1
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Seo Y, Rhim J, Kim JH. RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within. Exp Mol Med 2024; 56:1080-1106. [PMID: 38689093 PMCID: PMC11148060 DOI: 10.1038/s12276-024-01224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/02/2024] Open
Abstract
Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.
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Affiliation(s)
- Yoona Seo
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jiho Rhim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea.
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2
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Fagre C, Gilbert W. Beyond reader proteins: RNA binding proteins and RNA modifications in conversation to regulate gene expression. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1834. [PMID: 38444048 DOI: 10.1002/wrna.1834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/07/2024]
Abstract
Post-transcriptional mRNA modifications play diverse roles in gene expression and RNA function. In many cases, RNA modifications function by altering how cellular machinery such as RNA binding proteins (RBPs) interact with RNA substrates. For instance, N6-methyladenosine (m6A) is recognized by the well-characterized YTH domain-containing family of "reader" proteins. For other mRNA modifications, similar global readers of modification status have not been clearly defined. Rather, most interactions between RBPs and RNA modifications have a more complicated dependence on sequence context and binding modality. The current handful of studies that demonstrate modifications impacting protein binding likely represent only a fraction of the full landscape. In this review, we dissect the known instances of RNA modifications altering RBP binding, specifically m6A, N1-methyladenosine (m1A), 5-methylcytosine (m5C), pseudouridine (Ψ), and internal N7-methylguanosine. We then review the biochemical properties of these and other identified mRNA modifications including dihydrouridine (D), N4-acetylcytosine (ac4C), and 2'-O-Methylation (Nme). We focus on how these properties would be likely to impact RNA:RBP interactions, including by changes to hydrogen bond potential, base-stacking efficiency, and RNA conformational preferences. The effects of RNA modifications on secondary structure have been well-studied, and we briefly discuss how structural effects imparted by modifications can lead to protein binding changes. Finally, we discuss strategies for uncovering as-yet-to-be identified modification-sensitive RBP:RNA Interactions. Coordinating future efforts to intersect the epitranscriptome and the RNA-protein interactome will illuminate the rules governing RNA modification recognition and the mechanisms responsible for the biological consequences of mRNA modification. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Christian Fagre
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Wendy Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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3
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Alpuche-Lazcano SP, Scarborough RJ, Gatignol A. MicroRNAs and long non-coding RNAs during transcriptional regulation and latency of HIV and HTLV. Retrovirology 2024; 21:5. [PMID: 38424561 PMCID: PMC10905857 DOI: 10.1186/s12977-024-00637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) and human T cell leukemia virus (HTLV) have replicative and latent stages of infection. The status of the viruses is dependent on the cells that harbour them and on different events that change the transcriptional and post-transcriptional events. Non-coding (nc)RNAs are key factors in the regulation of retrovirus replication cycles. Notably, micro (mi)RNAs and long non-coding (lnc)RNAs are important regulators that can induce switches between active transcription-replication and latency of retroviruses and have important impacts on their pathogenesis. Here, we review the functions of miRNAs and lncRNAs in the context of HIV and HTLV. We describe how specific miRNAs and lncRNAs are involved in the regulation of the viruses' transcription, post-transcriptional regulation and latency. We further discuss treatment strategies using ncRNAs for HIV and HTLV long remission, reactivation or possible cure.
