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Xiao P, Meng L, Cui X, Liu X, Qin L, Meng F, Cai X, Kong D, An T, Wang H. VP0 Myristoylation Is Essential for Senecavirus A Replication. Pathogens 2024; 13:601. [PMID: 39057827 PMCID: PMC11280471 DOI: 10.3390/pathogens13070601] [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: 06/19/2024] [Revised: 07/19/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024] Open
Abstract
Many picornaviruses require the myristoylation of capsid proteins for viral replication. Myristoylation is a site-specific lipidation to the N-terminal G residue of viral proteins, which is catalyzed by the ubiquitous eukaryotic enzyme N-myristoyltransferase (NMT) by allocating the myristoyl group to the N-terminal G residue. IMP-1088 and DDD85646 are two inhibitors that can deprive NMT biological functions. Whether Senecavirus A (SVA) uses NMT to modify VP0 and regulate viral replication remains unclear. Here, we found that NMT inhibitors could inhibit SVA replication. NMT1 knock-out in BHK-21 cells significantly suppressed viral replication. In contrast, the overexpression of NMT1 in BHK-21 cells benefited viral replication. These results indicated that VP0 is a potential NMT1 substrate. Moreover, we found that the myristoylation of SVA VP0 was correlated to the subcellular distribution of this protein in the cytoplasm. Further, we evaluated which residues at the N-terminus of VP0 are essential for viral replication. The substitution of N-terminal G residue, the myristoylation site of VP0, produced a nonviable virus. The T residue at the fifth position of the substrates facilitates the binding of the substrates to NMT. And our results showed that the T residue at the fifth position of VP0 played a positive role in SVA replication. Taken together, we demonstrated that SVA VP0 myristoylation plays an essential role in SVA replication.
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Affiliation(s)
- Peiyu Xiao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
| | - Liang Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
| | - Xingyang Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
| | - Xinran Liu
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York, NY 10591, USA;
| | - Lei Qin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
| | - Fandan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
- Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin 150069, China
| | - Dongni Kong
- Institute of Veterinary Drug Control, No. 8 Nandajie, Zhongguancun, Haidian, Beijing 100081, China;
| | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin 150069, China
| | - Haiwei Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (P.X.); (L.M.); (X.C.); qinlei-@163.com (L.Q.); (F.M.); (X.C.)
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin 150069, China
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Hering M, Madi A, Sandhoff R, Ma S, Wu J, Mieg A, Richter K, Mohr K, Knabe N, Stichling D, Poschet G, Bestvater F, Frank L, Utikal J, Umansky V, Cui G. Sphinganine recruits TLR4 adaptors in macrophages and promotes inflammation in murine models of sepsis and melanoma. Nat Commun 2024; 15:6067. [PMID: 39025856 PMCID: PMC11258287 DOI: 10.1038/s41467-024-50341-w] [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: 06/24/2023] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
After recognizing its ligand lipopolysaccharide, Toll-like receptor 4 (TLR4) recruits adaptor proteins to the cell membrane, thereby initiating downstream signaling and triggering inflammation. Whether this recruitment of adaptor proteins is dependent solely on protein-protein interactions is unknown. Here, we report that the sphingolipid sphinganine physically interacts with the adaptor proteins MyD88 and TIRAP and promotes MyD88 recruitment in macrophages. Myeloid cell-specific deficiency in serine palmitoyltransferase long chain base subunit 2, which encodes the key enzyme catalyzing sphingolipid biosynthesis, decreases the membrane recruitment of MyD88 and inhibits inflammatory responses in in vitro bone marrow-derived macrophage and in vivo sepsis models. In a melanoma mouse model, serine palmitoyltransferase long chain base subunit 2 deficiency decreases anti-tumor myeloid cell responses and increases tumor growth. Therefore, sphinganine biosynthesis is required for the initiation of TLR4 signal transduction and serves as a checkpoint for macrophage pattern recognition in sepsis and melanoma mouse models.
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Affiliation(s)
- Marvin Hering
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim (UMM), Ruprecht-Karls University of Heidelberg, Mannheim, Germany.
- DKFZ Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany.
| | - Alaa Madi
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roger Sandhoff
- Lipid Pathobiochemistry Group (A411), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sicong Ma
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, China
| | - Jingxia Wu
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, China
| | - Alessa Mieg
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karsten Richter
- Electron Microscopy Core Facility (W230), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kerstin Mohr
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nora Knabe
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz (HI-TRON Mainz)-A Helmholtz Institute of the DKFZ, Mainz, Germany
| | - Diana Stichling
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Felix Bestvater
- Light Microscopy Core Facility (W210), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Larissa Frank
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Cellular Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim (UMM), Ruprecht-Karls University of Heidelberg, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany
| | - Viktor Umansky
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim (UMM), Ruprecht-Karls University of Heidelberg, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Guoliang Cui
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, China.
- Helmholtz Institute for Translational Oncology, Mainz (HI-TRON Mainz)-A Helmholtz Institute of the DKFZ, Mainz, Germany.
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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Huang P, Xiang T, Wang Q, Han L, Zheng S, Zhang D, Huang F, Duan B, Li J, Li H, Huang T. Protective effect of Xixin-Ganjiang herb pair for warming the lungs to dissolve phlegm in chronic obstructive pulmonary disease rats based on integrated network pharmacology and metabolomics. Biomed Chromatogr 2024; 38:e5851. [PMID: 38449348 DOI: 10.1002/bmc.5851] [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: 09/29/2023] [Revised: 01/21/2024] [Accepted: 02/03/2024] [Indexed: 03/08/2024]
Abstract
Xixin-Ganjiang herb pair (XGHP) is a classic combination for warming the lungs to dissolve phlegm and is often used to treat a variety of chronic lung diseases; it can treat the syndrome of cold phlegm obstruction of lungs. First, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to examine the composition of XGHP, and network pharmacology was used to predict its potential core targets and signaling pathways in the current study. Second, a rat model of chronic obstructive pulmonary disease (COPD) was established for assessing the anti-COPD activity of XGHP, and metabolomics was used to explore the biomarkers and metabolic pathways. Finally, the sample was validated using molecular docking and Western blotting. The integration of metabolomics and network pharmacology results identified 11 targets, 3 biomarkers, 3 pathways, and 2 metabolic pathways. Western blotting showed that XGHP effectively regulated the expression of core proteins via multiple signaling pathways (downregulation of toll-like receptor 4 [TLR4] and upregulation of serine/threonine-protein kinase 1 [p-AKT1] and nitric oxide synthase 3 [NOS3]). Molecular docking results showed that the 10 potentially active components of XGHP have good affinity with tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), matrix metalloproteinase 9 (MMP-9), TLR4, p-AKT1, and NOS3. Our findings suggest that XGHP may regulate glucolipid metabolism, improve energy supply, and inhibit inflammatory responses (TNF-α, IL-6, and MMP-9) via the PI3K-Akt signaling pathway and HIF-1 signaling pathway in the management of COPD.
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Affiliation(s)
- Ping Huang
- Department of Rehabilitation Medicine, General Hospital of Central Theater Command, Wuhan, China
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Ting Xiang
- Department of Rehabilitation Medicine, General Hospital of Central Theater Command, Wuhan, China
| | - Qiong Wang
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Lintao Han
- Pharmacy School, Hubei University of Chinese Medicine, Wuhan, China
- Key Laboratory of Traditional Chinese Medicine Resource and Prescription, Ministry of Education, Wuhan, China
| | - Sili Zheng
- Pharmacy School, Hubei University of Chinese Medicine, Wuhan, China
| | - Dongning Zhang
- Pharmacy School, Hubei University of Chinese Medicine, Wuhan, China
| | - Fang Huang
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Bailu Duan
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Jingjing Li
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Huamao Li
- Department of Rehabilitation Medicine, General Hospital of Central Theater Command, Wuhan, China
| | - Tao Huang
- Department of Orthopedics, Wuhan Red Cross Hospital, Wuhan, China
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Gu Y, Wei K, Wang J. Phase separation and transcriptional regulation in cancer development. J Biomed Res 2024; 38:307-321. [PMID: 39113127 PMCID: PMC11300516 DOI: 10.7555/jbr.37.20230214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 08/10/2024] Open
Abstract
Liquid-liquid phase separation, a novel biochemical phenomenon, has been increasingly studied for its medical applications. It underlies the formation of membrane-less organelles and is involved in many cellular and biological processes. During transcriptional regulation, dynamic condensates are formed through interactions between transcriptional elements, such as transcription factors, coactivators, and mediators. Cancer is a disease characterized by uncontrolled cell proliferation, but the precise mechanisms underlying tumorigenesis often remain to be elucidated. Emerging evidence has linked abnormal transcriptional condensates to several diseases, especially cancer, implying that phase separation plays an important role in tumorigenesis. Condensates formed by phase separation may have an effect on gene transcription in tumors. In the present review, we focus on the correlation between phase separation and transcriptional regulation, as well as how this phenomenon contributes to cancer development.
