1
|
Jeong C, Kim HJ. YabJ from Staphylococcus aureus entraps chlorides within its pocket. Biochem Biophys Res Commun 2024; 710:149892. [PMID: 38581951 DOI: 10.1016/j.bbrc.2024.149892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Chlorination is a potent disinfectant against various microorganisms, including bacteria and viruses, by inducing protein modifications and functional changes. Chlorine, in the form of sodium hypochlorite, stands out as the predominant sanitizer choice due to its cost-effectiveness and powerful antimicrobial properties. Upon exposure to chlorination, proteins undergo modifications, with amino acids experiencing alterations through the attachment of chloride or oxygen atoms. These modifications lead to shifts in protein function and the modulation of downstream signaling pathways, ultimately resulting in a bactericidal effect. However, certain survival proteins, such as chaperones or transcription factors, aid organisms in overcoming harsh chlorination conditions. The expression of YabJ, a highly conserved protein from Staphylococcus aureus, is regulated by a stress-activated sigma factor called sigma B (σB). This research revealed that S. aureus YabJ maintains its structural integrity even under intense chlorination conditions and harbors sodium hypochlorite molecules within its surface pocket. Notably, the pocket of S. aureus YabJ is primarily composed of amino acids less susceptible to chlorination-induced damage, rendering it resistant to such effects. This study elucidates how S. aureus YabJ evades the detrimental effects of chlorination and highlights its role in sequestering sodium hypochlorite within its structure. Consequently, this process enhances resilience and facilitates adaptation to challenging environmental conditions.
Collapse
Affiliation(s)
- Cheolwoo Jeong
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea
| | - Hyo Jung Kim
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea.
| |
Collapse
|
2
|
Kataoka H, Akiyoshi T, Uchida Y, Imaoka A, Terasaki T, Ohtani H. The Effects of N-Glycosylation on the Expression and Transport Activity of OATP1A2 and OATP2B1. J Pharm Sci 2024; 113:1376-1384. [PMID: 38432624 DOI: 10.1016/j.xphs.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
Organic anion transporting polypeptide (OATP)1A2 and OATP2B1 have potential N-glycosylation sites, but their influence remains unclear. This study aimed to identify the N-glycosylation sites of OATP1A2/2B1 and investigate their impact on the expression and function of OATP1A2/2B1. Human embryonic kidney cells expressing OATP1A2 or OATP2B1 (HEK293-OATP1A2/2B1) were exposed to tunicamycin, an N-glycosylation inhibitor, and a plasma membrane fraction (PMF) Western blot assay and an estrone 3-sulfate (E3S) uptake study were conducted. HEK293-OATP1A2/OATP2B1 cell lines with mutation(s) at potential N-glycosylation sites were established, and the Western blotting and uptake study were repeated. Tunicamycin reduced the PMF levels and E3S uptake of OATP1A2/OATP2B1. The Asn124Gln, Asn135Gln, and Asn492Gln mutations in OATP1A2 and Asn176Gln and Asn538Gln mutations in OATP2B1 reduced the molecular weights of the OATP molecules and their PMF levels. The PMF levels of OATP1A2 Asn124/135Gln, OATP1A2 Asn124/135/492Gln, and OATP2B1 Asn176/538Gln were further reduced. The maximum transport velocities of OATP1A2 Asn124Gln, OATP1A2 Asn135Gln, and OATP2B1 Asn176/538Gln were markedly reduced to 10 %, 4 %, and 10 % of the wild-type level, respectively. In conclusion, the N-glycans at Asn124 and Asn135 of OATP1A2 and those at Asn176 and Asn538 of OATP2B1 are essential for the plasma membrane expression of these molecules and also affect their transport function.
Collapse
Affiliation(s)
- Hiroki Kataoka
- Division of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Takeshi Akiyoshi
- Division of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan; Department of Clinical Pharmacy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yasuo Uchida
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima city 734-0037, Japan
| | - Ayuko Imaoka
- Division of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Tetsuya Terasaki
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Hisakazu Ohtani
- Division of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan; Department of Clinical Pharmacy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; Department of Pharmacy, Keio University Hospital, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| |
Collapse
|
3
|
Qiu K, Tian Y, Guo C, Liu O, Shi Y, Liu D, Luo T. Global proteomic analysis reveals lysine succinylation is involved in the pathogenesis of hypertrophic scar. J Proteomics 2024; 298:105155. [PMID: 38460743 DOI: 10.1016/j.jprot.2024.105155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
Lysine succinylation (Ksucc) is a recently identified posttranslational modification that is involved in many diseases. This study examined the role of Ksucc in the pathogenesis of hypertrophic scar (HS). The presence of Ksucc in human skin was measured by immunoblotting. Ksucc occurs in many skin proteins ranging from 25 to 250 kDa, and higher levels of Ksucc are found in HS skin than in normal skin. An immunoaffinity approach coupled with LC-MS/MS was used to characterize the first succinylome of human skin, and 159 Ksucc sites in 79 proteins were identified. Among these, there were 38 increased succinylated sites in 29 proteins but no decreased succinylated sites in HS compared with normal skin. A parallel reaction monitoring assay was performed to validate the results of the succinylome and showed that the levels of Ksucc in decorin and collagens, which are involved in the pathogenesis of HS, were increased in HS than in normal skin. In addition, increasing the level of Ksucc enhanced cell proliferation and upregulated the expression of fibrosis markers (α-SMA, COL1, and COL3) in human skin fibroblasts. Our results provide global insights into the functional role of Ksucc in hypertrophic scarring.
Collapse
Affiliation(s)
- Keqing Qiu
- Department of Dermatology, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yan Tian
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Chunyan Guo
- Department of Dermatology, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Ougen Liu
- Department of Dermatology, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yan Shi
- Department of Plastic, Medical Center of Burn Plastic and Wound Repair, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Dewu Liu
- Department of Plastic, Medical Center of Burn Plastic and Wound Repair, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China.
| | - Tao Luo
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330031, China.
| |
Collapse
|
4
|
Gao M, Shi J, Xiao X, Yao Y, Chen X, Wang B, Zhang J. PD-1 regulation in immune homeostasis and immunotherapy. Cancer Lett 2024; 588:216726. [PMID: 38401888 DOI: 10.1016/j.canlet.2024.216726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 02/26/2024]
Abstract
Harnessing the programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) axis is pivotal in autoimmunity and cancer immunotherapy. PD-1 receptors on immune cells engage with one of its ligands, PD-L1 or PD-L2, expressed on antigen-presenting cells or tumor cells, driving T-cell dysfunction and tumor immune escape. Thus, targeting PD-1/PD-L1 revitalizes cytotoxic T cells for cancer elimination. However, a majority of cancer patients don't respond to PD-1/PD-L1 blockade, and the underlying mechanisms remain partially understood. Recent studies have revealed that PD-1 expression levels or modifications impact the effectiveness of anti-PD-1/PD-L1 treatments. Therefore, understanding the molecular mechanisms governing PD-1 expression and modifications is crucial for innovating therapeutic strategies to enhance the efficacy of PD-1/PD-L1 inhibition. This article presents a comprehensive overview of advancements in PD-1 regulation and highlights their potential in modulating immune homeostasis and cancer immunotherapy, aiming to refine clinical outcomes.
Collapse
Affiliation(s)
- Minling Gao
- Department of Hepatobiliary and Pancreatic Surgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jie Shi
- Department of Hepatobiliary and Pancreatic Surgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xiangling Xiao
- Department of Hepatobiliary and Pancreatic Surgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yingmeng Yao
- Department of Hepatobiliary and Pancreatic Surgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xu Chen
- Chongqing University Medical School, Chongqing, 400044, China
| | - Bin Wang
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
| | - Jinfang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
5
|
Wang J, Wang Y, Jiang X, Xu M, Wang M, Wang R, Zheng B, Chen M, Ke Q, Long J. Unleashing the power of immune checkpoints: Post-translational modification of novel molecules and clinical applications. Cancer Lett 2024; 588:216758. [PMID: 38401885 DOI: 10.1016/j.canlet.2024.216758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
Immune checkpoint molecules play a pivotal role in the initiation, regulation, and termination of immune responses. Tumor cells exploit these checkpoints to dampen immune cell function, facilitating immune evasion. Clinical interventions target this mechanism by obstructing the binding of immune checkpoints to their ligands, thereby restoring the anti-tumor capabilities of immune cells. Notably, therapies centered on immune checkpoint inhibitors, particularly PD-1/PD-L1 and CTLA-4 blocking antibodies, have demonstrated significant clinical promise. However, a considerable portion of patients still encounter suboptimal efficacy and develop resistance. Recent years have witnessed an exponential surge in preclinical and clinical trials investigating novel immune checkpoint molecules such as TIM3, LAG3, TIGIT, NKG2D, and CD47, along with their respective ligands. The processes governing immune checkpoint molecules, from their synthesis to transmembrane deployment, interaction with ligands, and eventual degradation, are intricately tied to post-translational modifications. These modifications encompass glycosylation, phosphorylation, ubiquitination, neddylation, SUMOylation, palmitoylation, and ectodomain shedding. This discussion proceeds to provide a concise overview of the structural characteristics of several novel immune checkpoints and their ligands. Additionally, it outlines the regulatory mechanisms governed by post-translational modifications, offering insights into their potential clinical applications in immune checkpoint blockade.
Collapse
Affiliation(s)
- Jie Wang
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China.
| | - Yian Wang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Changsha, Hunan, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Meifang Xu
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Meifeng Wang
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Rong Wang
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Boshu Zheng
- Department of Pathology, Institute of Oncology & Diagnostic Pathology Center, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Mingfen Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Fujian Medical University, Fujian Medical University, Quanzhou, Fujian, China
| | - Qi Ke
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Jun Long
- Shenzhen Geim Graphene Center, Tsinghua-Berkeley Shenzhen Institute & Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China.
| |
Collapse
|
6
|
Temgire P, Arthur R, Kumar P. Neuroinflammation and the role of epigenetic-based therapies for Huntington's disease management: the new paradigm. Inflammopharmacology 2024:10.1007/s10787-024-01477-0. [PMID: 38653938 DOI: 10.1007/s10787-024-01477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Huntington's disease (HD) is an inherited, autosomal, neurodegenerative ailment that affects the striatum of the brain. Despite its debilitating effect on its patients, there is no proven cure for HD management as of yet. Neuroinflammation, excitotoxicity, and environmental factors have been reported to influence the regulation of gene expression by modifying epigenetic mechanisms. Aside focusing on the etiology, changes in epigenetic mechanisms have become a crucial factor influencing the interaction between HTT protein and epigenetically transcribed genes involved in neuroinflammation and HD. This review presents relevant literature on epigenetics with special emphasis on neuroinflammation and HD. It summarizes pertinent research on the role of neuroinflammation and post-translational modifications of chromatin, including DNA methylation, histone modification, and miRNAs. To achieve this about 1500 articles were reviewed via databases like PubMed, ScienceDirect, Google Scholar, and Web of Science. They were reduced to 534 using MeSH words like 'epigenetics, neuroinflammation, and HD' coupled with Boolean operators. Results indicated that major contributing factors to the development of HD such as mitochondrial dysfunction, excitotoxicity, neuroinflammation, and apoptosis are affected by epigenetic alterations. However, the association between neuroinflammation-altered epigenetics and the reported transcriptional changes in HD is unknown. Also, the link between epigenetically dysregulated genomic regions and specific DNA sequences suggests the likelihood that transcription factors, chromatin-remodeling proteins, and enzymes that affect gene expression are all disrupted simultaneously. Hence, therapies that target pathogenic pathways in HD, including neuroinflammation, transcriptional dysregulation, triplet instability, vesicle trafficking dysfunction, and protein degradation, need to be developed.
