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Wu W, Lin L, Zhao Y, Li H, Zhang R. Protein modification regulated autophagy in Bombyx mori and Drosophila melanogaster. Front Physiol 2023; 14:1281555. [PMID: 38028759 PMCID: PMC10665574 DOI: 10.3389/fphys.2023.1281555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Post-translational modifications refer to the chemical alterations of proteins following their biosynthesis, leading to changes in protein properties. These modifications, which encompass acetylation, phosphorylation, methylation, SUMOylation, ubiquitination, and others, are pivotal in a myriad of cellular functions. Macroautophagy, also known as autophagy, is a major degradation of intracellular components to cope with stress conditions and strictly regulated by nutrient depletion, insulin signaling, and energy production in mammals. Intriguingly, in insects, 20-hydroxyecdysone signaling predominantly stimulates the expression of most autophagy-related genes while concurrently inhibiting mTOR activity, thereby initiating autophagy. In this review, we will outline post-translational modification-regulated autophagy in insects, including Bombyx mori and Drosophila melanogaster, in brief. A more profound understanding of the biological significance of post-translational modifications in autophagy machinery not only unveils novel opportunities for autophagy intervention strategies but also illuminates their potential roles in development, cell differentiation, and the process of learning and memory processes in both insects and mammals.
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Affiliation(s)
- Wenmei Wu
- School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Luobin Lin
- School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Yuntao Zhao
- School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Huaqin Li
- Guangzhou Xinhua University, Guangzhou, Guangdong, China
| | - Rongxin Zhang
- School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
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Khan S, Khan M, Iqbal N, Dilshad N, Almufareh MF, Alsubaie N. Enhancing Sumoylation Site Prediction: A Deep Neural Network with Discriminative Features. Life (Basel) 2023; 13:2153. [PMID: 38004293 PMCID: PMC10672286 DOI: 10.3390/life13112153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Sumoylation is a post-translation modification (PTM) mechanism that involves many critical biological processes, such as gene expression, localizing and stabilizing proteins, and replicating the genome. Moreover, sumoylation sites are associated with different diseases, including Parkinson's and Alzheimer's. Due to its vital role in the biological process, identifying sumoylation sites in proteins is significant for monitoring protein functions and discovering multiple diseases. Therefore, in the literature, several computational models utilizing conventional ML methods have been introduced to classify sumoylation sites. However, these models cannot accurately classify the sumoylation sites due to intrinsic limitations associated with the conventional learning methods. This paper proposes a robust computational model (called Deep-Sumo) for predicting sumoylation sites based on a deep-learning algorithm with efficient feature representation methods. The proposed model employs a half-sphere exposure method to represent protein sequences in a feature vector. Principal Component Analysis is applied to extract discriminative features by eliminating noisy and redundant features. The discriminant features are given to a multilayer Deep Neural Network (DNN) model to predict sumoylation sites accurately. The performance of the proposed model is extensively evaluated using a 10-fold cross-validation test by considering various statistical-based performance measurement metrics. Initially, the proposed DNN is compared with the traditional learning algorithm, and subsequently, the performance of the Deep-Sumo is compared with the existing models. The validation results show that the proposed model reports an average accuracy of 96.47%, with improvement compared with the existing models. It is anticipated that the proposed model can be used as an effective tool for drug discovery and the diagnosis of multiple diseases.
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Affiliation(s)
- Salman Khan
- Department of Computer Science, Abdul Wali Khan University, Mardan 23200, Pakistan; (S.K.); (N.I.)
| | - Mukhtaj Khan
- Department of Information Technology, The University of Haripur, Haripur 22620, Pakistan;
| | - Nadeem Iqbal
- Department of Computer Science, Abdul Wali Khan University, Mardan 23200, Pakistan; (S.K.); (N.I.)
| | - Naqqash Dilshad
- Department of Convergence Engineering for Intelligent Drone, Sejong University, Seoul 05006, Republic of Korea;
| | - Maram Fahaad Almufareh
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Najah Alsubaie
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University (PNU), P.O. Box 84428, Riyadh 11671, Saudi Arabia
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Sahni T, Sharma S, Verma D, Kaur H, Kumar S. Exploration of novel syringic esters as antifungal agent against phytopathogenic fungi of maize: Structure-activity studies. J Basic Microbiol 2023; 63:1265-1278. [PMID: 37236164 DOI: 10.1002/jobm.202300040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/13/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023]
Abstract
The production of maize is limited by major diseases such as foliar blights, stalk rot, maydis leaf blight; banded leaf and sheath blight and many more. Synthesis of ecologically sustainable and naturally derived products can help us counter these diseases. Hence, Syringaldehyde (a natural occurring isolate) should explore as a viable option as green agrochemical. We performed a structure-activity study to optimize syringaldehyde and its physicochemical properties. A series of novel syringaldehyde esters was synthesized and investigated focusing on esters' nature of lipophillicity, and membrane affinity. Tri-chloro acetylated ester of syringaldehyde was emerged as broad-spectrum fungicide.
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Affiliation(s)
- Tanvi Sahni
- Department of Chemistry, Punjab Agricultural University, Ludhiana, India
| | - Sunita Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Diksha Verma
- Department of Chemistry, Punjab Agricultural University, Ludhiana, India
| | - Harleen Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sachin Kumar
- Department of Zoology, Punjab Agricultural University, Ludhiana, India
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54
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Liu M, Lin X, Cao K, Yang L, Xu H, Zhou X. Multi-Omic Analysis Reveals the Molecular Mechanism of UV-B Stress Resistance in Acetylated RcMYB44 in Rhododendron chrysanthum. Genes (Basel) 2023; 14:2022. [PMID: 38002965 PMCID: PMC10671296 DOI: 10.3390/genes14112022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Ultraviolet-B (UV-B) radiation is a significant environmental factor influencing the growth and development of plants. MYBs play an essential role in the processes of plant responses to abiotic stresses. In the last few years, the development of transcriptome and acetylated proteome technologies have resulted in further and more reliable data for understanding the UV-B response mechanism in plants. In this research, the transcriptome and acetylated proteome were used to analyze Rhododendron chrysanthum Pall. (R. chrysanthum) leaves under UV-B stress. In total, 2348 differentially expressed genes (DEGs) and 685 differentially expressed acetylated proteins (DAPs) were found. The transcriptome analysis revealed 232 MYB TFs; we analyzed the transcriptome together with the acetylated proteome, and screened 4 MYB TFs. Among them, only RcMYB44 had a complete MYB structural domain. To investigate the role of RcMYB44 under UV-B stress, a homology tree was constructed between RcMYB44 and Arabidopsis MYBs, and it was determined that RcMYB44 shares the same function with ATMYB44. We further constructed the hormone signaling pathway involved in RcMYB44, revealing the molecular mechanism of resistance to UV-B stress in R. chrysanthum. Finally, by comparing the transcriptome and the proteome, it was found that the expression levels of proteins and genes were inconsistent, which is related to post-translational modifications of proteins. In conclusion, RcMYB44 of R. chrysanthum is involved in mediating the growth hormone, salicylic acid, jasmonic acid, and abscisic acid signaling pathways to resist UV-B stress.
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Affiliation(s)
| | | | | | | | | | - Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China (H.X.)
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55
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Wang J, Wang F, Wang N, Zhang MY, Wang HY, Huang GL. Diagnostic and Prognostic Value of Protein Post-translational Modifications in Hepatocellular Carcinoma. J Clin Transl Hepatol 2023; 11:1192-1200. [PMID: 37577238 PMCID: PMC10412711 DOI: 10.14218/jcth.2022.00006s] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/03/2023] [Accepted: 02/21/2023] [Indexed: 07/03/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignant tumor with high incidence and cancer mortality worldwide. Post-translational modifications (PTMs) of proteins have a great impact on protein function. Almost all proteins can undergo PTMs, including phosphorylation, acetylation, methylation, glycosylation, ubiquitination, and so on. Many studies have shown that PTMs are related to the occurrence and development of cancers. The findings provide novel therapeutic targets for cancers, such as glypican-3 and mucin-1. Other clinical implications are also found in the studies of PTMs. Diagnostic or prognostic value, and response to therapy have been identified. In HCC, it has been shown that glycosylated alpha-fetoprotein (AFP) has a higher detection rate for early liver cancer than conventional AFP. In this review, we mainly focused on the diagnostic and prognostic value of PTM, in order to provide new insights into the clinical implication of PTM in HCC.
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Affiliation(s)
- Jing Wang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, China
- China-America Cancer Research Institute, Key Laboratory for Epigenetics of Dongguan City, Guangdong Medical University, Dongguan, Guangdong, China
| | - Fangfang Wang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, China
- China-America Cancer Research Institute, Key Laboratory for Epigenetics of Dongguan City, Guangdong Medical University, Dongguan, Guangdong, China
| | - Ning Wang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, China
- China-America Cancer Research Institute, Key Laboratory for Epigenetics of Dongguan City, Guangdong Medical University, Dongguan, Guangdong, China
| | - Mei-Yin Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Hui-Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Guo-Liang Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, China
- China-America Cancer Research Institute, Key Laboratory for Epigenetics of Dongguan City, Guangdong Medical University, Dongguan, Guangdong, China
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56
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Rajalingam A, Sekar K, Ganjiwale A. Identification of Potential Genes and Critical Pathways in Postoperative Recurrence of Crohn's Disease by Machine Learning And WGCNA Network Analysis. Curr Genomics 2023; 24:84-99. [PMID: 37994325 PMCID: PMC10662376 DOI: 10.2174/1389202924666230601122334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 11/24/2023] Open
Abstract
Background Crohn's disease (CD) is a chronic idiopathic inflammatory bowel disease affecting the entire gastrointestinal tract from the mouth to the anus. These patients often experience a period of symptomatic relapse and remission. A 20 - 30% symptomatic recurrence rate is reported in the first year after surgery, with a 10% increase each subsequent year. Thus, surgery is done only to relieve symptoms and not for the complete cure of the disease. The determinants and the genetic factors of this disease recurrence are also not well-defined. Therefore, enhanced diagnostic efficiency and prognostic outcome are critical for confronting CD recurrence. Methods We analysed ileal mucosa samples collected from neo-terminal ileum six months after surgery (M6=121 samples) from Crohn's disease dataset (GSE186582). The primary aim of this study is to identify the potential genes and critical pathways in post-operative recurrence of Crohn's disease. We combined the differential gene expression analysis with Recursive feature elimination (RFE), a machine learning approach to get five critical genes for the postoperative recurrence of Crohn's disease. The features (genes) selected by different methods were validated using five binary classifiers for recurrence and remission samples: Logistic Regression (LR), Decision tree classifier (DT), Support Vector Machine (SVM), Random Forest classifier (RF), and K-nearest neighbor (KNN) with 10-fold cross-validation. We also performed weighted gene co-expression network analysis (WGCNA) to select specific modules and feature genes associated with Crohn's disease postoperative recurrence, smoking, and biological sex. Combined with other biological interpretations, including Gene Ontology (GO) analysis, pathway enrichment, and protein-protein interaction (PPI) network analysis, our current study sheds light on the in-depth research of CD diagnosis and prognosis in postoperative recurrence. Results PLOD2, ZNF165, BOK, CX3CR1, and ARMCX4, are the important genes identified from the machine learning approach. These genes are reported to be involved in the viral protein interaction with cytokine and cytokine receptors, lysine degradation, and apoptosis. They are also linked with various cellular and molecular functions such as Peptidyl-lysine hydroxylation, Central nervous system maturation, G protein-coupled chemoattractant receptor activity, BCL-2 homology (BH) domain binding, Gliogenesis and negative regulation of mitochondrial depolarization. WGCNA identified a gene co-expression module that was primarily involved in mitochondrial translational elongation, mitochondrial translational termination, mitochondrial translation, mitochondrial respiratory chain complex, mRNA splicing via spliceosome pathways, etc.; Both the analysis result emphasizes that the mitochondrial depolarization pathway is linked with CD recurrence leading to oxidative stress in promoting inflammation in CD patients. Conclusion These key genes serve as the novel diagnostic biomarker for the postoperative recurrence of Crohn's disease. Thus, among other treatment options present until now, these biomarkers would provide success in both diagnosis and prognosis, aiming for a long-lasting remission to prevent further complications in CD.
