51
|
Tang X, Dong H, Fang Z, Li J, Yang Q, Yao T, Pan Z. Ubiquitin-like modifier 1 ligating enzyme 1 relieves cisplatin-induced premature ovarian failure by reducing endoplasmic reticulum stress in granulosa cells. Reprod Biol Endocrinol 2022; 20:84. [PMID: 35610622 PMCID: PMC9128268 DOI: 10.1186/s12958-022-00956-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 05/14/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Ubiquitin-like modifier 1 ligating enzyme 1 (UFL1), the ligase of the UFMylation system, has recently been reported to be involved in apoptosis and endoplasmic reticulum stress (ER stress) in a variety of diseases. Premature ovarian failure (POF) is a gynecological disease that severely reduces the fertility of women, especially in female cancer patients receiving chemotherapy drugs. Whether UFL1 is involved in protection against chemotherapy-induced POF and its mechanism remain unclear. METHODS In this study, we examined the function of UFL1 in ovarian dysfunction and granulosa cell (GC) apoptosis induced by cisplatin through histological examination and cell viability analysis. We used western blotting, quantitative real-time PCR (qPCR) and immunofluorescence (IF) to detect the expression of UFL1 and the levels of ER stress specific markers. Enzyme linked immunosorbent assays were used to detect the levels of follicle-stimulating hormone (FSH) and estrogen (E2) in ovaries and GCs. In addition, we used infection with lentiviral particle suspensions to knock down and overexpress UFL1 in ovaries and GCs, respectively. RESULTS Our data showed that the expression of UFL1 was reduced in POF model ovaries, accompanied by ER stress. In vitro, cisplatin induced a stress-related increase in UFL1 expression in GCs and enhanced ER stress, which was aggravated by UFL1 knockdown and alleviated by UFL1 overexpression. Furthermore, UFL1 knockdown resulted in a decrease in ovarian follicle number, an increase in atretic follicles, and decreased expression of AMH and FSHR. Conversely, the overexpression of UFL1 reduced cisplatin-induced damage to the ovary in vitro. CONCLUSIONS Our research indicated that UFL1 regulates cisplatin-induced ER stress and apoptosis in GCs, and participates in protection against cisplatin-induced POF, providing a potential therapeutic target for the clinical prevention of chemotherapeutic drug-induced POF.
Collapse
Affiliation(s)
- Xiangting Tang
- Basic Medical College, Nanchang University, Nanchang, 330006, China
| | - Hao Dong
- The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Zhi Fang
- The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Jingyi Li
- Basic Medical College, Nanchang University, Nanchang, 330006, China
| | - Qi Yang
- Basic Medical College, Nanchang University, Nanchang, 330006, China
| | - Ting Yao
- Basic Medical College, Nanchang University, Nanchang, 330006, China
| | - Zezheng Pan
- Basic Medical College, Nanchang University, Nanchang, 330006, China.
| |
Collapse
|
52
|
Yan H, Xu JJ, Ali I, Zhang W, Jiang M, Li G, Teng Y, Zhu G, Cai Y. CDK5RAP3, an essential regulator of checkpoint, interacts with RPL26 and maintains the stability of cell growth. Cell Prolif 2022; 55:e13240. [PMID: 35509151 PMCID: PMC9136512 DOI: 10.1111/cpr.13240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/22/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE AND MATERIALS CDK5RAP3 (CDK5 regulatory subunit associated protein 3) was originally identified as a binding protein of CDK5. It is a crucial gene controlling biological functions, such as cell proliferation, apoptosis, invasion, and metastasis. Although previous studies have also shown that CDK5RAP3 is involved in a variety of signalling pathways, however, the mechanism of CDK5RAP3 remains largely undefined. This study utilized MEFs from conditional knockout mice to inhibit CDK5RAP3 and knockdown CDK5RAP3 in MCF7 to explore the role of CDK5RAP3 in cell growth, mitosis, and cell death. RESULTS CDK5RAP3 was found to be widely distributed throughout the centrosome, spindle, and endoplasmic reticulum, indicating that it is involved in regulating a variety of cellular activities. CDK5RAP3 deficiency resulted in instability of cell growth. CDK5RAP3 deficiency partly blocks the cell cycle in G2 /M by downregulating CDK1 (Cyclin-dependent kinase 1) and CCNB1 (Cyclin B1) expression levels. The cell proliferation rate was decreased, thereby slowing down the cell growth rate. Furthermore, the results showed that CDK5RAP3 interacts with RPL26 (ribosome protein L26) to regulate the mTOR pathway. CDK5RAP3 and RPL26 deficiency inhibited mTOR/p-mTOR protein and induce autophagy, resulting in an upregulation of the percentage of apoptosis, and the upregulated percentage of apoptosis also slowed cell growth. CONCLUSIONS Our experiments show that CDK5RAP3 interacts with RPL26 and maintains the stability of cell growth. It shows that CDK5RAP3 plays an important role in cell growth and can be used as the target of gene medicine.
Collapse
Affiliation(s)
- Hongchen Yan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jun-Jie Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ilyas Ali
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ming Jiang
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guiping Li
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Teng
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Guangxun Zhu
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
53
|
Liang Q, Jin Y, Xu S, Zhou J, Mao J, Ma X, Wang M, Cong YS. Human UFSP1 translated from an upstream near-cognate initiation codon functions as an active UFM1-specific protease. J Biol Chem 2022; 298:102016. [PMID: 35525273 PMCID: PMC9168615 DOI: 10.1016/j.jbc.2022.102016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a recently identified ubiquitin-like posttranslational modification with important biological functions. However, the regulatory mechanisms governing UFM1 modification of target proteins (UFMylation) and the cellular processes controlled by UFMylation remain largely unknown. It has been previously shown that a UFM1-specific protease (UFSP2) mediates the maturation of the UFM1 precursor and drives the de-UFMylation reaction. Furthermore, it has long been thought that UFSP1, an ortholog of UFSP2, is inactive in many organisms, including human, because it lacks an apparent protease domain when translated from the canonical start codon (445AUG). Here, we demonstrate using the combination of site-directed mutagenesis, CRISPR/Cas9–mediated genome editing, and mass spectrometry approaches that translation of human UFSP1 initiates from an upstream near-cognate codon, 217CUG, via eukaryotic translation initiation factor eIF2A-mediated translational initiation rather than from the annotated 445AUG, revealing the presence of a catalytic protease domain containing a Cys active site. Moreover, we show that both UFSP1 and UFSP2 mediate maturation of UFM1 and de-UFMylation of target proteins. This study demonstrates that human UFSP1 functions as an active UFM1-specific protease, thus contributing to our understanding of the UFMylation/de-UFMylation process.
