1
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Zhou Z, Zheng X, Zhao J, Yuan A, Lv Z, Shao G, Peng B, Dong MQ, Xu Q, Xu X, Li J. ULK1-dependent phosphorylation of PKM2 antagonizes O-GlcNAcylation and regulates the Warburg effect in breast cancer. Oncogene 2024:10.1038/s41388-024-03035-y. [PMID: 38632437 DOI: 10.1038/s41388-024-03035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024]
Abstract
Pyruvate kinase M2 (PKM2) is a central metabolic enzyme driving the Warburg effect in tumor growth. Previous investigations have demonstrated that PKM2 is subject to O-linked β-N-acetylglucosamine (O-GlcNAc) modification, which is a nutrient-sensitive post-translational modification. Here we found that unc-51 like autophagy activating kinase 1 (ULK1), a glucose-sensitive kinase, interacts with PKM2 and phosphorylates PKM2 at Ser333. Ser333 phosphorylation antagonizes PKM2 O-GlcNAcylation, promotes its tetramer formation and enzymatic activity, and decreases its nuclear localization. As PKM2 is known to have a nuclear role in regulating c-Myc, we also show that PKM2-S333 phosphorylation inhibits c-Myc expression. By downregulating glucose consumption and lactate production, PKM2 pS333 attenuates the Warburg effect. Through mouse xenograft assays, we demonstrate that the phospho-deficient PKM2-S333A mutant promotes tumor growth in vivo. In conclusion, we identified a ULK1-PKM2-c-Myc axis in inhibiting breast cancer, and a glucose-sensitive phosphorylation of PKM2 in modulating the Warburg effect.
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Affiliation(s)
- Zibin Zhou
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiyuan Zheng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Jianxin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Aiyun Yuan
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Zhuan Lv
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Guangcan Shao
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Quan Xu
- Department of Rehabilitation Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, China.
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China.
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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2
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Ye J, He X, Wang S, Dong MQ, Wu F, Lu S, Feng F. Test-Time Training for Deep MS/MS Spectrum Prediction Improves Peptide Identification. J Proteome Res 2024; 23:550-559. [PMID: 38153036 DOI: 10.1021/acs.jproteome.3c00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In bottom-up proteomics, peptide-spectrum matching is critical for peptide and protein identification. Recently, deep learning models have been used to predict tandem mass spectra of peptides, enabling the calculation of similarity scores between the predicted and experimental spectra for peptide-spectrum matching. These models follow the supervised learning paradigm, which trains a general model using paired peptides and spectra from standard data sets and directly employs the model on experimental data. However, this approach can lead to inaccurate predictions due to differences between the training data and the experimental data, such as sample types, enzyme specificity, and instrument calibration. To tackle this problem, we developed a test-time training paradigm that adapts the pretrained model to generate experimental data-specific models, namely, PepT3. PepT3 yields a 10-40% increase in peptide identification depending on the variability in training and experimental data. Intriguingly, when applied to a patient-derived immunopeptidomic sample, PepT3 increases the identification of tumor-specific immunopeptide candidates by 60%. Two-thirds of the newly identified candidates are predicted to bind to the patient's human leukocyte antigen isoforms. To facilitate access of the model and all the results, we have archived all the intermediate files in Zenodo.org with identifier 8231084.
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Affiliation(s)
- Jianbai Ye
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiangnan He
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shujuan Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Feng Wu
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shan Lu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Fuli Feng
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
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3
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Shi L, Ma H, Wang J, Ma M, Zhao H, Li Z, Wang JH, Wu S, Zhou Z, Dong MQ, Li Z. An EMC-Hpo-Yki axis maintains intestinal homeostasis under physiological and pathological conditions. Development 2023; 150:dev201958. [PMID: 38031990 DOI: 10.1242/dev.201958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
Balanced control of stem cell proliferation and differentiation underlines tissue homeostasis. Disruption of tissue homeostasis often results in many diseases. However, how endogenous factors influence the proliferation and differentiation of intestinal stem cells (ISCs) under physiological and pathological conditions remains poorly understood. Here, we find that the evolutionarily conserved endoplasmic reticulum membrane protein complex (EMC) negatively regulates ISC proliferation and intestinal homeostasis. Compromising EMC function in progenitors leads to excessive ISC proliferation and intestinal homeostasis disruption. Mechanistically, the EMC associates with and stabilizes Hippo (Hpo) protein, the key component of the Hpo signaling pathway. In the absence of EMC, Yorkie (Yki) is activated to promote ISC proliferation due to Hpo destruction. The EMC-Hpo-Yki axis also functions in enterocytes to maintain intestinal homeostasis. Importantly, the levels of the EMC are dramatically diminished in tunicamycin-treated animals, leading to Hpo destruction, thereby resulting in intestinal homeostasis disruption due to Yki activation. Thus, our study uncovers the molecular mechanism underlying the action of the EMC in intestinal homeostasis maintenance under physiological and pathological conditions and provides new insight into the pathogenesis of tunicamycin-induced tumorigenesis.
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Affiliation(s)
- Lin Shi
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Hubing Ma
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jinjun Wang
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Meifang Ma
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Hang Zhao
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhengran Li
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shian Wu
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zizhang Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhouhua Li
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
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4
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Zheng JX, Du TY, Shao GC, Ma ZH, Jiang ZD, Hu W, Suo F, He W, Dong MQ, Du LL. Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers. Nat Commun 2023; 14:8334. [PMID: 38097609 PMCID: PMC10721834 DOI: 10.1038/s41467-023-44151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. In several fission yeast species, single-gene KMDs belonging to the wtf gene family exert selfish killing by expressing a toxin and an antidote through alternative transcription initiation. Here we investigate how the toxin and antidote products of a wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs PY motifs (Leu/Pro-Pro-X-Tyr) in its N-terminal cytosolic tail to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
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Affiliation(s)
- Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tong-Yang Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhu-Hui Ma
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wen Hu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wanzhong He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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5
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McDonald NA, Tao L, Dong MQ, Shen K. SAD-1 kinase controls presynaptic phase separation by relieving SYD-2/Liprin-α autoinhibition. PLoS Biol 2023; 21:e3002421. [PMID: 38048304 PMCID: PMC10695385 DOI: 10.1371/journal.pbio.3002421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Neuronal development orchestrates the formation of an enormous number of synapses that connect the nervous system. In developing presynapses, the core active zone structure has been found to assemble through liquid-liquid phase separation. Here, we find that the phase separation of Caenorhabditis elegans SYD-2/Liprin-α, a key active zone scaffold, is controlled by phosphorylation. We identify the SAD-1 kinase as a regulator of SYD-2 phase separation and determine presynaptic assembly is impaired in sad-1 mutants and increased by overactivation of SAD-1. Using phosphoproteomics, we find SAD-1 phosphorylates SYD-2 on 3 sites that are critical to activate phase separation. Mechanistically, SAD-1 phosphorylation relieves a binding interaction between 2 folded domains in SYD-2 that inhibits phase separation by an intrinsically disordered region (IDR). We find synaptic cell adhesion molecules localize SAD-1 to nascent synapses upstream of active zone formation. We conclude that SAD-1 phosphorylates SYD-2 at developing synapses, activating its phase separation and active zone assembly.
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Affiliation(s)
- Nathan A. McDonald
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Li Tao
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, People’s Republic of China
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
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6
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Zhao H, Shi L, Li Z, Kong R, Jia L, Lu S, Wang JH, Dong MQ, Guo X, Li Z. Diamond controls epithelial polarity through the dynactin-dynein complex. Traffic 2023; 24:552-563. [PMID: 37642208 DOI: 10.1111/tra.12917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/10/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Epithelial polarity is critical for proper functions of epithelial tissues, tumorigenesis, and metastasis. The evolutionarily conserved transmembrane protein Crumbs (Crb) is a key regulator of epithelial polarity. Both Crb protein and its transcripts are apically localized in epithelial cells. However, it remains not fully understood how they are targeted to the apical domain. Here, using Drosophila ovarian follicular epithelia as a model, we show that epithelial polarity is lost and Crb protein is absent in the apical domain in follicular cells (FCs) in the absence of Diamond (Dind). Interestingly, Dind is found to associate with different components of the dynactin-dynein complex through co-IP-MS analysis. Dind stabilizes dynactin and depletion of dynactin results in almost identical defects as those observed in dind-defective FCs. Finally, both Dind and dynactin are also required for the apical localization of crb transcripts in FCs. Thus our data illustrate that Dind functions through dynactin/dynein-mediated transport of both Crb protein and its transcripts to the apical domain to control epithelial apico-basal (A/B) polarity.
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Affiliation(s)
- Hang Zhao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Lin Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhengran Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Ruiyan Kong
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Lemei Jia
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Shan Lu
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Xuan Guo
- Life Science Institute, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Zhouhua Li
- College of Life Sciences, Capital Normal University, Beijing, China
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7
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Zou CX, Ma ZH, Jiang ZD, Pan ZQ, Xu DD, Suo F, Shao GC, Dong MQ, Du LL. The ortholog of human REEP1-4 is required for autophagosomal enclosure of ER-phagy/nucleophagy cargos in fission yeast. PLoS Biol 2023; 21:e3002372. [PMID: 37939137 PMCID: PMC10659188 DOI: 10.1371/journal.pbio.3002372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 11/20/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023] Open
Abstract
Selective macroautophagy of the endoplasmic reticulum (ER) and the nucleus, known as ER-phagy and nucleophagy, respectively, are processes whose mechanisms remain inadequately understood. Through an imaging-based screen, we find that in the fission yeast Schizosaccharomyces pombe, Yep1 (also known as Hva22 or Rop1), the ortholog of human REEP1-4, is essential for ER-phagy and nucleophagy but not for bulk autophagy. In the absence of Yep1, the initial phase of ER-phagy and nucleophagy proceeds normally, with the ER-phagy/nucleophagy receptor Epr1 coassembling with Atg8. However, ER-phagy/nucleophagy cargos fail to reach the vacuole. Instead, nucleus- and cortical-ER-derived membrane structures not enclosed within autophagosomes accumulate in the cytoplasm. Intriguingly, the outer membranes of nucleus-derived structures remain continuous with the nuclear envelope-ER network, suggesting a possible outer membrane fission defect during cargo separation from source compartments. We find that the ER-phagy role of Yep1 relies on its abilities to self-interact and shape membranes and requires its C-terminal amphipathic helices. Moreover, we show that human REEP1-4 and budding yeast Atg40 can functionally substitute for Yep1 in ER-phagy, and Atg40 is a divergent ortholog of Yep1 and REEP1-4. Our findings uncover an unexpected mechanism governing the autophagosomal enclosure of ER-phagy/nucleophagy cargos and shed new light on the functions and evolution of REEP family proteins.