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Affiliation(s)
- Aruna Rajalingam
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka, 560056, India
| | - Kanagaraj Sekar
- Laboratory for Structural Biology and Bio-computing, Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Anjali Ganjiwale
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka, 560056, India
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57
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Greiner JV, Glonek T. Adenosine Triphosphate (ATP) and Protein Aggregation in Age-Related Vision-Threatening Ocular Diseases. Metabolites 2023; 13:1100. [PMID: 37887425 PMCID: PMC10609282 DOI: 10.3390/metabo13101100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Protein aggregation is the etiopathogenesis of the three most profound vision-threatening eye diseases: age-related cataract, presbyopia, and age-related macular degeneration. This perspective organizes known information on ATP and protein aggregation with a fundamental unrecognized function of ATP. With recognition that maintenance of protein solubility is related to the high intracellular concentration of ATP in cells, tissues, and organs, we hypothesize that (1) ATP serves a critical molecular function for organismal homeostasis of proteins and (2) the hydrotropic feature of ATP prevents pathological protein aggregation while assisting in the maintenance of protein solubility and cellular, tissue, and organismal function. As such, the metabolite ATP plays an extraordinarily important role in the prevention of protein aggregation in the leading causes of vision loss or blindness worldwide.
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Affiliation(s)
- Jack V. Greiner
- Schepens Eye Research Institute of Massachusetts Eye & Ear Infirmary, Boston, MA 02114, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA
- Clinical Eye Research of Boston, Boston, MA 01890, USA;
| | - Thomas Glonek
- Clinical Eye Research of Boston, Boston, MA 01890, USA;
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58
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Hu J, Sha W, Yuan S, Wu J, Huang Y. Aggregation, Transmission, and Toxicity of the Microtubule-Associated Protein Tau: A Complex Comprehension. Int J Mol Sci 2023; 24:15023. [PMID: 37834471 PMCID: PMC10573976 DOI: 10.3390/ijms241915023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
The microtubule-associated protein tau is an intrinsically disordered protein containing a few short and transient secondary structures. Tau physiologically associates with microtubules (MTs) for its stabilization and detaches from MTs to regulate its dynamics. Under pathological conditions, tau is abnormally modified, detaches from MTs, and forms protein aggregates in neuronal and glial cells. Tau protein aggregates can be found in a number of devastating neurodegenerative diseases known as "tauopathies", such as Alzheimer's disease (AD), frontotemporal dementia (FTD), corticobasal degeneration (CBD), etc. However, it is still unclear how the tau protein is compacted into ordered protein aggregates, and the toxicity of the aggregates is still debated. Fortunately, there has been considerable progress in the study of tau in recent years, particularly in the understanding of the intercellular transmission of pathological tau species, the structure of tau aggregates, and the conformational change events in the tau polymerization process. In this review, we summarize the concepts of tau protein aggregation and discuss the views on tau protein transmission and toxicity.
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Affiliation(s)
- Jiaxin Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; (J.H.); (W.S.); (S.Y.)
| | - Wenchi Sha
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; (J.H.); (W.S.); (S.Y.)
| | - Shuangshuang Yuan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; (J.H.); (W.S.); (S.Y.)
| | - Jiarui Wu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; (J.H.); (W.S.); (S.Y.)
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yunpeng Huang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; (J.H.); (W.S.); (S.Y.)
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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Khandelwal M, Rout RK. PRMxAI: protein arginine methylation sites prediction based on amino acid spatial distribution using explainable artificial intelligence. BMC Bioinformatics 2023; 24:376. [PMID: 37794362 PMCID: PMC10548713 DOI: 10.1186/s12859-023-05491-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Protein methylation, a post-translational modification, is crucial in regulating various cellular functions. Arginine methylation is required to understand crucial biochemical activities and biological functions, like gene regulation, signal transduction, etc. However, some experimental methods, including Chip-Chip, mass spectrometry, and methylation-specific antibodies, exist for the prediction of methylated proteins. These experimental methods are expensive and tedious. As a result, computational methods based on machine learning play an efficient role in predicting arginine methylation sites. RESULTS In this research, a novel method called PRMxAI has been proposed to predict arginine methylation sites. The proposed PRMxAI extract sequence-based features, such as dipeptide composition, physicochemical properties, amino acid composition, and information theory-based features (Arimoto, Havrda-Charvat, Renyi, and Shannon entropy), to represent the protein sequences into numerical format. Various machine learning algorithms are implemented to select the better classifier, such as Decision trees, Naive Bayes, Random Forest, Support vector machines, and K-nearest neighbors. The random forest algorithm is selected as the underlying classifier for the PRMxAI model. The performance of PRMxAI is evaluated by employing 10-fold cross-validation, and it yields 87.17% and 90.40% accuracy on mono-methylarginine and di-methylarginine data sets, respectively. This research also examines the impact of various features on both data sets using explainable artificial intelligence. CONCLUSIONS The proposed PRMxAI shows the effectiveness of the features for predicting arginine methylation sites. Additionally, the SHapley Additive exPlanation method is used to interpret the predictive mechanism of the proposed model. The results indicate that the proposed PRMxAI model outperforms other state-of-the-art predictors.
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Affiliation(s)
- Monika Khandelwal
- Computer Science and Engineering Department, National Institute of Technology Srinagar, Hazratbal, Srinagar, J&K 190006 India
| | - Ranjeet Kumar Rout
- Computer Science and Engineering Department, National Institute of Technology Srinagar, Hazratbal, Srinagar, J&K 190006 India
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60
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Yao J, Wang ZN, Liu H, Jin H, Zhang Y. Survey of Acetylation for Thermoanaerobacter tengcongensis. Appl Biochem Biotechnol 2023; 195:6081-6097. [PMID: 36809429 DOI: 10.1007/s12010-023-04361-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 02/23/2023]
Abstract
Non-histone protein acetylation is involved in key cellular processes both in eukaryotes and prokaryotes. Acetylation in bacteria is used to modify proteins involved in metabolism and allow the bacteria to adapt to their environment. TTE (Thermoanaerobacter tengcongensis) is an anaerobic, thermophilic saccharolytic bacterium that grows at extreme temperature range between 50 and 80 ℃. The annotated TTE proteome contains less than 3000 proteins. We analyzed the proteome and acetylome of TTE using 2DLC-MS/MS (2-dimensional liquid chromatography mass spectrum). We evaluated the ability of mass spectrometry technology to cover a relatively small proteome as much as possible. And we also observed wide spread of acetylation in TTE, which changed under different temperatures. A total of 2082 proteins were identified, which accounts for about 82% of the database. A total of 2050 (~ 98%) proteins were quantified in at least one culture condition and 1818 proteins were quantified in all 4 conditions. The result also consisted 3457 acetylation sites corresponding to 827 distinct proteins, which covered 40% of the proteins identified. Bioinformatics analysis reported that proteins related to replication, recombination, repair, and extracellular structure cell wall biogenesis had more than half members acetylated, while energy production, carbohydrate transport, and metabolism related proteins were least acetylated. Our result suggested that acetylation affects the ATP-related energy metabolism and energy-dependent biosynthesis process. Comparing the enzymes related with lysine acetylation and acetyl-CoA (acetyl-coenzyme A) metabolism, we suggested that the acetylation of TTE took a non-enzymatic mechanism and affected by abundance of acetyl-CoA.
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Affiliation(s)
- Jun Yao
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Ze-Ning Wang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hang Liu
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Jin
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| | - Yang Zhang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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Zhou WH, Luo Y, Li RX, Degrace P, Jourdan T, Qiao F, Chen LQ, Zhang ML, Du ZY. Inhibition of mitochondrial fatty acid β-oxidation activates mTORC1 pathway and protein synthesis via Gcn5-dependent acetylation of Raptor in zebrafish. J Biol Chem 2023; 299:105220. [PMID: 37660921 PMCID: PMC10540046 DOI: 10.1016/j.jbc.2023.105220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Pharmacological inhibition of mitochondrial fatty acid oxidation (FAO) has been clinically used to alleviate certain metabolic diseases by remodeling cellular metabolism. However, mitochondrial FAO inhibition also leads to mechanistic target of rapamycin complex 1 (mTORC1) activation-related protein synthesis and tissue hypertrophy, but the mechanism remains unclear. Here, by using a mitochondrial FAO inhibitor (mildronate or etomoxir) or knocking out carnitine palmitoyltransferase-1, we revealed that mitochondrial FAO inhibition activated the mTORC1 pathway through general control nondepressible 5-dependent Raptor acetylation. Mitochondrial FAO inhibition significantly promoted glucose catabolism and increased intracellular acetyl-CoA levels. In response to the increased intracellular acetyl-CoA, acetyltransferase general control nondepressible 5 activated mTORC1 by catalyzing Raptor acetylation through direct interaction. Further investigation also screened Raptor deacetylase histone deacetylase class II and identified histone deacetylase 7 as a potential regulator of Raptor. These results provide a possible mechanistic explanation for the mTORC1 activation after mitochondrial FAO inhibition and also bring light to reveal the roles of nutrient metabolic remodeling in regulating protein acetylation by affecting acetyl-CoA production.
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Affiliation(s)
- Wen-Hao Zhou
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Yuan Luo
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Rui-Xin Li
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Pascal Degrace
- Pathophysiology of Dyslipidemia Research Group, INSERM UMR1231 CTM (Center for Translational and Molecular Medicine) Ex-Lipids, Nutrition, Cancer, Université de Bourgogne Franche-Comté, Dijon, France
| | - Tony Jourdan
- Pathophysiology of Dyslipidemia Research Group, INSERM UMR1231 CTM (Center for Translational and Molecular Medicine) Ex-Lipids, Nutrition, Cancer, Université de Bourgogne Franche-Comté, Dijon, France
| | - Fang Qiao
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Li-Qiao Chen
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Mei-Ling Zhang
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China
| | - Zhen-Yu Du
- LANEH, School of Life Sciences, East China Normal University, Shanghai, P.R. China.