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Affiliation(s)
- Sergio P Alpuche-Lazcano
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - Robert J Scarborough
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Anne Gatignol
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Medicine, Division of Infectious Diseases, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
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4
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Que Z, Yang K, Wang N, Li S, Li T. Functional Role of RBP in Osteosarcoma: Regulatory Mechanism and Clinical Therapy. Anal Cell Pathol (Amst) 2023; 2023:9849719. [PMID: 37426488 PMCID: PMC10328736 DOI: 10.1155/2023/9849719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023] Open
Abstract
Malignant bone neoplasms can be represented by osteosarcoma (OS), which accounts for 36% of all sarcomas. To reduce tumor malignancy, extensive efforts have been devoted to find an ideal target from numerous candidates, among which RNA-binding proteins (RBPs) have shown their unparalleled competitiveness. With the special structure of RNA-binding domains, RBPs have the potential to establish relationships with RNAs or small molecules and are considered regulators of different sections of RNA processes, including splicing, transport, translation, and degradation of RNAs. RBPs have considerable significant roles in various cancers, and experiments revealed that there was a strong association of RBPs with tumorigenesis and tumor cell progression. Regarding OS, RBPs are a new orientation, but achievements in hand are noteworthy. Higher or lower expression of RBPs was first found in tumor cells compared to normal tissue. By binding to different molecules, RBPs are capable of influencing tumor cell phenotypes through different signaling pathways or other axes, and researches on medical treatment have been largely inspired. Exploring the prognostic and therapeutic values of RBPs in OS is a hotspot where diverse avenues on regulating RBPs have achieved dramatical effects. In this review, we briefly summarize the contribution of RBPs and their binding molecules to OS oncogenicity and generally introduce distinctive RBPs as samples. Moreover, we focus on the attempts to differentiate RBP's opposite functions in predicting prognosis and collect possible strategies for treatment. Our review provides forwards insight into improving the understanding of OS and suggests RBPs as potential biomarkers for therapies.
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Affiliation(s)
- Ziyuan Que
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Kang Yang
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Nan Wang
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Shuying Li
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Tao Li
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
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5
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Li Q, Zhao Y, Xu C, Liang Y, Zhao Y, He Q, Li J, Chen K, Qiao H, Liu N, Ma J, Chen L, Li Y. Chemotherapy-Induced Senescence Reprogramming Promotes Nasopharyngeal Carcinoma Metastasis by circRNA-Mediated PKR Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205668. [PMID: 36683218 PMCID: PMC10015868 DOI: 10.1002/advs.202205668] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/23/2022] [Indexed: 05/13/2023]
Abstract
Senescence is associated with tumor metastasis and chemotherapy resistance, yet the mechanisms remain elusive. Here, it is identified that nasopharyngeal carcinoma (NPC) patients who developed distant metastasis are characterized by senescence phenotypes, in which circWDR37 is a key regulator. CircWDR37 deficiency limits cisplatin or gemcitabine-induced senescent NPC cells from proliferation, migration, and invasion. Mechanistically, circWDR37 binds to and dimerizes double-stranded RNA-activated protein kinase R (PKR) to initiate PKR autophosphorylation and activation. Independent of its kinase activity, phosphorylated PKR induces I-kappaB kinase beta (IKKβ) phosphorylation, binds to and releases RELA from NF-κB inhibitor alpha (IκBα) to trigger nuclear factor kappa B (NF-κB) activation, thereby stimulating cyclin D1 (CCND1) and senescence-associated secretory phenotype component gene transcription in a circWDR37-dependent manner. Low circWDR37 levels correlate with chemotherapy response and favorable survival in NPC patients treated with gemcitabine or cisplatin induction chemotherapy. This study uncovers a new mechanism of circWDR37 activated PKR in senescence-driven metastasis and provides appealing therapeutic targets in NPC.
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Affiliation(s)
- Qian Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yu‐Heng Zhao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Cheng Xu
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ye‐Lin Liang
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yin Zhao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Qing‐Mei He
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jun‐Yan Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Kai‐Lin Chen
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Han Qiao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Na Liu
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jun Ma
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Lei Chen
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ying‐Qin Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
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6
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A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus. Int J Mol Sci 2022; 23:ijms231911752. [PMID: 36233053 PMCID: PMC9569428 DOI: 10.3390/ijms231911752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022] Open
Abstract
RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to trigger effective silencing, with a notable exception in the spiny lobsters where repeated attempts at dsRNA induced RNAi have demonstrated extremely ineffective gene knockdown. A comparison of the core RNAi machinery in transcriptomic data from spiny lobsters (Panulirus ornatus) and the closely related slipper lobsters (Thenus australiensis, where silencing is highly effective) revealed that both lobsters possess all proteins involved in the small interfering and microRNA pathways, and that there was little difference at both the sequence and domain architecture level. Comparing the expression of these genes however demonstrated that T. australiensis had significantly higher expression in the transcripts encoding proteins which directly interact with dsRNA when compared to P. ornatus, validated via qPCR. These results suggest that low expression of the core RNAi genes may be hindering the silencing response in P. ornatus, and suggest that it may be critical to enhance the expression of these genes to induce efficient silencing in spiny lobsters.
