1
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Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms. Life Sci Alliance 2024; 7:e202302501. [PMID: 38803235 PMCID: PMC11109482 DOI: 10.26508/lsa.202302501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the developmental transcription factor CCAAT/enhancer-binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This choice between alternative start sites depends on sequence features of the CEBPA transcript, including a regulatory uORF, but the molecular basis is not fully understood. Here, we identify the factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescent reporter coupled with CRISPRi screening. Our screen uncovered a role of the ribosome rescue factor PELOTA (PELO) in promoting the expression of the longer C/EBPα isoform by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin kinase. Our work uncovers further links between ribosome recycling and translation reinitiation that regulate a key transcription factor, with implications for normal hematopoiesis and leukemogenesis.
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Affiliation(s)
- Samantha G Fernandez
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lucas Ferguson
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Nicholas T Ingolia
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
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2
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Ni J, Li S, Lai Y, Wang Z, Wang D, Tan Y, Fan Y, Lu J, Yao YF. Global profiling of ribosomal protein acetylation reveals essentiality of acetylation homeostasis in maintaining ribosome assembly and function. Nucleic Acids Res 2023; 51:10411-10427. [PMID: 37742082 PMCID: PMC10602876 DOI: 10.1093/nar/gkad768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Acetylation is a global post-translational modification that regulates various cellular processes. Bacterial acetylomic studies have revealed extensive acetylation of ribosomal proteins. However, the role of acetylation in regulating ribosome function remains poorly understood. In this study, we systematically profiled ribosomal protein acetylation and identified a total of 289 acetylated lysine residues in 52 ribosomal proteins (r-proteins) from Salmonella Typhimurium. The majority of acetylated lysine residues of r-proteins were found to be regulated by both acetyltransferase Pat and metabolic intermediate acetyl phosphate. Our results show that acetylation plays a critical role in the assembly of the mature 70S ribosome complex by modulating r-proteins binding to rRNA. Moreover, appropriate acetylation is important for the interactions between elongation factors and polysomes, as well as regulating ribosome translation efficiency and fidelity. Dysregulation of acetylation could alter bacterial sensitivity to ribosome-targeting antibiotics. Collectively, our data suggest that the acetylation homeostasis of ribosomes is crucial for their assembly and function. Furthermore, this mechanism may represent a universal response to environmental signals across different cell types.
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Affiliation(s)
- Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shuxian Li
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanan Lai
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zuoqiang Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yongcong Tan
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yongqiang Fan
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Jie Lu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
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3
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Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBP α. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524343. [PMID: 36711859 PMCID: PMC9882168 DOI: 10.1101/2023.01.16.524343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the hematopoietic transcription factor CCAAT-enhancer binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This alternative initiation depends on sequence features of the CEBPA transcript, including a regulatory upstream open reading frame (uORF), but the molecular basis is not fully understood. Here we identify trans-acting factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescence reporter coupled with CRISPRi screening. Our screen uncovered a role for the ribosome rescue factor PELOTA (PELO) in promoting expression of the longer C/EBPα isoform, by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin (mTOR) kinase. Our work provides further mechanistic insights into coupling between ribosome recycling and translation reinitiation in regulation of a key transcription factor, with implications for normal hematopoiesis and leukemiagenesis.
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Affiliation(s)
| | - Lucas Ferguson
- Department of Molecular and Cell Biology, University of California, Berkeley
| | - Nicholas T. Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley
- Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley
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4
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Scarpin MR, Simmons CH, Brunkard JO. Translating across kingdoms: target of rapamycin promotes protein synthesis through conserved and divergent pathways in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7016-7025. [PMID: 35770874 PMCID: PMC9664230 DOI: 10.1093/jxb/erac267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
mRNA translation is the growth rate-limiting step in genome expression. Target of rapamycin (TOR) evolved a central regulatory role in eukaryotes as a signaling hub that monitors nutrient availability to maintain homeostasis and promote growth, largely by increasing the rate of translation initiation and protein synthesis. The dynamic pathways engaged by TOR to regulate translation remain debated even in well-studied yeast and mammalian models, however, despite decades of intense investigation. Recent studies have firmly established that TOR also regulates mRNA translation in plants through conserved mechanisms, such as the TOR-LARP1-5'TOP signaling axis, and through pathways specific to plants. Here, we review recent advances in our understanding of the regulation of mRNA translation in plants by TOR.