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Affiliation(s)
- Yan Gu
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Ke Wei
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jun Wang
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Peng Z, Ding YN, Yang ZM, Li XJ, Zhuang Z, Lu Y, Tang QS, Hang CH, Li W. Neuron-targeted liposomal coenzyme Q10 attenuates neuronal ferroptosis after subarachnoid hemorrhage by activating the ferroptosis suppressor protein 1/coenzyme Q10 system. Acta Biomater 2024; 179:325-339. [PMID: 38561074 DOI: 10.1016/j.actbio.2024.03.023] [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: 12/18/2023] [Revised: 03/07/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
Subarachnoid hemorrhage (SAH) is primarily attributed to the rupture of intracranial aneurysms and is associated with a high incidence of disability and mortality. SAH disrupts the blood‒brain barrier, leading to the release of iron ions from blood within the subarachnoid space, subsequently inducing neuronal ferroptosis. A recently discovered protein, known as ferroptosis suppressor protein 1 (FSP1), exerts anti-ferroptotic effects by facilitating the conversion of oxidative coenzyme Q 10 (CoQ10) to its reduced form, which effectively scavenges reactive oxygen radicals and mitigates iron-induced ferroptosis. In our investigation, we observed an increase in FSP1 levels following SAH. However, the depletion of CoQ10 caused by SAH hindered the biological function of FSP1. Therefore, we created neuron-targeted liposomal CoQ10 by introducing the neuron-targeting peptide Tet1 onto the surface of liposomal CoQ10. Our objective was to determine whether this formulation could activate the FSP1 system and subsequently inhibit neuronal ferroptosis. Our findings revealed that neuron-targeted liposomal CoQ10 effectively localized to neurons at the lesion site after SAH. Furthermore, it facilitated the upregulation of FSP1, reduced the accumulation of malondialdehyde and reactive oxygen species, inhibited neuronal ferroptosis, and exerted neuroprotective effects both in vitro and in vivo. Our study provides evidence that supplementation with CoQ10 can effectively activate the FSP1 system. Additionally, we developed a neuron-targeted liposomal CoQ10 formulation that can be selectively delivered to neurons at the site of SAH. This innovative approach represents a promising therapeutic strategy for neuronal ferroptosis following SAH. STATEMENT OF SIGNIFICANCE: Subarachnoid hemorrhage (SAH) is primarily attributed to the rupture of intracranial aneurysms and is associated with a high incidence of disability and mortality. Ferroptosis suppressor protein 1 (FSP1), exerts anti-ferroptotic effects by facilitating the conversion of oxidative coenzyme Q 10 (CoQ10) to its reduced form, which effectively scavenges reactive oxygen radicals and mitigates iron-induced ferroptosis. In our investigation, we observed an increase in FSP1 levels following SAH. However, the depletion of CoQ10 caused by SAH hindered the biological function of FSP1. Therefore, we created neuron-targeted liposomal CoQ10. We find that it effectively localized to neurons at the lesion site after SAH and activated the FSP1/CoQ10 system. This innovative approach represents a promising therapeutic strategy for neuronal ferroptosis following SAH and other central nervous system diseases characterized by disruption of the blood-brain barrier.
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Affiliation(s)
- Zheng Peng
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
| | - Yi-Nan Ding
- Department of Interventional Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
| | | | - Xiao-Jian Li
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
| | - Zong Zhuang
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
| | - Yue Lu
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
| | - Qiu-Sha Tang
- Medical School of Southeast University, Nanjing, China.
| | - Chun-Hua Hang
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
| | - Wei Li
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
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Lu M, Wang X, Sun N, Huang S, Yang L, Li D. Metabolomics of cerebrospinal fluid reveals candidate diagnostic biomarkers to distinguish between spinal muscular atrophy type II and type III. CNS Neurosci Ther 2024; 30:e14718. [PMID: 38615366 PMCID: PMC11016346 DOI: 10.1111/cns.14718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/13/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024] Open
Abstract
AIMS Classification of spinal muscular atrophy (SMA) is associated with the clinical prognosis; however, objective classification markers are scarce. This study aimed to identify metabolic markers in the cerebrospinal fluid (CSF) of children with SMA types II and III. METHODS CSF samples were collected from 40 patients with SMA (27 with type II and 13 with type III) and analyzed for metabolites. RESULTS We identified 135 metabolites associated with SMA types II and III. These were associated with lysine degradation and arginine, proline, and tyrosine metabolism. We identified seven metabolites associated with the Hammersmith Functional Motor Scale: 4-chlorophenylacetic acid, adb-chminaca,(+/-)-, dodecyl benzenesulfonic acid, norethindrone acetate, 4-(undecan-5-yl) benzene-1-sulfonic acid, dihydromaleimide beta-d-glucoside, and cinobufagin. Potential typing biomarkers, N-cyclohexylformamide, cinobufagin, cotinine glucuronide, N-myristoyl arginine, 4-chlorophenylacetic acid, geranic acid, 4-(undecan-5-yl) benzene, and 7,8-diamino pelargonate, showed good predictive performance. Among these, N-myristoyl arginine was unaffected by the gene phenotype. CONCLUSION This study identified metabolic markers are promising candidate prognostic factors for SMA. We also identified the metabolic pathways associated with the severity of SMA. These assessments can help predict the outcomes of screening SMA classification biomarkers.
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Affiliation(s)
- Mengnan Lu
- Department of Pediatricsthe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Xueying Wang
- Department of Pediatricsthe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Na Sun
- Department of Pediatricsthe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Shaoping Huang
- Department of Pediatricsthe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Lin Yang
- Department of Pediatricsthe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Dan Li
- Department of Pediatricsthe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
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Rode S, Kaur H, Sharma M, Shah V, Singh SS, Gubyad M, Ghosh DK, Sircar D, Kumar P, Roy P, Sharma AK. Characterization of Type1 Lipid Transfer Protein from Citrus sinensis: Unraveling its potential as an antimicrobial and insecticidal agent. Int J Biol Macromol 2024; 265:130811. [PMID: 38490399 DOI: 10.1016/j.ijbiomac.2024.130811] [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: 09/30/2023] [Revised: 12/27/2023] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
Lipid Transfer Protein1 (LTP1) is a cationic, multifaceted protein belonging to the pathogenesis-related protein (PR14) family. Despite being involved in diverse physiological processes and defense mechanisms, the precise in-vivo role of LTP1 remains undiscovered. This work presents the characterization of recombinant Citrus sinensis LTP1 (CsLTP1) along with lipid binding studies through in-silico and in-vitro approaches. CsLTP1 demonstrated great thermal and pH stability with a huge biotechnological potential. It showed in-vitro binding capacity with jasmonic acid and lipids involved in regulating plant immune responses. Gene expression profiling indicated a significant upregulation of CsLTP1 in Candidatus-infected Citrus plants. CsLTP1 disrupted the cell membrane integrity of various pathogens, making it a potent antimicrobial agent. Further, in-vivo antimicrobial and insecticidal properties of CsLTP1 have been explored. The impact of exogenous CsLTP1 treatment on rice crop metabolism for managing blight disease has been studied using GC-MS. CsLTP1 triggered crucial metabolic pathways in rice plants while controlling the blight disease. CsLTP1 effectively inhibited Helicoverpa armigera larvae by impeding mid-gut α-amylase activity and obstructing its developmental stages. This study highlights the pivotal role of CsLTP1 in plant defense by offering insights for developing multi-target therapeutic agent or disease-resistant varieties to comprehensively tackle the challenges towards crop protection.
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Affiliation(s)
- Surabhi Rode
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Harry Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Monica Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Vivek Shah
- Division of Crop Protection, ICAR Central Institute for Cotton Research, Nagpur, India
| | - Shiv Shakti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Mrugendra Gubyad
- Plant Virology Laboratory, Central Citrus Research Institute, Nagpur, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, Central Citrus Research Institute, Nagpur, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Partha Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India.
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Yuan Y, Li P, Li J, Zhao Q, Chang Y, He X. Protein lipidation in health and disease: molecular basis, physiological function and pathological implication. Signal Transduct Target Ther 2024; 9:60. [PMID: 38485938 PMCID: PMC10940682 DOI: 10.1038/s41392-024-01759-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 03/18/2024] Open
Abstract
Posttranslational modifications increase the complexity and functional diversity of proteins in response to complex external stimuli and internal changes. Among these, protein lipidations which refer to lipid attachment to proteins are prominent, which primarily encompassing five types including S-palmitoylation, N-myristoylation, S-prenylation, glycosylphosphatidylinositol (GPI) anchor and cholesterylation. Lipid attachment to proteins plays an essential role in the regulation of protein trafficking, localisation, stability, conformation, interactions and signal transduction by enhancing hydrophobicity. Accumulating evidence from genetic, structural, and biomedical studies has consistently shown that protein lipidation is pivotal in the regulation of broad physiological functions and is inextricably linked to a variety of diseases. Decades of dedicated research have driven the development of a wide range of drugs targeting protein lipidation, and several agents have been developed and tested in preclinical and clinical studies, some of which, such as asciminib and lonafarnib are FDA-approved for therapeutic use, indicating that targeting protein lipidations represents a promising therapeutic strategy. Here, we comprehensively review the known regulatory enzymes and catalytic mechanisms of various protein lipidation types, outline the impact of protein lipidations on physiology and disease, and highlight potential therapeutic targets and clinical research progress, aiming to provide a comprehensive reference for future protein lipidation research.
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Affiliation(s)
- Yuan Yuan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyuan Li
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianghui Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Xingxing He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
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9
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Chang I, Loo YL, Patel J, Nguyen JT, Kim JK, Krebsbach PH. Targeting of lysosomal-bound protein mEAK-7 for cancer therapy. Front Oncol 2024; 14:1375498. [PMID: 38532930 PMCID: PMC10963491 DOI: 10.3389/fonc.2024.1375498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
mEAK-7 (mammalian EAK-7 or MTOR-associated protein, eak-7 homolog), is an evolutionarily conserved lysosomal membrane protein that is highly expressed in several cancer cells. Multiple recent studies have identified mEAK-7 as a positive activator of mTOR (mammalian/mechanistic target of rapamycin) signaling via an alternative mTOR complex, implying that mEAK-7 plays an important role in the promotion of cancer proliferation and migration. In addition, structural analyses investigating interactions between mEAK-7 and V-ATPase, a protein complex responsible for regulating pH homeostasis in cellular compartments, have suggested that mEAK-7 may contribute to V-ATPase-mediated mTORC1 activation. The C-terminal α-helix of mEAK-7 binds to the D and B subunits of the V-ATPase, creating a pincer-like grip around its B subunit. This binding undergoes partial disruption during ATP hydrolysis, potentially enabling other proteins such as mTOR to bind to the α-helix of mEAK-7. mEAK-7 also promotes chemoresistance and radiation resistance by sustaining DNA damage-mediated mTOR signaling through interactions with DNA-PKcs (DNA-dependent protein kinase catalytic subunit). Taken together, these findings indicate that mEAK-7 may be a promising therapeutic target against tumors. However, the precise molecular mechanisms and signal transduction pathways of mEAK-7 in cancer remain largely unknown, motivating the need for further investigation. Here, we summarize the current known roles of mEAK-7 in normal physiology and cancer development by reviewing the latest studies and discuss potential future developments of mEAK-7 in targeted cancer therapy.