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Zu G, Sun Z, Chen Y, Geng J, Lv J, You Z, Jiang C, Sheng Q, Nie Z. The acetyltransferase BmCBP changes the acetylation modification of BmSP3 and affects its protein expression in silkworm, Bombyx mori. Mol Biol Rep 2023; 50:8509-8521. [PMID: 37642757 DOI: 10.1007/s11033-023-08699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Protein acetylation is an important post-translational modification (PTM) that widely exists in organisms. As a reversible PTM, acetylation modification can regulate the function of proteins with high efficiency. In the previous study, the acetylation sites of silkworm proteins were identified on a large scale by nano-HPLC/MS/MS (nanoscale high performance liquid chromatography-tandem secondary mass spectrometry), and a total of 11 acetylation sites were discovered on Bombyx mori nutrient-storage protein SP3 (BmSP3). The purpose of this study was to investigate the effect of acetylation level on BmSP3. METHODS AND RESULTS In this study, the acetylation of BmSP3 was further verified by immunoprecipitation (IP) and Western blotting. Then, it was confirmed that acetylation could up-regulate the expression of BmSP3 by improving its protein stability in BmN cells. Co-IP and RNAi experiments showed acetyltransferase BmCBP could bind to BmSP3 and catalyze its acetylation modification, then regulate the expression of BmSP3. Furthermore, the knock-down of BmCBP could improve the ubiquitination level of BmSP3. Both acetylation and ubiquitination occur on the side chain of lysine residues, therefore, we speculated that the acetylation of BmSP3 catalyzed by BmCBP could competitively inhibit its ubiquitination modification and improve its protein stability by inhibiting ubiquitin-mediated proteasome degradation pathway, and thereby increase the expression and intracellular accumulation. CONCLUSIONS BmCBP catalyzes the acetylation of BmSP3 and may improve the stability of BmSP3 by competitive ubiquitination. This conclusion provides a new functional basis for the extensive involvement of acetylation in the regulation of nutrient storage and utilization in silkworm, Bombyx mori.
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Affiliation(s)
- Guowei Zu
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zihan Sun
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Yanmei Chen
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jiasheng Geng
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jiao Lv
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zhengying You
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Caiying Jiang
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Qing Sheng
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zuoming Nie
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
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Yayli G, Bernardini A, Mendoza Sanchez PK, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA co-activator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. Cell Rep 2023; 42:113099. [PMID: 37682711 PMCID: PMC10591836 DOI: 10.1016/j.celrep.2023.113099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
To understand the function of multisubunit complexes, it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here, we demonstrate that the core modules of ATAC (ADA-two-A-containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription co-activator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, a SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histone proteins. In contrast, ATAC complex subunits cannot be detected in the cytoplasm of mammalian cells. However, an endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble using co-translational pathways, but their subcellular localization, cytoplasmic abundance, and functions are distinct.
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Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
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Yi Y, Lan X, Li Y, Yan C, Lv J, Zhang T, Jiang W. Fatty acid synthesis and oxidation regulate human endoderm differentiation by mediating SMAD3 nuclear localization via acetylation. Dev Cell 2023; 58:1670-1687.e4. [PMID: 37516106 DOI: 10.1016/j.devcel.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/02/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
Metabolic remodeling is one of the earliest events that occur during cell differentiation. Here, we define fatty acid metabolism as a key player in definitive endoderm differentiation from human embryonic stem cells. Fatty acid β-oxidation is enhanced while lipogenesis is decreased, and this is due to the phosphorylation of lipogenic enzyme acetyl-CoA carboxylase by AMPK. More importantly, inhibition of fatty acid synthesis by either its inhibitors or AMPK agonist significantly promotes human endoderm differentiation, while blockade of fatty acid oxidation impairs differentiation. Mechanistically, reduced de novo fatty acid synthesis and enhanced fatty acid β-oxidation both contribute to the accumulation of intracellular acetyl-CoA, which guarantees the acetylation of SMAD3 and further causes nuclear localization to promote endoderm differentiation. Thus, our current study identifies a fatty acid synthesis/oxidation shift during early differentiation and presents an instructive role for fatty acid metabolism in regulating human endoderm differentiation.
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Affiliation(s)
- Ying Yi
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yinglei Li
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Chenchao Yan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Jing Lv
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; College of Life Science, Cangzhou Normal University, Cangzhou 061000, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China.
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65
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Bozdemir N, Uysal F. Histone acetyltransferases and histone deacetyl transferases play crucial role during oogenesis and early embryo development. Genesis 2023; 61:e23518. [PMID: 37226850 DOI: 10.1002/dvg.23518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/26/2023]
Abstract
Dynamic epigenetic regulation is critical for proper oogenesis and early embryo development. During oogenesis, fully grown germinal vesicle oocytes develop to mature Metaphase II oocytes which are ready for fertilization. Fertilized oocyte proliferates mitotically until blastocyst formation and the process is called early embryo development. Throughout oogenesis and early embryo development, spatio-temporal gene expression takes place, and this dynamic gene expression is controlled with the aid of epigenetics. Epigenetic means that gene expression can be altered without changing DNA itself. Epigenome is regulated through DNA methylation and histone modifications. While DNA methylation generally ends up with repression of gene expression, histone modifications can result in expression or repression depending on type of modification, type of histone protein and its specific residue. One of the modifications is histone acetylation which generally ends up with gene expression. Histone acetylation occurs through the addition of acetyl group onto amino terminal of the core histone proteins by histone acetyltransferases (HATs). Contrarily, histone deacetylation is associated with repression of gene expression, and it is catalyzed by histone deacetylases (HDACs). This review article focuses on what is known about alterations in the expression of HATs and HDACs and emphasizes importance of HATs and HDACs during oogenesis and early embryo development.
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Affiliation(s)
- Nazlican Bozdemir
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, Turkey
| | - Fatma Uysal
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, Turkey
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66
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Wang Y, Hu T, He Y, Su C, Wang Z, Zhou X. N-terminal acetylation of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus is critical for its viral pathogenicity. Virology 2023; 586:1-11. [PMID: 37473501 DOI: 10.1016/j.virol.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
N-terminal acetylation (N-acetylation) is one of the most common protein modifications and plays crucial roles in viability and stress responses in animals and plants. However, very little is known about N-acetylation of viral proteins. Here, we identified the Thr residue at position 2 (Thr-2) in the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus (TYLCCNB-βC1) as a novel N-acetylation site. Furthermore, the effects of TYLCCNB-βC1 N-acetylation on its function as a pathogenicity factor were determined via N-acetylation mutants in Nicotiana benthamiana plants. We found that N-acetylation of TYLCCNB-βC1 is critical for its self-interaction in the nucleus and viral pathogenesis, and that removal of N-acetylation of TYLCCNB-βC1 attenuated tomato yellow leaf curl China virus-induced symptoms and led to accelerated degradation of TYLCCNB-βC1 through the ubiquitin-proteasome system. Our data reveal a protective effect of N-acetylation of TYLCCNB-βC1 on its pathogenesis and demonstrate an antagonistic crosstalk between N-acetylation and ubiquitination in this geminiviral protein.
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Affiliation(s)
- Yaqin Wang
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Tao Hu
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yuting He
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chenlu Su
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000, China.
| | - Xueping Zhou
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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67
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Cignarella A, Boscaro C, Albiero M, Bolego C, Barton M. Post-Transcriptional and Epigenetic Regulation of Estrogen Signaling. J Pharmacol Exp Ther 2023; 386:288-297. [PMID: 37391222 DOI: 10.1124/jpet.123.001613] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/17/2023] [Accepted: 06/16/2023] [Indexed: 07/02/2023] Open
Abstract
Post-translational and epigenetic regulation are important mechanisms controlling functions of genes and proteins. Although the "classic" estrogen receptors (ERs) have been acknowledged to function in mediating estrogen effects via transcriptional mechanisms, estrogenic agents modulate the turnover of several proteins via post-transcriptional and post-translational pathways including epigenetics. For instance, the metabolic and angiogenic action of G-protein coupled estrogen receptor (GPER) in vascular endothelial cells has been recently elucidated. By interacting with GPER, 17β-estradiol and the GPER agonist G1 enhance endothelial stability of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) and capillary tube formation by increasing ubiquitin-specific peptidase 19 levels, thereby reducing PFKFB3 ubiquitination and proteasomal degradation. In addition to ligands, the functional expression and trafficking of ERs can be modulated by post-translational modification, including palmitoylation. MicroRNAs (miRNAs), the most abundant form of endogenous small RNAs in humans, regulate multiple target genes and are at the center of the multi-target regulatory network. This review also discusses the emerging evidence of how miRNAs affect glycolytic metabolism in cancer, as well as their regulation by estrogens. Restoring dysregulated miRNA expression represents a promising strategy to counteract the progression of cancer and other disease conditions. Accordingly, estrogen post-transcriptional regulatory and epigenetic mechanisms represent novel targets for pharmacological and nonpharmacological intervention for the treatment and prevention of hormone-sensitive noncommunicable diseases, including estrogen-sensitive cancers of the reproductive system in women. SIGNIFICANCE STATEMENT: The effects of estrogen are mediated by several mechanisms that are not limited to the transcriptional regulation of target genes. Slowing down the turnover of master regulators of metabolism by estrogens allows cells to rapidly adapt to environmental cues. Identification of estrogen-targeted microRNAs may lead to the development of novel RNA therapeutics that disrupt pathological angiogenesis in estrogen-dependent cancers.
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Affiliation(s)
- Andrea Cignarella
- Departments of Medicine (A.C., Ca.B., M.A.) and Pharmaceutical and Pharmacological Sciences (Ch.B.), University of Padova, Padova, Italy; and Molecular Internal Medicine, University of Zürich and Andreas Grüntzig Foundation, Zürich, Switzerland (M.B.)
| | - Carlotta Boscaro
- Departments of Medicine (A.C., Ca.B., M.A.) and Pharmaceutical and Pharmacological Sciences (Ch.B.), University of Padova, Padova, Italy; and Molecular Internal Medicine, University of Zürich and Andreas Grüntzig Foundation, Zürich, Switzerland (M.B.)
| | - Mattia Albiero
- Departments of Medicine (A.C., Ca.B., M.A.) and Pharmaceutical and Pharmacological Sciences (Ch.B.), University of Padova, Padova, Italy; and Molecular Internal Medicine, University of Zürich and Andreas Grüntzig Foundation, Zürich, Switzerland (M.B.)
| | - Chiara Bolego
- Departments of Medicine (A.C., Ca.B., M.A.) and Pharmaceutical and Pharmacological Sciences (Ch.B.), University of Padova, Padova, Italy; and Molecular Internal Medicine, University of Zürich and Andreas Grüntzig Foundation, Zürich, Switzerland (M.B.)
| | - Matthias Barton
- Departments of Medicine (A.C., Ca.B., M.A.) and Pharmaceutical and Pharmacological Sciences (Ch.B.), University of Padova, Padova, Italy; and Molecular Internal Medicine, University of Zürich and Andreas Grüntzig Foundation, Zürich, Switzerland (M.B.)
