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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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2
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Zhang H, Liu W, Wu Y, Chen C. USP3: Key deubiquitylation enzyme in human diseases. Cancer Sci 2024; 115:2094-2106. [PMID: 38651282 PMCID: PMC11247611 DOI: 10.1111/cas.16178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024] Open
Abstract
Ubiquitination and deubiquitylation are pivotal posttranslational modifications essential for regulating cellular protein homeostasis and are implicated in the development of human diseases. Ubiquitin-specific protease 3 (USP3), a member of the ubiquitin-specific protease family, serves as a key deubiquitylation enzyme, playing a critical role in diverse cellular processes including the DNA damage response, cell cycle regulation, carcinogenesis, tumor cell proliferation, migration, and invasion. Despite notable research efforts, our current understanding of the intricate and context-dependent regulatory networks governing USP3 remains incomplete. This review aims to comprehensively synthesize existing published works on USP3, elucidating its multifaceted roles, functions, and regulatory mechanisms, while offering insights for future investigations. By delving into the complexities of USP3, this review strives to provide a foundation for a more nuanced understanding of its specific roles in various cellular processes. Furthermore, the exploration of USP3's regulatory networks may uncover novel therapeutic strategies targeting this enzyme in diverse human diseases, thereby holding promising clinical implications. Overall, an in-depth comprehension of USP3's functions and regulatory pathways is crucial for advancing our knowledge and developing targeted therapeutic approaches for human diseases.
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Affiliation(s)
- Hongyan Zhang
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunmingChina
- Medical SchoolKunming University of Science and TechnologyKunmingChina
| | - Wenjing Liu
- The Third Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Yingying Wu
- The First Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Ceshi Chen
- The Third Affiliated Hospital, Kunming Medical UniversityKunmingChina
- Academy of Biomedical EngineeringKunming Medical UniversityKunmingChina
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Qi Y, Rezaeian AH, Wang J, Huang D, Chen H, Inuzuka H, Wei W. Molecular insights and clinical implications for the tumor suppressor role of SCF FBXW7 E3 ubiquitin ligase. Biochim Biophys Acta Rev Cancer 2024; 1879:189140. [PMID: 38909632 DOI: 10.1016/j.bbcan.2024.189140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
FBXW7 is one of the most well-characterized F-box proteins, serving as substrate receptor subunit of SKP1-CUL1-F-box (SCF) E3 ligase complexes. SCFFBXW7 is responsible for the degradation of various oncogenic proteins such as cyclin E, c-MYC, c-JUN, NOTCH, and MCL1. Therefore, FBXW7 functions largely as a major tumor suppressor. In keeping with this notion, FBXW7 gene mutations or downregulations have been found and reported in many types of malignant tumors, such as endometrial, colorectal, lung, and breast cancers, which facilitate the proliferation, invasion, migration, and drug resistance of cancer cells. Therefore, it is critical to review newly identified FBXW7 regulation and tumor suppressor function under physiological and pathological conditions to develop effective strategies for the treatment of FBXW7-altered cancers. Since a growing body of evidence has revealed the tumor-suppressive activity and role of FBXW7, here, we updated FBXW7 upstream and downstream signaling including FBXW7 ubiquitin substrates, the multi-level FBXW7 regulatory mechanisms, and dysregulation of FBXW7 in cancer, and discussed promising cancer therapies targeting FBXW7 regulators and downstream effectors, to provide a comprehensive picture of FBXW7 and facilitate the study in this field.
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Affiliation(s)
- Yihang Qi
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Abdol-Hossein Rezaeian
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingchao Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Daoyuan Huang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hong Chen
- Vascular Biology Program, Department of Surgery, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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Wen J, Wan L, Chen W, Dong X. The prognostic value of ubiquitin/ubiquitin-like-related genes along with immune cell infiltration and clinicopathological features in osteosarcoma. J Orthop Surg Res 2024; 19:356. [PMID: 38879525 PMCID: PMC11179372 DOI: 10.1186/s13018-024-04781-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/03/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Ubiquitin/ubiquitin-like (Ub/UBL)-related genes have been reported to be associated with the survival of osteosarcoma patients but have not yet been systematically explored. METHODS The prognostic value of Ub/UBL-related genes, immune cell infiltration and clinicopathological features of patients were explored by Cox and LASSO regression analyses. A prognostic model was established and then validated in the GSE21257 dataset. The differential expression of hub genes in osteosarcoma was confirmed by qRT-PCR, western blotting and immunohistochemistry. RESULTS Tripartite Motif Containing 8 (TRIM8) and Ubiquitin Like With PHD And Ring Finger Domains 2 (UHRF2) were screened as genes with prognostic value in osteosarcoma. Kaplan-Meier analysis and scatter plots indicated that patients in the high gene significance score group tended to have a worse prognosis. The concordance index, calibration analysis and receiver operating characteristic analysis suggested that the model had good prediction accuracy and high sensitivity and specificity. Decision curve analysis revealed that patients could obtain greater net benefit from this model. Functional analyses of the differentially expressed genes indicated that they were involved in important functions and pathways. TRIM8 and UHRF2 were confirmed to be highly expressed in osteosarcoma cell lines and tissues. CONCLUSIONS TRIM8 and UHRF2 are potential prognostic genes in osteosarcoma, and these results provide insights into the roles of these genes and their implications for patient outcomes.
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Affiliation(s)
- Jian Wen
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, China
- JXHC Key Laboratory of Digital Orthopaedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, 330006, Jiangxi, China
- Department of Orthopedics, Pingxiang People's Hospital, The Sixth Clinical College of Gannan Medical University, Pingxiang, 337000, China
| | - Lijia Wan
- Department of Child Healthcare, Hunan Provincial Maternal and Child Health Hospital, Changsha, 410008, Hunan, China
| | - Wenming Chen
- Department of Orthopedics, Pingxiang People's Hospital, The Sixth Clinical College of Gannan Medical University, Pingxiang, 337000, China.
| | - Xieping Dong
- JXHC Key Laboratory of Digital Orthopaedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, 330006, Jiangxi, China.
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Wan B, Cheng M, He T, Zhang L. UCHL5 promotes hepatocellular carcinoma progression by promoting glycolysis through activating Wnt/β-catenin pathway. BMC Cancer 2024; 24:618. [PMID: 38773433 PMCID: PMC11110341 DOI: 10.1186/s12885-023-11317-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 08/18/2023] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is highly malignant with a dismal prognosis, although the available therapies are insufficient. No efficient ubiquitinase has been identified as a therapeutic target for HCC despite the complicating role that of proteins ubiquitination plays in the malignant development of HCC. METHODS The expression of ubiquitin carboxyl terminal hydrolase L5 (UCHL5) in HCC tumor tissue and adjacent normal tissue was determined using the cancer genome atlas (TCGA) database and was validated using real-time quantitative polymerase chain reaction (RT-qRCR), Western blot and immunohistochemistry (IHC), and the relation of UCHL5 with patient clinical prognosis was explored. The expression of UCHL5 was knocked down and validated, and the effect of UCHL5 on the biological course of HCC was explored using cellular assays. To clarify the molecular mechanism of action of UCHL5 affecting HCC, expression studies of Adenosine triphosphate adenosine triphosphate (ATP), extracellular acidification (ECAR), and glycolysis-related enzymes were performed. The effects of UCHL5 on β-catenin ubiquitination and Wnt signaling pathways were explored in depth and validated using cellular functionalities. Validation was also performed in vivo. RESULTS In the course of this investigation, we discovered that UCHL5 was strongly expressed in HCC at both cellular and tissue levels. The prognosis of patients with high UCHL5 expression is considerably worse than that of those with low UCHL5 expression. UCHL5 has been shown to increase the degree of glycolysis in HCC cells with the impact of stimulating the proliferation and metastasis of HCC cells in both in vivo and in vitro. UCHL5 downregulates its degree of ubiquitination by binding to β-catenin, which activates the Wnt/β-catenin pathway and accelerates HCC cell glycolysis. Thereby promoting the growth of the HCC. CONCLUSIONS In summary, we have demonstrated for the first time that UCHL5 is a target of HCC and promotes the progression of hepatocellular carcinoma by promoting glycolysis through the activation of the Wnt/β-catenin pathway. UCHL5 may thus serve as a novel prognostic marker and therapeutic target for the treatment of HCC.
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Affiliation(s)
- Baishun Wan
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, No. 127, Dongming Road, Zhengzhou, Henan Province, 450008, China
| | - Ming Cheng
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, No. 127, Dongming Road, Zhengzhou, Henan Province, 450008, China
| | - Tao He
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, No. 127, Dongming Road, Zhengzhou, Henan Province, 450008, China
| | - Ling Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, No. 127, Dongming Road, Zhengzhou, Henan Province, 450008, China.
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González R, Félix MA. Caenorhabditis elegans immune responses to microsporidia and viruses. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105148. [PMID: 38325500 DOI: 10.1016/j.dci.2024.105148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
The model organism Caenorhabditis elegans is susceptible to infection by obligate intracellular pathogens, specifically microsporidia and viruses. These intracellular pathogens infect intestinal cells, or, for some microsporidia, epidermal cells. Strikingly, intestinal cell infections by viruses or microsporidia trigger a common transcriptional response, activated in part by the ZIP-1 transcription factor. Among the strongest activated genes in this response are ubiquitin-pathway members and members of the pals family, an intriguing gene family with cross-regulations of different members of genomic clusters. Some of the induced genes participate in host defense against the pathogens, for example through ubiquitin-mediated inhibition. Other mechanisms defend the host specifically against viral infections, including antiviral RNA interference and uridylation. These various immune responses are altered by environmental factors and by intraspecific genetic variation of the host. These pathogens were first isolated 15 years ago and much remains to be discovered using C. elegans genetics; also, other intracellular pathogens of C. elegans may yet to be discovered.
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Affiliation(s)
- Rubén González
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France.