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Affiliation(s)
- Chen-Xi Zou
- National Institute of Biological Sciences, Beijing, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Zhu-Hui Ma
- National Institute of Biological Sciences, Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, China
| | - Zhao-Qian Pan
- National Institute of Biological Sciences, Beijing, China
| | - Dan-Dan Xu
- National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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8
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Cao Y, Dong MQ. TransitID maps translocated proteins en masse through tandem proximity labeling and enrichment. Sci Bull (Beijing) 2023; 68:2139-2141. [PMID: 37633830 DOI: 10.1016/j.scib.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Affiliation(s)
- Yong Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
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9
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Cao Y, Liu XT, Mao PZ, Chen ZL, Tarn C, Dong MQ. Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers. J Proteome Res 2023; 22:2593-2607. [PMID: 37494005 DOI: 10.1021/acs.jproteome.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
When it comes to mass spectrometry data analysis for identification of peptide pairs linked by N-hydroxysuccinimide (NHS) ester cross-linkers, search engines bifurcate in their setting of cross-linkable sites. Some restrict NHS ester cross-linkable sites to lysine (K) and protein N-terminus, referred to as K only for short, whereas others additionally include serine (S), threonine (T), and tyrosine (Y) by default. Here, by setting amino acids with chemically inert side chains such as glycine (G), valine (V), and leucine (L) as cross-linkable sites, which serves as a negative control, we show that software-identified STY-cross-links are only as reliable as GVL-cross-links. This is true across different NHS ester cross-linkers including DSS, DSSO, and DSBU, and across different search engines including MeroX, xiSearch, and pLink. Using a published data set originated from synthetic peptides, we demonstrate that STY-cross-links indeed have a high false discovery rate. Further analysis revealed that depending on the data and the search engine used to analyze the data, up to 65% of the STY-cross-links identified are actually K-K cross-links of the same peptide pairs, up to 61% are actually K-mono-links, and the rest tend to contain short peptides at high risk of false identification.
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Affiliation(s)
- Yong Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Xin-Tong Liu
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Peng-Zhi Mao
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ching Tarn
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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10
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Sun RX, Zuo MQ, Zhang JS, Dong MQ. Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry. J Am Soc Mass Spectrom 2023. [PMID: 37463304 DOI: 10.1021/jasms.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1- to 5-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.
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Affiliation(s)
- Rui-Xiang Sun
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Ji-Shuai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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11
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McDonald NA, Tao L, Dong MQ, Shen K. SAD-1 kinase controls presynaptic phase separation by relieving SYD-2/Liprin-α autoinhibition. bioRxiv 2023:2023.06.12.544643. [PMID: 37398223 PMCID: PMC10312667 DOI: 10.1101/2023.06.12.544643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Neuronal development orchestrates the formation of an enormous number of synapses that connect the nervous system. In developing presynapses, the core active zone structure has been found to assemble through a liquid-liquid phase separation. Here, we find that the phase separation of SYD-2/Liprin-α, a key active zone scaffold, is controlled by phosphorylation. Using phosphoproteomics, we identify the SAD-1 kinase to phosphorylate SYD-2 and a number of other substrates. Presynaptic assembly is impaired in sad-1 mutants and increased by overactivation of SAD-1. We determine SAD-1 phosphorylation of SYD-2 at three sites is critical to activate its phase separation. Mechanistically, phosphorylation relieves a binding interaction between two folded SYD-2 domains that inhibits phase separation by an intrinsically disordered region. We find synaptic cell adhesion molecules localize SAD-1 to nascent synapses upstream of active zone formation. We conclude that SAD-1 phosphorylates SYD-2 at developing synapses, enabling its phase separation and active zone assembly.
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Affiliation(s)
| | - Li Tao
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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12
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Florens L, Dong MQ, LaBaer J. Second Special Issue on Methods for Omics Research: Proteome Research and Beyond. J Proteome Res 2023; 22:1381-1384. [PMID: 37143351 DOI: 10.1021/acs.jproteome.3c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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13
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Li J, Ahmad M, Sang L, Zhan Y, Wang Y, Yan Y, Liu Y, Mi W, Lu M, Dai Y, Zhang R, Dong MQ, Yang YG, Wang X, Sun J, Li J. O-GlcNAcylation promotes the cytosolic localization of the m 6A reader YTHDF1 and colorectal cancer tumorigenesis. J Biol Chem 2023; 299:104738. [PMID: 37086786 DOI: 10.1016/j.jbc.2023.104738] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/24/2023] Open
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is an emerging post-translation modification that couples metabolism with cellular signal transduction by crosstalk with phosphorylation and ubiquitination to orchestrate various biological processes. The mechanisms underlying the involvement of O-GlcNAc modifications in N6-methyladenosine (m6A) regulation are not fully characterized. Herein we show that O-GlcNAc modifies the m6A mRNA reader YTHDF1 and fine-tunes its nuclear translocation by the exportin protein Crm1. First we present evidence that YTHDF1 interacts with the sole O-GlcNAc transferase (OGT). Second, we verified Ser196/Ser197/Ser198 as the YTHDF1 O-GlcNAcylation sites, as described in numerous chemoproteomic studies. Then we constructed the O-GlcNAc-deficient YTHDF1-S196A/S197F/S198A (AFA) mutant, which significantly attenuated O-GlcNAc signals. Moreover, we revealed that YTHDF1 is a nucleocytoplasmic protein, whose nuclear export is mediated by Crm1. Furthermore, O-GlcNAcylation increases the cytosolic portion of YTHDF1 by enhancing binding with Crm1, thus upregulating downstream target (e.g. c-Myc) expression. Molecular dynamics simulations suggest that O-GlcNAcylation at S197 promotes the binding between the nuclear export signal motif and Crm1 through increasing hydrogen bonding. Mouse xenograft assays further demonstrate that YTHDF1-AFA mutants decreased the colon cancer mass and size via decreasing c-Myc expression. In sum, we found that YTHDF1 is a nucleocytoplasmic protein, whose cytosolic localization is dependent on O-GlcNAc modification. We propose that the OGT-YTHDF1-c-Myc axis underlies colorectal cancer tumorigenesis.
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Affiliation(s)
- Jie Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Muhammad Ahmad
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Lei Sang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Yahui Zhan
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Yonghong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yue Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Weixiao Mi
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Mei Lu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Yu Dai
- Department of Stomatology, Shenzhen Peoples Hospital, the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
| | - Rou Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China; Beijing National Laboratory for Molecular Sciences, Beijing 100190, China.
| | - Jianwei Sun
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China.
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China.
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Fan Q, Li XM, Zhai C, Li B, Li ST, Dong MQ. Somatic nuclear blebbing in Caenorhabditis elegans is not a feature of organismal aging but a potential indicator of germline proliferation in early adulthood. G3 (Bethesda) 2023; 13:jkad029. [PMID: 36735812 PMCID: PMC10085788 DOI: 10.1093/g3journal/jkad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Abnormal nuclear morphology is suggested to be a hallmark of aging and one such abnormality is nuclear blebbing. However, little is known about whether and how nuclear blebbing participates in animal aging, and what regulates it. In this study, we show that the frequency of nuclear blebbing in the hypodermis increases during aging in wild-type C. elegans. These nuclear blebs are enveloped by the nuclear lamina, the inner and the outer nuclear membrane, and 42% of them contain chromatin. Although nuclear blebbing could lead to DNA loss if chromatin-containing blebs detach and fuse with lysosomes, we find by time-lapse imaging that nuclear blebs rarely detach, and the estimated lifetime of a nuclear bleb is 772 h or 32 days. The amount of DNA lost through nuclear blebbing is estimated to be about 0.1% of the total DNA loss by adult Day 11. Furthermore, the frequency of nuclear blebbing does not correlate with the rate of aging in C. elegans. Old age does not necessarily induce nuclear blebbing, neither does starvation, heat stress, or oxidative stress. Intriguingly, we find that proliferation of germ cells promotes nuclear blebbing.
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Affiliation(s)
- Qiang Fan
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Xue-Mei Li
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Chao Zhai
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Bin Li
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Shang-Tong Li
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Meng-Qiu Dong
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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15
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Li N, Chen S, Xu K, He MT, Dong MQ, Zhang QC, Gao N. Structural basis of membrane skeleton organization in red blood cells. Cell 2023; 186:1912-1929.e18. [PMID: 37044097 DOI: 10.1016/j.cell.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023]
Abstract
The spectrin-based membrane skeleton is a ubiquitous membrane-associated two-dimensional cytoskeleton underneath the lipid membrane of metazoan cells. Mutations of skeleton proteins impair the mechanical strength and functions of the membrane, leading to several different types of human diseases. Here, we report the cryo-EM structures of the native spectrin-actin junctional complex (from porcine erythrocytes), which is a specialized short F-actin acting as the central organizational unit of the membrane skeleton. While an α-/β-adducin hetero-tetramer binds to the barbed end of F-actin as a flexible cap, tropomodulin and SH3BGRL2 together create an absolute cap at the pointed end. The junctional complex is strengthened by ring-like structures of dematin in the middle actin layers and by patterned periodic interactions with tropomyosin over its entire length. This work serves as a structural framework for understanding the assembly and dynamics of membrane skeleton and offers insights into mechanisms of various ubiquitous F-actin-binding factors in other F-actin systems.
