1
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Howes JM, Harper MT. Application of the Cellular Thermal Shift Assay (CETSA) to validate drug target engagement in platelets. Platelets 2024; 35:2354833. [PMID: 38767506 DOI: 10.1080/09537104.2024.2354833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
Small molecule drugs play a major role in the study of human platelets. Effective action of a drug requires it to bind to one or more targets within the platelet (target engagement). However, although in vitro assays with isolated proteins can be used to determine drug affinity to these targets, additional factors affect target engagement and its consequences in an intact platelet, including plasma membrane permeability, intracellular metabolism or compartmentalization, and level of target expression. Mechanistic interpretation of the effect of drugs on platelet activity requires comprehensive investigation of drug binding in the proper cellular context, i.e. in intact platelets. The Cellular Thermal Shift Assay (CETSA) is a valuable method to investigate target engagement within complex cellular environments. The assay is based on the principle that drug binding to a target protein increases that protein's thermal stability. In this technical report, we describe the application of CETSA to platelets. We highlight CETSA as a quick and informative technique for confirming the direct binding of drugs to platelet protein targets, providing a platform for understanding the mechanism of action of drugs in platelets, and which will be a valuable tool for investigating platelet signaling and function.
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Affiliation(s)
| | - Matthew T Harper
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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2
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Davis CK, Bathula S, Jeong S, Arruri V, Choi J, Subramanian S, Ostrom CM, Vemuganti R. An antioxidant and anti-ER stress combination therapy elevates phosphorylation of α-Syn at serine 129 and alleviates post-TBI PD-like pathology in a sex-specific manner in mice. Exp Neurol 2024; 377:114795. [PMID: 38657855 DOI: 10.1016/j.expneurol.2024.114795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/13/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Clinical studies have shown that traumatic brain injury (TBI) increases the onset of Parkinson's disease (PD) in later life by >50%. Oxidative stress, endoplasmic reticulum (ER) stress, and inflammation are the major drivers of both TBI and PD pathologies. We presently evaluated if curtailing oxidative stress and ER stress concomitantly using a combination of apocynin and tert-butylhydroquinone and salubrinal during the acute stage after TBI in mice reduces the severity of late-onset PD-like pathology. The effect of multiple low doses of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) on post-TBI neurodegeneration was also evaluated. The combo therapy elevated the level of phosphorylation at serine 129 (pS129) of α-Syn in the pericontusional cortex of male mice at 72 h post-TBI. Motor and cognitive deficits induced by TBI lasted at least 3 months and the combo therapy curtailed these deficits in both sexes. At 3 months post-TBI, male mice given combo therapy exhibited significantly lesser α-Syn aggregates in the SN and higher TH+ cells in the SNpc, compared to vehicle control. However, the aggregate number was not significantly different between groups of female mice. Moreover, TBI-induced loss of TH+ cells was negligible in female mice irrespective of treatment. The MPTP treatment aggravated PD-like pathology in male mice but had a negligible effect on the loss of TH+ cells in female mice. Thus, the present study indicates that mitigation of TBI-induced oxidative stress and ER stress at the acute stage could potentially reduce the risk of post-TBI PD-like pathology at least in male mice, plausibly by elevating pS129-α-Syn level.
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Affiliation(s)
- Charles K Davis
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | | | - Soomin Jeong
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - Vijay Arruri
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Jeongwoo Choi
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Shruti Subramanian
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Carlie M Ostrom
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Neuroscience Training Program, University of Wisconsin, Madison, WI, USA; William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.
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3
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Bahram Sangani N, Koetsier J, Mélius J, Kutmon M, Ehrhart F, Evelo CT, Curfs LMG, Reutelingsperger CP, Eijssen LMT. A novel insight into neurological disorders through HDAC6 protein-protein interactions. Sci Rep 2024; 14:14666. [PMID: 38918466 PMCID: PMC11199618 DOI: 10.1038/s41598-024-65094-1] [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: 02/07/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Due to its involvement in physiological and pathological processes, histone deacetylase 6 (HDAC6) is considered a promising pharmaceutical target for several neurological manifestations. However, the exact regulatory role of HDAC6 in the central nervous system (CNS) is still not fully understood. Hence, using a semi-automated literature screening technique, we systematically collected HDAC6-protein interactions that are experimentally validated and reported in the CNS. The resulting HDAC6 network encompassed 115 HDAC6-protein interactions divided over five subnetworks: (de)acetylation, phosphorylation, protein complexes, regulatory, and aggresome-autophagy subnetworks. In addition, 132 indirect interactions identified through HDAC6 inhibition were collected and categorized. Finally, to display the application of our HDAC6 network, we mapped transcriptomics data of Alzheimer's disease, Parkinson's disease, and Amyotrophic Lateral Sclerosis on the network and highlighted that in the case of Alzheimer's disease, alterations predominantly affect the HDAC6 phosphorylation subnetwork, whereas differential expression within the deacetylation subnetwork is observed across all three neurological disorders. In conclusion, the HDAC6 network created in the present study is a novel and valuable resource for the understanding of the HDAC6 regulatory mechanisms, thereby providing a framework for the integration and interpretation of omics data from neurological disorders and pharmacodynamic assessments.
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Affiliation(s)
- Nasim Bahram Sangani
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD, Maastricht, The Netherlands.
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands.
| | - Jarno Koetsier
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands
| | - Jonathan Mélius
- DataHub, Maastricht University & Maastricht UMC+, P. Debyelaan 15, 6229 HX, Maastricht, The Netherlands
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, Research Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, Research Institute for Mental Health and Neuroscience (MHeNs), Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Chris T Evelo
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of Bioinformatics - BiGCaT, Research Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Leopold M G Curfs
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands
| | - Chris P Reutelingsperger
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands
| | - Lars M T Eijssen
- Department of Bioinformatics - BiGCaT, Research Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, Research Institute for Mental Health and Neuroscience (MHeNs), Maastricht University, 6200 MD, Maastricht, The Netherlands
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4
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Wang S, Li H, Liu X, Yin T, Li T, Zheng M, Liu M, Meng X, Zhou J, Wang Y, Chen Y. VHL suppresses UBE3B-mediated breast tumor growth and metastasis. Cell Death Dis 2024; 15:446. [PMID: 38914543 PMCID: PMC11196597 DOI: 10.1038/s41419-024-06844-x] [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: 01/07/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/26/2024]
Abstract
Protein homeostasis is predominantly governed through post-translational modification (PTM). UBE3B, identified as an oncoprotein, exhibits elevated protein levels in breast cancer. However, the impact of PTM on UBE3B remains unexplored. In this study, we show that VHL is a bona fide E3 ligase for UBE3B. Mechanistically, VHL directly binds to UBE3B, facilitating its lysine 48 (K48)-linked polyubiquitination at K286 and K427 in a prolyl hydroxylase (PHD)-independent manner. Consequently, this promotes the proteasomal degradation of UBE3B. The K286/427R mutation of UBE3B dramatically abolishes the inhibitory effect of VHL on breast tumor growth and lung metastasis. Additionally, the protein levels of UBE3B and VHL exhibit a negative correlation in breast cancer tissues. These findings delineate an important layer of UBE3B regulation by VHL.
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Affiliation(s)
- Shuo Wang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Huiyan Li
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiong Liu
- School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Tingting Yin
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Tingru Li
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Miaomiao Zheng
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Min Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiaoqian Meng
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Yijie Wang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China.
| | - Yan Chen
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China.
- School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, China.
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5
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Liang F, Jin J, Li Q, Duan J, Jiang A, Chen X, Geng H, Wu K, Yu F, Zhao X, Zhou Y, Hu D, Chen L. DOT1L/H3K79me2 represses HIV-1 reactivation via recruiting DCAF1. Cell Rep 2024; 43:114368. [PMID: 38905100 DOI: 10.1016/j.celrep.2024.114368] [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: 01/03/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/23/2024] Open
Abstract
DOT1L mediates the methylation of histone H3 at lysine 79 and, in turn, the transcriptional activation or repression in a context-dependent manner, yet the regulatory mechanisms and functions of DOT1L/H3K79me remain to be fully explored. Following peptide affinity purification and proteomic analysis, we identified that DCAF1-a component of the E3 ligase complex involved in HIV regulation-is associated with H3K79me2 and DOT1L. Interestingly, blocking the expression or catalytic activity of DOT1L or repressing the expression of DCAF1 significantly enhances the tumor necrosis factor alpha (TNF-α)/nuclear factor κB (NF-κB)-induced reactivation of the latent HIV-1 genome. Mechanistically, upon TNF-α/NF-κB activation, DCAF1 is recruited to the HIV-1 long terminal repeat (LTR) by DOT1L and H3K79me2. Recruited DCAF1 subsequently induces the ubiquitination of NF-κB and restricts its accumulation at the HIV-1 LTR. Altogether, our findings reveal a feedback modulation of HIV reactivation by DOT1L-mediated histone modification regulation and highlight the potential of targeting the DOT1L/DCAF1 axis as a therapeutic strategy for HIV treatment.
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Affiliation(s)
- Fenfei Liang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiaxing Jin
- State Key Laboratory of Experimental Hematology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qiming Li
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiangkai Duan
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ao Jiang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoqing Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huichao Geng
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Wu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fei Yu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaolu Zhao
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Zhou
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Deqing Hu
- State Key Laboratory of Experimental Hematology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Cancer Institute and Hospital of Tianjin Medical University, Tianjin 300060, China.
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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6
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Wang X, Lv X, Ma J, Xu G. UFMylation: An integral post-translational modification for the regulation of proteostasis and cellular functions. Pharmacol Ther 2024; 260:108680. [PMID: 38878974 DOI: 10.1016/j.pharmthera.2024.108680] [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: 04/07/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is covalently conjugated to protein substrates via a cascade of enzymatic reactions, a process known as UFMylation. UFMylation orchestrates an array of vital biological functions, including maintaining endoplasmic reticulum (ER) homeostasis, facilitating protein biogenesis, promoting cellular differentiation, regulating DNA damage response, and participating in cancer-associated signaling pathways. UFMylation has rapidly evolved into one of the forefront research areas within the last few years, yet much remains to be uncovered. In this review, first, UFMylation and its cellular functions associated with diseases are briefly introduced. Then, we summarize the proteomic approaches for identifying UFMylation substrates and explore the impact of UFMylation on gene transcription, protein translation, and maintenance of ER homeostasis. Next, we highlight the intricate regulation between UFMylation and two protein degradation pathways, the ubiquitin-proteasome system and the autophagy-lysosome pathway, and explore the potential of UFMylation system as a drug target. Finally, we discuss emerging perspectives in the UFMylation field. This review may provide valuable insights for drug discovery targeting the UFMylation system.
