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Wang G, Wang Y, Wang K, Zhao H, Liu M, Liang W, Li D. Perillaldehyde Functions as a Potential Antifungal Agent by Triggering Metacaspase-Independent Apoptosis in Botrytis cinerea. Microbiol Spectr 2023; 11:e0052623. [PMID: 37191530 PMCID: PMC10269628 DOI: 10.1128/spectrum.00526-23] [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: 02/17/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023] Open
Abstract
Botrytis cinerea, the causal agent of gray mold, is an important plant pathogen causing preharvest and postharvest diseases. Due to the extensive use of commercial fungicides, fungicide-resistant strains have emerged. Natural compounds with antifungal properties are widely present in various kinds of organisms. Perillaldehyde (PA), derived from the plant species Perilla frutescens, is generally recognized as a potent antimicrobial substance and to be safe to humans and the environment. In this study, we demonstrated that PA could significantly inhibit the mycelial growth of B. cinerea and reduced its pathogenicity on tomato leaves. We also found that PA had a significant protective effect on tomato, grape, and strawberry. The antifungal mechanism of PA was investigated by measuring the reactive oxygen species (ROS) accumulation, the intracellular Ca2+ level, the mitochondrial membrane potential, DNA fragmentation, and phosphatidylserine exposure. Further analyses revealed that PA promoted protein ubiquitination and induced autophagic activities and then triggered protein degradation. When the two metacaspase genes, BcMca1 and BcMca2, were knocked out from B. cinerea, all mutants did not exhibit reduced sensitivity to PA. These findings demonstrated that PA could induce metacaspase-independent apoptosis in B. cinerea. Based on our results, we proposed that PA could be used as an effective control agent for gray mold management. IMPORTANCE Botrytis cinerea causes gray mold disease, is considered one of the most important dangerous pathogens worldwide, and leads to severe economic losses worldwide. Due to the lack of resistant varieties of B. cinerea, gray mold control has mainly relied on application of synthetic fungicides. However, long-term and extensive use of synthetic fungicides has increased fungicide resistance in B. cinerea and is harmful to humans and the environment. In this study, we found that perillaldehyde has a significant protective effect on tomato, grape, and strawberry. We further characterized the antifungal mechanism of PA on B. cinerea. Our results indicated that PA induced apoptosis that was independent of metacaspase function.
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Affiliation(s)
- Guanbo Wang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yadi Wang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Kunchun Wang
- The Linzi Center for Agricultural and Rural Development, Zibo, China
| | - Haonan Zhao
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mengjie Liu
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Delong Li
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Pang K, Wang W, Qin J, Shi Z, Hao L, Ma Y, Xu H, Wu Z, Pan D, Chen Z, Han C. Role of protein phosphorylation in cell signaling, disease, and the intervention therapy. MedComm (Beijing) 2022; 3:e175. [PMID: 36349142 PMCID: PMC9632491 DOI: 10.1002/mco2.175] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is an important post-transcriptional modification involving an extremely wide range of intracellular signaling transduction pathways, making it an important therapeutic target for disease intervention. At present, numerous drugs targeting protein phosphorylation have been developed for the treatment of various diseases including malignant tumors, neurological diseases, infectious diseases, and immune diseases. In this review article, we analyzed 303 small-molecule protein phosphorylation kinase inhibitors (PKIs) registered and participated in clinical research obtained in a database named Protein Kinase Inhibitor Database (PKIDB), including 68 drugs approved by the Food and Drug Administration of the United States. Based on previous classifications of kinases, we divided these human protein phosphorylation kinases into eight groups and nearly 50 families, and delineated their main regulatory pathways, upstream and downstream targets. These groups include: protein kinase A, G, and C (AGC) and receptor guanylate cyclase (RGC) group, calmodulin-dependent protein kinase (CaMK) group, CMGC [Cyclin-dependent kinases (CDKs), Mitogen-activated protein kinases (MAPKs), Glycogen synthase kinases (GSKs), and Cdc2-like kinases (CLKs)] group, sterile (STE)-MAPKs group, tyrosine kinases (TK) group, tyrosine kinase-like (TKL) group, atypical group, and other groups. Different groups and families of inhibitors stimulate or inhibit others, forming an intricate molecular signaling regulatory network. This review takes newly developed new PKIs as breakthrough point, aiming to clarify the regulatory network and relationship of each pathway, as well as their roles in disease intervention, and provide a direction for future drug development.