Collapse
Affiliation(s)
- Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yaqi Jin
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Shiwen Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xiaohe Ma
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| |
Collapse
|
54
|
Snider DL, Park M, Murphy KA, Beachboard DC, Horner SM. Signaling from the RNA sensor RIG-I is regulated by ufmylation. Proc Natl Acad Sci U S A 2022; 119:e2119531119. [PMID: 35394863 PMCID: PMC9169834 DOI: 10.1073/pnas.2119531119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/28/2022] [Indexed: 01/23/2023] Open
Abstract
The RNA-binding protein RIG-I is a key initiator of the antiviral innate immune response. The signaling that mediates the antiviral response downstream of RIG-I is transduced through the adaptor protein MAVS and results in the induction of type I and III interferons (IFNs). This signal transduction occurs at endoplasmic reticulum (ER)–mitochondrial contact sites, to which RIG-I and other signaling proteins are recruited following their activation. RIG-I signaling is highly regulated to prevent aberrant activation of this pathway and dysregulated induction of IFN. Previously, we identified UFL1, the E3 ligase of the ubiquitin-like modifier conjugation system called ufmylation, as one of the proteins recruited to membranes at ER–mitochondrial contact sites in response to RIG-I activation. Here, we show that UFL1, as well as the process of ufmylation, promote IFN induction in response to RIG-I activation. We found that following RNA virus infection, UFL1 is recruited to the membrane-targeting protein 14–3-3ε and that this complex is then recruited to activated RIG-I to promote downstream innate immune signaling. Importantly, we found that 14–3-3ε has an increase in UFM1 conjugation following RIG-I activation. Additionally, loss of cellular ufmylation prevents the interaction of 14–3-3ε with RIG-I, which abrogates the interaction of RIG-I with MAVS and thus the downstream signal transduction that induces IFN. Our results define ufmylation as an integral regulatory component of the RIG-I signaling pathway and as a posttranslational control for IFN induction.
Collapse
Affiliation(s)
- Daltry L. Snider
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Moonhee Park
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Kristen A. Murphy
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Dia C. Beachboard
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Stacy M. Horner
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
- Department of Medicine, Duke University Medical Center, Durham, NC 27710
| |
Collapse
|
55
|
Reggiori F, Molinari M. ER-phagy: mechanisms, regulation and diseases connected to the lysosomal clearance of the endoplasmic reticulum. Physiol Rev 2022; 102:1393-1448. [PMID: 35188422 PMCID: PMC9126229 DOI: 10.1152/physrev.00038.2021] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
ER-phagy (reticulo-phagy) defines the degradation of portions of the endoplasmic reticulum (ER) within lysosomes or vacuoles. It is part of the self-digestion (i.e., auto-phagic) programs recycling cytoplasmic material and organelles, which rapidly mobilize metabolites in cells confronted with nutrient shortage. Moreover, selective clearance of ER subdomains participates to the control of ER size and activity during ER stress, the re-establishment of ER homeostasis after ER stress resolution and the removal of ER parts, in which aberrant and potentially cytotoxic material has been segregated. ER-phagy relies on the individual and/or concerted activation of the ER-phagy receptors, ER peripheral or integral membrane proteins that share the presence of LC3/Atg8-binding motifs in their cytosolic domains. ER-phagy involves the physical separation of portions of the ER from the bulk ER network, and their delivery to the endolysosomal/vacuolar catabolic district. This last step is accomplished by a variety of mechanisms including macro-ER-phagy (in which ER fragments are sequestered by double-membrane autophagosomes that eventually fuse with lysosomes/vacuoles), micro-ER-phagy (in which ER fragments are directly engulfed by endosomes/lysosomes/vacuoles), or direct fusion of ER-derived vesicles with lysosomes/vacuoles. ER-phagy is dysfunctional in specific human diseases and its regulators are subverted by pathogens, highlighting its crucial role for cell and organism life.
Collapse
Affiliation(s)
- Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, grid.4830.fUniversity of Groningen, Netherlands
| | - Maurizio Molinari
- Protein Folding and Quality Control, grid.7722.0Institute for Research in Biomedicine, Bellinzona, Switzerland
| |
Collapse
|
56
|
Cheng Y, Niu Z, Cai Y, Zhang W. Emerging role of UFMylation in secretory cells involved in the endocrine system by maintaining ER proteostasis. Front Endocrinol (Lausanne) 2022; 13:1085408. [PMID: 36743909 PMCID: PMC9894094 DOI: 10.3389/fendo.2022.1085408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/13/2022] [Indexed: 01/21/2023] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like molecule (UBL) discovered almost two decades ago, but our knowledge about the cellular and molecular mechanisms of this novel protein post-translational modification is still very fragmentary. In this review, we first summarize the core enzymes and factors involved in the UFMylation cascade, which, similar to ubiquitin, is consecutively catalyzed by UFM1-activating enzyme 5 (UBA5), UFM1-conjugating enzyme 1 (UFC1) and UFM1-specific ligase 1 (UFL1). Inspired by the substantial implications of UFM1 machinery in the secretory pathway, we next concentrate on the puzzling role of UFMylation in maintaining ER protein homeostasis, intending to illustrate the underlying mechanisms and future perspectives. At last, given a robust ER network is a hallmark of healthy endocrine secretory cells, we emphasize the function of UFM1 modification in physiology and pathology in the context of endocrine glands pancreas and female ovaries, aiming to provide precise insight into other internal glands of the endocrine system.
Collapse
Affiliation(s)
- Yun Cheng
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zikang Niu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Wei Zhang,
| |
Collapse
|
57
|
Park J, Lee J, Kim JH, Lee J, Park H, Lim C. ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD. Nucleic Acids Res 2021; 49:11294-11311. [PMID: 34551427 PMCID: PMC8565315 DOI: 10.1093/nar/gkab834] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
C9ORF72-derived dipeptide repeat proteins have emerged as the pathogenic cause of neurodegeneration in amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). However, the mechanisms underlying their expression are not fully understood. Here, we demonstrate that ZNF598, the rate-limiting factor for ribosome-associated quality control (RQC), co-translationally titrates the expression of C9ORF72-derived poly(GR) protein. A Drosophila genetic screen identified key RQC factors as potent modifiers of poly(GR)-induced neurodegeneration. ZNF598 overexpression in human neuroblastoma cells inhibited the nuclear accumulation of poly(GR) protein and decreased its cytotoxicity, whereas ZNF598 deletion had opposing effects. Poly(GR)-encoding sequences in the reporter RNAs caused translational stalling and generated ribosome-associated translation products, sharing molecular signatures with canonical RQC substrates. Furthermore, ZNF598 and listerin 1, the RQC E3 ubiquitin-protein ligase, promoted poly(GR) degradation via the ubiquitin-proteasome pathway. An ALS-relevant ZNF598R69C mutant displayed loss-of-function effects on poly(GR) expression, as well as on general RQC. Moreover, RQC function was impaired in C9-ALS patient-derived neurons, whereas lentiviral overexpression of ZNF598 lowered their poly(GR) expression and suppressed proapoptotic caspase-3 activation. Taken together, we propose that an adaptive nature of the RQC-relevant ZNF598 activity allows the co-translational surveillance to cope with the atypical expression of pathogenic poly(GR) protein, thereby acquiring a neuroprotective function in C9-ALS/FTD.
Collapse
Affiliation(s)
- Jumin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jongbo Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ji-Hyung Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Heeju Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| |
Collapse
|
58
|
Sheng L, Li J, Rao S, Yang Z, Huang Y. Cyclin-Dependent Kinase 5 Regulatory Subunit Associated Protein 3: Potential Functions and Implications for Development and Disease. Front Oncol 2021; 11:760429. [PMID: 34722315 PMCID: PMC8551632 DOI: 10.3389/fonc.2021.760429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Cyclin-dependent kinase 5 (CDK5) regulatory subunit associated protein 3 (CDK5RAP3, also named as C53 or LZAP) was initially identified as a binding protein of CDK5 activator p35. To date, CDK5RAP3 has been reported to interact with a range of proteins involved in cellular events ranging from cell cycle, apoptosis, and invasion to UFMylation modification and endoplasmic reticulum stress. Owing to its crucial roles in cellular processes, CDK5RAP3 is demonstrated to be not only an active participant in embryonic and mammalian tissue development, but also a key regulator in the onset and progress of human cancers such as head and neck squamous cell carcinoma, gastric cancer, hepatocellular cancer, lung cancer, kidney cancer and breast cancer. Notwithstanding, the detailed function of CDK5RAP3 and its mechanism remain poorly defined. Here, we briefly described a history of the discovery of CDK5RAP3, and systematically overviewed its gene structural and distribution features. We also focused on the known functions of this protein and its implications for embryogenesis and tissue development, as well as diseases especially carcinoma. This review may facilitate to understand the molecular and functional basis of CDK5RAP3 and its association with development and disease, and provide a reasonable idea for novel therapeutic opportunities targeting CDK5RAP3.
