1
|
Nazir A, Shad M, Rehman HM, Azim N, Sajjad M. Application of SUMO fusion technology for the enhancement of stability and activity of lysophospholipase from Pyrococcus abyssi. World J Microbiol Biotechnol 2024; 40:183. [PMID: 38722449 DOI: 10.1007/s11274-024-03998-w] [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: 02/11/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
Abstract
Heterologous production of proteins in Escherichia coli has raised several challenges including soluble production of target proteins, high levels of expression and purification. Fusion tags can serve as the important tools to overcome these challenges. SUMO (small ubiquitin-related modifier) is one of these tags whose fusion to native protein sequence can enhance its solubility and stability. In current research, a simple, efficient and cost-effective method is being discussed for the construction of pET28a-SUMO vector. In order to improve the stability and activity of lysophospholipase from Pyrococcus abyssi (Pa-LPL), a 6xHis-SUMO tag was fused to N-terminal of Pa-LPL by using pET28a-SUMO vector. Recombinant SUMO-fused enzyme (6 H-S-PaLPL) works optimally at 35 °C and pH 6.5 with remarkable thermostability at 35-95 °C. Thermo-inactivation kinetics of 6 H-S-PaLPL were also studied at 35-95 °C with first order rate constant (kIN) of 5.58 × 10- 2 h-1 and half-life of 12 ± 0 h at 95 °C. Km and Vmax for the hydrolysis of 4-nitrophenyl butyrate were calculated to be 2 ± 0.015 mM and 3882 ± 22.368 U/mg, respectively. 2.4-fold increase in Vmax of Pa-LPL was observed after fusion of 6xHis-SUMO tag to its N-terminal. It is the first report on the utilization of SUMO fusion tag to enhance the overall stability and activity of Pa-LPL. Fusion of 6xHis-SUMO tag not only aided in the purification process but also played a crucial role in increasing the thermostability and activity of the enzyme. SUMO-fused enzyme, thus generated, can serve as an important candidate for degumming of vegetable oils at industrial scale.
Collapse
Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
| |
Collapse
|
2
|
Sahu M, Rani N, Kumar P. Simulation and Computational Study of RING Domain Mutants of BRCA1 and Ube2k in AD/PD Pathophysiology. Mol Biotechnol 2024; 66:1095-1115. [PMID: 38172369 DOI: 10.1007/s12033-023-01006-4] [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: 06/09/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Lysine-based post-translational modification (PTM) such as acylation, acetylation, deamination, methylation, SUMOylation, and ubiquitination has proven to be a major regulator of gene expression, chromatin structure, protein stability, protein-protein interaction, protein degradation, and cellular localization. However, besides all the PTMs, ubiquitination stands as the second most common PTM after phosphorylation that is involved in the etiology of neurodegenerative diseases (NDDs) namely, Alzheimer's disease (AD) and Parkinson's disease (PD). NDDs are characterized by the accumulation of misfolded protein aggregates in the brain that lead to disease-related gene mutation and irregular protein homeostasis. The ubiquitin-proteasome system (UPS) is in charge of degrading these misfolded proteins, which involve an interplay of E1, E2, E3, and deubiquitinase enzymes. Impaired UPS has been commonly observed in NDDs and E3 ligases are the key members of the UPS, thus, dysfunction of the same can accelerate the neurodegeneration process. Therefore, the aim of this study is firstly, to find E3 ligases that are common in both AD and PD through data mining. Secondly, to study the impact of mutation on its structure and function. The study deciphered 74 E3 ligases that were common in both AD and PD. Later, 10 hub genes were calculated of which protein-protein interaction, pathway enrichment, lysine site prediction, domain, and motif analysis were performed. The results predicted BRCA1, PML, and TRIM33 as the top three putative lysine-modified E3 ligases involved in AD and PD pathogenesis. However, based on structural characterization, BRCA1 was taken further to study RING domain mutation that inferred K32Y, K32L, K32C, K45V, K45Y, and K45G as potential mutants that alter the structural and functional ability of BRCA1 to interact with Ube2k, E2-conjugating enzyme. The most probable mutant observed after molecular dynamics simulation of 50 ns is K32L. Therefore, our study concludes BRCA1, a potential E3 ligase common in AD and PD, and RING domain mutation at sites K32 and K45 possibly disturbs its interaction with its E2, Ube2k.
Collapse
Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Neetu Rani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
| |
Collapse
|
3
|
Floros KV, Fairchild CK, Li J, Zhang K, Roberts JL, Kurupi R, Hu B, Kraskauskiene V, Hosseini N, Shen S, Inge MM, Smith-Fry K, Li L, Sotiriou A, Dalton KM, Jose A, Abdelfadiel EI, Xing Y, Hill RD, Slaughter JM, Shende M, Lorenz MR, Hinojosa MR, Belvin BR, Lai Z, Boikos SA, Stamatouli AM, Lewis JP, Manjili MH, Valerie K, Li R, Banito A, Poklepovic A, Koblinski JE, Siggers T, Dozmorov MG, Jones KB, Radhakrishnan SK, Faber AC. Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in Synovial Sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591023. [PMID: 38712286 PMCID: PMC11071469 DOI: 10.1101/2024.04.25.591023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Synovial Sarcoma (SS) is driven by the SS18::SSX fusion oncoprotein. and is ultimately refractory to therapeutic approaches. SS18::SSX alters ATP-dependent chromatin remodeling BAF (mammalian SWI/SNF) complexes, leading to the degradation of canonical (cBAF) complex and amplified presence of an SS18::SSX-containing non-canonical BAF (ncBAF or GBAF) that drives an SS-specific transcription program and tumorigenesis. We demonstrate that SS18::SSX activates the SUMOylation program and SSs are sensitive to the small molecule SAE1/2 inhibitor, TAK-981. Mechanistically, TAK-981 de-SUMOylates the cBAF subunit SMARCE1, stabilizing and restoring cBAF on chromatin, shifting away from SS18::SSX-ncBAF-driven transcription, associated with DNA damage and cell death and resulting in tumor inhibition across both human and mouse SS tumor models. TAK-981 synergized with cytotoxic chemotherapy through increased DNA damage, leading to tumor regression. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, positioning the in-clinic TAK-981 to treat SS.