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Affiliation(s)
- Kun Pang
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Wei Wang
- Department of Medical CollegeSoutheast UniversityNanjingJiangsuChina
| | - Jia‐Xin Qin
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Zhen‐Duo Shi
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Yu‐Yang Ma
- Graduate SchoolBengbu Medical CollegeBengbuAnhuiChina
| | - Hao Xu
- Graduate SchoolBengbu Medical CollegeBengbuAnhuiChina
| | - Zhuo‐Xun Wu
- Department of Pharmaceutical SciencesCollege of Pharmacy and Health SciencesSt. John's University, QueensNew YorkNew YorkUSA
| | - Deng Pan
- Graduate SchoolBengbu Medical CollegeBengbuAnhuiChina
| | - Zhe‐Sheng Chen
- Department of Pharmaceutical SciencesCollege of Pharmacy and Health SciencesSt. John's University, QueensNew YorkNew YorkUSA
| | - Cong‐Hui Han
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
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Genetic Variants Associated with Neuropeptide Y Autoantibody Levels in Newly Diagnosed Individuals with Type 1 Diabetes. Genes (Basel) 2022; 13:genes13050869. [PMID: 35627254 PMCID: PMC9142038 DOI: 10.3390/genes13050869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/30/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
(1) Autoantibodies to the leucine variant of neuropeptide Y (NPY-LA) have been found in individuals with type 1 diabetes (T1D). We investigated the association between the levels of NPY-LA and single nucleotide polymorphisms (SNP) to better understand the genetic regulatory mechanisms of autoimmunity in T1D and the functional impacts of increased NPY-LA levels. (2) NPY-LA measurements from serum and SNP genotyping were done on 560 newly diagnosed individuals with T1D. SNP imputation with the 1000 Genomes reference panel was followed by an association analysis between the SNPs and measured NPY-LA levels. Additionally, functional enrichment and pathway analyses were done. (3) Three loci (DGKH, DCAF5, and LINC02261) were associated with NPY-LA levels (p-value < 1.5 × 10−6), which indicates an association with neurologic and vascular disorders. SNPs associated with variations in expression levels were found in six genes (including DCAF5). The pathway analysis showed that NPY-LA was associated with changes in gene transcription, protein modification, immunological functions, and the MAPK pathway. (4) Conclusively, we found NPY-LA to be significantly associated with three loci (DGKH, DCAF5, and LINC02261), and based on our findings we hypothesize that the presence of NPY-LA is associated with the regulation of the immune system and possibly neurologic and vascular disorders.
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The inhibition of TRIM35-mediated TIGAR ubiquitination enhances mitochondrial fusion and alleviates renal ischemia-reperfusion injury. Int J Biol Macromol 2022; 209:725-736. [PMID: 35421414 DOI: 10.1016/j.ijbiomac.2022.04.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 11/23/2022]
Abstract
Tripartite motif 35 (TRIM35) is a member of the tripartite motif protein family and has been recognized to play a key role in immune-inflammatory diseases. However, the role of TRIM35 in renal ischemia-reperfusion injury (IRI) remains unclear. Our study proved that knockdown of TRIM35 alleviates kidney IRI by inhibiting oxidative stress and enhancing mitochondrial fusion. In addition, our experimental results found that TRIM35 interacts with TP53-induced glycolysis and apoptosis regulator (TIGAR) and promotes the polyubiquitination of TIGAR and induces its degradation in the proteasome pathway. Furthermore, TIGAR knockdown significantly inhibited mitochondrial fusion. These results indicate that TRIM35 is a potential therapeutic target for renal IRI.