Collapse
Affiliation(s)
- Linna Sheng
- Department of Pathophysiology, Basic Medical College of Nanchang University, Nanchang, China.,Graduate College of Nanchang University, Nanchang, China
| | - Jiaxuan Li
- Nanchang Joint Program, Queen Mary School, Nanchang University, Nanchang, China
| | - Shengfang Rao
- Department of Nuclear Medicine, Nanchang University Hospital, Nanchang, China
| | - Zhijun Yang
- Department of Pathophysiology, Basic Medical College of Nanchang University, Nanchang, China
| | - Yonghong Huang
- Department of Pathophysiology, Basic Medical College of Nanchang University, Nanchang, China
| |
Collapse
|
59
|
Clavel M, Dagdas Y. Proteasome and selective autophagy: Brothers-in-arms for organelle quality control. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102106. [PMID: 34487948 DOI: 10.1016/j.pbi.2021.102106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Maintaining the integrity of organelles despite the cellular disturbances that arise during stress is essential for life. To ensure organelle proteostasis (protein homeostasis), plants have evolved multitiered quality control mechanisms that work together to repair or recycle the damaged organelles. Despite recent advances, our understanding of plant organelle quality control mechanisms is far from complete. Especially, the crosstalk between different quality control pathways remains elusive. Here, we highlight recent advances on organelle quality control, focusing on the targeted protein degradation pathways that maintain the homeostasis of the endoplasmic reticulum (ER), chloroplast, and mitochondria. We discuss how plant cells decide to employ different degradation pathways and propose tools that could be used to discover the missing components in organelle quality control.
Collapse
Affiliation(s)
- Marion Clavel
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| |
Collapse
|
60
|
Park J, Park J, Lee J, Lim C. The trinity of ribosome-associated quality control and stress signaling for proteostasis and neuronal physiology. BMB Rep 2021. [PMID: 34488933 PMCID: PMC8505234 DOI: 10.5483/bmbrep.2021.54.9.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Translating ribosomes accompany co-translational regulation of nascent polypeptide chains, including subcellular targeting, protein folding, and covalent modifications. Ribosome-associated quality control (RQC) is a co-translational surveillance mechanism triggered by ribosomal collisions, an indication of atypical translation. The ribosome-associated E3 ligase ZNF598 ubiquitinates small subunit proteins at the stalled ribosomes. A series of RQC factors are then recruited to dissociate and triage aberrant translation intermediates. Regulatory ribosomal stalling may occur on endogenous transcripts for quality gene expression, whereas ribosomal collisions are more globally induced by ribotoxic stressors such as translation inhibitors, ribotoxins, and UV radiation. The latter are sensed by ribosome-associated kinases GCN2 and ZAKα, activating integrated stress response (ISR) and ribotoxic stress response (RSR), respectively. Hierarchical crosstalks among RQC, ISR, and RSR pathways are readily detectable since the collided ribosome is their common substrate for activation. Given the strong implications of RQC factors in neuronal physiology and neurological disorders, the interplay between RQC and ribosome-associated stress signaling may sustain proteostasis, adaptively determine cell fate, and contribute to neural pathogenesis. The elucidation of underlying molecular principles in relevant human diseases should thus provide unexplored therapeutic opportunities.
Collapse
Affiliation(s)
- Jumin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongmin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| |
Collapse
|
61
|
Abstract
Ufmylation is a post-translational modification essential for regulating key cellular processes. A three-enzyme cascade involving E1, E2 and E3 is required for UFM1 attachment to target proteins. How UBA5 (E1) and UFC1 (E2) cooperatively activate and transfer UFM1 is still unclear. Here, we present the crystal structure of UFC1 bound to the C-terminus of UBA5, revealing how UBA5 interacts with UFC1 via a short linear sequence, not observed in other E1-E2 complexes. We find that UBA5 has a region outside the adenylation domain that is dispensable for UFC1 binding but critical for UFM1 transfer. This region moves next to UFC1’s active site Cys and compensates for a missing loop in UFC1, which exists in other E2s and is needed for the transfer. Overall, our findings advance the understanding of UFM1’s conjugation machinery and may serve as a basis for the development of ufmylation inhibitors. Ufmylation is a well-established ubiquitin-like protein modification, but its mechanism is largely unclear. Here, the authors present a crystal structure of the ufmylation-specific E1-E2 complex, revealing differences to the ubiquitination machinery and mechanistic details of the ufmylation process.
Collapse
|
62
|
Briere LC, Walker MA, High FA, Cooper C, Rogers CA, Callahan CJ, Ishimura R, Ichimura Y, Caruso PA, Sharma N, Brokamp E, Koziura ME, Mohammad SS, Dale RC, Riley LG, Phillips JA, Komatsu M, Sweetser DA. A description of novel variants and review of phenotypic spectrum in UBA5-related early epileptic encephalopathy. Cold Spring Harb Mol Case Stud 2021; 7:a005827. [PMID: 33811063 PMCID: PMC8208045 DOI: 10.1101/mcs.a005827] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/10/2021] [Indexed: 12/22/2022] Open
Abstract
Early infantile epileptic encephalopathy-44 (EIEE44, MIM: 617132) is a previously described condition resulting from biallelic variants in UBA5, a gene involved in a ubiquitin-like post-translational modification system called UFMylation. Here we report five children from four families with biallelic pathogenic variants in UBA5 All five children presented with global developmental delay, epilepsy, axial hypotonia, appendicular hypertonia, and a movement disorder, including dystonia in four. Affected individuals in all four families have compound heterozygous pathogenic variants in UBA5 All have the recurrent mild c.1111G > A (p.Ala371Thr) variant in trans with a second UBA5 variant. One patient has the previously described c.562C > T (p. Arg188*) variant, two other unrelated patients have a novel missense variant, c.907T > C (p.Cys303Arg), and the two siblings have a novel missense variant, c.761T > C (p.Leu254Pro). Functional analyses demonstrate that both the p.Cys303Arg variant and the p.Leu254Pro variants result in a significant decrease in protein function. We also review the phenotypes and genotypes of all 15 previously reported families with biallelic UBA5 variants, of which two families have presented with distinct phenotypes, and we describe evidence for some limited genotype-phenotype correlation. The overlap of motor and developmental phenotypes noted in our cohort and literature review adds to the increasing understanding of genetic syndromes with movement disorders-epilepsy.