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Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
| | - Siyi Chen
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China; Changping Laboratory Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Kui Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Ting He
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China; National Biomedical Imaging Center, Peking University, Beijing 100871, China.
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16
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Yan S, Peng B, Kan S, Shao G, Xiahou Z, Tang X, Chen YX, Dong MQ, Liu X, Xu X, Li J. Polo-like kinase 1 (PLK1) O-GlcNAcylation is essential for dividing mammalian cells and inhibits uterine carcinoma. J Biol Chem 2023; 299:102887. [PMID: 36626982 PMCID: PMC9932112 DOI: 10.1016/j.jbc.2023.102887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/09/2023] Open
Abstract
The O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) mediates intracellular O-GlcNAcylation modification. O-GlcNAcylation occurs on Ser/Thr residues and is important for numerous physiological processes. OGT is essential for dividing mammalian cells and is involved in many human diseases; however, many of its fundamental substrates during cell division remain unknown. Here, we focus on the effect of OGT on polo-like kinase 1 (PLK1), a mitotic master kinase that governs DNA replication, mitotic entry, chromosome segregation, and mitotic exit. We show that PLK1 interacts with OGT and is O-GlcNAcylated. By utilizing stepped collisional energy/higher-energy collisional dissociation mass spectrometry, we found a peptide fragment of PLK1 that is modified by O-GlcNAc. Further mutation analysis of PLK1 shows that the T291A mutant decreases O-GlcNAcylation. Interestingly, T291N is a uterine carcinoma mutant in The Cancer Genome Atlas. Our biochemical assays demonstrate that T291A and T291N both increase PLK1 stability. Using stable H2B-GFP cells, we found that PLK1-T291A and PLK1-T291N mutants display chromosome segregation defects and result in misaligned and lagging chromosomes. In mouse xenograft models, we demonstrate that the O-GlcNAc-deficient PLK1-T291A and PLK1-T291N mutants enhance uterine carcinoma in animals. Hence, we propose that OGT partially exerts its mitotic function through O-GlcNAcylation of PLK1, which might be one mechanism by which elevated levels of O-GlcNAc promote tumorigenesis.
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Affiliation(s)
- Sheng Yan
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Shifeng Kan
- Zaozhuang Municipal Hospital, Shandong, China
| | - Guangcan Shao
- National Institute of Biological Sciences, Beijing, China
| | - Zhikai Xiahou
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Xiangyan Tang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Xiao Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China.
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong, China.
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China.
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17
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Dai S, Tang X, Li L, Ishidate T, Ozturk AR, Chen H, Dude AL, Yan YH, Dong MQ, Shen EZ, Mello CC. A family of C. elegans VASA homologs control Argonaute pathway specificity and promote transgenerational silencing. Cell Rep 2022; 40:111265. [PMID: 36070689 PMCID: PMC9887883 DOI: 10.1016/j.celrep.2022.111265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/01/2022] [Accepted: 08/04/2022] [Indexed: 02/02/2023] Open
Abstract
Germline Argonautes direct transcriptome surveillance within perinuclear membraneless organelles called nuage. In C. elegans, a family of Vasa-related Germ Line Helicase (GLH) proteins localize in and promote the formation of nuage. Previous studies have implicated GLH proteins in inherited silencing, but direct roles in small-RNA production, Argonaute binding, or mRNA targeting have not been identified. Here we show that GLH proteins compete with each other to control Argonaute pathway specificity, bind directly to Argonaute target mRNAs, and promote the amplification of small RNAs required for transgenerational inheritance. We show that the ATPase cycle of GLH-1 regulates direct binding to the Argonaute WAGO-1, which engages amplified small RNAs. Our findings support a dynamic and direct role for GLH proteins in inherited silencing beyond their role as structural components of nuage.
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Affiliation(s)
- Siyuan Dai
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA; Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Xiaoyin Tang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Lili Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Takao Ishidate
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Ahmet R Ozturk
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Hao Chen
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Altair L Dude
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - En-Zhi Shen
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
| | - Craig C Mello
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Worcester, MA 01605, USA.
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18
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Xu N, Liu Y, Nai S, Tao Y, Ding Y, Jia L, Geng Q, Li J, Bai Y, Wei GH, Dong MQ, Luo L, Zhao M, Xu X, Li XX, Li J, Huang L. UBE3D Is Involved in Blue Light-Induced Retinal Damage by Regulating Double-Strand Break Repair. Invest Ophthalmol Vis Sci 2022; 63:7. [PMID: 36094642 PMCID: PMC9482326 DOI: 10.1167/iovs.63.10.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose Age-related macular degeneration (AMD) is currently the leading cause of blindness worldwide. Previously, we identified ubiquitin-protein ligase E3D (UBE3D) as an AMD-associated protein for East Asian populations, and here we further demonstrate that UBE3D could be associated with DNA damage response. Methods The established I-SceI-inducible GFP reporter system was used to explore the effect of UBE3D on homologous recombination. Immunoprecipitation-mass spectrometry (MS) was used to explore potential UBE3D-interacting proteins and validated with coimmunoprecipitation assays and the pulldown assays. Micrococcal nuclease (MNase) assays were used to investigate the function of UBE3D on heterochromatin de-condensation upon DNA damage. An aged mouse model of blue light-induced eye damage was constructed, and electroretinography (ERG) and optical coherence tomography (OCT) were performed to compare the differences between wild-type and UBE3D+/- mice. Results First, we show that GFP-UBE3D is recruited to damage sites by PCNA, through a PCNA-interacting protein (PIP) box. Furthermore, UBE3D interacts with KAP1 via R377R378 and oxidation of the AMD-associated V379M mutation abolishes KAP1-UBE3D binding. By MNase assays, UBE3D depletion reduces the chromatin relaxation levels upon DNA damage. In addition, UBE3D depletion renders less KAP1 recruitment. Compared with wild type, blue light induces less damage in UBE3D+/- mice as measured by ERG and OCT, consistent with our biochemical results. Conclusions Hence, we propose that one potential mechanism that UBE3D-V379M contributes to AMD pathogenesis might be via defective DNA damage repair linked with oxidative stress and our results offered a potential direction for the treatment of AMD.
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Affiliation(s)
- Ningda Xu
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Yue Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shanshan Nai
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University, Chaoyang District, Beijing, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, China
| | - Lemei Jia
- National Institute of Biological Sciences, Beijing, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Jie Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yujing Bai
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Linyi Luo
- Department of Ophthalmology and Visual Sciences, Affiliated Dongguan Hospital, Southern Medical University, Guangdong, China
| | - Mingwei Zhao
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xiao-Xin Li
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
- Department of Ophthalmology, Xiamen Eye Center of Xiamen University, Xiamen, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Lvzhen Huang
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
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Shi Y, Yan S, Shao GC, Wang J, Jian YP, Liu B, Yuan Y, Qin K, Nai S, Huang X, Wang Y, Chen Z, Chen X, Dong MQ, Geng Y, Xu ZX, Li J. O-GlcNAcylation stabilizes the autophagy-initiating kinase ULK1 by inhibiting chaperone-mediated autophagy upon HPV infection. J Biol Chem 2022; 298:102341. [PMID: 35931119 PMCID: PMC9436821 DOI: 10.1016/j.jbc.2022.102341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 01/02/2023] Open
Abstract
Human papillomaviruses (HPVs) cause a subset of head and neck squamous cell carcinomas (HNSCCs). Previously, we demonstrated that HPV16 oncogene E6 or E6/E7 transduction increases the abundance of O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT), but OGT substrates affected by this increase are unclear. Here, we focus on the effects of O-GlcNAcylation on HPV-positive HNSCCs. We found that upon HPV infection, Unc-51-like kinase 1 (ULK1), an autophagy-initiating kinase, is hyper-O-GlcNAcylated, stabilized, and linked with autophagy elevation. Through mass spectrometry, we identified that ULK1 is O-GlcNAcylated at Ser409, which is distinct from the previously reported Thr635/Thr754 sites. It has been demonstrated that PKCα mediates phosphorylation of ULK1 at Ser423, which attenuates its stability by shunting ULK1 to the chaperone-mediated autophagy (CMA) pathway. Using biochemical assays, we demonstrate that ULK1 Ser409Ser410 O-GlcNAcylation antagonizes its phosphorylation at Ser423. Moreover, mutations of Ser409A and its neighboring site Ser410A (2A) render ULK1 less stable by promoting interaction with the CMA chaperone HSC70 (heat shock cognate 70 kDa protein). Furthermore, ULK1-2A mutants attenuate the association of ULK1 with STX17, which is vital for the fusion between autophagosomes and lysosomes. Analysis of The Cancer Genome Atlas (TCGA) database reveals that ULK1 is upregulated in HPV-positive HNSCCs, and its level positively correlates with HNSCC patient survival. Overall, our work demonstrates that O-GlcNAcylation of ULK1 is altered in response to environmental changes. O-GlcNAcylation of ULK1 at Ser409 and perhaps Ser410 stabilizes ULK1, which might underlie the molecular mechanism of HPV-positive HNSCC patient survival.