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Affiliation(s)
- Xiaohui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Xiaowei Lv
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Jingjing Ma
- Department of Pharmacy, The Fourth Affiliated Hospital of Soochow University, Suzhou Dushu Lake Hospital, Medical Center of Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China; Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China.
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7
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Mou J, Ning XL, Wang XY, Hou SY, Meng FB, Zhou C, Wu JW, Li C, Jia T, Wu X, Wu Y, Chen Y, Li GB. X-ray Structure-Guided Discovery of a Potent Benzimidazole Glutaminyl Cyclase Inhibitor That Shows Activity in a Parkinson's Disease Mouse Model. J Med Chem 2024; 67:8730-8756. [PMID: 38817193 DOI: 10.1021/acs.jmedchem.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The secretory glutaminyl cyclase (sQC) and Golgi-resident glutaminyl cyclase (gQC) are responsible for N-terminal protein pyroglutamation and associated with various human diseases. Although several sQC/gQC inhibitors have been reported, only one inhibitor, PQ912, is currently undergoing clinic trials for the treatment of Alzheimer's disease. We report an X-ray crystal structure of sQC complexed with PQ912, revealing that the benzimidazole makes "anchor" interactions with the active site zinc ion and catalytic triad. Structure-guided design and optimization led to a series of new benzimidazole derivatives exhibiting nanomolar inhibition for both sQC and gQC. In a MPTP-induced Parkinson's disease (PD) mouse model, BI-43 manifested efficacy in mitigating locomotor deficits through reversing dopaminergic neuronal loss, reducing microglia, and decreasing levels of the sQC/gQC substrates, α-synuclein, and CCL2. This study not only offers structural basis and new leads for drug discovery targeting sQC/gQC but also provides evidence supporting sQC/gQC as potential targets for PD treatment.
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Affiliation(s)
- Jun Mou
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xiang-Li Ning
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xin-Yue Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shu-Yan Hou
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Fan-Bo Meng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Cong Zhou
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jing-Wei Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Chunyan Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Tao Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xiaoai Wu
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yongping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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8
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Williams ET, Schiefelbein K, Schuster M, Ahmed IMM, De Vries M, Beveridge R, Zerbe O, Hartrampf N. Rapid flow-based synthesis of post-translationally modified peptides and proteins: a case study on MYC's transactivation domain. Chem Sci 2024; 15:8756-8765. [PMID: 38873065 PMCID: PMC11168107 DOI: 10.1039/d4sc00481g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 05/04/2024] [Indexed: 06/15/2024] Open
Abstract
Protein-protein interactions of c-Myc (MYC) are often regulated by post-translational modifications (PTMs), such as phosphorylation, and crosstalk thereof. Studying these interactions requires proteins with unique PTM patterns, which are challenging to obtain by recombinant methods. Standard peptide synthesis and native chemical ligation can produce such modified proteins, but are time-consuming and therefore typically limited to the study of individual PTMs. Herein, we report the development of flow-based methods for the rapid synthesis of phosphorylated MYC sequences (up to 84 AA), and demonstrate the versatility of this approach for the incorporation of other PTMs (N ε-methylation, sulfation, acetylation, glycosylation) and combinations thereof. Peptides containing up to seven PTMs and phosphorylation at up to five sites were successfully prepared and isolated in high yield and purity. We further produced ten PTM-decorated analogues of the MYC Transactivation Domain (TAD) to screen for binding to the tumor suppressor protein, Bin1, using heteronuclear NMR and native mass spectrometry. We determined the effects of phosphorylation and glycosylation on the strength of the MYC:Bin1 interaction, and reveal an influence of MYC sequence length on binding. Our platform for the rapid synthesis of MYC sequences up to 84 AA with distinct PTM patterns thus enables the systematic study of PTM function at a molecular level, and offers a convenient way for expedited screening of constructs.
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Affiliation(s)
- Elyse T Williams
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kevin Schiefelbein
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ikhlas M M Ahmed
- Department for Pure and Applied Chemistry, University of Strathclyde 295 Cathedral St Glasgow G1 1XL UK
| | - Marije De Vries
- Department for Pure and Applied Chemistry, University of Strathclyde 295 Cathedral St Glasgow G1 1XL UK
| | - Rebecca Beveridge
- Department for Pure and Applied Chemistry, University of Strathclyde 295 Cathedral St Glasgow G1 1XL UK
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nina Hartrampf
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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9
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Gutierrez Reyes CD, Alejo-Jacuinde G, Perez Sanchez B, Chavez Reyes J, Onigbinde S, Mogut D, Hernández-Jasso I, Calderón-Vallejo D, Quintanar JL, Mechref Y. Multi Omics Applications in Biological Systems. Curr Issues Mol Biol 2024; 46:5777-5793. [PMID: 38921016 PMCID: PMC11202207 DOI: 10.3390/cimb46060345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Traditional methodologies often fall short in addressing the complexity of biological systems. In this regard, system biology omics have brought invaluable tools for conducting comprehensive analysis. Current sequencing capabilities have revolutionized genetics and genomics studies, as well as the characterization of transcriptional profiling and dynamics of several species and sample types. Biological systems experience complex biochemical processes involving thousands of molecules. These processes occur at different levels that can be studied using mass spectrometry-based (MS-based) analysis, enabling high-throughput proteomics, glycoproteomics, glycomics, metabolomics, and lipidomics analysis. Here, we present the most up-to-date techniques utilized in the completion of omics analysis. Additionally, we include some interesting examples of the applicability of multi omics to a variety of biological systems.
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Affiliation(s)
| | - Gerardo Alejo-Jacuinde
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX 79409, USA; (G.A.-J.); (B.P.S.)
| | - Benjamin Perez Sanchez
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX 79409, USA; (G.A.-J.); (B.P.S.)
| | - Jesus Chavez Reyes
- Center of Basic Sciences, Department of Physiology and Pharmacology, Autonomous University of Aguascalientes, Aguascalientes 20392, Mexico; (J.C.R.); (I.H.-J.); (D.C.-V.); (J.L.Q.)
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Damir Mogut
- Department of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Irma Hernández-Jasso
- Center of Basic Sciences, Department of Physiology and Pharmacology, Autonomous University of Aguascalientes, Aguascalientes 20392, Mexico; (J.C.R.); (I.H.-J.); (D.C.-V.); (J.L.Q.)
| | - Denisse Calderón-Vallejo
- Center of Basic Sciences, Department of Physiology and Pharmacology, Autonomous University of Aguascalientes, Aguascalientes 20392, Mexico; (J.C.R.); (I.H.-J.); (D.C.-V.); (J.L.Q.)
| | - J. Luis Quintanar
- Center of Basic Sciences, Department of Physiology and Pharmacology, Autonomous University of Aguascalientes, Aguascalientes 20392, Mexico; (J.C.R.); (I.H.-J.); (D.C.-V.); (J.L.Q.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
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10
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Granato DC, Carnielli CM, Trino LD, Busso-Lopes AF, Câmara GA, Normando AGC, Filho HVR, Domingues R, Yokoo S, Pauletti BA, Patroni FM, Santos-Silva AR, Lopes MA, Brandão TB, Prado-Ribeiro AC, Lopes-de Oliveira PS, Telles GP, Paes Leme AF. Mapping Conformational Changes in the Saliva Proteome Potentially Associated with Oral Cancer Aggressiveness. J Proteome Res 2024; 23:2148-2159. [PMID: 38785273 PMCID: PMC11166140 DOI: 10.1021/acs.jproteome.4c00093] [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: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
Diverse proteomics-based strategies have been applied to saliva to quantitatively identify diagnostic and prognostic targets for oral cancer. Considering that these targets may be regulated by events that do not imply variation in protein abundance levels, we hypothesized that changes in protein conformation can be associated with diagnosis and prognosis, revealing biological processes and novel targets of clinical relevance. For this, we employed limited proteolysis-mass spectrometry in saliva samples to explore structural alterations, comparing the proteome of healthy control and oral squamous cell carcinoma (OSCC) patients with and without lymph node metastasis. Thirty-six proteins with potential structural rearrangements were associated with clinical patient features including transketolase and its interacting partners. Moreover, N-glycosylated peptides contribute to structural rearrangements of potential diagnostic and prognostic markers. Altogether, this approach utilizes saliva proteins to search for targets for diagnosing and prognosing oral cancer and can guide the discovery of potential regulated sites beyond protein-level abundance.
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Affiliation(s)
- Daniela C. Granato
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Carolina M. Carnielli
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Luciana D. Trino
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Ariane F. Busso-Lopes
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Guilherme A. Câmara
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Ana Gabriela C. Normando
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Helder V. R. Filho
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Romênia
R. Domingues
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Sami Yokoo
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Bianca A. Pauletti
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Fabio M. Patroni
- Centro
de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-875, Brazil
| | - Alan R. Santos-Silva
- Departamento
de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP 13414-903, Brazil
| | - Márcio A. Lopes
- Departamento
de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP 13414-903, Brazil
| | - Thaís Bianca Brandão
- Instituto
do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo 01246-000, Brazil
| | | | - Paulo. S. Lopes-de Oliveira
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Guilherme P. Telles
- Instituto
de Computação, Universidade
Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-852, Brazil
| | - Adriana F. Paes Leme
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
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11
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Liu S, Dai W, Jin B, Jiang F, Huang H, Hou W, Lan J, Jin Y, Peng W, Pan J. Effects of super-enhancers in cancer metastasis: mechanisms and therapeutic targets. Mol Cancer 2024; 23:122. [PMID: 38844984 PMCID: PMC11157854 DOI: 10.1186/s12943-024-02033-8] [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: 04/19/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Metastasis remains the principal cause of cancer-related lethality despite advancements in cancer treatment. Dysfunctional epigenetic alterations are crucial in the metastatic cascade. Among these, super-enhancers (SEs), emerging as new epigenetic regulators, consist of large clusters of regulatory elements that drive the high-level expression of genes essential for the oncogenic process, upon which cancer cells develop a profound dependency. These SE-driven oncogenes play an important role in regulating various facets of metastasis, including the promotion of tumor proliferation in primary and distal metastatic organs, facilitating cellular migration and invasion into the vasculature, triggering epithelial-mesenchymal transition, enhancing cancer stem cell-like properties, circumventing immune detection, and adapting to the heterogeneity of metastatic niches. This heavy reliance on SE-mediated transcription delineates a vulnerable target for therapeutic intervention in cancer cells. In this article, we review current insights into the characteristics, identification methodologies, formation, and activation mechanisms of SEs. We also elaborate the oncogenic roles and regulatory functions of SEs in the context of cancer metastasis. Ultimately, we discuss the potential of SEs as novel therapeutic targets and their implications in clinical oncology, offering insights into future directions for innovative cancer treatment strategies.