Collapse
|
4
|
Zhang T, Su F, Wang B, Liu L, Lu Y, Su H, Ling R, Yue P, Dai H, Yang T, Yang J, Chen R, Wu R, Zhu K, Zhao D, Hou X. Ubiquitin specific peptidase 38 epigenetically regulates KLF transcription factor 5 to augment malignant progression of lung adenocarcinoma. Oncogene 2024; 43:1190-1202. [PMID: 38409551 DOI: 10.1038/s41388-024-02985-7] [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: 04/04/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Protein ubiquitination is a common post-translational modification and a critical mechanism for regulating protein stability. This study aimed to explore the role and potential molecular mechanism of ubiquitin-specific peptidase 38 (USP38) in the progression of lung adenocarcinoma (LUAD). USP38 expression was significantly higher in patients with LUAD than in their counterparts, and higher USP38 expression was closely associated with a worse prognosis. USP38 silencing suppresses the proliferation of LUAD cells in vitro and impedes the tumorigenic activity of cells in xenograft mouse models in vivo. Further, we found that USP38 affected the protein stability of transcription factor Krüppel-like factors 5 (KLF5) by inhibiting its degradation. Subsequent mechanistic investigations showed that the N-terminal of USP38 (residues 1-400aa) interacted with residues 1-200aa of KLF5, thereby stabilizing the KLF5 protein by deubiquitination. Moreover, we found that PIAS1-mediated SUMOylation of USP38 was promoted, whereas SENP2-mediated de-SUMOylation of USP38 suppressed the deubiquitination effects of USP38 on KLF5. Additionally, our results demonstrated that KLF5 overexpression restored the suppression of the malignant properties of LUAD cells by USP38 knockdown. SUMOylation of USP38 enhances the deubiquitination and stability of KLF5, thereby augmenting the malignant progression of LUAD.
Collapse
Affiliation(s)
- Tao Zhang
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Fei Su
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China.
| | - Bofang Wang
- The second clinical medical college of Lanzhou University, Lanzhou, Gansu, PR China
| | - Lixin Liu
- Department of Thoracic Surgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Yongbin Lu
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Hongxin Su
- Department of Radiotherapy, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Ruijiang Ling
- Department of Thoracic Surgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Peng Yue
- Department of Thoracic Surgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Huanyu Dai
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Tianning Yang
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Jingru Yang
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Rui Chen
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Ruiyue Wu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, PR China
| | - Kaili Zhu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, PR China
| | - Da Zhao
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China.
| | - Xiaoming Hou
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, Gansu, PR China.
| |
Collapse
|
5
|
Zhan X, Yang Y, Li Q, He F. The role of deubiquitinases in cardiac disease. Expert Rev Mol Med 2024; 26:e3. [PMID: 38525836 PMCID: PMC11062144 DOI: 10.1017/erm.2024.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/10/2023] [Accepted: 12/28/2023] [Indexed: 03/26/2024]
Abstract
Deubiquitinases are a group of proteins that identify and digest monoubiquitin chains or polyubiquitin chains attached to substrate proteins, preventing the substrate protein from being degraded by the ubiquitin-proteasome system. Deubiquitinases regulate cellular autophagy, metabolism and oxidative stress by acting on different substrate proteins. Recent studies have revealed that deubiquitinases act as a critical regulator in various cardiac diseases, and control the onset and progression of cardiac disease through a board range of mechanism. This review summarizes the function of different deubiquitinases in cardiac disease, including cardiac hypertrophy, myocardial infarction and diabetes mellitus-related cardiac disease. Besides, this review briefly recapitulates the role of deubiquitinases modulators in cardiac disease, providing the potential therapeutic targets in the future.
Collapse
Affiliation(s)
- Xiaona Zhan
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Yi Yang
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Qing Li
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Fan He
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| |
Collapse
|
6
|
Kalani L, Kim BH, Vincent JB, Ausió J. MeCP2 ubiquitination and sumoylation, in search of a function†. Hum Mol Genet 2023; 33:1-11. [PMID: 37694858 DOI: 10.1093/hmg/ddad150] [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: 08/04/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023] Open
Abstract
MeCP2 (Methyl CpG binding protein 2) is an intrinsically disordered protein that binds to methylated genome regions. The protein is a critical transcriptional regulator of the brain, and its mutations account for 95% of Rett syndrome (RTT) cases. Early studies of this neurodevelopmental disorder revealed a close connection with dysregulations of the ubiquitin system (UbS), notably as related to UBE3A, a ubiquitin ligase involved in the proteasome-mediated degradation of proteins. MeCP2 undergoes numerous post-translational modifications (PTMs), including ubiquitination and sumoylation, which, in addition to the potential functional outcomes of their monomeric forms in gene regulation and synaptic plasticity, in their polymeric organization, these modifications play a critical role in proteasomal degradation. UbS-mediated proteasomal degradation is crucial in maintaining MeCP2 homeostasis for proper function and is involved in decreasing MeCP2 in some RTT-causing mutations. However, regardless of all these connections to UbS, the molecular details involved in the signaling of MeCP2 for its targeting by the ubiquitin-proteasome system (UPS) and the functional roles of monomeric MeCP2 ubiquitination and sumoylation remain largely unexplored and are the focus of this review.
Collapse
Affiliation(s)
- Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, 27 King's College Cir, Toronto, ON M5S 1A8, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| |
Collapse
|
7
|
Liu F, Chen S, Ming X, Li H, Zeng Z, Lv Y. Sortilin-induced lipid accumulation and atherogenesis are suppressed by HNF1b SUMOylation promoted by flavone of Polygonatum odoratum. J Zhejiang Univ Sci B 2023; 24:998-1013. [PMID: 37961802 PMCID: PMC10646395 DOI: 10.1631/jzus.b2200682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 11/15/2023]
Abstract
This study aims to investigate the impact of hepatocyte nuclear factor 1β (HNF1b) on macrophage sortilin-mediated lipid metabolism and aortic atherosclerosis and explore the role of the flavone of Polygonatum odoratum (PAOA-flavone)-promoted small ubiquitin-related modifier (SUMO) modification in the atheroprotective efficacy of HNF1b. HNF1b was predicted to be a transcriptional regulator of sortilin expression via bioinformatics, dual-luciferase reporter gene assay, and chromatin immunoprecipitation. HNF1b overexpression decreased sortilin expression and cellular lipid contents in THP-1 macrophages, leading to a depression in atherosclerotic plaque formation in low-density lipoprotein (LDL) receptor-deficient (LDLR-/-) mice. Multiple SUMO1-modified sites were identified on the HNF1b protein and co-immunoprecipitation confirmed its SUMO1 modification. The SUMOylation of HNF1b protein enhanced the HNF1b-inhibited effect on sortilin expression and reduced lipid contents in macrophages. PAOA-flavone treatment promoted SUMO-activating enzyme subunit 1 (SAE1) expression and SAE1-catalyzed SUMOylation of the HNF1b protein, which prevented sortilin-mediated lipid accumulation in macrophages and the formation of atherosclerotic plaques in apolipoprotein E-deficient (ApoE-/-) mice. Interference with SAE1 abrogated the improvement in lipid metabolism in macrophage cells and atheroprotective efficacy in vivo upon PAOA-flavone administration. In summary, HNF1b transcriptionally suppressed sortilin expression and macrophage lipid accumulation to inhibit aortic lipid deposition and the development of atherosclerosis. This anti-atherosclerotic effect was enhanced by PAOA-flavone-facilitated, SAE1-catalyzed SUMOylation of the HNF1b protein.
