [PMID: 37279748 DOI: 10.1016/j.neuron.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 03/19/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023]
Abstract
Autophagy disorders prominently affect the brain, entailing neurodevelopmental and neurodegenerative phenotypes in adolescence or aging, respectively. Synaptic and behavioral deficits are largely recapitulated in mouse models with ablation of autophagy genes in brain cells. Yet, the nature and temporal dynamics of brain autophagic substrates remain insufficiently characterized. Here, we immunopurified LC3-positive autophagic vesicles (LC3-pAVs) from the mouse brain and proteomically profiled their content. Moreover, we characterized the LC3-pAV content that accumulates after macroautophagy impairment, validating a brain autophagic degradome. We reveal selective pathways for aggrephagy, mitophagy, and ER-phagy via selective autophagy receptors, and the turnover of numerous synaptic substrates, under basal conditions. To gain insight into the temporal dynamics of autophagic protein turnover, we quantitatively compared adolescent, adult, and aged brains, revealing critical periods of enhanced mitophagy or degradation of synaptic substrates. Overall, this resource unbiasedly characterizes the contribution of autophagy to proteostasis in the maturing, adult, and aged brain.
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Affiliation(s)
- Emmanouela Kallergi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | | | - Alessandro Matera
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Angeliki Kolaxi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | | | - Joern Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
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12
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Gibertini S, Ruggieri A, Cheli M, Maggi L. Protein Aggregates and Aggrephagy in Myopathies. Int J Mol Sci 2023; 24:ijms24098456. [PMID: 37176163 PMCID: PMC10179229 DOI: 10.3390/ijms24098456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
A number of muscular disorders are hallmarked by the aggregation of misfolded proteins within muscle fibers. A specialized form of macroautophagy, termed aggrephagy, is designated to remove and degrade protein aggregates. This review aims to summarize what has been studied so far about the direct involvement of aggrephagy and the activation of the key players, among others, p62, NBR1, Alfy, Tollip, Optineurin, TAX1BP1 and CCT2 in muscular diseases. In the first part of the review, we describe the aggrephagy pathway with the involved proteins; then, we illustrate the muscular disorder histologically characterized by protein aggregates, highlighting the role of aggrephagy pathway abnormalities in these muscular disorders.
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Affiliation(s)
- Sara Gibertini
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Alessandra Ruggieri
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Marta Cheli
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Lorenzo Maggi
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
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13
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Levy R, Alter Regev T, Paes W, Gumpert N, Cohen Shvefel S, Bartok O, Dayan-Rubinov M, Alon M, Shmueli M, Levin Y, Merbl Y, Ternette N, Samuels Y. Large-Scale Immuno-Peptidome Analysis Reveals Recurrent Post-Translational Splicing of Cancer and Immune-Associated Genes. Mol Cell Proteomics 2023; 22:100519. [PMID: 36828127 PMCID: PMC10119686 DOI: 10.1016/j.mcpro.2023.100519] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Post-translational spliced peptides (PTSPs) are a unique class of peptides that have been found to be presented by HLA-class-I molecules in cancer (1). Thus far, no consensus has been reached on the proportion of PTSPs in the immunopeptidome, with estimates ranging from 2% to as high as 45% and stirring significant debate (2-8). Furthermore, the role of the HLA-class-II pathway in PTSP presentation has been studied only in diabetes (9). Here, we exploit our large-scale cancer peptidomics database and our newly devised pipeline for filtering spliced peptide predictions to identify recurring spliced peptides, both for HLA-class-I and -II complexes. Our results indicate that HLA-class-I spliced peptides account for a low percentage of the immunopeptidome (less than 3.1%), yet are larger in number relative to other types of identified aberrant peptides. Therefore, spliced peptides significantly contribute to the repertoire of presented peptides in cancer cells. In addition, we identified HLA-class-II-bound spliced peptides, but to a lower extent (less than 0.5%). The identified spliced peptides include cancer- and immune-associated genes, such as the MITF oncogene, DAPK1 tumor suppressor and HLA-E, which were validated using synthetic peptides. The potential immunogenicity of the DAPK1- and HLA-E-derived PTSPs was also confirmed. In addition, a reanalysis of our published mouse single-cell clone immunopeptidome dataset showed that most of the spliced peptides were found repeatedly in a large number of the single-cell clones. Establishing a novel search-scheme for the discovery and evaluation of recurring PTSPs among cancer patients may assist in identifying potential novel targets for immunotherapy.
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Affiliation(s)
- Ronen Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Alter Regev
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nofar Gumpert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sapir Cohen Shvefel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osnat Bartok
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maria Dayan-Rubinov
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - MeravD Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nicola Ternette
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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14
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Mahapatra KK, Patra S, Mishra SR, Behera BP, Patil S, Bhutia SK. Autophagy for secretory protein: Therapeutic targets in cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 133:159-180. [PMID: 36707200 DOI: 10.1016/bs.apcsb.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autophagy, a classical cellular degradative catabolic process, also involves a functionally discrete non-degradative role in eukaryotic cells. It imparts critical regulatory function on conventional and unconventional protein secretion (degradative and secretory autophagy with distinct lysosomal degradation and extracellular expulsion, respectively) pathways. The N-amino terminal leader sequence containing proteins follows a conventional secretion pathway, while the leader-less proteins opt for secretory autophagy. The secretory autophagic process ensembles core autophagy machinery proteins, specifically ULK1/2, Beclin 1, LC3, and GABARAP, in coordination with Golgi re-assembly and stacking proteins (GRASPs). The secretory omegasomes fuse with the plasma membrane for the expulsion of cytosolic cargos to the extracellular environment. Alternatively, the secretory omegasomes also fuse with multi-vesicular bodies (MVBs) and harmonize ESCRTs (Complex I; TSG101) and Rab GTPase for their release to extracellular space. Autophagy has been associated with the secretion of diverse proteins involved in cellular signaling, inflammation, and carcinogenesis. Secreted proteins play an essential role in cancer by sustaining cell proliferation, inhibiting apoptosis, enhancing angiogenesis and metastasis, immune cell regulation, modulation of cellular energy metabolism, and resistance to anticancer drugs. The complexity of autophagy regulation during tumorigenesis is dependent on protein secretion pathways. Autophagy-regulated TOR-autophagy spatial coupling compartment complex energizes enhanced secretion of pro-inflammatory cytokines and leaderless proteins such as HMGB1. In conclusion, the chapter reviews the role of autophagy in regulating conventional and unconventional protein secretion pathways and its possible role in cancer.
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Affiliation(s)
- Kewal Kumar Mahapatra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Srimanta Patra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Soumya Ranjan Mishra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Bishnu Prasad Behera
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT, United States.
| | - Sujit Kumar Bhutia
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India.