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Affiliation(s)
- Shenglan Liu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Wei Dai
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Bei Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Feng Jiang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Hao Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Wen Hou
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Jinxia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou, 341000, China
| | - Yanli Jin
- College of Pharmacy, Jinan University Institute of Tumor Pharmacology, Jinan University, Guangzhou, 510632, China
| | - Weijie Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China.
| | - Jingxuan Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
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12
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Zhang N, Gao S, Peng H, Wu J, Li H, Gibson C, Wu S, Zhu J, Zheng Q. Chemical Proteomic Profiling of Protein Dopaminylation in Colorectal Cancer Cells. J Proteome Res 2024. [PMID: 38838187 DOI: 10.1021/acs.jproteome.4c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid of H3 (i.e., glutamine) and dopamine. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of its regulator, transglutaminase 2 (TGM2), in colon cancer cells. Due to the enzyme promiscuity of TGM2, nonhistone proteins have also been identified as dopaminylation targets; however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of dopaminylation sites were identified and attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that targeting these pathways may become a promising anticancer strategy.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Shuaixin Gao
- Human Nutrition Program, Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Haidong Peng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jinghua Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Huapeng Li
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Connor Gibson
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sophia Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Columbus Academy, Gahanna, Ohio 43230, United States
| | - Jiangjiang Zhu
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Human Nutrition Program, Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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13
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Ando K, Küçükali F, Doeraene E, Nagaraj S, Antonelli EM, Thazin Htut M, Yilmaz Z, Kosa AC, Lopez-Guitierrez L, Quintanilla-Sánchez C, Aydin E, Ramos AR, Mansour S, Turbant S, Schurmans S, Sleegers K, Erneux C, Brion JP, Leroy K. Alteration of gene expression and protein solubility of the PI 5-phosphatase SHIP2 are correlated with Alzheimer's disease pathology progression. Acta Neuropathol 2024; 147:94. [PMID: 38833073 PMCID: PMC11150309 DOI: 10.1007/s00401-024-02745-7] [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: 04/15/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
A recent large genome-wide association study has identified EGFR (encoding the epidermal growth factor EGFR) as a new genetic risk factor for late-onset AD. SHIP2, encoded by INPPL1, is taking part in the signalling and interactome of several growth factor receptors, such as the EGFR. While INPPL1 has been identified as one of the most significant genes whose RNA expression correlates with cognitive decline, the potential alteration of SHIP2 expression and localization during the progression of AD remains largely unknown. Here we report that gene expression of both EGFR and INPPL1 was upregulated in AD brains. SHIP2 immunoreactivity was predominantly detected in plaque-associated astrocytes and dystrophic neurites and its increase was correlated with amyloid load in the brain of human AD and of 5xFAD transgenic mouse model of AD. While mRNA of INPPL1 was increased in AD, SHIP2 protein undergoes a significant solubility change being depleted from the soluble fraction of AD brain homogenates and co-enriched with EGFR in the insoluble fraction. Using FRET-based flow cytometry biosensor assay for tau-tau interaction, overexpression of SHIP2 significantly increased the FRET signal while siRNA-mediated downexpression of SHIP2 significantly decreased FRET signal. Genetic association analyses suggest that some variants in INPPL1 locus are associated with the level of CSF pTau. Our data support the hypothesis that SHIP2 is an intermediate key player of EGFR and AD pathology linking amyloid and tau pathologies in human AD.
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Affiliation(s)
- Kunie Ando
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium.
| | - Fahri Küçükali
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Emilie Doeraene
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Siranjeevi Nagaraj
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Eugenia Maria Antonelli
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - May Thazin Htut
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Zehra Yilmaz
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute (UNI), 808 Route de Lennik, 1070, Brussels, Belgium
| | - Andreea-Claudia Kosa
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Lidia Lopez-Guitierrez
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Carolina Quintanilla-Sánchez
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Emmanuel Aydin
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Ana Raquel Ramos
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, 808 Route de Lennik, 1070, Brussels, Belgium
| | - Salwa Mansour
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute (UNI), 808 Route de Lennik, 1070, Brussels, Belgium
| | - Sabrina Turbant
- Biobanque Neuro-CEB, Hôpital de la Pitié-Salpétrière, Paris, France
- Plateforme de Ressources Biologiques (PRB), Hôpital de La Pitié-Salpêtrière, AP-HP, Paris, France
| | - Stéphane Schurmans
- Laboratory of Functional Genetics, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christophe Erneux
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, 808 Route de Lennik, 1070, Brussels, Belgium
| | - Jean-Pierre Brion
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium
| | - Karelle Leroy
- Alzheimer and Other Tauopathies Research Group, ULB Neuroscience Institute (UNI), ULB Center for Diabetes Research (UCDR), Faculty of Medicine, Université Libre de Bruxelles, 808 Route de Lennik, Bldg GE, 1070, Brussels, Belgium.
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14
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Amar D, Gay NR, Jimenez-Morales D, Jean Beltran PM, Ramaker ME, Raja AN, Zhao B, Sun Y, Marwaha S, Gaul DA, Hershman SG, Ferrasse A, Xia A, Lanza I, Fernández FM, Montgomery SB, Hevener AL, Ashley EA, Walsh MJ, Sparks LM, Burant CF, Rector RS, Thyfault J, Wheeler MT, Goodpaster BH, Coen PM, Schenk S, Bodine SC, Lindholm ME. The mitochondrial multi-omic response to exercise training across rat tissues. Cell Metab 2024; 36:1411-1429.e10. [PMID: 38701776 PMCID: PMC11152996 DOI: 10.1016/j.cmet.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/27/2023] [Accepted: 12/15/2023] [Indexed: 05/05/2024]
Abstract
Mitochondria have diverse functions critical to whole-body metabolic homeostasis. Endurance training alters mitochondrial activity, but systematic characterization of these adaptations is lacking. Here, the Molecular Transducers of Physical Activity Consortium mapped the temporal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats trained for 1, 2, 4, or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart, and skeletal muscle. The colon showed non-linear response dynamics, whereas mitochondrial pathways were downregulated in brown adipose and adrenal tissues. Protein acetylation increased in the liver, with a shift in lipid metabolism, whereas oxidative proteins increased in striated muscles. Exercise-upregulated networks were downregulated in human diabetes and cirrhosis. Knockdown of the central network protein 17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) elevated oxygen consumption, indicative of metabolic stress. We provide a multi-omic, multi-tissue, temporal atlas of the mitochondrial response to exercise training and identify candidates linked to mitochondrial dysfunction.
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Affiliation(s)
- David Amar
- Stanford University, Stanford, CA, USA; Insitro, San Francisco, CA, USA
| | | | | | | | | | | | | | - Yifei Sun
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - David A Gaul
- Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - Ashley Xia
- National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | - Martin J Walsh
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Lauren M Sparks
- Translational Research Institute AdventHealth, Orlando, FL, USA
| | | | | | - John Thyfault
- University of Kansas Medical Center, Kansas City, KS, USA
| | | | | | - Paul M Coen
- Translational Research Institute AdventHealth, Orlando, FL, USA
| | - Simon Schenk
- University of California, San Diego, La Jolla, CA, USA
| | - Sue C Bodine
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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15
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Lin H, Han Y, Sang Y, Wu Y, Tian M, Chen X, Lin X, Lin X. OTUD1 enhances gastric cancer aggressiveness by deubiquitinating EBV-encoded protein BALF1 to stabilize the apoptosis inhibitor Bcl-2. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167132. [PMID: 38565386 DOI: 10.1016/j.bbadis.2024.167132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
The Epstein-Barr virus (EBV) is implicated in several cancers, including EBV-associated gastric cancer (EBVaGC). This study focuses on EBV-encoded BALF1 (BamH1 A fragment leftward reading frame 1), a key apoptosis regulator in EBV-related cancers, whose specific impact on EBVaGC was previously unknown. Our findings indicate that BALF1 overexpression in gastric cancer cells significantly enhances their proliferation, migration, and resistance to chemotherapy-induced apoptosis, confirming BALF1's oncogenic potential. A novel discovery is that BALF1 undergoes degradation via the ubiquitin-proteasome pathway. Through analysis of 69 deubiquitinating enzymes (DUBs), ovarian tumor protease (OTU) domain-containing protein 1 (OTUD1) emerged as a vital regulator for maintaining BALF1 protein stability. Furthermore, BALF1 was found to play a role in regulating the stability of the B-cell lymphoma-2 (Bcl-2) protein, increasing its levels through deubiquitination. This mechanism reveals BALF1's multifaceted oncogenic role in gastric cancer, as it contributes both directly and indirectly to cancer progression, particularly by stabilizing Bcl-2, known for its anti-apoptotic characteristics. These insights significantly deepen our understanding of EBV's involvement in the pathogenesis of gastric cancer. The elucidation of OTUD1's role in BALF1 regulation and its influence on Bcl-2 stabilization provide new avenues for therapeutic intervention in EBVaGC, bridging the gap between viral oncogenesis and cellular protein regulation and offering a more holistic view of gastric cancer development under the influence of EBV.