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Affiliation(s)
- M Regina Scarpin
- Laboratory of Genetics, University of Wisconsin, Madison, WI, USA
- Department of Plant and Microbial Biology, University of California, Berkeley,CA, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA, USA
| | - Carl H Simmons
- Laboratory of Genetics, University of Wisconsin, Madison, WI, USA
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5
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Dentel B, Angeles-Perez L, Ren C, Jakkamsetti V, Holley AJ, Caballero D, Oh E, Gibson J, Pascual JM, Huber KM, Tu BP, Tsai PT. Increased glycine contributes to synaptic dysfunction and early mortality in Nprl2 seizure model. iScience 2022; 25:104334. [PMID: 35602938 PMCID: PMC9118754 DOI: 10.1016/j.isci.2022.104334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 09/16/2021] [Accepted: 04/26/2022] [Indexed: 10/25/2022] Open
Abstract
Targeted therapies for epilepsies associated with the mTORC1 signaling negative regulator GATOR1 are lacking. NPRL2 is a subunit of the GATOR1 complex and mutations in GATOR1 subunits, including NPRL2, are associated with epilepsy. To delineate the mechanisms underlying NPRL2-related epilepsies, we created a mouse (Mus musculus) model with neocortical loss of Nprl2. Mutant mice have increased mTORC1 signaling and exhibit spontaneous seizures. They also display abnormal synaptic function characterized by increased evoked and spontaneous EPSC and decreased evoked and spontaneous IPSC frequencies, respectively. Proteomic and metabolomics studies of Nprl2 mutants revealed alterations in known epilepsy-implicated proteins and metabolic pathways, including increases in the neurotransmitter, glycine. Furthermore, glycine actions on the NMDA receptor contribute to the electrophysiological and survival phenotypes of these mice. Taken together, in this neuronal Nprl2 model, we delineate underlying molecular, metabolic, and electrophysiological mechanisms contributing to mTORC1-related epilepsy, providing potential therapeutic targets for epilepsy.
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Affiliation(s)
- Brianne Dentel
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | | | - Chongyu Ren
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Vikram Jakkamsetti
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Andrew J. Holley
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Daniel Caballero
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Emily Oh
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Jay Gibson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Juan M. Pascual
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Kimberly M. Huber
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Benjamin P. Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Peter T. Tsai
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75235, USA
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75235, USA
- Departments of Pediatrics and Psychiatry, UT Southwestern Medical Center, Dallas, TX 75235, USA
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6
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Zhang JF, Xu W, Yang YX, Zhang LL, Wang T. Leucine Alters Blood Parameters and Regulates Hepatic Protein Synthesis via mTOR Activation in Intrauterine Growth Restriction Piglets. J Anim Sci 2022; 100:6562689. [PMID: 35366314 PMCID: PMC9053099 DOI: 10.1093/jas/skac109] [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: 03/03/2022] [Accepted: 03/29/2022] [Indexed: 11/12/2022] Open
Abstract
Neonatal piglets often suffer low birth weights and poor growth performance accompanied by the disruption of protein metabolism, when intrauterine growth restriction (IUGR) takes place during pregnancy, leading to a higher mortality and bigger economic loss than expected. Leucine has been proposed to function as a nutritional signal regulating protein synthesis in numerous studies. The aim of this study was to determine the effect of dietary leucine supplementation on the blood parameters and hepatic protein metabolism in IUGR piglets. Weaned piglets were assigned to one of four to treatments in a 2 × 2 factorial arrangement: (1) piglets fed a basal diet with normal birth weight; (2) piglets fed a basal diet plus 0.35% L-leucine with normal birth weight; (3) IUGR piglets fed a basal diet with low birth weight; (4) IUGR piglets fed a basal diet plus 0.35% L-leucine with low birth weight. The results showed that IUGR decreased serum aspartate aminotransferase and alkaline phosphatase activities, increased serum cortisol and prostaglandin E2 levels at 35 days of age (P < 0.05), suggesting the occurrence of liver dysfunction and stress response. Leucine supplementation increased serum alkaline phosphatase activity, and decreased serum cortisol levels at 35 days of age (P < 0.05). IUGR decreased the lysozyme activity and complement 3 level in serum (P < 0.05), which were prevented by dietary leucine supplementation. IUGR piglets showed increased hepatic DNA contents while showing reduced RNA/DNA ratio (P < 0.05). Piglets supplied with leucine had decreased RNA/DNA ratio in the liver (P < 0.05). Leucine supplementation stimulated hepatic protein anabolism through up-regulating protein synthesis related genes expression and activating the phosphorylation of mammalian/mechanistic target of rapamycin (mTOR) (P < 0.05). Moreover, IUGR inhibited the mRNA expression of hepatic protein degradation related genes, indicating a compensatory mechanism for the metabolic response. Dietary leucine supplementation attenuated the suppression of the protein catabolism induced by IUGR in liver. These results demonstrate that dietary leucine supplementation could alter the blood parameters, alleviated the disrupted protein metabolism induced by IUGR via enhanced mTOR phosphorylation to promote protein synthesis in weaned piglets.