Collapse
Affiliation(s)
- Pooja Temgire
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
| |
Collapse
|
7
|
Thimmappa PY, Nair AS, D'silva S, Aravind A, Mallya S, Soman SP, Guruprasad KP, Shastry S, Raju R, Prasad TSK, Joshi MB. Neutrophils display distinct post-translational modifications in response to varied pathological stimuli. Int Immunopharmacol 2024; 132:111950. [PMID: 38579564 DOI: 10.1016/j.intimp.2024.111950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/08/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
Neutrophils play a vital role in the innate immunity by perform effector functions through phagocytosis, degranulation, and forming extracellular traps. However, over-functioning of neutrophils has been associated with sterile inflammation such as Type 2 Diabetes, atherosclerosis, cancer and autoimmune disorders. Neutrophils exhibiting phenotypical and functional heterogeneity in both homeostatic and pathological conditions suggests distinct signaling pathways are activated in disease-specific stimuli and alter neutrophil functions. Hence, we examined mass spectrometry based post-translational modifications (PTM) of neutrophil proteins in response to pathologically significant stimuli, including high glucose, homocysteine and bacterial lipopolysaccharides representing diabetes-indicator, an activator of thrombosis and pathogen-associated molecule, respectively. Our data revealed that these aforesaid stimulators differentially deamidate, citrullinate, acetylate and methylate neutrophil proteins and align to distinct biological functions associated with degranulation, platelet activation, innate immune responses and metabolic alterations. The PTM patterns in response to high glucose showed an association with neutrophils extracellular traps (NETs) formation, homocysteine induced proteins PTM associated with signaling of systemic lupus erythematosus and lipopolysaccharides induced PTMs were involved in pathways related to cardiomyopathies. Our study provides novel insights into neutrophil PTM patterns and functions in response to varied pathological stimuli, which may serve as a resource to design therapeutic strategies for the management of neutrophil-centred diseases.
Collapse
Affiliation(s)
- Pooja Yedehalli Thimmappa
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Aswathy S Nair
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Sian D'silva
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Sreelakshmi Pathappillil Soman
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Kanive Parashiva Guruprasad
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Shamee Shastry
- Department of Immunohematology and Blood Transfusion, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | | | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India.
| |
Collapse
|
8
|
Yang Y, Yu F. Abnormal protein SUMOylation in liver disease: novel target for therapy. J Mol Med (Berl) 2024:10.1007/s00109-024-02440-w. [PMID: 38565749 DOI: 10.1007/s00109-024-02440-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/10/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
SUMOylation is an important protein post-translational modification (PTM) process, in which the small ubiquitin-like modifier (SUMO) protein covalently binds to the target protein and regulates stability, subcellular localization, and protein-protein interaction of the target protein. Protein SUMOylation exerts crucial regulatory function in the liver, and its abnormalities are associated with various liver-related disease processes. This review focuses on the biological functions of protein SUMOylation in liver-related diseases in recent years, summarizes the molecular mechanisms of SUMOylation in the replication of hepatitis viruses and the occurrence of hepatocellular carcinoma, and discusses the significance of SUMOylation in liver-related disorders, which is essential for understanding liver biological processes and formulating therapeutic strategies.
Collapse
Affiliation(s)
- Yanfang Yang
- Department of Central Laboratory, Guizhou Provincial People's Hospital, Guiyang, 550002, China.
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, China.
| | - Fuxun Yu
- Department of Central Laboratory, Guizhou Provincial People's Hospital, Guiyang, 550002, China.
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, China.
| |
Collapse
|
9
|
Feichtner A, Enzler F, Kugler V, Hoppe K, Mair S, Kremser L, Lindner H, Huber RG, Stelzl U, Stefan E, Torres-Quesada O. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions. Cell Mol Life Sci 2024; 81:162. [PMID: 38568213 PMCID: PMC10991009 DOI: 10.1007/s00018-024-05204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.
Collapse
Affiliation(s)
- Andreas Feichtner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
| | - Valentina Kugler
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Katharina Hoppe
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Sophia Mair
- Department of Cardiac Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
- Vascage, Center of Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, 138671, Singapore
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
| |
Collapse
|
10
|
Zhu Z, Ren W, Li S, Gao L, Zhi K. Functional significance of O-linked N-acetylglucosamine protein modification in regulating autophagy. Pharmacol Res 2024; 202:107120. [PMID: 38417774 DOI: 10.1016/j.phrs.2024.107120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Autophagy is a core molecular pathway that preserves cellular and organismal homeostasis. Being susceptible to nutrient availability and stress, eukaryotic cells recycle or degrade internal components via membrane transport pathways to provide sustainable biological molecules and energy sources. The dysregulation of this highly conserved physiological process has been strongly linked to human disease. Post-translational modification, a mechanism that regulates protein function, plays a crucial role in autophagy regulation. O-linked N-acetylglucosamine protein modification (O-GlcNAcylation), a monosaccharide post-translational modification of intracellular proteins, is essential in nutritional and stress regulatory mechanisms. O-GlcNAcylation has emerged as an essential regulatory mechanism of autophagy. It regulates autophagy throughout its lifetime by targeting the core components of the autophagy regulatory network. This review provides an overview of the O-GlcNAcylation of autophagy-associated proteins and their regulation and function in the autophagy pathway. Therefore, this article may contribute to further understanding of the role of O-GlcNAc-regulated autophagy and provide new perspectives for the treatment of human diseases.
Collapse
Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| |
Collapse
|
11
|
Nalehua MR, Zaia J. A critical evaluation of ultrasensitive single-cell proteomics strategies. Anal Bioanal Chem 2024; 416:2359-2369. [PMID: 38358530 DOI: 10.1007/s00216-024-05171-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Success of mass spectrometry characterization of the proteome of single cells allows us to gain a greater understanding than afforded by transcriptomics alone but requires clear understanding of the tradeoffs between analytical throughput and precision. Recent advances in mass spectrometry acquisition techniques, including updated instrumentation and sample preparation, have improved the quality of peptide signals obtained from single cell data. However, much of the proteome remains uncharacterized, and higher throughput techniques often come at the expense of reduced sensitivity and coverage, which diminish the ability to measure proteoform heterogeneity, including splice variants and post-translational modifications, in single cell data analysis. Here, we assess the growing body of ultrasensitive single-cell approaches and their tradeoffs as researchers try to balance throughput and precision in their experiments.
Collapse
Affiliation(s)
| | - Joseph Zaia
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Biochemistry and Cell Biology, Boston University, Boston, MA, USA.
| |
Collapse
|
12
|
Cheng C, Yao H, Li H, Liu J, Liu Z, Wu Y, Zhu L, Hu H, Fang Z, Wu L. Blockade of the deubiquitinating enzyme USP48 degrades oncogenic HMGA2 and inhibits colorectal cancer invasion and metastasis. Acta Pharm Sin B 2024; 14:1624-1643. [PMID: 38572092 PMCID: PMC10985028 DOI: 10.1016/j.apsb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 04/05/2024] Open
Abstract
HMGA2, a pivotal transcription factor, functions as a versatile regulator implicated in the progression of diverse aggressive malignancies. In this study, mass spectrometry was employed to identify ubiquitin-specific proteases that potentially interact with HMGA2, and USP48 was identified as a deubiquitinating enzyme of HMGA2. The enforced expression of USP48 significantly increased HMGA2 protein levels by inhibiting its degradation, while the deprivation of USP48 promoted HMGA2 degradation, thereby suppressing tumor invasion and metastasis. We discovered that USP48 undergoes SUMOylation at lysine 258, which enhances its binding affinity to HMGA2. Through subsequent phenotypic screening of small molecules, we identified DUB-IN-2 as a remarkably potent pharmacological inhibitor of USP48. Interestingly, the small-molecule inhibitor targeting USP48 induces destabilization of HMGA2. Clinically, upregulation of USP48 or HMGA2 in cancerous tissues is indicative of poor prognosis for patients with colorectal cancer (CRC). Collectively, our study not only elucidates the regulatory mechanism of DUBs involved in HMGA2 stability and validates USP48 as a potential therapeutic target for CRC, but also identifies DUB-IN-2 as a potent inhibitor of USP48 and a promising candidate for CRC treatment.
Collapse
Affiliation(s)
- Can Cheng
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Hanhui Yao
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Heng Li
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Comprehensive Surgery, Anhui Provincial Cancer Hospital, West District of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Jingwen Liu
- Anhui Provincial Hospital Health Management Center, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Zhengyi Liu
- Department of Breast Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou 450003, China
| | - Yang Wu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Liang Zhu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Hejie Hu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Zhengdong Fang
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Liang Wu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| |
Collapse
|
13
|
Hosen N. Identification of cancer-specific cell surface targets for CAR-T cell therapy. Inflamm Regen 2024; 44:17. [PMID: 38549116 PMCID: PMC10979572 DOI: 10.1186/s41232-024-00329-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
One should identify appropriate cell surface targets to develop new CAR-T cells. Currently, lineage-specific antigens such as CD19 or B cell maturation antigen (BCMA) are being used as targets for CAR-T cells. However, in most cancers, lineage-specific antigens cannot be used as targets because targeting normal counterparts expressing them causes fatal toxicity. Cancer-specific transcripts have been extensively searched for using transcriptome analysis, but only a few candidates were reported. We have been working on identifying tumor-specific antigen structures, for example constitutively activated conformer of integrin b7 in multiple myeloma. Recently, several researchers have been working on a logic gate system that can react only when two antigens are expressed on the cell surface.