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Affiliation(s)
- Hanbin Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou 350122, China
| | - Yuting Han
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou 350122, China
| | - Yuchao Sang
- Anxi County Hospital, Quanzhou 362400, China
| | - Yuecheng Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou 350122, China
| | - Mengyue Tian
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou 350122, China
| | - Xintan Chen
- Anxi County Hospital, Quanzhou 362400, China
| | - Xu Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou 350122, China; Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou 350122, China.
| | - Xinjian Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou 350122, China; Anxi County Hospital, Quanzhou 362400, China.
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16
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Li C, Yi J, Jie H, Liu Z, Li S, Zeng Z, Zhou Y. Acetylation of ELMO1 correlates with Rac1 activity and colorectal cancer progress. Exp Cell Res 2024; 439:114068. [PMID: 38750717 DOI: 10.1016/j.yexcr.2024.114068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/27/2024]
Abstract
Acetylation, a critical regulator of diverse cellular processes, holds significant implications in various cancer contexts. Further understanding of the acetylation patterns of key cancer-driven proteins is crucial for advancing therapeutic strategies in cancer treatment. This study aimed to unravel the acetylation patterns of Engulfment and Cell Motility Protein 1 (ELMO1) and its relevance to the pathogenesis of colorectal cancer (CRC). Immunoprecipitation and mass spectrometry precisely identified lysine residue 505 (K505) as a central acetylation site in ELMO1. P300 emerged as the acetyltransferase for ELMO1 K505 acetylation, while SIRT2 was recognized as the deacetylase. Although K505 acetylation minimally affected ELMO1's localization and stability, it played a crucial role in mediating ELMO1-Dock180 interaction, thereby influencing Rac1 activation. Functionally, ELMO1 K505 acetylation proved to be a pivotal factor in CRC progression, exerting its influence on key cellular processes. Clinical analysis of CRC samples unveiled elevated ELMO1 acetylation in primary tumors, indicating a potential association with CRC pathologies. This work provides insights into ELMO1 acetylation and its significance in advancing potentially therapeutic interventions in CRC treatment.
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Affiliation(s)
- Chuangkun Li
- Department of General Surgery, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Hunan, China
| | - Jianmei Yi
- Department of General Surgery, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Hunan, China
| | - Haiqing Jie
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhihang Liu
- The "Double-First Class" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, China
| | - Shujuan Li
- Department of Pharmacy, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ziwei Zeng
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi Zhou
- Department of General Surgery, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Hunan, China.
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Munro V, Kelly V, Messner CB, Kustatscher G. Cellular control of protein levels: A systems biology perspective. Proteomics 2024; 24:e2200220. [PMID: 38012370 DOI: 10.1002/pmic.202200220] [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: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.
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Affiliation(s)
- Victoria Munro
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Van Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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18
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Feng YR, Zhang Q, Miao JK, Yang T, Chen J, Chen HY, Mou QH, Xiang XL, Long D, Wei QH, Wu Y, Li TY. Association of the retinol to all-trans retinoic acid pathway with autism spectrum disorder. World J Pediatr 2024:10.1007/s12519-024-00815-0. [PMID: 38789720 DOI: 10.1007/s12519-024-00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex group of neurodevelopmental disorders. Research has highlighted a close association between the retinoic acid (RA) signaling pathway and ASD. This study investigates alterations in the vitamin A (VA, retinol) to RA metabolic pathway in children with ASD and speculates on the underlying reasons for these changes. We propose a subtype characterized by downregulated RA signaling in ASD, laying the groundwork for precise diagnosis and treatment research. METHODS We included 489 children with ASD and 280 typically developing (TD) children. Those with ASD underwent evaluations of core symptoms and neuro-developmental levels, which were conducted by professional developmental behavior physicians using assessment scales. Serum VA and all-trans RA (atRA) levels were determined by high-performance liquid chromatography and ultra-high-performance liquid chromatography-tandem mass spectrometry. The expression levels and concentrations of enzyme molecules such as retinol dehydrogenase 10 were assessed using quantitative polymerase chain reaction and enzyme-linked immunosorbent assay. RESULTS Children with ASD exhibited reduced serum atRA, accompanied by a downregulation of atRA synthesis enzymes. The reduction in serum atRA levels was linked not only to VA levels but also to the aberrant expression of metabolic enzymes responsible for atRA. Furthermore, the serum atRA levels in children with ASD were more strongly correlated with core symptoms and neurodevelopmental levels than VA levels. CONCLUSION Children with ASD exhibited a dual regulation of reduced serum atRA levels, influenced by both VA levels and abnormal expression of atRA metabolic enzymes.
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Affiliation(s)
- Yu-Ru Feng
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Qian Zhang
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Jing-Kun Miao
- Department of Pediatrics, Women and Children' Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Ting Yang
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Jie Chen
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Hong-Yu Chen
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Qiu-Hong Mou
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Xue-Li Xiang
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Dan Long
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Qiu-Hong Wei
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Yuan Wu
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China
| | - Ting-Yu Li
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, No 136, 2nd Zhongshan Rd, Yuzhong District, Chongqing, China.
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19
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Wang H, Zhang J, Wei Z, Chen S, Zheng J, Li Y. The prognostic implications and tumor-promoting functions of CHSY3 in gastric cancer. Front Immunol 2024; 15:1364979. [PMID: 38812506 PMCID: PMC11133601 DOI: 10.3389/fimmu.2024.1364979] [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: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/31/2024] Open
Abstract
Chondroitin sulfate synthase 3 (CHSY3) is an important enzyme that regulates glycosylation, but its role in tumors has not been determined. Here, we showed that high CHSY3 expression promotes proliferation in gastric cancer (GC) cells and is associated with poor prognosis in GC patients. We analyzed the immunohistochemistry data of 150 gastric cancer patients to determine the clinicopathological and survival significance of CHSY3. Immunofluorescence was used to detect the colocalization of CHSY3 with infiltrating immune cells. Additionally, CHSY3 was predominantly found in tumor tissues and showed higher abundance compared to matched adjacent tissues. High CHSY3 expression was associated with more advanced tumor stage, higher recurrence risk and worse survival. Immunohistochemistry and bioinformatic analysis revealed that CHSY3 expression was significantly positively correlated with tumor-associated macrophage (TAM) infiltration. Moreover, after knocking down CHSY3, the proliferation of cells was decreased, and the migration ability was reduced, as shown by scratch, monoclonal and transwell assays. In conclusion, this study revealed that CHSY3 has a tumor-promoting effect on GC, suggesting a novel therapeutic strategy against this disease.
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Affiliation(s)
- Han Wang
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Junchang Zhang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Zhuoqi Wei
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Songyao Chen
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jiabin Zheng
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yong Li
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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20
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Liu L, Chen Y, Wu W, Chen Q, Tian Z, Huang J, Ren H, Zhang J, Du X, Zhuang M, Wang P. A multilevel investigation to reveal the regulatory mechanism of lignin accumulation in juice sac granulation of pomelo. BMC PLANT BIOLOGY 2024; 24:390. [PMID: 38730367 PMCID: PMC11088010 DOI: 10.1186/s12870-024-05095-4] [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: 02/15/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024]
Abstract
Granulation of juice sacs is a physiological disorder, which affects pomelo fruit quality. Here, the transcriptome and ubiquitinome of the granulated juice sacs were analyzed in Guanxi pomelo. We found that lignin accumulation in the granulated juice sacs was regulated at transcription and protein modification levels. In transcriptome data, we found that the genes in lignin biosynthesis pathway and antioxidant enzyme system of the granulated juice sacs were significantly upregulated. However, in ubiquitinome data, we found that ubiquitinated antioxidant enzymes increased in abundance but the enzyme activities decreased after the modification, which gave rise to reactive oxygen species (ROS) contents in granulated juice sacs. This finding suggests that ubiquitination level of the antioxidant enzymes is negatively correlated with the enzyme activities. Increased H2O2 is considered to be a signaling molecule to activate the key gene expressions in lignin biosynthesis pathway, which leads to the lignification in granulated juice sacs of pomelo. This regulatory mechanism in juice sac granulation of pomelo was further confirmed through the verification experiment using tissue culture by adding H2O2 or dimethylthiourea (DMTU). Our findings suggest that scavenging H2O2 and other ROS are important for reducing lignin accumulation, alleviating juice sac granulation and improving pomelo fruit quality.
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Affiliation(s)
- Luning Liu
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yiran Chen
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilin Wu
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiuyou Chen
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhijiao Tian
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiakang Huang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huaqing Ren
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiacheng Zhang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Du
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mulai Zhuang
- Bureau of Agriculture and Rural Affairs of Pinghe County, Pinghe, China
| | - Ping Wang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.
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21
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Gan PR, Wu H, Zhu YL, Shu Y, Wei Y. Glycolysis, a driving force of rheumatoid arthritis. Int Immunopharmacol 2024; 132:111913. [PMID: 38603855 DOI: 10.1016/j.intimp.2024.111913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024]
Abstract
Resident synoviocytes and synovial microvasculature, together with immune cells from circulation, contribute to pannus formation, the main pathological feature of rheumatoid arthritis (RA), leading to destruction of adjacent cartilage and bone. Seeds, fibroblast-like synoviocytes (FLSs), macrophages, dendritic cells (DCs), B cells, T cells and endothelial cells (ECs) seeds with high metabolic demands undergo metabolic reprogramming from oxidative phosphorylation to glycolysis in response to poor soil of RA synovium with hypoxia, nutrient deficiency and inflammatory stimuli. Glycolysis provides rapid energy supply and biosynthetic precursors to support pathogenic growth of these seeds. The metabolite lactate accumulated during this process in turn condition the soil microenvironment and affect seeds growth by modulating signalling pathways and directing lactylation modifications. This review explores in depth the survival mechanism of seeds with high metabolic demands in the poor soil of RA synovium, providing useful support for elucidating the etiology of RA. In addition, we discuss the role and major post-translational modifications of proteins and enzymes linked to glycolysis to inspire the discovery of novel anti-rheumatic targets.