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France
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Qiu H, Liang J, Yang G, Xie Z, Wang Z, Wang L, Zhang J, Nanda HS, Zhou H, Huang Y, Peng X, Lu C, Chen H, Zhou Y. Application of exosomes in tumor immunity: recent progresses. Front Cell Dev Biol 2024; 12:1372847. [PMID: 38633106 PMCID: PMC11021734 DOI: 10.3389/fcell.2024.1372847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Exosomes are small extracellular vesicles secreted by cells, ranging in size from 30 to 150 nm. They contain proteins, nucleic acids, lipids, and other bioactive molecules, which play a crucial role in intercellular communication and material transfer. In tumor immunity, exosomes present various functions while the following two are of great importance: regulating the immune response and serving as delivery carriers. This review starts with the introduction of the formation, compositions, functions, isolation, characterization, and applications of exosomes, and subsequently discusses the current status of exosomes in tumor immunotherapy, and the recent applications of exosome-based tumor immunity regulation and antitumor drug delivery. Finally, current challenge and future prospects are proposed and hope to demonstrate inspiration for targeted readers in the field.
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Affiliation(s)
- Haiyan Qiu
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Junting Liang
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Guang Yang
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zhenyu Xie
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zhenpeng Wang
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Liyan Wang
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Jingying Zhang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
| | - Himansu Sekhar Nanda
- Biomedical Engineering and Technology Lab, Discipline of Mechanical Engineering, PDPM Indian Institute of Information Technology Design and Manufacturing Jabalpur, Jabalpur, Madhya Pradesh, India
| | - Hui Zhou
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Yong Huang
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xinsheng Peng
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Chengyu Lu
- School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Huizhi Chen
- School of Pharmacy, Guangdong Medical University, Dongguan, China
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
| | - Yubin Zhou
- School of Pharmacy, Guangdong Medical University, Dongguan, China
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
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8
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Li Q, Wu P, Du Q, Hanif U, Hu H, Li K. cGAS-STING, an important signaling pathway in diseases and their therapy. MedComm (Beijing) 2024; 5:e511. [PMID: 38525112 PMCID: PMC10960729 DOI: 10.1002/mco2.511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Since cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway was discovered in 2013, great progress has been made to elucidate the origin, function, and regulating mechanism of cGAS-STING signaling pathway in the past decade. Meanwhile, the triggering and transduction mechanisms have been continuously illuminated. cGAS-STING plays a key role in human diseases, particularly DNA-triggered inflammatory diseases, making it a potentially effective therapeutic target for inflammation-related diseases. Here, we aim to summarize the ancient origin of the cGAS-STING defense mechanism, as well as the triggers, transduction, and regulating mechanisms of the cGAS-STING. We will also focus on the important roles of cGAS-STING signal under pathological conditions, such as infections, cancers, autoimmune diseases, neurological diseases, and visceral inflammations, and review the progress in drug development targeting cGAS-STING signaling pathway. The main directions and potential obstacles in the regulating mechanism research and therapeutic drug development of the cGAS-STING signaling pathway for inflammatory diseases and cancers will be discussed. These research advancements expand our understanding of cGAS-STING, provide a theoretical basis for further exploration of the roles of cGAS-STING in diseases, and open up new strategies for targeting cGAS-STING as a promising therapeutic intervention in multiple diseases.
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Affiliation(s)
- Qijie Li
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
| | - Ping Wu
- Department of Occupational DiseasesThe Second Affiliated Hospital of Chengdu Medical College (China National Nuclear Corporation 416 Hospital)ChengduSichuanChina
| | - Qiujing Du
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
| | - Ullah Hanif
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
| | - Hongbo Hu
- Center for Immunology and HematologyState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Ka Li
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
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Li M, Dai M, Cheng B, Li S, Guo E, Fu J, Ma T, Yu B. Strategies that regulate LSD1 for novel therapeutics. Acta Pharm Sin B 2024; 14:1494-1507. [PMID: 38572094 PMCID: PMC10985039 DOI: 10.1016/j.apsb.2024.01.005] [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: 08/19/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 04/05/2024] Open
Abstract
Histone methylation plays crucial roles in regulating chromatin structure and gene transcription in epigenetic modifications. Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is universally overexpressed in various diseases. LSD1 dysregulation is closely associated with cancer, viral infections, and neurodegenerative diseases, etc., making it a promising therapeutic target. Several LSD1 inhibitors and two small-molecule degraders (UM171 and BEA-17) have entered the clinical stage. LSD1 can remove methyl groups from histone 3 at lysine 4 or lysine 9 (H3K4 or H3K9), resulting in either transcription repression or activation. While the roles of LSD1 in transcriptional regulation are well-established, studies have revealed that LSD1 can also be dynamically regulated by other factors. For example, the expression or activity of LSD1 can be regulated by many proteins that form transcriptional corepressor complexes with LSD1. Moreover, some post-transcriptional modifications and cellular metabolites can also regulate LSD1 expression or its demethylase activity. Therefore, in this review, we will systematically summarize how proteins involved in the transcriptional corepressor complex, various post-translational modifications, and metabolites act as regulatory factors for LSD1 activity.
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Affiliation(s)
- Meng Li
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Mengge Dai
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Bing Cheng
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Shaotong Li
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Enhui Guo
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Junwei Fu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Ma
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
- Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Henan Normal University, Xinxiang 453007, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450000, China
- Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Henan Normal University, Xinxiang 453007, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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Ha J, Kim M, Park JS, Lee Y, Lee JY, Shin JC, Seo D, Park SS, You J, Jung SM, Kim HY, Mizuno S, Takahashi S, Kim SJ, Park SH. SERTAD1 initiates NLRP3-mediated inflammasome activation through restricting NLRP3 polyubiquitination. Cell Rep 2024; 43:113752. [PMID: 38341852 DOI: 10.1016/j.celrep.2024.113752] [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: 08/07/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 02/13/2024] Open
Abstract
We here demonstrate that SERTAD1 is an adaptor protein responsible for the regulation of lysine 63 (K63)-linked NLRP3 polyubiquitination by the Cullin1 E3 ubiquitin ligase upon inflammasome activation. SERTAD1 specifically binds to NLRP3 but not to other inflammasome sensors. This endogenous interaction increases after inflammasome activation, interfering with the interaction between NLRP3 and Cullin1. Interleukin (IL)-1β and IL-18 secretion, as well as the cleavage of gasdermin D, are decreased in SERTAD1 knockout bone-marrow-derived macrophages, together with reduced formation of the NLRP3 inflammasome complex. Additionally, SERTAD1-deficient mice show attenuated severity of monosodium-uric-acid-induced peritonitis and experimental autoimmune encephalomyelitis. Analysis of public datasets indicates that expression of SERTAD1 mRNA is significantly increased in the patients of autoimmune diseases. Thus, our findings uncover a function of SERTAD1 that specifically reduces Cullin1-mediated NLRP3 polyubiquitination via direct binding to NLRP3, eventually acting as a crucial factor to regulate the initiation of NLRP3-mediated inflammasome activation.
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Affiliation(s)
- Jihoon Ha
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Minbeom Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin Seok Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yerin Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jae Young Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin-Cheol Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dongyeob Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seong Shil Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jiyeon You
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Su Myung Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hye Young Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8578, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8578, Japan
| | - Seong-Jin Kim
- GILO Institute, GILO Foundation, Seoul 06668, Republic of Korea
| | - Seok Hee Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea; SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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11
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Ma J, Yan L, Yang J, He Y, Wu L. Effect of Modification Strategies on the Biological Activity of Peptides/Proteins. Chembiochem 2024; 25:e202300481. [PMID: 38009768 DOI: 10.1002/cbic.202300481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 11/29/2023]
Abstract
Covalent attachment of biologically active peptides/proteins with functional moieties is an effective strategy to control their biodistribution, pharmacokinetics, enzymatic digestion, and toxicity. This review focuses on the characteristics of different modification strategies and their effects on the biological activity of peptides/proteins and illustrates their relevant applications and potential.
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Affiliation(s)
- Jian Ma
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingkui Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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12
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Spano D, Catara G. Targeting the Ubiquitin-Proteasome System and Recent Advances in Cancer Therapy. Cells 2023; 13:29. [PMID: 38201233 PMCID: PMC10778545 DOI: 10.3390/cells13010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Ubiquitination is a reversible post-translational modification based on the chemical addition of ubiquitin to proteins with regulatory effects on various signaling pathways. Ubiquitination can alter the molecular functions of tagged substrates with respect to protein turnover, biological activity, subcellular localization or protein-protein interaction. As a result, a wide variety of cellular processes are under ubiquitination-mediated control, contributing to the maintenance of cellular homeostasis. It follows that the dysregulation of ubiquitination reactions plays a relevant role in the pathogenic states of human diseases such as neurodegenerative diseases, immune-related pathologies and cancer. In recent decades, the enzymes of the ubiquitin-proteasome system (UPS), including E3 ubiquitin ligases and deubiquitinases (DUBs), have attracted attention as novel druggable targets for the development of new anticancer therapeutic approaches. This perspective article summarizes the peculiarities shared by the enzymes involved in the ubiquitination reaction which, when deregulated, can lead to tumorigenesis. Accordingly, an overview of the main pharmacological interventions based on targeting the UPS that are in clinical use or still in clinical trials is provided, also highlighting the limitations of the therapeutic efficacy of these approaches. Therefore, various attempts to circumvent drug resistance and side effects as well as UPS-related emerging technologies in anticancer therapeutics are discussed.
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Affiliation(s)
- Daniela Spano
- Institute for Endocrinology and Experimental Oncology “G. Salvatore”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
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13
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Lemma B, Zhang D, Vamisetti GB, Wentz BG, Suga H, Brik A, Lubkowski J, Fushman D. Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation. Nat Commun 2023; 14:7212. [PMID: 37938554 PMCID: PMC10632358 DOI: 10.1038/s41467-023-43025-4] [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: 03/11/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Post-translational modification of proteins with polyubiquitin chains is a critical cellular signaling mechanism in eukaryotes with implications in various cellular states and processes. Unregulated ubiquitin-mediated protein degradation can be detrimental to cellular homeostasis, causing numerous diseases including cancers. Recently, macrocyclic peptides were developed that selectively target long Lysine-48-linked polyubiquitin chains (tetra-ubiquitin) to inhibit ubiquitin-proteasome system, leading to attenuation of tumor growth in vivo. However, structural determinants of the chain length and linkage selectivity by these cyclic peptides remained unclear. Here, we uncover the mechanism underlying cyclic peptide's affinity and binding selectivity by combining X-ray crystallography, solution NMR, and biochemical studies. We found that the peptide engages three consecutive ubiquitins that form a ring around the peptide and determined requirements for preferential selection of a specific trimer moiety in longer polyubiquitin chains. The structural insights gained from this work will guide the development of next-generation cyclic peptides with enhanced anti-cancer activity.
