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Book ; Online: Reversible Ubiquitylation in Plant Biology

Genschik, Pascal / Goring, Daphne / Fu, Hongyong

2015

Abstract: ... and regulatorye in almost all aspects of cellular and organismal processes in plants. Its pervasive regula mechanisms.- ... signaling components, key metabolic enzymes, and critical mechanistic components of major cellular processes ... Reversible ubiquitylation plays an important regulatory role in almost all aspects of cellular and ...

Abstract	Reversible ubiquitylation plays an important regulatory role in almost all aspects of cellular and organismal processes in plants. Its pervasive regulatory role in plant biology is primarily due to the involvement of a large set of ubiquitin system constituents (encoded by approximately 6% Arabidopsis genome), the huge number of important cellular proteins targeted as substrates, and various drastic effects on the modified proteins. The major components of the ubiquitin system include a large set of enzymes and proteins involved in ubiquitin conjugation (E1s, E2s, and E3s) and deconjugation (deubiquitinases of different classes) and post ubiquitin conjugation components such as ubiquitin receptors, endocytic machineries, and 26S proteasome. The established substrates include transcriptional activators and repressors, signaling components, key metabolic enzymes, and critical mechanistic components of major cellular processes and regulatory mechanisms.- Post-translational modification of proteins by reversible ubiquitylation could drastically affects the modified proteins by proteolytic processing and turnover, altering catalytic activity, subcellular targeting, and protein-protein interaction. Continued efforts are being carried out to identify novel substrates critical for various cellular and organismal processes, to determine effects of reversible ubiquitylation on the modified substrates, to determine signaling determinants triggering reversible ubiquitylation of specific substrates, to illustrate individual components of the ubiquitin system for their in vivo functions and involved mechanistic roles, and to determine mechanistic roles of modification acting on critical components of major cellular processes and regulatory mechanisms. The aim of this special topic is to serve as a platform to report most recent advances on those above listed current research endeavors.- We welcome article types including original research, review, mini review, method, and perspective/opinion/hypothesis
Keywords	Botany ; Science (General)
Size	1 electronic resource (115 p.)
Publisher	Frontiers Media SA
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT020090907
ISBN	9782889194414 ; 2889194418
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article: Decoding histone ubiquitylation.

Chen, Jennifer J / Stermer, Dylan / Tanny, Jason C

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 968398

Abstract: ... the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division ... development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream ... Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and ...

Abstract	Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and lies at the heart of DNA damage repair signaling. The histone residues targeted for ubiquitylation are often highly conserved through evolution, and extensive functional studies of the enzymes that catalyze the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division, development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream consequences of these modifications have only recently begun to be appreciated on a molecular level. Here we review the structure and function of proteins that act as effectors or "readers" of histone ubiquitylation. We highlight lessons learned about how ubiquitin recognition lends specificity and function to intermolecular interactions in the context of transcription and DNA repair, as well as what this might mean for how we think about histone modifications more broadly.
Language	English
Publishing date	2022-08-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.968398
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Article ; Online: The regulation of necroptosis by ubiquitylation.

Chen, Yiliang / Ren, Wenqing / Wang, Qingsong / He, Yuan / Ma, Dan / Cai, Zhenyu

Apoptosis : an international journal on programmed cell death

2022 Volume 27, Issue 9-10, Page(s) 668–684

Abstract: ... inflammatory, infectious, and degenerative diseases. Ubiquitylation is a widespread ... pathway. An enhanced understanding of the ubiquitylation enzymes and regulatory proteins in necroptotic ... RIPK3 and the mixed lineage kinase domain-like protein, MLKL. Necroptosis must be strictly regulated ...