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15
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Kaposi's sarcoma-associated herpesvirus (KSHV) utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies. PLoS Pathog 2023; 19:e1011080. [PMID: 36634147 PMCID: PMC9876383 DOI: 10.1371/journal.ppat.1011080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 01/25/2023] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposi's sarcoma (KS). We previously demonstrated that the KSHV Kaposin B (KapB) protein promotes inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). PBs modify gene expression by silencing or degrading labile messenger RNAs (mRNAs), including many transcripts that encode inflammatory or angiogenic proteins associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via phosphorylation of the autophagy regulatory protein, Beclin. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin phosphorylation or autophagic flux. Moreover, we showed that PB disassembly mediated by KSHV or KapB, depended on autophagy genes and the selective autophagy receptor NDP52/CALCOCO2 and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection.
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16
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Mucopolysaccharidoses: Cellular Consequences of Glycosaminoglycans Accumulation and Potential Targets. Int J Mol Sci 2022; 24:ijms24010477. [PMID: 36613919 PMCID: PMC9820209 DOI: 10.3390/ijms24010477] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/09/2022] [Accepted: 12/24/2022] [Indexed: 12/30/2022] Open
Abstract
Mucopolysaccharidoses (MPSs) constitute a heterogeneous group of lysosomal storage disorders characterized by the lysosomal accumulation of glycosaminoglycans (GAGs). Although lysosomal dysfunction is mainly affected, several cellular organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, and their related process are also impaired, leading to the activation of pathophysiological cascades. While supplying missing enzymes is the mainstream for the treatment of MPS, including enzyme replacement therapy (ERT), hematopoietic stem cell transplantation (HSCT), or gene therapy (GT), the use of modulators available to restore affected organelles for recovering cell homeostasis may be a simultaneous approach. This review summarizes the current knowledge about the cellular consequences of the lysosomal GAGs accumulation and discusses the use of potential modulators that can reestablish normal cell function beyond ERT-, HSCT-, or GT-based alternatives.
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17
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Martínez-Férriz A, Ferrando A, Fathinajafabadi A, Farràs R. Ubiquitin-mediated mechanisms of translational control. Semin Cell Dev Biol 2022; 132:146-154. [PMID: 34952788 DOI: 10.1016/j.semcdb.2021.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/15/2022]
Abstract
mRNAs translation to proteins constitutes an important step of cellular gene expression that is highly regulated in response to different extracellular stimuli and stress situations. The fine control of protein synthesis is carried out both qualitatively and quantitatively, depending on the cellular demand at each moment. Post-translational modifications, in turn regulated by intracellular signaling pathways, play a key role in translation regulation. Among them, ubiquitination, whose role is becoming increasingly important in the control of translation, determines a correct balance between protein synthesis and degradation. In this review we focus on the role of ubiquitination (both degradative K48-linkage type and non-degradative K63-linkage type and monoubiquitination) in eukaryotic translation, both at the pre-translational level during the biogenesis/degradation of the components of translational machinery as well as at the co-translational level under stressful conditions. We also discuss other ubiquitin-dependent regulatory mechanisms of mRNA protection and resumption of translation after stress removal, where the ubiquitination of ribosomal proteins and associated regulatory proteins play an important role in the global rhythm of translation.
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Affiliation(s)
- Arantxa Martínez-Férriz
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alihamze Fathinajafabadi
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
| | - Rosa Farràs
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
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18
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Weinberg J, Gaur M, Swaroop A, Taylor A. Proteostasis in aging-associated ocular disease. Mol Aspects Med 2022; 88:101157. [PMID: 36459837 PMCID: PMC9742340 DOI: 10.1016/j.mam.2022.101157] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022]
Abstract
Vision impairment has devastating consequences for the quality of human life. The cells and tissues associated with the visual process must function throughout one's life span and maintain homeostasis despite exposure to a variety of insults. Maintenance of the proteome is termed proteostasis, and is vital for normal cellular functions, especially at an advanced age. Here we describe basic aspects of proteostasis, from protein synthesis and folding to degradation, and discuss the current status of the field with a particular focus on major age-related eye diseases: age-related macular degeneration, cataract, and glaucoma. Our intent is to allow vision scientists to determine where and how to harness the proteostatic machinery for extending functional homeostasis in the aging retina, lens, and trabecular meshwork. Several common themes have emerged despite these tissues having vastly different metabolisms. Continued exposure to insults, including chronic stress with advancing age, increases proteostatic burden and reduces the fidelity of the degradation machineries including the ubiquitin-proteasome and the autophagy-lysosome systems that recognize and remove damaged proteins. This "double jeopardy" results in an exponential accumulation of cytotoxic proteins with advancing age. We conclude with a discussion of the challenges in maintaining an appropriate balance of protein synthesis and degradation pathways, and suggest that harnessing proteostatic capacities should provide new opportunities to design interventions for attenuating age-related eye diseases before they limit sight.
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Affiliation(s)
- Jasper Weinberg
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, 02111, USA
| | - Mohita Gaur
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Allen Taylor
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, 02111, USA.
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19
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Yuan M, Tu B, Li H, Pang H, Zhang N, Fan M, Bai J, Wang W, Shu Z, DuFort CC, Huo S, Zhai J, Yao K, Wang L, Ying H, Zhu WG, Fu D, Hu Z, Zhao Y. Cancer-associated fibroblasts employ NUFIP1-dependent autophagy to secrete nucleosides and support pancreatic tumor growth. NATURE CANCER 2022; 3:945-960. [PMID: 35982178 DOI: 10.1038/s43018-022-00426-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Cancer-associated fibroblasts (CAFs) are one of the most prominent and active components in the pancreatic tumor microenvironment. Our data show that CAFs are critical for survival from pancreatic ductal adenocarcinoma (PDAC) on glutamine deprivation. Specifically, we uncovered a role for nucleosides, which are secreted by CAFs through autophagy in a nuclear fragile X mental retardation-interacting protein 1 (NUFIP1)-dependent manner, increased glucose utilization and promoted growth of PDAC. Moreover, we demonstrate that CAF-derived nucleosides induced glucose consumption under glutamine-deprived conditions and displayed a dependence on MYC. Using an orthotopic mouse model of PDAC, we found that inhibiting nucleoside secretion by targeting NUFIP1 in the stroma reduced tumor weight. This finding highlights a previously unappreciated metabolic network within pancreatic tumors in which diverse nutrients are used to promote growth in an austere tumor microenvironment.