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Affiliation(s)
- Pei-Rong Gan
- College of Pharmacy, Anhui University of Chinese Medicine, Qian Jiang Road 1, Hefei 230012, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China
| | - Hong Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Qian Jiang Road 1, Hefei 230012, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China.
| | - Yu-Long Zhu
- College of Pharmacy, Anhui University of Chinese Medicine, Qian Jiang Road 1, Hefei 230012, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China
| | - Yin Shu
- College of Pharmacy, Anhui University of Chinese Medicine, Qian Jiang Road 1, Hefei 230012, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China
| | - Yi Wei
- College of Pharmacy, Anhui University of Chinese Medicine, Qian Jiang Road 1, Hefei 230012, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China
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22
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Wang C, Yang J, Xu Z, Lv L, Chen S, Hong M, Liu JH. Promoter regulatory mode evolution enhances the high multidrug resistance of tmexCD1-toprJ1. mBio 2024; 15:e0021824. [PMID: 38564664 PMCID: PMC11077950 DOI: 10.1128/mbio.00218-24] [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: 01/24/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Antibiotic resistance could rapidly emerge from acquiring the mobile antibiotic resistance genes, which are commonly evolved from an intrinsic gene. The emergence of the plasmid-borne mobilized efflux pump gene cluster tmexCD1-toprJ1 renders the last-resort antibiotic tigecycline ineffective, although its evolutionary mechanism remains unclear. In this study, we investigate the regulatory mechanisms of the progenitor NfxB-MexCD-OprJ, a chromosomally encoded operon that does not mediate antibiotic resistance in the wild-type version, and its homologs, TNfxB1-TMexCD1-TOprJ1 mediating high-level tigecycline resistance, and TNfxB3-TMexCD3-TOprJ1. Mechanistic studies demonstrated that in nfxB-mexCD-oprJ, MexCD expression was under a weaker promoter, PmexC and inhibited by a strong repressor NfxB. For tmexCD1-toprJ1, TMexCD1 was highly expressed owing to the presence of a strong promoter, PtmexC1, and an inactive suppressor, TNfxB1, with a T39R mutation that rendered it unable to bind to promoter DNA. In tnfxB3-tmexCD3-toprJ1b, TMexCD3 expression was intermediate because of the local regulator TNfxB3, which binds to two inverted repeat sequences of PtmexC. Additionally, TNfxB3 exhibited lower protein expression and weaker DNA binding affinity than its ancestor NfxB, together with their promoter activities difference explaining the different expression levels of tmexCD-toprJ homologs. Distinct fitness burdens on these homologs-carrying bacteria were observed due to the corresponding expression level, which might be associated with their global prevalence. In summary, our data depict the mechanisms underlying the evolution and dissemination of an important mobile antibiotic resistance gene from an intrinsic chromosomal gene.IMPORTANCEAs antibiotic resistance seriously challenges global health, tigecycline is one of the few effective drugs in the pipeline against infections caused by multidrug-resistant pathogens. Our previous work identified a novel tigecycline resistance efflux pump gene cluster tmexCD1-toprJ1 in animals and humans, together with its various variants, a rising clinical concern. Herein, this study focused on how the local regulation modes of tmexCD1-toprJ1 evolved to a highly expressed efflux pump. Through comparative analysis between three tnfxB-tmexCD-toprJ homologs and their progenitor nfxB-mexCD-oprJ, modes, we demonstrated the evolutionary dynamics from a chromosomal silent gene to an active state. We found the de-repression of the local regulator and an increase of the promoter activity work together to promote a high production of drug efflux machines and enhance multidrug resistance. Our findings revealed that TMexCD1-TOprJ1 adopts a distinct evolutionary path to achieve higher multidrug resistance, urgently needing tight surveillance.
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Affiliation(s)
- Chengzhen Wang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Jun Yang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Luchao Lv
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
| | - Jian-Hua Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
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23
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Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [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: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
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Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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24
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Li Q, Lin J, Ma H, Yuan L, Liu X, Xiong J, Miao W, Yang M, Ge F. Identification and Functional Analysis of Lysine 2-Hydroxyisobutyrylation in Cyanobacteria. J Proteome Res 2024; 23:1689-1701. [PMID: 38565891 DOI: 10.1021/acs.jproteome.3c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cyanobacteria are the oldest prokaryotic photoautotrophic microorganisms and have evolved complicated post-translational modification (PTM) machinery to respond to environmental stress. Lysine 2-hydroxyisobutyrylation (Khib) is a newly identified PTM that is reported to play important roles in diverse biological processes, however, its distribution and function in cyanobacteria have not been reported. Here, we performed the first systematic studies of Khib in a model cyanobacterium Synechococcus sp. strain PCC 7002 (Syn7002) using peptide prefractionation, pan-Khib antibody enrichment, and high-accuracy mass spectrometry (MS) analysis. A total of 1875 high-confidence Khib sites on 618 proteins were identified, and a large proportion of Khib sites are present on proteins in the cellular metabolism, protein synthesis, and photosynthesis pathways. Using site-directed mutagenesis and functional studies, we showed that Khib of glutaredoxin (Grx) affects the efficiency of the PS II reaction center and H2O2 resistance in Syn7002. Together, this study provides novel insights into the functions of Khib in cyanobacteria and suggests that reversible Khib may influence the stress response and photosynthesis in both cyanobacteria and plants.
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Affiliation(s)
- Qiaoya Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Lin
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Ma
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430070, China
| | - Jie Xiong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Miao
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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25
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Sun Y, Xie Z, Jin L, Qin T, Zhan C, Huang J. Histone deacetylase OsHDA716 represses rice chilling tolerance by deacetylating OsbZIP46 to reduce its transactivation function and protein stability. THE PLANT CELL 2024; 36:1913-1936. [PMID: 38242836 PMCID: PMC11062455 DOI: 10.1093/plcell/koae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Low temperature is a major environmental factor limiting plant growth and crop production. Epigenetic regulation of gene expression is important for plant adaptation to environmental changes, whereas the epigenetic mechanism of cold signaling in rice (Oryza sativa) remains largely elusive. Here, we report that the histone deacetylase (HDAC) OsHDA716 represses rice cold tolerance by interacting with and deacetylating the transcription factor OsbZIP46. The loss-of-function mutants of OsHDA716 exhibit enhanced chilling tolerance, compared with the wild-type plants, while OsHDA716 overexpression plants show chilling hypersensitivity. On the contrary, OsbZIP46 confers chilling tolerance in rice through transcriptionally activating OsDREB1A and COLD1 to regulate cold-induced calcium influx and cytoplasmic calcium elevation. Mechanistic investigation showed that OsHDA716-mediated OsbZIP46 deacetylation in the DNA-binding domain reduces the DNA-binding ability and transcriptional activity as well as decreasing OsbZIP46 protein stability. Genetic evidence indicated that OsbZIP46 deacetylation mediated by OsHDA716 reduces rice chilling tolerance. Collectively, these findings reveal that the functional interplay between the chromatin regulator and transcription factor fine-tunes the cold response in plant and uncover a mechanism by which HDACs repress gene transcription through deacetylating nonhistone proteins and regulating their biochemical functions.
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Affiliation(s)
- Ying Sun
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Zizhao Xie
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Tian Qin
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Chenghang Zhan
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
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Min Y, Yu H, Li Q. Transcriptional and post-translational regulation of MITF mediated by bHLH domain during the melanogenesis and melanocyte proliferation in Crassostrea gigas. Int J Biol Macromol 2024; 266:131138. [PMID: 38547943 DOI: 10.1016/j.ijbiomac.2024.131138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Melanocyte differentiation is orchestrated by the master regulator transcription factor MITF. However, its ability to discern distinct binding sites linked to effective gene regulation remains poorly understood. This study aims to assess how co-activator acetyltransferase interacts with MITF to modulate their related lysine action, thereby mediating downstream gene regulation, including DNA affinity, stability, transcriptional activity, particularly in the process of shell pigmentation. Here, we have demonstrated that the CgMITF protein can be acetylated, further enabling selective amplification of the melanocyte maturation program. Collaboration with transcriptional co-regulator p300 advances MITF dynamically interplay with downstream targeted gene promoters. We have established that MITF activation was partially dependent on the bHLH domain, which was well conserved across species. The bHLH domain contained conserved lysine residues, including K6 and K43, which interacted with the E-box motif of downstream targeted-genes. Mutations at K6 and K43 lead to a decrease in the binding affinity of the E-box motif. CgMITF protein bound to the E-box motif within the promoter regions of the tyrosinase-related genes, contributing to melanogenesis, and also interacted with the E-box motif within the TBX2 promoter regions, associated with melanocyte proliferation. We elucidated how the bHLH domain links the transcriptional regulation and acetylation modifications in the melanocyte development in C. gigas.
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Affiliation(s)
- Yue Min
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Ri-Wen, Yang YH, Zhang TN, Liu CF, Yang N. Targeting epigenetic and post-translational modifications regulating pyroptosis for the treatment of inflammatory diseases. Pharmacol Res 2024; 203:107182. [PMID: 38614373 DOI: 10.1016/j.phrs.2024.107182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Inflammatory diseases, including infectious diseases, diabetes-related diseases, arthritis-related diseases, neurological diseases, digestive diseases, and tumor, continue to threaten human health and impose a significant financial burden despite advancements in clinical treatment. Pyroptosis, a pro-inflammatory programmed cell death pathway, plays an important role in the regulation of inflammation. Moderate pyroptosis contributes to the activation of native immunity, whereas excessive pyroptosis is associated with the occurrence and progression of inflammation. Pyroptosis is complicated and tightly controlled by various factors. Accumulating evidence has confirmed that epigenetic modifications and post-translational modifications (PTMs) play vital roles in the regulation of pyroptosis. Epigenetic modifications, which include DNA methylation and histone modifications (such as methylation and acetylation), and post-translational modifications (such as ubiquitination, phosphorylation, and acetylation) precisely manipulate gene expression and protein functions at the transcriptional and post-translational levels, respectively. In this review, we summarize the major pathways of pyroptosis and focus on the regulatory roles and mechanisms of epigenetic and post-translational modifications of pyroptotic components. We also illustrate these within pyroptosis-associated inflammatory diseases. In addition, we discuss the effects of novel therapeutic strategies targeting epigenetic and post-translational modifications on pyroptosis, and provide prospective insight into the regulation of pyroptosis for the treatment of inflammatory diseases.