Abstract	Necroptosis is a programmed necrosis that is mediated by receptor-interacting protein kinases RIPK1, RIPK3 and the mixed lineage kinase domain-like protein, MLKL. Necroptosis must be strictly regulated to maintain normal tissue homeostasis, and dysregulation of necroptosis leads to the development of various inflammatory, infectious, and degenerative diseases. Ubiquitylation is a widespread post-translational modification that is essential for balancing numerous physiological processes. Over the past decade, considerable progress has been made in the understanding of the role of ubiquitylation in regulating necroptosis. Here, we will discuss the regulatory functions of ubiquitylation in necroptosis signaling pathway. An enhanced understanding of the ubiquitylation enzymes and regulatory proteins in necroptotic signaling pathway will be exploited for the development of new therapeutic strategies for necroptosis-related diseases.
MeSH term(s)	Apoptosis/genetics ; Humans ; Necroptosis/genetics ; Necrosis/genetics ; Protein Kinases/genetics ; Protein Kinases/metabolism ; Ubiquitination
Chemical Substances	Protein Kinases (EC 2.7.-)
Language	English
Publishing date	2022-08-08
Publishing country	Netherlands
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1452360-7
ISSN	1573-675X ; 1360-8185
ISSN (online)	1573-675X
ISSN	1360-8185
DOI	10.1007/s10495-022-01755-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Decoding histone ubiquitylation

Jennifer J. Chen / Dylan Stermer / Jason C. Tanny

Frontiers in Cell and Developmental Biology, Vol

2022 Volume 10

Abstract	Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and lies at the heart of DNA damage repair signaling. The histone residues targeted for ubiquitylation are often highly conserved through evolution, and extensive functional studies of the enzymes that catalyze the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division, development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream consequences of these modifications have only recently begun to be appreciated on a molecular level. Here we review the structure and function of proteins that act as effectors or “readers” of histone ubiquitylation. We highlight lessons learned about how ubiquitin recognition lends specificity and function to intermolecular interactions in the context of transcription and DNA repair, as well as what this might mean for how we think about histone modifications more broadly.
Keywords	histone modification readers ; ubiquitin signaling ; histone ubiquitylation ; PRC1 and PRC2 recruitment ; DOT1l ; 53BP1 ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Non-proteolytic ubiquitylation in cellular signaling and human disease.

Liao, Yongrong / Sumara, Izabela / Pangou, Evanthia

Communications biology

2022 Volume 5, Issue 1, Page(s) 114

Abstract: ... in cellular signaling and in disease-mediating processes. Our review, may advance our understanding of the non ... trafficking, DNA repair and cell cycle. Emerging evidence demonstrates that dysfunction of non-proteolytic ... the current knowledge and the latest concepts on how non-proteolytic ubiquitylation pathways are involved ...

Abstract	Ubiquitylation is one of the most common post-translational modifications (PTMs) of proteins that frequently targets substrates for proteasomal degradation. However it can also result in non-proteolytic events which play important functions in cellular processes such as intracellular signaling, membrane trafficking, DNA repair and cell cycle. Emerging evidence demonstrates that dysfunction of non-proteolytic ubiquitylation is associated with the development of multiple human diseases. In this review, we summarize the current knowledge and the latest concepts on how non-proteolytic ubiquitylation pathways are involved in cellular signaling and in disease-mediating processes. Our review, may advance our understanding of the non-degradative ubiquitylation process.
MeSH term(s)	DNA Repair ; Humans ; Protein Processing, Post-Translational ; Signal Transduction ; Ubiquitination
Language	English
Publishing date	2022-02-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03060-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ubiquitylation of PHYTOSULFOKINE RECEPTOR 1 modulates the defense response in tomato.

Hu, Zhangjian / Fang, Hanmo / Zhu, Changan / Gu, Shaohan / Ding, Shuting / Yu, Jingquan / Shi, Kai

Plant physiology

2023 Volume 192, Issue 3, Page(s) 2507–2522

Abstract: ... 1 (PSKR1) and initiates intercellular signaling to coordinate different physiological processes ... proteasome degradation pathway. Using multiple protein-protein interactions and ubiquitylation analyses ... ubiquitylation at Lys-748 and Lys-905 sites to control PSKR1 abundance ...