Collapse
Affiliation(s)
- Naoki Hosen
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, 2-2, Yamada-Oka, Suita, 565-0871, Osaka, Japan.
| |
Collapse
|
14
|
Zhang F, Jiang R, Sun S, Wu C, Yu Q, Awadasseid A, Wang J, Zhang W. Recent advances and mechanisms of action of PD-L1 degraders as potential therapeutic agents. Eur J Med Chem 2024; 268:116267. [PMID: 38422701 DOI: 10.1016/j.ejmech.2024.116267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/01/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
PD-L1 is an important immune checkpoint protein that can bind to T cells' PD-1 receptor, thereby promoting immune escape from tumors. In recent years, many researchers have developed strategies to degrade PD-L1 to improve the effect of immunotherapy. The study of degrading PD-L1 provides new opportunities for immunotherapy. Here, we mainly summarize and review the current active molecules and mechanisms that mediate the degradation of immature and mature PD-L1 during the post-translational modification stages, involving PD-L1 phosphorylation, glycosylation, palmitoylation, ubiquitination, and the autophagy-lysosomal process. This review expects that by degrading PD-L1 protein, we will not only gain a better understanding of oncogenic mechanisms involving tumor PD-L1 protein but also provide a new way to improve immunotherapy.
Collapse
Affiliation(s)
- Feng Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ruiya Jiang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shishi Sun
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Caiyun Wu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qimeng Yu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Annoor Awadasseid
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China; Moganshan Institute, Zhejiang University of Technology, Deqing, China
| | - Jianwei Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Wen Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China.
| |
Collapse
|
15
|
Jiang Y, Hu L, Wang B, Zhang B, Shao M, Meng L, Xu Y, Chen R, Li M, Du C. Disrupting PIAS3-mediated SUMOylation of MLK3 ameliorates poststroke neuronal damage and deficits in cognitive and sensorimotor behaviors. Cell Mol Life Sci 2024; 81:119. [PMID: 38456949 PMCID: PMC10924033 DOI: 10.1007/s00018-024-05166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/25/2024] [Accepted: 02/03/2024] [Indexed: 03/09/2024]
Abstract
Activated small ubiquitin-like modifiers (SUMOs) have been implicated in neuropathological processes following ischemic stroke. However, the target proteins of SUMOylation and their contribution to neuronal injury remain to be elucidated. MLK3 (mixed-lineage kinase 3), a member of the mitogen-activated protein kinase kinase kinase (MAPKKK) family, is a critical regulator of neuronal lesions following cerebral ischemia. Here, we found that SUMOylation of MLK3 increases in both global and focal ischemic rodent models and primary neuronal models of oxygen and glucose deprivation (OGD). SUMO1 conjugation at the Lys401 site of MLK3 promoted its activation, stimulated its downstream p38/c-Jun N-terminal kinase (JNK) cascades, and led to cell apoptosis. The interaction of MLK3 with PIAS3, a SUMO ligase, was elevated following ischemia and reperfusion. The PINIT domain of PIAS3 was involved in direct interactions with MLK3. Overexpression of the PINIT domain of PIAS3 disrupted the MLK3-PIAS3 interaction, inhibited SUMOylation of MLK3, suppressed downstream signaling, and reduced cell apoptosis and neurite damage. In rodent ischemic models, the overexpression of the PINIT domain reduced brain lesions and alleviated deficits in learning, memory, and sensorimotor functions. Our findings demonstrate that brain ischemia-induced MLK3 SUMOylation by PIAS3 is a potential target against poststroke neuronal lesions and behavioral impairments.
Collapse
Affiliation(s)
- Yu Jiang
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Lulu Hu
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Baixue Wang
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Bingge Zhang
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Mengwen Shao
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Li Meng
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yan Xu
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Rourou Chen
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Meng Li
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| | - Caiping Du
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| |
Collapse
|
16
|
Zhang B, Guan Y, Zeng D, Wang R. Arginine methylation and respiratory disease. Transl Res 2024:S1931-5244(24)00046-X. [PMID: 38453053 DOI: 10.1016/j.trsl.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Arginine methylation, a vital post-translational modification, plays a pivotal role in numerous cellular functions such as signal transduction, DNA damage response and repair, regulation of gene transcription, mRNA splicing, and protein interactions. Central to this modification is the role of protein arginine methyltransferases (PRMTs), which have been increasingly recognized for their involvement in the pathogenesis of various respiratory diseases. This review begins with an exploration of the biochemical underpinnings of arginine methylation, shedding light on the intricate molecular regulatory mechanisms governed by PRMTs. It then delves into the impact of arginine methylation and the dysregulation of arginine methyltransferases in diverse pulmonary disorders. Concluding with a focus on the therapeutic potential and recent advancements in PRMT inhibitors, this article aims to offer novel perspectives and therapeutic avenues for the management and treatment of respiratory diseases.
Collapse
Affiliation(s)
- Binbin Zhang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui Province, PR China
| | - Youhong Guan
- Department of Infectious Diseases, Hefei Second People's Hospital, Hefei 230001, Anhui Province, PR China
| | - Daxiong Zeng
- Department of Pulmonary and Critical Care Medicine, Dushu Lake Hospital Affiliated to Soochow University, Medical Center of Soochow University, Suzhou 215006, Jiangsu Province, PR China.
| | - Ran Wang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui Province, PR China.
| |
Collapse
|
17
|
Tong C, Chang X, Qu F, Bian J, Wang J, Li Z, Xu X. Overview of the development of protein arginine methyltransferase modulators: Achievements and future directions. Eur J Med Chem 2024; 267:116212. [PMID: 38359536 DOI: 10.1016/j.ejmech.2024.116212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
Protein methylation is a post-translational modification (PTM) that organisms undergo. This process is considered a part of epigenetics research. In recent years, there has been an increasing interest in protein methylation, particularly histone methylation, as research has advanced. Methylation of histones is a dynamic process that is subject to fine control by histone methyltransferases and demethylases. In addition, many non-histone proteins also undergo methylation, and these modifications collectively regulate physiological phenomena, including RNA transcription, translation, signal transduction, DNA damage response, and cell cycle. Protein arginine methylation is a crucial aspect of protein methylation, which plays a significant role in regulating the cell cycle and repairing DNA. It is also linked to various diseases. Therefore, protein arginine methyltransferases (PRMTs) that are involved in this process have gained considerable attention as a potential therapeutic target for treating diseases. Several PRMT inhibitors are in phase I/II clinical trials. This paper aims to introduce the structure, biochemical functions, and bioactivity assays of PRMTs. Additionally, we will review the structure-function of currently popular PRMT inhibitors. Through the analysis of various data on known PRMT inhibitors, we hope to provide valuable assistance for future drug design and development.
Collapse
Affiliation(s)
- Chao Tong
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Xiujin Chang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Fangui Qu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China.
| | - Zhiyu Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China.
| | - Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China.
| |
Collapse
|
18
|
Pang PP, Zhang HY, Zhang DC, Tang JX, Gong Y, Guo YC, Zheng CB. Investigating the impact of protein S-sulfhydration modification on vascular diseases: A comprehensive review. Eur J Pharmacol 2024; 966:176345. [PMID: 38244760 DOI: 10.1016/j.ejphar.2024.176345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/22/2024]
Abstract
The post-translational modification of cysteine through redox reactions, especially S-sulfhydration, plays a critical role in regulating protein activity, interactions, and spatial arrangement. This review focuses on the impact of protein S-sulfhydration on vascular function and its implications in vascular diseases. Dysregulated S-sulfhydration has been linked to the development of vascular pathologies, including aortic aneurysms and dissections, atherosclerosis, and thrombotic diseases. The H2S signaling pathway and the enzyme cystathionine γ-lyase (CSE), which is responsible for H2S generation, are identified as key regulators of vascular function. Additionally, potential therapeutic targets for the treatment of vascular diseases, such as the H2S donor GYY4137 and the HDAC inhibitor entinostat, are discussed. The review also emphasizes the antithrombotic effects of H2S in regulating platelet aggregation and thrombosis. The aim of this review is to enhance our understanding of the function and mechanism of protein S-sulfhydration modification in vascular diseases, and to provide new insights into the clinical application of this modification.
Collapse
Affiliation(s)
- Pan-Pan Pang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China
| | - Hong-Ye Zhang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China
| | - Ding-Cheng Zhang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China
| | - Jia-Xiang Tang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China
| | - Yu Gong
- Yunnan Provincial Hospital of Infection Disease/ Yunnan AIDS Care Center/ Yunnan Mental Health Center, Kunming, 650301, China
| | - Yu-Chen Guo
- University of Sydney Pharmacy School, Sydney, 2006, Australia
| | - Chang-Bo Zheng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, 650500, China; College of Modern Biomedical Industry, Kunming Medical University, Kunming, 650500, China; Yunnan Vaccine Laboratory, Kunming, 650500, China.
| |
Collapse
|
19
|
Yang Y, Li W, Yang H, Zhang Y, Zhang S, Xu F, Hao Y, Cao W, Du G, Wang J. Research progress on the regulatory mechanisms of FOXC1 expression in cancers and its role in drug resistance. Gene 2024; 897:148079. [PMID: 38101711 DOI: 10.1016/j.gene.2023.148079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
The Forkhead box C1 (FOXC1) transcription factor is an important member of the FOX family. After initially being identified in triple-negative breast cancer (TNBC) with significant oncogenic function, FOXC1 was subsequently demonstrated to be involved in the development of more than 16 types of cancers. In recent years, increasing studies have focused on the deregulatory mechanisms of FOXC1 expression and revealed that FOXC1 expression was regulated at multiple levels including transcriptional regulation, post-transcription regulation and post-translational modification. Moreover, dysregulation of FOXC1 is also implicated in drug resistance in various types of cancer, especially in breast cancer, which further emphasizes the translational and clinical significance of FOXC1 as a therapeutic target in cancer treatment. This review summarizes recent findings on mechanisms of FOXC1 dysregulation in cancers and its role in chemoresistance, which will help to better understand the oncogenic role of FOXC1, overcome FOXC1-mediated drug resistance and develop targeted therapy for FOXC1 in cancers.
Collapse
Affiliation(s)
- Yihui Yang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Wan Li
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Hong Yang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yizhi Zhang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Sen Zhang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Fang Xu
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yue Hao
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Wanxin Cao
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Guanhua Du
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Jinhua Wang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| |
Collapse
|
20
|
Trujillo MN, Jennings EQ, Hoffman EA, Zhang H, Phoebe AM, Mastin GE, Kitamura N, Reisz JA, Megill E, Kantner D, Marcinkiewicz MM, Twardy SM, Lebario F, Chapman E, McCullough RL, D'Alessandro A, Snyder NW, Cusanovich DA, Galligan JJ. Lactoylglutathione promotes inflammatory signaling in macrophages through histone lactoylation. Mol Metab 2024; 81:101888. [PMID: 38307385 PMCID: PMC10869261 DOI: 10.1016/j.molmet.2024.101888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
Chronic, systemic inflammation is a pathophysiological manifestation of metabolic disorders. Inflammatory signaling leads to elevated glycolytic flux and a metabolic shift towards aerobic glycolysis and lactate generation. This rise in lactate corresponds with increased generation of lactoylLys modifications on histones, mediating transcriptional responses to inflammatory stimuli. Lactoylation is also generated through a non-enzymatic S-to-N acyltransfer from the glyoxalase cycle intermediate, lactoylglutathione (LGSH). Here, we report a regulatory role for LGSH in mediating histone lactoylation and inflammatory signaling. In the absence of the primary LGSH hydrolase, glyoxalase 2 (GLO2), RAW264.7 macrophages display significant elevations in LGSH and histone lactoylation with a corresponding potentiation of the inflammatory response when exposed to lipopolysaccharides. An analysis of chromatin accessibility shows that lactoylation is associated with more compacted chromatin than acetylation in an unstimulated state; upon stimulation, however, regions of the genome associated with lactoylation become markedly more accessible. Lastly, we demonstrate a spontaneous S-to-S acyltransfer of lactate from LGSH to CoA, yielding lactoyl-CoA. This represents the first known mechanism for the generation of this metabolite. Collectively, these data suggest that LGSH, and not intracellular lactate, is the primary driving factor facilitating histone lactoylation and a major contributor to inflammatory signaling.