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Affiliation(s)
- Insoon Chang
- Section of Endodontics, Division of Regenerative and Reconstructive Sciences, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yi-Ling Loo
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jay Patel
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Joe Truong Nguyen
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Oral Immunobiology Unit, National Institutes of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Jin Koo Kim
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Paul H Krebsbach
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
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10
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Kremer A, Ryaykenen T, Haraszti RA. Systematic optimization of siRNA productive uptake into resting and activated T cells ex vivo. Biomed Pharmacother 2024; 172:116285. [PMID: 38382331 DOI: 10.1016/j.biopha.2024.116285] [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: 11/24/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024] Open
Abstract
RNA-based medicines are ideally suited for precise modulation of T cell phenotypes in anti-cancer immunity, in autoimmune diseases and for ex vivo modulation of T-cell-based therapies. Therefore, understanding productive siRNA uptake to T cells is of particular importance. Most studies used unmodified siRNAs or commercially available siRNAs with undisclosed chemical modification patterns to show functionality in T cells. Despite being an active field of research, robust siRNA delivery to T cells still represents a formidable challenge. Therefore, a systematic approach is needed to further optimize and understand productive siRNA uptake pathways to T cells. Here, we compared conjugate-mediated and nanoparticle-mediated delivery of siRNAs to T cells in the context of fully chemically modified RNA constructs. We showed that lipid-conjugate-mediated delivery outperforms lipid-nanoparticle-mediated and extracellular-vesicle-mediated delivery in activated T cells ex vivo. Yet, ex vivo manipulation of T cells without the need of activation is of great therapeutic interest for CAR-T, engineered TCR-T and allogeneic donor lymphocyte applications. We are first to report productive siRNA uptake into resting T cells using lipid-conjugate-mediated delivery. Interestingly, we observed strong dependence of silencing activity on lipid-conjugate-identity in resting T cells but not in activated T cells. This phenomenon is consistent with our early uptake kinetics data. Lipid-conjugates also enabled delivery of siRNA to all mononuclear immune cell types, including both lymphoid and myeloid lineages. These findings are expected to be broadly applicable for ex vivo modulation of immune cell therapies.
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Affiliation(s)
- A Kremer
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Germany; Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University Tuebingen, Germany
| | - T Ryaykenen
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Germany; Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University Tuebingen, Germany
| | - R A Haraszti
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Germany; Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University Tuebingen, Germany.
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11
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Kava E, Garbelotti CV, Lopes JLS, Costa-Filho AJ. Myristoylated GRASP55 dimerizes in the presence of model membranes. J Biomol Struct Dyn 2024:1-12. [PMID: 38361284 DOI: 10.1080/07391102.2024.2317973] [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: 10/13/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
The Golgi Reassembly and Stacking Proteins (GRASPs) are engaged in various functions within the cell, both in unconventional secretion mechanisms and structuring and organizing the Golgi apparatus. Understanding their specific role in each situation still requires more structural and functional data at the molecular level. GRASP55 is one of the GRASP members in mammals, anchored to the membrane via the myristoylation of a Gly residue at its N-terminus. Therefore, co-translational modifications, such as myristoylation, are fundamental when considering a strategy to obtain detailed information on the interactions between GRASP55 and membranes. Despite its functional relevance, the N-terminal myristoylation has been underappreciated in the studies reported to date, compromising the previously proposed models for GRASP-membrane interactions. Here, we investigated the synergy between the presence of the membrane and the formation of oligomeric structures of myristoylated GRASP55, using a series of biophysical techniques to perform the structural characterization of the lipidated GRASP55 and its interaction with biological lipid model membranes. Our data fulfill an unexplored gap: the adequate evaluation of the presence of lipidations and lipid membranes on the structure-function dyad of GRASPs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Emanuel Kava
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Carolina V Garbelotti
- Laboratório de Fisiologia Ecológica de Plantas, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Luiz S Lopes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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12
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Liu F, Qu PY, Li JP, Yang LN, Geng YJ, Lu JY, Zhang Y, Li S. Arabidopsis protein S-acyl transferases positively mediate BR signaling through S-acylation of BSK1. Proc Natl Acad Sci U S A 2024; 121:e2322375121. [PMID: 38315835 PMCID: PMC10873554 DOI: 10.1073/pnas.2322375121] [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: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Protein S-acyl transferases (PATs) catalyze S-acylation, a reversible post-translational modification critical for membrane association, trafficking, and stability of substrate proteins. Many plant proteins are potentially S-acylated but few have corresponding PATs identified. By using genomic editing, confocal imaging, pharmacological, genetic, and biochemical assays, we demonstrate that three Arabidopsis class C PATs positively regulate BR signaling through S-acylation of BRASSINOSTEROID-SIGNALING KINASE1 (BSK1). PAT19, PAT20, and PAT22 associate with the plasma membrane (PM) and the trans-Golgi network/early endosome (TGN/EE). Functional loss of all three genes results in a plethora of defects, indicative of reduced BR signaling and rescued by enhanced BR signaling. PAT19, PAT20, and PAT22 interact with BSK1 and are critical for the S-acylation of BSK1, and for BR signaling. The PM abundance of BSK1 was reduced by functional loss of PAT19, PAT20, and PAT22 whereas abolished by its S-acylation-deficient point mutations, suggesting a key role of S-acylation in its PM targeting. Finally, an active BR analog induces vacuolar trafficking and degradation of PAT19, PAT20, or PAT22, suggesting that the S-acylation of BSK1 by the three PATs serves as a negative feedback module in BR signaling.
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Affiliation(s)
- Fei Liu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Peng-Yu Qu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Ji-Peng Li
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
| | - Li-Na Yang
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
| | - Yuan-Jun Geng
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
| | - Jin-Yu Lu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Yan Zhang
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Sha Li
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
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13
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Xu S, Xu X, Wang Z, Wu R. A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability. Angew Chem Int Ed Engl 2024; 63:e202315286. [PMID: 38117010 PMCID: PMC10981938 DOI: 10.1002/anie.202315286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
The N-termini of proteins can regulate their degradation, and the same protein with different N-termini may have distinct dynamics. Recently, it was found that N-terminal glycine can serve as a degron recognized by two E3 ligases, but N-terminal glycine was also reported to stabilize proteins. Here we developed a chemoenzymatic method for selective enrichment of proteoforms with N-terminal glycine and integrated dual protease cleavage to further improve the enrichment specificity. Over 2000 unique peptides with protein N-terminal glycine were analyzed from >1000 proteins, and most of them are previously unknown, indicating the effectiveness of the current method to capture low-abundance proteoforms with N-terminal glycine. The degradation rates of proteoforms with N-terminal glycine were quantified along with those of proteins from the whole proteome. Bioinformatic analyses reveal that proteoforms with N-terminal glycine with the fastest and slowest degradation rates have different functions and localizations. Membrane proteins with N-terminal glycine and proteins with N-terminal glycine from the N-terminal methionine excision degrade more rapidly. Furthermore, the secondary structures, adjacent amino acid residues, and protease specificities for N-terminal glycine are also vital for protein degradation. The results advance our understanding of the effects of N-terminal glycine on protein properties and functions.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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14
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Gamerdinger M, Deuerling E. Cotranslational sorting and processing of newly synthesized proteins in eukaryotes. Trends Biochem Sci 2024; 49:105-118. [PMID: 37919225 DOI: 10.1016/j.tibs.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023]
Abstract
Ribosomes interact with a variety of different protein biogenesis factors that guide newly synthesized proteins to their native 3D shapes and cellular localization. Depending on the type of translated substrate, a distinct set of cotranslational factors must interact with the ribosome in a timely and coordinated manner to ensure proper protein biogenesis. While cytonuclear proteins require cotranslational maturation and folding factors, secretory proteins must be maintained in an unfolded state and processed cotranslationally by transport and membrane translocation factors. Here we explore the specific cotranslational processing steps for cytonuclear, secretory, and membrane proteins in eukaryotes and then discuss how the nascent polypeptide-associated complex (NAC) cotranslationally sorts these proteins into the correct protein biogenesis pathway.
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Affiliation(s)
- Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany.
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany.
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15
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Hong S, Huh SU. Members of the Capsicum annuum CaTrxh Family Respond to High Temperature and Exhibit Dynamic Hetero/Homo Interactions. Int J Mol Sci 2024; 25:1729. [PMID: 38339006 PMCID: PMC10855718 DOI: 10.3390/ijms25031729] [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: 12/17/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Climate change adversely affects the water and temperature conditions required for plant growth, leading to a decrease in yield. In high temperatures, oxidative stress causes cellular damage in plant cells, which is a negative factor for crop production. Thioredoxin (Trx) is a small redox protein containing a conserved WC(G/P)PC motif that catalyzes the exchange of disulfide bonds. It is known to play an important role in maintaining cellular redox homeostasis. Trx proteins are widely distributed across various subcellular locations, and they play a crucial role in responding to cellular stresses. In this study, seven CaTrxh-type genes present in pepper were identified and the CaTrxh-type family was classified into three subgroups. CaTrxh genes responded to heat stress. Moreover, subcellular locations of the CaTrxh family exhibited dynamic patterns in normal conditions, and we observed relocalizations in heat stress conditions. Each CaTrxh family protein member formed homo-/heteromeric protein complexes in BiFC assay. Unexpectedly, subgroup III CaTrxh9 and CaTrxh10 can recruit subgroup I and II CaTrxh proteins into the plasma membrane. Thus, the function of the CaTrxh-type family is expected to play a protective role in the cell in response to high-temperature stress via protein complex formations. CaTrxh may have potential applications in the development of crops with enhanced tolerance to oxidative stress.