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Affiliation(s)
- Betsegaw Lemma
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Di Zhang
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Ganga B Vamisetti
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200008, Israel
| | - Bryan G Wentz
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200008, Israel.
| | - Jacek Lubkowski
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - David Fushman
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
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14
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Li D, Xia W, Cui X, Zhao M, Huang K, Wang X, Shen J, Chen H, Zhu L. The putatively high-altitude adaptation of macaque monkeys: Evidence from the fecal metabolome and gut microbiome. Evol Appl 2023; 16:1708-1720. [PMID: 38020871 PMCID: PMC10660799 DOI: 10.1111/eva.13595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 12/01/2023] Open
Abstract
Animals living in high-altitude environments, such as the Tibetan Plateau, must face harsh environmental conditions (e.g., hypoxia, cold, and strong UV radiation). These animals' physiological adaptations (e.g., increased red cell production and turnover rate) might also be associated with the gut microbial response. Bilirubin is a component of red blood cell turnover or destruction and is excreted into the intestine and reduced to urobilinoids and/or urobilinogen by gut bacteria. Here, we found that the feces of macaques living in high-altitude regions look significantly browner (with a high concentration of stercobilin, a component from urobilinoids) than those living in low-altitude regions. We also found that gut microbes involved in urobilinogen reduction (e.g., beta-glucuronidase) were enriched in the high-altitude mammal population compared to the low-altitude population. Moreover, the spatial-temporal change in gut microbial function was more profound in the low-altitude macaques than in the high-altitude population, which might be attributed to profound changes in food resources in the low-altitude regions. Therefore, we conclude that a high-altitude environment's stress influences living animals and their symbiotic microbiota.
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Affiliation(s)
- Dayong Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Wancai Xia
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Xinyuan Cui
- College of Life ScienceNanjing Normal UniversityNanjingChina
| | - Mei Zhao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Kai Huang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Xueyu Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | | | - Hua Chen
- Mingke BiotechnologyHangzhouChina
| | - Lifeng Zhu
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjingChina
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15
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Farooqi AA, Rakhmetova V, Kapanova G, Tanbayeva G, Mussakhanova A, Abdykulova A, Ryskulova AG. Role of Ubiquitination and Epigenetics in the Regulation of AhR Signaling in Carcinogenesis and Metastasis: "Albatross around the Neck" or "Blessing in Disguise". Cells 2023; 12:2382. [PMID: 37830596 PMCID: PMC10571945 DOI: 10.3390/cells12192382] [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: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
The molecular mechanisms and signal transduction cascades evoked by the activation of aryl hydrocarbon receptor (AhR) are becoming increasingly understandable. AhR is a ligand-activated transcriptional factor that integrates environmental, dietary and metabolic cues for the pleiotropic regulation of a wide variety of mechanisms. AhR mediates transcriptional programming in a ligand-specific, context-specific and cell-type-specific manner. Pioneering cutting-edge research works have provided fascinating new insights into the mechanistic role of AhR-driven downstream signaling in a wide variety of cancers. AhR ligands derived from food, environmental contaminants and intestinal microbiota strategically activated AhR signaling and regulated multiple stages of cancer. Although AhR has classically been viewed and characterized as a ligand-regulated transcriptional factor, its role as a ubiquitin ligase is fascinating. Accordingly, recent evidence has paradigmatically shifted our understanding and urged researchers to drill down deep into these novel and clinically valuable facets of AhR biology. Our rapidly increasing realization related to AhR-mediated regulation of the ubiquitination and proteasomal degradation of different proteins has started to scratch the surface of intriguing mechanisms. Furthermore, AhR and epigenome dynamics have shown previously unprecedented complexity during multiple stages of cancer progression. AhR not only transcriptionally regulated epigenetic-associated molecules, but also worked with epigenetic-modifying enzymes during cancer progression. In this review, we have summarized the findings obtained not only from cell-culture studies, but also from animal models. Different clinical trials are currently being conducted using AhR inhibitors and PD-1 inhibitors (Pembrolizumab and nivolumab), which confirm the linchpin role of AhR-related mechanistic details in cancer progression. Therefore, further studies are required to develop a better comprehension of the many-sided and "diametrically opposed" roles of AhR in the regulation of carcinogenesis and metastatic spread of cancer cells to the secondary organs.
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Affiliation(s)
- Ammad Ahmad Farooqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 54000, Pakistan
| | - Venera Rakhmetova
- Department of Internal Diseases, Medical University of Astana, Astana 010000, Kazakhstan
| | - Gulnara Kapanova
- Faculty of Medicine and healthcare, Al-Farabi Kazakh National University, 71 Al-Farabi Ave, Almaty 050040, Kazakhstan (G.T.)
- Scientific Center of Anti-Infectious Drugs, 75 Al-Farabi Ave, Almaty 050040, Kazakhstan
| | - Gulnur Tanbayeva
- Faculty of Medicine and healthcare, Al-Farabi Kazakh National University, 71 Al-Farabi Ave, Almaty 050040, Kazakhstan (G.T.)
| | - Akmaral Mussakhanova
- Department of Public Health and Management, Astana Medical University, Astana 010000, Kazakhstan;
| | - Akmaral Abdykulova
- Department of General Medical Practice, General Medicine Faculty, Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan;
| | - Alma-Gul Ryskulova
- Department of Public Health and Social Sciences, Kazakhstan Medical University “KSPH”, Utenos Str. 19A, Almaty 050060, Kazakhstan;
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16
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Harit K, Bhattacharjee R, Matuschewski K, Becker J, Kalinke U, Schlüter D, Nishanth G. The deubiquitinating enzyme OTUD7b protects dendritic cells from TNF-induced apoptosis by stabilizing the E3 ligase TRAF2. Cell Death Dis 2023; 14:480. [PMID: 37516734 PMCID: PMC10387084 DOI: 10.1038/s41419-023-06014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 07/31/2023]
Abstract
The cytokine tumor necrosis factor (TNF) critically regulates the intertwined cell death and pro-inflammatory signaling pathways of dendritic cells (DCs) via ubiquitin modification of central effector molecules, but the intrinsic molecular switches deciding on either pathway are incompletely defined. Here, we uncover that the ovarian tumor deubiquitinating enzyme 7b (OTUD7b) prevents TNF-induced apoptosis of DCs in infection, resulting in efficient priming of pathogen-specific CD8+ T cells. Mechanistically, OTUD7b stabilizes the E3 ligase TNF-receptor-associated factor 2 (TRAF2) in human and murine DCs by counteracting its K48-ubiquitination and proteasomal degradation. TRAF2 in turn facilitates K63-linked polyubiquitination of RIPK1, which mediates activation of NF-κB and MAP kinases, IL-12 production, and expression of anti-apoptotic cFLIP and Bcl-xL. We show that mice with DC-specific OTUD7b-deficiency displayed DC apoptosis and a failure to induce CD8+ T cell-mediated brain pathology, experimental cerebral malaria, in a murine malaria infection model. Together, our data identify the deubiquitinating enzyme OTUD7b as a central molecular switch deciding on survival of human and murine DCs and provides a rationale to manipulate DC responses by targeting their ubiquitin network downstream of the TNF receptor pathway.
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Affiliation(s)
- Kunjan Harit
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany
| | - Rituparna Bhattacharjee
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany
| | - Kai Matuschewski
- Department of Molecular Parasitology, Institute of Biology, Humboldt University, 10115, Berlin, Germany
| | - Jennifer Becker
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Dirk Schlüter
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany
| | - Gopala Nishanth
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany.
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17
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Sallam M, Wilson PW, Andersson B, Schmutz M, Benavides C, Dominguez-Gasca N, Sanchez-Rodriguez E, Rodriguez-Navarro AB, Dunn IC, De Koning DJ, Johnsson M. Genetic markers associated with bone composition in Rhode Island Red laying hens. Genet Sel Evol 2023; 55:44. [PMID: 37386416 DOI: 10.1186/s12711-023-00818-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Bone damage has welfare and economic impacts on modern commercial poultry and is known as one of the major challenges in the poultry industry. Bone damage is particularly common in laying hens and is probably due to the physiological link between bone and the egg laying process. Previous studies identified and validated quantitative trait loci (QTL) for bone strength in White Leghorn laying hens based on several measurements, including bone composition measurements on the cortex and medulla of the tibia bone. In a previous pedigree-based analysis, bone composition measurements showed heritabilities ranging from 0.18 to 0.41 and moderate to strong genetic correlations with tibia strength and density. Bone composition was measured using infrared spectroscopy and thermogravimetry. The aim of this study was to combine these bone composition measurements with genotyping data via a genome-wide association study (GWAS) to investigate genetic markers that contribute to genetic variance in bone composition in Rhode Island Red laying hens. In addition, we investigated the genetic correlations between bone composition and bone strength. RESULTS We found novel genetic markers that are significantly associated with cortical lipid, cortical mineral scattering, medullary organic matter, and medullary mineralization. Composition of the bone organic matter showed more significant associations than bone mineral composition. We also found interesting overlaps between the GWAS results for tibia composition traits, particularly for cortical lipid and tibia strength. Bone composition measurements by infrared spectroscopy showed more significant associations than thermogravimetry measurements. Based on the results of infrared spectroscopy, cortical lipid showed the highest genetic correlations with tibia density, which was negative (- 0.20 ± 0.04), followed by cortical CO3/PO4 (0.18 ± 0.04). Based on the results of thermogravimetry, medullary organic matter% and mineral% showed the highest genetic correlations with tibia density (- 0.25 ± 0.04 and 0.25 ± 0.04, respectively). CONCLUSIONS This study detected novel genetic associations for bone composition traits, particularly those involving organic matter, that could be used as a basis for further molecular genetic investigations. Tibia cortical lipids displayed the strongest genetic associations of all the composition measurements, including a significantly high genetic correlation with tibia density and strength. Our results also highlighted that cortical lipid may be a key measurement for further avian bone studies.