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Kyrodimos E, Chrysovergis A, Mastronikolis N, Tsiambas E, Manaios L, Roukas D, Pantos P, Ragos V, Peschos D, Papanikolaou V. Impact of Ubiquitination Signaling Pathway Modifications on Oral Carcinoma. CANCER DIAGNOSIS & PROGNOSIS 2022; 2:1-6. [PMID: 35399999 DOI: 10.21873/cdp.10069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022]
Abstract
Among intra-cellular homeostasis mechanisms, ubiquitination plays a critical role in protein metabolism regulation by degrading proteins via activating a broad spectrum of ubiquitin chains. In fact, ubiquitination and sumoylation signaling pathways are characterized by increased complexity regarding the molecules and their interactions. The Ubiquitin-Proteasome System (Ub-PS) recognizes and targets a broad spectrum of protein substrates. Ubiquitin conjugation modifies each substrate protein determining its biochemical fate (degradation). A major functional activity of Ub-PS is autophagy mechanism regulation. Interestingly, Ub-PS promotes all stages of bulk autophagy (initiation, execution, and termination). Autophagy is a crucial catabolic process that provides protein degradation and for this reason the interaction with Ub-PS is crucial. Furthermore, ubiquitination controls and regulates specific types of protein targets. Ub-PS is also involved in oxidative cellular stress and DNA damage response. Additionally, the functional role of Ub-PS in ribosome machinery regulation seems to be crucial. Concerning carcinogenesis, Ub-PS is involved in malignant disease development and progression by negatively affecting the corresponding TGF-B-, MEEK/MAPK/ERK-JNK- dependent signaling pathways. In the current review article, we describe the role of Ub-PS biochemical modifications and alterations in oral squamous cell carcinoma (OSCC).
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Affiliation(s)
- Efthimios Kyrodimos
- 1st ENT Department, Hippocration Hospital, National and Kapodistrian University, Athens, Greece
| | - Aristeidis Chrysovergis
- 1st ENT Department, Hippocration Hospital, National and Kapodistrian University, Athens, Greece
| | | | - Evangelos Tsiambas
- Department of Cytology, Molecular Unit, 417 Veterans Army Hospital (NIMTS), Athens, Greece.,Department of Maxillofacial, Medical School, University of Ioannina, Ioannina, Greece
| | | | - Dimitrios Roukas
- Department of Psychiatry, 417 Veterans Army Hospital (NIMTS), Athens, Greece
| | - Pavlos Pantos
- 1st ENT Department, Hippocration Hospital, National and Kapodistrian University, Athens, Greece
| | - Vasileios Ragos
- Department of Maxillofacial, Medical School, University of Ioannina, Ioannina, Greece
| | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Ioannina, Greece
| | - Vasileios Papanikolaou
- 1st ENT Department, Hippocration Hospital, National and Kapodistrian University, Athens, Greece
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6
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Usman B, Zhao N, Nawaz G, Qin B, Liu F, Liu Y, Li R. CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice ( Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins. Int J Mol Sci 2021; 22:ijms22063225. [PMID: 33810044 PMCID: PMC8004693 DOI: 10.3390/ijms22063225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
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7
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Suresh HG, Pascoe N, Andrews B. The structure and function of deubiquitinases: lessons from budding yeast. Open Biol 2020; 10:200279. [PMID: 33081638 PMCID: PMC7653365 DOI: 10.1098/rsob.200279] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification that regulates diverse cellular processes in eukaryotic cells. The specificity of ubiquitin (Ub) signalling for different bioprocesses and pathways is dictated by the large variety of mono-ubiquitination and polyubiquitination events, including many possible chain architectures. Deubiquitinases (DUBs) reverse or edit Ub signals with high sophistication and specificity, forming an integral arm of the Ub signalling machinery, thus impinging on fundamental cellular processes including DNA damage repair, gene expression, protein quality control and organellar integrity. In this review, we discuss the many layers of DUB function and regulation, with a focus on insights gained from budding yeast. Our review provides a framework to understand key aspects of DUB biology.
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Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Natasha Pascoe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Brenda Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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8
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Li JC, Chang X, Chen Y, Li XZ, Zhang XL, Yang SM, Hu CJ, Zhang H. Loss of the Tumor Suppressor HACE1 Contributes to Cancer Progression. Curr Drug Targets 2020; 20:1018-1028. [PMID: 30827236 DOI: 10.2174/1389450120666190227184654] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/20/2019] [Accepted: 02/14/2019] [Indexed: 12/15/2022]
Abstract
HACE1 belongs to the family of HECT domain-containing E3 ligases, which plays an important role in the occurrence, invasion and metastatic process in many human malignancies. HACE1 is a tumor suppressor gene that is reduced in most cancer tissues compared to adjacent normal tissue. The loss or knocking out of HACE1 leads to enhanced tumor growth, invasion, and metastasis; in contrast, the overexpression of HACE1 can inhibit the development of tumors. Hypermethylation reduces the expression of HACE1, thereby promoting tumor development. HACE1 can inhibit the development of inflammation or tumors via the ubiquitination pathway. Therefore, HACE1 may be a potential therapeutic target, providing new strategies for disease prevention and treatment.