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68
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Franco J. Pear pollen self-awareness is the result of acetylation of an inorganic pyrophosphatase leading to pollen tube tip swelling. THE PLANT CELL 2023; 35:3392-3393. [PMID: 37352196 PMCID: PMC10473187 DOI: 10.1093/plcell/koad185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Affiliation(s)
- Jessica Franco
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA
- Department of Plant Pathology, Washington State University, Pullman, WA 20855, USA
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69
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Tang C, Wang P, Zhu X, Qi K, Xie Z, Zhang H, Li X, Gao H, Gu T, Gu C, Li S, de Graaf BHJ, Zhang S, Wu J. Acetylation of inorganic pyrophosphatase by S-RNase signaling induces pollen tube tip swelling by repressing pectin methylesterase. THE PLANT CELL 2023; 35:3544-3565. [PMID: 37306489 PMCID: PMC10473231 DOI: 10.1093/plcell/koad162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
Self-incompatibility (SI) is a widespread genetically determined system in flowering plants that prevents self-fertilization to promote gene flow and limit inbreeding. S-RNase-based SI is characterized by the arrest of pollen tube growth through the pistil. Arrested pollen tubes show disrupted polarized growth and swollen tips, but the underlying molecular mechanism is largely unknown. Here, we demonstrate that the swelling at the tips of incompatible pollen tubes in pear (Pyrus bretschneideri [Pbr]) is mediated by the SI-induced acetylation of the soluble inorganic pyrophosphatase (PPA) PbrPPA5. Acetylation at Lys-42 of PbrPPA5 by the acetyltransferase GCN5-related N-acetyltransferase 1 (GNAT1) drives accumulation of PbrPPA5 in the nucleus, where it binds to the transcription factor PbrbZIP77, forming a transcriptional repression complex that inhibits the expression of the pectin methylesterase (PME) gene PbrPME44. The function of PbrPPA5 as a transcriptional repressor does not require its PPA activity. Downregulating PbrPME44 resulted in increased levels of methyl-esterified pectins in growing pollen tubes, leading to swelling at their tips. These observations suggest a mechanism for PbrPPA5-driven swelling at the tips of pollen tubes during the SI response. The targets of PbrPPA5 include genes encoding cell wall-modifying enzymes, which are essential for building a continuous sustainable mechanical structure for pollen tube growth.
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Affiliation(s)
- Chao Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Xiaoxuan Zhu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Zhihua Xie
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Hao Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Xiaoqiang Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Hongru Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Tingting Gu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Gu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Shan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Shaoling Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
| | - Juyou Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Islam A, Chakraborty A, Sarker AH, Aryal UK, Sharma G, Boldogh I, Hazra T. Site-specific acetylation of polynucleotide kinase 3'-phosphatase (PNKP) regulates its distinct role in DNA repair pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545973. [PMID: 37645927 PMCID: PMC10461918 DOI: 10.1101/2023.06.21.545973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mammalian polynucleotide kinase 3'-phosphatase (PNKP) is a dual-function DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, which generate 3'-OH and 5'-phosphate termini respectively, as substrates for DNA polymerase and DNA ligase to complete DNA repair. PNKP is thus involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes, which involve distinct sets of proteins. In this study, we report that PNKP is acetylated at two lysine (K142 and K226) residues. While K142 (AcK142) is constitutively acetylated by p300, CBP acetylates K226 (AcK226) only after DSB induction. Co-immunoprecipitation analysis using antibodies specific for PNKP peptides containing AcK142 or AcK226 of PNKP showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP only with DSBR proteins. Although acetylation at these residues did not significantly affect the enzymatic activity of PNKP in vitro, cells expressing nonacetylable PNKP (K142R or K226R) accumulated DNA damage, specifically in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This observation is consistent with the reported degradation of CBP but not p300 in HD cells. Moreover, genomes of HD cells progressively accumulated DSBs specifically in the transcribed genes. Chromatin-immunoprecipitation analysis using anti-AcK142 or anti-AcK226 antibodies demonstrated an association of Ac-PNKP with the transcribed genes, consistent with PNKP's role in transcription-coupled repair. Thus, our findings collectively demonstrate that acetylation at two lysine residues located in different domains of PNKP regulates its functionally distinct role in BER/SSBR vs. DSBR.
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Affiliation(s)
- Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Altaf H Sarker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, IN 47907, USA
| | - Gulshan Sharma
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tapas Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
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71
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Gryniukova A, Kaiser F, Myziuk I, Alieksieieva D, Leberecht C, Heym PP, Tarkhanova OO, Moroz YS, Borysko P, Haupt VJ. AI-Powered Virtual Screening of Large Compound Libraries Leads to the Discovery of Novel Inhibitors of Sirtuin-1. J Med Chem 2023; 66:10241-10251. [PMID: 37499195 DOI: 10.1021/acs.jmedchem.3c00128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The discovery of new scaffolds and chemotypes via high-throughput screening is tedious and resource intensive. Yet, there are millions of small molecules commercially available, rendering comprehensive in vitro tests intractable. We show how smart algorithms reduce large screening collections to target-specific sets of just a few hundred small molecules, allowing for a much faster and more cost-effective hit discovery process. We showcase the application of this virtual screening strategy by preselecting 434 compounds for Sirtuin-1 inhibition from a library of 2.6 million compounds, corresponding to 0.02% of the original library. Multistage in vitro validation ultimately confirmed nine chemically novel inhibitors. When compared to a competitive benchmark study for Sirtuin-1, our method shows a 12-fold higher hit rate. The results demonstrate how AI-driven preselection from large screening libraries allows for a massive reduction in the number of small molecules to be tested in vitro while still retaining a large number of hits.
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Affiliation(s)
| | | | - Iryna Myziuk
- Enamine Ltd, 78 Chervonotkatska Str., 02094 Kyïv, Ukraine
| | | | | | - Peter P Heym
- Sum of Squares, Lange Straße 41, 04509 Delitzsch, Germany
| | | | - Yurii S Moroz
- Chemspace LLC, 85 Chervonotkatska Str., 03190 Kyïv, Ukraine
- Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Petro Borysko
- Enamine Ltd, 78 Chervonotkatska Str., 02094 Kyïv, Ukraine
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Yayli G, Bernardini A, Sanchez PKM, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA coactivator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551787. [PMID: 37577620 PMCID: PMC10418265 DOI: 10.1101/2023.08.03.551787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
To understand the function of multisubunit complexes it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the core modules of ATAC (ADA-Two-A-Containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histones proteins. In contrast, fully assembled ATAC complex cannot be detected in the cytoplasm of mammalian cells. However, endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related coactivators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic abundance and functions are distinct.
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Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
| | - HT Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research, Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moleculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Medicale, U1258, Illkirch, France
- Universite de Strasbourg, Illkirch, France
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73
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Wang Q, Peng W, Yang Y, Wu Y, Han R, Ding T, Zhang X, Liu J, Liu J, Yang J. Global analysis of lysine acetylation in the brain cortex of K18-hACE2 mice infected with SARS-CoV-2. Proteomics 2023; 23:e2300096. [PMID: 37309728 DOI: 10.1002/pmic.202300096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected hundreds of millions of people all over the world and thus threatens human life. Clinical evidence shows that SARS-CoV-2 infection can cause several neurological consequences, but the existing antiviral drugs and vaccines have failed to stop its spread. Therefore, an understanding of the response to SARS-CoV-2 infection of hosts is vital to find a resultful therapy. Here, we employed a K18-hACE2 mouse infection model and LC-MS/MS to systematically evaluate the acetylomes of brain cortexes in the presence and absence of SARS-CoV-2 infection. Using a label-free strategy, 3829 lysine acetylation (Kac) sites in 1735 histone and nonhistone proteins were identified. Bioinformatics analyses indicated that SARS-CoV-2 infection might lead to neurological consequences via acetylation or deacetylation of important proteins. According to a previous study, we found 26 SARS-CoV-2 proteins interacted with 61 differentially expressed acetylated proteins with high confidence and identified one acetylated SARS-CoV-2 protein nucleocapsid phosphoprotein. We greatly expanded the known set of acetylated proteins and provide the first report of the brain cortex acetylome in this model and thus a theoretical basis for future research on the pathological mechanisms and therapies of neurological consequences after SARS-CoV-2 infection.
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Affiliation(s)
- Qiaochu Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wanjun Peng
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yehong Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Wu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Rong Han
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Ding
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xutong Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiangning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, CAMS and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jiangfeng Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juntao Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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74
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Guzman UH, Aksnes H, Ree R, Krogh N, Jakobsson ME, Jensen LJ, Arnesen T, Olsen JV. Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae. Nat Commun 2023; 14:4517. [PMID: 37500638 PMCID: PMC10374663 DOI: 10.1038/s41467-023-40224-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Protein N-terminal (Nt) acetylation is one of the most abundant modifications in eukaryotes, covering ~50-80 % of the proteome, depending on species. Cells with defective Nt-acetylation display a wide array of phenotypes such as impaired growth, mating defects and increased stress sensitivity. However, the pleiotropic nature of these effects has hampered our understanding of the functional impact of protein Nt-acetylation. The main enzyme responsible for Nt-acetylation throughout the eukaryotic kingdom is the N-terminal acetyltransferase NatA. Here we employ a multi-dimensional proteomics approach to analyze Saccharomyces cerevisiae lacking NatA activity, which causes global proteome remodeling. Pulsed-SILAC experiments reveals that NatA-deficient strains consistently increase degradation of ribosomal proteins compared to wild type. Explaining this phenomenon, thermal proteome profiling uncovers decreased thermostability of ribosomes in NatA-knockouts. Our data are in agreement with a role for Nt-acetylation in promoting stability for parts of the proteome by enhancing the avidity of protein-protein interactions and folding.
