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Koli S, Shetty S. Ribosomal dormancy at the nexus of ribosome homeostasis and protein synthesis. Bioessays 2024; 46:e2300247. [PMID: 38769702 DOI: 10.1002/bies.202300247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/05/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Dormancy or hibernation is a non-proliferative state of cells with low metabolic activity and gene expression. Dormant cells sequester ribosomes in a translationally inactive state, called dormant/hibernating ribosomes. These dormant ribosomes are important for the preservation of ribosomes and translation shut-off. While recent studies attempted to elucidate their modes of formation, the regulation and roles of the diverse dormant ribosomal populations are still largely understudied. The mechanistic details of the formation of dormant ribosomes in stress and especially their disassembly during recovery remain elusive. In this review, we discuss the roles of dormant ribosomes and their potential regulatory mechanisms. Furthermore, we highlight the paradigms that need to be answered in the field of ribosomal dormancy.
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Affiliation(s)
- Saloni Koli
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Sunil Shetty
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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2
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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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3
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Lu L, Ye Z, Zhang R, Olsen JV, Yuan Y, Mao Y. ETD-Based Proteomic Profiling Improves Arginine Methylation Identification and Reveals Novel PRMT5 Substrates. J Proteome Res 2024; 23:1014-1027. [PMID: 38272855 DOI: 10.1021/acs.jproteome.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Protein arginine methylations are important post-translational modifications (PTMs) in eukaryotes, regulating many biological processes. However, traditional collision-based mass spectrometry methods inevitably cause neutral losses of methylarginines, preventing the deep mining of biologically important sites. Herein we developed an optimized mass spectrometry workflow based on electron-transfer dissociation (ETD) with supplemental activation for proteomic profiling of arginine methylation in human cells. Using symmetric dimethylarginine (sDMA) as an example, we show that the ETD-based optimized workflow significantly improved the identification and site localization of sDMA. Quantitative proteomics identified 138 novel sDMA sites as potential PRMT5 substrates in HeLa cells. Further biochemical studies on SERBP1, a newly identified PRMT5 substrate, confirmed the coexistence of sDMA and asymmetric dimethylarginine in the central RGG/RG motif, and loss of either methylation caused increased the recruitment of SERBP1 to stress granules under oxidative stress. Overall, our optimized workflow not only enabled the identification and localization of extensive, nonoverlapping sDMA sites in human cells but also revealed novel PRMT5 substrates whose sDMA may play potentially important biological functions.
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Affiliation(s)
- Lingzi Lu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Sun Yat-sen University, Guangzhou 510006, China
| | - Zilu Ye
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Rou Zhang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Sun Yat-sen University, Guangzhou 510006, China
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Yanqiu Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Sun Yat-sen University, Guangzhou 510006, China
| | - Yang Mao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Sun Yat-sen University, Guangzhou 510006, China
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4
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Zhou J, Wang T, Zhang H, Liu J, Wei P, Xu R, Yan Q, Chen G, Li W, Gao SJ, Lu C. KSHV vIL-6 promotes SIRT3-induced deacetylation of SERBP1 to inhibit ferroptosis and enhance cellular transformation by inducing lipoyltransferase 2 mRNA degradation. PLoS Pathog 2024; 20:e1012082. [PMID: 38470932 PMCID: PMC10959363 DOI: 10.1371/journal.ppat.1012082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Ferroptosis, a defensive strategy commonly employed by the host cells to restrict pathogenic infections, has been implicated in the development and therapeutic responses of various types of cancer. However, the role of ferroptosis in oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV)-induced cancers remains elusive. While a growing number of non-histone proteins have been identified as acetylation targets, the functions of these modifications have yet to be revealed. Here, we show KSHV reprogramming of host acetylation proteomics following cellular transformation of rat primary mesenchymal precursor. Among them, SERPINE1 mRNA binding protein 1 (SERBP1) deacetylation is increased and required for KSHV-induced cellular transformation. Mechanistically, KSHV-encoded viral interleukin-6 (vIL-6) promotes SIRT3 deacetylation of SERBP1, preventing its binding to and protection of lipoyltransferase 2 (Lipt2) mRNA from mRNA degradation resulting in ferroptosis. Consequently, a SIRT3-specific inhibitor, 3-TYP, suppresses KSHV-induced cellular transformation by inducing ferroptosis. Our findings unveil novel roles of vIL-6 and SERBP1 deacetylation in regulating ferroptosis and KSHV-induced cellular transformation, and establish the vIL-6-SIRT3-SERBP1-ferroptosis pathways as a potential new therapeutic target for KSHV-associated cancers.
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Affiliation(s)
- Jing Zhou
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Tianjiao Wang
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Haoran Zhang
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Jianhong Liu
- Department of Pathology, Changzhou Third People’s Hospital, Changzhou, People’s Republic of China
| | - Pengjun Wei
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Ruoqi Xu
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Qin Yan
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
- Changzhou Medical Center, Nanjing Medical University, Nanjing, People’s Republic of China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Guochun Chen
- Department of Infectious Diseases, Changzhou Third People’s Hospital, Changzhou, People’s Republic of China
| | - Wan Li
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
- Changzhou Medical Center, Nanjing Medical University, Nanjing, People’s Republic of China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Shou-Jiang Gao
- Tumor Virology Program, UPMC Hillman Cancer Center, and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chun Lu
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
- Changzhou Medical Center, Nanjing Medical University, Nanjing, People’s Republic of China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People’s Republic of China
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5
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Silencing of Ago-2 Interacting Protein SERBP1 Relieves KCC2 Repression by miR-92 in Neurons. Cells 2022; 11:cells11061052. [PMID: 35326503 PMCID: PMC8947033 DOI: 10.3390/cells11061052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play important roles in modulating miRNA-mediated mRNA target repression. Argonaute2 (Ago2) is an essential component of the RNA-induced silencing complex (RISC) that plays a central role in silencing mechanisms via small non-coding RNA molecules known as siRNAs and miRNAs. Small RNAs loaded into Argonaute proteins catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and mRNA target destabilization. In previous studies we have shown that KCC2, a neuronal Cl (−) extruding K (+) Cl (−) co-transporter 2, is regulated by miR-92 in neuronal cells. Searching for Ago2 partners by immunoprecipitation and LC-MS/MS analysis, we isolated among other proteins the Serpine mRNA binding protein 1 (SERBP1) from SH-SY5Y neuroblastoma cells. Exploring the role of SERBP1 in miRNA-mediated gene silencing in SH-SY5Y cells and primary hippocampal neurons, we demonstrated that SERBP1 silencing regulates KCC2 expression through the 3′ untranslated region (UTR). In addition, we found that SERBP1 as well as Ago2/miR-92 complex bind to KCC2 3′UTR. Finally, we demonstrated the attenuation of miR-92-mediated repression of KCC2 3′UTR by SERBP1 silencing. These findings advance our knowledge regarding the miR-92-mediated modulation of KCC2 translation in neuronal cells and highlight SERBP1 as a key component of this gene regulation.