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Affiliation(s)
- Meng Yuan
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Bo Tu
- Molecular and Cellular Oncology Department, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hengchao Li
- Department of Pancreatic Surgery, Huashan hospital, Institute of Pancreatic Disease, FuDan University, Shanghai, China
| | - Huanhuan Pang
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Nan Zhang
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Minghe Fan
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jingru Bai
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Wei Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, NHC Key Laboratory of Medical Immunology, Beijing, China
| | - Zhaoqi Shu
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Christopher C DuFort
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sihan Huo
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jie Zhai
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ke Yao
- Department of Pancreatic Surgery, Huashan hospital, Institute of Pancreatic Disease, FuDan University, Shanghai, China
| | - Lina Wang
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Haoqiang Ying
- Molecular and Cellular Oncology Department, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei-Guo Zhu
- Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Deliang Fu
- Department of Pancreatic Surgery, Huashan hospital, Institute of Pancreatic Disease, FuDan University, Shanghai, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
| | - Ying Zhao
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
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20
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Houghton OH, Mizielinska S, Gomez-Suaga P. The Interplay Between Autophagy and RNA Homeostasis: Implications for Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Front Cell Dev Biol 2022; 10:838402. [PMID: 35573690 PMCID: PMC9096704 DOI: 10.3389/fcell.2022.838402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/14/2022] [Indexed: 01/18/2023] Open
Abstract
Amyotrophic lateral sclerosis and frontotemporal dementia are neurodegenerative disorders that lie on a disease spectrum, sharing genetic causes and pathology, and both without effective therapeutics. Two pathways that have been shown to play major roles in disease pathogenesis are autophagy and RNA homeostasis. Intriguingly, there is an increasing body of evidence suggesting a critical interplay between these pathways. Autophagy is a multi-stage process for bulk and selective clearance of malfunctional cellular components, with many layers of regulation. Although the majority of autophagy research focuses on protein degradation, it can also mediate RNA catabolism. ALS/FTD-associated proteins are involved in many stages of autophagy and autophagy-mediated RNA degradation, particularly converging on the clearance of persistent pathological stress granules. In this review, we will summarise the progress in understanding the autophagy-RNA homeostasis interplay and how that knowledge contributes to our understanding of the pathobiology of ALS/FTD.
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Affiliation(s)
- O H Houghton
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,UK Dementia Research Institute at King's College London, London, United Kingdom
| | - S Mizielinska
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,UK Dementia Research Institute at King's College London, London, United Kingdom
| | - P Gomez-Suaga
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Cáceres, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, Spain
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21
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Hammarström D, Øfsteng SJ, Jacobsen NB, Flobergseter KB, Rønnestad BR, Ellefsen S. Ribosome accumulation during early phase resistance training in humans. Acta Physiol (Oxf) 2022; 235:e13806. [PMID: 35213791 PMCID: PMC9540306 DOI: 10.1111/apha.13806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/04/2022] [Accepted: 02/21/2022] [Indexed: 12/16/2022]
Abstract
Aim To describe ribosome biogenesis during resistance training, its relation to training volume and muscle growth. Methods A training group (n = 11) performed 12 sessions (3‐4 sessions per week) of unilateral knee extension with constant and variable volume (6 and 3‐9 sets per session respectively) allocated to either leg. Ribosome abundance and biogenesis markers were assessed from vastus lateralis biopsies obtained at baseline, 48 hours after sessions 1, 4, 5, 8, 9 and 12, and after eight days of de‐training, and from a control group (n = 8). Muscle thickness was measured before and after the intervention. Results Training led to muscle growth (3.9% over baseline values, 95% CrI: [0.2, 7.5] vs. control) with concomitant increases in total RNA, ribosomal RNA, upstream binding factor (UBF) and ribosomal protein S6 with no differences between volume conditions. Total RNA increased rapidly in response to the first four sessions (8.6% [5.6, 11.7] per session), followed by a plateau and peak values after session 8 (49.5% [34.5, 66.5] above baseline). Total RNA abundance was associated with UBF protein levels (5.0% [0.2, 10.2] per unit UBF), and the rate of increase in total RNA levels predicted hypertrophy (0.3 mm [0.1, 0.4] per %‐point increase in total RNA per session). After de‐training, total RNA decreased (−19.3% [−29.0, −8.1]) without muscle mass changes indicating halted biosynthesis of ribosomes. Conclusion Ribosomes accumulate in the initial phase of resistance training with abundances sensitive to training cessation and associated with UBF protein levels. The average accumulation rate predicts muscle training‐induced hypertrophy.
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Affiliation(s)
- Daniel Hammarström
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
- Swedish School of Sport and Health Sciences Stockholm Sweden
| | - Sjur J. Øfsteng
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Nicolai B. Jacobsen
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Krister B. Flobergseter
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Bent R. Rønnestad
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Stian Ellefsen
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
- Innlandet Hospital Trust Lillehammer Norway
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22
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Gundelfinger ED, Karpova A, Pielot R, Garner CC, Kreutz MR. Organization of Presynaptic Autophagy-Related Processes. Front Synaptic Neurosci 2022; 14:829354. [PMID: 35368245 PMCID: PMC8968026 DOI: 10.3389/fnsyn.2022.829354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Brain synapses pose special challenges on the quality control of their protein machineries as they are far away from the neuronal soma, display a high potential for plastic adaptation and have a high energy demand to fulfill their physiological tasks. This applies in particular to the presynaptic part where neurotransmitter is released from synaptic vesicles, which in turn have to be recycled and refilled in a complex membrane trafficking cycle. Pathways to remove outdated and damaged proteins include the ubiquitin-proteasome system acting in the cytoplasm as well as membrane-associated endolysosomal and the autophagy systems. Here we focus on the latter systems and review what is known about the spatial organization of autophagy and endolysomal processes within the presynapse. We provide an inventory of which components of these degradative systems were found to be present in presynaptic boutons and where they might be anchored to the presynaptic apparatus. We identify three presynaptic structures reported to interact with known constituents of membrane-based protein-degradation pathways and therefore may serve as docking stations. These are (i) scaffolding proteins of the cytomatrix at the active zone, such as Bassoon or Clarinet, (ii) the endocytic machinery localized mainly at the peri-active zone, and (iii) synaptic vesicles. Finally, we sketch scenarios, how presynaptic autophagic cargos are tagged and recruited and which cellular mechanisms may govern membrane-associated protein turnover in the presynapse.
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Affiliation(s)
- Eckart D. Gundelfinger
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Institute of Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
- *Correspondence: Eckart D. Gundelfinger,
| | - Anna Karpova
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Rainer Pielot
- Institute of Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Craig C. Garner
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Michael R. Kreutz
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
- Center for Molecular Neurobiology (ZMNH), University Hospital Hamburg-Eppendorf, Hamburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
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23
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Smith PR, Pandit SC, Loerch S, Campbell ZT. The space between notes: emerging roles for translationally silent ribosomes. Trends Biochem Sci 2022; 47:477-491. [PMID: 35246374 DOI: 10.1016/j.tibs.2022.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 01/02/2023]
Abstract
In addition to their central functions in translation, ribosomes can adopt inactive structures that are fully assembled yet devoid of mRNA. We describe how the abundance of idle eukaryotic ribosomes is influenced by a broad range of biological conditions spanning viral infection, nutrient deprivation, and developmental cues. Vacant ribosomes may provide a means to exclude ribosomes from translation while also shielding them from degradation, and the variable identity of factors that occlude ribosomes may impart distinct functionality. We propose that regulated changes in the balance of idle and active ribosomes provides a means to fine-tune translation. We provide an overview of idle ribosomes, describe what is known regarding their function, and highlight questions that may clarify their biological roles.
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Affiliation(s)
- Patrick R Smith
- The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX, USA
| | - Sapna C Pandit
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Sarah Loerch
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Zachary T Campbell
- The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX, USA; The Center for Advanced Pain Studies (CAPS), University of Texas at Dallas, Richardson, TX, USA.