Collapse
Affiliation(s)
- Fang Liu
- Guangxi Key Laboratory of Diabetic Systems Medicine & Institute of Basic Medical Sciences, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin 541199, China
| | - Shirui Chen
- Guangxi Key Laboratory of Diabetic Systems Medicine & Institute of Basic Medical Sciences, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin 541199, China
| | - Xinyue Ming
- Guangxi Key Laboratory of Diabetic Systems Medicine & Institute of Basic Medical Sciences, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin 541199, China
| | - Huijuan Li
- Guangxi Key Laboratory of Diabetic Systems Medicine & Institute of Basic Medical Sciences, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin 541199, China
| | - Zhaoming Zeng
- Hunan Mingshun Pharmaceutical Co., Ltd., Shaodong 422800, China. ,
| | - Yuncheng Lv
- Guangxi Key Laboratory of Diabetic Systems Medicine & Institute of Basic Medical Sciences, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin 541199, China.
| |
Collapse
|
8
|
Jing H, Strader LC. AUXIN RESPONSE FACTOR protein accumulation and function. Bioessays 2023; 45:e2300018. [PMID: 37584215 PMCID: PMC10592145 DOI: 10.1002/bies.202300018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
Auxin is a key regulator of plant developmental processes. Its effects on transcription are mediated by the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. ARFs tightly control specific auxin responses necessary for proper plant growth and development. Recent research has revealed that regulated ARF protein accumulation and ARF nucleo-cytoplasmic partitioning can determine auxin transcriptional outputs. In this review, we explore these recent findings and consider the potential for regulated ARF accumulation in driving auxin responses in plants.
Collapse
Affiliation(s)
- Hongwei Jing
- Department of Biology, Duke University, Durham, NC 27008, USA
| | | |
Collapse
|
9
|
Marino R, Buccarello L, Hassanzadeh K, Akhtari K, Palaniappan S, Corbo M, Feligioni M. A novel cell-permeable peptide prevents protein SUMOylation and supports the mislocalization and aggregation of TDP-43. Neurobiol Dis 2023; 188:106342. [PMID: 37918759 DOI: 10.1016/j.nbd.2023.106342] [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: 06/16/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023] Open
Abstract
SUMOylation is a post-translational modification (PTM) that exerts a regulatory role in different cellular processes, including protein localization, aggregation, and biological activities. It consists of the dynamic formation of covalent isopeptide bonds between a family member of the Small Ubiquitin Like Modifiers (SUMOs) and the target proteins. Interestingly, it is a cellular mechanism implicated in several neurodegenerative pathologies and potentially it could become a new therapeutic target; however, there are very few pharmacological tools to modulate the SUMOylation process. In this study, we have designed and tested the activity of a novel small cell-permeable peptide, COV-1, in a neuroblastoma cell line that specifically prevents protein SUMOylation. COV-1 inhibits UBC9-protein target interaction and efficiently decreases global SUMO-1ylation. Moreover, it can perturb RanGAP-1 perinuclear localization by inducing the downregulation of UBC9. In parallel, we found that COV-1 causes an increase in the ubiquitin degradation system up to its engulfment while enhancing the autophagic flux. Surprisingly, COV-1 modifies protein aggregation, and specifically it mislocalizes TDP-43 within cells, inducing its aggregation and co-localization with SUMO-1. These data suggest that COV-1 could be taken into future consideration as an interesting pharmacological tool to study the cellular cascade effects of SUMOylation prevention.
Collapse
Affiliation(s)
- R Marino
- EBRI Rita Levi-Montalcini Foundation, Rome 00161, Italy
| | | | - K Hassanzadeh
- EBRI Rita Levi-Montalcini Foundation, Rome 00161, Italy
| | - K Akhtari
- Department of Physics, University of Kurdistan, Sanandaj 871, Iran
| | - S Palaniappan
- EBRI Rita Levi-Montalcini Foundation, Rome 00161, Italy
| | - M Corbo
- Department of Neurorehabilitation Sciences, Casa di Cura Igea, Milan 20144, Italy
| | - M Feligioni
- EBRI Rita Levi-Montalcini Foundation, Rome 00161, Italy; Department of Neurorehabilitation Sciences, Casa di Cura Igea, Milan 20144, Italy..
| |
Collapse
|
10
|
Wu W, Huang C. SUMOylation and DeSUMOylation: Prospective therapeutic targets in cancer. Life Sci 2023; 332:122085. [PMID: 37722589 DOI: 10.1016/j.lfs.2023.122085] [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: 08/05/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
The SUMO family is a type of ubiquitin-like protein modification molecule. Its protein modification mechanism is similar to that of ubiquitination: both involve modifier-activating enzyme E1, conjugating enzyme E2 and substrate-specific ligase E3. However, polyubiquitination can lead to the degradation of substrate proteins, while poly-SUMOylation only leads to the degradation of substrate proteins through the proteasome pathway after being recognized by ubiquitin as a signal factor. There are currently five reported subtypes in the SUMO family, namely SUMO1-5. As a reversible dynamic modification, intracellular sentrin/SUMO-specific proteases (SENPs) mainly regulate the reverse reaction pathway of SUMOylation. The SUMOylation modification system affects the localization, activation and turnover of proteins in cells and participates in regulating most nuclear and extranuclear molecular reactions. Abnormal expression of proteins related to the SUMOylation pathway is commonly observed in tumors, indicating that this pathway is closely related to tumor occurrence, metastasis and invasion. This review mainly discusses the composition of members in the protein family related to SUMOylation pathways, mutual connections between SUMOylation and other post-translational modifications on proteins as well as therapeutic drugs developed based on these pathways.