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7
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Sleman S, Hao H, Najmuldeen H, Jalal P, Saeed N, Othman D, Qian Z. Human Cytomegalovirus UL24 and UL43 Cooperate to Modulate the Expression of Immunoregulatory UL16 Binding Protein 1. Viral Immunol 2022; 35:529-544. [PMID: 36179070 DOI: 10.1089/vim.2022.0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human cytomegalovirus (HCMV) UL24 and UL43 are tegument proteins that have recently been shown to interact with each other in a yeast two-hybrid system. By their overexpression in MRC5 cells, we demonstrate that these viral proteins interact with several important host proteins, especially Dicer and trans-activation response RNA binding protein. As these hots proteins are involved in regulating the production of cellular micro-RNAs, the cytomegalovirus (CMV) proteins could interfere with their actions to favor viral replication directly or through an immune escape mechanism. Double knockout of UL24 and UL43 does not show a remarkable effect on CMV entry or replication, but it significantly downregulates the expression of CMV-encoded miR-UL59, which is thought to regulate the expression of a downstream target UL16 binding protein 1 (ULBP1). Interestingly, the double knockout increases the expression of the ULBP1 recognized by the NKG2D activating receptor of natural killer cells. This study investigates the potential role of several proteins encoded by HCMV in regulating the host cellular environment to favor escape from immunity, and it also provides some basis for the future development of RNA-targeted small molecules to control HCMV infection.
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Affiliation(s)
- Sirwan Sleman
- College of Veterinary Medicine, University of Sulaimani, Sulaymaniyah, Iraq.,Medical Laboratory Analysis, College of Health Science, Cihan University of Sulaimaniya, Sulaymaniyah, Iraq.,Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Hongyun Hao
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Hastyar Najmuldeen
- Medical Laboratory Analysis, College of Health Science, Cihan University of Sulaimaniya, Sulaymaniyah, Iraq.,Biology Department, College of Sciences, University of Sulaimani, Sulaymaniyah, Iraq
| | - Paywast Jalal
- Biology Department, College of Sciences, University of Sulaimani, Sulaymaniyah, Iraq
| | - Nahla Saeed
- College of Veterinary Medicine, University of Sulaimani, Sulaymaniyah, Iraq
| | - Dyary Othman
- College of Veterinary Medicine, University of Sulaimani, Sulaymaniyah, Iraq
| | - Zhikang Qian
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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8
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Peng T, He Y, Wang T, Yu J, Ma X, Zhou Z, Sheng Y, Li L, Peng H, Li S, Zou J, Yuan Y, Zhao Y, Shi H, Li F, Liu W, Hu K, Lu X, Zhang G, Wang F. Discovery of a Novel Small-Molecule Inhibitor Disrupting TRBP-Dicer Interaction against Hepatocellular Carcinoma via the Modulation of microRNA Biogenesis. J Med Chem 2022; 65:11010-11033. [PMID: 35695407 DOI: 10.1021/acs.jmedchem.2c00189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are key players in human hepatocellular carcinoma (HCC) tumorigenesis. Therefore, small molecules targeting components of miRNA biogenesis may provide new therapeutic means for HCC treatment. By a high-throughput screening and structural simplification, we identified a small molecule, CIB-3b, which suppresses the growth and metastasis of HCC in vitro and in vivo by modulating expression profiles of miRNAome and proteome in HCC cells. Mechanistically, CIB-3b physically binds to transactivation response (TAR) RNA-binding protein 2 (TRBP) and disrupts the TRBP-Dicer interaction, thereby altering the activity of Dicer and mature miRNA production. Structure-activity relationship study via the synthesis of 45 CIB-3b derivatives showed that some compounds exhibited a similar inhibitory effect on miRNA biogenesis to CIB-3b. These results support TRBP as a potential therapeutic target in HCC and warrant further development of CIB-3b along with its analogues as a novel therapeutic strategy for the treatment of HCC.