Collapse
Affiliation(s)
- Marissa N Trujillo
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Erin Q Jennings
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Emely A Hoffman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Hao Zhang
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Aiden M Phoebe
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Grace E Mastin
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Naoya Kitamura
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emily Megill
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA, USA
| | - Daniel Kantner
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA, USA
| | - Mariola M Marcinkiewicz
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA, USA
| | - Shannon M Twardy
- Department of Pharmaceutical Sciences, The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Felicidad Lebario
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Rebecca L McCullough
- Department of Pharmaceutical Sciences, The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA, USA
| | - Darren A Cusanovich
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA; Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - James J Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA.
| |
Collapse
|
21
|
Chang X, Zhu Y, Chen Y, Li L. DeepNphos: A deep-learning architecture for prediction of N-phosphorylation sites. Comput Biol Med 2024; 170:108079. [PMID: 38295472 DOI: 10.1016/j.compbiomed.2024.108079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
Abstract
MOTIVATION Phosphorylation, a prevalent post-translational modification, plays a crucial role in regulating cellular activities. This process encompasses O-phosphorylation (e.g., phosphoserine) and N-phosphorylation (e.g., phospho-lysine (pK), phospho-arginine (pR), and phospho-histidine (pH)). While significant research has focused on O-phosphorylation, resulting in the development of various algorithms for predicting O-phosphorylation sites with commendable performance, there has been a notable absence of models designed to predict N-phosphorylation sites. This study introduces an integrated model named DeepNphos, designed to predict N-phosphorylation sites. This model is developed based on the analysis of thousands of experimentally identified pK, pR and pH sites. RESULTS Observing that the Convolutional Neural Network (CNN) model, incorporating the One-Hot encoding feature, demonstrates favorable performance in comparison to other models when predicting pK, pR, and pH sites. Additionally, pK exhibits similarities to other lysine modification types, and integrating the CNN model with a deep-transfer learning (DTL) strategy based on tens of thousands of known lysine modification sites could enhance pK prediction performance. In contrast, pR exhibits little similarity to other arginine modification types, and the integration of DTL has minimal impact on pR prediction performance. Furthermore, the decision was made to refrain from incorporating the DTL strategy in predicting pH sites, given the scarcity of histidine modification sites beyond those associated with pH. The final classifiers for predicting pK, pR, and pH sites achieve AUC values of 0.856, 0.805 and 0.802 for ten-fold cross-validation, respectively. Overall, DeepNphos is the first classifier for predicting N-phosphorylation sites, accessible at https://github.com/ChangXulinmessi/DeepNPhos.
Collapse
Affiliation(s)
- Xulin Chang
- College of Computer Science and Technology, Qingdao University, Qingdao, 266071, China
| | - Yafei Zhu
- College of Computer Science and Technology, Qingdao University, Qingdao, 266071, China
| | - Yu Chen
- College of Computer Science and Technology, Qingdao University, Qingdao, 266071, China
| | - Lei Li
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266000, China.
| |
Collapse
|
22
|
Baba K, Uemura K, Nakazato R, Ijaz F, Takahashi S, Ikegami K. Δ3-tubulin impairs mitotic spindle morphology and increases nuclear size in pancreatic cancer cells. Med Mol Morphol 2024; 57:59-67. [PMID: 37930423 DOI: 10.1007/s00795-023-00373-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/14/2023] [Indexed: 11/07/2023]
Abstract
Cancer cell proliferation is affected by post-translational modifications of tubulin. Especially, overexpression or depletion of enzymes for modifications on the tubulin C-terminal region perturbs dynamic instability of the spindle body. Those modifications include processing of C-terminal amino acids of α-tubulin; detyrosination, and a removal of penultimate glutamic acid (Δ2). We previously found a further removal of the third last glutamic acid, which generates so-called Δ3-tubulin. The effects of Δ3-tubulin on spindle integrities and cell proliferation remain to be elucidated. In this study, we investigated the impacts of forced expression of Δ3-tubulin on the structure of spindle bodies and cell division in a pancreatic cancer cell line, PANC-1. Overexpression of HA-tagged Δ3-tubulin impaired the morphology and orientation of spindle bodies during cell division in PANC-1 cells. In particular, spindle bending was most significantly increased. Expression of EGFP-tagged Δ3-tubulin driven by the endogenous promoter of human TUBA1B also deformed and misoriented spindle bodies. Spindle bending and condensation defects were significantly observed by EGFP-Δ3-tubulin expression. Furthermore, EGFP-Δ3-tubulin expression increased the nuclear size in a dose-dependent manner of EGFP-Δ3-tubulin expression. The expression of EGFP-Δ3-tubulin tended to slow down cell proliferation. Taken together, our results demonstrate that Δ3-tubulin affects the spindle integrity and cell division.
Collapse
Affiliation(s)
- Kenta Baba
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Kenichiro Uemura
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Ryota Nakazato
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Faryal Ijaz
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Shinya Takahashi
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Koji Ikegami
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
| |
Collapse
|
23
|
Subedi GP, Roberts ET, Davis AR, Kremer PG, Amster IJ, Barb AW. A comprehensive assessment of selective amino acid 15N-labeling in human embryonic kidney 293 cells for NMR spectroscopy. J Biomol NMR 2024:10.1007/s10858-023-00434-3. [PMID: 38407675 DOI: 10.1007/s10858-023-00434-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/31/2023] [Indexed: 02/27/2024]
Abstract
A large proportion of human proteins contain post-translational modifications that cannot be synthesized by prokaryotes. Thus, mammalian expression systems are often employed to characterize structure/function relationships using NMR spectroscopy. Here we define the selective isotope labeling of secreted, post-translationally modified proteins using human embryonic kidney (HEK)293 cells. We determined that alpha-[15N]- atoms from 10 amino acids experience minimal metabolic scrambling (C, F, H, K, M, N, R, T, W, Y). Two more interconvert to each other (G, S). Six others experience significant scrambling (A, D, E, I, L, V). We also demonstrate that tuning culture conditions suppressed V and I scrambling. These results define expectations for 15N-labeling in HEK293 cells.
Collapse
Affiliation(s)
- Ganesh P Subedi
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Elijah T Roberts
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - Paul G Kremer
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
| |
Collapse
|
24
|
Corre M, Lebreton A. Regulation of cold-inducible RNA-binding protein (CIRBP) in response to cellular stresses. Biochimie 2024; 217:3-9. [PMID: 37037339 DOI: 10.1016/j.biochi.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023]
Abstract
Cold-inducible RNA-Binding Protein (CIRBP) is a general stress-response factor in vertebrates harboring two domains: an RNA-recognition motif and a regulatory domain rich in RG/RGG motifs. CIRBP has been described to bind mRNAs upon various stress conditions (cold, infections, UV, hypoxia …) and regulate their stability and translation. The proteins encoded by its targets are involved in key stress-responsive cellular pathways including apoptosis, inflammation, cell proliferation or translation, thus allowing their coordination. Due to its role in regulating central cellular functions, the expression of CIRBP is tightly controlled. We review here current understanding of the multiple mechanistic layers affecting CIRBP expression and function. Beyond transcriptional regulation by cold-responsive elements and the use of alternative promoters and transcription start sites, CIRBP undergoes various alternative splicing (AS) events which, depending on conditions, modulate the stability of CIRBP transcripts and/or impact the sequence of the encoded polypeptide. Typically, whilst CIRBP expression is induced in the context of hypothermia or viral infection, AS events preferentially address alternative isoforms towards mRNA degradation pathways in response to heat stress or to bacterial-secreted pore forming toxins. Post-translational modifications of CIRBP, mostly in its RGG domain, also condition CIRBP subcellular localization and access to its targets, thereby promoting or inhibiting their expression. For instance, phosphorylation and methylation events gate CIRBP nuclear to cytoplasmic translocation and control its recruitment to stress granules. Considering the therapeutic potential of modulating the expression and function of this central player in stress responses, a fine understanding of CIRBP regulation mechanisms deserves further attention.
Collapse
Affiliation(s)
- Morgane Corre
- Institut de biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Alice Lebreton
- Institut de biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France; INRAE, Micalis Institute, 78350, Jouy-en-Josas, France.
| |
Collapse
|
25
|
Guo Y, Cheng R, Wang Y, Gonzalez ME, Zhang H, Liu Y, Kleer CG, Xue L. Regulation of EZH2 protein stability: new mechanisms, roles in tumorigenesis, and roads to the clinic. EBioMedicine 2024; 100:104972. [PMID: 38244292 PMCID: PMC10835131 DOI: 10.1016/j.ebiom.2024.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The importance of EZH2 as a key methyltransferase has been well documented theoretically. Practically, the first EZH2 inhibitor Tazemetostat (EPZ6438), was approved by FDA in 2020 and is used in clinic. However, for most solid tumors it is not as effective as desired and the scope of clinical indications is limited, suggesting that targeting its enzymatic activity may not be sufficient. Recent technologies focusing on the degradation of EZH2 protein have drawn attention due to their potential robust effects. This review focuses on the molecular mechanisms that regulate EZH2 protein stability via post-translational modifications (PTMs), mainly including ubiquitination, phosphorylation, and acetylation. In addition, we discuss recent advancements of multiple proteolysis targeting chimeras (PROTACs) strategies and the latest degraders that can downregulate EZH2 protein. We aim to highlight future directions to expand the application of novel EZH2 inhibitors by targeting both EZH2 enzymatic activity and protein stability.