Collapse
Affiliation(s)
- Lauren C Briere
- Department of Pediatrics, Division of Medical Genetics and Metabolism, and Center for Genomic Medicine, Massachusetts 02114, USA
| | - Melissa A Walker
- Department of Neurology, Division of Neurogenetics, Child Neurology, Massachusetts 02114, USA
| | - Frances A High
- Department of Pediatrics, Division of Medical Genetics and Metabolism, Massachusetts 02114, USA
| | - Cynthia Cooper
- Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Cassandra A Rogers
- Department of Pediatrics, Division of Medical Genetics and Metabolism, and Center for Genomic Medicine, Massachusetts 02114, USA
| | - Christine J Callahan
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Ryosuke Ishimura
- Department of Biochemistry, Niigata University School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Yoshinobu Ichimura
- Department of Biochemistry, Niigata University School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Paul A Caruso
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Mary E Koziura
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Shekeeb S Mohammad
- Kids Neuroscience Center & Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Russell C Dale
- Kids Neuroscience Center & Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and Children's Medical Research Institute, Westmead, New South Wales 2145, Australia
- Discipline of Child & Adolescent Health, University of Sydney, Sydney, New South Wales 2006, Australia
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
- Department of Physiology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - David A Sweetser
- Department of Pediatrics, Division of Medical Genetics and Metabolism, and Center for Genomic Medicine, Massachusetts 02114, USA
| |
Collapse
|
63
|
UFMylation inhibits the proinflammatory capacity of interferon-γ-activated macrophages. Proc Natl Acad Sci U S A 2021; 118:2011763118. [PMID: 33372156 DOI: 10.1073/pnas.2011763118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Macrophages activated with interferon-γ (IFN-γ) in combination with other proinflammatory stimuli, such as lipopolysaccharide or tumor necrosis factor-α (TNF-α), respond with transcriptional and cellular changes that enhance clearance of intracellular pathogens at the risk of damaging tissues. IFN-γ effects must therefore be carefully balanced with inhibitory mechanisms to prevent immunopathology. We performed a genome-wide CRISPR knockout screen in a macrophage cell line to identify negative regulators of IFN-γ responses. We discovered an unexpected role of the ubiquitin-fold modifier (Ufm1) conjugation system (herein UFMylation) in inhibiting responses to IFN-γ and lipopolysaccharide. Enhanced IFN-γ activation in UFMylation-deficient cells resulted in increased transcriptional responses to IFN-γ in a manner dependent on endoplasmic reticulum stress responses involving Ern1 and Xbp1. Furthermore, UFMylation in myeloid cells is required for resistance to influenza infection in mice, indicating that this pathway modulates in vivo responses to infection. These findings provide a genetic roadmap for the regulation of responses to a key mediator of cellular immunity and identify a molecular link between the UFMylation pathway and immune responses.
Collapse
|
64
|
Yip MCJ, Shao S. Detecting and Rescuing Stalled Ribosomes. Trends Biochem Sci 2021; 46:731-743. [PMID: 33966939 DOI: 10.1016/j.tibs.2021.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Ribosomes that stall inappropriately during protein synthesis harbor proteotoxic components linked to cellular stress and neurodegenerative diseases. Molecular mechanisms that rescue stalled ribosomes must selectively detect rare aberrant translational complexes and process the heterogeneous components. Ribosome-associated quality control pathways eliminate problematic messenger RNAs and nascent proteins on stalled translational complexes. In addition, recent studies have uncovered general principles of stall recognition upstream of quality control pathways and fail-safe mechanisms that ensure nascent proteome integrity. Here, we discuss developments in our mechanistic understanding of the detection and rescue of stalled ribosomal complexes in eukaryotes.
Collapse
Affiliation(s)
- Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
65
|
Molinari M. ER-phagy responses in yeast, plants, and mammalian cells and their crosstalk with UPR and ERAD. Dev Cell 2021; 56:949-966. [PMID: 33765438 DOI: 10.1016/j.devcel.2021.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 12/24/2022]
Abstract
ER-phagy, literally endoplasmic reticulum (ER)-eating, defines the constitutive or regulated clearance of ER portions within metazoan endolysosomes or yeast and plant vacuoles. The advent of electron microscopy led to the first observations of ER-phagy over 60 years ago, but only recently, with the discovery of a set of regulatory proteins named ER-phagy receptors, has it been dissected mechanistically. ER-phagy receptors are activated by a variety of pleiotropic and ER-centric stimuli. They promote ER fragmentation and engage luminal, membrane-bound, and cytosolic factors, eventually driving lysosomal clearance of select ER domains along with their content. After short historical notes, this review introduces the concept of ER-phagy responses (ERPRs). ERPRs ensure lysosomal clearance of ER portions expendable during nutrient shortage, nonfunctional, present in excess, or containing misfolded proteins. They cooperate with unfolded protein responses (UPRs) and with ER-associated degradation (ERAD) in determining ER size, function, and homeostasis.
Collapse
Affiliation(s)
- Maurizio Molinari
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
66
|
Kulsuptrakul J, Wang R, Meyers NL, Ott M, Puschnik AS. A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection. Cell Rep 2021; 34:108859. [PMID: 33730579 PMCID: PMC8893346 DOI: 10.1016/j.celrep.2021.108859] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Hepatitis A virus (HAV) is a positive-sense RNA virus causing acute inflammation of the liver. Here, using a genome-scale CRISPR screen, we provide a comprehensive picture of the cellular factors that are exploited by HAV. We identify genes involved in sialic acid/ganglioside biosynthesis and members of the eukaryotic translation initiation factor complex, corroborating their putative roles for HAV. Additionally, we uncover all components of the cellular machinery for UFMylation, a ubiquitin-like protein modification. We show that HAV translation specifically depends on UFM1 conjugation of the ribosomal protein RPL26. Furthermore, we find that components related to the yeast Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex are required for viral translation independent of controlling viral poly(A) tails or RNA stability. Finally, we demonstrate that pharmacological inhibition of the TRAMP-like complex decreases HAV replication in hepatocyte cells and human liver organoids, thus providing a strategy for host-directed therapy of HAV infection. To identify host factors required for the infection with hepatitis A virus, Kulsuptrakul et al. conducted a genome-wide CRISPR knockout screen in human hepatocytes. They reveal that UFMylation of the ribosomal protein RPL26 as well as the polyadenylation activity of a TRAMP-like complex enhance viral translation.
Collapse
Affiliation(s)
| | - Ruofan Wang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | |
Collapse
|
67
|
Cao Z, Li S, Liu H, Li W, Sun Y, Li Z, Jia M, Su M. The UFSP2/UFMylation Pathway Is Involved in Silica-Induced Pulmonary Injury. DNA Cell Biol 2021; 40:589-594. [PMID: 33600261 DOI: 10.1089/dna.2020.6421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Silicosis is an irreversible occupational pulmonary disease that is characterized as progressed pulmonary fibrosis. In this study, we investigated the changes of UFSP2 and the related UFMylation in silica-induced pulmonary injury mice models. The experimental silicosis models were prepared by intratracheal injection of silica particles, and the lung samples were harvested at the first or the seventh day after treatment. We found that the UFSP2 expression in the 1-day models was comparable, whereas it was upregulated in the 7-day models. Consistently, the UFMylation in the lung tissues of the 7-day models was activated. In addition, we observed the CADM2, an adhesion molecule, was reported to associate with epithelial-mesenchymal transition, was upregulated in the lungs of 7-day models. In contrast, it remained comparable in the 1-day models. Our data indicated that the UFSP2/UFMylation pathway and the CADM2 might be involved in the silica-induced pulmonary injury.
Collapse
Affiliation(s)
- Zhenju Cao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Shanshan Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Hangqi Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Wendi Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Yi Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Zichen Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Mei Jia
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Ming Su
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| |
Collapse
|
68
|
Witting KF, Mulder MP. Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma. Biomolecules 2021; 11:biom11020255. [PMID: 33578803 PMCID: PMC7916544 DOI: 10.3390/biom11020255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Post-translational modification with Ubiquitin-like proteins represents a complex signaling language regulating virtually every cellular process. Among these post-translational modifiers is Ubiquitin-fold modifier (UFM1), which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Originally identified to be involved embryonic development, its biological function remains enigmatic. Recent research reveals that UFM1 regulates a variety of cellular events ranging from DNA repair to autophagy and ER stress response implicating its involvement in a variety of diseases. Given the contribution of UFM1 to numerous pathologies, the enzymes of the UFM1 cascade represent attractive targets for pharmacological inhibition. Here we discuss the current understanding of this cryptic post-translational modification especially its contribution to disease as well as expand on the unmet needs of developing chemical and biochemical tools to dissect its role.