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Affiliation(s)
- Yingxin Shi
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing 100048, China
| | - Sheng Yan
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing 100048, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jinglong Wang
- Qingdao University Medical College Affiliated Hospital, Qingdao, Shandong 266000, China
| | - Yong-Ping Jian
- School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Bo Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yanqiu Yuan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Ke Qin
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Shanshan Nai
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenghui Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yiqun Geng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Zhi-Xiang Xu
- School of Life Sciences, Henan University, Kaifeng, Henan 475004, China.
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing 100048, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
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20
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Guan L, Wu B, Li T, Beer LA, Sharma G, Li M, Lee CN, Liu S, Yang C, Huang L, Frederick DT, Boland GM, Shao G, Svitkina TM, Cai KQ, Chen F, Dong MQ, Mills GB, Schuchter LM, Karakousis GC, Mitchell TC, Flaherty KT, Speicher DW, Chen YH, Herlyn M, Amaravadi RK, Xu X, Guo W. HRS phosphorylation drives immunosuppressive exosome secretion and restricts CD8 + T-cell infiltration into tumors. Nat Commun 2022; 13:4078. [PMID: 35835783 PMCID: PMC9283393 DOI: 10.1038/s41467-022-31713-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/30/2022] [Indexed: 02/03/2023] Open
Abstract
The lack of tumor infiltration by CD8+ T cells is associated with poor patient response to anti-PD-1 therapy. Understanding how tumor infiltration is regulated is key to improving treatment efficacy. Here, we report that phosphorylation of HRS, a pivotal component of the ESCRT complex involved in exosome biogenesis, restricts tumor infiltration of cytolytic CD8+ T cells. Following ERK-mediated phosphorylation, HRS interacts with and mediates the selective loading of PD-L1 to exosomes, which inhibits the migration of CD8+ T cells into tumors. In tissue samples from patients with melanoma, CD8+ T cells are excluded from the regions where tumor cells contain high levels of phosphorylated HRS. In murine tumor models, overexpression of phosphorylated HRS increases resistance to anti-PD-1 treatment, whereas inhibition of HRS phosphorylation enhances treatment efficacy. Our study reveals a mechanism by which phosphorylation of HRS in tumor cells regulates anti-tumor immunity by inducing PD-L1+ immunosuppressive exosomes, and suggests HRS phosphorylation blockade as a potential strategy to improve the efficacy of cancer immunotherapy.
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Affiliation(s)
- Lei Guan
- grid.25879.310000 0004 1936 8972Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Bin Wu
- grid.25879.310000 0004 1936 8972Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ting Li
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Lynn A. Beer
- grid.251075.40000 0001 1956 6678Molecular & Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104 USA
| | - Gaurav Sharma
- grid.25879.310000 0004 1936 8972Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Mingyue Li
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Chin Nien Lee
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Shujing Liu
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Changsong Yang
- grid.25879.310000 0004 1936 8972Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Lili Huang
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Dennie T. Frederick
- grid.38142.3c000000041936754XDivision of Medical Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
| | - Genevieve M. Boland
- grid.32224.350000 0004 0386 9924Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA MA02114 USA
| | - Guangcan Shao
- grid.410717.40000 0004 0644 5086National Institute of Biological Sciences, Beijing, 102206 P. R. China
| | - Tatyana M. Svitkina
- grid.25879.310000 0004 1936 8972Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kathy Q. Cai
- grid.249335.a0000 0001 2218 7820Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA 19111 USA
| | - Fangping Chen
- grid.251075.40000 0001 1956 6678Histotechnology Facility, The Wistar Institute, Philadelphia, PA 19104 USA
| | - Meng-Qiu Dong
- grid.410717.40000 0004 0644 5086National Institute of Biological Sciences, Beijing, 102206 P. R. China
| | - Gordon B. Mills
- grid.5288.70000 0000 9758 5690Division of Oncological Science, School of Medicine and Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201 USA
| | - Lynn M. Schuchter
- grid.25879.310000 0004 1936 8972Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Giorgos C. Karakousis
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Tara C. Mitchell
- grid.25879.310000 0004 1936 8972Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Keith T. Flaherty
- grid.38142.3c000000041936754XDivision of Medical Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
| | - David W. Speicher
- grid.251075.40000 0001 1956 6678Molecular & Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104 USA
| | - Youhai H. Chen
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Meenhard Herlyn
- grid.251075.40000 0001 1956 6678Molecular & Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104 USA
| | - Ravi K. Amaravadi
- grid.25879.310000 0004 1936 8972Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Xiaowei Xu
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Wei Guo
- grid.25879.310000 0004 1936 8972Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
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21
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Mi C, Zhang L, Huang G, Shao G, Yang F, You X, Dong MQ, Sun S, Sui SF. Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32. Sci Adv 2022; 8:eabi5603. [PMID: 35080977 PMCID: PMC8791620 DOI: 10.1126/sciadv.abi5603] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and exist in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast. Here, we present cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states. All the structures show a dimeric architecture assembled by two triangle-shaped monomers, while the monomer in the apo state exhibits both open and closed conformations, and the monomer in the Ypt32-bound form only captures the closed conformation. Located in the interior of the monomer, Ypt32 binds with both core TRAPP/TRAPPI and Trs120 via its nucleotide-binding domain and binds with Trs31 via its hypervariable domain. Combined with functional analysis, the structures provide insights into the assembly of TRAPPII and the mechanism of the specific activation of Ypt31/Ypt32 by TRAPPII.
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Affiliation(s)
- Chenchen Mi
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li Zhang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guoqiang Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangcan Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fan Yang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xin You
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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22
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Li WJ, Wang CW, Tao L, Yan YH, Zhang MJ, Liu ZX, Li YX, Zhao HQ, Li XM, He XD, Xue Y, Dong MQ. Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. Nat Commun 2021; 12:4568. [PMID: 34315882 PMCID: PMC8316574 DOI: 10.1038/s41467-021-24816-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 07/01/2021] [Indexed: 12/22/2022] Open
Abstract
Insulin/IGF-1 Signaling (IIS) is known to constrain longevity by inhibiting the transcription factor FOXO. How phosphorylation mediated by IIS kinases regulates lifespan beyond FOXO remains unclear. Here, we profile IIS-dependent phosphorylation changes in a large-scale quantitative phosphoproteomic analysis of wild-type and three IIS mutant Caenorhabditis elegans strains. We quantify more than 15,000 phosphosites and find that 476 of these are differentially phosphorylated in the long-lived daf-2/insulin receptor mutant. We develop a machine learning-based method to prioritize 25 potential lifespan-related phosphosites. We perform validations to show that AKT-1 pT492 inhibits DAF-16/FOXO and compensates the loss of daf-2 function, that EIF-2α pS49 potently inhibits protein synthesis and daf-2 longevity, and that reduced phosphorylation of multiple germline proteins apparently transmits reduced DAF-2 signaling to the soma. In addition, an analysis of kinases with enriched substrates detects that casein kinase 2 (CK2) subunits negatively regulate lifespan. Our study reveals detailed functional insights into longevity.
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Affiliation(s)
- Wen-Jun Li
- School of Life Sciences, Peking University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Chen-Wei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu, China
| | - Li Tao
- National Institute of Biological Sciences, Beijing, China
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing, China
| | - Mei-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
- Annoroad Gene Tech. Co., Ltd., Beijing, China
| | - Ze-Xian Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-Xin Li
- National Institute of Biological Sciences, Beijing, China
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Han-Qing Zhao
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Mei Li
- School of Life Sciences, Peking University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Xian-Dong He
- National Institute of Biological Sciences, Beijing, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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23
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Wang YY, Zhang J, Liu XM, Li Y, Sui J, Dong MQ, Ye K, Du LL. Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1. EMBO J 2021; 40:e107497. [PMID: 34169534 DOI: 10.15252/embj.2020107497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.
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Affiliation(s)
- Ying-Ying Wang
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Jianxiu Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - Yulu Li
- National Institute of Biological Sciences, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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24
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Kim H, Ding YH, Zhang G, Yan YH, Conte D, Dong MQ, Mello CC. HDAC1 SUMOylation promotes Argonaute-directed transcriptional silencing in C. elegans. eLife 2021; 10:e63299. [PMID: 34003109 PMCID: PMC8131101 DOI: 10.7554/elife.63299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/23/2021] [Indexed: 12/30/2022] Open
Abstract
Eukaryotic cells use guided search to coordinately control dispersed genetic elements. Argonaute proteins and their small RNA cofactors engage nascent RNAs and chromatin-associated proteins to direct transcriptional silencing. The small ubiquitin-like modifier (SUMO) has been shown to promote the formation and maintenance of silent chromatin (called heterochromatin) in yeast, plants, and animals. Here, we show that Argonaute-directed transcriptional silencing in Caenorhabditis elegans requires SUMOylation of the type 1 histone deacetylase HDA-1. Our findings suggest how SUMOylation promotes the association of HDAC1 with chromatin remodeling factors and with a nuclear Argonaute to initiate de novo heterochromatin silencing.
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Affiliation(s)
- Heesun Kim
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Yue-He Ding
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Gangming Zhang
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Yong-Hong Yan
- National Institute of Biological SciencesBeijingChina
| | - Darryl Conte
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Meng-Qiu Dong
- National Institute of Biological SciencesBeijingChina
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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25
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Kim H, Ding YH, Lu S, Zuo MQ, Tan W, Conte D, Dong MQ, Mello CC. PIE-1 SUMOylation promotes germline fates and piRNA-dependent silencing in C. elegans. eLife 2021; 10:e63300. [PMID: 34003111 PMCID: PMC8131105 DOI: 10.7554/elife.63300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
Germlines shape and balance heredity, integrating and regulating information from both parental and foreign sources. Insights into how germlines handle information have come from the study of factors that specify or maintain the germline fate. In early Caenorhabditis elegans embryos, the CCCH zinc finger protein PIE-1 localizes to the germline where it prevents somatic differentiation programs. Here, we show that PIE-1 also functions in the meiotic ovary where it becomes SUMOylated and engages the small ubiquitin-like modifier (SUMO)-conjugating machinery. Using whole-SUMO-proteome mass spectrometry, we identify HDAC SUMOylation as a target of PIE-1. Our analyses of genetic interactions between pie-1 and SUMO pathway mutants suggest that PIE-1 engages the SUMO machinery both to preserve the germline fate in the embryo and to promote Argonaute-mediated surveillance in the adult germline.