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RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication. J Virol 2022; 96:e0196221. [PMID: 35266803 DOI: 10.1128/jvi.01962-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no effective treatment is available. DENV relies heavily on the host cellular machinery for productive infection. Here, we show that the scaffold protein RACK1, which is part of the DENV replication complex, mediates infection by binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to an RNA interference screen-identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV genome. Genetic ablation of Vigilin or SERBP1 rendered cells poorly susceptible to DENV, as well as related flaviviruses, by hampering the translation and replication steps. Finally, we established that a Vigilin or SERBP1 mutant lacking RACK1 binding but still interacting with the viral RNA is unable to mediate DENV infection. We propose that RACK1 recruits Vigilin and SERBP1, linking the DENV genome to the translation machinery for efficient infection. IMPORTANCE We recently identified the scaffolding RACK1 protein as an important host-dependency factor for dengue virus (DENV), a positive-stranded RNA virus responsible for the most prevalent mosquito-borne viral disease worldwide. Here, we have performed the first RACK1 interactome in human cells and identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV RNA to regulate viral replication. Importantly, Vigilin and SERBP1 interact with RACK1 and the DENV viral RNA (vRNA) to mediate viral replication. Overall, our results suggest that RACK1 acts as a binding platform at the surface of the 40S ribosomal subunit to recruit Vigilin and SERBP1, which may therefore function as linkers between the viral RNA and the translation machinery to facilitate infection.
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7
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Ko S, Yeom E, Chun YL, Mun H, Howard-McGuire M, Millison NT, Jung J, Lee KP, Lee C, Lee KS, Delaney JR, Yoon JH. Profiling of RNA-binding Proteins Interacting With Glucagon and Adipokinetic Hormone mRNAs. J Lipid Atheroscler 2022; 11:55-72. [PMID: 35118022 PMCID: PMC8792818 DOI: 10.12997/jla.2022.11.1.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/05/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Glucagon in mammals and its homolog (adipokinetic hormone [AKH] in Drosophila melanogaster) are peptide hormones which regulate lipid metabolism by breaking down triglycerides. Although regulatory mechanisms of glucagon and AKH expression have been widely studied, post-transcriptional gene expression of glucagon has not been investigated thoroughly. In this study, we aimed to profile proteins binding with Gcg messenger RNA (mRNA) in mouse and Akh mRNA in Drosophila. METHODS Drosophila Schneider 2 (S2) and mouse 3T3-L1 cell lysates were utilized for affinity pull down of Akh and Gcg mRNA respectively using biotinylated anti-sense DNA oligoes against target mRNAs. Mass spectrometry and computational network analysis revealed mRNA-interacting proteins residing in functional proximity. RESULTS We observed that 1) 91 proteins interact with Akh mRNA from S2 cell lysates, 2) 34 proteins interact with Gcg mRNA from 3T3-L1 cell lysates. 3) Akh mRNA interactome revealed clusters of ribosomes and known RNA-binding proteins (RBPs). 4) Gcg mRNA interactome revealed mRNA-binding proteins including Plekha7, zinc finger protein, carboxylase, lipase, histone proteins and a cytochrome, Cyp2c44. 5) Levels of Gcg mRNA and its interacting proteins are elevated in skeletal muscles isolated from old mice compared to ones from young mice. CONCLUSION Akh mRNA in S2 cells are under active translation in a complex of RBPs and ribosomes. Gcg mRNA in mouse precursor adipocyte is in a condition distinct from Akh mRNA due to biochemical interactions with a subset of RBPs and histones. We anticipate that our study contributes to investigating regulatory mechanisms of Gcg and Akh mRNA decay, translation, and localization.
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Affiliation(s)
- Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Eunbyul Yeom
- Neurophysiology and Metabolism Research Group, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Yoo Lim Chun
- Department of Biomedical Science, Graduation School, Kyung Hee University, Seoul, Korea
| | - Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Marina Howard-McGuire
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Nathan T. Millison
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Junyang Jung
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Kwang-Pyo Lee
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kyu-Sun Lee
- Neurophysiology and Metabolism Research Group, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Joe R. Delaney
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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8
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Nishimura T, Fujii K, Nakamura H, Naruki S, Sakai H, Kimura H, Miyazawa T, Takagi M, Furuya N, Marko-Varga G, Kato H, Saji H. Protein co-expression network-based profiles revealed from laser-microdissected cancerous cells of lung squamous-cell carcinomas. Sci Rep 2021; 11:20209. [PMID: 34642392 PMCID: PMC8511190 DOI: 10.1038/s41598-021-99695-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/30/2021] [Indexed: 01/06/2023] Open
Abstract
No therapeutic targets have been identified for lung squamous cell cancer (SqCC) which is the second most prevalent lung cancer because its molecular profiles remain unclear. This study aimed to unveil disease-related protein networks by proteomic and bioinformatic assessment of laser-microdissected cancerous cells from seven SqCCs compared with eight representative lung adenocarcinomas. We identified three network modules significant to lung SqCC using weighted gene co-expression network analysis. One module was intrinsically annotated to keratinization and cell proliferation of SqCC, accompanied by hypoxia-induced aerobic glycolysis, in which key regulators were activated (HIF1A, ROCK2, EFNA1-5) and highly suppressed (KMT2D). The other two modules were significant for translational initiation, nonsense-mediated mRNA decay, inhibited cell death, and interestingly, eIF2 signaling, in which key regulators, MYC and MLXIPL, were highly activated. Another key regulator LARP1, the master regulator in cap-dependent translation, was highly suppressed although upregulations were observed for hub proteins including EIF3F and LARP1 targeted ribosomal proteins, among which PS25 is the key ribosomal protein in IRES-dependent translation. Our results suggest an underlying progression mechanism largely caused by switching to the cap-independent, IRES-dependent translation of mRNA subsets encoding oncogenic proteins. Our findings may help to develop therapeutic strategies to improve patient outcomes.