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24
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Rojas-Sanchez G, García-Miranda A, Montes-Alvarado JB, Cotzomi-Ortega I, Sarmiento-Salinas FL, Jimenez-Ignacio EE, Ramírez-Ramírez D, Romo-Rodríguez RE, Reyes-Leyva J, Vallejo-Ruiz V, Pazos-Salazar NG, Maycotte P. Chloroquine Induces ROS-mediated Macrophage Migration Inhibitory Factor Secretion and Epithelial to Mesenchymal Transition in ER-positive Breast Cancer Cell Lines. J Mammary Gland Biol Neoplasia 2021; 26:341-355. [PMID: 34813005 DOI: 10.1007/s10911-021-09503-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/10/2021] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is the leading cause of cancer-related death in women in the world. Since tumor cells employ autophagy as a survival pathway, it has been proposed that autophagy inhibition could be beneficial for cancer treatment. There are several onging clinical trials where autophagy is being inhibited (using chloroquine, CQ or hydroxychloroquine, HCQ) along with chemotherapy with promising results. However, there is also in vitro evidence in which autophagy inhibition can induce epithelial to mesenchymal transition (EMT) in cancer cells, indicating that, at least in some cases, this strategy could be detrimental for cancer patients. In this study, we found that the genetic inhibition of autophagy primed cells for EMT by inducing a decrease in E-cadherin protein levels, while CQ treatment decreased E-cadherin levels, induced morphological changes related to EMT, increased EMT-related transcription factor (EMT-TF) expression and migration in estrogen receptor positive (ER +) BC cell lines. Importantly, CQ treatment increased intracellular reactive oxygen species (ROS) which induced the secretion of macrophage migration inhibitory factor (MIF), a pro-inflammatory cytokine related to malignancy. Both ROS production and MIF secretion were responsible for the mesenchymal morphology and increased migratory capacity induced by CQ. Our results indicate that CQ treatment increased malignancy by inducing ROS production, MIF secretion and EMT and suggest that autophagy inhibition in ER + BC patients might have detrimental effects. Our data indicates that a careful selection of patients should be performed in order to determine who will benefit the most from autophagy inhibition with available pharmacological agents for the treatment of breast cancer.
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Affiliation(s)
- Guadalupe Rojas-Sanchez
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, 72570, Mexico
| | - Alin García-Miranda
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
- Facultad de Ciencias Químicas Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, 39090, Mexico
| | - José Benito Montes-Alvarado
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
| | - Israel Cotzomi-Ortega
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, 72570, Mexico
| | - Fabiola Lilí Sarmiento-Salinas
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, 72570, Mexico
| | - Eduardo Eleazar Jimenez-Ignacio
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
- Instituto Tecnológico Superior de Coatzacoalcos, Coatzacoalcos, 96536, Mexico
| | - Dalia Ramírez-Ramírez
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
| | - Rubí Esmeralda Romo-Rodríguez
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
| | - Julio Reyes-Leyva
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
| | - Verónica Vallejo-Ruiz
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico
| | - Nidia Gary Pazos-Salazar
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, 72570, Mexico
| | - Paola Maycotte
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Km 4.5 Carretera Atlixco-Metepec HGZ5, Puebla, 74360, Mexico.
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25
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Chauhan S, Jena KK, Mehto S, Chauhan NR, Sahu R, Dhar K, Yadav R, Krishna S, Jaiswal P, Chauhan S. Innate immunity and inflammophagy: balancing the defence and immune homeostasis. FEBS J 2021; 289:4112-4131. [PMID: 34826185 DOI: 10.1111/febs.16298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/27/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022]
Abstract
Extensive crosstalk exists between autophagy and innate immune signalling pathways. The stimuli that induce pattern recognition receptor (PRR)-mediated innate immune signalling pathways, also upregulate autophagy. The purpose of this increased autophagy is to eliminate the stimuli and/or suppress the inflammatory pathways by targeted degradation of PRRs or intermediary proteins (termed 'inflammophagy'). By executing these functions, autophagy dampens excess inflammation triggered by the innate immune signalling pathways. Thus, autophagy helps in the maintenance of the body's innate immune homeostasis to protect from inflammatory and autoimmune diseases. Many autophagy-dependent mechanisms that could control innate immune signalling have been studied over the last few years. However, still, the understanding is incomplete, and studies that are more systematic should be undertaken to delineate the mechanisms of inflammophagy. Here, we discuss the available knowledge of crosstalk between autophagy and PRR signalling pathways.
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Affiliation(s)
- Swati Chauhan
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Kautilya Kumar Jena
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Subhash Mehto
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Nishant Ranjan Chauhan
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Rinku Sahu
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Kollori Dhar
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Rina Yadav
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Sivaram Krishna
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Pundrik Jaiswal
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Santosh Chauhan
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
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26
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Cattelani C, Lesiak D, Liebscher G, Singer II, Stasyk T, Wallnöfer MH, Heberle AM, Corti C, Hess MW, Pfaller K, Kwiatkowski M, Pramstaller PP, Hicks AA, Thedieck K, Müller T, Huber LA, Eca Guimaraes de Araujo M. The SZT2 Interactome Unravels New Functions of the KICSTOR Complex. Cells 2021; 10:2711. [PMID: 34685691 PMCID: PMC8534408 DOI: 10.3390/cells10102711] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/20/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
Seizure threshold 2 (SZT2) is a component of the KICSTOR complex which, under catabolic conditions, functions as a negative regulator in the amino acid-sensing branch of mTORC1. Mutations in this gene cause a severe neurodevelopmental and epileptic encephalopathy whose main symptoms include epilepsy, intellectual disability, and macrocephaly. As SZT2 remains one of the least characterized regulators of mTORC1, in this work we performed a systematic interactome analysis under catabolic and anabolic conditions. Besides numerous mTORC1 and AMPK signaling components, we identified clusters of proteins related to autophagy, ciliogenesis regulation, neurogenesis, and neurodegenerative processes. Moreover, analysis of SZT2 ablated cells revealed increased mTORC1 signaling activation that could be reversed by Rapamycin or Torin treatments. Strikingly, SZT2 KO cells also exhibited higher levels of autophagic components, independent of the physiological conditions tested. These results are consistent with our interactome data, in which we detected an enriched pool of selective autophagy receptors/regulators. Moreover, preliminary analyses indicated that SZT2 alters ciliogenesis. Overall, the data presented form the basis to comprehensively investigate the physiological functions of SZT2 that could explain major molecular events in the pathophysiology of developmental and epileptic encephalopathy in patients with SZT2 mutations.
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Affiliation(s)
- Cecilia Cattelani
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy; (C.C.); (P.P.P.); (A.A.H.)
| | - Dominik Lesiak
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
| | - Gudrun Liebscher
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
| | - Isabel I. Singer
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
| | - Taras Stasyk
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
| | - Moritz H. Wallnöfer
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
| | - Alexander M. Heberle
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria; (A.M.H.); (M.K.); (K.T.)