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Affiliation(s)
| | - Sung Un Huh
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea;
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16
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Zhang B, Yu Y, Fox BW, Liu Y, Thirumalaikumar VP, Skirycz A, Lin H, Schroeder FC. Amino acid and protein specificity of protein fatty acylation in C. elegans. Proc Natl Acad Sci U S A 2024; 121:e2307515121. [PMID: 38252833 PMCID: PMC10835129 DOI: 10.1073/pnas.2307515121] [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: 05/08/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Protein lipidation plays critical roles in regulating protein function and localization. However, the chemical diversity and specificity of fatty acyl group utilization have not been investigated using untargeted approaches, and it is unclear to what extent structures and biosynthetic origins of S-acyl moieties differ from N- and O-fatty acylation. Here, we show that fatty acylation patterns in Caenorhabditis elegans differ markedly between different amino acid residues. Hydroxylamine capture revealed predominant cysteine S-acylation with 15-methylhexadecanoic acid (isoC17:0), a monomethyl branched-chain fatty acid (mmBCFA) derived from endogenous leucine catabolism. In contrast, enzymatic protein hydrolysis showed that N-terminal glycine was acylated almost exclusively with straight-chain myristic acid, whereas lysine was acylated preferentially with two different mmBCFAs and serine was acylated promiscuously with a broad range of fatty acids, including eicosapentaenoic acid. Global profiling of fatty acylated proteins using a set of click chemistry-capable alkyne probes for branched- and straight-chain fatty acids uncovered 1,013 S-acylated proteins and 510 hydroxylamine-resistant N- or O-acylated proteins. Subsets of S-acylated proteins were labeled almost exclusively by either a branched-chain or a straight-chain probe, demonstrating acylation specificity at the protein level. Acylation specificity was confirmed for selected examples, including the S-acyltransferase DHHC-10. Last, homology searches for the identified acylated proteins revealed a high degree of conservation of acylation site patterns across metazoa. Our results show that protein fatty acylation patterns integrate distinct branches of lipid metabolism in a residue- and protein-specific manner, providing a basis for mechanistic studies at both the amino acid and protein levels.
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Affiliation(s)
- Bingsen Zhang
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Yan Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Bennett W. Fox
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Yinong Liu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | | | | | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- HHMI, Cornell University, Ithaca, NY14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - Frank C. Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
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17
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Harada H, Moriya K, Kobuchi H, Ishihara N, Utsumi T. Protein N-myristoylation plays a critical role in the mitochondrial localization of human mitochondrial complex I accessory subunit NDUFB7. Sci Rep 2023; 13:22991. [PMID: 38151566 PMCID: PMC10752898 DOI: 10.1038/s41598-023-50390-z] [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: 09/18/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023] Open
Abstract
The present study examined human N-myristoylated proteins that specifically localize to mitochondria among the 1,705 human genes listed in MitoProteome, a mitochondrial protein database. We herein employed a strategy utilizing cellular metabolic labeling with a bioorthogonal myristic acid analog in transfected COS-1 cells established in our previous studies. Four proteins, DMAC1, HCCS, NDUFB7, and PLGRKT, were identified as N-myristoylated proteins that specifically localize to mitochondria. Among these proteins, DMAC1 and NDUFB7 play critical roles in the assembly of complex I of the mitochondrial respiratory chain. DMAC1 functions as an assembly factor, and NDUFB7 is an accessory subunit of complex I. An analysis of the intracellular localization of non-myristoylatable G2A mutants revealed that protein N-myristoylation occurring on NDUFB7 was important for the mitochondrial localization of this protein. Furthermore, an analysis of the role of the CHCH domain in NDUFB7 using Cys to Ser mutants revealed that it was essential for the mitochondrial localization of NDUFB7. Therefore, the present results showed that NDUFB7, a vital component of human mitochondrial complex I, was N-myristoylated, and protein N-myrisotylation and the CHCH domain were both indispensable for the specific targeting and localization of NDUFB7 to mitochondria.
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Affiliation(s)
- Haruna Harada
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Koko Moriya
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Hirotsugu Kobuchi
- Department of Cell Chemistry, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Naotada Ishihara
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Toshihiko Utsumi
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.
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18
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Koukos PI, Dehghani-Ghahnaviyeh S, Velez-Vega C, Manchester J, Tieleman DP, Duca JS, Souza PCT, Cournia Z. Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications. J Chem Theory Comput 2023; 19:8901-8918. [PMID: 38019969 DOI: 10.1021/acs.jctc.3c00604] [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: 12/01/2023]
Abstract
Protein lipidations are vital co/post-translational modifications that tether lipid tails to specific protein amino acids, allowing them to anchor to biological membranes, switch their subcellular localization, and modulate association with other proteins. Such lipidations are thus crucial for multiple biological processes including signal transduction, protein trafficking, and membrane localization and are implicated in various diseases as well. Examples of lipid-anchored proteins include the Ras family of proteins that undergo farnesylation; actin and gelsolin that are myristoylated; phospholipase D that is palmitoylated; glycosylphosphatidylinositol-anchored proteins; and others. Here, we develop parameters for cysteine-targeting farnesylation, geranylgeranylation, and palmitoylation, as well as glycine-targeting myristoylation for the latest version of the Martini 3 coarse-grained force field. The parameters are developed using the CHARMM36m all-atom force field parameters as reference. The behavior of the coarse-grained models is consistent with that of the all-atom force field for all lipidations and reproduces key dynamical and structural features of lipid-anchored peptides, such as the solvent-accessible surface area, bilayer penetration depth, and representative conformations of the anchors. The parameters are also validated in simulations of the lipid-anchored peripheral membrane proteins Rheb and Arf1, after comparison with independent all-atom simulations. The parameters, along with mapping schemes for the popular martinize2 tool, are available for download at 10.5281/zenodo.7849262 and also as supporting information.
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Affiliation(s)
- Panagiotis I Koukos
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Sepehr Dehghani-Ghahnaviyeh
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John Manchester
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4 Alberta, Canada
- Centre for Molecular Simulation, University of Calgary, Calgary T2N 1N4 Alberta, Canada
| | - José S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, (MMSB, UMR 5086), CNRS & University of Lyon, 69367 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69364 Lyon, France
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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19
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Prasad A, Sharma S, Prasad M. Post translational modifications at the verge of plant-geminivirus interaction. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194983. [PMID: 37717937 DOI: 10.1016/j.bbagrm.2023.194983] [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: 05/31/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
Plant-virus interaction is a complex phenomenon and involves the communication between plant and viral factors. Viruses have very limited coding ability yet, they are able to cause infection which results in huge agro-economic losses throughout the globe each year. Post-translational modifications (PTMs) are covalent modifications of proteins that have a drastic effect on their conformation, stability and function. Like the host proteins, geminiviral proteins are also subject to PTMs and these modifications greatly expand the diversity of their functions. Additionally, these viral proteins can also interact with the components of PTM pathways and modulate them. Several studies have highlighted the importance of PTMs such as phosphorylation, ubiquitination, SUMOylation, myristoylation, S-acylation, acetylation and methylation in plant-geminivirus interaction. PTMs also regulate epigenetic modifications during geminivirus infection which determines viral gene expression. In this review, we have summarized the role of PTMs in regulating geminiviral protein function, influence of PTMs on viral gene expression and how geminiviral proteins interact with the components of PTM pathways to modulate their function.
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Affiliation(s)
- Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
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20
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Abstract
N-myristoyltransferase 1 (NMT1) is an indispensable eukaryotic enzyme that catalyses the transfer of myristoyl groups to the amino acid terminal residues of numerous proteins. This catalytic process is required for the growth and development of many eukaryotes and viruses. Elevated expression and activity of NMT1 is observed to varying degrees in a variety of tumour types (e.g. colon, lung and breast tumours). Furthermore, an elevated level of NMT1 in tumours is associated with poor survival. Therefore, a relationship exists between NMT1 and tumours. In this review, we discuss the underlying mechanisms by which NMT1 is associated with tumour development from the perspective of oncogene signalling, involvement in cellular metabolism, and endoplasmic reticulum stress. Several NMT inhibitors used in cancer treatment are introduced. The review will provide some directions for future research.Key MessagesElevated expression and activity of NMT1 is observed to varying degrees in a variety of tumour types which creates the possibility of targeting NMT1 in tumours.NMT1-mediated myristoylation plays a pivotal role in cancer cell metabolism and may be particularly relevant to cancer metastasis and drug resistance. These insights can be used to direct potential therapeutic avenues for NMT1 inhibitors.
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Affiliation(s)
- Hong Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Xu
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Thoracic OncologyShanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Thoracic OncologyShanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Medical Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongxia Qiao
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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21
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Anwar MU, van der Goot FG. Refining S-acylation: Structure, regulation, dynamics, and therapeutic implications. J Cell Biol 2023; 222:e202307103. [PMID: 37756661 PMCID: PMC10533364 DOI: 10.1083/jcb.202307103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
With a limited number of genes, cells achieve remarkable diversity. This is to a large extent achieved by chemical posttranslational modifications of proteins. Amongst these are the lipid modifications that have the unique ability to confer hydrophobicity. The last decade has revealed that lipid modifications of proteins are extremely frequent and affect a great variety of cellular pathways and physiological processes. This is particularly true for S-acylation, the only reversible lipid modification. The enzymes involved in S-acylation and deacylation are only starting to be understood, and the list of proteins that undergo this modification is ever-increasing. We will describe the state of knowledge on the enzymes that regulate S-acylation, from their structure to their regulation, how S-acylation influences target proteins, and finally will offer a perspective on how alterations in the balance between S-acylation and deacylation may contribute to disease.
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Affiliation(s)
- Muhammad U. Anwar
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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22
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Rigante D, Leoni C, Onesimo R, Giorgio V, Trevisan V, Zampino G. Aberrant N-myristoylation as a prelude to autoimmune manifestations in patients with SHOC2 mutations. Autoimmun Rev 2023; 22:103462. [PMID: 37793491 DOI: 10.1016/j.autrev.2023.103462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Affiliation(s)
- Donato Rigante
- Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Università Cattolica Sacro Cuore, Rome, Italy.