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Affiliation(s)
- Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan. .,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.
| | - Kiyonaga Fujii
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.,Laboratory of Analytical Chemistry, Daiichi University of Pharmacy, Fukuoka, Fukuoka, 815-8511, Japan
| | - Haruhiko Nakamura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Saeko Naruki
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Kanagawa, 216-8511, Japan
| | - Hiroki Sakai
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Hiroyuki Kimura
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Tomoyuki Miyazawa
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Masayuki Takagi
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Kanagawa, 216-8511, Japan
| | - Naoki Furuya
- Division of Respiratory Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Gyorgy Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Harubumi Kato
- Tokyo Medical University, Tokyo, 160-0023, Japan.,International University of Health and Welfare, Tokyo, 107-8402, Japan
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
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Baudin A, Moreno-Romero AK, Xu X, Selig EE, Penalva LOF, Libich DS. Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes. Front Mol Biosci 2021; 8:744707. [PMID: 34631798 PMCID: PMC8497785 DOI: 10.3389/fmolb.2021.744707] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/07/2021] [Indexed: 11/18/2022] Open
Abstract
RNA binding proteins (RBPs) are essential for critical biological processes such as translation regulation and mRNA processing, and misfunctions of these proteins are associated with diseases such as cancer and neurodegeneration. SERBP1 (SERPINE1 mRNA Binding Protein 1) is an RBP that comprises two RG/RGG repeat regions yet lacks other recognizable RNA-binding motifs. It is involved in mRNA maturation, and translational regulation. It was initially identified as a hyaluronic acid binding protein, but recent studies have identified central roles for SERBP1 in brain function and development, especially neurogenesis and synaptogenesis. SERBP1 regulates One-carbon metabolism and epigenetic modification of histones, and increased SERBP1 expression in cancers such as leukemia, ovarian, prostate, liver and glioblastoma is correlated with poor patient outcomes. Despite these important regulatory roles for SERBP1, little is known about its structural and dynamic properties, nor about the molecular mechanisms governing its interaction with mRNA. Here, we define SERBP1 as an intrinsically disordered protein, containing highly conserved elements that were shown to be functionally important. The RNA binding activity of SERBP1 was explored using solution NMR and other biophysical techniques. The outcome of these experiments revealed that SERBP1 preferentially samples compact conformations including a central, stable α-helix and show that SERBP1 recognizes G-rich RNA sequences at the C-terminus involving the RGG box and neighboring residues. Despite the role in RNA recognition, the RGG boxes do not seem to stabilize the central helix and the central helix does not participate in RNA binding. Further, SERBP1 undergoes liquid-liquid phase separation, mediated by salt and RNA, and both RGG boxes are necessary for the efficient formation of condensed phases. Together, these results provide a foundation for understanding the molecular mechanisms of SERBP1 functions in physiological and pathological processes.
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Affiliation(s)
- Antoine Baudin
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Alma K Moreno-Romero
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Xiaoping Xu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Emily E Selig
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Luiz O F Penalva
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Cell Systems and Anatomy, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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10
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Baudin A, Xu X, Libich DS. The 1H, 15N and 13C resonance assignments of the C-terminal domain of Serpine mRNA binding protein 1 (SERBP1). BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:461-466. [PMID: 34436734 PMCID: PMC9990118 DOI: 10.1007/s12104-021-10046-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
SERBP1 is a multifunctional mRNA-binding protein that has been shown to play a regulatory role in a number of biological processes such as thrombosis, DNA damage repair, and the cellular response to nutrient deprivation. Additionally, SERBP1 is upregulated in glioblastoma, leukemia as well as liver, prostrate and ovarian cancers where it has been implicated in metastatic disease and poor patient outcomes. SERBP1 binds target mRNA, stabilizing and regulating the post-translational expression of the transcript. Since SERBP1 lacks canonical RNA-binding motifs such as RRM domains or zinc fingers, its target recognition and binding mechanisms are not well understood. Recent reports suggest that it is capable of recognizing both RNA sequence motifs and structured domains. Here we report the production and purification of the intrinsically disordered C-terminal domain of SERBP1, the assignment of the 1H, 13C, 15N backbone resonances of the protein by solution-state NMR, and secondary structure predictions. We show that the protein is not entirely disordered and identify an α-helix that was stable under the experimental conditions. This work is the first step toward understanding the structural basis underpinning the molecular mechanisms of SERBP1 functions, particularly interactions with mRNA targets.
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Affiliation(s)
- Antoine Baudin
- Department of Biochemistry and Structural Biology, and Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Xiaoping Xu
- Department of Biochemistry and Structural Biology, and Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - David S Libich
- Department of Biochemistry and Structural Biology, and Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA.