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Affiliation(s)
- Ri-Wen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yu-Hang Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Tie-Ning Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Chun-Feng Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Ni Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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Zhang N, Gao S, Peng H, Wu J, Li H, Gibson C, Wu S, Zhu J, Zheng Q. Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591460. [PMID: 38712070 PMCID: PMC11071480 DOI: 10.1101/2024.04.27.591460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid residue of H3 ( i.e. , glutamine) and dopamine. In our previous studies, we discovered that the dynamics of this post-translational modification (including installation, removal, and replacement) were regulated by a single enzyme, transglutaminase 2 (TGM2), through reversible transamination. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of TGM2 in colon cancer cells. Due to the enzyme promiscuity of TGM2, non-histone proteins have also been identified as targets of dopaminylation on glutamine residues, however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of modification sites of these dopaminylated proteins were identified, attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that to block the installation of protein dopaminylation may become a promising anti-cancer strategy. TOC
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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30
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Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science 2024; 384:eadl2528. [PMID: 38452047 DOI: 10.1126/science.adl2528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.
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Affiliation(s)
- Rohith Krishna
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Jue Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Woody Ahern
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Pascal Sturmfels
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Indrek Kalvet
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | | | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ryan McHugh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Dionne Vafeados
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | | | - Andrew Hitchcock
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Evans Brackenbrough
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Minkyung Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
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31
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Que Y, Qiu Y, Ding Z, Zhang S, Wei R, Xia J, Lin Y. The role of molecular chaperone CCT/TRiC in translation elongation: A literature review. Heliyon 2024; 10:e29029. [PMID: 38596045 PMCID: PMC11002246 DOI: 10.1016/j.heliyon.2024.e29029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Protein synthesis from mRNA is an energy-intensive and strictly controlled biological process. Translation elongation is a well-coordinated and multifactorial step in translation that ensures the accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of messenger RNA (mRNA). Which undergoes dynamic regulation due to cellular state and environmental determinants. An expanding body of research points to translational elongation as a crucial process that controls the translation of an mRNA through multiple feedback mechanisms. Molecular chaperones are key players in protein homeostasis to keep the balance between protein synthesis, folding, assembly, and degradation. Chaperonin-containing tailless complex polypeptide 1 (CCT) or tailless complex polypeptide 1 ring complex (TRiC) is an essential eukaryotic molecular chaperone that plays an essential role in assisting cellular protein folding and suppressing protein aggregation. In this review, we give an overview of the factors that influence translation elongation, focusing on different functions of molecular chaperones in translation elongation, including how they affect translation rates and post-translational modifications. We also provide an understanding of the mechanisms by which the molecular chaperone CCT plays multiple roles in the elongation phase of eukaryotic protein synthesis.
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Affiliation(s)
- Yueyue Que
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yudan Qiu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Zheyu Ding
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Shanshan Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Rong Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Jianing Xia
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yingying Lin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
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Zhang S, Cheng Y, Guan Y, Wen J, Chen Z. Hydrogen Sulfide Exerted a Pro-Angiogenic Role by Promoting the Phosphorylation of VEGFR2 at Tyr797 and Ser799 Sites in Hypoxia-Reoxygenation Injury. Int J Mol Sci 2024; 25:4340. [PMID: 38673925 PMCID: PMC11050214 DOI: 10.3390/ijms25084340] [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: 03/05/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The protective effects of hydrogen sulfide (H2S) against ischemic brain injury and its role in promoting angiogenesis have been established. However, the specific mechanism underlying these effects remains unclear. This study is designed to investigate the regulatory impact and mechanism of H2S on VEGFR2 phosphorylation. Following expression and purification, the recombinant His-VEGFR2 protein was subjected to LC-PRM/MS analysis to identify the phosphorylation sites of VEGFR2 upon NaHS treatment. Adenovirus infection was used to transfect primary rat brain artery endothelial cells (BAECs) with the Ad-VEGFR2WT, Ad-VEGFR2Y797F, and Ad-VEGFR2S799A plasmids. The expression of VEGFR2 and recombinant Flag-VEGFR2, along with Akt phosphorylation, cell proliferation, and LDH levels, was assessed. The migratory capacity and tube-forming potential of BAECs were assessed using wound healing, transwell, and tube formation assays. NaHS notably enhanced the phosphorylation of VEGFR2 at Tyr797 and Ser799 sites. These phosphorylation sites were identified as crucial for mediating the protective effects of NaHS against hypoxia-reoxygenation (H/R) injury. NaHS significantly enhanced the Akt phosphorylation, migratory capacity, and tube formation of BAECs and upregulated the expression of VEGFR2 and recombinant proteins. These findings suggest that Tyr797 and Ser799 sites of VEGFR2 serve as crucial mediators of H2S-induced pro-angiogenic effects and protection against H/R injury.
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Affiliation(s)
- Sen Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Yongfeng Cheng
- Clinical Medical College, Anhui Medical University, Hefei 230012, China;
| | - Yining Guan
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Jiyue Wen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Zhiwu Chen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
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Li X, Cai P, Tang X, Wu Y, Zhang Y, Rong X. Lactylation Modification in Cardiometabolic Disorders: Function and Mechanism. Metabolites 2024; 14:217. [PMID: 38668345 PMCID: PMC11052226 DOI: 10.3390/metabo14040217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Cardiovascular disease (CVD) is recognized as the primary cause of mortality and morbidity on a global scale, and developing a clear treatment is an important tool for improving it. Cardiometabolic disorder (CMD) is a syndrome resulting from the combination of cardiovascular, endocrine, pro-thrombotic, and inflammatory health hazards. Due to their complex pathological mechanisms, there is a lack of effective diagnostic and treatment methods for cardiac metabolic disorders. Lactylation is a type of post-translational modification (PTM) that plays a regulatory role in various cellular physiological processes by inducing changes in the spatial conformation of proteins. Numerous studies have reported that lactylation modification plays a crucial role in post-translational modifications and is closely related to cardiac metabolic diseases. This article discusses the molecular biology of lactylation modifications and outlines the roles and mechanisms of lactylation modifications in cardiometabolic disorders, offering valuable insights for the diagnosis and treatment of such conditions.
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Affiliation(s)
- Xu Li
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Pingdong Cai
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xinyuan Tang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yingzi Wu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yue Zhang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xianglu Rong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangzhou 510006, China; (X.L.); (P.C.); (X.T.); (Y.W.)
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangzhou 510006, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, Guangzhou 510006, China
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM, State Administration of Traditional Chinese Medicine, Guangzhou 510006, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
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Rrustemi T, Meyer K, Roske Y, Uyar B, Akalin A, Imami K, Ishihama Y, Daumke O, Selbach M. Pathogenic mutations of human phosphorylation sites affect protein-protein interactions. Nat Commun 2024; 15:3146. [PMID: 38605029 PMCID: PMC11009412 DOI: 10.1038/s41467-024-46794-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.
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Affiliation(s)
| | - Katrina Meyer
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Bora Uyar
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Altuna Akalin
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Kanagawa, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Oliver Daumke
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany.
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Zhang S, Yu Q, Li Z, Zhao Y, Sun Y. Protein neddylation and its role in health and diseases. Signal Transduct Target Ther 2024; 9:85. [PMID: 38575611 PMCID: PMC10995212 DOI: 10.1038/s41392-024-01800-9] [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: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.
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Affiliation(s)
- Shizhen Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Qing Yu
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, China
| | - Zhijian Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
| | - Yi Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
- Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, Hangzhou, 310024, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.
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Xu GE, Yu P, Hu Y, Wan W, Shen K, Cui X, Wang J, Wang T, Cui C, Chatterjee E, Li G, Cretoiu D, Sluijter JPG, Xu J, Wang L, Xiao J. Exercise training decreases lactylation and prevents myocardial ischemia-reperfusion injury by inhibiting YTHDF2. Basic Res Cardiol 2024:10.1007/s00395-024-01044-2. [PMID: 38563985 DOI: 10.1007/s00395-024-01044-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/19/2024] [Accepted: 03/02/2024] [Indexed: 04/04/2024]
Abstract
Exercise improves cardiac function and metabolism. Although long-term exercise leads to circulating and micro-environmental metabolic changes, the effect of exercise on protein post-translational lactylation modifications as well as its functional relevance is unclear. Here, we report that lactate can regulate cardiomyocyte changes by improving protein lactylation levels and elevating intracellular N6-methyladenosine RNA-binding protein YTHDF2. The intrinsic disorder region of YTHDF2 but not the RNA m6A-binding activity is indispensable for its regulatory function in influencing cardiomyocyte cell size changes and oxygen glucose deprivation/re-oxygenation (OGD/R)-stimulated apoptosis via upregulating Ras GTPase-activating protein-binding protein 1 (G3BP1). Downregulation of YTHDF2 is required for exercise-induced physiological cardiac hypertrophy. Moreover, myocardial YTHDF2 inhibition alleviated ischemia/reperfusion-induced acute injury and pathological remodeling. Our results here link lactate and lactylation modifications with RNA m6A reader YTHDF2 and highlight the physiological importance of this innovative post-transcriptional intrinsic regulation mechanism of cardiomyocyte responses to exercise. Decreasing lactylation or inhibiting YTHDF2/G3BP1 might represent a promising therapeutic strategy for cardiac diseases.
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Affiliation(s)
- Gui-E Xu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Pujiao Yu
- Department of Cardiology, Shanghai Gongli Hospital, Shanghai, 200135, China
| | - Yuxue Hu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Wensi Wan
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Keting Shen
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Xinxin Cui
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Jiaqi Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Tianhui Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Caiyue Cui
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Emeli Chatterjee
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Dragos Cretoiu
- Department of Medical Genetics, Carol Davila University of Medicine and Pharmacy, 020031, Bucharest, Romania
- Materno-Fetal Assistance Excellence Unit, Alessandrescu-Rusescu National Institute for Mother and Child Health, 011062, Bucharest, Romania
| | - Joost P G Sluijter
- Department of Cardiology, Laboratory of Experimental Cardiology, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
- UMC Utrecht Regenerative Medicine Center, Circulatory Health Research Center, University Medical Center Utrecht, Utrecht University, Utrecht, 3508GA, The Netherlands
| | - Jiahong Xu
- Department of Cardiology, Shanghai Gongli Hospital, Shanghai, 200135, China.
| | - Lijun Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China.