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Corrado Corti
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy; (C.C.); (P.P.P.); (A.A.H.)
| | - Michael W. Hess
- Institute of Histology and Embryology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.W.H.); (K.P.)
| | - Kristian Pfaller
- Institute of Histology and Embryology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.W.H.); (K.P.)
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria; (A.M.H.); (M.K.); (K.T.)
| | - Peter P. Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy; (C.C.); (P.P.P.); (A.A.H.)
| | - Andrew A. Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy; (C.C.); (P.P.P.); (A.A.H.)
| | - Kathrin Thedieck
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria; (A.M.H.); (M.K.); (K.T.)
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
- Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Thomas Müller
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Lukas A. Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
- Austrian Drug Screening Institute, ADSI, 6020 Innsbruck, Austria
| | - Mariana Eca Guimaraes de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.C.); (D.L.); (G.L.); (I.I.S.); (T.S.); (M.H.W.); (L.A.H.)
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27
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Molecular mechanisms of mammalian autophagy. Biochem J 2021; 478:3395-3421. [PMID: 34554214 DOI: 10.1042/bcj20210314] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitin-proteasome pathway (UPP) and autophagy play integral roles in cellular homeostasis. As part of their normal life cycle, most proteins undergo ubiquitination for some form of redistribution, localization and/or functional modulation. However, ubiquitination is also important to the UPP and several autophagic processes. The UPP is initiated after specific lysine residues of short-lived, damaged or misfolded proteins are conjugated to ubiquitin, which targets these proteins to proteasomes. Autophagy is the endosomal/lysosomal-dependent degradation of organelles, invading microbes, zymogen granules and macromolecules such as protein, carbohydrates and lipids. Autophagy can be broadly separated into three distinct subtypes termed microautophagy, chaperone-mediated autophagy and macroautophagy. Although autophagy was once thought of as non-selective bulk degradation, advancements in the field have led to the discovery of several selective forms of autophagy. Here, we focus on the mechanisms of primary and selective mammalian autophagy pathways and highlight the current knowledge gaps in these molecular pathways.
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28
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Inhibition of Scavenger Receptor Class B Type 1 (SR-B1) Expression and Activity as a Potential Novel Target to Disrupt Cholesterol Availability in Castration-Resistant Prostate Cancer. Pharmaceutics 2021; 13:pharmaceutics13091509. [PMID: 34575583 PMCID: PMC8467449 DOI: 10.3390/pharmaceutics13091509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023] Open
Abstract
There have been several studies that have linked elevated scavenger receptor class b type 1 (SR-B1) expression and activity to the development and progression of castration-resistant prostate cancer (CRPC). SR-B1 facilitates the influx of cholesterol to the cell from lipoproteins in systemic circulation. This influx of cholesterol may be important for many cellular functions, including the synthesis of androgens. Castration-resistant prostate cancer tumors can synthesize androgens de novo to supplement the loss of exogenous sources often induced by androgen deprivation therapy. Silencing of SR-B1 may impact the ability of prostate cancer cells, particularly those of the castration-resistant state, to maintain the intracellular supply of androgens by removing a supply of cholesterol. SR-B1 expression is elevated in CRPC models and has been linked to poor survival of patients. The overarching belief has been that cholesterol modulation, through either synthesis or uptake inhibition, will impact essential signaling processes, impeding the proliferation of prostate cancer. The reduction in cellular cholesterol availability can impede prostate cancer proliferation through both decreased steroid synthesis and steroid-independent mechanisms, providing a potential therapeutic target for the treatment of prostate cancer. In this article, we discuss and highlight the work on SR-B1 as a potential novel drug target for CRPC management.
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29
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He L, Qian X, Cui Y. Advances in ER-Phagy and Its Diseases Relevance. Cells 2021; 10:cells10092328. [PMID: 34571977 PMCID: PMC8465915 DOI: 10.3390/cells10092328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
As an important form of selective autophagy in cells, ER-phagy (endoplasmic reticulum-selective autophagy), the autophagic degradation of endoplasmic reticulum (ER), degrades ER membranes and proteins to maintain cellular homeostasis. The relationship between ER-phagy and human diseases, including neurodegenerative disorders, cancer, and other metabolic diseases has been unveiled by extensive research in recent years. Starting with the catabolic process of ER-phagy and key mediators in this pathway, this paper reviews the advances in the mechanism of ER-phagy and its diseases relevance. We hope to provide some enlightenment for further study on ER-phagy and the development of novel therapeutic strategies for related diseases.
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Affiliation(s)
- Lingang He
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, China; (L.H.); (X.Q.)
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Xuehong Qian
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, China; (L.H.); (X.Q.)
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Yixian Cui
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, China; (L.H.); (X.Q.)
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
- Correspondence: ; Tel.: +86-27-87267099
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30
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Agellon LB, Michalak M. A View of the Endoplasmic Reticulum Through the Calreticulin Lens. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 59:1-11. [PMID: 34050859 DOI: 10.1007/978-3-030-67696-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Calreticulin is well known as an ER-resident protein that serves as the major endoplasmic reticulum (ER) Ca2+ binding protein. This protein has been the major topic of discussion in an international workshop that has been meeting for a quarter of a century. In sharing information about this protein, the field also witnessed remarkable insights into the importance of the ER as an organelle and the role of ER Ca2+ in coordinating ER and cellular functions. Recent technological advances have helped to uncover the contributions of calreticulin in maintaining Ca2+ homeostasis in the ER and to unravel its involvement in a multitude of cellular processes as highlighted in this collection of articles. The continuing revelations of unexpected involvement of calreticulin and Ca2+ in many critical aspects of cellular function promises to further improve insights into the significance of this protein in the promotion of physiology as well as prevention of pathology.
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Affiliation(s)
- Luis B Agellon
- School of Human Nutrition, McGill University, Ste. Anne de Bellevue, QC, Canada.
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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31
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Autophagy Modulators in Cancer: Focus on Cancer Treatment. Life (Basel) 2021; 11:life11080839. [PMID: 34440583 PMCID: PMC8401266 DOI: 10.3390/life11080839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
Uncontrolled autophagy has been associated with the development and progression of various cancers that are resistant to cancer therapy. Therefore, many efforts to modulate uncontrolled autophagy as a cancer treatment have been attempted, from basic science to clinical trials. However, it remains difficult to equally apply autophagy modulators to cancer therapy because autophagy is a double-edged sword in cancer: it can be tumor-suppressive or tumor-protective. Therefore, the precise mechanisms of autophagy modulators and their varied responsiveness to each cancer type should be addressed in detail. This study will describe the precise mechanisms of developing various autophagy modulators, their current therapeutic applications and future perspectives.