| | - Chiara Leoni
- Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Roberta Onesimo
- Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Valentina Giorgio
- Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Università Cattolica Sacro Cuore, Rome, Italy
| | - Valentina Trevisan
- Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Università Cattolica Sacro Cuore, Rome, Italy
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23
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Geng S, Lu R, Zhang Y, Wu Y, Xie L, Caldwell B, Pradhan K, Yi Z, Hou J, Xu F, Chen X, Li L. Monocytes reprogrammed by 4-PBA potently contribute to the resolution of inflammation and atherosclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563200. [PMID: 37961551 PMCID: PMC10634693 DOI: 10.1101/2023.10.19.563200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Chronic inflammation initiated by inflammatory monocytes underlies the pathogenesis of atherosclerosis. However, approaches that can effectively resolve chronic low-grade inflammation targeting monocytes are not readily available. The small chemical compound 4-phenylbutyric acid (4-PBA) exhibits broad anti-inflammatory effects in reducing atherosclerosis. Selective delivery of 4-PBA reprogrammed monocytes may hold novel potential in providing targeted and precision therapeutics for the treatment of atherosclerosis. Methods Systems analyses integrating single-cell RNA-sequencing and complementary immunological approaches characterized key resolving characteristics as well as defining markers of reprogrammed monocytes trained by 4-PBA. Molecular mechanisms responsible for monocyte reprogramming was assessed by integrated biochemical and genetic approaches. The inter-cellular propagation of homeostasis resolution was evaluated by co-culture assays with donor monocytes trained by 4-PBA and recipient naïve monocytes. The in vivo effects of monocyte resolution and atherosclerosis prevention by 4-PBA were assessed with the high fat diet-fed ApoE -/- mouse model with i.p. 4-PBA administration. Furthermore, the selective efficacy of 4-PBA trained monocytes were examined by i.v. transfusion of ex vivo trained monocytes by 4-PBA into recipient high fat diet-fed ApoE -/- mice. Results In this study, we found that monocytes can be potently reprogrammed by 4-PBA into an immune-resolving state characterized by reduced adhesion and enhanced expression of anti-inflammatory mediator CD24. Mechanistically, 4-PBA reduced the expression of ICAM-1 via reducing peroxisome stress and attenuating SYK-mTOR signaling. Concurrently, 4-PBA enhanced the expression of resolving mediator CD24 through promoting PPARγ neddylation mediated by TOLLIP. 4-PBA trained monocytes can effectively propagate anti-inflammation activity to neighboring monocytes through CD24. Our data further demonstrated that 4-PBA trained monocytes effectively reduce atherosclerosis pathogenesis when administered in vivo . Conclusion Our study describes a robust and effective approach to generate resolving monocytes, characterizes novel mechanisms for targeted monocyte reprogramming, and offers a precision-therapeutics for atherosclerosis based on delivering reprogrammed resolving monocytes.
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24
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Pedretti M, Favretto F, Troilo F, Giovannoni M, Conter C, Mattei B, Dominici P, Travaglini-Allocatelli C, Di Matteo A, Astegno A. Role of myristoylation in modulating PCaP1 interaction with calmodulin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108003. [PMID: 37717348 DOI: 10.1016/j.plaphy.2023.108003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/09/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023]
Abstract
Plasma membrane-associated Cation-binding Protein 1 (PCaP1) belongs to the plant-unique DREPP protein family with largely unknown biological functions but ascertained roles in plant development and calcium (Ca2+) signaling. PCaP1 is anchored to the plasma membrane via N-myristoylation and a polybasic cluster, and its N-terminal region can bind Ca2+/calmodulin (CaM). However, the molecular determinants of PCaP1-Ca2+-CaM interaction and the functional impact of myristoylation in the complex formation and Ca2+ sensitivity of CaM remained to be elucidated. Herein, we investigated the direct interaction between Arabidopsis PCaP1 (AtPCaP1) and CaM1 (AtCaM1) using both myristoylated and non-myristoylated peptides corresponding to the N-terminal region of AtPCaP1. ITC analysis showed that AtCaM1 forms a high affinity 1:1 complex with AtPCaP1 peptides and the interaction is strictly Ca2+-dependent. Spectroscopic and kinetic Ca2+ binding studies showed that the myristoylated peptide dramatically increased the Ca2+-binding affinity of AtCaM1 and slowed the Ca2+ dissociation rates from both the C- and N-lobes, thus suggesting that the myristoylation modulates the mechanism of AtPCaP1 recognition by AtCaM1. Furthermore, NMR and CD spectroscopy revealed that the structure of both the N- and C-lobes of Ca2+-AtCaM1 changes markedly in the presence of the myristoylated AtPCaP1 peptide, which assumes a helical structure in the final complex. Overall, our results indicate that AtPCaP1 biological function is strictly related to the presence of multiple ligands, i.e., the myristoyl moiety, Ca2+ ions and AtCaM1 and only a full characterization of their equilibria will allow for a complete molecular understanding of the putative role of PCaP1 as signal protein.
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Affiliation(s)
- Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Filippo Favretto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Carolina Conter
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy.
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
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25
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Nascimento IJDS, Cavalcanti MDAT, de Moura RO. Exploring N-myristoyltransferase as a promising drug target against parasitic neglected tropical diseases. Eur J Med Chem 2023; 258:115550. [PMID: 37336067 DOI: 10.1016/j.ejmech.2023.115550] [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: 05/15/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Neglected tropical diseases (NTDs) constitute a group of approximately 20 infectious diseases that mainly affect the impoverished population without basic sanitation in tropical countries. These diseases are responsible for many deaths worldwide, costing billions of dollars in public health investment to treat and control these infections. Among them are the diseases caused by protozoa of the Trypanosomatid family, which constitute Trypanosoma cruzi (Chagas disease), Trypanosoma brucei (sleeping sickness), and Leishmaniasis. In addition, there is a classification of other diseases, called the big three, AIDS, tuberculosis, and malaria, which are endemic in countries with tropical conditions. Despite the high mortality rates, there is still a gap in the treatment. The drugs have a high incidence of side effects and protozoan resistance, justifying the investment in developing new alternatives. In fact, the Target-Based Drug Design (TBDD) approach is responsible for identifying several promising compounds, and among the targets explored through this approach, N-myristoyltransferase (NMT) stands out. It is an enzyme related to the co-translational myristoylation of N-terminal glycine in various peptides. The myristoylation process is a co-translation that occurs after removing the initiator methionine. This process regulates the assembly of protein complexes and stability, which justifies its potential as a drug target. In order to propose NMT as a potential target for parasitic diseases, this review will address the entire structure and function of this enzyme and the primary studies demonstrating its promising potential against Leishmaniasis, T. cruzi, T. brucei, and malaria. We hope our information can help researchers worldwide search for potential drugs against these diseases that have been threatening the health of the world's population.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Cesmac University Center, Pharmacy Departament, Maceió, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil.
| | - Misael de Azevedo Teotônio Cavalcanti
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Ricardo Olimpio de Moura
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
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26
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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27
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Wang H, Xu X, Wang Y, Xue X, Guo W, Guo S, Qiu S, Cui J, Qiao Y. NMT1 sustains ICAM-1 to modulate adhesion and migration of tumor cells. Cell Signal 2023:110739. [PMID: 37269961 DOI: 10.1016/j.cellsig.2023.110739] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/17/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Protein modifications have significant effects on tumorigenesis. N-Myristoylation is one of the most important lipidation modifications, and N-myristoyltransferase 1 (NMT1) is the main enzyme required for this process. However, the mechanism underlying how NMT1 modulates tumorigenesis remains largely unclear. Here, we found that NMT1 sustains cell adhesion and suppresses tumor cell migration. Intracellular adhesion molecule 1 (ICAM-1) was a potential functional downstream effector of NMT1, and its N-terminus could be N-myristoylated. NMT1 prevented ubiquitination and proteasome degradation of ICAM-1 by inhibiting Ub E3 ligase F-box protein 4, which prolonged the half-life of ICAM1 protein. Correlations between NMT1 and ICAM-1 were observed in liver and lung cancers, which were associated with metastasis and overall survival. Therefore, carefully designed strategies focusing on NMT1 and its downstream effectors might be helpful to treat tumors.
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Affiliation(s)
- Hong Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xin Xu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, China
| | - Yikun Wang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, China
| | - Xiangfei Xue
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, China
| | - Wanxin Guo
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, China
| | - Susu Guo
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, China
| | - Shiyu Qiu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, China
| | - Jiangtao Cui
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, China
| | - Yongxia Qiao
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.
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28
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Sakamaki JI, Mizushima N. Cell biology of protein-lipid conjugation. Cell Struct Funct 2023; 48:99-112. [PMID: 37019684 PMCID: PMC10721952 DOI: 10.1247/csf.23016] [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: 03/11/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Protein-lipid conjugation is a widespread modification involved in many biological processes. Various lipids, including fatty acids, isoprenoids, sterols, glycosylphosphatidylinositol, sphingolipids, and phospholipids, are covalently linked with proteins. These modifications direct proteins to intracellular membranes through the hydrophobic nature of lipids. Some of these membrane-binding processes are reversible through delipidation or by reducing the affinity to membranes. Many signaling molecules undergo lipid modification, and their membrane binding is important for proper signal transduction. The conjugation of proteins to lipids also influences the dynamics and function of organellar membranes. Dysregulation of lipidation has been associated with diseases such as neurodegenerative diseases. In this review, we first provide an overview of diverse forms of protein-lipid conjugation and then summarize the catalytic mechanisms, regulation, and roles of these modifications.Key words: lipid, lipidation, membrane, organelle, protein modification.
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Affiliation(s)
- Jun-ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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29
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Jamar G, Pisani LP. Inflammatory crosstalk between saturated fatty acids and gut microbiota-white adipose tissue axis. Eur J Nutr 2023; 62:1077-1091. [PMID: 36484808 DOI: 10.1007/s00394-022-03062-z] [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: 06/20/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE High-fat diets have different metabolic responses via gut dysbiosis. In this review, we discuss the complex interaction between the intake of long- and medium-chain saturated fatty acids (SFAs), gut microbiota, and white adipose tissue (WAT) dysfunction, particularly focusing on the type of fat. RESULTS The evidence for the impact of dietary SFAs on the gut microbiota-WAT axis has been mostly derived from in vitro and animal models, but there is now also evidence emerging from human studies. Most current reports show that, in response to high long- and medium-chain SFA diets, WAT functions are altered and can be modulated from microbial metabolites in several manners; and it appears to be also modified under conditions of obesity. SFAs overconsumption can reduce bacterial content and disrupt the gut environment. Both long- and medium-chain SFAs may contribute to proinflammatory cytokines release and TLR4 cascade signaling, either by regulation of endotoxemia markers or myristoylated protein. Palmitic and stearic acids have pathological effects on the intestinal epithelium, microbes, and inflammatory and lipogenic WAT profiles. While myristic and lauric acids display somewhat controversial outcomes, from probiotic effects and contribution to weight loss to cardiometabolic alterations from WAT inflammation. CONCLUSION Identifying an interference of distinct types of SFA in the binomial gut microbiota-WAT may elucidate essential mechanisms of metabolic endotoxemia, which may be the key to triggering obesity, innovating the therapeutic tools for this disease.