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Affiliation(s)
- Heesun Kim
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Yue-He Ding
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Shan Lu
- National Institute of Biological SciencesBeijingChina
| | - Mei-Qing Zuo
- National Institute of Biological SciencesBeijingChina
| | - Wendy Tan
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Darryl Conte
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Meng-Qiu Dong
- National Institute of Biological SciencesBeijingChina
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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26
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Xia SL, Li M, Chen B, Wang C, Yan YH, Dong MQ, Qi YB. The LRR-TM protein PAN-1 interacts with MYRF to promote its nuclear translocation in synaptic remodeling. eLife 2021; 10:67628. [PMID: 33950834 PMCID: PMC8099431 DOI: 10.7554/elife.67628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
Neural circuits develop through a plastic phase orchestrated by genetic programs and environmental signals. We have identified a leucine-rich-repeat domain transmembrane protein PAN-1 as a factor required for synaptic rewiring in C. elegans. PAN-1 localizes on cell membrane and binds with MYRF, a membrane-bound transcription factor indispensable for promoting synaptic rewiring. Full-length MYRF was known to undergo self-cleavage on ER membrane and release its transcriptional N-terminal fragment in cultured cells. We surprisingly find that MYRF trafficking to cell membrane before cleavage is pivotal for C. elegans development and the timing of N-MYRF release coincides with the onset of synaptic rewiring. On cell membrane PAN-1 and MYRF interact with each other via their extracellular regions. Loss of PAN-1 abolishes MYRF cell membrane localization, consequently blocking myrf-dependent neuronal rewiring process. Thus, through interactions with a cooperating factor on the cell membrane, MYRF may link cell surface activities to transcriptional cascades required for development.
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Affiliation(s)
- Shi-Li Xia
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Meng Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bing Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chao Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Yingchuan B Qi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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27
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Pan ZQ, Shao GC, Liu XM, Chen Q, Dong MQ, Du LL. Atg1 kinase in fission yeast is activated by Atg11-mediated dimerization and cis-autophosphorylation. eLife 2020; 9:58073. [PMID: 32909946 PMCID: PMC7511232 DOI: 10.7554/elife.58073] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/10/2020] [Indexed: 12/28/2022] Open
Abstract
Autophagy is a proteolytic pathway that is conserved from yeasts to mammals. Atg1 kinase is essential for autophagy, but how its activity is controlled remains insufficiently understood. Here, we show that, in the fission yeast Schizosaccharomyces pombe, Atg1 kinase activity requires Atg11, the ortholog of mammalian FIP200/RB1CC1, but does not require Atg13, Atg17, or Atg101. Remarkably, a 62 amino acid region of Atg11 is sufficient for the autophagy function of Atg11 and for supporting the Atg1 kinase activity. This region harbors an Atg1-binding domain and a homodimerization domain. Dimerizing Atg1 is the main role of Atg11, as it can be bypassed by artificially dimerizing Atg1. In an Atg1 dimer, only one Atg1 molecule needs to be catalytically active, suggesting that Atg1 activation can be achieved through cis-autophosphorylation. We propose that mediating Atg1 oligomerization and activation may be a conserved function of Atg11/FIP200 family proteins and cis-autophosphorylation may be a general mechanism of Atg1 activation.
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Affiliation(s)
- Zhao-Qian Pan
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - Quan Chen
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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28
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Lv L, Chen P, Cao L, Li Y, Zeng Z, Cui Y, Wu Q, Li J, Wang JH, Dong MQ, Qi X, Han T. Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation. eLife 2020; 9:59994. [PMID: 32804079 PMCID: PMC7462607 DOI: 10.7554/elife.59994] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular-glue degraders mediate interactions between target proteins and components of the ubiquitin-proteasome system to cause selective protein degradation. Here, we report a new molecular glue HQ461 discovered by high-throughput screening. Using loss-of-function and gain-of-function genetic screening in human cancer cells followed by biochemical reconstitution, we show that HQ461 acts by promoting an interaction between CDK12 and DDB1-CUL4-RBX1 E3 ubiquitin ligase, leading to polyubiquitination and degradation of CDK12-interacting protein Cyclin K (CCNK). Degradation of CCNK mediated by HQ461 compromised CDK12 function, leading to reduced phosphorylation of a CDK12 substrate, downregulation of DNA damage response genes, and cell death. Structure-activity relationship analysis of HQ461 revealed the importance of a 5-methylthiazol-2-amine pharmacophore and resulted in an HQ461 derivate with improved potency. Our studies reveal a new molecular glue that recruits its target protein directly to DDB1 to bypass the requirement of a substrate-specific receptor, presenting a new strategy for targeted protein degradation.
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Affiliation(s)
- Lu Lv
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Peihao Chen
- National Institute of Biological Sciences, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Longzhi Cao
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yamei Li
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhi Zeng
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yue Cui
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Qingcui Wu
- National Institute of Biological Sciences, Beijing, China
| | - Jiaojiao Li
- National Institute of Biological Sciences, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Ting Han
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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29
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Zeng C, Weng C, Wang X, Yan YH, Li WJ, Xu D, Hong M, Liao S, Dong MQ, Feng X, Xu C, Guang S. Functional Proteomics Identifies a PICS Complex Required for piRNA Maturation and Chromosome Segregation. Cell Rep 2020; 27:3561-3572.e3. [PMID: 31216475 DOI: 10.1016/j.celrep.2019.05.076] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/08/2019] [Accepted: 05/20/2019] [Indexed: 01/19/2023] Open
Abstract
piRNAs play significant roles in suppressing transposons and nonself nucleic acids, maintaining genome integrity, and defending against viral infections. In C. elegans, piRNA precursors are transcribed in the nucleus and are subjected to a number of processing and maturation steps. The biogenesis of piRNAs is not fully understood. We use functional proteomics in C. elegans and identify a piRNA biogenesis and chromosome segregation (PICS) complex. The PICS complex contains TOFU-6, PID-1, PICS-1, TOST-1, and ERH-2, which exhibit dynamic localization among different subcellular compartments. In the germlines, the PICS complex contains TOFU-6/PICS-1/ERH-2/PID-1, is largely concentrated at the perinuclear granule zone, and engages in piRNA processing. During embryogenesis, the TOFU-6/PICS-1/ERH-2/TOST-1 complex accumulates in the nucleus and plays essential roles in chromosome segregation. The functions of these factors in mediating chromosome segregation are independent of piRNA production. We speculate that differential compositions of PICS factors may help cells coordinate distinct cellular processes.
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Affiliation(s)
- Chenming Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Chenchun Weng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xiaoyang Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Jun Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Demin Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Minjie Hong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Shanhui Liao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China.
| | - Chao Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China.
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, Anhui 230027, P.R. China.
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30
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Zhao D, Zou CX, Liu XM, Jiang ZD, Yu ZQ, Suo F, Du TY, Dong MQ, He W, Du LL. A UPR-Induced Soluble ER-Phagy Receptor Acts with VAPs to Confer ER Stress Resistance. Mol Cell 2020; 79:963-977.e3. [PMID: 32735772 DOI: 10.1016/j.molcel.2020.07.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/01/2020] [Accepted: 07/20/2020] [Indexed: 01/07/2023]
Abstract
Autophagic degradation of the endoplasmic reticulum (ER-phagy) is triggered by ER stress in diverse organisms. However, molecular mechanisms governing ER stress-induced ER-phagy remain insufficiently understood. Here we report that ER stress-induced ER-phagy in the fission yeast Schizosaccharomyces pombe requires Epr1, a soluble Atg8-interacting ER-phagy receptor. Epr1 localizes to the ER through interacting with integral ER membrane proteins VAPs. Bridging an Atg8-VAP association is the main ER-phagy role of Epr1, as it can be bypassed by an artificial Atg8-VAP tether. VAPs contribute to ER-phagy not only by tethering Atg8 to the ER membrane, but also by maintaining the ER-plasma membrane contact. Epr1 is upregulated during ER stress by the unfolded protein response (UPR) regulator Ire1. Loss of Epr1 reduces survival against ER stress. Conversely, increasing Epr1 expression suppresses the ER-phagy defect and ER stress sensitivity of cells lacking Ire1. Our findings expand and deepen the molecular understanding of ER-phagy.
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Affiliation(s)
- Dan Zhao
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Chen-Xi Zou
- College of Life Sciences, Beijing Normal University, 100875 Beijing, China; National Institute of Biological Sciences, 102206 Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Zhong-Qiu Yu
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Tong-Yang Du
- College of Life Sciences, Beijing Normal University, 100875 Beijing, China; National Institute of Biological Sciences, 102206 Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, 102206 Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China
| | - Wanzhong He
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, 102206 Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China.
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31
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Liang X, Zuo MQ, Zhang Y, Li N, Ma C, Dong MQ, Gao N. Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. Nat Commun 2020; 11:3542. [PMID: 32669547 PMCID: PMC7363849 DOI: 10.1038/s41467-020-17237-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.