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32
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Grisan F, Iannucci LF, Surdo NC, Gerbino A, Zanin S, Di Benedetto G, Pozzan T, Lefkimmiatis K. PKA compartmentalization links cAMP signaling and autophagy. Cell Death Differ 2021; 28:2436-2449. [PMID: 33742135 PMCID: PMC8328970 DOI: 10.1038/s41418-021-00761-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
Autophagy is a highly regulated degradative process crucial for maintaining cell homeostasis. This important catabolic mechanism can be nonspecific, but usually occurs with fine spatial selectivity (compartmentalization), engaging only specific subcellular sites. While the molecular machines driving autophagy are well understood, the involvement of localized signaling events in this process is not well defined. Among the pathways that regulate autophagy, the cyclic AMP (cAMP)/protein kinase A (PKA) cascade can be compartmentalized in distinct functional units called microdomains. However, while it is well established that, depending on the cell type, cAMP can inhibit or promote autophagy, the role of cAMP/PKA microdomains has not been tested. Here we show not only that the effects on autophagy of the same cAMP elevation differ in different cell types, but that they depend on a highly complex sub-compartmentalization of the signaling cascade. We show in addition that, in HT-29 cells, in which autophagy is modulated by cAMP rising treatments, PKA activity is strictly regulated in space and time by phosphatases, which largely prevent the phosphorylation of soluble substrates, while membrane-bound targets are less sensitive to the action of these enzymes. Interestingly, we also found that the subcellular distribution of PKA type-II regulatory PKA subunits hinders the effect of PKA on autophagy, while displacement of type-I regulatory PKA subunits has no effect. Our data demonstrate that local PKA activity can occur independently of local cAMP concentrations and provide strong evidence for a link between localized PKA signaling events and autophagy.
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Affiliation(s)
- Francesca Grisan
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Liliana F Iannucci
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nicoletta C Surdo
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Andrea Gerbino
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Sofia Zanin
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Giulietta Di Benedetto
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Neuroscience Institute, National Research Council, Padua, Italy
| | - Tullio Pozzan
- Neuroscience Institute, National Research Council, Padua, Italy
| | - Konstantinos Lefkimmiatis
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy.
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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33
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Autophagy Modulators in Cancer Therapy. Int J Mol Sci 2021; 22:ijms22115804. [PMID: 34071600 PMCID: PMC8199315 DOI: 10.3390/ijms22115804] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 05/24/2021] [Indexed: 02/06/2023] Open
Abstract
Autophagy is a process of self-degradation that plays an important role in removing damaged proteins, organelles or cellular fragments from the cell. Under stressful conditions such as hypoxia, nutrient deficiency or chemotherapy, this process can also become the strategy for cell survival. Autophagy can be nonselective or selective in removing specific organelles, ribosomes, and protein aggregates, although the complete mechanisms that regulate aspects of selective autophagy are not fully understood. This review summarizes the most recent research into understanding the different types and mechanisms of autophagy. The relationship between apoptosis and autophagy on the level of molecular regulation of the expression of selected proteins such as p53, Bcl-2/Beclin 1, p62, Atg proteins, and caspases was discussed. Intensive studies have revealed a whole range of novel compounds with an anticancer activity that inhibit or activate regulatory pathways involved in autophagy. We focused on the presentation of compounds strongly affecting the autophagy process, with particular emphasis on those that are undergoing clinical and preclinical cancer research. Moreover, the target points, adverse effects and therapeutic schemes of autophagy inhibitors and activators are presented.
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34
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Vega-Vásquez P, Mosier NS, Irudayaraj J. Hormesis-Inducing Essential Oil Nanodelivery System Protects Plants against Broad Host-Range Necrotrophs. ACS NANO 2021; 15:8338-8349. [PMID: 33881823 DOI: 10.1021/acsnano.0c09759] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Botrytis cinerea, a broad host-range necrotrophic (BHN) phytopathogen, establishes compatible interactions with hosts by deploying multigene infection strategies, rendering simply inherited resistance ineffective to fight off this pathogen. Since essential oils (EOs) serve as intermediators during phytobiome communication, we hypothesize that they have the potential to enhance the quantitative disease resistance against BHN by eliciting the adaptive stress response (hormesis) in plants. However, using EOs is challenging due to their poor solubility in water. Nanoemulsification of EOs enhances not only the solubility of EOs but also their potency and stability. Here, we demonstrate the potential use of essential oil nanoemulsions (EONEs) to control infections caused by BHN. Using basic engineering principles of nanocarrier design, we demonstrate the efficacy of a robust EONEs design for controlling B. cinerea infection in a model plant, Arabidopsis thaliana. Our nanoemulsion delivery system significantly enhanced the disease resistance of the host by reducing the necrotic area by up to 50% compared to untreated plants. RNA-seq analysis indicated that successful treatments upregulated autophagy, ROS scavenging, and activation of the jasmonic acid signaling pathway.
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Affiliation(s)
- Pablo Vega-Vásquez
- Laboratory of Renewable Resources Engineering (LORRE), Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nathan S Mosier
- Laboratory of Renewable Resources Engineering (LORRE), Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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35
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Metabolic needs of the kidney graft undergoing normothermic machine perfusion. Kidney Int 2021; 100:301-310. [PMID: 33857572 DOI: 10.1016/j.kint.2021.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/18/2021] [Accepted: 04/02/2021] [Indexed: 12/14/2022]
Abstract
Normothermic machine perfusion (NMP) is emerging as a novel preservation strategy. During NMP, the organ is maintained in a metabolically active state that may not only provide superior organ preservation, but that also facilitates viability testing before transplantation, and ex situ resuscitation of marginal kidney grafts. Although the prevailing perfusion protocols for renal NMP are refined from initial pioneering studies concerning short periods of NMP, it could be argued that these protocols are not optimally tailored to address the putatively compromised metabolic plasticity of marginal donor grafts (i.e., in the context of viability testing and/or preservation), or to meet the metabolic prerequisites associated with prolonged perfusions and the required anabolic state in the context of organ regeneration. Herein, we provide a theoretical framework for the metabolic requirements for renal NMP. Aspects are discussed along the lines of carbohydrates, fatty acids, amino acids, and micronutrients required for optimal NMP of an isolated kidney. In addition, considerations for monitoring aspects of metabolic status during NMP are discussed.
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36
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Hydroxychloroquine Potentiates Apoptosis Induced by PPAR α Antagonist in 786-O Clear Cell Renal Cell Carcinoma Cells Associated with Inhibiting Autophagy. PPAR Res 2021; 2021:6631605. [PMID: 33959154 PMCID: PMC8075691 DOI: 10.1155/2021/6631605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/14/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the major pathological pattern of renal cell carcinoma. The ccRCC cells exhibit a certain degree of inherent drug resistance due to some genetic mutations. In recent years, peroxisome proliferator-activated receptor-α (PPARα) antagonists have been reported as a targeted therapeutic drug capable of inducing apoptosis and cell cycle arrest in the ccRCC cell line. Autophagy, which can be induced by stress in eukaryotic cells, plays a complex role in the proliferation, survival, and death of tumor cells. In our study, we found that the expression of PPARα was low in highly differentiated ccRCC tissues and 786-O cell line but high in poorly differentiated ccRCC tissues. The level of PPARα expression in ccRCC tissues is correlated to the grade of differentiation, but not to the sex or age of ccRCC patients. The findings also revealed that the PPARα antagonist GW6471 can lower cell viability and induce autophagy in the 786-O ccRCC cell line. This autophagy can be inhibited by hydroxychloroquine. When treated with a combination of hydroxychloroquine and GW6471, the viability of the 786-O cells was decreased further when compared to the treatment with GW6471 or hydroxychloroquine alone, and apoptosis was promoted. Meanwhile, when human kidney 2 cells were cotreated with hydroxychloroquine and GW6471, cell viability was only slightly influenced. Hence, our finding indicates that the combination of GW6471 and hydroxychloroquine may constitute a novel and potentially effective treatment for ccRCC. Furthermore, this approach is likely to be safe owing to its minimal effects on normal renal tissues.