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Affiliation(s)
- Moh Sallam
- Swedish University of Agricultural Sciences, 75651, Uppsala, Sweden.
| | - Peter W Wilson
- Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, Scotland, UK
| | | | | | - Cristina Benavides
- Departamento de Mineralogia y Petrologia, Universidad de Granada, 18002, Granada, Spain
| | | | | | | | - Ian C Dunn
- Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, Scotland, UK
| | | | - Martin Johnsson
- Swedish University of Agricultural Sciences, 75651, Uppsala, Sweden
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18
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Chen L, Li Y, Chen Y. KLHL7 promotes hepatocellular carcinoma progression and molecular therapy resistance by degrading RASA2. iScience 2023; 26:106914. [PMID: 37378318 PMCID: PMC10291331 DOI: 10.1016/j.isci.2023.106914] [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: 09/25/2022] [Revised: 12/27/2022] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common aggressive tumor with a poor prognosis, and patients often seem to be refractory to the use of therapeutic drugs. In this study, we found that the KLHL7 expression was upregulated in HCC that was associated with poor patient prognosis. KLHL7 has been found to promote HCC development in both in vitro and in vivo experiments. Mechanistically, RASA2, a RAS GAP, was identified as a substrate of KLHL7. Upregulation of KLHL7 by growth factors promotes K48-linked polyubiquitination of RASA2 for degradation via the proteasomal pathway. Our in vivo experiments revealed that inhibition of KLHL7 in combination with lenvatinib treatment resulted in efficient killing of HCC cells. Together, these findings demonstrate a role for KLHL7 in HCC and reveal a mechanism by which growth factors regulate the RAS-MAPK pathway. It represents a potential therapeutic target for HCC.
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Affiliation(s)
- Lin Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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19
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Kang J, Huang M, Li J, Zhang K, Zhu C, Liu S, Zhou Z, Wang T, Wang Z. Enterovirus D68 VP3 Targets the Interferon Regulatory Factor 7 To Inhibit Type I Interferon Response. Microbiol Spectr 2023; 11:e0413822. [PMID: 37125923 PMCID: PMC10269600 DOI: 10.1128/spectrum.04138-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/09/2023] [Indexed: 05/02/2023] Open
Abstract
Enterovirus D68 (EV-D68) is a globally emerging pathogen causing severe respiratory illnesses mainly in children. The protease from EV-D68 could impair type I interferon (IFN-I) production. However, the role of the EV-D68 structural protein in antagonizing host antiviral responses remains largely unknown. We showed that the EV-D68 structural protein VP3 interacted with IFN regulatory factor 7 (IRF7), and this interaction suppressed the phosphorylation and nuclear translocation of IRF7 and then repressed the transcription of IFN. Furthermore, VP3 inhibited the TNF receptor associated factor 6 (TRAF6)-induced ubiquitination of IRF7 by competitive interaction with IRF7. IRF7Δ305-503 showed much weaker interaction ability to VP3, and VP3Δ41-50 performed weaker interaction ability with IRF7. The VP3 from enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) was also found to interact with the IRF7 protein. These results indicate that the enterovirus structural protein VP3 plays a pivotal role in subverting host innate immune responses and may be a potential target for antiviral drug research. IMPORTANCE EV-D68 is a globally emerging pathogen that causes severe respiratory illnesses. Here, we report that EV-D68 inhibits innate immune responses by targeting IRF7. Further investigations revealed that the structural protein VP3 inhibited the TRAF6-induced ubiquitination of IRF7 by competitive interaction with IRF7. These results indicate that the control of IRF7 by VP3 may be a mechanism by which EV-D68 represses IFN-I production.
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Affiliation(s)
- Jun Kang
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Mengqian Huang
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Jinyu Li
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Keke Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Cheng Zhu
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Sihua Liu
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Zhenwei Zhou
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Tao Wang
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Zhiyun Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
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20
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Chen B, Hasan MM, Zhang H, Zhai Q, Waliullah ASM, Ping Y, Zhang C, Oyama S, Mimi MA, Tomochika Y, Nagashima Y, Nakamura T, Kahyo T, Ogawa K, Kaneda D, Yoshida M, Setou M. UBL3 Interacts with Alpha-Synuclein in Cells and the Interaction Is Downregulated by the EGFR Pathway Inhibitor Osimertinib. Biomedicines 2023; 11:1685. [PMID: 37371780 DOI: 10.3390/biomedicines11061685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Ubiquitin-like 3 (UBL3) acts as a post-translational modification (PTM) factor and regulates protein sorting into small extracellular vesicles (sEVs). sEVs have been reported as vectors for the pathology propagation of neurodegenerative diseases, such as α-synucleinopathies. Alpha-synuclein (α-syn) has been widely studied for its involvement in α-synucleinopathies. However, it is still unknown whether UBL3 interacts with α-syn, and is influenced by drugs or compounds. In this study, we investigated the interaction between UBL3 and α-syn, and any ensuing possible functional and pathological implications. We found that UBL3 can interact with α-syn by the Gaussia princeps based split luciferase complementation assay in cells and immunoprecipitation, while cysteine residues at its C-terminal, which are considered important as PTM factors for UBL3, were not essential for the interaction. The interaction was upregulated by 1-methyl-4-phenylpyridinium exposure. In drug screen results, the interaction was significantly downregulated by the treatment of osimertinib. These results suggest that UBL3 interacts with α-syn in cells and is significantly downregulated by epidermal growth factor receptor (EGFR) pathway inhibitor osimertinib. Therefore, the UBL3 pathway may be a new therapeutic target for α-synucleinopathies in the future.
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Affiliation(s)
- Bin Chen
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Md Mahmudul Hasan
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Hengsen Zhang
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Qing Zhai
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - A S M Waliullah
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Yashuang Ping
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Chi Zhang
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Soho Oyama
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Mst Afsana Mimi
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Yuna Tomochika
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Yu Nagashima
- Institute for Medical Photonics Research, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Shizuoka, Japan
| | - Tomohiko Nakamura
- Department of Neurology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Tomoaki Kahyo
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
| | - Kenji Ogawa
- Laboratory of Veterinary Epizootiology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa 252-0880, Kanagawa, Japan
| | - Daita Kaneda
- Choju Medical Institute, Fukushimura Hospital, Yamanaka-19-14 Noyoricho, Toyohashi 441-8124, Aichi, Japan
| | - Minoru Yoshida
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
- RIKEN Center for Sustainable Resource Science, Wako 351-0198, Saitama, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
- Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, 1-20-1 Handayama, Higashi-Ku, Hamamatsu 431-3192, Shizuoka, Japan
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21
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Lee J, Ha J, Kim JH, Seo D, Kim M, Lee Y, Park SS, Choi D, Park JS, Lee YJ, Yang S, Yang KM, Jung SM, Hong S, Koo SH, Bae YS, Kim SJ, Park SH. Peli3 ablation ameliorates acetaminophen-induced liver injury through inhibition of GSK3β phosphorylation and mitochondrial translocation. Exp Mol Med 2023; 55:1218-1231. [PMID: 37258579 PMCID: PMC10318043 DOI: 10.1038/s12276-023-01009-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/07/2023] [Accepted: 03/15/2023] [Indexed: 06/02/2023] Open
Abstract
The signaling pathways governing acetaminophen (APAP)-induced liver injury have been extensively studied. However, little is known about the ubiquitin-modifying enzymes needed for the regulation of APAP-induced liver injury. Here, we examined whether the Pellino3 protein, which has E3 ligase activity, is needed for APAP-induced liver injury and subsequently explored its molecular mechanism. Whole-body Peli3-/- knockout (KO) and adenovirus-mediated Peli3 knockdown (KD) mice showed reduced levels of centrilobular cell death, infiltration of immune cells, and biomarkers of liver injury, such as alanine aminotransferase (ALT) and aspartate aminotransferase (AST), upon APAP treatment compared to wild-type (WT) mice. Peli3 deficiency in primary hepatocytes decreased mitochondrial and lysosomal damage and reduced the mitochondrial reactive oxygen species (ROS) levels. In addition, the levels of phosphorylation at serine 9 in the cytoplasm and mitochondrial translocation of GSK3β were decreased in primary hepatocytes obtained from Peli3-/- KO mice, and these reductions were accompanied by decreases in JNK phosphorylation and mitochondrial translocation. Pellino3 bound more strongly to GSK3β compared with JNK1 and JNK2 and induced the lysine 63 (K63)-mediated polyubiquitination of GSK3β. In rescue experiments, the ectopic expression of wild-type Pellino3 in Peli3-/- KO hepatocytes restored the mitochondrial translocation of GSK3β, but this restoration was not obtained with expression of a catalytically inactive mutant of Pellino3. These findings are the first to suggest a mechanistic link between Pellino3 and APAP-induced liver injury through the modulation of GSK3β polyubiquitination.
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Affiliation(s)
- Jaewon Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jihoon Ha
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jun-Hyeong Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- KoBio Labs, Seongnam, 13488, Republic of Korea
| | - Dongyeob Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minbeom Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yerin Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seong Shil Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Dahee Choi
- Department of Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Jin Seok Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Young Jae Lee
- Department of Biochemistry, Gachon University School of Medicine, Incheon, 21999, Republic of Korea
| | - Siyoung Yang
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | | | - Su Myung Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Suntaek Hong
- Department of Biochemistry, Gachon University School of Medicine, Incheon, 21999, Republic of Korea
| | - Seung-Hoi Koo
- Department of Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Yong-Soo Bae
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seong-Jin Kim
- Medpacto Inc., Seoul, 06668, Republic of Korea.
- GILO Institute, GILO Foundation, Seoul, 06668, Republic of Korea.
| | - Seok Hee Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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22
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Yao S, Xie M, Hu M, Cui X, Wu H, Li X, Hu P, Tong C, Yu X. Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1118339. [PMID: 37021309 PMCID: PMC10067767 DOI: 10.3389/fpls.2023.1118339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.