Collapse
|
69
|
Qazi IH, Cao Y, Yang H, Angel C, Pan B, Zhou G, Han H. Impact of Dietary Selenium on Modulation of Expression of Several Non-Selenoprotein Genes Related to Key Ovarian Functions, Female Fertility, and Proteostasis: a Transcriptome-Based Analysis of the Aging Mice Ovaries. Biol Trace Elem Res 2021; 199:633-648. [PMID: 32430805 DOI: 10.1007/s12011-020-02192-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/10/2020] [Indexed: 02/07/2023]
Abstract
Female reproductive (ovarian) aging is characterized by a marked decline in quantity and quality of follicles and oocytes, as well as alterations in the surrounding ovarian stroma. In our previous report, we have shown that dietary selenium (Se) insufficiency and supplementation differentially impacted the reproductive efficiency in aging mice; however, the precise understanding of such modulation is still incomplete. In the present study, we sought to determine the impact of low (mildly low level) and moderately high (medium level) Se diets on expression profile of non-selenoprotein genes in the ovaries of aging mice. For this purpose, the aged mice were divided in two groups and fed either a low Se (Se-L; 0.08 mg Se/kg) diet or a moderately high Se (Se-M; 0.33 mg Se/kg) diet. RNA-seq analysis revealed that a total of 168 genes were differentially expressed between the two groups. From these, 72 and 96 differentially expressed genes (DEGs) were found to be upregulated and downregulated, respectively. Gene Ontology (GO) and pathways enrichment (KEGG) analyses revealed that these DEGs were enriched in several key GO terms and biological pathways including PI3K-Akt signaling pathway, steroid hormone biosynthesis, signaling pathways regulating pluripotency of stem cells, Hippo signaling pathway, ovarian steroidogenesis, and Wnt signaling pathway. Further filtering of RNA-seq data revealed that several DEGs such as Star, Hsd3b6, Scd1, Bmp7, Aqp8, Gas1, Fzd1, and Wwc1 were implicated in key ovarian- and fertility-related functions. In addition, some of the DEGs were related to ER homeostasis and/or proteostasis. These results highlight that dietary low and moderately high (medium level) Se diets, in addition to modulation of selenoproteins, can also have an impact on expression of several non-selenoprotein genes in the ovaries of aging mice. To sum up, these findings add more value to our understanding of Se modulation of ovarian functions and female fertility and will pave a way for the focused mechanistic and functional studies in this domain.
Collapse
Affiliation(s)
- Izhar Hyder Qazi
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Department of Veterinary Anatomy & Histology, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, 67210, Sindh, Pakistan
| | - Yutao Cao
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Haoxuan Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Christiana Angel
- Department of Veterinary Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Department of Veterinary Parasitology, Faculty of Veterinary Sciences, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, 67210, Sindh, Pakistan
| | - Bo Pan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangbin Zhou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Hongbing Han
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
70
|
Quintero M, Liu S, Xia Y, Huang Y, Zou Y, Li G, Hu L, Singh N, Blumberg R, Cai Y, Xu H, Li H. Cdk5rap3 is essential for intestinal Paneth cell development and maintenance. Cell Death Dis 2021; 12:131. [PMID: 33504792 PMCID: PMC7841144 DOI: 10.1038/s41419-021-03401-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
Intestinal Paneth cells are professional exocrine cells that play crucial roles in maintenance of homeostatic microbiome, modulation of mucosal immunity, and support for stem cell self-renewal. Dysfunction of these cells may lead to the pathogenesis of human diseases such as inflammatory bowel disease (IBD). Cdk5 activator binding protein Cdk5rap3 (also known as C53 and LZAP) was originally identified as a binding protein of Cdk5 activator p35. Although previous studies have indicated its involvement in a wide range of signaling pathways, the physiological function of Cdk5rap3 remains largely undefined. In this study, we found that Cdk5rap3 deficiency resulted in very early embryonic lethality, indicating its indispensable role in embryogenesis. To further investigate its function in the adult tissues and organs, we generated intestinal epithelial cell (IEC)-specific knockout mouse model to examine its role in intestinal development and tissue homeostasis. IEC-specific deletion of Cdk5rap3 led to nearly complete loss of Paneth cells and increased susceptibility to experimentally induced colitis. Interestingly, Cdk5rap3 deficiency resulted in downregulation of key transcription factors Gfi1 and Sox9, indicating its crucial role in Paneth cell fate specification. Furthermore, Cdk5rap3 is highly expressed in mature Paneth cells. Paneth cell-specific knockout of Cdk5rap3 caused partial loss of Paneth cells, while inducible acute deletion of Cdk5rap3 resulted in disassembly of the rough endoplasmic reticulum (RER) and abnormal zymogen granules in the mature Paneth cells, as well as loss of Paneth cells. Together, our results provide definitive evidence for the essential role of Cdk5rap3 in Paneth cell development and maintenance.
Collapse
Affiliation(s)
- Michaela Quintero
- Department of Biochemistry & Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Siyang Liu
- Department of Biochemistry & Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Yanhua Xia
- Faculty of Basic Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Yonghong Huang
- Faculty of Basic Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Yi Zou
- Department of Metabolic Endocrinology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ge Li
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Ling Hu
- Department of Metabolic Endocrinology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Nagendra Singh
- Department of Biochemistry & Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Richard Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hong Xu
- Faculty of Basic Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Honglin Li
- Department of Biochemistry & Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
| |
Collapse
|
71
|
Wang L, Ye Y. Clearing Traffic Jams During Protein Translocation Across Membranes. Front Cell Dev Biol 2021; 8:610689. [PMID: 33490075 PMCID: PMC7820333 DOI: 10.3389/fcell.2020.610689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Protein translocation across membranes is a critical facet of protein biogenesis in compartmentalized cells as proteins synthesized in the cytoplasm often need to traverse across lipid bilayers via proteinaceous channels to reach their final destinations. It is well established that protein biogenesis is tightly linked to various protein quality control processes, which monitor errors in protein folding, modification, and localization. However, little is known about how cells cope with translocation defective polypeptides that clog translocation channels (translocons) during protein translocation. This review summarizes recent studies, which collectively reveal a set of translocon-associated quality control strategies for eliminating polypeptides stuck in protein-conducting channels in the endoplasmic reticulum and mitochondria.