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Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Magnus E Jakobsson
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Biosciences, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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75
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Huynh TQ, Tran VN, Thai VC, Nguyen HA, Nguyen NTG, Tran MK, Nguyen TPT, Le CA, Ho LTN, Surian NU, Chen S, Nguyen TTH. Genomic alterations involved in fluoroquinolone resistance development in Staphylococcus aureus. PLoS One 2023; 18:e0287973. [PMID: 37494330 PMCID: PMC10370734 DOI: 10.1371/journal.pone.0287973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
AIM Fluoroquinolone (FQ) is a potent antibiotic class. However, resistance to this class emerges quickly which hinders its application. In this study, mechanisms leading to the emergence of multidrug-resistant (MDR) Staphylococcus aureus (S. aureus) strains under FQ exposure were investigated. METHODOLOGY S. aureus ATCC 29213 was serially exposed to ciprofloxacin (CIP), ofloxacin (OFL), or levofloxacin (LEV) at sub-minimum inhibitory concentrations (sub-MICs) for 12 days to obtain S. aureus -1 strains and antibiotic-free cultured for another 10 days to obtain S. aureus-2 strains. The whole genome (WGS) and target sequencing were applied to analyze genomic alterations; and RT-qPCR was used to access the expressions of efflux-related genes, alternative sigma factors, and genes involved in FQ resistance. RESULTS A strong and irreversible increase of MICs was observed in all applied FQs (32 to 128 times) in all S. aureus-1 and remained 16 to 32 times in all S. aureus-2. WGS indicated 10 noticeable mutations occurring in all FQ-exposed S. aureus including 2 insdel mutations in SACOL0573 and rimI; a synonymous mutation in hslO; and 7 missense mutations located in an untranslated region. GrlA, was found mutated (R570H) in all S. aureus-1 and -2. Genes encoding for efflux pumps and their regulator (norA, norB, norC, and mgrA); alternative sigma factors (sigB and sigS); acetyltransferase (rimI); methicillin resistance (fmtB); and hypothetical protein BJI72_0645 were overexpressed in FQ-exposed strains. CONCLUSION The emergence of MDR S. aureus was associated with the mutations in the FQ-target sequences and the overexpression of efflux pump systems and their regulators.
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Affiliation(s)
- Thuc Quyen Huynh
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Van Nhi Tran
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Van Chi Thai
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hoang An Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Ngoc Thuy Giang Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Minh Khang Tran
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thi Phuong Truc Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Cat Anh Le
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Le Thanh Ngan Ho
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | | | - Swaine Chen
- Genome Institute of Singapore, Singapore, Singapore
| | - Thi Thu Hoai Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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76
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Huang Y, Zhu C, Pan L, Zhang Z. The role of Mycobacterium tuberculosis acetyltransferase and protein acetylation modifications in tuberculosis. Front Cell Infect Microbiol 2023; 13:1218583. [PMID: 37560320 PMCID: PMC10407107 DOI: 10.3389/fcimb.2023.1218583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023] Open
Abstract
Tuberculosis (TB) is a widespread infectious disease caused by Mycobacterium tuberculosis (M. tb), which has been a significant burden for a long time. Post-translational modifications (PTMs) are essential for protein function in both eukaryotic and prokaryotic cells. This review focuses on the contribution of protein acetylation to the function of M. tb and its infected macrophages. The acetylation of M. tb proteins plays a critical role in virulence, drug resistance, regulation of metabolism, and host anti-TB immune response. Similarly, the PTMs of host proteins induced by M. tb are crucial for the development, treatment, and prevention of diseases. Host protein acetylation induced by M. tb is significant in regulating host immunity against TB, which substantially affects the disease's development. The review summarizes the functions and mechanisms of M. tb acetyltransferase in virulence and drug resistance. It also discusses the role and mechanism of M. tb in regulating host protein acetylation and immune response regulation. Furthermore, the current scenario of isoniazid usage in M. tb therapy treatment is examined. Overall, this review provides valuable information that can serve as a preliminary basis for studying pathogenic research, developing new drugs, exploring in-depth drug resistance mechanisms, and providing precise treatment for TB.
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Affiliation(s)
| | | | - Liping Pan
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing TB and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zongde Zhang
- Laboratory of Molecular Biology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing TB and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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van den Beukel MD, Stoelinga AEC, van der Meer AJ, van der Meulen S, Zhang L, Tushuizen ME, van Hoek B, Trouw LA. Antibodies against multiple post-translationally modified proteins aid in diagnosis of autoimmune hepatitis and associate with complete biochemical response to treatment. Front Med (Lausanne) 2023; 10:1195747. [PMID: 37564051 PMCID: PMC10411548 DOI: 10.3389/fmed.2023.1195747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/14/2023] [Indexed: 08/12/2023] Open
Abstract
Background (Auto)immune mediated and cholestatic liver disease (AILD) includes autoimmune hepatitis (AIH), primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). Especially AIH is characterized by the presence of autoantibodies and elevated serum immunoglobulins. In rheumatoid arthritis, autoantibodies against post-translational modifications (PTMs) such as citrullination (Cit) and carbamylation (CarP) are used as diagnostic and prognostic markers, respectively. We studied the presence of six anti-PTM antibodies in patients with the three AILDs and non-AILD. Methods Antibodies against six PTMs (malondialdehyde-acetaldehyde adducts (MAA), advanced glycation end-products (AGE), CarP, acetylation (AL), Cit, and nitration (NT)) were tested in sera of patients with AILD (n = 106), non-AILD (n = 101) and compared with healthy controls (HC) (n = 100). Levels and positivity were correlated with clinical and biochemical features in a well-defined cohort of untreated AIH patients. Results Anti-PTM antibodies were more often detectable in sera from AILD patients compared with HCs (anti-MAA: 67.9% vs. 2.0%, anti-AGE: 36.8% vs. 4.0%, anti-CarP: 47.2% vs. 5.0% and anti-AL: 18.9% vs. 5.0%). In untreated AIH, time to complete biochemical response (CBR) was associated with anti-MAA, anti-AGE, anti-CarP and anti-AL antibodies. Significantly more patients with at least three anti-PTM antibodies attained CBR at 12 months of treatment (13 vs. 3 p = 0.01). Conclusion Anti-PTM antibodies are frequently present in AILD. The presence of anti-MAA, anti-AGE and anti-CarP antibodies correlates with the presence of AIH within this cohort. In AIH, harboring at least three anti-PTM antibody responses is positively associated with CBR. Determination of anti-PTM antibodies in liver disease may have diagnostic and prognostic value.
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Affiliation(s)
| | - Anna E. C. Stoelinga
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Adriaan J. van der Meer
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Stef van der Meulen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Lu Zhang
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Maarten E. Tushuizen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Bart van Hoek
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Leendert A. Trouw
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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Hsu YH, Chao CN, Huang HY, Zhao PW, Hsu PH, Shen CH, Chen SY, Fang CY. Histone deacetylase III interactions with BK polyomavirus large tumor antigen may affect protein stability. Virol J 2023; 20:155. [PMID: 37464367 DOI: 10.1186/s12985-023-02128-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Human polyomavirus BK (BKPyV) causes associated nephropathy and contributes to urinary tract cancer development in renal transplant recipients. Large tumor antigen (LT) is an early protein essential in the polyomavirus life cycle. Protein acetylation plays a critical role in regulating protein stability, so this study investigated the acetylation of the BKPyV LT protein. METHODS The BKPyV LT nucleotide was synthesized, and the protein was expressed by transfection into permissive cells. The BKPyV LT protein was immunoprecipitated and subjected to LC-MS/MS analysis to determine the acetylation residues. The relative lysine was then mutated to arginine in the LT nucleotide and BKPyV genome to analyze the role of LT lysine acetylation in the BKPyV life cycle. RESULTS BKPyV LT acetylation sites were identified at Lys3 and Lys230 by mass spectrometry. HDAC3 and HDAC8 and their deacetylation activity are required for BKPyV LT expression. In addition, mutations of Lys3 and Lys230 to arginine increased LT expression, and the interaction of HDAC3 and LT was confirmed by coimmunoprecipitation. CONCLUSIONS HDAC3 is a newly identified protein that interacts with BKPyV LT, and LT acetylation plays a vital role in the BKPyV life cycle.
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Affiliation(s)
- Yueh-Han Hsu
- Division of Nephrology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
- Department of Nursing, Min-Hwei Junior College of Health Care Management, Tainan, Taiwan
| | - Chun-Nun Chao
- Department of Pediatrics, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Hsin-Yi Huang
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Pei-Wen Zhao
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chiayi Christian Hospital, Chia-Yi, Taiwan
| | - San-Yuan Chen
- Department of Chinese Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan.
- Department of Sports Management, Chia Nan University of Pharmacy & Science, Tainan City, Taiwan.
| | - Chiung-Yao Fang
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan.
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Yang YH, Wen R, Yang N, Zhang TN, Liu CF. Roles of protein post-translational modifications in glucose and lipid metabolism: mechanisms and perspectives. Mol Med 2023; 29:93. [PMID: 37415097 DOI: 10.1186/s10020-023-00684-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
The metabolism of glucose and lipids is essential for energy production in the body, and dysregulation of the metabolic pathways of these molecules is implicated in various acute and chronic diseases, such as type 2 diabetes, Alzheimer's disease, atherosclerosis (AS), obesity, tumor, and sepsis. Post-translational modifications (PTMs) of proteins, which involve the addition or removal of covalent functional groups, play a crucial role in regulating protein structure, localization function, and activity. Common PTMs include phosphorylation, acetylation, ubiquitination, methylation, and glycosylation. Emerging evidence indicates that PTMs are significant in modulating glucose and lipid metabolism by modifying key enzymes or proteins. In this review, we summarize the current understanding of the role and regulatory mechanisms of PTMs in glucose and lipid metabolism, with a focus on their involvement in disease progression associated with aberrant metabolism. Furthermore, we discuss the future prospects of PTMs, highlighting their potential for gaining deeper insights into glucose and lipid metabolism and related diseases.
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Affiliation(s)
- Yu-Hang Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China
| | - Ri Wen
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China
| | - Ni Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China
| | - Tie-Ning Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China.
| | - Chun-Feng Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China.
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80
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Crotti S, Menicatti M, Pallecchi M, Bartolucci G. Tandem mass spectrometry approaches for recognition of isomeric compounds mixtures. MASS SPECTROMETRY REVIEWS 2023; 42:1244-1260. [PMID: 34841547 DOI: 10.1002/mas.21757] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 06/07/2023]
Abstract
The present review aims to collect the published literature pertaining the recognition of isobaric compounds (isomers or stereoisomers) using the features of tandem mass spectrometry (MS) experiments without any chromatographic separation or chemical modification (derivatization or isotopic enrichment) of the analytes. MS/MS methods possess high selectivity, wide dynamic range and high throughput capabilities. Generally, tandem MS has limited capability for distinguishing isomers that fragment similarly. However, some MS/MS methods have been developed and positively applied to isomers discrimination. Among the literature on this topic, the applications that fit on the review subject can be summarized as follow: (1) chiral discrimination by the kinetic method, (2) the use energy-resolved tandem mass spectra and the survival yield (SY) representation, (3) the kinetics evaluation of the ion-molecule interaction and (4) the postprocessing mathematical algorithm to resolve the isomers in MS/MS signal.