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11
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Salilew-Wondim D, Tesfaye D, Rings F, Held-Hoelker E, Miskel D, Sirard MA, Tholen E, Schellander K, Hoelker M. The global gene expression outline of the bovine blastocyst: reflector of environmental conditions and predictor of developmental capacity. BMC Genomics 2021; 22:408. [PMID: 34082721 PMCID: PMC8176733 DOI: 10.1186/s12864-021-07693-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022] Open
Abstract
Background Morphological evaluation of embryos has been used to screen embryos for transfer. However, the repeatability and accuracy of this method remains low. Thus, evaluation of an embryo’s gene expression signature with respect to its developmental capacity could provide new opportunities for embryo selection. Since the gene expression outline of an embryo is considered as an aggregate of its intrinsic characteristics and culture conditions, we have compared transcriptome profiles of in vivo and in vitro derived blastocysts in relation to pregnancy outcome to unravel the discrete effects of developmental competence and environmental conditions on bovine embryo gene expression outlines. To understand whether the gene expression patterns could be associated with blastocyst developmental competency, the global transcriptome profile of in vivo (CVO) and in vitro (CVT) derived competent blastocysts that resulted in pregnancy was investigated relative to that of in vivo (NVO) and in vitro (NVT) derived blastocysts which did not establish initial pregnancy, respectively while to unravel the effects of culture condition on the transcriptome profile of embryos, the transcriptional activity of the CVO group was compared to the CVT group and the NVO group was compared to the NVT ones. Results A total of 700 differentially expressed genes (DEGs) were identified between CVO and NVO blastocysts. These gene transcripts represent constitutive regions, indel variants, 3′-UTR sequence variants and novel transcript regions. The majority (82%) of these DEGs, including gene clusters like ATP synthases, eukaryotic translation initiation factors, ribosomal proteins, mitochondrial ribosomal proteins, NADH dehydrogenase and cytochrome c oxidase subunits were enriched in the CVO group. These DEGs were involved in pathways associated with glycolysis/glycogenesis, citrate acid cycle, pyruvate metabolism and oxidative phosphorylation. Similarly, a total of 218 genes were differentially expressed between CVT and NVT groups. Of these, 89%, including TPT1, PDIA6, HSP90AA1 and CALM, were downregulated in the CVT group and those DEGs were overrepresented in pathways related to protein processing, endoplasmic reticulum, spliceasome, ubiquitone mediated proteolysis and steroid biosynthesis. On the other hand, although both the CVT and CVO blastocyst groups resulted in pregnancy, a total of 937 genes were differential expressed between the two groups. Compared to CVO embryos, the CVT ones exhibited downregulation of gene clusters including ribosomal proteins, mitochondrial ribosomal protein, eukaryotic translation initiation factors, ATP synthases, NADH dehydrogenase and cytochrome c oxidases. Nonetheless, downregulation of these genes could be associated with pre and postnatal abnormalities observed after transfer of in vitro embryos. Conclusion The present study provides a detailed inventory of differentially expressed gene signatures and pathways specifically reflective of the developmental environment and future developmental capacities of bovine embryos suggesting that transcriptome activity observed in blastocysts could be indicative of further pregnancy success but also adaptation to culture environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07693-0.
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Affiliation(s)
- Dessie Salilew-Wondim
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Dawit Tesfaye
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, 3105 Rampart Rd, CO, 80521, Fort Collins, USA
| | - Franca Rings
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Eva Held-Hoelker
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Dennis Miskel
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Marc-Andre Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des sciences de l'agriculture et de l'alimentation, INAF, Pavillon des services, Université Laval (Québec), G1V 0A6, Quebec City, Canada
| | - Ernst Tholen
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Karl Schellander
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Michael Hoelker
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany. .,Department of Animal Science, Biotechnology & Reproduction in farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
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12
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Melo-Hanchuk TD, Colleti C, Saito Â, Mendes MCS, Carvalheira JBC, Vassallo J, Kobarg J. Intracellular hyaluronic acid-binding protein 4 (HABP4): a candidate tumor suppressor in colorectal cancer. Oncotarget 2020; 11:4325-4337. [PMID: 33245729 PMCID: PMC7679031 DOI: 10.18632/oncotarget.27804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Hyaluronic Acid-binding protein 4 (HABP4) is a regulatory protein of 57 kDa that is functionally involved in transcription regulation and RNA metabolism and shows several characteristics common to oncoproteins or tumor suppressors, including altered expression in cancer tissues, nucleus/cytoplasm shuttling, intrinsic lack of protein structure, complex interactomes and post translational modifications. Its gene has been found in a region on chromosome 9q22.3-31, which contains SNP haplotypes occurring in individuals with a high risk for familial colon cancer. To test a possible role of HABP4 in tumorigenesis we generated knockout mice by the CRISPR/Cas9 method and treated the animals with azoxymethane (AOM)/dextran sodium sulfate (DSS) for induction of colon tumors. HABP4-/- mice, compared to wild type mice, had more and larger tumors, and expressed more of the proliferation marker proteins Cyclin-D1, CDK4 and PCNA. Furthermore, the cells of the bottom of the colon crypts in the HABP4-/- mice divided more rapidly. Next, we generated also HABP4-/- HCT 116 cells, in cell culture and found again an increased proliferation in clonogenic assays in comparison to wild-type cells. Our study of the protein expression levels of HABP4 in human colon cancer samples, through immunohistochemistry assays, showed, that 30% of the tumors analyzed had low expression of HABP4. Our data suggest that HABP4 is involved in proliferation regulation of colon cells in vitro and in vivo and that it is a promising new candidate for a tumor suppressor protein that can be explored both in the diagnosis and possibly therapy of colon cancer.
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Affiliation(s)
- Talita Diniz Melo-Hanchuk
- 2Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil
- *These authors contributed equally to this work
| | - Carolina Colleti
- 1School of Pharmaceutical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
- *These authors contributed equally to this work
| | - Ângela Saito
- 3Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- *These authors contributed equally to this work
| | - Maria Carolina Santos Mendes
- 4Division of Oncology, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - José Barreto Campello Carvalheira
- 4Division of Oncology, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Jose Vassallo
- 5Laboratory of Investigative Pathology, CIPED, Faculty of Medical Sciences, State University of Campinas, Campinas, SP, Brazil
| | - Jörg Kobarg
- 1School of Pharmaceutical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
- Correspondence to: Jörg Kobarg, email:
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13
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Kužmová E, Zawada Z, Navrátil M, Günterová J, Kraus T. Flow cytometric determination of cell cycle progression via direct labeling of replicated DNA. Anal Biochem 2020; 614:114002. [PMID: 33159846 DOI: 10.1016/j.ab.2020.114002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 01/14/2023]
Abstract
The reported method allows for a simple and rapid monitoring of DNA replication and cell cycle progression in eukaryotic cells in vitro. The DNA of replicating cells is labeled by incorporation of a metabolically-active fluorescent (Cy3) deoxyuridine triphosphate derivative, which is delivered into the cells by a synthetic transporter (SNTT1). The cells are then fixed, stained with DAPI and analyzed by flow cytometry. Thus, this protocol obviates post-labeling steps, which are indispensable in currently used incorporation assays (BrdU, EdU). The applicability of the protocol is demonstrated in analyses of cell cycles of adherent (U-2 OS, HeLa S3, RAW 264.7, J774 A.1, Chem-1, U-87 MG) and suspension (CCRF-CEM, MOLT-4, THP-1, HL-60, JURKAT) cell cultures, including those affected by a DNA polymerase inhibitor (aphidicolin). Owing to a short incorporation time (5-60 min) and reduced number of steps, the protocol can be completed within 1-2 h with a minimal cell loss and with excellent reproducibility.