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Affiliation(s)
- Giovana Jamar
- Post-Graduate Program in Nutrition, Federal University of São Paulo-UNIFESP, São Paulo, SP, Brazil
- Department of Biosciences, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo-UNIFESP, Rua Silva Jardim, 136/311, Vila Mathias, Santos, SP, 11015-020, Brazil
| | - Luciana Pellegrini Pisani
- Post-Graduate Program in Nutrition, Federal University of São Paulo-UNIFESP, São Paulo, SP, Brazil.
- Department of Biosciences, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo-UNIFESP, Rua Silva Jardim, 136/311, Vila Mathias, Santos, SP, 11015-020, Brazil.
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30
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Islam S, Akhand MRN, Hasan M. Evolutionary trend of bovine β-defensin proteins toward functionality prediction: A domain-based bioinformatics study. Heliyon 2023; 9:e14158. [PMID: 36938430 PMCID: PMC10015202 DOI: 10.1016/j.heliyon.2023.e14158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Defensins are small cationic cysteine-rich and amphipathic peptides that form of three-dimensional β-strand structure connected by disulfide bonds. Defensins form key elements of the innate immune system of multicellular organisms. They not only possess broad-spectrum antimicrobial activity but also have diverse roles, including cell signaling, ion channel agitation, toxic functions, and enzyme inhibitor activities in various animals. Although the role of β-defensins in immune responses against infectious agents and reproduction could be significant, inadequate genomic information is available to explain the whole β-defensin repertoire in cattle. No domain or motif-based functional analyses have been previously reported. In addition, how do defensins possess this magnitude of functions in the immune system is still not clear. Our present study, therefore, investigated the sequence divergence and evolutionary relations of bovine defensin proteins with those of humans. Our domain-based evolutionary analysis revealed four major clusters with significant domain variation while reserving a main antimicrobial activity. Our study revealed the β-defensin domain as the ancestor domain, and it is preserved in the first group of defensin protein with no α-helix in its structure. Due to natural selection, some domains have evolved independently within clusters II and III, while some proteins have lost their domain characteristics. Cluster IV contains the most recently evolved domains. Some proteins of all but cluster I might have adopted the functional characteristics of α-defensins which is largely absent in cattle. The proteins show different patterns of disulfide bridges and multiple signature patterns which might render them specialized functions in different tissue to combat against various pathogens.
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Affiliation(s)
- Saiful Islam
- Department of Physiology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Mst Rubaiat Nazneen Akhand
- Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet-3100, Bangladesh
- Corresponding author.
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
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Myristic acid as a checkpoint to regulate STING-dependent autophagy and interferon responses by promoting N-myristoylation. Nat Commun 2023; 14:660. [PMID: 36750575 PMCID: PMC9905541 DOI: 10.1038/s41467-023-36332-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023] Open
Abstract
Stimulator of interferon gene (STING)-triggered autophagy is crucial for the host to eliminate invading pathogens and serves as a self-limiting mechanism of STING-induced interferon (IFN) responses. Thus, the mechanisms that ensure the beneficial effects of STING activation are of particular importance. Herein, we show that myristic acid, a type of long-chain saturated fatty acid (SFA), specifically attenuates cGAS-STING-induced IFN responses in macrophages, while enhancing STING-dependent autophagy. Myristic acid inhibits HSV-1 infection-induced innate antiviral immune responses and promotes HSV-1 replication in mice in vivo. Mechanistically, myristic acid enhances N-myristoylation of ARF1, a master regulator that controls STING membrane trafficking. Consequently, myristic acid facilitates STING activation-triggered autophagy degradation of the STING complex. Thus, our work identifies myristic acid as a metabolic checkpoint that contributes to immune homeostasis by balancing STING-dependent autophagy and IFN responses. This suggests that myristic acid and N-myristoylation are promising targets for the treatment of diseases caused by aberrant STING activation.
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32
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Byrne DP, Shrestha S, Daly LA, Marensi V, Ramakrishnan K, Eyers CE, Kannan N, Eyers PA. Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2. Biochem J 2023; 480:141-160. [PMID: 36520605 PMCID: PMC9988210 DOI: 10.1042/bcj20220474] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Pseudokinases, so named because they lack one or more conserved canonical amino acids that define their catalytically active relatives, have evolved a variety of biological functions in both prokaryotic and eukaryotic organisms. Human PSKH2 is closely related to the canonical kinase PSKH1, which maps to the CAMK family of protein kinases. Primates encode PSKH2 in the form of a pseudokinase, which is predicted to be catalytically inactive due to loss of the invariant catalytic Asp residue. Although the biological role(s) of vertebrate PSKH2 proteins remains unclear, we previously identified species-level adaptions in PSKH2 that have led to the appearance of kinase or pseudokinase variants in vertebrate genomes alongside a canonical PSKH1 paralog. In this paper we confirm that, as predicted, PSKH2 lacks detectable protein phosphotransferase activity, and exploit structural informatics, biochemistry and cellular proteomics to begin to characterise vertebrate PSKH2 orthologues. AlphaFold 2-based structural analysis predicts functional roles for both the PSKH2 N- and C-regions that flank the pseudokinase domain core, and cellular truncation analysis confirms that the N-terminal domain, which contains a conserved myristoylation site, is required for both stable human PSKH2 expression and localisation to a membrane-rich subcellular fraction containing mitochondrial proteins. Using mass spectrometry-based proteomics, we confirm that human PSKH2 is part of a cellular mitochondrial protein network, and that its expression is regulated through client-status within the HSP90/Cdc37 molecular chaperone system. HSP90 interactions are mediated through binding to the PSKH2 C-terminal tail, leading us to predict that this region might act as both a cis and trans regulatory element, driving outputs linked to the PSKH2 pseudokinase domain that are important for functional signalling.
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Affiliation(s)
- Dominic P. Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Safal Shrestha
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, U.S.A
| | - Leonard A. Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Vanessa Marensi
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Krithika Ramakrishnan
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, U.S.A
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, U.S.A
| | - Patrick A. Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
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Shang S, Liu J, Hua F. Protein acylation: mechanisms, biological functions and therapeutic targets. Signal Transduct Target Ther 2022; 7:396. [PMID: 36577755 PMCID: PMC9797573 DOI: 10.1038/s41392-022-01245-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/27/2022] [Accepted: 11/06/2022] [Indexed: 12/30/2022] Open
Abstract
Metabolic reprogramming is involved in the pathogenesis of not only cancers but also neurodegenerative diseases, cardiovascular diseases, and infectious diseases. With the progress of metabonomics and proteomics, metabolites have been found to affect protein acylations through providing acyl groups or changing the activities of acyltransferases or deacylases. Reciprocally, protein acylation is involved in key cellular processes relevant to physiology and diseases, such as protein stability, protein subcellular localization, enzyme activity, transcriptional activity, protein-protein interactions and protein-DNA interactions. Herein, we summarize the functional diversity and mechanisms of eight kinds of nonhistone protein acylations in the physiological processes and progression of several diseases. We also highlight the recent progress in the development of inhibitors for acyltransferase, deacylase, and acylation reader proteins for their potential applications in drug discovery.
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Affiliation(s)
- Shuang Shang
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| | - Jing Liu
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| | - Fang Hua
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
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Post-Translational Modifications by Lipid Metabolites during the DNA Damage Response and Their Role in Cancer. Biomolecules 2022; 12:biom12111655. [DOI: 10.3390/biom12111655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Genomic DNA damage occurs as an inevitable consequence of exposure to harmful exogenous and endogenous agents. Therefore, the effective sensing and repair of DNA damage are essential for maintaining genomic stability and cellular homeostasis. Inappropriate responses to DNA damage can lead to genomic instability and, ultimately, cancer. Protein post-translational modifications (PTMs) are a key regulator of the DNA damage response (DDR), and recent progress in mass spectrometry analysis methods has revealed that a wide range of metabolites can serve as donors for PTMs. In this review, we will summarize how the DDR is regulated by lipid metabolite-associated PTMs, including acetylation, S-succinylation, N-myristoylation, palmitoylation, and crotonylation, and the implications for tumorigenesis. We will also discuss potential novel targets for anti-cancer drug development.
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Protein Myristoylation Plays a Role in the Nuclear Entry of the Parvovirus Minute Virus of Mice. J Virol 2022; 96:e0111822. [PMID: 35950857 PMCID: PMC9472656 DOI: 10.1128/jvi.01118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Being nonpathogenic to humans, rodent parvoviruses (PVs) are naturally oncolytic viruses with great potential as anti-cancer agents. As these viruses replicate in the host cell nucleus, they must gain access to the nucleus during infection. The PV minute virus of mice (MVM) and several other PVs transiently disrupt the nuclear envelope (NE) and enter the nucleus through the resulting breaks. However, the molecular basis of this unique nuclear entry pathway remains uncharacterized. In this study, we used MVM as a model to investigate the molecular mechanism by which PVs induce NE disruption during viral nuclear entry. By combining bioinformatics analyses, metabolic labeling assays, mutagenesis, and pharmacological inhibition, we identified a functional myristoylation site at the sequence 78GGKVGH83 of the unique portion of the capsid protein VP1 (VP1u) of MVM. Performing proteolytic cleavage studies with a peptide containing this myristoylation site or with purified virions, we found tryptophan at position 77 of MVM VP1u is susceptible to chymotrypsin cleavage, implying this cleavage exposes G (glycine) 78 at the N-terminus of VP1u for myristoylation. Subsequent experiments using inhibitors of myristoylation and cellular proteases with MVM-infected cells, or an imaging-based quantitative NE permeabilization assay, further indicate protein myristoylation and a chymotrypsin-like activity are essential for MVM to locally disrupt the NE during viral nuclear entry. We thus propose a model for the nuclear entry of MVM in which NE disruption is mediated by VP1u myristoylation after the intact capsid undergoes proteolytic processing to expose the required N-terminal G for myristoylation. IMPORTANCE Rodent parvoviruses (PVs), including minute virus of mice (MVM), have the ability to infect and kill cancer cells and thereby possess great potential in anti-cancer therapy. In fact, some of these viruses are currently being investigated in both preclinical studies and clinical trials to treat a wide variety of cancers. However, the detailed mechanism of how PVs enter the cell nucleus remains unknown. In this study, we for the first time demonstrated a chemical modification called "myristoylation" of a MVM protein plays an essential role in the nuclear entry of the virus. We also showed, in addition to protein myristoylation, a chymotrypsin-like activity, which may come from cellular proteasomes, is required for MVM to get myristoylated and enter the nucleus. These findings deepen our understanding on how MVM and other related PVs infect host cells and provide new insights for the development of PV-based anti-cancer therapies.