Collapse
Affiliation(s)
- Yunyun Guo
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Rui Cheng
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Yuqing Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Maria E Gonzalez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Hongshan Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yang Liu
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
| | - Celina G Kleer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Lixiang Xue
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
| |
Collapse
|
26
|
Chavarría C, Ivagnes R, Zeida A, Piñeyro MD, Souza JM. Revisiting the role of 3-nitrotyrosine residues in the formation of alpha-synuclein oligomers and fibrils. Arch Biochem Biophys 2024; 752:109858. [PMID: 38104957 DOI: 10.1016/j.abb.2023.109858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Nitration of tyrosine residues in alpha-synuclein (a-syn) has been detected in different synucleinopathies, including Parkinson's disease. The potential role of 3-nitrotyrosine formation in a-syn, as an oxidative post-translational modification, is still elusive. In this work, we generated well-characterized tyrosine nitrated a-syn monomers and studied their capability to form oligomers and fibrils. We constructed tyrosine to phenylalanine mutants, containing a single tyrosine residue, a-syn mutant Y(125/133/136)F and Y(39/125/133)F) and assessed the impact in a-syn biophysical properties. Nitrated wild-type a-syn and the Y-F mutants, with one 3-nitrotyrosine residue in either the protein's N-terminal or C-terminal region, showed inhibition of fibril formation but retained the capacity of oligomer formation. The inhibition of a-syn fibrillation occurs even when an important amount of unmodified a-syn is still present. We characterized oligomers from both nitrated and non-nitrated forms of the wild-type protein and the mutant forms obtained. Our results indicate that the formation of 3-nitrotyrosine in a-syn could induce an off-pathway oligomer formation which may have an important impact in the development of synucleinopathies.
Collapse
Affiliation(s)
- Cecilia Chavarría
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - Rodrigo Ivagnes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - María Dolores Piñeyro
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - José M Souza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay.
| |
Collapse
|
27
|
Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| |
Collapse
|
28
|
Fu ZW, Fan SH, Liu HF, Hua W. Proteome-wide identification of methylglyoxalated proteins in rapeseed (Brassica napus L.). Plant Physiol Biochem 2024; 207:108319. [PMID: 38183900 DOI: 10.1016/j.plaphy.2023.108319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Methylglyoxal (MG), a highly reactive cellular metabolite, is crucial for plant growth and environmental responses. MG may function by modifying its target proteins, but little is known about MG-modified proteins in plants. Here, MG-modified proteins were pulled down by an antibody against methylglyoxalated proteins and detected using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. We identified 543 candidate proteins which are involved in multiple enzymatic activities and metabolic processes. A great number of candidate proteins were predicted to localize to cytoplasm, chloroplast, and nucleus, consistent with the known subcellular compartmentalization of MG. By further analyzing the raw LC-MS/MS data, we obtained 42 methylglyoxalated peptides in 35 proteins and identified 10 methylglyoxalated lysine residues in a myrosinase-binding protein (BnaC06G0061400ZS). In addition, we demonstrated that MG modifies the glycolate oxidase and β-glucosidase to enhance and inhibit the enzymatic activity, respectively. Together, our study contributes to the investigation of the MG-modified proteins and their potential roles in rapeseed.
Collapse
Affiliation(s)
- Zheng-Wei Fu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Shi-Hang Fan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hong-Fang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| |
Collapse
|
29
|
Hardtke HA, Zhang YJ. Collaborators or competitors: the communication between RNA polymerase II and the nucleosome during eukaryotic transcription. Crit Rev Biochem Mol Biol 2024:1-19. [PMID: 38288999 DOI: 10.1080/10409238.2024.2306365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/12/2024] [Indexed: 04/22/2024]
Abstract
Decades of scientific research have been devoted to unraveling the intricacies of eukaryotic transcription since the groundbreaking discovery of eukaryotic RNA polymerases in the late 1960s. RNA polymerase II, the polymerase responsible for mRNA synthesis, has always attracted the most attention. Despite its structural resemblance to its bacterial counterpart, eukaryotic RNA polymerase II faces a unique challenge in progressing transcription due to the presence of nucleosomes that package DNA in the nuclei. In this review, we delve into the impact of RNA polymerase II and histone signaling on the progression of eukaryotic transcription. We explore the pivotal points of interactions that bridge the RNA polymerase II and histone signaling systems. Finally, we present an analysis of recent cryo-electron microscopy structures, which captured RNA polymerase II-nucleosome complexes at different stages of the transcription cycle. The combination of the signaling crosstalk and the direct visualization of RNA polymerase II-nucleosome complexes provides a deeper understanding of the communication between these two major players in eukaryotic transcription.
Collapse
Affiliation(s)
- Haley A Hardtke
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Y Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| |
Collapse
|
30
|
Tahara S, Okumura G, Matsuo T, Shibuya A, Shibuya K. Essential role of CD155 glycosylation in functional binding to DNAM-1 on natural killer cells. Int Immunol 2024:dxae005. [PMID: 38289706 DOI: 10.1093/intimm/dxae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Indexed: 02/01/2024] Open
Abstract
CD155 is highly expressed on tumor cells and augments or inhibits the cytotoxic activities of natural killer (NK) cells and T cells through its receptor ligands DNAM-1 and T cell immunoglobulin immunoreceptor tyrosine-based inhibitory motif domain (TIGIT), respectively. Although CD155 is heavily glycosylated, the role of glycosylation of CD155 in the cytotoxic activity of effector lymphocytes remains unknown. Here, we show that the N-linked glycosylation at residue 105 (N105 glycosylation) in the first immunoglobulin-like domain of CD155 is involved in the binding of CD155 to both DNAM-1 and TIGIT. The N105 glycosylation also plays an essential role to induce signaling in both DNAM-1 and TIGIT reporter cells. Moreover, we show that the N105 glycosylation of CD155 contributes preferentially to DNAM-1-mediated activating signal over TIGIT-mediated inhibitory signal in NK cells. Our results demonstrated the important role of the N105 glycosylation of CD155 in DNAM-1 and TIGIT functions and shed new light on the understanding of tumor immune responses.
Collapse
Affiliation(s)
- Saeko Tahara
- Department of Immunology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
- School of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Genki Okumura
- Department of Immunology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
- Doctoral Program of Biomedical Sciences, Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Tomohei Matsuo
- Department of Immunology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
- Doctoral Program of Clinical Sciences, Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Akira Shibuya
- Department of Immunology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
- R&D Center for Innovative Drug Discovery, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kazuko Shibuya
- Department of Immunology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
- R&D Center for Innovative Drug Discovery, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| |
Collapse
|
31
|
Gong H, Zhong H, Cheng L, Li LP, Zhang DK. Post-translational protein lactylation modification in health and diseases: a double-edged sword. J Transl Med 2024; 22:41. [PMID: 38200523 PMCID: PMC10777551 DOI: 10.1186/s12967-023-04842-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
As more is learned about lactate, it acts as both a product and a substrate and functions as a shuttle system between different cell populations to provide the energy for sustaining tumor growth and proliferation. Recent discoveries of protein lactylation modification mediated by lactate play an increasingly significant role in human health (e.g., neural and osteogenic differentiation and maturation) and diseases (e.g., tumors, fibrosis and inflammation, etc.). These views are critically significant and first described in detail in this review. Hence, here, we focused on a new target, protein lactylation, which may be a "double-edged sword" of human health and diseases. The main purpose of this review was to describe how protein lactylation acts in multiple physiological and pathological processes and their potential mechanisms through an in-depth summary of preclinical in vitro and in vivo studies. Our work aims to provide new ideas for treating different diseases and accelerate translation from bench to bedside.
Collapse
Affiliation(s)
- Hang Gong
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Huang Zhong
- Department of Gastroenterology, Zigong First People's Hospital, Zigong, Sichuan, China
| | - Long Cheng
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Liang-Ping Li
- Department of Gastroenterology, Sichuan Academy of Medical Sciences and Sichuan People's Hospital, Chengdu, Sichuan, China.
| | - De-Kui Zhang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, Gansu, China.
| |
Collapse
|
32
|
Elsäßer G, Seidl T, Pfannstiel J, Schaller A, Stührwohldt N. Characterization of Prolyl-4-Hydroxylase Substrate Specificity Using Pichia pastoris as an Efficient Eukaryotic Expression System. Methods Mol Biol 2024; 2731:59-80. [PMID: 38019426 DOI: 10.1007/978-1-0716-3511-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The use of eukaryotic expression systems facilitates the heterologous expression of complex eukaryotic proteins in their post-translationally modified and biologically active state, as a prerequisite for subsequent biochemical characterization and functional analysis. Here we describe the complete workflow for the expression of Arabidopsis thaliana prolyl-4-hydroxylases (P4Hs) in the methylotrophic yeast Pichia pastoris (renamed as Komagataella phaffii), for the extraction of the recombinant enzymes, purification by affinity chromatography, and characterization of P4H activity and specificity toward oligopeptide substrates by mass spectrometry. We expressed eight of the 13 Arabidopsis P4Hs and show that they are all active against proline-rich extensin-derived peptides. However, three of them differed in substrate specificity and were also able to hydroxylate the CLEL9 signaling peptide, featuring a single proline within its mature peptide sequence.
Collapse
Affiliation(s)
- Gerith Elsäßer
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Tim Seidl
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Module, University of Hohenheim, Stuttgart, Germany
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Nils Stührwohldt
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
| |
Collapse
|
33
|
May MA, Tomanek L. Uncovering the roles of sirtuin activity and food availability during the onset of the heat shock response in the California mussel (Mytilus californianus): Implications for antioxidative stress responses. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110902. [PMID: 37690509 DOI: 10.1016/j.cbpb.2023.110902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/13/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Sirtuins are a class of NAD+-dependent deacylases, with known regulatory roles in energy metabolism and cellular stress responses in vertebrates. Previous work using marine mussels have suggested a similar role in invertebrates, providing a potential mechanism linking food availability and thermal sensitivity in Mytilids. Sirtuin inhibitors affect mussels' recovery from environmental stressors, including acute heat shock and well-fed mussels exposed to sirtuin inhibitors and/or acute heat shock respond differently than poorly fed mussels, at the protein and whole-organism levels. While this implies a relationship between sirtuins, food availability, and temperature, the direct effects of sirtuin inhibitors (nicotinamide and suramin) on sirtuin activity or their putative effectors have not been explicitly tested. In this study, adult Mytilus californianus were acclimated to a low or high food availability and exposed to one of the following treatments: control, acute heat shock, sirtuin inhibitors, or acute heat shock and sirtuin inhibitors. Mussels increased sirtuin activity during early recovery (5 h) from sirtuin inhibition and acute heat shock, but only if acclimated to a high food availability. Redox balance was also impacted in mussels acclimated to high food availability and exposed to sirtuin inhibitors, signifying interactions between ration, acute heat shock, and sirtuin inhibitors. Additionally, we found a correlation between sirtuin and superoxide dismutase activities, suggesting a potential regulatory role of oxidative stress by sirtuins. Following prolonged recovery (17 h), we found increased sirtuin activity in mussels acclimated to low food availability, indicating that endogenous sirtuin activity may be related to food availability in mussels.