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Affiliation(s)
- Ting Peng
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujiao He
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Tao Wang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jialing Yu
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofang Ma
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zongyuan Zhou
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuwen Sheng
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingyu Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huipan Peng
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Sheng Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jiawei Zou
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yi Yuan
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yongyun Zhao
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Hailong Shi
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fu Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Wanli Liu
- Ministry of Education Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Kaifeng Hu
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoxia Lu
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Xiongan Institute of Innovation, Chinese Academy of Sciences, Hebei 071700, China
| | - Fei Wang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Xiongan Institute of Innovation, Chinese Academy of Sciences, Hebei 071700, China
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9
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Vannamahaxay S, Sornpet B, Pringproa K, Patchanee P, Chuammitri P. Transcriptome analysis of infected Crandell Rees Feline Kidney (CRFK) cells by canine parvovirus type 2c Laotian isolates. Gene X 2022; 822:146324. [PMID: 35182681 DOI: 10.1016/j.gene.2022.146324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/22/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
The advent of RNA sequencing technology provides insight into the dynamic nature of tremendous transcripts within Crandell-Reese feline kidney (CRFK) cells in response to canine parvovirus (CPV-2c) infection. A total of 1,603 genes displayed differentially expressed genes (DEGs), including 789 up-regulated genes and 814 downregulated genes in the infected cells. Gene expression profiles have shown a subtle pattern of defense mechanism and immune response to CPV through significant DEGs when extensively examined via Gene Ontology (GO) and pathway analysis. Prospective GO analysis was performed and identified several enriched GO biological process terms with significant participating roles in the immune system process and defense response to virus pathway. A Gene network was constructed using the 22 most significantly enriched genes of particular interests in defense response to virus pathways to illustrate the key pathways. Eleven genes (C1QBP, CD40, HYAL2, IFNB1, IFNG, IL12B, IL6, IRF3, LSM14A, MAVS, NLRC5) were identified, which are directly related to the defense response to the virus. Results of transcriptome profiling permit us to understand the heterogeneity of DEGs during in vitro experimental study of CPV infection, reflecting a unique transcriptome signature for the CPV virus. Our findings also demonstrate a distinct scenario of enhanced CPV responses in CRFK cells for viral clearance that involved multistep and perplexity of biological processes. Collectively, our data have given a fundamental role in anti-viral immunity as our highlights of this study, thus providing outlooks on future research priorities to be important in studying CPV.
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Affiliation(s)
- Soulasack Vannamahaxay
- Department of Veterinary Medicine, Faculty of Agriculture, National University of Laos, Vientiane, Lao Democratic People's Republic
| | - Benjaporn Sornpet
- Central Laboratory, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Kidsadagon Pringproa
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Prapas Patchanee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; Integrative Research Center for Veterinary Preventive Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phongsakorn Chuammitri
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; Research Center of Producing and Development of Products and Innovations for Animal Health and Production, Chiang Mai University, Chiang Mai 50100, Thailand.
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10
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Wang K, Cui P, Ni R, Gong H, Li H, Yan W, Fu X, Chen L, Lei C, Wang H, Yang X. Chicken-Derived Pattern Recognition Receptor chLGP2 Inhibits the Replication and Proliferation of Infectious Bronchitis Virus. Front Microbiol 2022; 12:810215. [PMID: 35145497 PMCID: PMC8824401 DOI: 10.3389/fmicb.2021.810215] [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: 11/06/2021] [Accepted: 12/17/2021] [Indexed: 12/03/2022] Open
Abstract
The widespread nature and economic importance of Infectious bronchitis virus (IBV) and interactions between IBV and the host immune response remain poorly understood. Understanding the mechanism of virus recognition via innate immunity can help resist IBV invasion. Retinoic acid-induced gene I-like receptor (RLRs) recognize virus RNA in virus infection, and LGP2 is a member of RLRs. According to the current studies, LGP2 exhibited certain inhibition in the virus, and there is a lack of investigation for chicken’s LGP2. It is important to figure out the role of chLGP2 in host immune recognition of IBV. Our results showed that chLGP2 inhibited the proliferation of IBV Beaudette in cells. Also, chLGP2 can identify and combine with IBV RNA. The domains of chLGP2 were separately expressed and inspired by related literature, and the chLGP2 K30A mutant was constructed. Our results suggested its structural integrity and the adenosine triphosphatase (ATPase) activity are critical for IBV inhibiting activity. chTRBP was selected after CO-IP and Mass spectrometry test. We found chTRBP and chLGP2 are the interacting partners and promote mutual expression. Our study showed that chTRBP could also suppress IBV infections via chLGP2, which provided a basis for future innate immunity research for IBV.