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Affiliation(s)
- J F Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - W Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Y X Yang
- Bluestar Adisseo Nanjing Co. Ltd., Nanjing 210000, China
| | - L L Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - T Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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7
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Terrey M, Adamson SI, Chuang JH, Ackerman SL. Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology. eLife 2021; 10:e66904. [PMID: 33899734 PMCID: PMC8075583 DOI: 10.7554/elife.66904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent quality control pathways such as no-go decay (NGD), non-stop decay (NSD), and nonsense-mediated decay (NMD) govern protein synthesis and proteostasis by resolving non-translating ribosomes and preventing the production of potentially toxic peptides derived from faulty and aberrant mRNAs. However, how translation is altered and the in vivo defects that arise in the absence of these pathways are poorly understood. Here, we show that the NGD/NSD factors Pelo and Hbs1l are critical in mice for cerebellar neurogenesis but expendable for survival of these neurons after development. Analysis of mutant mouse embryonic fibroblasts revealed translational pauses, alteration of signaling pathways, and translational reprogramming. Similar effects on signaling pathways, including mTOR activation, the translatome and mouse cerebellar development were observed upon deletion of the NMD factor Upf2. Our data reveal that these quality control pathways that function to mitigate errors at distinct steps in translation can evoke similar cellular responses.
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Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
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8
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Terrey M, Adamson SI, Gibson AL, Deng T, Ishimura R, Chuang JH, Ackerman SL. GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis. eLife 2020; 9:e62731. [PMID: 33186095 PMCID: PMC7665888 DOI: 10.7554/elife.62731] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of a tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here, we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant GTPases function in the same pathway to mitigate ribosome pausing. As observed in Gtpbp2-/- mice (Ishimura et al., 2016), GCN2-mediated activation of the integrated stress response (ISR) was apparent in the Gtpbp1-/- brain. We observed decreased mTORC1 signaling which increased neuronal death, whereas ISR activation was neuroprotective. Our data demonstrate that GTPBP1 functions as an important quality control mechanism during translation elongation and suggest that translational signaling pathways intricately interact to regulate neuronal homeostasis during defective elongation.
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Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Alana L Gibson
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Tianda Deng
- Division of Biological Sciences, Section of Molecular Biology, University of California, San DiegoSan DiegoUnited States
| | - Ryuta Ishimura
- The Jackson Laboratory for Mammalian GeneticsBar HarborUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
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9
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Si J, Shi X, Sun S, Zou B, Li Y, An D, Lin X, Gao Y, Long F, Pang B, Liu X, Liu T, Chi W, Chen L, Dimitrov DS, Sun Y, Du X, Yin W, Gao G, Min J, Wei L, Liao X. Hematopoietic Progenitor Kinase1 (HPK1) Mediates T Cell Dysfunction and Is a Druggable Target for T Cell-Based Immunotherapies. Cancer Cell 2020; 38:551-566.e11. [PMID: 32860752 DOI: 10.1016/j.ccell.2020.08.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 05/17/2020] [Accepted: 07/31/2020] [Indexed: 01/02/2023]
Abstract
Ameliorating T cell exhaustion and enhancing effector function are promising strategies for the improvement of immunotherapies. Here, we show that the HPK1-NFκB-Blimp1 axis mediates T cell dysfunction. High expression of MAP4K1 (which encodes HPK1) correlates with increased T cell exhaustion and with worse patient survival in several cancer types. In MAP4K1KO mice, tumors grow slower than in wild-type mice and infiltrating T cells are less exhausted and more active and proliferative. We further show that genetic depletion, pharmacological inhibition, or proteolysis targeting chimera (PROTAC)-mediated degradation of HPK1 improves the efficacy of CAR-T cell-based immunotherapies in diverse preclinical mouse models of hematological and solid tumors. These strategies are more effective than genetically depleting PD-1 in CAR-T cells. Thus, we demonstrate that HPK1 is a mediator of T cell dysfunction and an attractive druggable target to improve immune therapy responses.