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Affiliation(s)
- Shengli Yao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - XiaoBo Cui
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haoming Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Xiaohua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Peng Hu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoli Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
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23
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Sui N, Zhang R, Jiang Y, Yu H, Xu G, Wang J, Zhu Y, Xie Z, Hu J, Jiang S. Nonstructural protein 2A2 from Duck hepatitis A virus type 1 inhibits interferon beta production by interaction with mitochondrial antiviral signaling protein and TANK-binding kinase 1. Vet Microbiol 2023; 280:109679. [PMID: 36822034 DOI: 10.1016/j.vetmic.2023.109679] [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: 09/13/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Type I interferon (IFN-I) is essential for the regulation of host-virus interactions, and viruses have evolved strategies to escape the host immune response. Duck hepatitis A virus type 1 (DHAV-1) causes severe liver necrosis and hemorrhage, neurological symptoms, and high mortality in ducklings. However, how DHAV-1 interacts with the duck innate immune system remains unclear. In this study, DHAV-1-encoded proteins were cloned, and DHAV-1 2A2 was shown to strongly suppress IFN-β-luciferase activity, triggered by Sendai virus and polyriboinosinic polyribocytidylic acid [poly(I:C)], along with the transcription of IFN-β and downstream antiviral genes, including OASL, PKR, and TNF-a. In addition, 2A2 interacts with the central adaptor proteins mitochondrial antiviral signaling (MAVS) and TANK-binding kinase 1 (TBK1) by its N-terminal 1-100 amino acids (aa), thus leading to the inhibition of IFN-β production. Importantly, the deletion of the N-terminal 1-100 aa region of 2A2 abolished inhibition of IFN-I production. Moreover, the transmembrane domain of the MAVS protein and the ubiquitin domain of TBK1 were demonstrated to be required for interaction with DHAV-1 2A2. These findings revealed a novel strategy by which DHAV-1 hijacks cellular immunosurveillance and provided new insights into controlling the disease.
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Affiliation(s)
- Nana Sui
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Ruihua Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Yue Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Honglei Yu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Guige Xu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Jingyu Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Yanli Zhu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Zhijing Xie
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China
| | - Jiaqing Hu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China; Shandong GreenBlue Biotechnology Co. Ltd. Economic development zone, Tai'an 271400, China.
| | - Shijin Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271018, China.
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24
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Cassidy K, Zhao H. Redefining the Scope of Targeted Protein Degradation: Translational Opportunities in Hijacking the Autophagy-Lysosome Pathway. Biochemistry 2023; 62:580-587. [PMID: 34569233 DOI: 10.1021/acs.biochem.1c00330] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The advent of multi-specific targeted protein degradation (TPD) therapies has made it possible to drug targets that have long been considered to be inaccessible. For this reason, the foremost TPD modalities - molecular glues and proteolysis targeting chimeras (PROTACs) -have been widely adopted and developed in therapeutic programs across the pharmaceutical and biotechnology industries. While there are many clear advantages to these two approaches, there are also blind spots. Specifically, PROTACs and molecular glues are inherently mechanistically analogous in that targets of both are degraded via the 26s proteasome; however, not all disease-relevant targets are suitable for ubiquitin proteasome system (UPS)-mediated degradation. The alternative mammalian protein degradation pathway, the autophagy-lysosome system (or ALS), is capable of degrading targets that elude the UPS such as long-lived proteins, insoluble protein aggregates, and even abnormal organelles. Emerging TPD strategies- such as ATTEC, AUTAC, and LYTAC- take advantage of the substrate diversity of the ALS to greatly expand the clinical utility of TPD. In this Perspective, we will discuss the array of current TPD modalities, with a focus on critical evaluation of these novel ALS-mediated degradation techniques.
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Affiliation(s)
- Katelyn Cassidy
- Discovery Biology, BioPharmaceuticals R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Heng Zhao
- Discovery Biology, BioPharmaceuticals R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
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25
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Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination. Chem 2023. [DOI: 10.1016/j.chempr.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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26
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Wang H, Li H, Gao W, Xie J. PrUb-EL: A hybrid framework based on deep learning for identifying ubiquitination sites in Arabidopsis thaliana using ensemble learning strategy. Anal Biochem 2022; 658:114935. [PMID: 36206844 DOI: 10.1016/j.ab.2022.114935] [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: 07/08/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022]
Abstract
Identification of ubiquitination sites is central to many biological experiments. Ubiquitination is a kind of post-translational protein modification (PTM). It is a key mechanism for increasing protein diversity and plays a vital role in regulating cell function. In recent years, many models have been developed to predict ubiquitination sites in humans, mice and yeast. However, few studies have predicted ubiquitination sites in Arabidopsis thaliana. In view of this, a deep network model named PrUb-EL is proposed to predict ubiquitination sites in Arabidopsis thaliana. Firstly, six features based on the protein sequence are extracted with amino acid index database (AAindex), dipeptide deviates from the expected mean (DDE), dipeptide composition (DPC), blocks substitution matrix (BLOSUM62), enhanced amino acid composition (EAAC) and binary encoding. Secondly, the synthetic minority over-sampling technique (SMOTE) is utilized to process the imbalanced data set. Then a new classifier named DG is presented, which includes Dense block, Residual block and Gated recurrent unit (GRU) block. Finally, each of six feature extraction methods is integrated into the DG model, and the ensemble learning strategy is used to gain the final prediction result. Experimental results show that PrUb-EL has good predictive ability with the accuracy (ACC) and area under the ROC curve (auROC) values of 91.00% and 97.70% using 5-fold cross-validation, respectively. Note that the values of ACC and auROC are 88.58% and 96.09% in the independent test, respectively. Compared with previous studies, our model has significantly improved performance thus it is an excellent method for identifying ubiquitination sites in Arabidopsis thaliana. The datasets and code used for the article are available at https://github.com/Tom-Wangy/PreUb-EL.git.
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Affiliation(s)
- Houqiang Wang
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China
| | - Hong Li
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China.
| | - Weifeng Gao
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China
| | - Jin Xie
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China
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27
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Ciaston I, Dobosz E, Potempa J, Koziel J. The subversion of toll-like receptor signaling by bacterial and viral proteases during the development of infectious diseases. Mol Aspects Med 2022; 88:101143. [PMID: 36152458 PMCID: PMC9924004 DOI: 10.1016/j.mam.2022.101143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/29/2022] [Accepted: 09/09/2022] [Indexed: 02/05/2023]
Abstract
Toll-like receptors (TLRs) are pattern recognition receptors (PRRs) that respond to pathogen-associated molecular patterns (PAMPs). The recognition of specific microbial ligands by TLRs triggers an innate immune response and also promotes adaptive immunity, which is necessary for the efficient elimination of invading pathogens. Successful pathogens have therefore evolved strategies to subvert and/or manipulate TLR signaling. Both the impairment and uncontrolled activation of TLR signaling can harm the host, causing tissue destruction and allowing pathogens to proliferate, thus favoring disease progression. In this context, microbial proteases are key virulence factors that modify components of the TLR signaling pathway. In this review, we discuss the role of bacterial and viral proteases in the manipulation of TLR signaling, highlighting the importance of these enzymes during the development of infectious diseases.
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Affiliation(s)
- Izabela Ciaston
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ewelina Dobosz
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Potempa
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Department of Oral Health and Systemic Disease, University of Louisville School of Dentistry, University of Louisville, Louisville, KY, USA.
| | - Joanna Koziel
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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28
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Huang N, Sun X, Li P, Liu X, Zhang X, Chen Q, Xin H. TRIM family contribute to tumorigenesis, cancer development, and drug resistance. Exp Hematol Oncol 2022; 11:75. [PMID: 36261847 PMCID: PMC9583506 DOI: 10.1186/s40164-022-00322-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
The tripartite-motif (TRIM) family represents one of the largest classes of putative single protein RING-finger E3 ubiquitin ligases. TRIM family is involved in a variety of cellular signaling transductions and biological processes. TRIM family also contributes to cancer initiation, progress, and therapy resistance, exhibiting oncogenic and tumor-suppressive functions in different human cancer types. Moreover, TRIM family members have great potential to serve as biomarkers for cancer diagnosis and prognosis. In this review, we focus on the specific mechanisms of the participation of TRIM family members in tumorigenesis, and cancer development including interacting with dysregulated signaling pathways such as JAK/STAT, PI3K/AKT, TGF-β, NF-κB, Wnt/β-catenin, and p53 hub. In addition, many studies have demonstrated that the TRIM family are related to tumor resistance; modulate the epithelial–mesenchymal transition (EMT) process, and guarantee the acquisition of cancer stem cells (CSCs) phenotype. In the end, we havediscussed the potential of TRIM family members for cancer therapeutic targets.
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Affiliation(s)
- Ning Huang
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.,PharmaLegacy Laboratories Co.,Ltd, Shengrong Road No.388, Zhangjiang High-tech Park, Pudong New Area, Shanghai, China
| | - Xiaolin Sun
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China
| | - Peng Li
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China
| | - Xin Liu
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.,PharmaLegacy Laboratories Co.,Ltd, Shengrong Road No.388, Zhangjiang High-tech Park, Pudong New Area, Shanghai, China
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.
| | - Qian Chen
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy & General Surgery of Minhang Hospital, Fudan University, Shanghai, 201203, China.
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29
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Yu K, Wang Y, Zheng Y, Liu Z, Zhang Q, Wang S, Zhao Q, Zhang X, Li X, Xu RH, Liu ZX. qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast. Nucleic Acids Res 2022; 51:D479-D487. [PMID: 36165955 PMCID: PMC9825568 DOI: 10.1093/nar/gkac820] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 09/14/2022] [Indexed: 01/29/2023] Open
Abstract
Post-translational modifications (PTMs) are critical molecular mechanisms that regulate protein functions temporally and spatially in various organisms. Since most PTMs are dynamically regulated, quantifying PTM events under different states is crucial for understanding biological processes and diseases. With the rapid development of high-throughput proteomics technologies, massive quantitative PTM proteome datasets have been generated. Thus, a comprehensive one-stop data resource for surfing big data will benefit the community. Here, we updated our previous phosphorylation dynamics database qPhos to the qPTM (http://qptm.omicsbio.info). In qPTM, 11 482 553 quantification events among six types of PTMs, including phosphorylation, acetylation, glycosylation, methylation, SUMOylation and ubiquitylation in four different organisms were collected and integrated, and the matched proteome datasets were included if available. The raw mass spectrometry based false discovery rate control and the recurrences of identifications among datasets were integrated into a scoring system to assess the reliability of the PTM sites. Browse and search functions were improved to facilitate users in swiftly and accurately acquiring specific information. The results page was revised with more abundant annotations, and time-course dynamics data were visualized in trend lines. We expected the qPTM database to be a much more powerful and comprehensive data repository for the PTM research community.