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Affiliation(s)
- Sara Crotti
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Marta Menicatti
- Dipartimento Neurofarba, Università di Firenze, Florence, Italy
| | - Marco Pallecchi
- Dipartimento Neurofarba, Università di Firenze, Florence, Italy
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81
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Kirsch-Volders M, Fenech M. Towards prevention of aneuploidy-associated cellular senescence and aging: more questions than answers? MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108474. [PMID: 37866738 DOI: 10.1016/j.mrrev.2023.108474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
The aim of this review is to discuss how aneuploidy contributes to the aging process, and to identify plausible strategies for its prevention. After an overview of mechanisms leading to aneuploidy and the major features of cellular senescence, we discuss the link between (i) aneuploidy and cellular senescence; (ii) aneuploidy and aging; and (iii) cellular senescence and aging. We also consider (i) interactions between aneuploidy, micronuclei, cellular senescence and aging, (ii) the potential of nutritional treatments to prevent aneuploidy-associated senescence and aging, and (iii) knowledge and technological gaps. Evidence for a causal link between aneuploidy, senescence and aging is emerging. In vitro, aneuploidy accompanies the entry into cellular senescence and can itself induce senescence. How aneuploidy contributes in vivo to cellular senescence is less clear. Several routes depending on aneuploidy and/or senescence converge towards chronic inflammation, the major driver of unhealthy aging. Aneuploidy can induce the pro-inflammatory Senescence Associated Secretory Phenotype (SASP), either directly or as a result of micronucleus (MN) induction leading to leakage of DNA into the cytoplasm and triggering of the cGAS-STING pathway of innate immune response. A major difficulty in understanding the impact of aneuploidy on senescence and aging in vivo, results from the heterogeneity of cellular senescence in different tissues at the cytological and molecular level. Due to this complexity, there is at the present time no biomarker or biomarker combination characteristic for all types of senescent cells. In conclusion, a deeper understanding of the critical role aneuploidy plays in cellular senescence and aging is essential to devise practical strategies to protect human populations from aneuploidy-associated pathologies. We discuss emerging evidence, based on in vitro and in vivo studies, that adequate amounts of specific micronutrients are essential for prevention of aneuploidy in humans and that precise nutritional intervention may be essential to help avoid the scourge of aneuploidy-driven diseases.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Michael Fenech
- Clinical and Health Sciences, University of South Australia, SA 5000, Australia; Genome Health Foundation, North Brighton, SA 5048, Australia.
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82
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Pan B, Gardner SM, Schultz K, Perez RM, Deng S, Shimogawa M, Sato K, Rhoades E, Marmorstein R, Petersson EJ. Semi-Synthetic CoA-α-Synuclein Constructs Trap N-Terminal Acetyltransferase NatB for Binding Mechanism Studies. J Am Chem Soc 2023; 145:14019-14030. [PMID: 37319422 PMCID: PMC10728591 DOI: 10.1021/jacs.3c03887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases. A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here, we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes as well as their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Sarah M. Gardner
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kollin Schultz
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryann M. Perez
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Sunbin Deng
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marie Shimogawa
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Kohei Sato
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Elizabeth Rhoades
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
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83
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Lu Z, Qian P, Chang J, He X, Zhang H, Wu J, Zhang T, Wu J. Multi-omics analysis explores the effect of chronic exercise on liver metabolic reprogramming in mice. Front Cell Dev Biol 2023; 11:1199902. [PMID: 37408533 PMCID: PMC10318136 DOI: 10.3389/fcell.2023.1199902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/09/2023] [Indexed: 07/07/2023] Open
Abstract
Background: The effect of exercise on human metabolism is obvious. However, the effect of chronic exercise on liver metabolism in mice is less well described. Methods: The healthy adult mice running for 6 weeks as exercise model and sedentary mice as control were used to perform transcriptomic, proteomic, acetyl-proteomics, and metabolomics analysis. In addition, correlation analysis between transcriptome and proteome, and proteome and metabolome was conducted as well. Results: In total, 88 mRNAs and 25 proteins were differentially regulated by chronic exercise. In particular, two proteins (Cyp4a10 and Cyp4a14) showed consistent trends (upregulated) at transcription and protein levels. KEGG enrichment analysis indicated that Cyp4a10 and Cyp4a14 are mainly involved in fatty acid degradation, retinol metabolism, arachidonic acid metabolism and PPAR signaling pathway. For acetyl-proteomics analysis, 185 differentially acetylated proteins and 207 differentially acetylated sites were identified. Then, 693 metabolites in positive mode and 537 metabolites in negative mode were identified, which were involved in metabolic pathways such as fatty acid metabolism, citrate cycle and glycolysis/gluconeogenesis. Conclusion: Based on the results of transcriptomic, proteomics, acetyl-proteomics and metabolomics analysis, chronic moderate intensity exercise has certain effects on liver metabolism and protein synthesis in mice. Chronic moderate intensity exercise may participate in liver energy metabolism by influencing the expression of Cyp4a14, Cyp4a10, arachidonic acid and acetyl coenzyme A and regulating fatty acid degradation, arachidonic acid metabolism, fatty acyl metabolism and subsequent acetylation.
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Affiliation(s)
- Zhaoxu Lu
- Children’s Hospital Capital Institute of Pediatrics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Ping Qian
- Children’s Hospital Capital Institute of Pediatrics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Jiahui Chang
- Children’s Hospital Capital Institute of Pediatrics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Xuejia He
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing, China
| | - Haifeng Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Experimental Center, Capital Institute of Pediatrics, Beijing, China
| | - Jian Wu
- School of Kinesiology and Health, Capital University of Physical Education and Sports, Beijing, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Jianxin Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
- Beijing Tongren Hospital, Capital Medical University, Beijing, China
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84
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Ding Y, Bi Q, Huang D, Liao J, Yang L, Luo X, Yang P, Li Y, Yao C, Wei W, Zhang J, Li J, Huang Y, Guo DA. A novel integrated automatic strategy for amino acid composition analysis of seeds from 67 species. Food Chem 2023; 426:136670. [PMID: 37354578 DOI: 10.1016/j.foodchem.2023.136670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/06/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
The composition and quantity of amino acids (AAs) in seeds are complicated due to the various origins and modifications of different species. In this study, a novel automatic neutral loss filtering (ANLF) strategy based on accurate mass searching by Python was developed to analyze the free and hydrolyzed AA-phenyl isothiocyanate (PITC) derivatives from seeds of Gymnosperm and Angiosperm phyla. Compared with traditional strategies, ANLF showed much higher accuracy in screening AA derivatives by filtering nitrogen-containing non-AA compounds and efficiency in processing large datasets. Meanwhile, the content phenotype of 20 proteinogenic AAs from seeds of these two families was characterized by a 35-min HPLC method combined with an automated peak-matching strategy. AA profiles of 232 batches of seeds from 67 species, consisting of 19 proteinogenic AAs, 21 modified AAs, and 77 unknown AAs, would be a good reference for their application in food and medicine.
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Affiliation(s)
- Yelin Ding
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qirui Bi
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dongdong Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingmei Liao
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lin Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaoxiao Luo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peilei Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yun Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenlong Wei
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jianqing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiayuan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yong Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - De-An Guo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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85
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Kiouri DP, Ntallis C, Kelaidonis K, Peana M, Tsiodras S, Mavromoustakos T, Giuliani A, Ridgway H, Moore GJ, Matsoukas JM, Chasapis CT. Network-Based Prediction of Side Effects of Repurposed Antihypertensive Sartans against COVID-19 via Proteome and Drug-Target Interactomes. Proteomes 2023; 11:21. [PMID: 37368467 DOI: 10.3390/proteomes11020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
The potential of targeting the Renin-Angiotensin-Aldosterone System (RAAS) as a treatment for the coronavirus disease 2019 (COVID-19) is currently under investigation. One way to combat this disease involves the repurposing of angiotensin receptor blockers (ARBs), which are antihypertensive drugs, because they bind to angiotensin-converting enzyme 2 (ACE2), which in turn interacts with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. However, there has been no in silico analysis of the potential toxicity risks associated with the use of these drugs for the treatment of COVID-19. To address this, a network-based bioinformatics methodology was used to investigate the potential side effects of known Food and Drug Administration (FDA)-approved antihypertensive drugs, Sartans. This involved identifying the human proteins targeted by these drugs, their first neighbors, and any drugs that bind to them using publicly available experimentally supported data, and subsequently constructing proteomes and protein-drug interactomes. This methodology was also applied to Pfizer's Paxlovid, an antiviral drug approved by the FDA for emergency use in mild-to-moderate COVID-19 treatment. The study compares the results for both drug categories and examines the potential for off-target effects, undesirable involvement in various biological processes and diseases, possible drug interactions, and the potential reduction in drug efficiency resulting from proteoform identification.
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Affiliation(s)
- Despoina P Kiouri
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Charalampos Ntallis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - Graham J Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V6Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - John M Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
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86
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Nishiura M, Hori Y, Umeno M, Kikuchi K. Visualization of multiple localizations of GLUT4 by fluorescent probes of PYP-tag with designed unnatural warhead. Chem Sci 2023; 14:5925-5935. [PMID: 37293637 PMCID: PMC10246691 DOI: 10.1039/d3sc00724c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
Within a cell, multiple copies of the same protein coexist in different pathways and behave differently. Being able to individually analyze the constant actions of proteins in a cell is crucial to know the pathways through which they pass and which physiological functions they are deeply involved in. However, until now, it has been difficult to distinguish protein copies with distinct translocation properties by fluorescence labeling with different colors in living cells. In this study, we have created an unnatural ligand with an unprecedented protein-tag labeling property in living cells and overcome the above-mentioned problem. Of special interest is that some fluorescent probes with the ligand can selectively and efficiently label intracellular proteins without binding to cell-surface proteins, even if the proteins are present on the cell membrane. We also developed a cell-membrane impermeable fluorescent probe that selectively labels cell-surface proteins without labeling of intracellular proteins. These localization-selective properties enabled us to visually discriminate two kinetically distinct glucose transporter 4 (GLUT4) molecules that show different multiple subcellular localization and translocation dynamics in live cells. Taking advantage of the probes, we revealed that N-glycosylation of GLUT4 influences intracellular localization. Furthermore, we were able to visually distinguish active GLUT4 molecules that underwent membrane translocation at least twice within an hour from those that remained intracellularly, discovering previously unrecognized dynamic behaviors of GLUT4. This technology provides not only a valuable tool for study on multiple localization and dynamics of proteins but also important information on diseases caused by protein translocation dysfunction.