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Affiliation(s)
- Kailu Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Pengfei Cui
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Ruiqi Ni
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Huiling Gong
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hao Li
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Wenjun Yan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Xue Fu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Liang Chen
- Deyang Animal Disease Control Center, Deyang, China
| | - Changwei Lei
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hongning Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Xin Yang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
- *Correspondence: Xin Yang,
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11
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Sharma NR, Zheng ZM. RNA Granules in Antiviral Innate Immunity: A Kaposi's Sarcoma-Associated Herpesvirus Journey. Front Microbiol 2022; 12:794431. [PMID: 35069491 PMCID: PMC8767106 DOI: 10.3389/fmicb.2021.794431] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022] Open
Abstract
RNA granules are cytoplasmic, non-membranous ribonucleoprotein compartments that form ubiquitously and are often referred to as foci for post-transcriptional gene regulation. Recent research on RNA processing bodies (PB) and stress granules (SG) has shown wide implications of these cytoplasmic RNA granules and their components in suppression of RNA translation as host intracellular innate immunity against infecting viruses. Many RNA viruses either counteract or co-opt these RNA granules; however, many fundamental questions about DNA viruses with respect to their interaction with these two RNA granules remain elusive. Kaposi’s sarcoma-associated herpesvirus (KSHV), a tumor-causing DNA virus, exhibits two distinct phases of infection and encodes ∼90 viral gene products during the lytic phase of infection compared to only a few (∼5) during the latent phase. Thus, productive KSHV infection relies heavily on the host cell translational machinery, which often links to the formation of PB and SG. One major question is how KSHV counteracts the hostile environment of RNA granules for its productive infection. Recent studies demonstrated that KSHV copes with the translational suppression by cellular RNA granules, PB and SG, by expressing ORF57, a viral RNA-binding protein, during KSHV lytic infection. ORF57 interacts with Ago2 and GW182, two major components of PB, and prevents the scaffolding activity of GW182 at the initial stage of PB formation in the infected cells. ORF57 also interacts with protein kinase R (PKR) and PKR-activating protein (PACT) to block PKR dimerization and kinase activation, and thus inhibits eIF2α phosphorylation and SG formation. The homologous immediate-early regulatory protein ICP27 of herpes simplex virus type 1 (HSV-1), but not the EB2 protein of Epstein-Barr virus (EBV), shares this conserved inhibitory function with KSHV ORF57 on PB and SG. Through KSHV ORF57 studies, we have learned much about how a DNA virus in the infected cells is equipped to evade host antiviral immunity for its replication and productive infection. KSHV ORF57 would be an excellent viral target for development of anti-KSHV-specific therapy.
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Affiliation(s)
- Nishi R Sharma
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard University, New Delhi, India
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
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12
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Shatoff E, Bundschuh R. dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA-protein binding. Bioinformatics 2022; 38:687-693. [PMID: 34668517 DOI: 10.1093/bioinformatics/btab724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/15/2021] [Accepted: 10/15/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION RNA-binding proteins are fundamental to many cellular processes. Double-stranded RNA-binding proteins (dsRBPs) in particular are crucial for RNA interference, mRNA elongation, A-to-I editing, host defense, splicing and a multitude of other important mechanisms. Since dsRBPs require double-stranded RNA to bind, their binding affinity depends on the competition among all possible secondary structures of the target RNA molecule. Here, we introduce a quantitative model that allows calculation of the effective affinity of dsRBPs to any RNA given a principal affinity and the sequence of the RNA, while fully taking into account the entire secondary structure ensemble of the RNA. RESULTS We implement our model within the ViennaRNA folding package while maintaining its O(N3) time complexity. We validate our quantitative model by comparing with experimentally determined binding affinities and stoichiometries for transactivation response element RNA-binding protein (TRBP). We also find that the change in dsRBP binding affinity purely due to the presence of alternative RNA structures can be many orders of magnitude and that the predicted affinity of TRBP for pre-miRNA-like constructs correlates with experimentally measured processing rates. AVAILABILITY AND IMPLEMENTATION Our modified version of the ViennaRNA package is available for download at http://bioserv.mps.ohio-state.edu/dsRBPBind, is free to use for research and educational purposes, and utilizes simple get/set methods for footprint size, concentration, cooperativity, principal dissociation constant and overlap.