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Affiliation(s)
| | | | | | | | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Siyu Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaolong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaoxing Li
- Precision Medicine Institute, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rui-Hua Xu
- Correspondence may also be addressed to Rui-Hua Xu. Tel: +86 20 8734 3228; Fax: +86 20 8734 3392;
| | - Ze-Xian Liu
- To whom correspondence should be addressed. Tel: +86 20 8734 2025; Fax: +86 20 8734 2522;
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30
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Singh M, Singh A, Yadav N, Yadav DK. Current perspectives of ubiquitination and SUMOylation in abiotic stress tolerance in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:993194. [PMID: 36212351 PMCID: PMC9533872 DOI: 10.3389/fpls.2022.993194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Post-translational modification (PTM) is a critical and rapid mechanism to regulate all the major cellular processes through the modification of diverse protein substrates. Substrate-specific covalent attachment of ubiquitin and Small Ubiquitin-Like Modifier (SUMO) with the target proteins, known as ubiquitination and SUMOylation, respectively, are crucial PTMs that regulate almost every process in the cell by modulating the stability and fidelity of the proteins. Ubiquitination and SUMOylation play a very significant role to provide tolerance to the plants in adverse environmental conditions by activating/deactivating the pre-existing proteins to a great extent. We reviewed the importance of ubiquitination and SUMOylation in plants, implicating its prospects in various abiotic stress regulations. An exhaustive study of molecular mechanisms of ubiquitination and SUMOylation of plant proteins and their role will contribute to the understanding of physiology underlying mitigation of the abiotic stresses and survival in plants. It will be helpful to strategize the improvement of crops for abiotic stress tolerance.
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Affiliation(s)
- Madhavi Singh
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Ananya Singh
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Neelam Yadav
- Department of Botany, University of Allahabad, Prayagraj, India
| | - Dinesh Kumar Yadav
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
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31
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Sikander R, Arif M, Ghulam A, Worachartcheewan A, Thafar MA, Habib S. Identification of the ubiquitin–proteasome pathway domain by hyperparameter optimization based on a 2D convolutional neural network. Front Genet 2022; 13:851688. [PMID: 35937990 PMCID: PMC9355632 DOI: 10.3389/fgene.2022.851688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
The major mechanism of proteolysis in the cytosol and nucleus is the ubiquitin–proteasome pathway (UPP). The highly controlled UPP has an effect on a wide range of cellular processes and substrates, and flaws in the system can lead to the pathogenesis of a number of serious human diseases. Knowledge about UPPs provide useful hints to understand the cellular process and drug discovery. The exponential growth in next-generation sequencing wet lab approaches have accelerated the accumulation of unannotated data in online databases, making the UPP characterization/analysis task more challenging. Thus, computational methods are used as an alternative for fast and accurate identification of UPPs. Aiming this, we develop a novel deep learning-based predictor named “2DCNN-UPP” for identifying UPPs with low error rate. In the proposed method, we used proposed algorithm with a two-dimensional convolutional neural network with dipeptide deviation features. To avoid the over fitting problem, genetic algorithm is employed to select the optimal features. Finally, the optimized attribute set are fed as input to the 2D-CNN learning engine for building the model. Empirical evidence or outcomes demonstrates that the proposed predictor achieved an overall accuracy and AUC (ROC) value using 10-fold cross validation test. Superior performance compared to other state-of-the art methods for discrimination the relations UPPs classification. Both on and independent test respectively was trained on 10-fold cross validation method and then evaluated through independent test. In the case where experimentally validated ubiquitination sites emerged, we must devise a proteomics-based predictor of ubiquitination. Meanwhile, we also evaluated the generalization power of our trained modal via independent test, and obtained remarkable performance in term of 0.862 accuracy, 0.921 sensitivity, 0.803 specificity 0.803, and 0.730 Matthews correlation coefficient (MCC) respectively. Four approaches were used in the sequences, and the physical properties were calculated combined. When used a 10-fold cross-validation, 2D-CNN-UPP obtained an AUC (ROC) value of 0.862 predicted score. We analyzed the relationship between UPP protein and non-UPP protein predicted score. Last but not least, this research could effectively analyze the large scale relationship between UPP proteins and non-UPP proteins in particular and other protein problems in general and our research work might improve computational biological research. Therefore, we could utilize the latest features in our model framework and Dipeptide Deviation from Expected Mean (DDE) -based protein structure features for the prediction of protein structure, functions, and different molecules, such as DNA and RNA.
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Affiliation(s)
- Rahu Sikander
- School of Computer Science and Technology, Xidian University, Xi’an, China
- *Correspondence: Rahu Sikander, ; Apilak Worachartcheewan,
| | - Muhammad Arif
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Ali Ghulam
- Computerization and Network Section, Sindh Agriculture University, Tando Jam, Pakistan
| | - Apilak Worachartcheewan
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
- *Correspondence: Rahu Sikander, ; Apilak Worachartcheewan,
| | - Maha A. Thafar
- Department of Computer Science, Collage of Computer and Information Technology, Taif University, Taif, Saudi Arabia
| | - Shabana Habib
- Department of Information Technology, College of Computer, Qassim University, Buraydah, Saudi Arabia
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32
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Chen BR, Sleckman BP. The regulation of DNA end resection by chromatin response to DNA double strand breaks. Front Cell Dev Biol 2022; 10:932633. [PMID: 35912102 PMCID: PMC9335370 DOI: 10.3389/fcell.2022.932633] [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: 04/30/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) constantly arise upon exposure to genotoxic agents and during physiological processes. The timely repair of DSBs is important for not only the completion of the cellular functions involving DSBs as intermediates, but also the maintenance of genome stability. There are two major pathways dedicated to DSB repair: homologous recombination (HR) and non-homologous end joining (NHEJ). The decision of deploying HR or NHEJ to repair DSBs largely depends on the structures of broken DNA ends. DNA ends resected to generate extensive single-strand DNA (ssDNA) overhangs are repaired by HR, while those remaining blunt or minimally processed can be repaired by NHEJ. As the generation and repair of DSB occurs within the context of chromatin, the resection of broken DNA ends is also profoundly affected by the state of chromatin flanking DSBs. Here we review how DNA end resection can be regulated by histone modifications, chromatin remodeling, and the presence of ssDNA structure through altering the accessibility to chromatin and the activity of pro- and anti-resection proteins.
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Affiliation(s)
- Bo-Ruei Chen
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Bo-Ruei Chen,
| | - Barry P. Sleckman
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
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33
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Salari S, Bamorovat M, Sharifi I, Almani PGN. Global distribution of treatment resistance gene markers for leishmaniasis. J Clin Lab Anal 2022; 36:e24599. [PMID: 35808933 PMCID: PMC9396204 DOI: 10.1002/jcla.24599] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/19/2022] [Accepted: 06/28/2022] [Indexed: 01/02/2023] Open
Abstract
Background Pentavalent antimonials (Sb(V)) such as meglumine antimoniate (Glucantime®) and sodium stibogluconate (Pentostam®) are used as first‐line treatments for leishmaniasis, either alone or in combination with second‐line drugs such as amphotericin B (Amp B), miltefosine (MIL), methotrexate (MTX), or cryotherapy. Therapeutic aspects of these drugs are now challenged because of clinical resistance worldwide. Methods We reviewedthe recent original studies were assessed by searching in electronic databases such as Scopus, Pubmed, Embase, and Web of Science. Results Studies on molecular biomarkers involved in drug resistance are essential for monitoring the disease. We reviewed genes and mechanisms of resistance to leishmaniasis, and the geographical distribution of these biomarkers in each country has also been thoroughly investigated. Conclusion Due to the emergence of resistant genes mainly in anthroponotic Leishmania species such as L. donovani and L. tropica, as the causative agents of ACL and AVL, respectively, selection of an appropriate treatment modality is essential. Physicians should be aware of the presence of such resistance for the selection of proper treatment modalities in endemic countries.
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Affiliation(s)
- Samira Salari
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Bamorovat
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Iraj Sharifi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
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34
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Lan W, Qiu Y, Xu Y, Liu Y, Miao Y. Ubiquitination and Ubiquitin-Like Modifications as Mediators of Alternative Pre-mRNA Splicing in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:869870. [PMID: 35646014 PMCID: PMC9134077 DOI: 10.3389/fpls.2022.869870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Alternative splicing (AS) is a common post-transcriptional regulatory process in eukaryotes. AS has an irreplaceable role during plant development and in response to environmental stress as it evokes differential expression of downstream genes or splicing factors (e.g., serine/arginine-rich proteins). Numerous studies have reported that loss of AS capacity leads to defects in plant growth and development, and induction of stress-sensitive phenotypes. A role for post-translational modification (PTM) of AS components has emerged in recent years. These modifications are capable of regulating the activity, stability, localization, interaction, and folding of spliceosomal proteins in human cells and yeast, indicating that PTMs represent another layer of AS regulation. In this review, we summarize the recent reports concerning ubiquitin and ubiquitin-like modification of spliceosome components and analyze the relationship between spliceosome and the ubiquitin/26S proteasome pathway in plants. Based on the totality of the evidence presented, we further speculate on the roles of protein ubiquitination mediated AS in plant development and environmental response.
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35
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Zhao S, Zhang C, Xu J, Liu S, Yu L, Chen S, Wen H, Li Z, Liu N. Dppa3 facilitates self-renewal of embryonic stem cells by stabilization of pluripotent factors. Stem Cell Res Ther 2022; 13:169. [PMID: 35477484 PMCID: PMC9044575 DOI: 10.1186/s13287-022-02846-8] [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: 09/14/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Developmental pluripotency-associated 3 (Dppa3, also called Stella or PGC7) is a principal maternal protein specially expressed in pre-implantation embryos, embryonic stem cells (ES cells) and primordial germ cells (PGCs). It plays critical role in the regulating of DNA methylation in zygotes and oocytes. However, the effect of Dppa3 in ES cells on the stability of proteins is still unclear. METHODS In this study, we first identified the potential interacting proteins with Dppa3 using immunoprecipitation-mass spectrometry (IP-MS). After GO analysis, we further constructed Dppa3-silenced ES cells and ES cell lines overexpressing with different lengths of Dppa3 to explore the mechanisms of Dppa3 on protein stability. RESULTS IP-MS results showed that Dppa3 interacted with quite a few subunits of 26S proteasome. Full length of Dppa3 stabilized Uhrf1 and Nanog by inhibiting its degradation. Silencing Dppa3 promoted degradation of Nanog protein. CONCLUSIONS Our results indicated that Dppa3 safeguard the stability of Uhrf1 and Nanog by inhibiting proteasome-associated degradation in ES cells. These findings shed light on new function of Dppa3 in maintaining stability of proteins and provides a valuable resource for understanding the roles of Dppa3 in embryonic stem cells.