Abstract	Phytosulfokine (PSK) is a danger-associated molecular pattern recognized by PHYTOSULFOKINE RECEPTOR 1 (PSKR1) and initiates intercellular signaling to coordinate different physiological processes, especially in the defense response to the necrotrophic fungus Botrytis cinerea. The activity of peptide receptors is largely influenced by different posttranslational modifications, which determine intercellular peptide signal outputs. To date, the posttranslational modification to PHYTOSULFOKINE RECEPTOR 1 (PSKR1) remains largely unknown. Here, we show that tomato (Solanum lycopersicum) PSKR1 is regulated by the ubiquitin/proteasome degradation pathway. Using multiple protein-protein interactions and ubiquitylation analyses, we identified that plant U-box E3 ligases PUB12 and PUB13 interacted with PSKR1, among which PUB13 caused PSKR1 ubiquitylation at Lys-748 and Lys-905 sites to control PSKR1 abundance. However, this posttranslational modification was attenuated upon addition of PSK. Moreover, the disease symptoms observed in PUB13 knock-down and overexpression lines demonstrated that PUB13 significantly suppressed the PSK-initiated defense response. This highlights an important regulatory function for the turnover of a peptide receptor by E3 ligase-mediated ubiquitylation in the plant defense response.
MeSH term(s)	Arabidopsis Proteins/metabolism ; Plant Proteins/metabolism ; Receptors, Cell Surface/metabolism ; Receptors, Peptide/metabolism ; Signal Transduction/physiology ; Solanum lycopersicum/genetics ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
Chemical Substances	Arabidopsis Proteins ; Plant Proteins ; Receptors, Cell Surface ; Receptors, Peptide ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2023-03-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiad188
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Article ; Online: Ubiquitylation of RUNX3 by RNA-binding ubiquitin ligase MEX3C promotes tumorigenesis in lung adenocarcinoma.

He, Zelai / Zhang, Huijun / Xiao, Haibo / Zhang, Xiangyu / Xu, Hongbo / Sun, Ruifen / Li, Siwen

Journal of translational medicine

2024 Volume 22, Issue 1, Page(s) 216

Abstract: ... Knockdown of MEX3C dramatically decreased cell proliferation, migration, and invasion, and accelerated ... quantitative PCR. The involvement of MEX3C in the growth and metastasis of LUAD cells was measured by EdU assay ... and H1299 cells had significantly higher levels of MEX3C expression compared to control HBE cells ...

Abstract	Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer, but the early diagnosis rate is low. The RNA-binding ubiquitin ligase MEX3C promotes tumorigenesis in several cancers but its mechanism of action in LUAD is unclear. In this study, the biological activity of MEX3C was assessed in LUAD. MEX3C and RUNX3 mRNA levels in the tissues of LUAD patients were determined using reverse transcription‑quantitative PCR. The involvement of MEX3C in the growth and metastasis of LUAD cells was measured by EdU assay, CCK-8, colony formation, Transwell assay, TUNEL, and flow cytometry. Expression of apoptosis and epithelial-mesenchymal transition related proteins were determined using western blotting analysis. LUAD cells transfected with si-MEX3C were administered to mice subcutaneously to monitor tumor progression and metastasis. We found that MEX3C is strongly upregulated in LUAD tissue sections, and involved in proliferation and migration. A549 and H1299 cells had significantly higher levels of MEX3C expression compared to control HBE cells. Knockdown of MEX3C dramatically decreased cell proliferation, migration, and invasion, and accelerated apoptosis. Mechanistically, we demonstrate MEX3C induces ubiquitylation and degradation of tumor suppressor RUNX3. Moreover, RUNX3 transcriptionally represses Suv39H1, as revealed by RNA pull-down and chromatin immunoprecipitation assays. The in vivo mice model demonstrated that knockdown of MEX3C reduced LUAD growth and metastasis significantly. Collectively, we reveal a novel MEX3C-RUNX3-Suv39H1 signaling axis driving LUAD pathogenesis. Targeting MEX3C may represent a promising therapeutic strategy against LUAD.
MeSH term(s)	Animals ; Humans ; Mice ; Adenocarcinoma of Lung/genetics ; Adenocarcinoma of Lung/pathology ; Cell Line, Tumor ; Cell Movement/genetics ; Cell Proliferation/genetics ; Cell Transformation, Neoplastic/genetics ; Gene Expression Regulation, Neoplastic ; Ligases/genetics ; Ligases/metabolism ; Lung Neoplasms/pathology ; MicroRNAs/genetics ; RNA/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Ligases (EC 6.-) ; MEX3C protein, human ; MicroRNAs ; RNA (63231-63-0) ; RNA-Binding Proteins ; Ubiquitin ; Runx3 protein, human
Language	English
Publishing date	2024-02-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2118570-0
ISSN	1479-5876 ; 1479-5876
ISSN (online)	1479-5876
ISSN	1479-5876
DOI	10.1186/s12967-023-04700-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dopamine enhances recovery after traumatic brain injury through ubiquitylation and autophagic degradation of RIPK1.