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China.
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Life Science, Shanghai University, Nantong, 226011, China.
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, 200444, China.
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Idrees S, Paudel KR, Sadaf T, Hansbro PM. Uncovering domain motif interactions using high-throughput protein-protein interaction detection methods. FEBS Lett 2024; 598:725-742. [PMID: 38439692 DOI: 10.1002/1873-3468.14841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 02/18/2024] [Indexed: 03/06/2024]
Abstract
Protein-protein interactions (PPIs) are often mediated by short linear motifs (SLiMs) in one protein and domain in another, known as domain-motif interactions (DMIs). During the past decade, SLiMs have been studied to find their role in cellular functions such as post-translational modifications, regulatory processes, protein scaffolding, cell cycle progression, cell adhesion, cell signalling and substrate selection for proteasomal degradation. This review provides a comprehensive overview of the current PPI detection techniques and resources, focusing on their relevance to capturing interactions mediated by SLiMs. We also address the challenges associated with capturing DMIs. Moreover, a case study analysing the BioGrid database as a source of DMI prediction revealed significant known DMI enrichment in different PPI detection methods. Overall, it can be said that current high-throughput PPI detection methods can be a reliable source for predicting DMIs.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Tayyaba Sadaf
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
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Li Z, Chen J, Huang H, Zhan Q, Wang F, Chen Z, Lu X, Sun G. Post-translational modifications in diabetic cardiomyopathy. J Cell Mol Med 2024; 28:e18158. [PMID: 38494853 PMCID: PMC10945092 DOI: 10.1111/jcmm.18158] [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: 07/30/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024] Open
Abstract
The increasing attention towards diabetic cardiomyopathy as a distinctive complication of diabetes mellitus has highlighted the need for standardized diagnostic criteria and targeted treatment approaches in clinical practice. Ongoing research is gradually unravelling the pathogenesis of diabetic cardiomyopathy, with a particular emphasis on investigating various post-translational modifications. These modifications dynamically regulate protein function in response to changes in the internal and external environment, and their disturbance of homeostasis holds significant relevance for the development of chronic ailments. This review provides a comprehensive overview of the common post-translational modifications involved in the initiation and progression of diabetic cardiomyopathy, including O-GlcNAcylation, phosphorylation, methylation, acetylation and ubiquitination. Additionally, the review discusses drug development strategies for targeting key post-translational modification targets, such as agonists, inhibitors and PROTAC (proteolysis targeting chimaera) technology that targets E3 ubiquitin ligases.
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Affiliation(s)
- Zhi Li
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Jie Chen
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Hailong Huang
- Department of Obstetrics and GynecologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Qianru Zhan
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Fengzhi Wang
- Department of Neurology, People's Hospital of Liaoning ProvincePeople's Hospital of China Medical UniversityShenyangChina
| | - Zihan Chen
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
| | - Xinwei Lu
- Department of CardiologySiping Central People's HospitalSipingChina
| | - Guozhe Sun
- Department of CardiologyThe First Hospital of China Medical UniversityShenyangChina
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Bu W, Di J, Zhao J, Liu R, Wu Y, Ran J, Li T. Dynein Light Intermediate Chains Exhibit Different Arginine Methylation Patterns. J Clin Lab Anal 2024; 38:e25030. [PMID: 38525916 PMCID: PMC11033342 DOI: 10.1002/jcla.25030] [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: 01/29/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND The motor protein dynein is integral to retrograde transport along microtubules and interacts with numerous cargoes through the recruitment of cargo-specific adaptor proteins. This interaction is mediated by dynein light intermediate chain subunits LIC1 (DYNC1LI1) and LIC2 (DYNC1LI2), which govern the adaptor binding and are present in distinct dynein complexes with overlapping and unique functions. METHODS Using bioinformatics, we analyzed the C-terminal domains (CTDs) of LIC1 and LIC2, revealing similar structural features but diverse post-translational modifications (PTMs). The methylation status of LIC2 and the proteins involved in this modification were examined through immunoprecipitation and immunoblotting analyses. The specific methylation sites on LIC2 were identified through a site-directed mutagenesis analysis, contributing to a deeper understanding of the regulatory mechanisms of the dynein complex. RESULTS We found that LIC2 is specifically methylated at the arginine 397 residue, a reaction that is catalyzed by protein arginine methyltransferase 1 (PRMT1). CONCLUSIONS The distinct PTMs of the LIC subunits offer a versatile mechanism for dynein to transport diverse cargoes efficiently. Understanding how these PTMs influence the functions of LIC2, and how they differ from LIC1, is crucial for elucidating the role of dynein-related transport pathways in a range of diseases. The discovery of the arginine 397 methylation site on LIC2 enhances our insight into the regulatory PTMs of dynein functions.
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Affiliation(s)
- Weiwen Bu
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Jie Di
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Junkui Zhao
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Ruming Liu
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
| | - Yue Wu
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life SciencesShandong Normal UniversityJinanChina
| | - Jie Ran
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life SciencesShandong Normal UniversityJinanChina
| | - Te Li
- Department of Genetics and Cell Biology, Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Medicinal Chemical Biology, College of Life SciencesNankai UniversityTianjinChina
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40
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Korchak JA, Jeffery ED, Bandyopadhyay S, Jordan BT, Lehe M, Watts EF, Fenix A, Wilhelm M, Sheynkman GM. IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587549. [PMID: 38617311 PMCID: PMC11014528 DOI: 10.1101/2024.04.01.587549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of pre-defined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (LR RNAseq) data to predict potential protein isoforms with prior transcript evidence. Predicted tryptic isoform-specific peptides, which are specific to individual gene product isoforms, serve as "triggers" and "targets" in the IS-PRM method, Tomahto. Using the model human stem cell line WTC11, LR RNAseq data were generated and used to inform the generation of synthetic standards for 192 isoform-specific peptides (114 isoforms from 55 genes). These synthetic "trigger" peptides were labeled with super heavy tandem mass tags (TMT) and spiked into TMT-labeled WTC11 tryptic digest, predicted to contain corresponding endogenous "target" peptides. Compared to DDA mode, Tomahto increased detectability of isoforms by 3.6-fold, resulting in the identification of five previously unannotated isoforms. Our method detected protein isoform expression for 43 out of 55 genes corresponding to 54 resolved isoforms. This LR RNA seq-informed Tomahto targeted approach, called LRP-IS-PRM, is a new modality for generating protein-level evidence of alternative isoforms - a critical first step in designing functional studies and eventually clinical assays.
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Affiliation(s)
- Jennifer A. Korchak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Erin D. Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Saikat Bandyopadhyay
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ben T. Jordan
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Micah Lehe
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Emily F. Watts
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Aidan Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
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Garcia JPT, Tayo LL. Theoretical Studies of DNA Microarray Present Potential Molecular and Cellular Interconnectivity of Signaling Pathways in Immune System Dysregulation. Genes (Basel) 2024; 15:393. [PMID: 38674328 PMCID: PMC11049615 DOI: 10.3390/genes15040393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 04/28/2024] Open
Abstract
Autoimmunity is defined as the inability to regulate immunological activities in the body, especially in response to external triggers, leading to the attack of the tissues and organs of the host. Outcomes include the onset of autoimmune diseases whose effects are primarily due to dysregulated immune responses. In past years, there have been cases that show an increased susceptibility to other autoimmune disorders in patients who are already experiencing the same type of disease. Research in this field has started analyzing the potential molecular and cellular causes of this interconnectedness, bearing in mind the possibility of advancing drugs and therapies for the treatment of autoimmunity. With that, this study aimed to determine the correlation of four autoimmune diseases, which are type 1 diabetes (T1D), psoriasis (PSR), systemic sclerosis (SSc), and systemic lupus erythematosus (SLE), by identifying highly preserved co-expressed genes among datasets using WGCNA. Functional annotation was then employed to characterize these sets of genes based on their systemic relationship as a whole to elucidate the biological processes, cellular components, and molecular functions of the pathways they are involved in. Lastly, drug repurposing analysis was performed to screen candidate drugs for repositioning that could regulate the abnormal expression of genes among the diseases. A total of thirteen modules were obtained from the analysis, the majority of which were associated with transcriptional, post-transcriptional, and post-translational modification processes. Also, the evaluation based on KEGG suggested the possible role of TH17 differentiation in the simultaneous onset of the four diseases. Furthermore, clomiphene was the top drug candidate for regulating overexpressed hub genes; meanwhile, prilocaine was the top drug for regulating under-expressed hub genes. This study was geared towards utilizing transcriptomics approaches for the assessment of microarray data, which is different from the use of traditional genomic analyses. Such a research design for investigating correlations among autoimmune diseases may be the first of its kind.
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Affiliation(s)
- Jon Patrick T. Garcia
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
- School of Graduate Studies, Mapúa University, Manila 1002, Philippines
| | - Lemmuel L. Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
- Department of Biology, School of Medicine and Health Sciences, Mapúa University, Makati 1200, Philippines
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Di Gregorio J, Di Giuseppe L, Terreri S, Rossi M, Battafarano G, Pagliarosi O, Flati V, Del Fattore A. Protein Stability Regulation in Osteosarcoma: The Ubiquitin-like Modifications and Glycosylation as Mediators of Tumor Growth and as Targets for Therapy. Cells 2024; 13:537. [PMID: 38534381 DOI: 10.3390/cells13060537] [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: 02/14/2024] [Revised: 03/11/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024] Open
Abstract
The identification of new therapeutic targets and the development of innovative therapeutic approaches are the most important challenges for osteosarcoma treatment. In fact, despite being relatively rare, recurrence and metastatic potential, particularly to the lungs, make osteosarcoma a deadly form of cancer. In fact, although current treatments, including surgery and chemotherapy, have improved survival rates, the disease's recurrence and metastasis are still unresolved complications. Insights for analyzing the still unclear molecular mechanisms of osteosarcoma development, and for finding new therapeutic targets, may arise from the study of post-translational protein modifications. Indeed, they can influence and alter protein structure, stability and function, and cellular interactions. Among all the post-translational modifications, ubiquitin-like modifications (ubiquitination, deubiquitination, SUMOylation, and NEDDylation), as well as glycosylation, are the most important for regulating protein stability, which is frequently altered in cancers including osteosarcoma. This review summarizes the relevance of ubiquitin-like modifications and glycosylation in osteosarcoma progression, providing an overview of protein stability regulation, as well as highlighting the molecular mediators of these processes in the context of osteosarcoma and their possible targeting for much-needed novel therapy.