Collapse
Affiliation(s)
- Melissa A May
- Florida Gulf Coast University, Fort Myers, FL 33965, USA; California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Lars Tomanek
- California Polytechnic State University, San Luis Obispo, CA 93407, USA
| |
Collapse
|
34
|
Yang Y, Mei G, Yang L, Luo T, Wu R, Peng S, Peng Z, Cui J, Cheng Y. PCB126 impairs human sperm functions by affecting post-translational modifications and mitochondrial functions. Chemosphere 2024; 346:140532. [PMID: 37918541 DOI: 10.1016/j.chemosphere.2023.140532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Over the past few decades, there has been a consistent decline in semen quality across the globe, with environmental pollution being identified as the primary cause. Among the various contaminants present in the environment, persistent organic pollutants (POPs) have garnered significant attention due to their high toxicity, slow degradation, bio-accumulation, and long-range migration. PCBs, which include 210 congeners, are a crucial type of POPs that are known to have harmful effects on the environment and human health. Among the various PCB congeners, 3,3',4,4',5-pentachlorobiphenyl (PCB126) is a typical environmental endocrine-disrupting chemical that is widely distributed and has been associated with several health hazards. However, the impact and mechanism of PCB126 on human sperm function has not been fully elucidated. We aimed to investigate the effects of different concentrations of PCB126 (0.01, 0.1, 1, 10 μg/mL) on sperm motility, viability, hyperactivation, and acrosome reaction after incubation for different periods (1 and 2 h), delving deeper into the molecular mechanism of human sperm dysfunction caused by PCB126. First, we investigated the link between PCB126 treatment and the occurrence of protein modifications that are critical to sperm function regulation, such as tyrosine phosphorylation and lysine glutarylation. Second, we examined the potential impact of PCB126 on different parameters related to mitochondrial function, including reactive oxygen species, malondialdehyde levels, mitochondrial membrane potential, mitochondria respiration and adenosine triphosphate generation. Our findings indicate that exposure to environmental pollutants such as PCB126 in vitro may have a negative impact on human sperm functions by interfering with post-translational modifications and mitochondrial functions.
Collapse
Affiliation(s)
- Yebin Yang
- College of Chemistry and Biological Engineering, Yichun University, Yichun, China
| | - Guangquan Mei
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, Department of Chemistry and Bioengineering, Yichun University, Yichun, China; Key Laboratory of Jiangxi University for Applied Chemistry and Chemical Biology, Yichun University, Yichun, China
| | - Liu Yang
- College of Chemistry and Biological Engineering, Yichun University, Yichun, China
| | - Tao Luo
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Runwen Wu
- Center for Translational Medicine, Department of Medicine, Yichun University, Yichun, China
| | - Shenglin Peng
- Yichun People's Hospital, Jiangxi Province, Yichun, China
| | - Zhen Peng
- Yichun People's Hospital, Jiangxi Province, Yichun, China
| | - Jiajun Cui
- Center for Translational Medicine, Department of Medicine, Yichun University, Yichun, China
| | - Yimin Cheng
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, Department of Chemistry and Bioengineering, Yichun University, Yichun, China; Center for Translational Medicine, Department of Medicine, Yichun University, Yichun, China.
| |
Collapse
|
35
|
Ogawa-Ohnishi M, Matsubayashi Y. Extraction of Apoplastic Peptides for the Structural Elucidation of Mature Peptide Hormones in Arabidopsis. Methods Mol Biol 2024; 2731:81-87. [PMID: 38019427 DOI: 10.1007/978-1-0716-3511-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Various secreted peptides, including peptide hormones, are present in the apoplast, but their biochemical characterization remains a challenge due to their low abundance, difficulty in extraction, and interference from numerous secondary metabolites. Here, we describe a simple and straightforward protocol for the extraction of apoplastic peptides with a high purity. This protocol takes advantage of the fact that apoplastic peptides diffuse and accumulate in the culture medium when Arabidopsis seedlings are subjected to whole-plant submerged culture. The peptides in the culture medium are efficiently recovered by o-chlorophenol extraction followed by acetone precipitation. The recovered peptides can be subjected to nano-liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) without any additional clean-up. This procedure enables the structural elucidation of mature peptide hormones in the apoplast with the use of Arabidopsis plants that overexpress peptide hormone genes.
Collapse
|
36
|
Long J, Wang J, Dong Y, Yang J, Xie G, Tong Y. Prolyl isomerase Pin1 promotes autophagy and cancer cell viability through activating FoxO3 signalling. Cell Signal 2024; 113:110940. [PMID: 38084839 DOI: 10.1016/j.cellsig.2023.110940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/01/2023] [Accepted: 10/22/2023] [Indexed: 12/18/2023]
Abstract
Pin1-directed prolyl isomerization is a central common oncogenic mechanism to drive tumorigenic processes. However, the role of Pin1 in cellular autophagy is still poorly understood. Here we report that pharmacological inhibition of Pin1 decreased the formation of autophagosome/autolysosomes upon nutrient starvation. Inhibition of Pin1 reduced, whereas forced expression of Pin1 increased, the level of LC3 and viability of U2OS and PANC-1 cells. Pin1 could augment the accumulation of LC3 upon chloroquine treatment, while chloroquine also disturbed its function on cell viability. RNA-Seq and qPCR identified altered autophagic pathway upon Pin1 silencing. Mechanistically, FoxO3 was identified critical for Pin1-mediated autophagy. Knockdown of FoxO3 could rescue the changes of LC3 level and cellular viability caused by Pin1 overexpression. In xenograft mouse model, Pin1 reduced the sensitivity of PANC-1 to chloroquine while FoxO3 silencing could inhibit Pin1's function. Moreover, Pin1 could bind FoxO3 via its pS284-P motif, reduce its phosphorylation at T32, facilitate its nuclear retention, and therefore increased its transcriptional activity. S284A mutation of FoxO3 interfered with its T32 phosphorylation, reduced its nuclear localization and disrupted its function to support cell viability upon nutrient starvation. Furthermore, the protein level of Pin1 positively correlated with FoxO3 nuclear localization and LC3 level in pancreatic adenocarcinoma and osteosarcoma samples. Together, this study highlights an important role for Pin1-FoxO3 axis in regulating autophagy and cancer cell viability. Intervening in the Pin1-FoxO3 interaction would serve as an effective therapeutic strategy and the pS284-P motif of FoxO3 provides a potential target for drug design.
Collapse
Affiliation(s)
- Juan Long
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiaxin Wang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yuanyuan Dong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jian Yang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Gang Xie
- The Second Hospital of Traditional Chinese Medicine in Sichuan Province, Chengdu, Sichuan, China
| | - Ying Tong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
37
|
Chen Y, Jiang Z, Yang Y, Zhang C, Liu H, Wan J. The functions and mechanisms of post-translational modification in protein regulators of RNA methylation: Current status and future perspectives. Int J Biol Macromol 2023; 253:126773. [PMID: 37690652 DOI: 10.1016/j.ijbiomac.2023.126773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
RNA methylation, an epigenetic modification that does not alter gene sequence, may be important to diverse biological processes. Protein regulators of RNA methylation include "writers," "erasers," and "readers," which respectively deposit, remove, and recognize methylated RNA. RNA methylation, particularly N6-methyladenosine (m6A), 5-methylcytosine (m5C), N3-methylcytosine (m3C), N1-methyladenosine (m1A) and N7-methylguanosine (m7G), has been suggested as disease therapeutic targets. Despite advances in the structure and pharmacology of RNA methylation regulators that have improved drug discovery, regulating these proteins by various post-translational modifications (PTMs) has received little attention. PTM modifies protein structure and function, affecting all aspects of normal biology and pathogenesis, including immunology, cell differentiation, DNA damage repair, and tumors. It is becoming evident that RNA methylation regulators are also regulated by diverse PTMs. PTM of RNA methylation regulators induces their covalent linkage to new functional groups, hence modifying their activity and function. Mass spectrometry has identified many PTMs on protein regulators of RNA methylation. In this review, we describe the functions and PTM of protein regulators of RNA methylation and summarize the recent advances in the regulatory mode of human disease and its underlying mechanisms.
Collapse
Affiliation(s)
- Youming Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zuli Jiang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chenxing Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| |
Collapse
|
38
|
Liu X, Zhu B, Dai XW, Xu ZA, Li R, Qian Y, Lu YP, Zhang W, Liu Y, Zheng J. GBDT_KgluSite: An improved computational prediction model for lysine glutarylation sites based on feature fusion and GBDT classifier. BMC Genomics 2023; 24:765. [PMID: 38082413 PMCID: PMC10712101 DOI: 10.1186/s12864-023-09834-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Lysine glutarylation (Kglu) is one of the most important Post-translational modifications (PTMs), which plays significant roles in various cellular functions, including metabolism, mitochondrial processes, and translation. Therefore, accurate identification of the Kglu site is important for elucidating protein molecular function. Due to the time-consuming and expensive limitations of traditional biological experiments, computational-based Kglu site prediction research is gaining more and more attention. RESULTS In this paper, we proposed GBDT_KgluSite, a novel Kglu site prediction model based on GBDT and appropriate feature combinations, which achieved satisfactory performance. Specifically, seven features including sequence-based features, physicochemical property-based features, structural-based features, and evolutionary-derived features were used to characterize proteins. NearMiss-3 and Elastic Net were applied to address data imbalance and feature redundancy issues, respectively. The experimental results show that GBDT_KgluSite has good robustness and generalization ability, with accuracy and AUC values of 93.73%, and 98.14% on five-fold cross-validation as well as 90.11%, and 96.75% on the independent test dataset, respectively. CONCLUSION GBDT_KgluSite is an effective computational method for identifying Kglu sites in protein sequences. It has good stability and generalization ability and could be useful for the identification of new Kglu sites in the future. The relevant code and dataset are available at https://github.com/flyinsky6/GBDT_KgluSite .
Collapse
Affiliation(s)
- Xin Liu
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
| | - Bao Zhu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Xia-Wei Dai
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Zhi-Ao Xu
- School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Rui Li
- School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Yuting Qian
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Ya-Ping Lu
- School of Humanities and Arts, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, China
| | - Wenqing Zhang
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Yong Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
| | - Junnian Zheng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221002, China.
| |
Collapse
|
39
|
Mohammad Nezhady MA, Bajon E, Chemtob S. Disentangling the nonmetabolic roles of metabolites: lactate as a case study. Trends Endocrinol Metab 2023; 34:786-788. [PMID: 37739879 DOI: 10.1016/j.tem.2023.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
Many metabolites possess covalent and noncovalent signaling functions. However, ongoing research considers them mostly as ligands, neglecting their potential involvement in post-translational modifications. In this forum article, we discuss the dual signaling functions of metabolites, using lactate as a case study, and advocate for the use of multiple complementary techniques to disentangle their functions.