Luo, Hui / Liu, Ning / Lin, Chao

Cell communication and signaling : CCS

2024 Volume 22, Issue 1, Page(s) 134

Abstract: ... that DRD1 signaling prevented neural death, suppressed neuroinflammation, and restored many TBI-related ... after traumatic brain injury (TBI), its function and specific underlying mechanisms of action remain ... lesion volume and brain water content were measured. On days 7-13, behavioral tests were performed ...

Abstract	Background: Although the neurotransmitter dopamine (DA) plays a crucial pathophysiologic role after traumatic brain injury (TBI), its function and specific underlying mechanisms of action remain unclear. Methods: Adult male mice underwent controlled cortical impact (CCI). We administered DA intraperitoneally to mice for 14 consecutive days, starting 8 h before CCI. On day 3 after brain injury, cortical lesion volume and brain water content were measured. On days 7-13, behavioral tests were performed. Results: Herein we report that DA inhibits neural death after injury, which is mediated via the dopamine D1 receptor (DRD1). Our results also showed that DRD1 signaling promotes RIPK1 ubiquitination via the E3 ubiquitin ligase Chip and then degradation through autophagy. Importantly, in vivo data revealed that DRD1 signaling prevented neural death, suppressed neuroinflammation, and restored many TBI-related functional sequelae. Conclusions: These data reveal a novel mechanism involving dopamine, and suggest that DRD1 activation positively regulates Chip-mediated ubiquitylation of RIPK1-leading to its autophagic degradation.
MeSH term(s)	Animals ; Male ; Mice ; Autophagy/drug effects ; Brain/metabolism ; Brain Injuries, Traumatic/drug therapy ; Brain Injuries, Traumatic/metabolism ; Dopamine/metabolism ; Dopamine/pharmacology ; Mice, Inbred C57BL ; Ubiquitination ; Receptor-Interacting Protein Serine-Threonine Kinases/drug effects ; Receptor-Interacting Protein Serine-Threonine Kinases/metabolism
Chemical Substances	Dopamine (VTD58H1Z2X) ; Ripk1 protein, mouse (EC 2.7.11.1) ; Receptor-Interacting Protein Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2024-02-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126315-2
ISSN	1478-811X ; 1478-811X
ISSN (online)	1478-811X
ISSN	1478-811X
DOI	10.1186/s12964-024-01515-y
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Article ; Online: Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties.

Prus, Gabriela / Satpathy, Shankha / Weinert, Brian T / Narita, Takeo / Choudhary, Chunaram

Cell

2024 Volume 187, Issue 11, Page(s) 2875–2892.e21

Abstract: Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell ... sites involved in proteasomal degradation and cellular signaling. Sites in structured protein regions ... However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified ...