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Affiliation(s)
- Jacopo Di Gregorio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Laura Di Giuseppe
- Department of Clinical, Internal, Anaesthesiological and Cardiovascular Sciences, Sapienza University, 00185 Rome, Italy
| | - Sara Terreri
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Michela Rossi
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Giulia Battafarano
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Olivia Pagliarosi
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Vincenzo Flati
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Andrea Del Fattore
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
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43
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Yang L, Xu L, Guo J, Li A, Qi H, Wang J, Song S. SNAC1-OsERF103-OsSDG705 module mediates drought response in rice. THE NEW PHYTOLOGIST 2024; 241:2480-2494. [PMID: 38296835 DOI: 10.1111/nph.19552] [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: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Drought stress profoundly hampers both plant growth and crop yield. To combat this, plants have evolved intricate transcriptional regulation mechanisms as a pivotal strategy. Through a genetic screening with rice genome-scale mutagenesis pool under drought stress, we identified an APETALA2/Ethylene Responsive Factor, namely OsERF103, positively responds to drought tolerance in rice. Combining chromatin immunoprecipitation sequencing and RNA sequencing analyses, we pinpointed c. 1000 genes directly influenced by OsERF103. Further results revealed that OsERF103 interacts with Stress-responsive NAC1 (SNAC1), a positive regulator of drought tolerance in rice, to synergistically regulate the expression of key drought-related genes, such as OsbZIP23. Moreover, we found that OsERF103 recruits a Su(var)3-9,enhancer of zeste and trithorax-domain group protein 705, which encodes a histone 3 lysine 4 (H3K4)-specific methyltransferase to specifically affect the deposition of H3K4me3 at loci like OsbZIP23 and other genes linked to dehydration responses. Additionally, the natural alleles of OsERF103 are selected during the domestication of both indica and japonica rice varieties and exhibit significant geographic distribution. Collectively, our findings have unfurled a comprehensive mechanistic framework underlying the OsERF103-mediated cascade regulation of drought response. This discovery not only enhances our understanding of drought signaling but also presents a promising avenue for the genetic improvement of drought-tolerant rice cultivars.
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Affiliation(s)
- Lijia Yang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liang Xu
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiazhuo Guo
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Aipeng Li
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Haoyue Qi
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiaxuan Wang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiyong Song
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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44
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Zhou Y, Zheng Z, Wu S, Zhu J. Ubiquitin-conjugating enzyme E2 for regulating autophagy in diabetic cardiomyopathy: A mini-review. J Diabetes 2024; 16:e13511. [PMID: 38052719 PMCID: PMC10925883 DOI: 10.1111/1753-0407.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/18/2023] [Indexed: 12/07/2023] Open
Abstract
The prevalence of diabetic cardiomyopathy (DCM) increases year by year with the increase in the prevalence of diabetes mellitus (DM), which is one of the most serious cardiovascular complications of DM and a major cause of death in diabetic patients. Although the pathological molecular features of DCM have not been fully elucidated, increasing evidence suggests that impaired autophagy in cardiomyocytes plays a nonnegligible role in the development of DCM. It has been shown that SUMOylation [SUMO = small ubiquitin-like modifier], a post-translational modification of proteins, and its associated ubiquitin-proteasome system mediates protein quality control in the heart and plays an important role in the proteotoxic environment of the heart. Specifically, the expression of ubiquitin-conjugating enzyme E2 (Ubc9), the only SUMO-E2 enzyme, exerts a positive regulatory effect on autophagy in cardiomyocytes with potential cardioprotective effects. This review focuses on the role that autophagy plays in DCM and the potential for Ubc9-regulated autophagy pathways to ameliorate DCM, highlighting the potential of Ubc9 as an interventional target in DCM and providing new insights into the pathogenesis of the disease.
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Affiliation(s)
- Yueran Zhou
- Institute of Clinical Electrocardiology, First Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Zequn Zheng
- Institute of Clinical Electrocardiology, First Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Shenglin Wu
- Institute of Clinical Electrocardiology, First Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Jinxiu Zhu
- Institute of Clinical Electrocardiology, First Affiliated Hospital of Shantou University Medical CollegeShantouChina
- Longgang Maternity and Child Institute of Shantou University Medical College (Longgang District Maternity & Child Healthcare Hospital of Shenzhen City)ShenzhenChina
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45
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Wang Y, Engel T, Teng X. Post-translational regulation of the mTORC1 pathway: A switch that regulates metabolism-related gene expression. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195005. [PMID: 38242428 DOI: 10.1016/j.bbagrm.2024.195005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is a kinase complex that plays a crucial role in coordinating cell growth in response to various signals, including amino acids, growth factors, oxygen, and ATP. Activation of mTORC1 promotes cell growth and anabolism, while its suppression leads to catabolism and inhibition of cell growth, enabling cells to withstand nutrient scarcity and stress. Dysregulation of mTORC1 activity is associated with numerous diseases, such as cancer, metabolic disorders, and neurodegenerative conditions. This review focuses on how post-translational modifications, particularly phosphorylation and ubiquitination, modulate mTORC1 signaling pathway and their consequential implications for pathogenesis. Understanding the impact of phosphorylation and ubiquitination on the mTORC1 signaling pathway provides valuable insights into the regulation of cellular growth and potential therapeutic targets for related diseases.
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Affiliation(s)
- Yitao Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China; Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Tobias Engel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Xinchen Teng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
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46
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Suskiewicz MJ. The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments. Bioessays 2024; 46:e2300178. [PMID: 38247183 DOI: 10.1002/bies.202300178] [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: 09/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.
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Affiliation(s)
- Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS - Orléans, UPR 4301, affiliated with Université d'Orléans, Orléans, France
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47
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Peng Z, Schussheim B, Chatterjee P. PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.581983. [PMID: 38464112 PMCID: PMC10925343 DOI: 10.1101/2024.02.28.581983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and functional diversity of different protein types and uphold proteostasis, allowing cells to swiftly respond to environmental changes and intricately regulate complex biological processes. To this point, efforts to model the complex features of proteins have involved the training of large and expressive protein language models (pLMs) such as ESM-2 and ProtT5, which accurately encode structural, functional, and physicochemical properties of input protein sequences. However, the over 200 million sequences that these pLMs were trained on merely scratch the surface of proteomic diversity, as they neither input nor account for the effects of PTMs. In this work, we fill this major gap in protein sequence modeling by introducing PTM tokens into the pLM training regime. We then leverage recent advancements in structured state space models (SSMs), specifically Mamba, which utilizes efficient hardware-aware primitives to overcome the quadratic time complexities of Transformers. After adding a comprehensive set of PTM tokens to the model vocabulary, we train bidirectional Mamba blocks whose outputs are fused with state-of-the-art ESM-2 embeddings via a novel gating mechanism. We demonstrate that our resultant PTM-aware pLM, PTM-Mamba , improves upon ESM-2's performance on various PTM-specific tasks. PTM-Mamba is the first and only pLM that can uniquely input and represent both wild-type and PTM sequences, motivating downstream modeling and design applications specific to post-translationally modified proteins. To facilitate PTM-aware protein language modeling applications, we have made our model available at: https://huggingface.co/ChatterjeeLab/PTM-Mamba .
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48
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Lawer A, Schulz L, Sawyer R, Liu X. Harmony of Protein Tags and Chimeric Molecules Empowers Targeted Protein Ubiquitination and Beyond. Cells 2024; 13:426. [PMID: 38474390 DOI: 10.3390/cells13050426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Post-translational modifications (PTMs) are crucial mechanisms that underlie the intricacies of biological systems and disease mechanisms. This review focuses on the latest advancements in the design of heterobifunctional small molecules that hijack PTM machineries for target-specific modifications in living systems. A key innovation in this field is the development of proteolysis-targeting chimeras (PROTACs), which promote the ubiquitination of target proteins for proteasomal degradation. The past decade has seen several adaptations of the PROTAC concept to facilitate targeted (de)phosphorylation and acetylation. Protein fusion tags have been particularly vital in these proof-of-concept studies, aiding in the investigation of the functional roles of post-translationally modified proteins linked to diseases. This overview delves into protein-tagging strategies that enable the targeted modulation of ubiquitination, phosphorylation, and acetylation, emphasizing the synergies and challenges of integrating heterobifunctional molecules with protein tags in PTM research. Despite significant progress, many PTMs remain to be explored, and protein tag-assisted PTM-inducing chimeras will continue to play an important role in understanding the fundamental roles of protein PTMs and in exploring the therapeutic potential of manipulating protein modifications, particularly for targets not yet addressed by existing drugs.
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Affiliation(s)
- Aggie Lawer
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
| | - Luke Schulz
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Renata Sawyer
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
| | - Xuyu Liu
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
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49
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Helms A, Brodbelt JS. Mass Spectrometry Strategies for O-Glycoproteomics. Cells 2024; 13:394. [PMID: 38474358 DOI: 10.3390/cells13050394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Glycoproteomics has accelerated in recent decades owing to numerous innovations in the analytical workflow. In particular, new mass spectrometry strategies have contributed to inroads in O-glycoproteomics, a field that lags behind N-glycoproteomics due to several unique challenges associated with the complexity of O-glycosylation. This review will focus on progress in sample preparation, enrichment strategies, and MS/MS techniques for the identification and characterization of O-glycoproteins.
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Affiliation(s)
- Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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50
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Zhang H, Zhou Z, Guo J. The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species. Int J Mol Sci 2024; 25:2574. [PMID: 38473819 DOI: 10.3390/ijms25052574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.
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Affiliation(s)
- Haoran Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zengxuan Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinhu Guo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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