Collapse
Affiliation(s)
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
72
|
Schuren A, Boer I, Bouma E, Van de Weijer M, Costa A, Hubel P, Pichlmair A, Lebbink R, Wiertz E. The UFM1 Pathway Impacts HCMV US2-Mediated Degradation of HLA Class I. Molecules 2021; 26:molecules26020287. [PMID: 33430125 PMCID: PMC7827699 DOI: 10.3390/molecules26020287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
To prevent accumulation of misfolded proteins in the endoplasmic reticulum, chaperones perform quality control on newly translated proteins and redirect misfolded proteins to the cytosol for degradation by the ubiquitin-proteasome system. This pathway is called ER-associated protein degradation (ERAD). The human cytomegalovirus protein US2 induces accelerated ERAD of HLA class I molecules to prevent immune recognition of infected cells by CD8+ T cells. Using US2-mediated HLA-I degradation as a model for ERAD, we performed a genome-wide CRISPR/Cas9 library screen to identify novel cellular factors associated with ERAD. Besides the identification of known players such as TRC8, p97, and UBE2G2, the ubiquitin-fold modifier1 (UFM1) pathway was found to affect degradation of HLA-I. UFMylation is a post-translational modification resembling ubiquitination. Whereas we observe ubiquitination of HLA-I, no UFMylation was detected on HLA-I or several other proteins involved in degradation of HLA-I, suggesting that the UFM1 pathway impacts ERAD in a different manner than ubiquitin. Interference with the UFM1 pathway seems to specifically inhibit the ER-to-cytosol dislocation of HLA-I. In the absence of detectable UFMylation of HLA-I, UFM1 may contribute to US2-mediated HLA-I degradation by misdirecting protein sorting indirectly. Mass spectrometry analysis of US2-expressing cells showed that ribosomal proteins are a major class of proteins undergoing extensive UFMylation; the role of these changes in protein degradation may be indirect and remains to be established.
Collapse
Affiliation(s)
- A.B.C. Schuren
- Department of Medical Microbiology, University Medical Center Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands; (A.B.C.S.); (I.G.J.B.); (E.M.B.); (M.L.v.d.W.); (A.I.C.)
| | - I.G.J. Boer
- Department of Medical Microbiology, University Medical Center Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands; (A.B.C.S.); (I.G.J.B.); (E.M.B.); (M.L.v.d.W.); (A.I.C.)
| | - E.M. Bouma
- Department of Medical Microbiology, University Medical Center Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands; (A.B.C.S.); (I.G.J.B.); (E.M.B.); (M.L.v.d.W.); (A.I.C.)
- Department of Medical Microbiology, University Medical Center Groningen, Postbus 30001, 9700 RB Groningen, The Netherlands
| | - M.L. Van de Weijer
- Department of Medical Microbiology, University Medical Center Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands; (A.B.C.S.); (I.G.J.B.); (E.M.B.); (M.L.v.d.W.); (A.I.C.)
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - A.I. Costa
- Department of Medical Microbiology, University Medical Center Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands; (A.B.C.S.); (I.G.J.B.); (E.M.B.); (M.L.v.d.W.); (A.I.C.)
| | - P. Hubel
- Innate Immunity Laboratory, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried, D-82152 Munich, Germany; (P.H.); (A.P.)
- Core Facility Hohenheim, Universität Hohenheim, Emil-Wolff-Straße 12, D-70599 Stuttgart, Germany
| | - A. Pichlmair
- Innate Immunity Laboratory, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried, D-82152 Munich, Germany; (P.H.); (A.P.)
- School of Medicine, Institute of Virology, Technical University of Munich, Schneckenburgerstr 8, D-81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, D-85764 Neuherberg, Germany
| | - R.J. Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands; (A.B.C.S.); (I.G.J.B.); (E.M.B.); (M.L.v.d.W.); (A.I.C.)
- Correspondence: (R.J.L.); (E.J.H.J.W.); Tel.: +31-887550627 (R.J.L.); +31-887550862 (E.J.H.J.W.)
| | - E.J.H.J. Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands; (A.B.C.S.); (I.G.J.B.); (E.M.B.); (M.L.v.d.W.); (A.I.C.)
- Correspondence: (R.J.L.); (E.J.H.J.W.); Tel.: +31-887550627 (R.J.L.); +31-887550862 (E.J.H.J.W.)
| |
Collapse
|
73
|
Yang X, You C, Wang X, Gao L, Mo B, Liu L, Chen X. Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes. Genome Biol 2021; 22:15. [PMID: 33402203 PMCID: PMC7784310 DOI: 10.1186/s13059-020-02242-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Background Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular localization has not yet been well studied, thus limiting our mechanistic understanding of sRNA action. Results We investigate the cytoplasmic partitioning of sRNAs and their targets globally in maize (Zea mays, inbred line “B73”) and rice (Oryza sativa, cv. “Nipponbare”) by high-throughput sequencing of polysome-associated sRNAs and 3′ cleavage fragments, and find that both miRNAs and a subset of 21-nucleotide (nt)/22-nt siRNAs are enriched on membrane-bound polysomes (MBPs) relative to total polysomes (TPs) across different tissues. Most of the siRNAs are generated from transposable elements (TEs), and retrotransposons positively contributed to MBP overaccumulation of 22-nt TE-derived siRNAs (TE-siRNAs) as opposed to DNA transposons. Widespread occurrence of miRNA-mediated target cleavage is observed on MBPs, and a large proportion of these cleavage events are MBP-unique. Reproductive 21PHAS (21-nt phasiRNA-generating) and 24PHAS (24-nt phasiRNA-generating) precursors, which were commonly considered as noncoding RNAs, are bound by polysomes, and high-frequency cleavage of 21PHAS precursors by miR2118 and 24PHAS precursors by miR2275 is further detected on MBPs. Reproductive 21-nt phasiRNAs are enriched on MBPs as opposed to TPs, whereas 24-nt phasiRNAs are nearly completely devoid of polysome occupancy. Conclusions MBP overaccumulation is a conserved pattern for cytoplasmic partitioning of sRNAs, and endoplasmic reticulum (ER)-bound ribosomes function as an independent regulatory layer for miRNA-induced gene silencing and reproductive phasiRNA biosynthesis in maize and rice.
Collapse
Affiliation(s)
- Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
74
|
Phillips BP, Miller EA. Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum. J Cell Sci 2020; 133:133/22/jcs251983. [PMID: 33247003 PMCID: PMC7116877 DOI: 10.1242/jcs.251983] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.
Collapse
Affiliation(s)
- Ben P Phillips
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | |
Collapse
|
75
|
UFBP1, a key component in ufmylation, enhances drug sensitivity by promoting proteasomal degradation of oxidative stress-response transcription factor Nrf2. Oncogene 2020; 40:647-662. [PMID: 33219317 DOI: 10.1038/s41388-020-01551-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022]
Abstract
The key component in the UFM1 conjugation system, UFM1-binding and PCI domain-containing protein 1 (UFBP1), regulates many biological processes. Recently it has been shown that low UFBP1 protein level is associated with the worse outcome of gastric cancer patients. However, how it responses to the sensitivity of gastric cancer to chemotherapy drugs and the underlying molecular mechanism remain elusive. Here, we discovered that high UFBP1 expression increases the progression-free survival of advanced gastric cancer patients treated with platinum-based chemotherapy. Cell-line based studies unveiled that UFBP1 expression enhances while UFBP1 knockdown attenuates the sensitivity of gastric cancer cells to cisplatin. High-throughput SILAC-based quantitative proteomic analysis revealed that the protein level of aldo-keto reductase 1Cs (AKR1Cs) is significantly downregulated by UFBP1. Flow cytometry analysis showed that UFBP1 expression increases while UFBP1 knockdown reduces reactive oxygen species upon cisplatin treatment. We further disclosed that UFBP1 attenuates the gene expression of AKR1Cs and the transcription activity of the master oxidative stress-response transcription factor Nrf2 (nuclear factor erythroid-2-related factor 2). Detailed mechanistic studies manifested that UFBP1 promotes the formation of K48-linked polyubiquitin chains on Nrf2 and thus augments its proteasome-mediated degradation. Experiments using genetic depletion and pharmacological activation in vitro and in vivo demonstrated that UFBP1 enhances the sensitivity of gastric cancer cells to cisplatin through the Nrf2/AKR1C axis. Overall, this work discovered a novel prognostic biomarker for gastric cancer patients treated with platinum-based chemotherapy and elucidated the underlying molecular mechanism, which may benefit to future personalized chemotherapy.