Abstract	Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ubiquitylation site occupancy spans over four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and regulation of sites by proteasome inhibitors are strongly interrelated, and these attributes distinguish sites involved in proteasomal degradation and cellular signaling. Sites in structured protein regions exhibit longer half-lives and stronger upregulation by proteasome inhibitors than sites in unstructured regions. Importantly, we discovered a surveillance mechanism that rapidly and site-indiscriminately deubiquitylates all ubiquitin-specific E1 and E2 enzymes, protecting them against accumulation of bystander ubiquitylation. The work provides a systems-scale, quantitative view of ubiquitylation properties and reveals general principles of ubiquitylation-dependent governance.
MeSH term(s)	Ubiquitination ; Proteasome Endopeptidase Complex/metabolism ; Humans ; Ubiquitin/metabolism ; Ubiquitin-Conjugating Enzymes/metabolism ; Phosphorylation ; Proteasome Inhibitors/pharmacology ; Proteolysis
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Ubiquitin ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23) ; Proteasome Inhibitors
Language	English
Publishing date	2024-04-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2024.03.024
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: TRIM45 facilitates NASH-progressed HCC by promoting fatty acid synthesis via catalyzing FABP5 ubiquitylation.

Li, Xiaomian / He, Wenzhi / Chen, Xi / Zhang, Yangwenqing / Zhang, Jia / Liu, Fusheng / Li, Jinghua / Zhao, Dongli / Xia, Peng / Ma, Weijie / Wu, Tiangen / Wang, Haitao / Yuan, Yufeng

Oncogene

2024

Abstract: ... metabolism and oleic acid restored impaired proliferation and metastasis of TRIM45-deficient HCC cells. IP ... of which we focused on E3 ligase TRIM45. We found TRIM45 exacerbates HCC cells proliferation and metastasis in vitro ... diagnosis and therapy. In this study, we aim to identify shared transcriptional changes between NASH and HCC ...

Abstract	Non-alcoholic steatohepatitis (NASH) is rapidly surpassing viral hepatitis as the primary cause of hepatocellular carcinoma (HCC). However, understanding of NASH-progressed HCC remains poor, which might impede HCC diagnosis and therapy. In this study, we aim to identify shared transcriptional changes between NASH and HCC, of which we focused on E3 ligase TRIM45. We found TRIM45 exacerbates HCC cells proliferation and metastasis in vitro and in vivo. Further transcriptome analysis revealed TRIM45 predominantly affects fatty acid metabolism and oleic acid restored impaired proliferation and metastasis of TRIM45-deficient HCC cells. IP-tandem mass spectrum and FABP5 depriving experiment indicated that TRIM45 enhance fatty acid synthesis depending on FABP5 presence. Interestingly, we found TRIM45 directly added K33-type and K63-type poly-ubiquitin chains to FABP5 NLS domain, which ultimately promoted FABP5 nuclear translocation. Nuclear FABP5 interacted with PPARγ to facilitate downstream lipid synthesis gene expression. We observed TRIM45 accelerated NASH-to-HCC transition and exacerbated both NASH and NASH-HCC with the enhanced fatty acid production in vivo. Moreover, high concentration of fatty acid increased TRIM45 expression. The established mechanism was substantiated by gene expression correlation in TCGA-LIHC. Collectively, our research revealed a common lipid reprograming process in NASH and HCC and identified the cyclical amplification of the TRIM45-FABP5-PPARγ-fatty acid axis. This signaling pathway offers potential therapeutic targets for therapeutic intervention in NASH and NASH-progressed HCC.
Language	English
Publishing date	2024-05-16
Publishing country	England
Document type	Journal Article
ZDB-ID	639046-8
ISSN	1476-5594 ; 0950-9232
ISSN (online)	1476-5594
ISSN	0950-9232
DOI	10.1038/s41388-024-03056-7
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