Collapse
Affiliation(s)
- Wenyan Wu
- Kunming University of Science and Technology, Medical School, Kunming 650500, China
| | - Chao Huang
- Kunming University of Science and Technology, Medical School, Kunming 650500, China.
| |
Collapse
|
11
|
Choudhary D, Kaur A, Singh P, Chaudhary G, Kaur R, Bayan MF, Chandrasekaran B, Marji SM, Ayman R. Target protein degradation by protacs: A budding cancer treatment strategy. Pharmacol Ther 2023; 250:108525. [PMID: 37696366 DOI: 10.1016/j.pharmthera.2023.108525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023]
Abstract
Cancer is one of the most common causes of death. So, its lethal effect increases with time. Near about hundreds of cancers are known in humans. Cancer treatment is done to cure or prolonged remission, and shrinkage of the tumor. Cytotoxic agents, biological agents/targeted drugs, hormonal drugs, surgery, radiotherapy/proton therapy, chemotherapy, immunotherapy, and gene therapy are currently used in the treatment of cancer but their cost is high and cause various side effects. Seeing this, some new targeted strategies such as PROTACs are the need of the time. Proteolysis targeting chimera (PROTAC) has become one of the most discussed topics regarding cancer treatment. Few of the PROTAC molecules are in the trial phases. PROTACs have many advantages over other strategies such as modularity, compatibility, sub-stoichiometric activity, acting on undruggable targets, molecular design, and acts on intracellular targets, selectivity and specificity can be recruited for any cancer, versatility, and others. PROTACs are having some unclear questions on their pharmacokinetics, heavy-molecular weight, etc. PROTACs are anticipated to bring about a conversion in current healthcare and will emerge as booming treatments. In this review article we summarize PROTACs, their mechanism of action, uses, advantages, disadvantages, challenges, and future aspects for the successful development of potent PROTACs as a drug strategy.
Collapse
Affiliation(s)
- Diksha Choudhary
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Amritpal Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Pargat Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Gaurav Chaudhary
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Rajwinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India.
| | - Mohammad F Bayan
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan
| | | | - Saeed M Marji
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan
| | - Reema Ayman
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan
| |
Collapse
|
12
|
Alrosan AZ, Alrosan K, Heilat GB, Alsharedeh R, Abudalo R, Oqal M, Alqudah A, Elmaghrabi YA. Potential roles of NEDD4 and NEDD4L and their utility as therapeutic targets in high‑incidence adult male cancers (Review). Mol Clin Oncol 2023; 19:68. [PMID: 37614371 PMCID: PMC10442760 DOI: 10.3892/mco.2023.2664] [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: 02/18/2023] [Accepted: 07/07/2023] [Indexed: 08/25/2023] Open
Abstract
The term 'cancer' refers to >100 disorders that progressively manifest over time and are characterized by uncontrolled cell division. Although malignant growth can occur in virtually any human tissue, the underlying mechanisms underlying all forms of cancer are consistent. The International Agency for Research on Cancer's annual GLOBOCAN 2020 report provided an update on the global cancer incidence and mortality. Excluding non-melanoma skin cancer, the report predicts that there will be 19.3 million new cancer cases and >10 million cancer-related fatalities in 2023. Lung, prostate, and colon cancers are the most prevalent and lethal cancers in males. It was recognized that post-translational modifications (PTMs) of proteins are necessary for almost all cellular biological processes, as well as in cancer development and metastasis to other bodily organs. Thus, PTMs have a considerable impact on how proteins behave. Various PTMs may have harmful roles by affecting the hallmarks of cancer, metabolism and the regulation of the tumor microenvironment. PTMs and genetic changes/mutations are essential in carcinogenesis and cancer development. A pivotal PTM mechanism is protein ubiquitination. Of note, the rate-limiting stage of the protein ubiquitination cascade is hypothesized to be E3-ligase-mediated ubiquitination. Numerous studies revealed that the neural precursor cell expressed developmentally downregulated protein 4 (NEDD4) E3 ligase is among the E3 ubiquitin ligases that have essential roles in cellular processes. It regulates protein degradation and substrate ubiquitination. In addition, it has been shown that NEDD4 primarily functions as an oncogene in various malignancies but can also act as a tumor suppressor in certain types of tumor. In the present review, the roles of NEDD4 as an anticancer protein in various high-incidence male malignancies and the significance of NEDD4 as a potential cancer therapeutic target are discussed. In addition, the targeting of NEDD4 as a therapeutic strategy for the treatment of human malignancies is explored.
Collapse
Affiliation(s)
- Amjad Z. Alrosan
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Khaled Alrosan
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Ghaith B. Heilat
- Department of General Surgery and Urology, Faculty of Medicine, The Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Rawan Alsharedeh
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, The Yarmouk University, Irbid 21163, Jordan
| | - Rawan Abudalo
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Muna Oqal
- Department of Pharmaceutical Technology, Faculty of Pharmacy, The Hashemite University, Zarqa 13133, Jordan
| | - Abdelrahim Alqudah
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | | |
Collapse
|
13
|
Salas-Lloret D, Jansen NS, Nagamalleswari E, van der Meulen C, Gracheva E, de Ru AH, Otte HAM, van Veelen PA, Pichler A, Goedhart J, Vertegaal AC, González-Prieto R. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. SCIENCE ADVANCES 2023; 9:eadh2073. [PMID: 37531430 PMCID: PMC10396300 DOI: 10.1126/sciadv.adh2073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
Collapse
Affiliation(s)
- Daniel Salas-Lloret
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nicolette S. Jansen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Coen van der Meulen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ekaterina Gracheva
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - H. Anne Marie Otte
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Andrea Pichler
- Max Plank Institute for Immunobiology and Epigenetics, Freiburg, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| |
Collapse
|
14
|
Zhao Y, Zhou H, Zhao Y, Liang Z, Gong X, Yu J, Huang T, Yang C, Wu M, Xiao Y, Yang Y, Liu W, Wang X, Shu X, Bao J. BACE1 SUMOylation deregulates phosphorylation and ubiquitination in Alzheimer's disease pathology. J Neurochem 2023; 166:318-327. [PMID: 37286480 DOI: 10.1111/jnc.15870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023]
Abstract
BACE1 is essential for the generation of amyloid-β (Aβ) that likely initiates the toxicity in Alzheimer's disease (AD). BACE1 activity is mainly regulated by post-translational modifications, but the relationship between these modifications is not fully characterized. Here, we studied the effects of BACE1 SUMOylation on its phosphorylation and ubiquitination. We demonstrate that SUMOylation of BACE1 inhibits its phosphorylation at S498 and its ubiquitination in vitro. Conversely, BACE1 phosphorylation at S498 suppresses its SUMOylation, which results in promoting BACE1 degradation in vitro. Furthermore, an increase in BACE1 SUMOylation is associated with the progression of AD pathology, while its phosphorylation and ubiquitination are decreased in an AD mouse model. Our findings suggest that BACE1 SUMOylation reciprocally influences its phosphorylation and competes against its ubiquitination, which might provide a new insight into the regulations of BACE1 activity and Aβ accumulation.