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Affiliation(s)
- Elan Shatoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
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13
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Naudi-Fabra S, Blackledge M, Milles S. Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins. Biomolecules 2021; 12:biom12010027. [PMID: 35053175 PMCID: PMC8773649 DOI: 10.3390/biom12010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid–liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.
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14
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Ukhueduan B, Chukwurah E, Patel RC. Regulation of PKR activation and apoptosis during oxidative stress by TRBP phosphorylation. Int J Biochem Cell Biol 2021; 137:106030. [PMID: 34174402 DOI: 10.1016/j.biocel.2021.106030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/09/2021] [Accepted: 06/18/2021] [Indexed: 11/25/2022]
Abstract
Transactivation response element RNA-binding protein (TRBP or TARBP2) originally identified as a pro-viral cellular protein in human immunodeficiency virus (HIV) replication is also a regulator of microRNA biogenesis and cellular stress response. TRBP inhibits the catalytic activity of interferon-induced double-stranded RNA (dsRNA)-activated protein kinase (PKR) during viral infections and cell stress thereby regulating stress-induced signaling pathways. During cellular stress, PKR is catalytically activated transiently by its protein activator PACT and TRBP inhibits PKR to bring about a timely cellular recovery. We have previously established that TRBP phosphorylated after oxidative stress binds to and inhibits PKR more efficiently promoting cell survival. In this study, we investigated if phosphorylation of TRBP enhances its interaction with PACT to bring about additional PKR inhibition. Our data establishes that phosphorylation of TRBP has no effect on PACT-TRBP interaction and TRBP's inhibitory actions on PKR are mediated exclusively by its enhanced interaction with PKR. Cells lacking TRBP are more sensitive to apoptosis in response to oxidative stress and show persistent PKR activation. These results establish that PKR inhibition by stress-induced TRBP phosphorylation occurs by its direct binding to PKR and is important for preventing apoptosis due to sustained PKR activation.
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Affiliation(s)
- Benedicth Ukhueduan
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Evelyn Chukwurah
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Rekha C Patel
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
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15
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Onomoto K, Onoguchi K, Yoneyama M. Regulation of RIG-I-like receptor-mediated signaling: interaction between host and viral factors. Cell Mol Immunol 2021; 18:539-555. [PMID: 33462384 PMCID: PMC7812568 DOI: 10.1038/s41423-020-00602-7] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/17/2020] [Indexed: 01/31/2023] Open
Abstract
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are RNA sensor molecules that play essential roles in innate antiviral immunity. Among the three RLRs encoded by the human genome, RIG-I and melanoma differentiation-associated gene 5, which contain N-terminal caspase recruitment domains, are activated upon the detection of viral RNAs in the cytoplasm of virus-infected cells. Activated RLRs induce downstream signaling via their interactions with mitochondrial antiviral signaling proteins and activate the production of type I and III interferons and inflammatory cytokines. Recent studies have shown that RLR-mediated signaling is regulated by interactions with endogenous RNAs and host proteins, such as those involved in stress responses and posttranslational modifications. Since RLR-mediated cytokine production is also involved in the regulation of acquired immunity, the deregulation of RLR-mediated signaling is associated with autoimmune and autoinflammatory disorders. Moreover, RLR-mediated signaling might be involved in the aberrant cytokine production observed in coronavirus disease 2019. Since the discovery of RLRs in 2004, significant progress has been made in understanding the mechanisms underlying the activation and regulation of RLR-mediated signaling pathways. Here, we review the recent advances in the understanding of regulated RNA recognition and signal activation by RLRs, focusing on the interactions between various host and viral factors.