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MESH Headings
- Cell Nucleus/metabolism
- Cryoelectron Microscopy
- Humans
- Models, Molecular
- RNA, Ribosomal, 5S/isolation & purification
- RNA, Ribosomal, 5S/metabolism
- RNA, Ribosomal, 5S/ultrastructure
- RNA-Binding Proteins/isolation & purification
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Ribosomal Proteins/isolation & purification
- Ribosomal Proteins/metabolism
- Ribosomal Proteins/ultrastructure
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
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Affiliation(s)
- Xiaomeng Liang
- State Key Laboratory of Membrane Biology, School of Life Science, Tsinghua University, 100084, Beijing, China
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Mei-Qing Zuo
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Yunyang Zhang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Chengying Ma
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.
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32
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Florens L, Dong MQ, LaBaer J. New and Improved Tools for the Omics Crew. J Proteome Res 2020; 19:2525-2528. [PMID: 32610914 DOI: 10.1021/acs.jproteome.0c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Shi D, Zhao S, Zuo MQ, Zhang J, Hou W, Dong MQ, Cao Q, Lou H. The acetyltransferase Eco1 elicits cohesin dimerization during S phase. J Biol Chem 2020; 295:7554-7565. [PMID: 32312753 PMCID: PMC7261783 DOI: 10.1074/jbc.ra120.013102] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Indexed: 01/26/2023] Open
Abstract
Cohesin is a DNA-associated protein complex that forms a tripartite ring controlling sister chromatid cohesion, chromosome segregation and organization, DNA replication, and gene expression. Sister chromatid cohesion is established by the protein acetyltransferase Eco1, which acetylates two conserved lysine residues on the cohesin subunit Smc3 and thereby ensures correct chromatid separation in yeast (Saccharomyces cerevisiae) and other eukaryotes. However, the consequence of Eco1-catalyzed cohesin acetylation is unknown, and the exact nature of the cohesive state of chromatids remains controversial. Here, we show that self-interactions of the cohesin subunits Scc1/Rad21 and Scc3 occur in a DNA replication-coupled manner in both yeast and human cells. Using cross-linking MS-based and in vivo disulfide cross-linking analyses of purified cohesin, we show that a subpopulation of cohesin may exist as dimers. Importantly, upon temperature-sensitive and auxin-induced degron-mediated Eco1 depletion, the cohesin-cohesin interactions became significantly compromised, whereas deleting either the deacetylase Hos1 or the Eco1 antagonist Wpl1/Rad61 increased cohesin dimer levels by ∼20%. These results indicate that cohesin dimerizes in the S phase and monomerizes in mitosis, processes that are controlled by Eco1, Wpl1, and Hos1 in the sister chromatid cohesion-dissolution cycle. These findings suggest that cohesin dimerization is controlled by the cohesion cycle and support the notion that a double-ring cohesin model operates in sister chromatid cohesion.
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Affiliation(s)
- Di Shi
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Shuaijun Zhao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jingjing Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Wenya Hou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
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34
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Ma M, Liu JJ, Li Y, Huang Y, Ta N, Chen Y, Fu H, Ye MD, Ding Y, Huang W, Wang J, Dong MQ, Yu L, Wang HW. Author Correction: Cryo-EM structure and biochemical analysis reveal the basis of the functional difference between human PI3KC3-C1 and -C2. Cell Res 2020; 30:551-552. [PMID: 32284560 DOI: 10.1038/s41422-020-0311-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Meisheng Ma
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jun-Jie Liu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Li
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuwei Huang
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China
| | - Na Ta
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hua Fu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Ming-Da Ye
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Weijiao Huang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Li Yu
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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35
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Yu ZQ, Sun LL, Jiang ZD, Liu XM, Zhao D, Wang HT, He WZ, Dong MQ, Du LL. Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop to promote autophagy. Autophagy 2020; 16:2036-2051. [PMID: 31941401 PMCID: PMC7595586 DOI: 10.1080/15548627.2020.1713644] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroautophagy (autophagy) is driven by the coordinated actions of core autophagy-related (Atg) proteins. Atg8, the core Atg protein generally considered acting most downstream, has recently been shown to interact with other core Atg proteins via their Atg8-family-interacting motifs (AIMs). However, the extent, functional consequence, and evolutionary conservation of such interactions remain inadequately understood. Here, we show that, in the fission yeast Schizosaccharomyces pombe, Atg38, a subunit of the phosphatidylinositol 3-kinase (PtdIns3K) complex I, interacts with Atg8 via an AIM, which is highly conserved in Atg38 proteins of fission yeast species, but not conserved in Atg38 proteins of other species. This interaction recruits Atg38 to Atg8 on the phagophore assembly site (PAS) and consequently enhances PAS accumulation of the PtdIns3K complex I and Atg proteins acting downstream of the PtdIns3K complex I, including Atg8. The disruption of the Atg38-Atg8 interaction leads to the reduction of autophagosome size and autophagic flux. Remarkably, the loss of this interaction can be compensated by an artificial Atg14-Atg8 interaction. Our findings demonstrate that the Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop between Atg8 and the PtdIns3K complex I to promote efficient autophagosome formation, underscore the prevalence and diversity of AIM-mediated connections within the autophagic machinery, and reveal unforeseen flexibility of such connections. Abbreviations: AIM: Atg8-family-interacting motif; AP-MS: affinity purification coupled with mass spectrometry; Atg: autophagy-related; FLIP: fluorescence loss in photobleaching; PAS: phagophore assembly site; PB: piggyBac; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol 3-phosphate.
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Affiliation(s)
- Zhong-Qiu Yu
- National Institute of Biological Sciences , Beijing, China.,PTN Graduate Program, School of Life Sciences, Peking University , Beijing, China
| | - Ling-Ling Sun
- National Institute of Biological Sciences , Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences , Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences , Beijing, China
| | - Dan Zhao
- National Institute of Biological Sciences , Beijing, China
| | - Hai-Tao Wang
- National Institute of Biological Sciences , Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences , Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
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36
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Liu L, Zhang Y, Zhang J, Wang JH, Cao Q, Li Z, Campbell JL, Dong MQ, Lou H. Characterization of the dimeric CMG/pre-initiation complex and its transition into DNA replication forks. Cell Mol Life Sci 2019; 77:3041-3058. [PMID: 31728581 DOI: 10.1007/s00018-019-03333-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/17/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
The pre-initiation complex (pre-IC) has been proposed for two decades as an intermediate right before the maturation of the eukaryotic DNA replication fork. However, its existence and biochemical nature remain enigmatic. Here, through combining several enrichment strategies, we are able to isolate an endogenous dimeric CMG-containing complex (designated as d-CMG) distinct from traditional single CMG (s-CMG) and in vitro reconstituted dimeric CMG. D-CMG is assembled upon entry into the S phase and shortly matures into s-CMG/replisome, leading to the fact that only ~ 5% of the total CMG-containing complexes can be detected as d-CMG in vivo. Mass spectra reveal that RPA and DNA Pol α/primase co-purify with s-CMG, but not with d-CMG. Consistently, the former fraction is able to catalyze DNA unwinding and de novo synthesis, while the latter catalyzes neither. The two CMGs in d-CMG display flexibly orientated conformations under an electronic microscope. When DNA Pol α-primase is inactivated, d-CMG % rose up to 29%, indicating an incomplete pre-IC/fork transition. These findings reveal biochemical properties of the d-CMG/pre-IC and provide in vivo evidence to support the pre-IC/fork transition as a bona fide step in replication initiation.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Yue Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Jingjing Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Zhen Li
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, 91125, CA, USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences China Agricultural University, Beijing, China.
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37
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Nai S, Shi Y, Ru H, Ding Y, Geng Q, Li Z, Dong MQ, Xu X, Li J. Chk2-dependent phosphorylation of myosin phosphatase targeting subunit 1 (MYPT1) regulates centrosome maturation. Cell Cycle 2019; 18:2651-2659. [PMID: 31416392 PMCID: PMC6773232 DOI: 10.1080/15384101.2019.1654795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/17/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
Checkpoint kinase 2 (Chk2) is a pivotal effector kinase in the DNA damage response, with an emerging role in mitotic chromosome segregation. In this study, we show that Chk2 interacts with myosin phosphatase targeting subunit 1 (MYPT1), the targeting subunit of protein phosphatase 1cβ (PP1cβ). Previous studies have shown that MYPT1 is phosphorylated by CDK1 at S473 during mitosis, and subsequently docks to the polo-binding domain of PLK1 and dephosphorylates PLK1. Herein we present data that Chk2 phosphorylates MYPT1 at S507 in vitro and in vivo, which antagonizes pS473. Chk2 inhibition results in failure of γ-tubulin recruitment to the centrosomes, phenocopying Plk1 inhibition defects. These aberrancies were also observed in the MYPT1-S507A stable transfectants, suggesting that Chk2 exerts its effect on centrosomes via MYPT1. Collectively, we have identified a Chk2-MYPT1-PLK1 axis in regulating centrosome maturation. Abbreviations: Chk2: checkpoint kinase 2; MYPT1: myosin phosphatase targeting subunit 1; PP1cβ: protein phosphatase 1c β; Noc: nocodazole; IP: immunoprecipitation; IB: immunoblotting; LC-MS/MS: liquid chromatography-tandem mass spectrometry; Chk2: checkpoint kinase 2; KD: kinase domain; WT: wild type; Ub: ubiquitin; DAPI: 4',6-diamidino-2-phenylindole; IF: Immunofluorescence; IR: ionizing radiation; siCHK2: siRNA targeting CHK2.