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37
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Salovska B, Li W, Di Y, Liu Y. BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples. Anal Chem 2021; 93:3103-3111. [PMID: 33533601 DOI: 10.1021/acs.analchem.0c04293] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The data-independent acquisition (DIA) performed in the latest high-resolution, high-speed mass spectrometers offers a powerful analytical tool for biological investigations. The DIA mass spectrometry (DIA-MS) combined with the isotopic labeling approach holds a particular promise for increasing the multiplexity of DIA-MS analysis, which could assist the relative protein quantification and the proteome-wide turnover profiling. However, the wide MS1 isolation windows employed in conventional DIA methods lead to a limited efficiency in identifying and quantifying isotope-labeled peptide pairs through peptide fragment ions. Here, we optimized a high-selectivity DIA-MS named BoxCarmax that supports the analysis of complex samples, such as those generated from Stable isotope labeling by amino acids in cell culture (SILAC) and pulse SILAC (pSILAC) experiments. BoxCarmax enables multiplexed acquisition at both MS1 and MS2 levels, through the integration of BoxCar and MSX features, as well as a gas-phase separation strategy. We found BoxCarmax significantly improved the quantitative accuracy in SILAC and pSILAC samples by mitigating the ratio suppression of isotope-peptide pairs. We further applied BoxCarmax to measure protein degradation regulation during serum starvation stress in cultured cells, revealing valuable biological insights. Our study offered an alternative and accurate approach for the MS analysis of protein turnover and complex samples.
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Affiliation(s)
- Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut CT 06520, United States
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut CT 06520, United States
| | - Yi Di
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut CT 06520, United States
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut CT 06520, United States.,Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut CT 06510, United States
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38
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Li W, He P, Huang Y, Li YF, Lu J, Li M, Kurihara H, Luo Z, Meng T, Onishi M, Ma C, Jiang L, Hu Y, Gong Q, Zhu D, Xu Y, Liu R, Liu L, Yi C, Zhu Y, Ma N, Okamoto K, Xie Z, Liu J, He RR, Feng D. Selective autophagy of intracellular organelles: recent research advances. Theranostics 2021; 11:222-256. [PMID: 33391472 PMCID: PMC7681076 DOI: 10.7150/thno.49860] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Macroautophagy (hereafter called autophagy) is a highly conserved physiological process that degrades over-abundant or damaged organelles, large protein aggregates and invading pathogens via the lysosomal system (the vacuole in plants and yeast). Autophagy is generally induced by stress, such as oxygen-, energy- or amino acid-deprivation, irradiation, drugs, etc. In addition to non-selective bulk degradation, autophagy also occurs in a selective manner, recycling specific organelles, such as mitochondria, peroxisomes, ribosomes, endoplasmic reticulum (ER), lysosomes, nuclei, proteasomes and lipid droplets (LDs). This capability makes selective autophagy a major process in maintaining cellular homeostasis. The dysfunction of selective autophagy is implicated in neurodegenerative diseases (NDDs), tumorigenesis, metabolic disorders, heart failure, etc. Considering the importance of selective autophagy in cell biology, we systemically review the recent advances in our understanding of this process and its regulatory mechanisms. We emphasize the 'cargo-ligand-receptor' model in selective autophagy for specific organelles or cellular components in yeast and mammals, with a focus on mitophagy and ER-phagy, which are finely described as types of selective autophagy. Additionally, we highlight unanswered questions in the field, helping readers focus on the research blind spots that need to be broken.
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39
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Li C, Yao H, Wang H, Fang JY, Xu J. Repurposing screen identifies Amlodipine as an inducer of PD-L1 degradation and antitumor immunity. Oncogene 2020; 40:1128-1146. [PMID: 33323966 DOI: 10.1038/s41388-020-01592-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 02/08/2023]
Abstract
Cancer cell expression of PD-L1 leads to T cells exhaustion by transducing co-inhibitory signal, and further understanding the regulation of PD-L1 in cancer cells may provide additional therapeutic strategies. Here by drug repurposing screen, we identified amlodipine as a potent inhibitor of PD-L1 expression in cancer cells. Further survey of calcium-associated pathways revealed calpain-dependent stabilization of the PD-L1 protein. Intracellular calcium delivered an operational signal to calpain-dependent Beclin-1 cleavage, blocking autophagic degradation of PD-L1 accumulated on recycling endosome (RE). Blocking calcium flux by amlodipine depleted PD-L1 expression and increased CD8+ T-cell infiltration in tumor tissues but not in myocardium, causing dose-dependent tumor suppression in vivo. Rescuing PD-L1 expression eliminated the effects of amlodipine, suggesting the PD-L1-dependent effect of amlodipine. These results reveal a calcium-dependent mechanism controlling PD-L1 degradation, and highlight calcium flux blockade as a potential strategy for combinatorial immunotherapy.
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Affiliation(s)
- Chushu Li
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Han Yao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Huanbin Wang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Jie Xu
- Institutes of Biomedical Sciences, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China. .,Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, 200001, Shanghai, China.
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40
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Johnston HE, Samant RS. Alternative systems for misfolded protein clearance: life beyond the proteasome. FEBS J 2020; 288:4464-4487. [PMID: 33135311 DOI: 10.1111/febs.15617] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Protein misfolding is a major driver of ageing-associated frailty and disease pathology. Although all cells possess multiple, well-characterised protein quality control systems to mitigate the toxicity of misfolded proteins, how they are integrated to maintain protein homeostasis ('proteostasis') in health-and how their disintegration contributes to disease-is still an exciting and fast-paced area of research. Under physiological conditions, the predominant route for misfolded protein clearance involves ubiquitylation and proteasome-mediated degradation. When the capacity of this route is overwhelmed-as happens during conditions of acute environmental stress, or chronic ageing-related decline-alternative routes for protein quality control are activated. In this review, we summarise our current understanding of how proteasome-targeted misfolded proteins are retrafficked to alternative protein quality control routes such as juxta-nuclear sequestration and selective autophagy when the ubiquitin-proteasome system is compromised. We also discuss the molecular determinants of these alternative protein quality control systems, attempt to clarify distinctions between various cytoplasmic spatial quality control inclusion bodies (e.g., Q-bodies, p62 bodies, JUNQ, aggresomes, and aggresome-like induced structures 'ALIS'), and speculate on emerging concepts in the field that we hope will spur future research-with the potential to benefit the rational development of healthy ageing strategies.