Collapse
|
76
|
Dong HJ, Zhang R, Kuang Y, Wang XJ. Selective regulation in ribosome biogenesis and protein production for efficient viral translation. Arch Microbiol 2020; 203:1021-1032. [PMID: 33124672 PMCID: PMC7594972 DOI: 10.1007/s00203-020-02094-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022]
Abstract
As intracellular parasites, viruses depend heavily on host cell structures and their functions to complete their life cycle and produce new viral particles. Viruses utilize or modulate cellular translational machinery to achieve efficient replication; the role of ribosome biogenesis and protein synthesis in viral replication particularly highlights the importance of the ribosome quantity and/or quality in controlling viral protein synthesis. Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Here we summarize the recent literature on RBFs and RPs and their association with subcellular redistribution, post-translational modification, enzyme catalysis, and direct interaction with viral proteins. The advances described in this literature establish a rationale for targeting ribosome production and function in the design of the next generation of antiviral agents.
Collapse
Affiliation(s)
- Hui-Jun Dong
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Rui Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Yu Kuang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
77
|
Xiao J, Liu S, Yu T, Zhang R, Guo X, Jia Y, Shang C, Wang A, Jin Y, Lin P. UFMylation is associated with LPS-induced inflammatory response in goat endometrial epithelial cells. Reprod Domest Anim 2020; 55:1725-1734. [PMID: 32986296 DOI: 10.1111/rda.13832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/22/2020] [Indexed: 01/08/2023]
Abstract
The endometrium plays an important role in the defence against invading pathogens, although the mechanisms are not clear. UFMylation is a recently discovered novel ubiquitination-like modification system that plays a pivotal role in inflammation and the immune response. The purpose of this study was to investigate the effects of UFMylation on lipopolysaccharide (LPS)-induced inflammatory responses in immortalized goat endometrial epithelial cells (gEECs). Ubiquitin-fold modifier conjugating enzyme 1 (UFM1) and DDRGK domain containing 1 (DDRGK1) were mainly localized in the luminal epithelium and glandular epithelium of mouse and goat endometrial tissues. The expression levels of UFM1, ubiquitin-like modifier activating enzyme 5 (UBA5), UFM1 specific ligase 1 (UFL1) and DDRGK1, as key components of the UFMylation system, were significantly activated by 5 μg/mL LPS-induced inflammatory response in gEECs for 6 hr. Meanwhile, the expression levels of interleukin-6 (IL-6) were significantly upregulated, and tumour necrosis factor-α (TNF-α) was significantly down-regulated after overexpression of UFM1 in gEECs. Additionally, we observed UFM1 and DDRGK1 were markedly increased on LPS-stimulated mouse endometritis in vivo. In conclusion, the current study demonstrated that UFMylation was significantly activated by LPS and might be involved in regulating inflammatory response in gEECs.
Collapse
Affiliation(s)
- Jinbang Xiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Shouqin Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Tong Yu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Ruixue Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Xinyan Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Yanni Jia
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Chunmei Shang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Pengfei Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| |
Collapse
|
78
|
Banerjee S, Kumar M, Wiener R. Decrypting UFMylation: How Proteins Are Modified with UFM1. Biomolecules 2020; 10:E1442. [PMID: 33066455 PMCID: PMC7602216 DOI: 10.3390/biom10101442] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Besides ubiquitin (Ub), humans have a set of ubiquitin-like proteins (UBLs) that can also covalently modify target proteins. To date, less is known about UBLs than Ub and even less is known about the UBL called ubiquitin-fold modifier 1 (UFM1). Currently, our understanding of protein modification by UFM1 (UFMylation) is like a jigsaw puzzle with many missing pieces, and in some cases it is not even clear whether these pieces of data are in the right place. Here we review the current data on UFM1 from structural biology to biochemistry and cell biology. We believe that the physiological significance of protein modification by UFM1 is currently underestimated and there is more to it than meets the eye.
Collapse
Affiliation(s)
| | | | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.B.); (M.K.)
| |
Collapse
|
79
|
Petibon C, Malik Ghulam M, Catala M, Abou Elela S. Regulation of ribosomal protein genes: An ordered anarchy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1632. [PMID: 33038057 PMCID: PMC8047918 DOI: 10.1002/wrna.1632] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under:Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation
Collapse
Affiliation(s)
- Cyrielle Petibon
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| |
Collapse
|
80
|
Runnebohm AM, Richards KA, Irelan CB, Turk SM, Vitali HE, Indovina CJ, Rubenstein EM. Overlapping function of Hrd1 and Ste24 in translocon quality control provides robust channel surveillance. J Biol Chem 2020; 295:16113-16120. [PMID: 33033070 DOI: 10.1074/jbc.ac120.016191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Translocation of proteins across biological membranes is essential for life. Proteins that clog the endoplasmic reticulum (ER) translocon prevent the movement of other proteins into the ER. Eukaryotes have multiple translocon quality control (TQC) mechanisms to detect and destroy proteins that persistently engage the translocon. TQC mechanisms have been defined using a limited panel of substrates that aberrantly occupy the channel. The extent of substrate overlap among TQC pathways is unknown. In this study, we found that two TQC enzymes, the ER-associated degradation ubiquitin ligase Hrd1 and zinc metalloprotease Ste24, promote degradation of characterized translocon-associated substrates of the other enzyme in Saccharomyces cerevisiae Although both enzymes contribute to substrate turnover, our results suggest a prominent role for Hrd1 in TQC. Yeast lacking both Hrd1 and Ste24 exhibit a profound growth defect, consistent with overlapping function. Remarkably, two mutations that mildly perturb post-translational translocation and reduce the extent of aberrant translocon engagement by a model substrate diminish cellular dependence on TQC enzymes. Our data reveal previously unappreciated mechanistic complexity in TQC substrate detection and suggest that a robust translocon surveillance infrastructure maintains functional and efficient translocation machinery.
Collapse
Affiliation(s)
| | - Kyle A Richards
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | - Samantha M Turk
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Halie E Vitali
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | | |
Collapse
|
81
|
Stephani M, Picchianti L, Gajic A, Beveridge R, Skarwan E, Sanchez de Medina Hernandez V, Mohseni A, Clavel M, Zeng Y, Naumann C, Matuszkiewicz M, Turco E, Loefke C, Li B, Dürnberger G, Schutzbier M, Chen HT, Abdrakhmanov A, Savova A, Chia KS, Djamei A, Schaffner I, Abel S, Jiang L, Mechtler K, Ikeda F, Martens S, Clausen T, Dagdas Y. A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress. eLife 2020; 9:e58396. [PMID: 32851973 PMCID: PMC7515635 DOI: 10.7554/elife.58396] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the endoplasmic reticulum (ER). Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control in the ER.