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Affiliation(s)
- Miyako Nishiura
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Department of Chemistry, Faculty of Science, Kyushu University Fukuoka Fukuoka 819-0395 Japan
| | - Maho Umeno
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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87
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Liu W, Yuan Q, Cao S, Wang G, Liu X, Xia Y, Bian Y, Xu F, Chen Y. Review: Acetylation Mechanisms andTargeted Therapies in Cardiac Fibrosis. Pharmacol Res 2023; 193:106815. [PMID: 37290541 DOI: 10.1016/j.phrs.2023.106815] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Cardiac fibrosis is a common pathophysiological remodeling process that occurs in a variety of cardiovascular diseases and greatly influences heart structure and function, progressively leading to the development of heart failure. However, to date, few effective therapies for cardiac fibrosis exist. Abnormal proliferation, differentiation, and migration of cardiac fibroblasts are responsible for the excessive deposition of extracellular matrix in the myocardium. Acetylation, a widespread and reversible protein post-translational modification, plays an important role in the development of cardiac fibrosis by adding acetyl groups to lysine residues. Many acetyltransferases and deacetylases regulate the dynamic alterations of acetylation in cardiac fibrosis, regulating a range of pathogenic conditions including oxidative stress, mitochondrial dysfunction, and energy metabolism disturbance. In this review, we demonstrate the critical roles that acetylation modifications caused by different types of pathological injury play in cardiac fibrosis. Furthermore, we propose therapeutic acetylation-targeting strategies for the prevention and treatment of patients with cardiac fibrosis.
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Affiliation(s)
- Weikang Liu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Qiuhuan Yuan
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Shengchuan Cao
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Guoying Wang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Xiangguo Liu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Yanan Xia
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Yuan Bian
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China.
| | - Feng Xu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China.
| | - Yuguo Chen
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China.
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88
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Yi F, Cai C, Ruan B, Hao M, Yeo SK, Haas M, Yang F, Zhang X, Guan JL. Regulation of RB1CC1/FIP200 stability and autophagy function by CREBBP-mediated acetylation in an intrinsically disordered region. Autophagy 2023; 19:1662-1677. [PMID: 36394358 PMCID: PMC10262773 DOI: 10.1080/15548627.2022.2148432] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
Abstract
RB1CC1/FIP200 is an essential macroautophagy/autophagy protein that plays an important role in a variety of biological and disease processes through its canonical autophagy-dependent and -independent functions. However, it remains largely unknown whether post-translational modifications could regulate RB1CC1 and its associated autophagy functions. Here, we report acetylation of several lysine residues of RB1CC1 by acetyltransferase CREBBP (CREB binding protein), with K276 as the major CREBBP acetylation site. K276 is also identified as a ubiquitination site by mass spectrometry, and acetylation at this site reduces ubiquitination of RB1CC1 to inhibit its ubiquitin-dependent degradation. We also find that RB1CC1 contains an N-terminal intrinsically disordered region (IDR) capable of forming liquid-liquid phase separation (LLPS) in vitro, which may drive formation of RB1CC1 puncta with LLPS properties in cells independent of SQSTM1/p62 and other autophagy receptors CALCOCO2/NDP52, NBR1, TAX1BP1 and OPTN. Mutational analysis shows that both K276 acetylation and the N-terminal IDR containing it are important for maintaining canonical autophagy function of RB1CC1 in breast cancer cells. Our findings demonstrate regulation of RB1CC1 by a new post-translational mechanism and suggest potential therapeutic application of inducing RB1CC1 degradation through blocking K276 acetylation in the treatment of cancer and other diseases.Abbreviations: Baf-A1: bafilomycin A1; CREBBP/CBP: CREB binding protein; CHX: cycloheximide; EP300/p300: E1A binding protein p300; FRAP: fluorescence recovery after photobleaching; HADCs: histone deacetylases; IDR: intrinsically disordered region; LLPS: liquid-liquid phase separation; KAT2A/GCN5: lysine acetyltransferase 2A; KAT2B/PCAF: lysine acetyltransferase 2B; KAT5/TIP60: lysine acetyltransferase 5; KAT8/MOF: lysine acetyltransferase 8; NAM: nicotinamide; PAS: phagophore assembly site; PEG-8000: polyethylene glycol 8000; RB1CC1/FIP200: RB1 inducible coiled-coil 1; TSA: trichostatin A.
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Affiliation(s)
- Fei Yi
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Chunmiao Cai
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Banzhan Ruan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Mingang Hao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Syn Kok Yeo
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Michael Haas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Fuchun Yang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Xiaoting Zhang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267, USA
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89
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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90
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Ivanauskaite A, Rantala M, Laihonen L, Konert MM, Schwenner N, Mühlenbeck JS, Finkemeier I, Mulo P. Loss of Chloroplast GNAT Acetyltransferases Results in Distinct Metabolic Phenotypes in Arabidopsis. PLANT & CELL PHYSIOLOGY 2023; 64:549-563. [PMID: 37026998 DOI: 10.1093/pcp/pcad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/16/2023] [Indexed: 05/17/2023]
Abstract
Acetylation is one of the most common chemical modifications found on a variety of molecules ranging from metabolites to proteins. Although numerous chloroplast proteins have been shown to be acetylated, the role of acetylation in the regulation of chloroplast functions has remained mainly enigmatic. The chloroplast acetylation machinery in Arabidopsis thaliana consists of eight General control non-repressible 5 (GCN5)-related N-acetyltransferase (GNAT)-family enzymes that catalyze both N-terminal and lysine acetylation of proteins. Additionally, two plastid GNATs have also been reported to be involved in the biosynthesis of melatonin. Here, we have characterized six plastid GNATs (GNAT1, GNAT2, GNAT4, GNAT6, GNAT7 and GNAT10) using a reverse genetics approach with an emphasis on the metabolomes and photosynthesis of the knock-out plants. Our results reveal the impact of GNAT enzymes on the accumulation of chloroplast-related compounds, such as oxylipins and ascorbate, and the GNAT enzymes also affect the accumulation of amino acids and their derivatives. Specifically, the amount of acetylated arginine and proline was significantly decreased in the gnat2 and gnat7 mutants, respectively, as compared to the wild-type Col-0 plants. Additionally, our results show that the loss of the GNAT enzymes results in increased accumulation of Rubisco and Rubisco activase (RCA) at the thylakoids. Nevertheless, the reallocation of Rubisco and RCA did not have consequent effects on carbon assimilation under the studied conditions. Taken together, our results show that chloroplast GNATs affect diverse aspects of plant metabolism and pave way for future research into the role of protein acetylation.
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Affiliation(s)
- Aiste Ivanauskaite
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Marjaana Rantala
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Laura Laihonen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Minna M Konert
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Naike Schwenner
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Jens S Mühlenbeck
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Paula Mulo
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
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91
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Bertola N, Regis S, Bruno S, Mazzarello AN, Serra M, Lupia M, Sabatini F, Corsolini F, Ravera S, Cappelli E. Effects of Deacetylase Inhibition on the Activation of the Antioxidant Response and Aerobic Metabolism in Cellular Models of Fanconi Anemia. Antioxidants (Basel) 2023; 12:antiox12051100. [PMID: 37237966 DOI: 10.3390/antiox12051100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease characterized by a dysfunctional DNA repair and an oxidative stress accumulation due to defective mitochondrial energy metabolism, not counteracted by endogenous antioxidant defenses, which appear down-expressed compared to the control. Since the antioxidant response lack could depend on the hypoacetylation of genes coding for detoxifying enzymes, we treated lymphoblasts and fibroblasts mutated for the FANC-A gene with some histone deacetylase inhibitors (HDACi), namely, valproic acid (VPA), beta-hydroxybutyrate (OHB), and EX527 (a Sirt1 inhibitor), under basal conditions and after hydrogen peroxide addition. The results show that VPA increased catalase and glutathione reductase expression and activity, corrected the metabolic defect, lowered lipid peroxidation, restored the mitochondrial fusion and fission balance, and improved mitomycin survival. In contrast, OHB, despite a slight increase in antioxidant enzyme expressions, exacerbated the metabolic defect, increasing oxidative stress production, probably because it also acts as an oxidative phosphorylation metabolite, while EX527 showed no effect. In conclusion, the data suggest that VPA could be a promising drug to modulate the gene expression in FA cells, confirming that the antioxidant response modulation plays a pivotal in FA pathogenesis as it acts on both oxidative stress levels and the mitochondrial metabolism and dynamics quality.
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Affiliation(s)
- Nadia Bertola
- Department of Experimental Medicine, University of Genoa, Via De Toni 14, 16132 Genova, Italy
| | - Stefano Regis
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy
| | - Silvia Bruno
- Department of Experimental Medicine, University of Genoa, Via De Toni 14, 16132 Genova, Italy
| | | | - Martina Serra
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy
| | - Michela Lupia
- Haematology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy
| | - Federica Sabatini
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy
| | - Fabio Corsolini
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy
| | - Silvia Ravera
- Department of Experimental Medicine, University of Genoa, Via De Toni 14, 16132 Genova, Italy
| | - Enrico Cappelli
- Haematology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy
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92
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Elurbide J, Carte B, Guedes J, Aldabe R. NatB Catalytic Subunit Depletion Disrupts DNA Replication Initiation Leading to Senescence in MEFs. Int J Mol Sci 2023; 24:ijms24108724. [PMID: 37240070 DOI: 10.3390/ijms24108724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Alpha-aminoterminal acetyltransferase B (NatB) is a critical enzyme responsible for acetylating the aminoterminal end of proteins, thereby modifying approximately 21% of the proteome. This post-translational modification impacts protein folding, structure, stability, and interactions between proteins which, in turn, play a crucial role in modulating several biological functions. NatB has been widely studied for its role in cytoskeleton function and cell cycle regulation in different organisms, from yeast to human tumor cells. In this study, we aimed to understand the biological importance of this modification by inactivating the catalytic subunit of the NatB enzymatic complex, Naa20, in non-transformed mammal cells. Our findings demonstrate that depletion of NAA20 results in decreased cell cycle progression and DNA replication initiation, ultimately leading to the senescence program. Furthermore, we have identified NatB substrates that play a role in cell cycle progression, and their stability is compromised when NatB is inactivated. These results underscore the significance of N-terminal acetylation by NatB in regulating cell cycle progression and DNA replication.
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Affiliation(s)
- Jasmin Elurbide
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Beatriz Carte
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Joana Guedes
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA/UM), University of Minho, 4710-057 Braga, Portugal
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
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93
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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94
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Wang X, Jiang X, Li B, Zheng J, Guo J, Gao L, Du M, Weng X, Li L, Chen S, Zhang J, Fang L, Liu T, Wang L, Liu W, Neculai D, Sun Q. A regulatory circuit comprising the CBP and SIRT7 regulates FAM134B-mediated ER-phagy. J Cell Biol 2023; 222:e202201068. [PMID: 37043189 PMCID: PMC10103787 DOI: 10.1083/jcb.202201068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 11/14/2022] [Accepted: 02/21/2023] [Indexed: 04/13/2023] Open
Abstract
Macroautophagy (autophagy) utilizes a serial of receptors to specifically recognize and degrade autophagy cargoes, including damaged organelles, to maintain cellular homeostasis. Upstream signals spatiotemporally regulate the biological functions of selective autophagy receptors through protein post-translational modifications (PTM) such as phosphorylation. However, it is unclear how acetylation directly controls autophagy receptors in selective autophagy. Here, we report that an ER-phagy receptor FAM134B is acetylated by CBP acetyltransferase, eliciting intense ER-phagy. Furthermore, FAM134B acetylation promoted CAMKII-mediated phosphorylation to sustain a mode of milder ER-phagy. Conversely, SIRT7 deacetylated FAM134B to temper its activities in ER-phagy to avoid excessive ER degradation. Together, this work provides further mechanistic insights into how ER-phagy receptor perceives environmental signals for fine-tuning of ER homeostasis and demonstrates how nucleus-derived factors are programmed to control ER stress by modulating ER-phagy.