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Affiliation(s)
- Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic; University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Jana Günterová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic.
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14
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Ding G, Xu X, Li D, Chen Y, Wang W, Ping D, Jia S, Cao L. Fisetin inhibits proliferation of pancreatic adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation. Cell Death Dis 2020; 11:893. [PMID: 33093461 PMCID: PMC7582166 DOI: 10.1038/s41419-020-03019-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/05/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022]
Abstract
Pancreatic adenocarcinoma (PDAC) is an extremely malignant tumor that is associated with low survival rates. Fisetin is a natural flavonoid that shows diverse antitumor effects, including DNA damage, in various cancers. Increasing studies have demonstrated that epigenetic modifications play critical roles in DNA-damage response. However, the epigenetic regulation mechanism of fisetin in cancers is hardly studied. RFXAP is a critical transcription factor for MHC II molecules, however, its transcriptional role in PDAC is poorly understood. The anti-PDAC effect of fisetin was measured by CCK-8, flow cytometry, xenograft tumor nude mice model. DNA-damage levels were examined by immunofluorescence. Bioinformatics analysis was used to examine the expression of RFXAP and other genes involved in DNA-damage response. ChIP sequencing was used to explore the transcriptional role of RFXAP. The expression of target gene KDM4A was measured by qRT-PCR and western blots. KDM4A promoter activity was analyzed using dual-luciferase reporter assay. RFXAP overexpressing or silencing of PDAC cells was used to explore the effect of RFXAP in DNA damage induced by fisetin. We found that fisetin inhibited cell proliferation and induced DNA damage and S-phase arrest in PDAC. Expression of RFXAP and other DNA-damage response genes were upregulated by fisetin. We revealed that RFXAP expression was relatively low in PDAC and correlated with tumor stage and poor prognosis. Then we explored the transcriptional role of RFXAP and found that RFXAP targeted KDM4A, a special demethylase specific for tri- and dimethylated histone H3K36. We found that overexpression of RFXAP upregulated KDM4A and attenuated methylation of H3K36, thereby impairing DNA repair and enhancing the DNA damage induced by fisetin, while RFXAP silencing showed the opposite effect. We also found the function of fisetin in enhancing the effect of chemotherapy on pancreatic cancer cells. Our findings revealed that fisetin induced DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation, thus causing inhibition of proliferation in PDAC.
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Affiliation(s)
- Guoping Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Xiaodong Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Dan Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Department of General Surgery, School of Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310000, China
| | - Yuhao Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Emergency Department, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Weimin Wang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Department of General Surgery, Huzhou Hospital, Zhejiang University School of Medicine, Huzhou, 313003, Zhejiang, China
| | - Dongnan Ping
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China. .,Innovation Center for Minimally Invasive Technique and Device, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
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15
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Kosti A, de Araujo PR, Li WQ, Guardia GDA, Chiou J, Yi C, Ray D, Meliso F, Li YM, Delambre T, Qiao M, Burns SS, Lorbeer FK, Georgi F, Flosbach M, Klinnert S, Jenseit A, Lei X, Sandoval CR, Ha K, Zheng H, Pandey R, Gruslova A, Gupta YK, Brenner A, Kokovay E, Hughes TR, Morris QD, Galante PAF, Tiziani S, Penalva LOF. The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation. Genome Biol 2020; 21:195. [PMID: 32762776 PMCID: PMC7412812 DOI: 10.1186/s13059-020-02115-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiation and growth. Identification and characterization of oncogenic RBPs and their regulatory networks provide new opportunities for targeted therapy. RESULTS We identify the RNA-binding protein SERBP1 as a novel regulator of glioblastoma (GBM) development. High SERBP1 expression is prevalent in GBMs and correlates with poor patient survival and poor response to chemo- and radiotherapy. SERBP1 knockdown causes delay in tumor growth and impacts cancer-relevant phenotypes in GBM and glioma stem cell lines. RNAcompete identifies a GC-rich region as SERBP1-binding motif; subsequent genomic and functional analyses establish SERBP1 regulation role in metabolic routes preferentially used by cancer cells. An important consequence of these functions is SERBP1 impact on methionine production. SERBP1 knockdown decreases methionine levels causing a subsequent reduction in histone methylation as shown for H3K27me3 and upregulation of genes associated with neurogenesis, neuronal differentiation, and function. Further analysis demonstrates that several of these genes are downregulated in GBM, potentially through epigenetic silencing as indicated by the presence of H3K27me3 sites. CONCLUSIONS SERBP1 is the first example of an RNA-binding protein functioning as a central regulator of cancer metabolism and indirect modulator of epigenetic regulation in GBM. By bridging these two processes, SERBP1 enhances glioma stem cell phenotypes and contributes to GBM poorly differentiated state.
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Affiliation(s)
- Adam Kosti
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Patricia Rosa de Araujo
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Wei-Qing Li
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Jennifer Chiou
- Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX 78712 USA
| | - Caihong Yi
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Fabiana Meliso
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Yi-Ming Li
- Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Talia Delambre
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Mei Qiao
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Suzanne S. Burns
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Franziska K. Lorbeer
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Fanny Georgi
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Markus Flosbach
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Sarah Klinnert
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Anne Jenseit
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Xiufen Lei
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | | | - Kevin Ha
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Renu Pandey
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | | | - Yogesh K. Gupta
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Andrew Brenner
- Mays Cancer Center, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Erzsebet Kokovay
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Timothy R. Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
- Canadian Institute for Advanced Research, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1 Canada
| | - Quaid D. Morris
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1 Canada
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Stefano Tiziani
- Department of Nutritional Sciences, Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX 78712 USA
| | - Luiz O. F. Penalva
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
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16
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Mejías-Navarro F, Rodríguez-Real G, Ramón J, Camarillo R, Huertas P. ALC1/eIF4A1-mediated regulation of CtIP mRNA stability controls DNA end resection. PLoS Genet 2020; 16:e1008787. [PMID: 32392243 PMCID: PMC7241833 DOI: 10.1371/journal.pgen.1008787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 05/21/2020] [Accepted: 04/22/2020] [Indexed: 11/18/2022] Open
Abstract
During repair of DNA double-strand breaks, resection of DNA ends influences how these lesions will be repaired. If resection is activated, the break will be channeled through homologous recombination; if not, it will be simply ligated using the non-homologous end-joining machinery. Regulation of resection relies greatly on modulating CtIP, which can be done by modifying: i) its interaction partners, ii) its post-translational modifications, or iii) its cellular levels, by regulating transcription, splicing and/or protein stability/degradation. Here, we have analyzed the role of ALC1, a chromatin remodeler previously described as an integral part of the DNA damage response, in resection. Strikingly, we found that ALC1 affects resection independently of chromatin remodeling activity or its ability to bind damaged chromatin. In fact, it cooperates with the RNA-helicase eIF4A1 to help stabilize the most abundant splicing form of CtIP mRNA. This function relies on the presence of a specific RNA sequence in the 5' UTR of CtIP. Therefore, we describe an additional layer of regulation of CtIP-at the level of mRNA stability through ALC1 and eIF4A1.