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Affiliation(s)
- Shanshan Nai
- Beijing Key Laboratory of DNA damage Response, College of Life Sciences, Capital Normal University, Beijing, China
| | - Yingxin Shi
- Beijing Key Laboratory of DNA damage Response, College of Life Sciences, Capital Normal University, Beijing, China
| | - Huanwei Ru
- Beijing Key Laboratory of DNA damage Response, College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA damage Response, College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhe Li
- Beijing Key Laboratory of DNA damage Response, College of Life Sciences, Capital Normal University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA damage Response, College of Life Sciences, Capital Normal University, Beijing, China
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, China
| | - Jing Li
- Beijing Key Laboratory of DNA damage Response, College of Life Sciences, Capital Normal University, Beijing, China
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38
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Zhao K, Cheng S, Miao N, Xu P, Lu X, Zhang Y, Wang M, Ouyang X, Yuan X, Liu W, Lu X, Zhou P, Gu J, Zhang Y, Qiu D, Jin Z, Su C, Peng C, Wang JH, Dong MQ, Wan Y, Ma J, Cheng H, Huang Y, Yu Y. A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation. Nat Cell Biol 2019; 21:1261-1272. [PMID: 31570835 DOI: 10.1038/s41556-019-0396-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022]
Abstract
The repression of transposons by the Piwi-interacting RNA (piRNA) pathway is essential to protect animal germ cells. In Drosophila, Panoramix enforces transcriptional silencing by binding to the target-engaged Piwi-piRNA complex, although the precise mechanisms by which this occurs remain elusive. Here, we show that Panoramix functions together with a germline-specific paralogue of a nuclear export factor, dNxf2, and its cofactor dNxt1 (p15), to suppress transposon expression. The transposon RNA-binding protein dNxf2 is required for animal fertility and Panoramix-mediated silencing. Transient tethering of dNxf2 to nascent transcripts leads to their nuclear retention. The NTF2 domain of dNxf2 competes dNxf1 (TAP) off nucleoporins, a process required for proper RNA export. Thus, dNxf2 functions in a Panoramix-dNxf2-dependent TAP/p15 silencing (Pandas) complex that counteracts the canonical RNA exporting machinery and restricts transposons to the nuclear peripheries. Our findings may have broader implications for understanding how RNA metabolism modulates heterochromatin formation.
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Affiliation(s)
- Kang Zhao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Sha Cheng
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Na Miao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ping Xu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,National Engineering Laboratory of AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Xiaohua Lu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuhan Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Ming Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuan Ouyang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Yuan
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Weiwei Liu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xin Lu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Gu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiqun Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ding Qiu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhaohui Jin
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Chen Su
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua Wang
- Graduate School of Peking Union Medical College and Chinese Academy of Sciences of Medical Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Youzhong Wan
- National Engineering Laboratory of AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Cheng
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ying Huang
- University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. .,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yang Yu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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39
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Jones AX, Cao Y, Tang YL, Wang JH, Ding YH, Tan H, Chen ZL, Fang RQ, Yin J, Chen RC, Zhu X, She Y, Huang N, Shao F, Ye K, Sun RX, He SM, Lei X, Dong MQ. Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers. Nat Commun 2019; 10:3911. [PMID: 31477730 PMCID: PMC6718413 DOI: 10.1038/s41467-019-11917-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially. Cross-linking mass spectrometry can provide insights into protein structures and interactions but its scope depends on the reactivity of the cross-linker. Here, the authors develop Arg-Arg and Lys-Arg cross-linkers, which provide structural information elusive to the widely used Lys-Lys cross-linkers.
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Affiliation(s)
- Alexander X Jones
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yong Cao
- School of Life Sciences, Peking University, 100871, Beijing, China.,National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yu-Liang Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yue-He Ding
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Hui Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zhen-Lin Chen
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Run-Qian Fang
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jili Yin
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Rong-Chang Chen
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xing Zhu
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yang She
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Niu Huang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Keqiong Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Rui-Xiang Sun
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206, Beijing, China.
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40
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Chen ZL, Meng JM, Cao Y, Yin JL, Fang RQ, Fan SB, Liu C, Zeng WF, Ding YH, Tan D, Wu L, Zhou WJ, Chi H, Sun RX, Dong MQ, He SM. A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nat Commun 2019; 10:3404. [PMID: 31363125 PMCID: PMC6667459 DOI: 10.1038/s41467-019-11337-z] [Citation(s) in RCA: 220] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 06/20/2019] [Indexed: 01/05/2023] Open
Abstract
We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development. The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.
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Affiliation(s)
- Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Ming Meng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Cao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Ji-Li Yin
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Run-Qian Fang
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng-Bo Fan
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Liu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Feng Zeng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue-He Ding
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Long Wu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Jing Zhou
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chi
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui-Xiang Sun
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China.
| | - Si-Min He
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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41
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Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem 2019; 91:6953-6961. [PMID: 31045356 PMCID: PMC6625963 DOI: 10.1021/acs.analchem.9b00658] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,Faculty of Science , University of Zurich , 8006 Zurich , Switzerland
| | - Bruno C Amaral
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Philip Andrews
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Christoph Borchers
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada
| | - Nicolas I Brodie
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Yong Cao
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Stéphane Chaignepain
- CBMN, UMR 5248, CNRS , Université de Bordeaux, INP Bordeaux , Pessac 33607 , France
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Stéphane Claverol
- Centre de Génomique Fonctionnelle, Plateforme Protéome , Université de Bordeaux , Bordeaux 33000 , France
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Trisha Davis
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Gianluca Degliesposti
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Nufar Edinger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Michael Götze
- Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Francisco Gomes-Neto
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Fabio C Gozzo
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Craig Gutierrez
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Caroline Haupt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Franz Herzog
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Lan Huang
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Michael R Hoopmann
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Oleg Klykov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Zdeněk Kukačka
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Fan Liu
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Michael J MacCoss
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Karl Mechtler
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Ravit Mesika
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Robert L Moritz
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nagarjuna Nagaraj
- Biochemistry Core Facility , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Victor Nesati
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Ana G C Neves-Ferreira
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Robert Ninnis
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Petr Novák
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Francis J O'Reilly
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany
| | - Matthias Pelzing
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Evgeniy Petrotchenko
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Lolita Piersimoni
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Manolo Plasencia
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Tara Pukala
- Discipline of Chemistry, Faculty of Sciences , University of Adelaide , North Terrace, Adelaide , South Australia 5005 , Australia
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany.,Wellcome Trust Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , EH9 3BF Edinburgh , U.K
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Carolin Sailer
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Chris P Sarnowski
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,PhD Program in Systems Biology , University of Zurich and ETH Zurich , 8092 Zurich , Switzerland
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Yi Shi
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Moriya Slavin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Frank Sobott
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , 2020 Antwerp , Belgium.,The Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology , University of Leeds , LS2 9JT Leeds , U.K
| | - Victor Solis-Mezarino
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Heike Stephanowitz
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Florian Stengel
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Christian E Stieger
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Esben Trabjerg
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Michael Trnka
- UCSF Mass Spectrometry Facility , Genentech Hall, 600 16th Street , San Francisco , California 94158 , United States
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Yufei Xiang
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - Sule Yilmaz
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Alex Zelter
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Daniel Ziemianowicz
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
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42
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Liu G, Zheng X, Guan H, Cao Y, Qu H, Kang J, Ren X, Lei J, Dong MQ, Li X, Li H. Architecture of Saccharomyces cerevisiae SAGA complex. Cell Discov 2019; 5:25. [PMID: 31069110 PMCID: PMC6502868 DOI: 10.1038/s41421-019-0094-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 11/25/2022] Open
Affiliation(s)
- Gaochao Liu
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Xiangdong Zheng
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Haipeng Guan
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Yong Cao
- 2National Institute of Biological Sciences, Beijing, 102206 China
| | - Hongyuan Qu
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Junqing Kang
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Xiangle Ren
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Jianlin Lei
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Meng-Qiu Dong
- 2National Institute of Biological Sciences, Beijing, 102206 China
| | - Xueming Li
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Haitao Li
- 1MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China
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43
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Huang X, Sun S, Wang X, Fan F, Zhou Q, Lu S, Cao Y, Wang QW, Dong MQ, Yao J, Sui SF. Mechanistic insights into the SNARE complex disassembly. Sci Adv 2019; 5:eaau8164. [PMID: 30989110 PMCID: PMC6457932 DOI: 10.1126/sciadv.aau8164] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/19/2019] [Indexed: 05/16/2023]
Abstract
NSF (N-ethylmaleimide-sensitive factor) and α-SNAP (α-soluble NSF attachment protein) bind to the SNARE (soluble NSF attachment protein receptor) complex, the minimum machinery to mediate membrane fusion, to form a 20S complex, which disassembles the SNARE complex for reuse. We report the cryo-EM structures of the α-SNAP-SNARE subcomplex and the NSF-D1D2 domain in the 20S complex at 3.9- and 3.7-Å resolutions, respectively. Combined with the biochemical and electrophysiological analyses, we find that α-SNAPs use R116 through electrostatic interactions and L197 through hydrophobic interactions to apply force mainly on two positions of the VAMP protein to execute disassembly process. Furthermore, we define the interaction between the amino terminus of the SNARE helical bundle and the pore loop of the NSF-D1 domain and demonstrate its essential role as a potential anchor for SNARE complex disassembly. Our studies provide a rotation model of α-SNAP-mediated disassembly of the SNARE complex.
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Affiliation(s)
- Xuan Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaojing Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fenghui Fan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Zhou
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shan Lu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yong Cao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qiu-Wen Wang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jun Yao
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Corresponding author.