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Affiliation(s)
- Shuang Zhao
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Chuanyu Zhang
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Jia Xu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Siying Liu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Lu Yu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Shang Chen
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Hang Wen
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Zongjin Li
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Na Liu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China. .,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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36
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Park ES, Dezhbord M, Lee AR, Kim KH. The Roles of Ubiquitination in Pathogenesis of Influenza Virus Infection. Int J Mol Sci 2022; 23:ijms23094593. [PMID: 35562987 PMCID: PMC9105177 DOI: 10.3390/ijms23094593] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 01/14/2023] Open
Abstract
The ubiquitin system denotes a potent post-translational modification machinery that is capable of activation or deactivation of target proteins through reversible linkage of a single ubiquitin or ubiquitin chains. Ubiquitination regulates major cellular functions such as protein degradation, trafficking and signaling pathways, innate immune response, antiviral defense, and virus replication. The RNA sensor RIG-I ubiquitination is specifically induced by influenza A virus (IAV) to activate type I IFN production. Influenza virus modulates the activity of major antiviral proteins in the host cell to complete its full life cycle. Its structural and non-structural proteins, matrix proteins and the polymerase complex can regulate host immunity and antiviral response. The polymerase PB1-F2 of mutated 1918 IAV, adapts a novel IFN antagonist function by sending the DDX3 into proteasomal degradation. Ultimately the fate of virus is determined by the outcome of interplay between viral components and host antiviral proteins and ubiquitination has a central role in the encounter of virus and its host cell.
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Affiliation(s)
- Eun-Sook Park
- Institute of Biomedical Science and Technology, School of Medicine, Konkuk University, Seoul 05029, Korea;
| | - Mehrangiz Dezhbord
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
| | - Ah Ram Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
| | - Kyun-Hwan Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
- Correspondence: ; Tel.: +82-31-299-6126
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37
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Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022; 22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 204] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition.
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Affiliation(s)
- Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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38
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Li W, Jones K, Burke TJ, Hossain MA, Lariscy L. Epigenetic Regulation of Nucleotide Excision Repair. Front Cell Dev Biol 2022; 10:847051. [PMID: 35465333 PMCID: PMC9023881 DOI: 10.3389/fcell.2022.847051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.
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Abstract
Autophagy is an important life phenomenon in eukaryotic cells. Its main role is to remove and degrade its damaged organelles and excess biological macromolecules, and use degradation products to provide energy and rebuild the cell structure, playing an important role in maintaining cell homeostasis and cell life activities. Mitophagy is a form of macroautophagy. It has the beneficial effect of eliminating damaged mitochondria, thereby maintaining the integrity of the mitochondrial pool. Autophagy and mitophagy have a dual role in the development of cancer. On one hand, autophagy and mitophagy can maintain the normal physiological function of cells. On the other hand, excessive autophagy and mitophagy can lead to diseases. The present review introduces the mechanisms of autophagy and mitophagy, and the main related proteins, and introduce the correlation with cancers, providing a basis for the treatment of cancers through the understanding of these proteins.
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Affiliation(s)
- Hong-Ming Xu
- Department of Orthopaedic Surgery, Affiliated Cixi Hospital of Wenzhou Medical University, Cixi, Ningbo, People's Republic of China
| | - Fei Hu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, People's Republic of China
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40
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Jiang Z, Zhao Q, Chen L, Luo Y, Shen L, Cao Z, Wang Q. UBR3 promotes inflammation and apoptosis via DUSP1/p38 pathway in the nucleus pulposus cells of patients with intervertebral disc degeneration. Hum Cell 2022; 35:792-802. [PMID: 35332432 DOI: 10.1007/s13577-022-00693-6] [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: 12/20/2021] [Accepted: 03/15/2022] [Indexed: 11/04/2022]
Abstract
Intervertebral disc disease (IDD) is a primary cause of low back pain, affecting 5% of individuals. Previous study have shown that dual-specificity (Thr/Tyr) phosphatase 1 (DUSP1) regulates p38 MAPK activity and DUSP1 level is regulated by ubiquitination. As an E3 ubiquitin-protein ligase, UBR3 has been shown to regulate a variety of biological processes through ubiquitination. However, the role of UBR3/DUSP1/p38 in IDD remains to be elucidated. In the current study, we found that UBR3 was significantly increased in the nucleus pulposus tissues of IDD patients and was correlated with IDD severity. Silencing UBR3 promoted the growth, inhibited apoptosis, and inhibited inflammation in primary NPCs. Mechanism study suggested that UBR3 exerted its effects through p38. Co-immunoprecipitation assay indicated that UBR3 promoted DUSP1 ubiquitination. Overexpression of DUSP1 reversed the effect of UBR3 overexpression. Our data also supported that UBR3 was positively correlated with p-p38, but negatively correlated with DUSP1 in IDD. In summary, UBR3 promotes inflammation and apoptosis via inhibiting the p38 signaling pathway by DUSP1 ubiquitination in the NPCs of IDD patients. These findings highlight the importance of UBR3/DUSP1/p38 signaling pathway in IDD and provide new insights for the prevention and treatment of IDD.
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Affiliation(s)
- Zhenhuan Jiang
- Department of Orthopaedics, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Qinghua Zhao
- Department of Orthopaedics, School of Medicine, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Liang Chen
- Department of Orthopaedics, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Yifeng Luo
- Department of Radiology, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Lei Shen
- Department of Orthopaedics, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Zhihong Cao
- Department of Radiology, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China.
| | - Qiang Wang
- Department of Orthopaedics, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China.
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41
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The Next Frontier: Translational Development of Ubiquitination, SUMOylation, and NEDDylation in Cancer. Int J Mol Sci 2022; 23:ijms23073480. [PMID: 35408841 PMCID: PMC8999128 DOI: 10.3390/ijms23073480] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 01/01/2023] Open
Abstract
Post-translational modifications of proteins ensure optimized cellular processes, including proteostasis, regulated signaling, cell survival, and stress adaptation to maintain a balanced homeostatic state. Abnormal post-translational modifications are associated with cellular dysfunction and the occurrence of life-threatening diseases, such as cancer and neurodegenerative diseases. Therefore, some of the frequently seen protein modifications have been used as disease markers, while others are targeted for developing specific therapies. The ubiquitin and ubiquitin-like post-translational modifiers, namely, small ubiquitin-like modifier (SUMO) and neuronal precursor cell-expressed developmentally down-regulated protein 8 (NEDD8), share several features, such as protein structures, enzymatic cascades mediating the conjugation process, and targeted amino acid residues. Alterations in the regulatory mechanisms lead to aberrations in biological processes during tumorigenesis, including the regulation of tumor metabolism, immunological modulation of the tumor microenvironment, and cancer stem cell stemness, besides many more. Novel insights into ubiquitin and ubiquitin-like pathways involved in cancer biology reveal a potential interplay between ubiquitination, SUMOylation, and NEDDylation. This review outlines the current understandings of the regulatory mechanisms and assay capabilities of ubiquitination, SUMOylation, and NEDDylation. It will further highlight the role of ubiquitination, SUMOylation, and NEDDylation in tumorigenesis.
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42
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Lospinoso Severini L, Bufalieri F, Infante P, Di Marcotullio L. Proteolysis-Targeting Chimera (PROTAC): Is the Technology Looking at the Treatment of Brain Tumors? Front Cell Dev Biol 2022; 10:854352. [PMID: 35242765 PMCID: PMC8886235 DOI: 10.3389/fcell.2022.854352] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/31/2022] [Indexed: 12/23/2022] Open
Abstract
Post-translational modifications, such as ubiquitylation, need to be tightly controlled to guarantee the accurate localization and activity of proteins. Ubiquitylation is a dynamic process primarily responsible for proteasome-mediated degradation of substrate proteins and crucial for both normal homeostasis and disease. Alterations in ubiquitylation lead to the upregulation of oncoproteins and/or downregulation of tumor suppressors, thus concurring in tumorigenesis. PROteolysis-TArgeting Chimera (PROTAC) is an innovative strategy that takes advantage by the cell’s own Ubiquitin-Proteasome System (UPS). Each PROTAC molecule is composed by a ligand that recruits the target protein of interest (POI), a ligand specific for an E3 ubiquitin ligase enzyme, and a linker that connects these units. Upon binding to the POI, the PROTAC recruits the E3 inducing ubiquitylation-dependent proteasome degradation of the POI. To date, PROTAC technology has entered in clinical trials for several human cancers. Here, we will discuss the advantages and limitations of PROTACs development and safety considerations for their clinical application. Furthermore, we will review the potential of PROTAC strategy as therapeutic option in brain tumor, focusing on glioblastoma.
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Affiliation(s)
| | - Francesca Bufalieri
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy
| | - Paola Infante
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, Rome, Italy
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43
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Garg C, khan H, Kaur A, Singh TG, Sharma VK, Singh SK. Therapeutic Implications of Sonic Hedgehog Pathway in Metabolic Disorders: Novel Target for Effective Treatment. Pharmacol Res 2022; 179:106194. [DOI: 10.1016/j.phrs.2022.106194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022]
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44
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Wang BZ, Luo L, Vunjak-Novakovic G. RNA and Protein Delivery by Cell-Secreted and Bioengineered Extracellular Vesicles. Adv Healthc Mater 2022; 11:e2101557. [PMID: 34706168 PMCID: PMC8891029 DOI: 10.1002/adhm.202101557] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/28/2021] [Indexed: 12/22/2022]
Abstract
Extracellular vesicles (EVs) are carriers of biological signals through export and delivery of RNAs and proteins. Of increasing interest is the use of EVs as a platform for delivery of biomolecules. Preclinical studies have effectively used EVs to treat a number of diseases. Uniquely, endogenous machinery within cells can be manipulated in order to produce desirable loading of cargo within secreted EVs. In order to inform the development of such approaches, an understanding of the cellular mechanisms by which cargo is sorted to EVs is required. Here, the current knowledge of cargo sorting within EVs is reviewed. Here is given an overview of recent bioengineering approaches that leverage these advances. Methods of externally manipulating EV cargo are also discussed. Finally, a perspective on the current challenges of EVs as a drug delivery platform is offered. It is proposed that standardized bioengineering methods for therapeutic EV preparation will be required to create a well-defined clinical product.