Collapse
Affiliation(s)
- Yanna Zhao
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Hongyan Zhou
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Yan Zhao
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Zhen Liang
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Xiaokang Gong
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Jing Yu
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Tiantian Huang
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Chaoqin Yang
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Mengjuan Wu
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Yifan Xiao
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Youhua Yang
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Physiology, School of Medicine, Jianghan University, Wuhan, China
| | - Wei Liu
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Xiaochuan Wang
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiji Shu
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| | - Jian Bao
- Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, China
| |
Collapse
|
15
|
Wei J, Li M, Xue C, Chen S, Zheng L, Deng H, Tang F, Li G, Xiong W, Zeng Z, Zhou M. Understanding the roles and regulation patterns of circRNA on its host gene in tumorigenesis and tumor progression. J Exp Clin Cancer Res 2023; 42:86. [PMID: 37060016 PMCID: PMC10105446 DOI: 10.1186/s13046-023-02657-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Circular RNAs (circRNAs) are a novel type of endogenous non-coding RNAs, which are covalently closed loop structures formed by precursor mRNAs (pre-mRNAs) through back-splicing. CircRNAs are abnormally expressed in many tumors, and play critical roles in a variety of tumors as oncogenes or tumor suppressor genes by sponging miRNAs, regulating alternative splicing and transcription, cis-regulating host genes, interacting with RNA binding proteins (RBPs) or encoding polypeptides. Among them, the regulation of circRNAs on their corresponding host genes is a critical way for circRNAs to exit their functions. Accumulating evidence suggests that circRNAs are able to regulate the expression of host genes at the transcriptional level, post-transcriptional level, translational level, post-translational level, or by encoding polypeptides. Therefore, this paper mainly summarized the roles and association of circRNAs and their corresponding host genes in tumorigenesis and tumor progression, generalized the circRNAs that function synergistically or antagonistically with their host genes, and elaborated the mechanisms of mutual regulation between circRNAs and their host genes. More importantly, this review provides specific references for revealing the potential application of circRNAs combined with their host genes in tumor diagnosis, treatment and prognosis.
Collapse
Affiliation(s)
- Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
- Cancer Research Institute, Central South University, Changsha, 410078, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China.
| |
Collapse
|
16
|
Xiong ST, Ying YR, Long Z, Li JH, Zhang YB, Xiao TY, Zhao X. Zebrafish MARCH7 negatively regulates IFN antiviral response by degrading TBK1. Int J Biol Macromol 2023; 240:124384. [PMID: 37054851 DOI: 10.1016/j.ijbiomac.2023.124384] [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: 02/13/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Membrane-associated RING-CH-type finger (MARCH) proteins have been reported to regulate type I IFN production during host antiviral innate immunity. The present study reported the zebrafish MARCH family member, MARCH7, as a negative regulator in virus-triggered type I IFN induction via targeting TANK-binding kinase 1 (TBK1) for degradation. As an IFN-stimulated gene (ISG), we discovered that MARCH7 was significantly induced by spring viremia of carp virus (SVCV) or poly(I:C) stimulation. Ectopic expression of MARCH7 reduced the activity of IFN promoter and dampened the cellular antiviral responses triggered by SVCV and grass carp reovirus (GCRV), which concomitantly accelerated the viral replication. Accordingly, the knockdown of MARCH7 by siRNA transfection significantly promoted the transcription of ISG genes and inhibited SVCV replication. Mechanistically, we found that MARCH7 interacted with TBK1 and degraded it via K48-linked ubiquitination. Further characterization of truncated mutants of MARCH7 and TBK1 confirmed that the C-terminal RING of MARCH7 is essential in the MARCH7-mediated degradation of TBK1 and the negative regulation of IFN antiviral response. This study reveals a molecular mechanism by which zebrafish MARCH7 negatively regulates the IFN response by targeting TBK1 for protein degradation, providing new insights into the essential role of MARCH7 in antiviral innate immunity.
Collapse
Affiliation(s)
- Shu-Ting Xiong
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Yan-Rong Ying
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China
| | - Zhe Long
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Jun-Hua Li
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Yi-Bing Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Tiao-Yi Xiao
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Xiang Zhao
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| |
Collapse
|
17
|
Hartman ML, Czyz M. BCL-G: 20 years of research on a non-typical protein from the BCL-2 family. Cell Death Differ 2023:10.1038/s41418-023-01158-5. [PMID: 37031274 DOI: 10.1038/s41418-023-01158-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Proteins from the BCL-2 family control cell survival and apoptosis in health and disease, and regulate apoptosis-unrelated cellular processes. BCL-Gonad (BCL-G, also known as BCL2-like 14) is a non-typical protein of the family as its long isoform (BCL-GL) consists of BH2 and BH3 domains without the BH1 motif. BCL-G is predominantly expressed in normal testes and different organs of the gastrointestinal tract. The complexity of regulatory mechanisms of BCL-G expression and post-translational modifications suggests that BCL-G may play distinct roles in different types of cells and disorders. While several genetic alterations of BCL2L14 have been reported, gene deletions and amplifications prevail, which is also confirmed by the analysis of sequencing data for different types of cancer. Although the studies validating the phenotypic consequences of genetic manipulations of BCL-G are limited, the role of BCL-G in apoptosis has been undermined. Recent studies using gene-perturbation approaches have revealed apoptosis-unrelated functions of BCL-G in intracellular trafficking, immunomodulation, and regulation of the mucin scaffolding network. These studies were, however, limited mainly to the role of BCL-G in the gastrointestinal tract. Therefore, further efforts using state-of-the-art methods and various types of cells are required to find out more about BCL-G activities. Deciphering the isoform-specific functions of BCL-G and the BCL-G interactome may result in the designing of novel therapeutic approaches, in which BCL-G activity will be either imitated using small-molecule BH3 mimetics or inhibited to counteract BCL-G upregulation. This review summarizes two decades of research on BCL-G.