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Wang PY, Yang X, Guo L, Wang YW, Zhang WL, Sun YX, Li J, Gan CY, Long SY, Liu JJ, Fan SY, Huang AL, Hu JL. Establishment of a human cell line with a surface display system for screening and optimizing Na+-taurocholate cotransporting polypeptide-binding peptides. Front Microbiol 2022; 13:920280. [PMID: 36060770 PMCID: PMC9428559 DOI: 10.3389/fmicb.2022.920280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
One of the most desirable targets for HBV medications is the sodium taurocholate cotransporting polypeptide (NTCP), an entry receptor for the hepatitis B virus (HBV). N-myristoylated preS1 2–48 (Myrcludex B or Hepcludex), an NTCP-binding peptide from the large surface protein of HBV, has been developed as the first-in-class entry inhibitor. However, its relatively large molecular weight contributes to increased immunogenicity and antibody production. As a result, it is preferable to look for an NTCP-binding peptide with a smaller size. To do this, we developed a human cell surface display strategy and screened peptides based on preS1-21. PreS1-21 (genotype D) was extended by 7 random amino acids and fused with mCherry and FasL transmembrane domain. The pooled constructs were transfected into HEK293 cells by using the transposon/transposase system to create a library displaying various peptides on the cell surface with red fluorescence. On the other hand, we expressed NTCP protein fused with EGFP on HEK293 and used the membrane lysate containing NTCP-GFP as the bait protein to select peptides with increased NTCP affinity. After 7 cycles of selection, the deep sequencing results revealed that some polypeptides were more than 1,000 times enriched. Further screening of the mostly enriched 10 peptides yields the peptide preS1-21-pep3. Replacing the preS1-21 sequence of preS1-21-pep3 with those from different genotypes demonstrated that the consensus sequence of genotype A–F had the best performance. The peptide (Myr-preS1-21-pep3) was synthesized and tested on the HepG2-NTCP cell model. The results showed that Myr-preS1-21-pep3 is approximately 10 times more potent than the initial peptide Myr-preS1-21 in preventing HBV infection. In conclusion, we developed a new strategy for screening peptides binding to membrane proteins and identified a new NTCP-binding peptide with a much smaller size than Hepcludex.
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Affiliation(s)
- Pei-yun Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xue Yang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Lin Guo
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-wei Wang
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
- Laboratory for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Wen-lu Zhang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-xue Sun
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jie Li
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Chun-yang Gan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shao-yuan Long
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jia-jun Liu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shu-ying Fan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ai-long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- *Correspondence: Ai-long Huang,
| | - Jie-Li Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- Jie-Li Hu,
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Tan YC, Lee GH, Huang DQ, Lim SG. Future anti-HDV treatment strategies, including those aimed at HBV functional cure. Liver Int 2022; 43:1157-1169. [PMID: 35946084 DOI: 10.1111/liv.15387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/11/2022] [Accepted: 08/08/2022] [Indexed: 02/13/2023]
Abstract
HDV is a defective virus that uses the HBV surface antigen to enter hepatocytes. It is associated with an accelerated course of liver fibrosis progression and an increased risk of hepatocellular carcinoma. Negative HDV RNA 24 weeks after the end of therapy has been proposed as an endpoint but late relapses make this endpoint suboptimal, hence HBsAg loss appears to be more appropriate. Current HBV antiviral agents have poor activity against HDV hence the search for improved therapy. Drugs only active against HDV, such as lonafarnib, have shown efficacy in combination with nucleoside analogues and peginterferon, but do not lead to HBsAg loss. HBsAg loss sustained 24 weeks after the end of therapy with negative HBV DNA is termed functional cure. Agents that are being investigated for functional cure include those that inhibit replication such as entry inhibitors, polymerase inhibitors and capsid assembly modulators but seldom lead to functional cure. Agents that reduce HBV antigen load such as RNA interference and inhibitors of HBsAg secretion are promising. Immunomodulators on their own seldom achieve functional cure, hence these agents in combination to assess the optimal combination are being investigated. Consequently, agents leading to functional cure of HBV are ideal for both HBV and HDV.
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Affiliation(s)
- Yong Chuan Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Guan Huei Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Daniel Q Huang
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Seng Gee Lim
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
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38
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Functional characterization of FBXL7 as a novel player in human cancers. Cell Death Dis 2022; 8:342. [PMID: 35906197 PMCID: PMC9338262 DOI: 10.1038/s41420-022-01143-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
F-box and leucine-rich repeat protein 7 (FBXL7), an F-box protein responsible for substrate recognition by the SKP1-Cullin-1-F-box (SCF) ubiquitin ligases, plays an emerging role in the regulation of tumorigenesis and tumor progression. FBXL7 promotes polyubiquitylation and degradation of diverse substrates and is involved in many biological processes, including apoptosis, cell proliferation, cell migration and invasion, tumor metastasis, DNA damage, glucose metabolism, planar cell polarity, and drug resistance. In this review, we summarize the downstream substrates and upstream regulators of FBXL7. We then discuss its role in tumorigenesis and tumor progression as either an oncoprotein or a tumor suppressor, and further describe its aberrant expression and association with patient survival in human cancers. Finally, we provide future perspectives on validating FBXL7 as a cancer biomarker for diagnosis and prognosis and/or as a potential therapeutic target for anticancer treatment.
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Kakkanas A, Karamichali E, Koufogeorgou EI, Kotsakis SD, Georgopoulou U, Foka P. Targeting the YXXΦ Motifs of the SARS Coronaviruses 1 and 2 ORF3a Peptides by In Silico Analysis to Predict Novel Virus-Host Interactions. Biomolecules 2022; 12:1052. [PMID: 36008946 PMCID: PMC9405953 DOI: 10.3390/biom12081052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
The emerging SARS-CoV and SARS-CoV-2 belong to the family of "common cold" RNA coronaviruses, and they are responsible for the 2003 epidemic and the current pandemic with over 6.3 M deaths worldwide. The ORF3a gene is conserved in both viruses and codes for the accessory protein ORF3a, with unclear functions, possibly related to viral virulence and pathogenesis. The tyrosine-based YXXΦ motif (Φ: bulky hydrophobic residue-L/I/M/V/F) was originally discovered to mediate clathrin-dependent endocytosis of membrane-spanning proteins. Many viruses employ the YXXΦ motif to achieve efficient receptor-guided internalisation in host cells, maintain the structural integrity of their capsids and enhance viral replication. Importantly, this motif has been recently identified on the ORF3a proteins of SARS-CoV and SARS-CoV-2. Given that the ORF3a aa sequence is not fully conserved between the two SARS viruses, we aimed to map in silico structural differences and putative sequence-driven alterations of regulatory elements within and adjacently to the YXXΦ motifs that could predict variations in ORF3a functions. Using robust bioinformatics tools, we investigated the presence of relevant post-translational modifications and the YXXΦ motif involvement in protein-protein interactions. Our study suggests that the predicted YXXΦ-related features may confer specific-yet to be discovered-functions to ORF3a proteins, significant to the new virus and related to enhanced propagation, host immune regulation and virulence.
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Affiliation(s)
- Athanassios Kakkanas
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Eirini Karamichali
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Efthymia Ioanna Koufogeorgou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Stathis D. Kotsakis
- Laboratory of Bacteriology, Hellenic Pasteur Institute, 115-21 Athens, Greece;
| | - Urania Georgopoulou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Pelagia Foka
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
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Hanashima S, Mito K, Umegawa Y, Murata M, Hojo H. Lipid chain-driven interaction of a lipidated Src-family kinase Lyn with the bilayer membrane. Org Biomol Chem 2022; 20:6436-6444. [PMID: 35880995 DOI: 10.1039/d2ob01079h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Myristoylation is a process of ubiquitous protein modification, which promotes the interaction of lipidated proteins on cell surfaces, in conjunction with reversible S-palmitoylation. We report the cooperative lipid-lipid interaction of two acyl chains of proteins, which increases the protein-membrane interaction and facilitates selective targeting of membranes containing anionic lipids. Lyn is a member of the Src family kinases distributed on the membrane surface by N-myristoyl and neighbouring S-palmitoyl chain anchors at the unique N-terminus domain. We prepared N-terminal short segments of lipidated Lyn to investigate the behaviour of each acyl chain in the lipid composition-dependent membrane interaction by solid-state nuclear magnetic resonance (NMR) analysis. Solid-state 31P-NMR studies revealed that S-palmitoylation of N-myristoylated Lyn peptides increased the interaction between peptides and phospholipid head groups, particularly with the anionic phosphatidylserine-containing bilayers. The solid-state 2H-NMR of Lyn peptides with a perdeutero N-myristoyl chain indicated an increase (0.6-0.8 Å) in the extent of the N-myristoyl chain in the presence of nearby S-palmitoyl chains, probably through the interaction via the acyl chains. The cooperative hydrocarbon chain interaction of the two acyl chains of Lyn increased membrane binding by extending the hydrocarbon chains deeper into the membrane interior, thereby promoting the peptide-membrane surface interaction between the cationic peptide side chains and the anionic lipid head groups. This lipid-driven mechanism by S-palmitoylation promotes the partition of the lipidated proteins to the cytoplasmic surface of the cell membranes and may be involved in recruiting Lyn at the signalling domains rich in anionic lipids.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Kanako Mito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan. .,Forefront Research Center, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hironobu Hojo
- Forefront Research Center, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.,Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
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41
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Activation and turnover of the plant immune signaling kinase BIK1: a fine balance. Essays Biochem 2022; 66:207-218. [PMID: 35575190 DOI: 10.1042/ebc20210071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 12/19/2022]
Abstract
Mechanisms to sense and respond to pathogens have evolved in all species. The plant immune pathway is initiated by the activation of transmembrane receptor kinases that trigger phosphorylation relays resulting in cellular reprogramming. BOTRYTIS-INDUCED KINASE 1 (BIK1) is a direct substrate of multiple immune receptors in Arabidopsis thaliana and is a central regulator of plant immunity. Here, we review how BIK1 activity and protein stability are regulated by a dynamic interplay between phosphorylation and ubiquitination.