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44
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Weng C, Kosalka J, Berkyurek AC, Stempor P, Feng X, Mao H, Zeng C, Li WJ, Yan YH, Dong MQ, Morero NR, Zuliani C, Barabas O, Ahringer J, Guang S, Miska EA. The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans. Genes Dev 2019; 33:90-102. [PMID: 30567997 PMCID: PMC6317315 DOI: 10.1101/gad.319293.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/19/2018] [Indexed: 01/15/2023]
Abstract
Piwi-interacting RNAs (piRNAs) engage Piwi proteins to suppress transposons and nonself nucleic acids and maintain genome integrity and are essential for fertility in a variety of organisms. In Caenorhabditis elegans, most piRNA precursors are transcribed from two genomic clusters that contain thousands of individual piRNA transcription units. While a few genes have been shown to be required for piRNA biogenesis, the mechanism of piRNA transcription remains elusive. Here we used functional proteomics approaches to identify an upstream sequence transcription complex (USTC) that is essential for piRNA biogenesis. The USTC contains piRNA silencing-defective 1 (PRDE-1), SNPC-4, twenty-one-U fouled-up 4 (TOFU-4), and TOFU-5. The USTC forms unique piRNA foci in germline nuclei and coats the piRNA cluster genomic loci. USTC factors associate with the Ruby motif just upstream of type I piRNA genes. USTC factors are also mutually dependent for binding to the piRNA clusters and forming the piRNA foci. Interestingly, USTC components bind differentially to piRNAs in the clusters and other noncoding RNA genes. These results reveal the USTC as a striking example of the repurposing of a general transcription factor complex to aid in genome defense against transposons.
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Affiliation(s)
- Chenchun Weng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Joanna Kosalka
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Ahmet C Berkyurek
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Przemyslaw Stempor
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Hui Mao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chenming Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wen-Jun Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Natalia Rosalía Morero
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Julie Ahringer
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Eric A Miska
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
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45
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Chi H, Liu C, Yang H, Zeng WF, Wu L, Zhou WJ, Wang RM, Niu XN, Ding YH, Zhang Y, Wang ZW, Chen ZL, Sun RX, Liu T, Tan GM, Dong MQ, Xu P, Zhang PH, He SM. Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine. Nat Biotechnol 2018; 36:nbt.4236. [PMID: 30295672 DOI: 10.1038/nbt.4236] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 08/03/2018] [Indexed: 12/27/2022]
Abstract
We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70-85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset.
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Affiliation(s)
- Hao Chi
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Yang
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Feng Zeng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Long Wu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Jing Zhou
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Min Wang
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Nan Niu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue-He Ding
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China
| | - Zhao-Wei Wang
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Xiang Sun
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Liu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Guang-Ming Tan
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Pei-Heng Zhang
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Si-Min He
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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46
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Kaasbøll OJ, Gadicherla AK, Wang JH, Monsen VT, Hagelin EMV, Dong MQ, Attramadal H. Connective tissue growth factor (CCN2) is a matricellular preproprotein controlled by proteolytic activation. J Biol Chem 2018; 293:17953-17970. [PMID: 30262666 DOI: 10.1074/jbc.ra118.004559] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/23/2018] [Indexed: 11/06/2022] Open
Abstract
Connective tissue growth factor (CTGF; now often referred to as CCN2) is a secreted protein predominantly expressed during development, in various pathological conditions that involve enhanced fibrogenesis and tissue fibrosis, and in several cancers and is currently an emerging target in several early-phase clinical trials. Tissues containing high CCN2 activities often display smaller degradation products of full-length CCN2 (FL-CCN2). Interpretation of these observations is complicated by the fact that a uniform protein structure that defines biologically active CCN2 has not yet been resolved. Here, using DG44 CHO cells engineered to produce and secrete FL-CCN2 and cell signaling and cell physiological activity assays, we demonstrate that FL-CCN2 is itself an inactive precursor and that a proteolytic fragment comprising domains III (thrombospondin type 1 repeat) and IV (cystine knot) appears to convey all biologically relevant activities of CCN2. In congruence with these findings, purified FL-CCN2 could be cleaved and activated following incubation with matrix metalloproteinase activities. Furthermore, the C-terminal fragment of CCN2 (domains III and IV) also formed homodimers that were ∼20-fold more potent than the monomeric form in activating intracellular phosphokinase cascades. The homodimer elicited activation of fibroblast migration, stimulated assembly of focal adhesion complexes, enhanced RANKL-induced osteoclast differentiation of RAW264.7 cells, and promoted mammosphere formation of MCF-7 mammary cancer cells. In conclusion, CCN2 is synthesized and secreted as a preproprotein that is autoinhibited by its two N-terminal domains and requires proteolytic processing and homodimerization to become fully biologically active.
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Affiliation(s)
- Ole Jørgen Kaasbøll
- From the Institute for Surgical Research, Oslo University Hospital and University of Oslo, NO-0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, NO-0316 Oslo, Norway
| | - Ashish K Gadicherla
- From the Institute for Surgical Research, Oslo University Hospital and University of Oslo, NO-0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, NO-0316 Oslo, Norway
| | - Jian-Hua Wang
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Vivi Talstad Monsen
- From the Institute for Surgical Research, Oslo University Hospital and University of Oslo, NO-0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, NO-0316 Oslo, Norway
| | - Else Marie Valbjørn Hagelin
- From the Institute for Surgical Research, Oslo University Hospital and University of Oslo, NO-0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, NO-0316 Oslo, Norway
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Håvard Attramadal
- From the Institute for Surgical Research, Oslo University Hospital and University of Oslo, NO-0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, NO-0316 Oslo, Norway.
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47
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Zhou D, Zhu X, Zheng S, Tan D, Dong MQ, Ye K. Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate. Protein Cell 2018; 10:120-130. [PMID: 29557065 PMCID: PMC6340896 DOI: 10.1007/s13238-018-0526-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/04/2018] [Indexed: 11/25/2022] Open
Abstract
Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established. Here, we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 Å resolution, revealing a half-assembled subunit. Domains I, II and VI of 25S/5.8S rRNA pack tightly into a native-like substructure, but domains III, IV and V are not assembled. The structure contains 12 assembly factors and 19 ribosomal proteins, many of which are required for early processing of large subunit rRNA. The Brx1-Ebp2 complex would interfere with the assembly of domains IV and V. Rpf1, Mak16, Nsa1 and Rrp1 form a cluster that consolidates the joining of domains I and II. Our structure reveals a key intermediate on the path to establishing the global architecture of 60S subunits.
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Affiliation(s)
- Dejian Zhou
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Keqiong Ye
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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48
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Hu X, Li Z, Ding Y, Geng Q, Xiahou Z, Ru H, Dong MQ, Xu X, Li J. Chk1 modulates the interaction between myosin phosphatase targeting protein 1 (MYPT1) and protein phosphatase 1cβ (PP1cβ). Cell Cycle 2018; 17:421-427. [PMID: 29262732 PMCID: PMC5927650 DOI: 10.1080/15384101.2017.1418235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/11/2017] [Indexed: 01/05/2023] Open
Abstract
Polo-like kinase 1 (Plk1) is an instrumental kinase that modulates many aspects of the cell cycle. Previous investigations have indicated that Plk1 is a target of the DNA damage response, and Plk1 inhibition is dependent on ATM/ATR and Chk1. But the exact mechanism remains elusive. In a proteomic screen to identify Chk1-interacting proteins, we found that myosin phosphatase targeting protein 1 (MYPT1) was present in the immunocomplex. MYPT1 is phosphorylated by CDK1, thus recruiting protein phosphatase 1β (PP1cβ) to dephosphorylate and inactivate Plk1. Here we identified that Chk1 directly interacts with MYPT1 and preferentially phosphorylates MYPT1 at Ser20, which is essential for MYPT1-PP1cβ interaction and subsequent Plk1 dephosphorylation. Phosphorylation of Ser20 is abolished during mitotic damage when Chk1 is inhibited. The degradation of MYPT1 is also regulated by Chk1 phosphorylation. Our results thus unveil the underlying machinery that attenuates Plk1 activity during mitotic damage through Chk1-induced phosphorylation of MYPT1.
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Affiliation(s)
- Xiaomei Hu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhe Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhikai Xiahou
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Huanwei Ru
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
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49
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Mei K, Li Y, Wang S, Shao G, Wang J, Ding Y, Luo G, Yue P, Liu JJ, Wang X, Dong MQ, Wang HW, Guo W. Cryo-EM structure of the exocyst complex. Nat Struct Mol Biol 2018; 25:139-146. [PMID: 29335562 PMCID: PMC5971111 DOI: 10.1038/s41594-017-0016-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/07/2017] [Indexed: 12/22/2022]
Abstract
The exocyst is an evolutionarily conserved octameric protein complex that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane during exocytosis and is implicated in many cellular processes such as cell polarization, cytokinesis, ciliogenesis and tumor invasion. Using cryo-EM and chemical cross-linking MS (CXMS), we solved the structure of the Saccharomyces cerevisiae exocyst complex at an average resolution of 4.4 Å. Our model revealed the architecture of the exocyst and led to the identification of the helical bundles that mediate the assembly of the complex at its core. Sequence analysis suggests that these regions are evolutionarily conserved across eukaryotic systems. Additional cell biological data suggest a mechanism for exocyst assembly that leads to vesicle tethering at the plasma membrane.
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Affiliation(s)
- Kunrong Mei
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yan Li
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Shaoxiao Wang
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Guangcan Shao
- National Institute of Biological Sciences, Beijing, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, China
| | - Guangzuo Luo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Yue
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jun-Jie Liu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China. .,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. .,School of Life Sciences, Tsinghua University, Beijing, China. .,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.
| | - Wei Guo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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Zhang X, Wang JH, Tan D, Li Q, Li M, Gong Z, Tang C, Liu Z, Dong MQ, Lei X. Carboxylate-Selective Chemical Cross-Linkers for Mass Spectrometric Analysis of Protein Structures. Anal Chem 2018; 90:1195-1201. [DOI: 10.1021/acs.analchem.7b03789] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyun Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jian-Hua Wang
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Dan Tan
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Qiang Li
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Maodong Li
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhou Gong
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Chun Tang
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Zhirong Liu
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meng-Qiu Dong
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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