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Affiliation(s)
| | - Rahul S Samant
- Signalling Programme, The Babraham Institute, Cambridge, UK
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41
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Dhakal S, Macreadie I. Protein Homeostasis Networks and the Use of Yeast to Guide Interventions in Alzheimer's Disease. Int J Mol Sci 2020; 21:E8014. [PMID: 33126501 PMCID: PMC7662794 DOI: 10.3390/ijms21218014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's Disease (AD) is a progressive multifactorial age-related neurodegenerative disorder that causes the majority of deaths due to dementia in the elderly. Although various risk factors have been found to be associated with AD progression, the cause of the disease is still unresolved. The loss of proteostasis is one of the major causes of AD: it is evident by aggregation of misfolded proteins, lipid homeostasis disruption, accumulation of autophagic vesicles, and oxidative damage during the disease progression. Different models have been developed to study AD, one of which is a yeast model. Yeasts are simple unicellular eukaryotic cells that have provided great insights into human cell biology. Various yeast models, including unmodified and genetically modified yeasts, have been established for studying AD and have provided significant amount of information on AD pathology and potential interventions. The conservation of various human biological processes, including signal transduction, energy metabolism, protein homeostasis, stress responses, oxidative phosphorylation, vesicle trafficking, apoptosis, endocytosis, and ageing, renders yeast a fascinating, powerful model for AD. In addition, the easy manipulation of the yeast genome and availability of methods to evaluate yeast cells rapidly in high throughput technological platforms strengthen the rationale of using yeast as a model. This review focuses on the description of the proteostasis network in yeast and its comparison with the human proteostasis network. It further elaborates on the AD-associated proteostasis failure and applications of the yeast proteostasis network to understand AD pathology and its potential to guide interventions against AD.
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Affiliation(s)
| | - Ian Macreadie
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia;
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42
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Zielke S, Kardo S, Zein L, Mari M, Covarrubias-Pinto A, Kinzler MN, Meyer N, Stolz A, Fulda S, Reggiori F, Kögel D, van Wijk S. ATF4 links ER stress with reticulophagy in glioblastoma cells. Autophagy 2020; 17:2432-2448. [PMID: 33111629 DOI: 10.1080/15548627.2020.1827780] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Selective degradation of the endoplasmic reticulum (ER; reticulophagy) is a type of autophagy involved in the removal of ER fragments. So far, amino acid starvation as well as ER stress have been described as inducers of reticulophagy, which in turn restores cellular energy levels and ER homeostasis. Here, we explored the autophagy-inducing mechanisms that underlie the autophagic cell death (ACD)-triggering compound loperamide (LOP) in glioblastoma cells. Interestingly, LOP triggers upregulation of the transcription factor ATF4, which is accompanied by the induction of additional ER stress markers. Notably, knockout of ATF4 significantly attenuated LOP-induced autophagy and ACD. Functionally, LOP also specifically induces the engulfment of large ER fragments within autophagosomes and lysosomes as determined by electron and fluorescence microscopy. LOP-induced reticulophagy and cell death are predominantly mediated through the reticulophagy receptor RETREG1/FAM134B and, to a lesser extent, TEX264, confirming that reticulophagy receptors can promote ACD. Strikingly, apart from triggering LOP-induced autophagy and ACD, ATF4 is also required for LOP-induced reticulophagy. These observations highlight a key role for ATF4, RETREG1 and TEX264 in response to LOP-induced ER stress, reticulophagy and ACD, and establish a novel mechanistic link between ER stress and reticulophagy, with possible implications for additional models of drug-induced ER stress.Abbreviations: ACD: autophagic cell death; ATF6: activating transcription factor 6; ATL3: atlastin 3; BafA1: bafilomycin A1; CCPG1: cell cycle progression gene 1; co-IP: co-immunoprecipitation; DDIT3/CHOP: DNA damage inducible transcript 3; ER: endoplasmic reticulum; EIF2A/eIF2α: eukaryotic translation initiation factor 2A; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ERN1/IRE1α: endoplasmic reticulum to nucleus signaling 1; GABARAP: GABA type A receptor-associated protein; GBM: glioblastoma multiforme; HSPA5/BiP: heat shock protein family (Hsp70) member 5; LOP: loperamide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; RETREG1/FAM134B: reticulophagy regulator 1; RTN3L: reticulon 3 long; SEC62: SEC62 homolog, protein translocation factor; TEX264: testis-expressed 264, reticulophagy receptor; UPR: unfolded protein response.
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Affiliation(s)
- Svenja Zielke
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
| | - Simon Kardo
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
| | - Laura Zein
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Adriana Covarrubias-Pinto
- Institute of Biochemistry II, Goethe-University - Medical Faculty, University Hospital, Frankfurt, Germany
| | - Maximilian N Kinzler
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt, Germany
| | - Nina Meyer
- Experimental Neurosurgery, Goethe-University Hospital, Frankfurt, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II, Goethe-University - Medical Faculty, University Hospital, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Frankfurt, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Donat Kögel
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Germany.,Experimental Neurosurgery, Goethe-University Hospital, Frankfurt, Germany
| | - Sjoerd van Wijk
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
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43
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Abildgaard MH, Brynjólfsdóttir SH, Frankel LB. The Autophagy-RNA Interplay: Degradation and Beyond. Trends Biochem Sci 2020; 45:845-857. [PMID: 32828649 DOI: 10.1016/j.tibs.2020.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/06/2020] [Accepted: 07/23/2020] [Indexed: 02/08/2023]
Abstract
Autophagy is a highly conserved degradation pathway that ensures nutrient recycling and removal of unwanted substrates. This process has a fundamental role in stress adaptation and maintenance of cellular homeostasis. Here, we discuss emerging aspects of the autophagy-RNA interplay, including autophagy-mediated degradation of RNA, RNA-binding proteins (RBPs), and ribonucleoprotein (RNP) complexes. Beyond degradation, we review new roles for autophagy players in the secretion and intracellular transport of RNA and related complexes. We discuss the physiological importance of these events for RNA homeostasis and gene expression programs, as well as their implications for disease, including cancer and neurodegeneration. Lastly, we examine how post-transcriptional regulation of autophagy, through specialized processing and selective translation of key transcripts, challenges and updates our current view of autophagy complexity.
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Affiliation(s)
| | | | - Lisa B Frankel
- Danish Cancer Society Research Center, Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
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44
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Streit D, Shanmugam T, Garbelyanski A, Simm S, Schleiff E. The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1016. [PMID: 32806552 PMCID: PMC7464842 DOI: 10.3390/plants9081016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Thiruvenkadam Shanmugam
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Asen Garbelyanski
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
- Institute of Bioinformatics, University Medicine Greifswald, D-17475 Greifswald, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
- Frankfurt Institute of Advanced Studies (FIAS), D-60438 Frankfurt am Main, Germany
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