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Affiliation(s)
- Jingwen Si
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China; Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Xiangjun Shi
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China
| | - Shuhao Sun
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060 Guangzhou, China
| | - Yaopeng Li
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China
| | - Dongjie An
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China
| | - Xingyu Lin
- Zhuhai Yufan Biotechnologies Co., Ltd, Zhuhai, 519000 Guangdong, China
| | - Yan Gao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China; Department of Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, 100026 Beijing, China
| | - Fei Long
- Xi'an Yufan Biotechnologies Co., Ltd, Xi'an, 710032 Shaanxi, China
| | - Bo Pang
- Department of Clinical Laboratory, Guang'an Men Hospital, China Academy of Chinese Medical Sciences, 100053 Beijing, China
| | - Xing Liu
- Department of Anesthesiology, Third Xiangya Hospital, Central South University, Changsha, 410013 Hunan, China
| | - Tian Liu
- Department of Plastic Surgery, General Hospital of Southern Theater Command, PLA, Guangdong, 510010 Guangzhou, China
| | - Wenna Chi
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China
| | - Ligong Chen
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, University of Pittsburgh, Pittsburgh, PA 15216, USA
| | - Yan Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Science of CAAS, Lanzhou, 730050 Gansu, China
| | - Xinru Du
- Department of Orthopaedics, Beijing Chao-Yang Hospital, Capita Medical University, 100020 Beijing, China
| | - Wen Yin
- Department of Transfusion Medicine, Xijing Hospital, Air Force Military Medical University, Xi'an, 710032 Shaanxi, China
| | - Guangxun Gao
- Department of Hematology, Xijing Hospital, Air Force Military Medical University, Xi'an, 710032 Shaanxi, China
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060 Guangzhou, China.
| | - Xuebin Liao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China.
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10
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Xu W, Comhair SAA, Chen R, Hu B, Hou Y, Zhou Y, Mavrakis LA, Janocha AJ, Li L, Zhang D, Willard BB, Asosingh K, Cheng F, Erzurum SC. Integrative proteomics and phosphoproteomics in pulmonary arterial hypertension. Sci Rep 2019; 9:18623. [PMID: 31819116 PMCID: PMC6901481 DOI: 10.1038/s41598-019-55053-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023] Open
Abstract
Pulmonary arterial endothelial cells (PAEC) are mechanistically linked to origins of pulmonary arterial hypertension (PAH). Here, global proteomics and phosphoproteomics of PAEC from PAH (n = 4) and healthy lungs (n = 5) were performed using LC-MS/MS to confirm known pathways and identify new areas of investigation in PAH. Among PAH and control cells, 170 proteins and 240 phosphopeptides were differentially expressed; of these, 45 proteins and 18 phosphopeptides were located in the mitochondria. Pathologic pathways were identified with integrative bioinformatics and human protein-protein interactome network analyses, then confirmed with targeted proteomics in PAH PAEC and non-targeted metabolomics and targeted high-performance liquid chromatography of metabolites in plasma from PAH patients (n = 30) and healthy controls (n = 12). Dysregulated pathways in PAH include accelerated one carbon metabolism, abnormal tricarboxylic acid (TCA) cycle flux and glutamate metabolism, dysfunctional arginine and nitric oxide pathways, and increased oxidative stress. Functional studies in cells confirmed abnormalities in glucose metabolism, mitochondrial oxygen consumption, and production of reactive oxygen species in PAH. Altogether, the findings indicate that PAH is typified by changes in metabolic pathways that are primarily found in mitochondria.
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Affiliation(s)
- Weiling Xu
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America.
| | - Suzy A A Comhair
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ruoying Chen
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Bo Hu
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yuan Hou
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yadi Zhou
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Lori A Mavrakis
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Allison J Janocha
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ling Li
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Dongmei Zhang
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Belinda B Willard
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Kewal Asosingh
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Feixiong Cheng
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Serpil C Erzurum
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America. .,Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, United States of America.