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Affiliation(s)
- Fernando Mejías-Navarro
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Guillermo Rodríguez-Real
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Javier Ramón
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Rosa Camarillo
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Pablo Huertas
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- * E-mail:
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17
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Tsuboyama K, Osaki T, Matsuura-Suzuki E, Kozuka-Hata H, Okada Y, Oyama M, Ikeuchi Y, Iwasaki S, Tomari Y. A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. PLoS Biol 2020; 18:e3000632. [PMID: 32163402 PMCID: PMC7067378 DOI: 10.1371/journal.pbio.3000632] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/05/2020] [Indexed: 01/08/2023] Open
Abstract
Proteins are typically denatured and aggregated by heating at near-boiling temperature. Exceptions to this principle include highly disordered and heat-resistant proteins found in extremophiles, which help these organisms tolerate extreme conditions such as drying, freezing, and high salinity. In contrast, the functions of heat-soluble proteins in non-extremophilic organisms including humans remain largely unexplored. Here, we report that heat-resistant obscure (Hero) proteins, which remain soluble after boiling at 95°C, are widespread in Drosophila and humans. Hero proteins are hydrophilic and highly charged, and function to stabilize various "client" proteins, protecting them from denaturation even under stress conditions such as heat shock, desiccation, and exposure to organic solvents. Hero proteins can also block several different types of pathological protein aggregations in cells and in Drosophila strains that model neurodegenerative diseases. Moreover, Hero proteins can extend life span of Drosophila. Our study reveals that organisms naturally use Hero proteins as molecular shields to stabilize protein functions, highlighting their biotechnological and therapeutic potential.
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Affiliation(s)
- Kotaro Tsuboyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tatsuya Osaki
- Biomolecular and Cellular Engineering laboratory, Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Eriko Matsuura-Suzuki
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yuki Okada
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masaaki Oyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yoshiho Ikeuchi
- Biomolecular and Cellular Engineering laboratory, Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Yukihide Tomari
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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18
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Colleti C, Melo-Hanchuk TD, da Silva FRM, Saito Â, Kobarg J. Complex interactomes and post-translational modifications of the regulatory proteins HABP4 and SERBP1 suggest pleiotropic cellular functions. World J Biol Chem 2019; 10:44-64. [PMID: 31768228 PMCID: PMC6872977 DOI: 10.4331/wjbc.v10.i3.44] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 10/15/2019] [Indexed: 02/05/2023] Open
Abstract
The 57 kDa antigen recognized by the Ki-1 antibody, is also known as intracellular hyaluronic acid binding protein 4 and shares 40.7% identity and 67.4% similarity with serpin mRNA binding protein 1, which is also named CGI-55, or plasminogen activator inhibitor type-1-RNA binding protein-1, indicating that they might be paralog proteins, possibly with similar or redundant functions in human cells. Through the identification of their protein interactomes, both regulatory proteins have been functionally implicated in transcriptional regulation, mRNA metabolism, specifically RNA splicing, the regulation of mRNA stability, especially, in the context of the progesterone hormone response, and the DNA damage response. Both proteins also show a complex pattern of post-translational modifications, involving Ser/Thr phosphorylation, mainly through protein kinase C, arginine methylation and SUMOylation, suggesting that their functions and locations are highly regulated. Furthermore, they show a highly dynamic cellular localization pattern with localizations in both the cytoplasm and nucleus as well as punctuated localizations in both granular cytoplasmic protein bodies, upon stress, and nuclear splicing speckles. Several reports in the literature show altered expressions of both regulatory proteins in a series of cancers as well as mutations in their genes that may contribute to tumorigenesis. This review highlights important aspects of the structure, interactome, post-translational modifications, sub-cellular localization and function of both regulatory proteins and further discusses their possible functions and their potential as tumor markers in different cancer settings.
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Affiliation(s)
- Carolina Colleti
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Talita Diniz Melo-Hanchuk
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Flávia Regina Moraes da Silva
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Ângela Saito
- Laboratório Nacional de Biociências, CNPEM, Campinas 13083-970, Brazil
| | - Jörg Kobarg
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
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19
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Muto A, Sugihara Y, Shibakawa M, Oshima K, Matsuda T, Nadano D. The mRNA-binding protein Serbp1 as an auxiliary protein associated with mammalian cytoplasmic ribosomes. Cell Biochem Funct 2018; 36:312-322. [PMID: 30039520 DOI: 10.1002/cbf.3350] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/23/2018] [Accepted: 06/26/2018] [Indexed: 01/27/2023]
Abstract
While transcription plays an obviously important role in gene expression, translation has recently been emerged as a key step that defines the composition and quality of the proteome in the cell of higher eukaryotes including mammals. Selective translation is supposed to be regulated by the structural heterogeneity of cytoplasmic ribosomes including differences in protein composition and chemical modifications. However, the current knowledge on the heterogeneity of mammalian ribosomes is limited. Here, we report mammalian Serbp1 as a ribosome-associated protein. The translated products of Serbp1 gene, including the longest isoform, were found to be localized in the nucleolus as well as in the cytoplasm. Subcellular fractionation indicated that most of cytoplasmic Serbp1 molecules were precipitated by ultracentrifugation. Proteomic analysis identified Serbp1 in the cytoplasmic ribosomes of the rodent testis. Polysome profiling suggested that Serbp1, as a component of the small 40S subunit, was included in translating ribosomes (polysomes). Cosedimentation of Serbp1 with the 40S subunit was observed after dissociation of the ribosomal subunits. Serbp1 was also included in the ribosomes of human cancer cells, which may lead to a mechanistic understanding of an emerging link between Serbp1 and tumour progression. SIGNIFICANCE OF THE STUDY In mammalian cells, the final protein output of their genetic program is determined not only by controlling transcription but also by regulating the posttranscriptional events. Although mRNA-binding proteins and the cytoplasmic ribosome have long been recognized as central players in the posttranscriptional regulation, their physical and functional interactions are still far from a complete understanding. Here, we describe the intracellular localization of Serbp1, an mRNA-binding protein, and the inclusion of this protein in actively translating ribosomes in normal and cancer cells. These findings shed a new light into molecular mechanisms underlying Serbp1 action in translational gene regulation and tumour progression.