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Affiliation(s)
- Xinyi Wang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Xiao Jiang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Boran Li
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
| | - Jiahua Zheng
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
| | - Jiansheng Guo
- Center of Cryo-Electron Microscopy, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Gao
- Microscopy Core Facility, Westlake University, Hangzhou, China
| | - Mengjie Du
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Xialian Weng
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Ting Liu
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Liang Wang
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Wei Liu
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
| | - Dante Neculai
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Qiming Sun
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
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95
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Kulik L, Renner B, Laskowski J, Thurman JM, Michael Holers V. Highly pathogenic natural monoclonal antibody B4-IgM recognizes a post-translational modification comprised of acetylated N-terminal methionine followed by aspartic or glutamic acid. Mol Immunol 2023; 157:112-128. [PMID: 37018938 DOI: 10.1016/j.molimm.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 04/05/2023]
Abstract
The natural monoclonal antibody B4-IgM recognizes murine annexin 4 (mAn4) and exacerbates ischemia-reperfusion injury in many mouse models. During apoptosis, the intracellular mAn4 protein translocates to the membrane surface, remaining attached to the outer membrane leaflet where it is recognized by the anti-mAn4 B4-IgM antibody. B4-IgM does not recognize human annexin 4 (hAn4). However, the B4-IgM antibody epitope was detected by Western blot of unknown human proteins and by flow cytometry on all studied human cell lines undergoing apoptosis and on a minor subset of healthy cells. The B4-IgM antibody also recognizes the epitope on necrotic cells in cytoplasmic proteins, apparently entering through pores large enough to allow natural antibodies to penetrate the cells and bind to the epitope expressed on self-proteins. Using proteomics and site-directed mutagenesis, we found that B4-IgM binds to an epitope with post-translationally modified acetylated N-terminal methionine, followed by either glutamic or aspartic acid. The epitope is not induced by apoptosis or injury because this modification can also occur during protein translation. This finding reveals an additional novel mechanism whereby injured cells are detected by natural antibodies that initiate pathogenic complement activation through the recognition of epitopes that are shared across multiple proteins found in variable cell lines.
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96
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Fatema N, Fan C. Studying lysine acetylation of citric acid cycle enzymes by genetic code expansion. Mol Microbiol 2023; 119:551-559. [PMID: 36890576 PMCID: PMC10636775 DOI: 10.1111/mmi.15052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/10/2023]
Abstract
Lysine acetylation is one of the most abundant post-translational modifications in nature, affecting many key biological pathways in both prokaryotes and eukaryotes. It has not been long since technological advances led to understanding of the roles of acetylation in biological processes. Most of those studies were based on proteomic analyses, which have identified thousands of acetylation sites in a wide range of proteins. However, the specific role of individual acetylation event remains largely unclear, mostly due to the existence of multiple acetylation and dynamic changes of acetylation levels. To solve these problems, the genetic code expansion technique has been applied in protein acetylation studies, facilitating the incorporation of acetyllysine into a specific lysine position to generate a site-specifically acetylated protein. By this method, the effects of acetylation at a specific lysine residue can be characterized with minimal interferences. Here, we summarized the development of the genetic code expansion technique for lysine acetylation and recent studies on lysine acetylation of citrate acid cycle enzymes in bacteria by this approach, providing a practical application of the genetic code expansion technique in protein acetylation studies.
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Affiliation(s)
- Nour Fatema
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
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97
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Tanaka M, Takarada T, Nadanaka S, Kojima R, Hosoi K, Machiba Y, Kitagawa H, Yamada T. Influences of amino-terminal modifications on amyloid fibril formation of human serum amyloid A. Arch Biochem Biophys 2023; 742:109615. [PMID: 37105512 DOI: 10.1016/j.abb.2023.109615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023]
Abstract
Human serum amyloid A (SAA) is a precursor protein involved in AA amyloidosis. The N-terminal region of the SAA molecule is crucial for amyloid fibril formation, and therefore modifications in this region are considered to influence the pathogenesis of AA amyloidosis. In the present study, using the N-terminal peptide corresponding to the putative first helix region of the SAA molecule, we investigated the influences of N-terminal modifications on amyloid fibril formation. Spectroscopic analyses revealed that carbamoylation of the N-terminal amino group delayed the onset of amyloid fibril formation. From transmission electron microscopic observations, the N-terminal carbamoylated aggregate showed remarkably different morphologies from the unmodified control. In contrast, acetylation of the N-terminal amino group or truncation of N-terminal amino acid(s) considerably diminished amyloidogenic properties. Furthermore, we also tested the cell toxicity of each peptide aggregate on cultured cells by two cytotoxic assays. Irrespective of carbamoylation or acetylation, MTT assay revealed that SAA peptides reduced the reductive activity of MTT on cells, whereas no apparent increase in LDH release was observed during an LDH assay. In contrast, N-terminal truncation did not affect either MTT reduction or LDH release. These results suggest that N-terminal modification of SAA molecules can act as a switch to regulate susceptibility to AA amyloidosis.
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Affiliation(s)
- Masafumi Tanaka
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan.
| | - Toru Takarada
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Satomi Nadanaka
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Risa Kojima
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Kimiko Hosoi
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Yuki Machiba
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Hiroshi Kitagawa
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Toshiyuki Yamada
- Department of Clinical Laboratory Medicine, Jichi Medical University, Shimotsuke, 329-0498, Japan
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98
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Ortega MA, De Leon-Oliva D, Garcia-Montero C, Fraile-Martinez O, Boaru DL, Del Val Toledo Lobo M, García-Tuñón I, Royuela M, García-Honduvilla N, Bujan J, Guijarro LG, Alvarez-Mon M, Alvarez-Mon MÁ. Understanding HAT1: A Comprehensive Review of Noncanonical Roles and Connection with Disease. Genes (Basel) 2023; 14:genes14040915. [PMID: 37107673 PMCID: PMC10137880 DOI: 10.3390/genes14040915] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Histone acetylation plays a vital role in organizing chromatin, regulating gene expression and controlling the cell cycle. The first histone acetyltransferase to be identified was histone acetyltransferase 1 (HAT1), but it remains one of the least understood acetyltransferases. HAT1 catalyzes the acetylation of newly synthesized H4 and, to a lesser extent, H2A in the cytoplasm. However, 20 min after assembly, histones lose acetylation marks. Moreover, new noncanonical functions have been described for HAT1, revealing its complexity and complicating the understanding of its functions. Recently discovered roles include facilitating the translocation of the H3H4 dimer into the nucleus, increasing the stability of the DNA replication fork, replication-coupled chromatin assembly, coordination of histone production, DNA damage repair, telomeric silencing, epigenetic regulation of nuclear lamina-associated heterochromatin, regulation of the NF-κB response, succinyl transferase activity and mitochondrial protein acetylation. In addition, the functions and expression levels of HAT1 have been linked to many diseases, such as many types of cancer, viral infections (hepatitis B virus, human immunodeficiency virus and viperin synthesis) and inflammatory diseases (chronic obstructive pulmonary disease, atherosclerosis and ischemic stroke). The collective data reveal that HAT1 is a promising therapeutic target, and novel therapeutic approaches, such as RNA interference and the use of aptamers, bisubstrate inhibitors and small-molecule inhibitors, are being evaluated at the preclinical level.
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Affiliation(s)
- Miguel A Ortega
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Cancer Registry and Pathology Department, Principe de Asturias University Hospital, 28806 Alcala de Henares, Spain
| | - Diego De Leon-Oliva
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Cielo Garcia-Montero
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Oscar Fraile-Martinez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Diego Liviu Boaru
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - María Del Val Toledo Lobo
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Department of Biomedicine and Biotechnology, University of Alcalá, 28801 Alcala de Henares, Spain
| | - Ignacio García-Tuñón
- Department of Biomedicine and Biotechnology, University of Alcalá, 28801 Alcala de Henares, Spain
| | - Mar Royuela
- Department of Biomedicine and Biotechnology, University of Alcalá, 28801 Alcala de Henares, Spain
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Julia Bujan
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Luis G Guijarro
- Unit of Biochemistry and Molecular Biology, Department of System Biology (CIBEREHD), University of Alcalá, 28801 Alcala de Henares, Spain
| | - Melchor Alvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Immune System Diseases-Rheumatology, Oncology Service and Internal Medicine (CIBEREHD), University Hospital Príncipe de Asturias, 28806 Alcala de Henares, Spain
| | - Miguel Ángel Alvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
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99
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Pan B, Gardner S, Schultz K, Perez RM, Deng S, Shimogawa M, Sato K, Rhoades E, Marmorstein R, Petersson EJ. Semi-synthetic CoA-α-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535351. [PMID: 37066334 PMCID: PMC10104007 DOI: 10.1101/2023.04.03.535351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases (NATs). A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes and their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.
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100
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Choi HJ, Lee JY, Kim K. Glutathionylation on RNA-binding proteins: a regulator of liquid‒liquid phase separation in the pathogenesis of amyotrophic lateral sclerosis. Exp Mol Med 2023; 55:735-744. [PMID: 37009800 PMCID: PMC10167235 DOI: 10.1038/s12276-023-00978-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 04/04/2023] Open
Abstract
RNA-binding proteins (RBPs) containing low-sequence complexity domains mediate the formation of cellular condensates and membrane-less organelles with biological functions via liquid‒liquid phase separation (LLPS). However, the abnormal phase transition of these proteins induces the formation of insoluble aggregates. Aggregates are pathological hallmarks of neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS). The molecular mechanisms underlying aggregate formation by ALS-associated RPBs remain largely unknown. This review highlights emerging studies on various posttranslational modifications (PTMs) related to protein aggregation. We begin with the introduction of several ALS-associated RBPs that form aggregates induced by phase separation. In addition, we highlight our recent discovery of a new PTM involved in the phase transition during the pathogenesis of fused-in-sarcoma (FUS)-associated ALS. We suggest a molecular mechanism through which LLPS mediates glutathionylation in FUS-linked ALS. This review aims to provide a detailed overview of the key molecular mechanisms of LLPS-mediated aggregate formation by PTMs, which will help further the understanding of the pathogenesis and development of ALS therapeutics.
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Affiliation(s)
- Hyun-Jun Choi
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Sciences, Soonchunhyang University, Cheonan, 31151, Korea
| | - Ji Young Lee
- Department of Medical Biotechnology, Soonchunhyang University, Asan, 31538, Korea
- Department of Medical Science, Soonchunhyang University, Asan, 31538, Korea
| | - Kiyoung Kim
- Department of Medical Science, Soonchunhyang University, Asan, 31538, Korea.
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