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Onukwufor JO, Dirksen RT, Wojtovich AP. Iron Dysregulation in Mitochondrial Dysfunction and Alzheimer’s Disease. Antioxidants (Basel) 2022; 11:antiox11040692. [PMID: 35453377 PMCID: PMC9027385 DOI: 10.3390/antiox11040692] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
Alzheimer’s disease (AD) is a devastating progressive neurodegenerative disease characterized by neuronal dysfunction, and decreased memory and cognitive function. Iron is critical for neuronal activity, neurotransmitter biosynthesis, and energy homeostasis. Iron accumulation occurs in AD and results in neuronal dysfunction through activation of multifactorial mechanisms. Mitochondria generate energy and iron is a key co-factor required for: (1) ATP production by the electron transport chain, (2) heme protein biosynthesis and (3) iron-sulfur cluster formation. Disruptions in iron homeostasis result in mitochondrial dysfunction and energetic failure. Ferroptosis, a non-apoptotic iron-dependent form of cell death mediated by uncontrolled accumulation of reactive oxygen species and lipid peroxidation, is associated with AD and other neurodegenerative diseases. AD pathogenesis is complex with multiple diverse interacting players including Aβ-plaque formation, phosphorylated tau, and redox stress. Unfortunately, clinical trials in AD based on targeting these canonical hallmarks have been largely unsuccessful. Here, we review evidence linking iron dysregulation to AD and the potential for targeting ferroptosis as a therapeutic intervention for AD.
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Affiliation(s)
- John O. Onukwufor
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA; (R.T.D.); (A.P.W.)
- Correspondence:
| | - Robert T. Dirksen
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA; (R.T.D.); (A.P.W.)
| | - Andrew P. Wojtovich
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA; (R.T.D.); (A.P.W.)
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
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Mikec Š, Šimon M, Morton NM, Atanur SS, Konc J, Dovč P, Horvat S, Kunej T. Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. Mol Biol Rep 2022; 49:4619-4631. [PMID: 35347545 DOI: 10.1007/s11033-022-07309-0] [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: 01/10/2022] [Accepted: 02/25/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied. METHODS AND RESULTS In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness. Sequencing and RFLP were used to analyse sequence variants within Hif3a. To identify candidate regulatory variants, we performed literature screening and used databases and bioinformatics tools like Ensembl, MethPrimer, TargetScanMouse, miRDB, PolyAsite, RISE, LncRRIsearch, RNAfold, PredictProtein, CAIcal, and switches.ELM Resource. There are 90 sequence variants in Hif3a between the two mouse lines. While most Fat line variants locate within intronic regions, Lean line variants are mainly in 3' UTR. We constructed a map of Hif3a potential regulatory regions and identified 39 regulatory variants by integrating data on constrained and regulatory elements, CpGs, and miRNAs and lncRNAs binding sites. Moreover, 3' UTR and two exonic variants may influence mRNA stability, translation rate and protein functionality. We propose as priority candidates for further functional studies a missense (rs37398126) and synonymous (rs37739792) variants, and intronic (rs47471302) variant that overlap conserved element in promoter region and predicted lncRNAs binding site. CONCLUSION The results indicate a potential involvement of Hif3a in fat deposition. Additionally, approach used in the present study may serve as a general guideline for constructing an integrative gene map for prioritizing candidate gene variants with phenotypic effects.
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Affiliation(s)
- Špela Mikec
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Martin Šimon
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M Morton
- The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Santosh S Atanur
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK.,Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Janez Konc
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
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44
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Sherpa D, Chrustowicz J, Schulman BA. How the ends signal the end: Regulation by E3 ubiquitin ligases recognizing protein termini. Mol Cell 2022; 82:1424-1438. [PMID: 35247307 PMCID: PMC9098119 DOI: 10.1016/j.molcel.2022.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 12/31/2022]
Abstract
Specificity of eukaryotic protein degradation is determined by E3 ubiquitin ligases and their selective binding to protein motifs, termed "degrons," in substrates for ubiquitin-mediated proteolysis. From the discovery of the first substrate degron and the corresponding E3 to a flurry of recent studies enabled by modern systems and structural methods, it is clear that many regulatory pathways depend on E3s recognizing protein termini. Here, we review the structural basis for recognition of protein termini by E3s and how this recognition underlies biological regulation. Diverse E3s evolved to harness a substrate's N and/or C terminus (and often adjacent residues as well) in a sequence-specific manner. Regulation is achieved through selective activation of E3s and also through generation of degrons at ribosomes or by posttranslational means. Collectively, many E3 interactions with protein N and C termini enable intricate control of protein quality and responses to cellular signals.
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Affiliation(s)
- Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany.
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45
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Guns J, Vanherle S, Hendriks JJA, Bogie JFJ. Protein Lipidation by Palmitate Controls Macrophage Function. Cells 2022; 11:cells11030565. [PMID: 35159374 PMCID: PMC8834383 DOI: 10.3390/cells11030565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 01/27/2023] Open
Abstract
Macrophages are present in all tissues within our body, where they promote tissue homeostasis by responding to microenvironmental triggers, not only through clearance of pathogens and apoptotic cells but also via trophic, regulatory, and repair functions. To accomplish these divergent functions, tremendous dynamic fine-tuning of their physiology is needed. Emerging evidence indicates that S-palmitoylation, a reversible post-translational modification that involves the linkage of the saturated fatty acid palmitate to protein cysteine residues, directs many aspects of macrophage physiology in health and disease. By controlling protein activity, stability, trafficking, and protein–protein interactions, studies identified a key role of S-palmitoylation in endocytosis, inflammatory signaling, chemotaxis, and lysosomal function. Here, we provide an in-depth overview of the impact of S-palmitoylation on these cellular processes in macrophages in health and disease. Findings discussed in this review highlight the therapeutic potential of modulators of S-palmitoylation in immunopathologies, ranging from infectious and chronic inflammatory disorders to metabolic conditions.
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Affiliation(s)
- Jeroen Guns
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium; (J.G.); (S.V.); (J.J.A.H.)
- University MS Center, Hasselt University, 3500 Hasselt, Belgium
| | - Sam Vanherle
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium; (J.G.); (S.V.); (J.J.A.H.)
- University MS Center, Hasselt University, 3500 Hasselt, Belgium
| | - Jerome J. A. Hendriks
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium; (J.G.); (S.V.); (J.J.A.H.)
- University MS Center, Hasselt University, 3500 Hasselt, Belgium
| | - Jeroen F. J. Bogie
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium; (J.G.); (S.V.); (J.J.A.H.)
- University MS Center, Hasselt University, 3500 Hasselt, Belgium
- Correspondence: ; Tel.: +32-1126-9261
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46
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Bhandari S, Bisht KS, Merkler DJ. The Biosynthesis and Metabolism of the N-Acylated Aromatic Amino Acids: N-Acylphenylalanine, N-Acyltyrosine, N-Acyltryptophan, and N-Acylhistidine. Front Mol Biosci 2022; 8:801749. [PMID: 35047560 PMCID: PMC8762209 DOI: 10.3389/fmolb.2021.801749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
The fatty acid amides are a family of lipids composed of two chemical moieties, a fatty acid and a biogenic amine linked together in an amide bond. This lipid family is structurally related to the endocannabinoid anandamide (N-arachidonoylethanolamine) and, thus, is frequently referred to as a family of endocannabinoid-related lipids. The fatty acid amide family is divided into different classes based on the conjugate amine; anandamide being a member of the N-acylethanolamine class (NAE). Another class within the fatty acid amide family is the N-acyl amino acids (NA-AAs). The focus of this review is a sub-class of the NA-AAs, the N-acyl aromatic amino acids (NA-ArAAs). The NA-ArAAs are not broadly recognized, even by those interested in the endocannabinoids and endocannabinoid-related lipids. Herein, the NA-ArAAs that have been identified from a biological source will be highlighted and pathways for their biosynthesis, degradation, enzymatic modification, and transport will be presented. Also, information about the cellular functions of the NA-ArAAs will be placed in context with the data regarding the identification and metabolism of these N-acylated amino acids. A review of the current state-of-knowledge about the NA-ArAAs is to stimulate future research about this underappreciated sub-class of the fatty acid amide family.
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Affiliation(s)
- Suzeeta Bhandari
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Kirpal S Bisht
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - David J Merkler
- Department of Chemistry, University of South Florida, Tampa, FL, United States
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47
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Komaniecki G, Lin H. Lysine Fatty Acylation: Regulatory Enzymes, Research Tools, and Biological Function. Front Cell Dev Biol 2021; 9:717503. [PMID: 34368168 PMCID: PMC8339906 DOI: 10.3389/fcell.2021.717503] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022] Open
Abstract
Post-translational acylation of lysine side chains is a common mechanism of protein regulation. Modification by long-chain fatty acyl groups is an understudied form of lysine acylation that has gained increasing attention recently due to the characterization of enzymes that catalyze the addition and removal this modification. In this review we summarize what has been learned about lysine fatty acylation in the approximately 30 years since its initial discovery. We report on what is known about the enzymes that regulate lysine fatty acylation and their physiological functions, including tumorigenesis and bacterial pathogenesis. We also cover the effect of lysine fatty acylation on reported substrates. Generally, lysine fatty acylation increases the affinity of proteins for specific cellular membranes, but the physiological outcome depends greatly on the molecular context. Finally, we will go over the experimental tools that have been used to study lysine fatty acylation. While much has been learned about lysine fatty acylation since its initial discovery, the full scope of its biological function has yet to be realized.
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Affiliation(s)
- Garrison Komaniecki
- Graduate Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY, United States.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Hening Lin
- Graduate Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY, United States.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States.,Howard Hughes Medical Institute, Cornell University, Ithaca, NY, United States
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48
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Boto A, González CC, Hernández D, Romero-Estudillo I, Saavedra CJ. Site-selective modification of peptide backbones. Org Chem Front 2021. [DOI: 10.1039/d1qo00892g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exciting developments in the site-selective modification of peptide backbones are allowing an outstanding fine-tuning of peptide conformation, folding ability, and physico-chemical and biological properties.
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Affiliation(s)
- Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Iván Romero-Estudillo
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
- Catedrático CONACYT-CIQ-UAEM, Mexico
| | - Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain
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