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11
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Brandt C, Nolte H, Henschke S, Engström Ruud L, Awazawa M, Morgan DA, Gabel P, Sprenger HG, Hess ME, Günther S, Langer T, Rahmouni K, Fenselau H, Krüger M, Brüning JC. Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation. Cell 2019; 175:1321-1335.e20. [PMID: 30445039 DOI: 10.1016/j.cell.2018.10.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/10/2018] [Accepted: 10/02/2018] [Indexed: 12/17/2022]
Abstract
Adaptation of liver to the postprandial state requires coordinated regulation of protein synthesis and folding aligned with changes in lipid metabolism. Here we demonstrate that sensory food perception is sufficient to elicit early activation of hepatic mTOR signaling, Xbp1 splicing, increased expression of ER-stress genes, and phosphatidylcholine synthesis, which translate into a rapid morphological ER remodeling. These responses overlap with those activated during refeeding, where they are maintained and constantly increased upon nutrient supply. Sensory food perception activates POMC neurons in the hypothalamus, optogenetic activation of POMC neurons activates hepatic mTOR signaling and Xbp1 splicing, whereas lack of MC4R expression attenuates these responses to sensory food perception. Chemogenetic POMC-neuron activation promotes sympathetic nerve activity (SNA) subserving the liver, and norepinephrine evokes the same responses in hepatocytes in vitro and in liver in vivo as observed upon sensory food perception. Collectively, our experiments unravel that sensory food perception coordinately primes postprandial liver ER adaption through a melanocortin-SNA-mTOR-Xbp1s axis. VIDEO ABSTRACT.
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Affiliation(s)
- Claus Brandt
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Hendrik Nolte
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, Cologne 50931, Germany
| | - Sinika Henschke
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Linda Engström Ruud
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Motoharu Awazawa
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Donald A Morgan
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 3181 MERF, 375 Newton Rd., Iowa City, IA 52242, USA
| | - Paula Gabel
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | | | - Martin E Hess
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Thomas Langer
- Institute for Genetics, University of Cologne, Cologne 50931, Germany; Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Kamal Rahmouni
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 3181 MERF, 375 Newton Rd., Iowa City, IA 52242, USA
| | - Henning Fenselau
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
| | - Marcus Krüger
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, Cologne 50931, Germany
| | - Jens C Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; National Center for Diabetes Research (DZD), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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12
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Hoque A, Williamson NA, Ameen SS, Ciccotosto GD, Hossain MI, Oakhill JS, Ng DCH, Ang CS, Cheng HC. Quantitative proteomic analyses of dynamic signalling events in cortical neurons undergoing excitotoxic cell death. Cell Death Dis 2019; 10:213. [PMID: 30824683 PMCID: PMC6397184 DOI: 10.1038/s41419-019-1445-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/20/2019] [Accepted: 02/01/2019] [Indexed: 12/23/2022]
Abstract
Excitotoxicity, caused by overstimulation or dysregulation of ionotropic glutamate receptors (iGluRs), is a pathological process directing neuronal death in many neurological disorders. The aberrantly stimulated iGluRs direct massive influx of calcium ions into the affected neurons, leading to changes in expression and phosphorylation of specific proteins to modulate their functions and direct their participation in the signalling pathways that induce excitotoxic neuronal death. To define these pathways, we used quantitative proteomic approaches to identify these neuronal proteins (referred to as the changed proteins) and determine how their expression and/or phosphorylation dynamically changed in association with excitotoxic cell death. Our data, available in ProteomeXchange with identifier PXD008353, identified over 100 changed proteins exhibiting significant alterations in abundance and/or phosphorylation levels at different time points (5–240 min) in neurons after glutamate overstimulation. Bioinformatic analyses predicted that many of them are components of signalling networks directing defective neuronal morphology and functions. Among them, the well-known neuronal survival regulators including mitogen-activated protein kinases Erk1/2, glycogen synthase kinase 3 (GSK3) and microtubule-associated protein (Tau), were selected for validation by biochemical approaches, which confirmed the findings of the proteomic analysis. Bioinformatic analysis predicted Protein Kinase B (Akt), c-Jun kinase (JNK), cyclin-dependent protein kinase 5 (Cdk5), MAP kinase kinase (MEK), Casein kinase 2 (CK2), Rho-activated protein kinase (Rock) and Serum/glucocorticoid-regulated kinase 1 (SGK1) as the potential upstream kinases phosphorylating some of the changed proteins. Further biochemical investigation confirmed the predictions of sustained changes of the activation states of neuronal Akt and CK2 in excitotoxicity. Thus, future investigation to define the signalling pathways directing the dynamic alterations in abundance and phosphorylation of the identified changed neuronal proteins will help elucidate the molecular mechanism of neuronal death in excitotoxicity.
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Affiliation(s)
- Ashfaqul Hoque
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Metabolic Signalling Laboratory, St. Vincent's Institute for Medical Research, University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - S Sadia Ameen
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Giuseppe D Ciccotosto
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - M Iqbal Hossain
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jonathan S Oakhill
- Metabolic Signalling Laboratory, St. Vincent's Institute for Medical Research, University of Melbourne, Fitzroy, VIC, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, 3000, Australia
| | - Dominic C H Ng
- School of Biomedical Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Cell Signalling Research Laboratories, University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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