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Affiliation(s)
- Jun-Chen Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.,Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Xing Chang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Yang Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Xin-Zhe Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Xiang-Lian Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Guangxi 530021, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Chang-Jiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Hao Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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Dougherty SE, Maduka AO, Inada T, Silva GM. Expanding Role of Ubiquitin in Translational Control. Int J Mol Sci 2020; 21:E1151. [PMID: 32050486 PMCID: PMC7037965 DOI: 10.3390/ijms21031151] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advances in proteomics and cryo-electron microscopy have identified ubiquitin modifications of several ribosomal proteins and provided numerous insights on how this modification affects ribosome structure and function. The variety of pathways and functions of translation controlled by ubiquitin are determined by the various enzymes involved in ubiquitin conjugation and removal, by the ubiquitin chain type used, by the target sites of ubiquitination, and by the physiologic signals triggering its accumulation. Current research is now elucidating multiple ubiquitin-mediated mechanisms of translational control, including ribosome biogenesis, ribosome degradation, ribosome-associated protein quality control (RQC), and redox control of translation by ubiquitin (RTU). This review discusses the central role of ubiquitin in modulating the dynamism of the cellular proteome and explores the molecular aspects responsible for the expanding puzzle of ubiquitin signals and functions in translation.
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Affiliation(s)
- Shannon E. Dougherty
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Austin O. Maduka
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
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Doshi A, Sharma M, Prabha CR. Structural changes induced by L50P and I61T single mutations of ubiquitin affect cell cycle progression while impairing its regulatory and degradative functions in Saccharomyces cerevisiae. Int J Biol Macromol 2017; 99:128-140. [DOI: 10.1016/j.ijbiomac.2017.02.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
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Girnita L, Takahashi SI, Crudden C, Fukushima T, Worrall C, Furuta H, Yoshihara H, Hakuno F, Girnita A. Chapter Seven - When Phosphorylation Encounters Ubiquitination: A Balanced Perspective on IGF-1R Signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:277-311. [PMID: 27378760 DOI: 10.1016/bs.pmbts.2016.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell-surface receptors govern the critical information passage from outside to inside the cell and hence control important cellular decisions such as survival, growth, and differentiation. These receptors, structurally grouped into different families, utilize common intracellular signaling-proteins and pathways, yet promote divergent biological consequences. In rapid processing of extracellular signals to biological outcomes, posttranslational modifications offer a repertoire of protein processing options. Protein ubiquitination was originally identified as a signal for protein degradation through the proteasome system. It is now becoming increasingly recognized that both ubiquitin and ubiquitin-like proteins, all evolved from a common ubiquitin structural superfold, are used extensively by the cell and encompass signal tags for many different cellular fates. In this chapter we examine the current understanding of the ubiquitin regulation surrounding the insulin-like growth factor and insulin signaling systems, major members of the larger family of receptor tyrosine kinases (RTKs) and key regulators of fundamental physiological and pathological states.
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Affiliation(s)
- L Girnita
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
| | - S-I Takahashi
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - C Crudden
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - T Fukushima
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan; Department of Biological Sciences, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa, Japan
| | - C Worrall
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - H Furuta
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - H Yoshihara
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - F Hakuno
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - A Girnita
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Dermatology Department, Karolinska University Hospital, Stockholm, Sweden
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Torres M. Chapter Two - Heterotrimeric G Protein Ubiquitination as a Regulator of G Protein Signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:57-83. [PMID: 27378755 DOI: 10.1016/bs.pmbts.2016.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ubiquitin-mediated regulation of G proteins has been known for over 20 years as a result of discoveries made independently in yeast and vertebrate model systems for pheromone and photoreception, respectively. Since that time, several details underlying the cause and effect of G protein ubiquitination have been determined-including the initiating signals, responsible enzymes, trafficking pathways, and their effects on protein structure, function, interactions, and cell signaling. The collective body of evidence suggests that Gα subunits are the primary targets of ubiquitination. However, longstanding and recent results suggest that Gβ and Gγ subunits are also ubiquitinated, in some cases impacting cell polarization-a process essential for chemotaxis and polarized cell growth. More recently, evidence from mass spectrometry (MS)-based proteomics coupled with advances in PTM bioinformatics have revealed that protein families representing G protein subunits contain several structural hotspots for ubiquitination-most of which have not been investigated for a functional role in signal transduction. Taken together, our knowledge and understanding of heterotrimeric G protein ubiquitination as a regulator of G protein signaling-despite 20 years of research-is still emerging.