Collapse
Affiliation(s)
- Mohammad Ali Mohammad Nezhady
- Program in Molecular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada; Research Center of Sainte-Justine University Hospital, Montreal, QC H3T 1C5, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
| | - Emmanuel Bajon
- Research Center of Sainte-Justine University Hospital, Montreal, QC H3T 1C5, Canada
| | - Sylvain Chemtob
- Program in Molecular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada; Research Center of Sainte-Justine University Hospital, Montreal, QC H3T 1C5, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| |
Collapse
|
40
|
Zou H, Cao Y, Hao P, Jin Z, Ding R, Bai X, Zhang K, Xue Y. New insights into the downregulation of cytochrome P450 2E1 via nuclear factor κB-dependent pathways in immune-mediated liver injury. Heliyon 2023; 9:e22641. [PMID: 38046176 PMCID: PMC10687058 DOI: 10.1016/j.heliyon.2023.e22641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/06/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
The extent of immune-mediated hepatic damage (such as in viral hepatitis) is characterised by the downregulation of cytochrome P450s (CYPs), a class of drug-metabolising enzymes. However, whether this downregulation aids liver cells in maintaining their homeostasis or whether the damage is aggravated remains largely unexplored. Herein, we evaluated the effects of phosphorylation mediated by the protein kinase C (PKC)/cAMP-response element binding protein (CREB) and nitration mediated by inducible nitric oxide synthase (iNOS) on the downregulation of CYP2E1 during immune-mediated liver injury. Additionally, we investigated the regulatory mechanism mediated by the nuclear factor κB (NF-κB). The rat model of immune-mediated liver injury was replicated by administering a single i.v. injection of Bacillus Calmette-Guerin (BCG, 125 mg/kg) vaccine and three i.p. injections of ammonium pyrrolidine dithiocarbamate (25, 50, 100 mg/kg/d, days 11, 12, and 13); blood was then collected on day 14. Subsequently, the livers were extracted to identify the different pharmacokinetic and biochemical indicators involved in the process. Our study reports new findings on the dependence between PKC-mediated CREB phosphorylation in the anti-inflammatory pathway and nitration emergency induced by iNOS in pro-inflammatory pathways in the NF-κB pathway. The interaction of these two pathways leads to the downregulation and recovery of CYP2E1, thus alleviating inflammation and nitration stress. Our results confirm that BCG-mediated downregulation of CYP2E1 is linked to iNOS-induced nitration and PKC/NF-κB-mediated CREB phosphorylation, and that NF-κB is an important molecular target in this process. These findings suggest that the downregulation of CYP2E1 may be an autonomous process characteristic of liver cells, helping them adapt to environmental changes, alleviate further hypoxia in inflamed tissues, and minimise exposure to toxic and harmful metabolites.
Collapse
Affiliation(s)
- Huiqiong Zou
- Institute of Pharmacokinetics and Liver Molecular Pharmacology, Department of Pharmacology, Baotou Medical College, No. 31 Jianshe Road, Donghe District, Baotou 014060, China
| | - Yingying Cao
- Institute of Pharmacokinetics and Liver Molecular Pharmacology, Department of Pharmacology, Baotou Medical College, No. 31 Jianshe Road, Donghe District, Baotou 014060, China
| | - Peipei Hao
- Institute of Pharmacokinetics and Liver Molecular Pharmacology, Department of Pharmacology, Baotou Medical College, No. 31 Jianshe Road, Donghe District, Baotou 014060, China
| | - Ziqi Jin
- Institute of Pharmacokinetics and Liver Molecular Pharmacology, Department of Pharmacology, Baotou Medical College, No. 31 Jianshe Road, Donghe District, Baotou 014060, China
| | - Ruifeng Ding
- Department of Gastroenterology, First Affiliated Hospital, Baotou Medical College, No. 41 linyin Road, Kundurun District, Baotou 014010, China
| | - Xuefeng Bai
- Department of Pathology, Baotou Cancer Hospital, No. 18 Tuanjie Street, Qingshan District, Baotou 014000, China
| | - Kun Zhang
- Institute of Pharmacokinetics and Liver Molecular Pharmacology, Department of Pharmacology, Baotou Medical College, No. 31 Jianshe Road, Donghe District, Baotou 014060, China
| | - Yongzhi Xue
- Institute of Pharmacokinetics and Liver Molecular Pharmacology, Department of Pharmacology, Baotou Medical College, No. 31 Jianshe Road, Donghe District, Baotou 014060, China
| |
Collapse
|
41
|
Wang Z, Zhang C, Fan C, Liu Y. Post-translational modifications in stress granule and their implications in neurodegenerative diseases. Biochim Biophys Acta Gene Regul Mech 2023; 1866:194989. [PMID: 37751804 DOI: 10.1016/j.bbagrm.2023.194989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023]
Abstract
Stress granules (SGs) arise as formations of mRNAs and proteins in response to translation initiation inhibition during stress. These dynamic compartments adopt a fluidic nature through liquid-liquid phase separation (LLPS), exhibiting a composition subject to constant change within cellular contexts. Research has unveiled an array of post-translational modifications (PTMs) occurring on SG proteins, intricately orchestrating SG dynamics. In the realm of neurodegenerative diseases, pathological mutant proteins congregate into insoluble aggregates alongside numerous SG proteins, manifesting resilience against disassembly. Specific PTMs conspicuously label these aggregates, designating them for subsequent degradation. The strategic manipulation of aberrant SGs via PTMs emerges as a promising avenue for therapeutic intervention. This review discerns recent strides in comprehending the impact of PTMs on LLPS behavior and the assembly/disassembly kinetics of SGs. By delving into the roles of PTMs in governing SG dynamics, we augment our cognizance of the molecular underpinnings of neurodegeneration. Furthermore, we offer invaluable insights into potential targets for therapeutic intervention in neurodegenerative afflictions, encompassing conditions like amyotrophic lateral sclerosis and frontotemporal dementia.
Collapse
Affiliation(s)
- Zhangshun Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chen'ang Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chengyu Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| |
Collapse
|
42
|
Stonebraker AR, Hankin R, Kapp KL, Li P, Valentine SJ, Legleiter J. Charge within Nt17 peptides modulates huntingtin aggregation and initial lipid binding events. Biophys Chem 2023; 303:107123. [PMID: 37852163 PMCID: PMC10843285 DOI: 10.1016/j.bpc.2023.107123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/22/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Toxic aggregation of pathogenic huntingtin protein (htt) is implicated in Huntington's disease and influenced by various factors, including the first seventeen amino acids at the N-terminus (Nt17) and the presence of lipid membranes. Nt17 has a propensity to form an amphipathic α-helix in the presence of binding partners, which promotes α-helix rich oligomer formation and facilitates htt/lipid interactions. Within Nt17 are multiple sites that are subject to post-translational modification, including acetylation and phosphorylation. Acetylation can occur at lysine 6, 9, and/or 15 while phosphorylation can occur at threonine 3, serine 13, and/or serine 16. Such modifications impact aggregation and lipid binding through the alteration of various intra- and intermolecular interactions. When incubated with htt-exon1(46Q), free Nt17 peptides containing point mutations mimicking acetylation or phosphorylation reduced fibril formation and altered oligomer morphologies. Upon exposure to lipid vesicles, changes to peptide/lipid complexation were observed and peptide-containing oligomers demonstrated reduced lipid interactions.
Collapse
Affiliation(s)
- Alyssa R Stonebraker
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Rachel Hankin
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Kathryn L Kapp
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Peng Li
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Stephen J Valentine
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA; Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, USA; Department of Neuroscience, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, USA.
| |
Collapse
|
43
|
Wu W, Zheng J, Wang R, Wang Y. Ion channels regulate energy homeostasis and the progression of metabolic disorders: Novel mechanisms and pharmacology of their modulators. Biochem Pharmacol 2023; 218:115863. [PMID: 37863328 DOI: 10.1016/j.bcp.2023.115863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
The progression of metabolic diseases, featured by dysregulated metabolic signaling pathways, is orchestrated by numerous signaling networks. Among the regulators, ion channels transport ions across the membranes and trigger downstream signaling transduction. They critically regulate energy homeostasis and pathogenesis of metabolic diseases and are potential therapeutic targets for treating metabolic disorders. Ion channel blockers have been used to treat diabetes for decades by stimulating insulin secretion, yet with hypoglycemia and other adverse effects. It calls for deeper understanding of the largely elusive regulatory mechanisms, which facilitates the identification of new therapeutic targets and safe drugs against ion channels. In the article, we critically assess the two principal regulatory mechanisms, protein-channel interaction and post-translational modification on the activities of ion channels to modulate energy homeostasis and metabolic disorders through multiple novel mechanisms. Moreover, we discuss the multidisciplinary methods that provide the tools for elucidation of the regulatory mechanisms mediating metabolic disorders by ion channels. In terms of translational perspective, the mechanistic analysis of recently validated ion channels that regulate insulin resistance, body weight control, and adverse effects of current ion channel antagonists are discussed in details. Their small molecule modulators serve as promising new drug candidates to combat metabolic disorders.
Collapse
Affiliation(s)
- Wenyi Wu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Jianan Zheng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
| |
Collapse
|
44
|
Pourmirzaei M, Ramazi S, Esmaili F, Shojaeilangari S, Allahvardi A. Machine learning-based approaches for ubiquitination site prediction in human proteins. BMC Bioinformatics 2023; 24:449. [PMID: 38017391 PMCID: PMC10683244 DOI: 10.1186/s12859-023-05581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
Protein ubiquitination is a critical post-translational modification (PTMs) involved in numerous cellular processes. Identifying ubiquitination sites (Ubi-sites) on proteins offers valuable insights into their function and regulatory mechanisms. Due to the cost- and time-consuming nature of traditional approaches for Ubi-site detection, there has been a growing interest in leveraging artificial intelligence for computer-aided Ubi-site prediction. In this study, we collected experimentally verified Ubi-sites of human proteins from the dbPTM database, then conducted comprehensive state-of-the art computational methods along with standard evaluation metrics and a proper validation strategy for Ubi-site prediction. We presented the effectiveness of our framework by comparing ten machine learning (ML) based approaches in three different categories: feature-based conventional ML methods, end-to-end sequence-based deep learning (DL) techniques, and hybrid feature-based DL models. Our results revealed that DL approaches outperformed the classical ML methods, achieving a 0.902 F1-score, 0.8198 accuracy, 0.8786 precision, and 0.9147 recall as the best performance for a DL model using both raw amino acid sequences and hand-crafted features. Interestingly, our experimental results disclosed that the performance of DL methods had a positive correlation with the length of amino acid fragments, suggesting that utilizing the entire sequence can lead to more accurate predictions in future research endeavors. Additionally, we developed a meticulously curated benchmark for Ubi-site prediction in human proteins. This benchmark serves as a valuable resource for future studies, enabling fair and accurate comparisons between different methods. Overall, our work highlights the potential of ML, particularly DL techniques, in predicting Ubi-sites and furthering our knowledge of protein regulation through ubiquitination in cells.