Collapse
Affiliation(s)
- Mariusz L Hartman
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215, Lodz, Poland.
| | - Malgorzata Czyz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215, Lodz, Poland
| |
Collapse
|
18
|
Zhang Z, Xia S, Wang Z, Yin N, Chen J, Shao L. The SUMOylation of Human Cytomegalovirus Capsid Assembly Protein Precursor (UL80.5) Affects Its Interaction with Major Capsid Protein (UL86) and Viral Replication. Viruses 2023; 15:v15040931. [PMID: 37112911 PMCID: PMC10145422 DOI: 10.3390/v15040931] [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: 03/10/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Human Cytomegalovirus Capsid Assembly Protein Precursor (pAP, UL80.5) plays a key role in capsid assembly by forming an internal protein scaffold with Major Capsid Protein (MCP, UL86) and other capsid subunits. In this study, we revealed UL80.5 as a novel SUMOylated viral protein. We confirmed that UL80.5 interacted with the SUMO E2 ligase UBC9 (58-93aa) and could be covalently modified by SUMO1/SUMO2/SUMO3 proteins. 371Lysine located within a ψKxE consensus motif on UL80.5 carboxy-terminal was the major SUMOylation site. Interestingly, the SUMOylation of UL80.5 restrained its interaction with UL86 but had no effects on translocating UL86 into the nucleus. Furthermore, we showed that the removal of the 371lysine SUMOylation site of UL80.5 inhibited viral replication. In conclusion, our data demonstrates that SUMOylation plays an important role in regulating UL80.5 functions and viral replication.
Collapse
Affiliation(s)
- Zhigang Zhang
- Basic Medical College, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Sisi Xia
- Department of Biological Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Zhigang Wang
- Basic Medical College, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Nina Yin
- Basic Medical College, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Jun Chen
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Luyao Shao
- Basic Medical College, Hubei University of Chinese Medicine, Wuhan 430065, China
| |
Collapse
|
19
|
Fu W, Lei X, Lu Q, Zhang J, Guo J, Zhao J, Tong X, Hu X. UBE2K regulated by IGF2BP3 promotes cell proliferation and stemness in pancreatic ductal adenocarcinoma. Int J Oncol 2023; 62:52. [PMID: 36896783 PMCID: PMC10019758 DOI: 10.3892/ijo.2023.5500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/16/2023] [Indexed: 03/11/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a noteworthy malignant carcinoma with an unsatisfactory prognosis attributed to late diagnosis. Ubiquitin‑conjugating enzyme E2K (UBE2K) has been found to serve important roles in a number of diseases. However, its function and the exact molecular mechanism of UBE2K in PDAC remain to be elucidated. The present study discovered that UBE2K was expressed at high levels and indicated the poor prognosis of patients with PDAC. Following this, the CCK‑8, colony formation, and sphere formation assays showed that UBE2K promoted proliferation and the stemness phenotype of PDAC cells in vitro. Evidence from subcutaneous tumor‑bearing nude mice experiments further confirmed that UBE2K enhanced PDAC cell tumorigenesis in vivo. Additionally, the present study demonstrated that insulin‑like growth factor 2 RNA binding protein 3 (IGF2BP3) functioned as an RNA‑binding protein to increase UBE2K expression by enhancing the RNA stability of UBE2K. The knockdown or overexpression of IGF2BP3 could attenuate the change in cells growth induced by the overexpression or knockdown of UBE2K. In summary, the findings indicated the oncogenic roles of UBE2K in PDAC. In addition, IGF2BP3 and UBE2K constitute a functional axis to regulate the malignant progression of PDAC.
Collapse
Affiliation(s)
- Wen Fu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Xiangxiang Lei
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Ji Zhang
- Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P.R. China
| | - Jinhui Guo
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Jie Zhao
- Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P.R. China
| | - Xiangmin Tong
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Xiaoge Hu
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| |
Collapse
|
20
|
Yang Z, Zeng X, Zhao Y, Chen R. AlphaFold2 and its applications in the fields of biology and medicine. Signal Transduct Target Ther 2023; 8:115. [PMID: 36918529 PMCID: PMC10011802 DOI: 10.1038/s41392-023-01381-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/27/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with atomic-level accuracy. Protein structure prediction is one of the most challenging problems in computational biology and chemistry, and has puzzled scientists for 50 years. The advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much attention. Subsequent release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community, especially in the fields of biology and medicine. AF2 is thought to have a significant impact on structural biology and research areas that need protein structure information, such as drug discovery, protein design, prediction of protein function, et al. Though the time is not long since AF2 was developed, there are already quite a few application studies of AF2 in the fields of biology and medicine, with many of them having preliminarily proved the potential of AF2. To better understand AF2 and promote its applications, we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success, and particularly focus on reviewing its applications in the fields of biology and medicine. Limitations of current AF2 prediction will also be discussed.
Collapse
Affiliation(s)
- Zhenyu Yang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoxi Zeng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yi Zhao
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Runsheng Chen
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
| |
Collapse
|
21
|
Histone Modifications Represent a Key Epigenetic Feature of Epithelial-to-Mesenchyme Transition in Pancreatic Cancer. Int J Mol Sci 2023; 24:ijms24054820. [PMID: 36902253 PMCID: PMC10003015 DOI: 10.3390/ijms24054820] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Pancreatic cancer is one of the most lethal malignant diseases due to its high invasiveness, early metastatic properties, rapid disease progression, and typically late diagnosis. Notably, the capacity for pancreatic cancer cells to undergo epithelial-mesenchymal transition (EMT) is key to their tumorigenic and metastatic potential, and is a feature that can explain the therapeutic resistance of such cancers to treatment. Epigenetic modifications are a central molecular feature of EMT, for which histone modifications are most prevalent. The modification of histones is a dynamic process typically carried out by pairs of reverse catalytic enzymes, and the functions of these enzymes are increasingly relevant to our improved understanding of cancer. In this review, we discuss the mechanisms through which histone-modifying enzymes regulate EMT in pancreatic cancer.