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Affiliation(s)
- Bryan Z. Wang
- Department of Biomedical Engineering, 622 West 168th Street VC12-234, 10032, U.S.A
- Department of Medicine, 622 West 168th Street VC12-234, 10032, U.S.A
| | - Lori Luo
- Department of Medicine, 622 West 168th Street VC12-234, 10032, U.S.A
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, 622 West 168th Street VC12-234, 10032, U.S.A
- Department of Medicine, 622 West 168th Street VC12-234, 10032, U.S.A
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45
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Weidenbach K, Gutt M, Cassidy L, Chibani C, Schmitz RA. Small Proteins in Archaea, a Mainly Unexplored World. J Bacteriol 2022; 204:e0031321. [PMID: 34543104 PMCID: PMC8765429 DOI: 10.1128/jb.00313-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.
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Affiliation(s)
- Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Cynthia Chibani
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
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46
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Cancela F, Noceti O, Arbiza J, Mirazo S. Structural aspects of hepatitis E virus. Arch Virol 2022; 167:2457-2481. [PMID: 36098802 PMCID: PMC9469829 DOI: 10.1007/s00705-022-05575-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/04/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV) is a leading cause of acute hepatitis worldwide. Hepatitis E is an enterically transmitted zoonotic disease that causes large waterborne epidemic outbreaks in developing countries and has become an increasing public-health concern in industrialized countries. In this setting, the infection is usually acute and self-limiting in immunocompetent individuals, although chronic cases in immunocompromised patients have been reported, frequently associated with several extrahepatic manifestations. Moreover, extrahepatic manifestations have also been reported in immunocompetent individuals with acute HEV infection. HEV belongs to the alphavirus-like supergroup III of single-stranded positive-sense RNA viruses, and its genome contains three partially overlapping open reading frames (ORFs). ORF1 encodes a nonstructural protein with eight domains, most of which have not been extensively characterized: methyltransferase, Y domain, papain-like cysteine protease, hypervariable region, proline-rich region, X domain, Hel domain, and RNA-dependent RNA polymerase. ORF2 and ORF3 encode the capsid protein and a multifunctional protein believed to be involved in virion release, respectively. The novel ORF4 is only expressed in HEV genotype 1 under endoplasmic reticulum stress conditions, and its exact function has not yet been elucidated. Despite important advances in recent years, the biological and molecular processes underlying HEV replication remain poorly understood, primarily due to a lack of detailed information about the functions of the viral proteins and the mechanisms involved in host-pathogen interactions. This review summarizes the current knowledge concerning HEV proteins and their biological properties, providing updated detailed data describing their function and focusing in detail on their structural characteristics. Furthermore, we review some unclear aspects of the four proteins encoded by the ORFs, highlighting the current key information gaps and discussing potential novel experimental strategies for shedding light on those issues.
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Affiliation(s)
- Florencia Cancela
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ofelia Noceti
- grid.414402.70000 0004 0469 0889Programa Nacional de Trasplante Hepático y Unidad Docente Asistencial Centro Nacional de Tratamiento Hepatobiliopancreatico. Hospital Central de las Fuerzas Armadas, Montevideo, Uruguay
| | - Juan Arbiza
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Mirazo
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay ,Av. Alfredo Navarro 3051, PC 11600 Montevideo, Uruguay
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Chen Z, Liu X, Li F, Li C, Marquez-Lago T, Leier A, Webb GI, Xu D, Akutsu T, Song J. Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL. Methods Mol Biol 2022; 2499:205-219. [PMID: 35696083 DOI: 10.1007/978-1-0716-2317-6_11] [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] [Indexed: 06/15/2023]
Abstract
Among various types of protein post-translational modifications (PTMs), lysine PTMs play an important role in regulating a wide range of functions and biological processes. Due to the generation and accumulation of enormous amount of protein sequence data by ongoing whole-genome sequencing projects, systematic identification of different types of lysine PTM substrates and their specific PTM sites in the entire proteome is increasingly important and has therefore received much attention. Accordingly, a variety of computational methods for lysine PTM identification have been developed based on the combination of various handcrafted sequence features and machine-learning techniques. In this chapter, we first briefly review existing computational methods for lysine PTM identification and then introduce a recently developed deep learning-based method, termed MUscADEL (Multiple Scalable Accurate Deep Learner for lysine PTMs). Specifically, MUscADEL employs bidirectional long short-term memory (BiLSTM) recurrent neural networks and is capable of predicting eight major types of lysine PTMs in both the human and mouse proteomes. The web server of MUscADEL is publicly available at http://muscadel.erc.monash.edu/ for the research community to use.
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Affiliation(s)
- Zhen Chen
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Xuhan Liu
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Chen Li
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Tatiana Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Molecular and Translational Science, Faculty of Medicine, Hudson Institute of Medical Research, Monash University, Melbourne, VIC, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.
| | - Jiangning Song
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia.
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia.
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Zhou J, Ma X, Xu L, Liang Q, Mao J, Liu J, Wang M, Yuan J, Cong YS. Genomic profiling of the UFMylation family genes identifies UFSP2 as a potential tumour suppressor in colon cancer. Clin Transl Med 2021; 11:e642. [PMID: 34923774 PMCID: PMC8684770 DOI: 10.1002/ctm2.642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 01/16/2023] Open
Affiliation(s)
- Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
| | - Xiaohe Ma
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
| | - Lu Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
| | - Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
| | - Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
| | - Jiang Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
| | - Jiao Yuan
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medicine, Hangzhou Normal University, 2318 Yu hang tang Rd, Hangzhou, Zhejiang, 311121, China
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Wang J, Zhong W, Su H, Xu J, Yang D, Liu X, Zhu YZ. Histone Methyltransferase Dot1L Contributes to RIPK1 Kinase-Dependent Apoptosis in Cerebral Ischemia/Reperfusion. J Am Heart Assoc 2021; 10:e022791. [PMID: 34796721 PMCID: PMC9075366 DOI: 10.1161/jaha.121.022791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background Neuron apoptosis is a pivotal process for brain damage in cerebral ischemia. Dot1L (disruptor of telomeric silencing 1‐like) is only known histone H3K79 methyltransferase. It is not clear whether the role and mechanism of Dot1L on cerebral ischemia is related to regulate neuron apoptosis. Methods and Results We use a combination of mice middle cerebral artery occlusion stroke and neurons exposed to oxygen‐glucose deprivation followed by reoxygenation to investigate the role and mechanism of Dot1L on cerebral ischemia. We find knockdown or inhibition of Dot1L reversed ischemia‐induced neuronal apoptosis and attenuated the neurons injury treated by oxygen‐glucose deprivation followed by reoxygenation. Further, blockade of Dot1L prevents RIPK1 (receptor‐interacting protein kinase 1)‐dependent apoptosis through increased RIPK1 K63‐ubiquitylation and decreased formation of RIPK1/Caspase 8 complexes. In line with this, H3K79me3 enrichment in the promoter region of deubiquitin‐modifying enzyme A20 and deubiquitinase cylindromatosis gene promotes the increasing expression in oxygen‐glucose deprivation followed by reoxygenation ‐induced neuronal cells, on the contrary, oxygen‐glucose deprivation followed by reoxygenation decreases H3K79me3 level in the promoter region of ubiquitin‐modifying enzyme cIAP1 (cellular inhibitors of apoptosis proteins), and both these factors ultimately cause K63‐deubiquitination of RIPK1. Importantly, knockdown or inhibition of Dot1L in vivo attenuates apoptosis in middle cerebral artery occlusion mice and reduces the extent of middle cerebral artery occlusion ‐induced brain injury. Conclusions These data support for the first time, to our knowledge, that Dot1L regulating RIPK1 to the apoptotic death trigger contributes to cerebral ischemia injury. Therefore, targeting Dot1L serves as a new therapeutic strategy for ischemia stroke.
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Affiliation(s)
- Jinghuan Wang
- Department of Pharmacology School of PharmacyHuman Phenome InstituteFudan University Shanghai China
| | - Wen Zhong
- Department of Pharmacology School of PharmacyHuman Phenome InstituteFudan University Shanghai China
| | - Haibi Su
- Department of Pharmacology School of PharmacyHuman Phenome InstituteFudan University Shanghai China
| | - Jie Xu
- Department of Pharmacology School of PharmacyHuman Phenome InstituteFudan University Shanghai China
| | - Di Yang
- Department of Pharmacology School of PharmacyHuman Phenome InstituteFudan University Shanghai China
| | - Xinhua Liu
- Department of Pharmacology School of PharmacyHuman Phenome InstituteFudan University Shanghai China
| | - Yi Zhun Zhu
- Department of Pharmacology School of PharmacyHuman Phenome InstituteFudan University Shanghai China.,State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy Macau University of Science and Technology Macau China
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50
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Chen Y, Zhao Y, Yin Y, Jia X, Mao L. Mechanism of cargo sorting into small extracellular vesicles. Bioengineered 2021; 12:8186-8201. [PMID: 34661500 PMCID: PMC8806638 DOI: 10.1080/21655979.2021.1977767] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are special membranous structures released by almost every cell type that carry and protect some biomolecules from being degraded. They transport important signaling molecules involved in cell communication, migration, and numerous physiological processes. EVs can be categorized into two main types according to their size: i) small extracellular vesicles (sEVs), such as exosomes (30-150 nm), released from the fusion of multivesicular bodies (MVBs) with the plasma membrane, and ii) large EVs, such as microvesicles (100-1000 nm). These are no longer considered a waste product of cells, but regulators of intercellular communication, as they can transport specific repertoires of cargos, such as proteins, lipids, and nucleic acids to receptor cells to achieve cell-to-cell communication. This indicates the existence of different mechanisms, which controls the cargos sorting into EVs. This review mainly gives a description about the biological roles of the cargo and the sorting mechanisms of sEVs, especially exosomes.
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Affiliation(s)
- Yiwen Chen
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yuxue Zhao
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yiqian Yin
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaonan Jia
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
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