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Affiliation(s)
- M Torres
- Georgia Institute of Technology, School of Biology, Atlanta, GA, United States.
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English JG, Shellhammer JP, Malahe M, McCarter PC, Elston TC, Dohlman HG. MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. Sci Signal 2015; 8:ra5. [PMID: 25587192 DOI: 10.1126/scisignal.2005774] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Signaling pathways can behave as switches or rheostats, generating binary or graded responses to a given cell stimulus. We evaluated whether a single signaling pathway can simultaneously encode a switch and a rheostat. We found that the kinase Hog1 mediated a bifurcated cellular response: Activation and commitment to adaptation to osmotic stress are switchlike, whereas protein induction and the resolution of this commitment are graded. Through experimentation, bioinformatics analysis, and computational modeling, we determined that graded recovery is encoded through feedback phosphorylation and a gene induction program that is both temporally staggered and variable across the population. This switch-to-rheostat signaling mechanism represents a versatile stress adaptation system, wherein a broad range of inputs generate an "all-in" response that is later tuned to allow graded recovery of individual cells over time.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James P Shellhammer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael Malahe
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick C McCarter
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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The role of ubiquitination and sumoylation in diabetic nephropathy. BIOMED RESEARCH INTERNATIONAL 2014; 2014:160692. [PMID: 24991536 PMCID: PMC4065738 DOI: 10.1155/2014/160692] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/19/2014] [Indexed: 01/14/2023]
Abstract
Diabetic nephropathy (DN) is a common and characteristic microvascular complication of diabetes; the mechanisms that cause DN have not been clarified, and the epigenetic mechanism was promised in the pathology of DN. Furthermore, ubiquitination and small ubiquitin-like modifier (SUMO) were involved in the progression of DN. MG132, as a ubiquitin proteasome, could improve renal injury by regulating several signaling pathways, such as NF-κB, TGF-β, Nrf2-oxidative stress, and MAPK. In this review, we summarize how ubiquitination and sumoylation may contribute to the pathology of DN, which may be a potential treatment strategy of DN.
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When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Cell Commun Signal 2013; 11:52. [PMID: 23902637 PMCID: PMC3734146 DOI: 10.1186/1478-811x-11-52] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 07/26/2013] [Indexed: 11/10/2022] Open
Abstract
Ubiquitination, the covalent attachment of ubiquitin to target proteins, has emerged as a ubiquitous post-translational modification (PTM) whose function extends far beyond its original role as a tag for protein degradation identified three decades ago. Although sharing parallel properties with phosphorylation, ubiquitination distinguishes itself in important ways. Nevertheless, the interplay and crosstalk between ubiquitination and phosphorylation events have become a recurrent theme in cell signalling regulation. Understanding how these two major PTMs intersect to regulate signal transduction is an important research question. In this review, we first discuss the involvement of ubiquitination in the regulation of the EGF-mediated ERK signalling pathway via the EGF receptor, highlighting the interplay between ubiquitination and phosphorylation in this cancer-implicated system and addressing open questions. The roles of ubiquitination in pathways crosstalking to EGFR/MAPK signalling will then be discussed. In the final part of the review, we demonstrate the rich and versatile dynamics of crosstalk between ubiquitination and phosphorylation by using quantitative modelling and analysis of network motifs commonly observed in cellular processes. We argue that given the overwhelming complexity arising from inter-connected PTMs, a quantitative framework based on systems biology and mathematical modelling is needed to efficiently understand their roles in cell signalling.
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