Collapse
|
22
|
Patton BK, Madadi S, Briley SM, Ahmed AA, Pangas SA. Sumoylation regulates functional properties of the oocyte transcription factors SOHLH1 and NOBOX. FASEB J 2023; 37:e22747. [PMID: 36607631 PMCID: PMC10129296 DOI: 10.1096/fj.202201481r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
SOHLH1 and NOBOX are oocyte-expressed transcription factors with critical roles in ovary development and fertility. In mice, Sohlh1 and Nobox are essential for fertility through their regulation of the oocyte transcriptional network and cross-talk to somatic cells. Sumoylation is a posttranslational modification that regulates transcription factor function, and we previously showed that mouse oocytes deficient for sumoylation had an altered transcriptional landscape that included significant changes in NOBOX target genes. Here, we show that mouse SOHLH1 is modified by SUMO2/3 at lysine 345 and mutation of this residue alters SOHLH1 nuclear to cytoplasmic localization. In NOBOX, we identify a non-consensus SUMO site, K97, that eliminates NOBOX mono-SUMO2/3 conjugation, while a point mutation at K125 had no effect on NOBOX sumoylation. However, NOBOXK97R/K125R double mutants showed loss of mono-SUMO2/3 and altered higher molecular weight modifications, suggesting cooperation between these lysine's. NOBOXK97R and NOBOXK97R/K125R differentially regulated NOBOX promoter targets, with increased activity on the Gdf9 promoter, but no effect on the Pou5f1 promoter. These data implicate sumoylation as a novel regulatory mechanism for SOHLH1 and NOBOX, which may prove useful in refining their roles during oogenesis as well as their function during reprogramming to generate de novo germ cells.
Collapse
Affiliation(s)
- Bethany K. Patton
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Surabhi Madadi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Rice University, Houston, TX 77005
| | - Shawn M. Briley
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Avery A. Ahmed
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030
| | - Stephanie A. Pangas
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| |
Collapse
|
23
|
Huang S, Gao Y, Wang Y, Li F, Xiao W, Ge WP, Li Y, Xu P. Fluorescein-labeled ThUBD probe for super-sensitive visualization of polyubiquitination signal in situ cells. Talanta 2023; 253:123564. [PMID: 35710467 DOI: 10.1016/j.talanta.2022.123564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 12/13/2022]
Abstract
Ubiquitin-binding domains (UBDs) are modular elements that bind non-covalently to the ubiquitin and ubiquitin chains. The preferences of UBDs for ubiquitin chains of specific length and linkage are central to their functions. We demonstrated that an artificial tandem hybrid UBD (ThUBD) exhibits an unbiased high affinity to all ubiquitin chains and is a promising tool for global ubiquitination profiling research. In this study, we labeled fluorescein on the four cysteine residues in the N-terminal glutathione S-transferase (GST) tag of ThUBD, generating a fluorescein-labeled ThUBD (ThUBD-Flu) probe for direct polyubiquitination signal imaging and visualization. Compared to the canonical ubiquitin antibody method, the ThUBD-Flu is hyper-sensitive and accurate to detect ubiquitination signal. More importantly, the ThUBD-Flu probe provided, for the first time, a widely applicable, super-sensitive and unbiased technique for in situ detection of intracellular polyubiquitination signal through immunofluorescence staining, which was only achievable with recombinant fluorescence tag fused ubiquitin gene previously. We propose that ThUBD-Flu, combined with evolving microscopy technology, could serve as prototypes to track and trace cellular polyubiquitination signal in vivo.
Collapse
Affiliation(s)
- Shuai Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, PR China
| | - Yuan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, PR China
| | - Yonghong Wang
- Medical School of Guizhou University, Guiyang, 550025, China
| | - Fengzhi Li
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Weidi Xiao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, PR China
| | - Woo-Ping Ge
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, PR China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, PR China; School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, PR China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China; Medical School of Guizhou University, Guiyang, 550025, China; Second Clinical Medicine Collage, Guangzhou University Chinese Medicine, Guangzhou, 510006, China.
| |
Collapse
|
24
|
Dai Z, Chen L, Pan K, Zhao X, Xu W, Du J, Xing C. Multi-omics Analysis of the Role of PHGDH in Colon Cancer. Technol Cancer Res Treat 2023; 22:15330338221145994. [PMID: 36707056 PMCID: PMC9896097 DOI: 10.1177/15330338221145994] [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] [Indexed: 01/29/2023] Open
Abstract
Objectives: Serine metabolism is essential for tumor cells. Endogenous serine arises from de novo synthesis pathways. As the rate-limiting enzyme of this pathway, PHGDH is highly expressed in a variety of tumors including colon cancer. Therefore, targeted inhibition of PHGDH is an important strategy for anti-tumor therapy research. However, the specific gene expression and metabolic pathways regulated by PHGDH in colon cancer are still unclear. Our study was aimed to clarified the role of PHGDH in serine metabolism in colon cancer to provide new knowledge for in-depth understanding of serine metabolism and PHGDH function in colon cancer. Methods: In this study, we analyzed the gene expression and metabolic remodeling process of colon cancer cells (SW620) after targeted inhibition of PHGDH by gene transcriptomics and metabolomics. LC-MS analysis was performed in 293T cells to PHGDH gene transcription and protein post-translational modification under depriving exogenous serine. Results: We found that amino acid transporters, amino acid metabolism, lipid synthesis related pathways compensation and other processes are involved in the response process after PHGDH inhibition. And ATF4 mediated the transcriptional expression of PHGDH under exogenous serine deficiency conditions. While LC-MS analysis of post-translational modification revealed that PHGDH produced changes in acetylation sites after serine deprivation that the K289 site was lost, and a new acetylation site K21was produced. Conclusion: Our study performed transcriptomic and metabolomic analysis by inhibiting PHGDH, thus clarifying the role of PHGDH in gene transcription and metabolism in colon cancer cells. The mechanism of high PHGDH expression in colon cancer cells and the acetylation modification that occurs in PHGDH protein were also clarified by serine deprivation. In our study, the role of PHGDH in serine metabolism in colon cancer was clarified by multi-omics analysis to provide new knowledge for in-depth understanding of serine metabolism and PHGDH function in colon cancer.
Collapse
Affiliation(s)
- Zhihui Dai
- Department of General Surgery, The Second Affiliated Hospital of Soochow
University, Suzhou, China,Department of Colorectal Surgery, Affiliated Jinhua Hospital,
Zhejiang University School of Medicine, Jinhua, Zhejiang Province, China
| | - Lin Chen
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University
School of Medicine, Jinhua, Zhejiang Province, China
| | - KaiLing Pan
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University
School of Medicine, Jinhua, Zhejiang Province, China
| | - XiaoYa Zhao
- Jiangsu Key Laboratory of Molecular Medicine,
Medical
School of Nanjing University, Nanjing,
Jiangsu Province, China
| | - WenXia Xu
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University
School of Medicine, Jinhua, Zhejiang Province, China
| | - JinLin Du
- Department of Colorectal Surgery, Affiliated Jinhua Hospital,
Zhejiang University School of Medicine, Jinhua, Zhejiang Province, China,JinLin Du, Department of Colorectal
Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine,
Jinhua 321000, Zhejiang Province, China.