Collapse
Affiliation(s)
- Madlen Stephani
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Lorenzo Picchianti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Alexander Gajic
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Rebecca Beveridge
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Emilio Skarwan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | | | - Azadeh Mohseni
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Marion Clavel
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Yonglun Zeng
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Christin Naumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant BiochemistryHalleGermany
| | - Mateusz Matuszkiewicz
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences-SGGWWarsawPoland
| | - Eleonora Turco
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Christian Loefke
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Baiying Li
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Gerhard Dürnberger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Michael Schutzbier
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Hsiao Tieh Chen
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Alibek Abdrakhmanov
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Adriana Savova
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Khong-Sam Chia
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Irene Schaffner
- BOKU Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life SciencesViennaAustria
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant BiochemistryHalleGermany
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Karl Mechtler
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Fumiyo Ikeda
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu UniversityFukuokaJapan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC)ViennaAustria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of ViennaViennaAustria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| |
Collapse
|
82
|
Liu J, Guan D, Dong M, Yang J, Wei H, Liang Q, Song L, Xu L, Bai J, Liu C, Mao J, Zhang Q, Zhou J, Wu X, Wang M, Cong YS. UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nat Cell Biol 2020; 22:1056-1063. [PMID: 32807901 DOI: 10.1038/s41556-020-0559-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/14/2020] [Indexed: 11/09/2022]
Abstract
p53 is the most intensively studied tumour suppressor1. The regulation of p53 homeostasis is essential for its tumour-suppressive function2,3. Although p53 is regulated by an array of post-translational modifications, both during normal homeostasis and in stress-induced responses2-4, how p53 maintains its homeostasis remains unclear. UFMylation is a recently identified ubiquitin-like modification with essential biological functions5-7. Deficiency in this modification leads to embryonic lethality in mice and disease in humans8-12. Here, we report that p53 can be covalently modified by UFM1 and that this modification stabilizes p53 by antagonizing its ubiquitination and proteasome degradation. Mechanistically, UFL1, the UFM1 ligase6, competes with MDM2 to bind to p53 for its stabilization. Depletion of UFL1 or DDRGK1, the critical regulator of UFMylation6,13, decreases p53 stability and in turn promotes cell growth and tumour formation in vivo. Clinically, UFL1 and DDRGK1 expression are downregulated and positively correlated with levels of p53 in a high percentage of renal cell carcinomas. Our results identify UFMylation as a crucial post-translational modification for maintenance of p53 stability and tumour-suppressive function, and point to UFMylation as a promising therapeutic target in cancer.
Collapse
Affiliation(s)
- Jiang Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Di Guan
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Maogong Dong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Yang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Haibin Wei
- Institute of Cancer and Basic Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lizhi Song
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lu Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Junjie Bai
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Cui Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Qian Zhang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Xiaoying Wu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China.
| |
Collapse
|
83
|
|
84
|
Li C, Han T, Guo R, Chen P, Peng C, Prag G, Hu R. An Integrative Synthetic Biology Approach to Interrogating Cellular Ubiquitin and Ufm Signaling. Int J Mol Sci 2020; 21:ijms21124231. [PMID: 32545848 PMCID: PMC7352202 DOI: 10.3390/ijms21124231] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
Global identification of substrates for PTMs (post-translational modifications) represents a critical but yet dauntingly challenging task in understanding biology and disease pathology. Here we presented a synthetic biology approach, namely ‘YESS’, which coupled Y2H (yeast two hybrid) interactome screening with PTMs reactions reconstituted in bacteria for substrates identification and validation, followed by the functional validation in mammalian cells. Specifically, the sequence-independent Gateway® cloning technique was adopted to afford simultaneous transfer of multiple hit ORFs (open reading frames) between the YESS sub-systems. In proof-of-evidence applications of YESS, novel substrates were identified for UBE3A and UFL1, the E3 ligases for ubiquitination and ufmylation, respectively. Therefore, the YESS approach could serve as a potentially powerful tool to study cellular signaling mediated by different PTMs.
Collapse
Affiliation(s)
- Chuanyin Li
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Tianting Han
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Rong Guo
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Peng Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Chao Peng
- University of Chinese Academy of Sciences, Beijing 100049, China;
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Gali Prag
- The Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Ronggui Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
- Cancer Center, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 20072, China
- Correspondence:
| |
Collapse
|
85
|
Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE. A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. Cell 2020; 180:1160-1177.e20. [PMID: 32160526 DOI: 10.1016/j.cell.2020.02.017] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/04/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Selective autophagy of organelles is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few autophagosomal receptors and remodelers. By using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence human ER-phagy factors. Two pathways were unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which is opposite of general autophagy and is independent of AMPK. Second, ER-localized UFMylation is required for ER-phagy to repress the unfolded protein response via IRE1α. The UFL1 ligase is brought to the ER surface by DDRGK1 to UFMylate RPN1 and RPL26 and preferentially targets ER sheets for degradation, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.
Collapse
Affiliation(s)
- Jin Rui Liang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Emily Lingeman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thao Luong
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Saba Ahmed
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthias Muhar
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Truc Nguyen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
86
|
Wang S, Jia M, Su M, Hu X, Li J, Xu Y, Qiu W. Ufmylation Is Activated in Renal Cancer and Is Not Associated with von Hippel-Lindau Mutation. DNA Cell Biol 2020; 39:654-660. [PMID: 31999483 DOI: 10.1089/dna.2019.5225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Clear cell renal cell carcinoma is the most common in all of the renal cancers; however, it lacks ideal molecular target for treatment. In the present study, we identified that ufmylation, a novel ubiquitin-like modification, was significantly upregulated in renal cancer tissues. Ufmylation is known to be closely associated with endoplasmic reticulum (ER) stress and protein quality control. To explore the relation between ufmylation and protein degradation pathways in renal cancer cells, we pharmacologically altered the ubiquitin-proteasome (UPS) and autophagy pathways. We found that the ufmylation levels were not varied by autophagy activation or inhibition. Consistently, the LC3 conversion, as an important biomarker of autophagy, was comparable between renal caner tissues and para-cancer tissues, indicating that the increase of ufmylation in renal cancer may be not related with autophagy. In contrast, blocking UPS with MG132 activated ufmylation in renal cancer cells, suggesting that the activation of ufmylation in renal cancer may be associated with the UPS activity. However, the ufmylation levels were not associated with mutations of the von Hippel-Lindau (VHL) gene, a specific E3 ligase of the UPS and has high mutation rate in renal cancer. Besides, we found that sunitinib, a multi-targeted tyrosine kinase inhibitor, could significantly inhibit ufmylation, whereas overexpression of active Ufm1 partially inhibited the antitumor effects of sunitinib. These results highlight that ufmylation might be a novel molecular candidate for renal cancer.
Collapse
Affiliation(s)
- Sixu Wang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Mei Jia
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Ming Su
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Xinyi Hu
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jun Li
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yongde Xu
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Wei Qiu
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| |
Collapse
|
87
|
Gerakis Y, Quintero M, Li H, Hetz C. The UFMylation System in Proteostasis and Beyond. Trends Cell Biol 2019; 29:974-986. [PMID: 31703843 PMCID: PMC6917045 DOI: 10.1016/j.tcb.2019.09.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications are at the apex of cellular communication and eventually regulate every aspect of life. The identification of new post-translational modifiers is opening alternative avenues in understanding fundamental cell biology processes and may ultimately provide novel therapeutic opportunities. The ubiquitin-fold modifier 1 (UFM1) is a post-translational modifier discovered a decade ago but its biological significance has remained mostly unknown. The field has recently witnessed an explosion of research uncovering the implications of the pathway to cellular homeostasis in living organisms. We overview recent advances in the function and regulation of the UFM1 pathway, and its implications for cell physiology and disease.
Collapse
Affiliation(s)
- Yannis Gerakis
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP (Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias) Center for Geroscience (GERO), Brain Health and Metabolism, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Michaela Quintero
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP (Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias) Center for Geroscience (GERO), Brain Health and Metabolism, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA 94945, USA; Cellular and Molecular Biology Program, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.
| |
Collapse
|