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Affiliation(s)
- Akiko Muto
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoshihiko Sugihara
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Minami Shibakawa
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzi Oshima
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tsukasa Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Daita Nadano
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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20
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Vasamsetti BMK, Park YS, Cho NJ. VIG-1 is required for maintenance of genome stability in Caenorhabditis elegans. Anim Cells Syst (Seoul) 2018; 22:197-204. [PMID: 30460098 PMCID: PMC6138327 DOI: 10.1080/19768354.2018.1476410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 11/17/2022] Open
Abstract
To explore the function of VIG-1 in Caenorhabditis elegans, we analyzed the phenotypes of two vig-1 deletion mutants: vig-1(tm3383) and vig-1(ok2536). Both vig-1 mutants exhibited phenotypes associated with genome instability, such as a high incidence of males (Him) and increased embryonic lethality. These phenotypes became more evident in succeeding generations, implying that the germline of vig-1 accumulates DNA damage over generations. To examine whether vig-1 causes a defect in the DNA damage response, we treated worms with UV or camptothecin, a specific topoisomerase I inhibitor. We observed that the embryonic survival of the vig-1 mutants was reduced compared with that of the wild-type worms. Our results thus suggest that VIG-1 is required for maintaining genome stability in response to endogenous and exogenous genotoxic stresses.
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Affiliation(s)
| | - Yang-Seo Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea
| | - Nam Jeong Cho
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea
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21
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Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R. dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc Natl Acad Sci U S A 2018; 115:E2734-E2741. [PMID: 29507191 PMCID: PMC5866577 DOI: 10.1073/pnas.1718844115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic gene regulation is a complex process, often coordinated by the action of tens to hundreds of proteins. Although previous biochemical studies have identified many components of the basal machinery and various ancillary factors involved in gene regulation, numerous gene-specific regulators remain undiscovered. To comprehensively survey the proteome directing gene expression at a specific genomic locus of interest, we developed an in vitro nuclease-deficient Cas9 (dCas9)-targeted chromatin-based purification strategy, called "CLASP" (Cas9 locus-associated proteome), to identify and functionally test associated gene-regulatory factors. Our CLASP method, coupled to mass spectrometry and functional screens, can be efficiently adapted for isolating associated regulatory factors in an unbiased manner targeting multiple genomic loci across different cell types. Here, we applied our method to isolate the Drosophila melanogaster histone cluster in S2 cells to identify several factors including Vig and Vig2, two proteins that bind and regulate core histone H2A and H3 mRNA via interaction with their 3' UTRs.
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Affiliation(s)
- Chiahao Tsui
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Andrew Lu
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720;
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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22
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Bolger GB. The RNA-binding protein SERBP1 interacts selectively with the signaling protein RACK1. Cell Signal 2017; 35:256-263. [PMID: 28267599 DOI: 10.1016/j.cellsig.2017.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 12/19/2022]
Abstract
The RACK1 protein interacts with numerous proteins involved in signal transduction, the cytoskeleton, and mRNA splicing and translation. We used the 2-hybrid system to identify additional proteins interacting with RACK1 and isolated the RNA-binding protein SERBP1. SERPB1 shares amino acid sequence homology with HABP4 (also known as Ki-1/57), a component of the RNA spicing machinery that has been shown previously to interact with RACK1. Several different isoforms of SERBP1, generated by alternative mRNA splicing, interacted with RACK1 with indistinguishable interaction strength, as determined by a 2-hybrid beta-galactosidase assay. Analysis of deletion constructs of SERBP1 showed that the C-terminal third of the SERBP1 protein, which contains one of its two substrate sites for protein arginine N-methyltransferase 1 (PRMT1), is necessary and sufficient for it to interact with RACK1. Analysis of single amino acid substitutions in RACK1, identified in a reverse 2-hybrid screen, showed very substantial overlap with those implicated in the interaction of RACK1 with the cAMP-selective phosphodiesterase PDE4D5. These data are consistent with SERBP1 interacting selectively with RACK1, mediated by an extensive interaction surface on both proteins.
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Affiliation(s)
- Graeme B Bolger
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-3300, USA; Department of Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294-3300, USA.
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23
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Cho SW, Na W, Choi M, Kang SJ, Lee SG, Choi CY. Autophagy inhibits cell death induced by the anti-cancer drug morusin. Am J Cancer Res 2017; 7:518-530. [PMID: 28401008 PMCID: PMC5385640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 06/07/2023] Open
Abstract
Autophagy is a cellular process by which damaged organelles and dysfunctional proteins are degraded. Morusin is an anti-cancer drug isolated from the root bark of Morus alba. Morusin induces apoptosis in human prostate cancer cells by reducing STAT3 activity. In this study, we examined whether morusin induces autophagy and also examined the effects of autophagy on the morusin-induced apoptosis. Morusin induces LC3-II accumulation and ULK1 activation in HeLa cells. In addition, we found that induction of ULK1 Ser317 phosphorylation and reduction of ULK1 Ser757 phosphorylation occurred simultaneously during morusin-induced autophagy. Consistently, morusin induces autophagy by activation of AMPK and inhibition of mTOR activity. Next, we investigated the role of autophagy in morusin-induced apoptosis. Inhibition of autophagy by treating cells with the 3-methyladenine (3-MA) autophagic inhibitor induces high levels of morusin-mediated apoptosis, while treatment of cells with morusin alone induces moderate levels of apoptosis. Cell survival was greatly reduced when cells were treated with morusin and 3-MA. Taken together, morusin induces autophagy, which is an impediment for morusin-induced apoptosis, suggesting combined treatment of morusin with an autophagic inhibitor would increase the efficacy of morusin as an anti-cancer drug.