Collapse
Affiliation(s)
- Mahdi Pourmirzaei
- Department of Information Technology, Tarbiat Modares University, 14115-111, Tehran, Iran
| | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-111, Tehran, Iran
| | - Farzaneh Esmaili
- Department of Information Technology, Tarbiat Modares University, 14115-111, Tehran, Iran
| | - Seyedehsamaneh Shojaeilangari
- Biomedical Engineering Group, Department of Electrical and Information Technology, Iranian Research Organization for Science and Technology (IROST), 33535111, Tehran, Iran.
| | - Abdollah Allahvardi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-111, Tehran, Iran
| |
Collapse
|
45
|
Azmi MB, Jawed A, Ahmed SDH, Naeem U, Feroz N, Saleem A, Sardar K, Qureshi SA, Azim MK. Understanding the impact of structural modifications at the NNAT gene's post-translational acetylation site: in silico approach for predicting its drug-interaction role in anorexia nervosa. Eat Weight Disord 2023; 28:97. [PMID: 37987927 PMCID: PMC10663277 DOI: 10.1007/s40519-023-01618-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/22/2023] Open
Abstract
PURPOSE Anorexia nervosa (AN) is a neuropsychological public health concern with a socially disabling routine and affects a person's healthy relationship with food. The role of the NNAT (Neuronatin) gene in AN is well established. The impact of mutation at the protein's post-translational modification (PTM) site has been exclusively associated with the worsening of the protein's biochemical dynamics. METHODS To understand the relationship between genotype and phenotype, it is essential to investigate the appropriate molecular stability of protein required for proper biological functioning. In this regard, we investigated the PTM-acetylation site of the NNAT gene in terms of 19 other specific amino acid probabilities in place of wild type (WT) through various in silico algorithms. Based on the highest pathogenic impact computed through the consensus classifier tool, we generated 3 residue-specific (K59D, P, W) structurally modified 3D models of NNAT. These models were further tested through the AutoDock Vina tool to compute the molecular drug binding affinities and inhibition constant (Ki) of structural variants and WT 3D models. RESULTS With trained in silico machine learning algorithms and consensus classifier; the three structural modifications (K59D, P, W), which were also the most deleterious substitution at the acetylation site of the NNAT gene, showed the highest structural destabilization and decreased molecular flexibility. The validation and quality assessment of the 3D model of these structural modifications and WT were performed. They were further docked with drugs used to manage AN, it was found that the ΔGbind (kcal/mol) values and the inhibition constants (Ki) were relatively lower in structurally modified models as compared to WT. CONCLUSION We concluded that any future structural variation(s) at the PTM-acetylation site of the NNAT gene due to possible mutational consequences, will serve as a basis to explore its relationship with the propensity of developing AN. LEVEL OF EVIDENCE No level of evidence-open access bioinformatics research.
Collapse
Affiliation(s)
- Muhammad Bilal Azmi
- Department of Biochemistry, Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan.
| | - Areesha Jawed
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Syed Danish Haseen Ahmed
- Department of Biochemistry, Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Unaiza Naeem
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Nazia Feroz
- Department of Biochemistry, Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Arisha Saleem
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Kainat Sardar
- Department of Biochemistry, University of Karachi, Karachi, Pakistan
- Department of Chemistry, Bahria College NORE-1, Karachi, Pakistan
| | | | - M Kamran Azim
- Department of Biosciences, Mohammad Ali Jinnah University, Karachi, Pakistan
| |
Collapse
|
46
|
Ramalingam N, Dettmer U. α-Synuclein serine129 phosphorylation - the physiology of pathology. Mol Neurodegener 2023; 18:84. [PMID: 37953316 PMCID: PMC10641962 DOI: 10.1186/s13024-023-00680-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023] Open
Affiliation(s)
- Nagendran Ramalingam
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
47
|
Zhen X, Sun Y, Lin H, Huang Y, Liu T, Li Y, Peng H. Elucidating the role of nicotinamide N-methyltransferase-p53 axis in the progression of chronic kidney disease. PeerJ 2023; 11:e16301. [PMID: 37953778 PMCID: PMC10638915 DOI: 10.7717/peerj.16301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 11/14/2023] Open
Abstract
Background Chronic kidney disease (CKD) is a significant global health issue characterized by progressive loss of kidney function. Renal interstitial fibrosis (TIF) is a common feature of CKD, but current treatments are seldom effective in reversing TIF. Nicotinamide N-methyltransferase (NNMT) has been found to increase in kidneys with TIF, but its role in renal fibrosis is unclear. Methods Using mice with unilateral ureteral obstruction (UUO) and cultured renal interstitial fibroblast cells (NRK-49F) stimulated with transforming growth factor-β1 (TGF-β1), we investigated the function of NNMT in vivo and in vitro. Results We performed single-cell transcriptome sequencing (scRNA-seq) on the kidneys of mice and found that NNMT increased mainly in fibroblasts of UUO mice compared to sham mice. Additionally, NNMT was positively correlated with the expression of renal fibrosis-related genes after UUO injury. Knocking down NNMT expression reduced fibroblast activation and was accompanied by an increase in DNA methylation of p53 and a decrease in its phosphorylation. Conclusions Our findings suggest that chronic kidney injury leads to an accumulation of NNMT, which might decrease p53 methylation, and increase the expression and activity of p53. We propose that NNMT promotes fibroblast activation and renal fibrosis, making NNMT a novel target for preventing and treating renal fibrosis.
Collapse
Affiliation(s)
- Xin Zhen
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuxiang Sun
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongchun Lin
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuebo Huang
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tianwei Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuanqing Li
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Peng
- Nephrology Division, Department of Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
48
|
Miao T, Bai H. Identification of Acetylation Sites of Fatty Acid Synthase (FASN) by Mass Spectrometry and FASN Activity Assay. Bio Protoc 2023; 13:e4873. [PMID: 37969759 PMCID: PMC10632157 DOI: 10.21769/bioprotoc.4873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 09/24/2023] [Indexed: 11/17/2023] Open
Abstract
Lysine acetylation is a conserved post-translational modification and a key regulatory mechanism for various cellular processes, including metabolic control, epigenetic regulation, and cellular signaling transduction. Recent advances in mass spectrometry (MS) enable the extensive identification of acetylated lysine residues of histone and non-histone proteins. However, protein enrichment before MS analysis may be necessary to improve the detection of low-abundant proteins or proteins that exhibit low acetylation levels. Fatty acid synthase (FASN), an essential enzyme catalyzing the de novo synthesis of fatty acids, has been found to be acetylated in various species, from fruit flies to humans. Here, we describe a step-by-step process of antibody-based protein enrichment and sample preparation for acetylation identification of endogenous FASN protein by MS-based proteomics analysis. Meanwhile, we provide a protocol for nicotinamide adenine dinucleotide phosphate (NADPH) absorbance assay for FASN activity measurement, which is one of the primary functional readouts of de novo lipogenesis. Key features • A comprehensive protocol for protein immunoprecipitation and sample preparation for acetylation site identification by mass spectrometry. • Step-by-step procedures for measurement of FASN activity of fruit fly larvae using an absorbance assay.
Collapse
Affiliation(s)
- Ting Miao
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
49
|
Antuma LJ, Steiner I, Garamus VM, Boom RM, Keppler JK. Engineering artificial casein micelles for future food: Is casein phosphorylation necessary? Food Res Int 2023; 173:113315. [PMID: 37803629 DOI: 10.1016/j.foodres.2023.113315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 10/08/2023]
Abstract
Industrial-scale production of recombinant proteins for food products may become economically feasible but correct post-translational modification of proteins by microbial expression systems remains a challenge. For efficient production of hybrid products from bovine casein and recombinant casein, it is therefore of interest to evaluate the necessity of casein post-translational phosphorylation for the preparation of hybrid casein micelles and study their rennet-induced coagulation. Our results show that dephosphorylated casein was hardly incorporated into artificial casein micelles but was capable of stabilising calcium phosphate nanoclusters with an increased size through adsorption on their surface. Thereby, dephosphorylated casein formed larger colloidal particles with a decreased hydration. Furthermore, the presence of increasing amounts of dephosphorylated casein resulted in increasingly poor rennet coagulation behaviour, where dephosphorylated casein disrupted the formation of a coherent gel network by native casein. These results emphasise that post-translational phosphorylation of casein is crucial for their assembly into micelles and thereby for the production of dairy products for which the casein micelle structure is a prerequisite, such as many cheese varieties and yoghurt. Therefore, phosphorylation of future recombinant casein is essential to allow its use in the production of animal-free dairy products.
Collapse
Affiliation(s)
- Laurens J Antuma
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands.
| | - Isabell Steiner
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands.
| | - Vasil M Garamus
- Helmholtz Zentrum Hereon, Max-Planck Str. 1, D-21502 Geesthacht, Germany.
| | - Remko M Boom
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands.
| | - Julia K Keppler
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands.
| |
Collapse
|
50
|
Petchampai N, Isoe J, Balaraman P, Oscherwitz M, Carter BH, Sánchez CG, Scaraffia PY. Pyruvate kinase is post-translationally regulated by sirtuin 2 in Aedes aegypti mosquitoes. Insect Biochem Mol Biol 2023; 162:104015. [PMID: 37797713 PMCID: PMC10698509 DOI: 10.1016/j.ibmb.2023.104015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
We previously demonstrated that Aedes aegypti pyruvate kinase (AaPK) plays a key role in the regulation of both carbon and nitrogen metabolism in mosquitoes. To further elucidate whether AaPK can be post-translationally regulated by Ae. aegypti sirtuin 2 (AaSirt2), an NAD+-dependent deacetylase that catalyzes the removal of acetyl groups from acetylated lysine residues, we conducted a series of analysis in non-starved and starved female mosquitoes. Transcriptional and protein profiles of AaSirt2, analyzed by qPCR and western blots, indicated that the AaSirt2 is differentially modulated in response to sugar or blood feeding in mosquito tissues dissected at different times during the first gonotrophic cycle. We also found that AaSirt2 is localized in both cytosolic and mitochondrial cellular compartments of fat body and thorax. Multiple lysine-acetylated proteins were detected by western blotting in both cellular compartments. Furthermore, western blotting of immunoprecipitated proteins provided evidence that AaPK is lysine-acetylated and bound with AaSirt2 in the cytosolic fractions of fat body and thorax from non-starved and starved females. In correlation with these results, we also discovered that RNAi-mediated knockdown of AaSirt2 in the fat body of starved females significantly decreased AaPK protein abundance. Notably, survivorship of AaSirt2-deficient females maintained under four different nutritional regimens was not significantly affected. Taken together, our data reveal that AaPK is post-translationally regulated by AaSirt2.
Collapse
Affiliation(s)
- Natthida Petchampai
- Department of Tropical Medicine and Infectious Disease, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Jun Isoe
- Department of Entomology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Prashanth Balaraman
- Department of Tropical Medicine and Infectious Disease, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Max Oscherwitz
- Department of Entomology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Brendan H Carter
- Department of Tropical Medicine and Infectious Disease, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Cecilia G Sánchez
- Department of Tropical Medicine and Infectious Disease, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Patricia Y Scaraffia
- Department of Tropical Medicine and Infectious Disease, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
| |
Collapse
|