Chungen Xing, Department of General Surgery, The Second Affiliated Hospital of
Soochow University, Suzhou, China.
| | - Chungen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow
University, Suzhou, China
| |
Collapse
|
25
|
Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions. Int J Mol Sci 2022; 23:ijms232214075. [PMID: 36430551 PMCID: PMC9694962 DOI: 10.3390/ijms232214075] [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: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates.
Collapse
|
26
|
Zhang S, Jin B, Liang W, Guo A, Luo X, Pu L, Chen X, Cai X, Wang S. Identification and expression analysis of a new small ubiquitin-like modifier from Taenia pisiformis. Exp Parasitol 2022; 242:108403. [DOI: 10.1016/j.exppara.2022.108403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022]
|
27
|
SNRPD2 Is a Novel Substrate for the Ubiquitin Ligase Activity of the Salmonella Type III Secretion Effector SlrP. BIOLOGY 2022; 11:biology11101517. [PMID: 36290420 PMCID: PMC9598574 DOI: 10.3390/biology11101517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Simple Summary Salmonella is a genus of bacterial pathogens that can cause several diseases in humans and other animals. These bacteria can inject proteins known as effectors into animal cells through a secretion system. One of these effectors, SlrP, promotes the covalent addition of ubiquitin, a small eukaryotic protein, to specific host proteins, leading to an alteration of their stability or function. Here, we have performed a genetic screen to find new human targets of SlrP. In this way, we have identified SNRPD2, a core component of the spliceosome, the ribonucleoprotein complex that removes introns from eukaryotic pre-mRNA. SNRPD2 physically interacts with SlrP and is also a substrate of its ubiquitination activity. Lysines at positions 85 and 92 in SNRPD2 are among the residues that were ubiquitinated in the presence of SlrP. The identification of new host targets of Salmonella effectors contributes to a better understanding of the biological processes that are highjacked by these pathogens during infection, and can help in the design of future therapeutic strategies. Abstract SlrP is a protein with E3 ubiquitin ligase activity that is translocated by Salmonella enterica serovar Typhimurium into eukaryotic host cells through a type III secretion system. A yeast two-hybrid screen was performed to find new human partners for this protein. Among the interacting proteins identified by this screen was SNRPD2, a core component of the spliceosome. In vitro ubiquitination assays demonstrated that SNRPD2 is a substrate for the catalytic activity of SlrP, but not for other members of the NEL family of E3 ubiquitin ligases, SspH1 and SspH2. The lysine residues modified by this activity were identified by mass spectrometry. The identification of a new ubiquitination target for SlrP is a relevant contribution to the understanding of the role of this Salmonella effector.
Collapse
|
28
|
Chen JJ, Stermer D, Tanny JC. Decoding histone ubiquitylation. Front Cell Dev Biol 2022; 10:968398. [PMID: 36105353 PMCID: PMC9464978 DOI: 10.3389/fcell.2022.968398] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and lies at the heart of DNA damage repair signaling. The histone residues targeted for ubiquitylation are often highly conserved through evolution, and extensive functional studies of the enzymes that catalyze the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division, development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream consequences of these modifications have only recently begun to be appreciated on a molecular level. Here we review the structure and function of proteins that act as effectors or “readers” of histone ubiquitylation. We highlight lessons learned about how ubiquitin recognition lends specificity and function to intermolecular interactions in the context of transcription and DNA repair, as well as what this might mean for how we think about histone modifications more broadly.
Collapse
|
29
|
Cancer-Associated Dysregulation of Sumo Regulators: Proteases and Ligases. Int J Mol Sci 2022; 23:ijms23148012. [PMID: 35887358 PMCID: PMC9316396 DOI: 10.3390/ijms23148012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
SUMOylation is a post-translational modification that has emerged in recent decades as a mechanism involved in controlling diverse physiological processes and that is essential in vertebrates. The SUMO pathway is regulated by several enzymes, proteases and ligases being the main actors involved in the control of sumoylation of specific targets. Dysregulation of the expression, localization and function of these enzymes produces physiological changes that can lead to the appearance of different types of cancer, depending on the enzymes and target proteins involved. Among the most studied proteases and ligases, those of the SENP and PIAS families stand out, respectively. While the proteases involved in this pathway have specific SUMO activity, the ligases may have additional functions unrelated to sumoylation, which makes it more difficult to study their SUMO-associated role in cancer process. In this review we update the knowledge and advances in relation to the impact of dysregulation of SUMO proteases and ligases in cancer initiation and progression.
Collapse
|
30
|
Bullones-Bolaños A, Bernal-Bayard J, Ramos-Morales F. The NEL Family of Bacterial E3 Ubiquitin Ligases. Int J Mol Sci 2022; 23:7725. [PMID: 35887072 PMCID: PMC9320238 DOI: 10.3390/ijms23147725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/16/2022] Open
Abstract
Some pathogenic or symbiotic Gram-negative bacteria can manipulate the ubiquitination system of the eukaryotic host cell using a variety of strategies. Members of the genera Salmonella, Shigella, Sinorhizobium, and Ralstonia, among others, express E3 ubiquitin ligases that belong to the NEL family. These bacteria use type III secretion systems to translocate these proteins into host cells, where they will find their targets. In this review, we first introduce type III secretion systems and the ubiquitination process and consider the various ways bacteria use to alter the ubiquitin ligation machinery. We then focus on the members of the NEL family, their expression, translocation, and subcellular localization in the host cell, and we review what is known about the structure of these proteins, their function in virulence or symbiosis, and their specific targets.
Collapse
Affiliation(s)
| | | | - Francisco Ramos-Morales
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (A.B.-B.); (J.B.-B.)
| |
Collapse
|
31
|
Histone Modifications and Non-Coding RNAs: Mutual Epigenetic Regulation and Role in Pathogenesis. Int J Mol Sci 2022; 23:ijms23105801. [PMID: 35628612 PMCID: PMC9146199 DOI: 10.3390/ijms23105801] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 12/07/2022] Open
Abstract
In the last few years, more and more scientists have suggested and confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. This is particularly interesting for a better understanding of processes that occur in the development and progression of various diseases. Appearing on the preclinical stages of diseases, epigenetic aberrations may be prominent biomarkers. Being dynamic and reversible, epigenetic modifications could become targets for a novel option for therapy. Therefore, in this review, we are focusing on histone modifications and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
Collapse
|