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Affiliation(s)
- Sang Woo Cho
- Department of Biological Sciences, Sungkyunkwan UniversitySuwon 16419, Republic of Korea
| | - Wooju Na
- Department of Biological Sciences, Sungkyunkwan UniversitySuwon 16419, Republic of Korea
| | - Minji Choi
- Department of Science in Korean Medicine, College of Korean Medicine, Kyung Hee UniversitySeoul 02447, Republic of Korea
| | - Shin Jung Kang
- Department of Molecular Biology, Sejong UniversitySeoul 05006, Republic of Korea
| | - Seok-Geun Lee
- Department of Science in Korean Medicine, College of Korean Medicine, Kyung Hee UniversitySeoul 02447, Republic of Korea
- KHU-KIST Department of Converging Science & Technology, Kyung Hee UniversitySeoul 02447, Republic of Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan UniversitySuwon 16419, Republic of Korea
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24
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Wang P, Ma D, Wang J, Fang Q, Gao R, Wu W, Cao L, Hu X, Zhao J, Li Y. INPP4B-mediated DNA repair pathway confers resistance to chemotherapy in acute myeloid leukemia. Tumour Biol 2016; 37:12513-12523. [PMID: 27342972 DOI: 10.1007/s13277-016-5111-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022] Open
Abstract
INPP4B has been recently shown to be a poor prognostic marker and confer chemo- or radio-resistance in AML cells, whereas, the underlying mechanisms remain unclear. Herein, we aimed to explore the possible mechanisms mediated the resistance to chemotherapy in AML. We found that INPP4B-mediated resistance to genotoxic drug, cytarabine, was accompanied by lower p-H2AX accumulation in KG-1 cells, and INPP4B knockdown evidently sensitized KG-1 cells to cytarabine, meanwhile, p-H2AX expression was increased dramatically. Then, we observed that INPP4B knockdown inhibited the loss of p-H2AX expression after cytarabine removal in INPP4B-silenced KG-1 cells, whereas, in control KG-1 cells, the expression of p-H2AX was reduced in a time-dependent manner. Next, INPP4B knockdown can significantly downregulate ATM expression and subsequently inhibit the activation of ATM downstream targets of p-ATM, p-BRCA1, p-ATR, and p-RAD51. Furthermore, nuclear localization of p65 was inhibited after INPP4B knockdown, and reactivation of p65 can rescue the INPP4B knockdown-induced inhibition of ATM, p-ATM, p-BRCA1, p-ATR, and p-RAD51. Finally, INPP4B expression was positively correlated with ATM expression in AML cells, both INPP4B knockdown and KU55933 can significantly sensitize primary myeloid leukemic cells to cytarabine treatment.Collectively, these data suggest that enhanced ATM-dependent DNA repair is involved in resistance to chemotherapy in INPP4Bhigh AML, which could be mediated by p65 nuclear translocation, combination chemotherapy with INPP4B or DNA repair pathway inhibition represents a promising strategy in INPP4Bhigh AML.
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Affiliation(s)
- Ping Wang
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China.,GuiZhou Province Hematopoietic Stem Cell Transplantation Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Dan Ma
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China.,Department of Pharmacy, Affiliated BaiYun Hospital of Guizhou Medical University, Guiyang, 550014, China
| | - Jishi Wang
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China. .,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China. .,GuiZhou Province Hematopoietic Stem Cell Transplantation Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
| | - Qin Fang
- Department of Pharmacy, Affiliated BaiYun Hospital of Guizhou Medical University, Guiyang, 550014, China.,Department of Pharmacy, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Rui Gao
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China.,GuiZhou Province Hematopoietic Stem Cell Transplantation Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Weibing Wu
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China.,GuiZhou Province Hematopoietic Stem Cell Transplantation Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Lu Cao
- Department of Pharmacy, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Xiuying Hu
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China.,GuiZhou Province Hematopoietic Stem Cell Transplantation Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jiangyuan Zhao
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China.,GuiZhou Province Hematopoietic Stem Cell Transplantation Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.,Key Laboratory of Hematological Disease Diagnostic and Treat Centre of GuiZhou Province, Guiyang, 550004, China.,GuiZhou Province Hematopoietic Stem Cell Transplantation Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
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25
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Expression of Progesterone Receptor Membrane Component 1 (PGRMC1), Progestin and AdipoQ Receptor 7 (PAQPR7), and Plasminogen Activator Inhibitor 1 RNA-Binding Protein (PAIRBP1) in Glioma Spheroids In Vitro. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8065830. [PMID: 27340667 PMCID: PMC4908248 DOI: 10.1155/2016/8065830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/14/2016] [Accepted: 04/27/2016] [Indexed: 11/25/2022]
Abstract
Objective. Some effects of progesterone on glioma cells can be explained through the slow, genomic mediated response via nuclear receptors; the other effects suggest potential role of a fast, nongenomic action mediated by membrane-associated progesterone receptors. Methods. The effects of progesterone treatment on the expression levels of progesterone receptor membrane component 1 (PGRMC1), plasminogen activator inhibitor 1 RNA-binding protein (PAIRBP1), and progestin and adipoQ receptor 7 (PAQR7) on both mRNA and protein levels were investigated in spheroids derived from human glioma cell lines U-87 MG and LN-229. Results. The only significant alteration at the transcript level was the decrease in PGRMC1 mRNA observed in LN-229 spheroids treated with 30 ng/mL of progesterone. No visible alterations at the protein levels were observed using immunohistochemical analysis. Stimulation of U-87 MG spheroids resulted in an increase of PGRMC1 but a decrease of PAIRBP1 protein. Double immunofluorescent detection of PGRMC1 and PAIRBP1 identified the two proteins to be partially colocalized in the cells. Western blot analysis revealed the expected bands for PGRMC1 and PAIRBP1, whereas two bands were detected for PAQR7. Conclusion. The progesterone action is supposed to be mediated via membrane-associated progesterone receptors as the nuclear progesterone receptor was absent in tested spheroids.
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