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Affiliation(s)
- Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Kazuhide Onoguchi
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba, 260-8673, Japan.
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16
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Vaughn LS, Chukwurah E, Patel RC. Opposite actions of two dsRNA-binding proteins PACT and TRBP on RIG-I mediated signaling. Biochem J 2021; 478:493-510. [PMID: 33459340 PMCID: PMC7919947 DOI: 10.1042/bcj20200987] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
An integral aspect of innate immunity is the ability to detect foreign molecules of viral origin to initiate antiviral signaling via pattern recognition receptors (PRRs). One such receptor is the RNA helicase retinoic acid inducible gene 1 (RIG-I), which detects and is activated by 5'triphosphate uncapped double stranded RNA (dsRNA) as well as the cytoplasmic viral mimic dsRNA polyI:C. Once activated, RIG-I's CARD domains oligomerize and initiate downstream signaling via mitochondrial antiviral signaling protein (MAVS), ultimately inducing interferon (IFN) production. Another dsRNA binding protein PACT, originally identified as the cellular protein activator of dsRNA-activated protein kinase (PKR), is known to enhance RIG-I signaling in response to polyI:C treatment, in part by stimulating RIG-I's ATPase and helicase activities. TAR-RNA-binding protein (TRBP), which is ∼45% homologous to PACT, inhibits PKR signaling by binding to PKR as well as by sequestration of its' activators, dsRNA and PACT. Despite the extensive homology and similar structure of PACT and TRBP, the role of TRBP has not been explored much in RIG-I signaling. This work focuses on the effect of TRBP on RIG-I signaling and IFN production. Our results indicate that TRBP acts as an inhibitor of RIG-I signaling in a PACT- and PKR-independent manner. Surprisingly, this inhibition is independent of TRBP's post-translational modifications that are important for other signaling functions of TRBP, but TRBP's dsRNA-binding ability is essential. Our work has major implications on viral susceptibility, disease progression, and antiviral immunity as it demonstrates the regulatory interplay between PACT and TRBP IFN production.
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Affiliation(s)
- Lauren S. Vaughn
- Department of Biology, University of South Carolina, Columbia, SC 29210
| | | | - Rekha C Patel
- Department of Biology, University of South Carolina, Columbia, SC 29210
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17
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Zhou M, Lu W, Li B, Liu X, Li A. TARBP2 promotes tumor angiogenesis and metastasis by destabilizing antiangiogenic factor mRNAs. Cancer Sci 2021; 112:1289-1299. [PMID: 33484209 PMCID: PMC7935780 DOI: 10.1111/cas.14820] [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: 09/19/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor angiogenesis is a crucial step in the further growth and metastasis of solid tumors. However, its regulatory mechanism remains unclear. Here, we showed that TARBP2, an RNA‐binding protein, played a role in promoting tumor‐induced angiogenesis both in vitro and in vivo through degrading the mRNAs of antiangiogenic factors, including thrombospondin1/2 (THBS1/2), tissue inhibitor of metalloproteinases 1 (TIMP1), and serpin family F member 1 (SERPINF1), by targeting their 3′untranslated regions (3′UTRs). Overexpression of TARBP2 promotes tumor cell–induced angiogenesis, while its knockdown inhibits tumor angiogenesis. Clinical cohort analysis revealed that high expression level of TARBP2 was associated with poor survival of lung cancer and breast cancer patients. Mechanistically, TARBP2 physically interacts with the stem‐loop structure located in the 3′UTR of antiangiogenic transcripts, leading to mRNA destabilization by the dsRNA‐binding domains 1/2 (dsRBDs1/2). Notably, the expression level of TARBP2 in human tumor tissue is negatively correlated with the expression of antiangiogenic factors, including THBS1/2, and brain‐specific angiogenesis inhibitor 1 (BAI1). Moreover, TARBP2 expression is strongly associated with tumor angiogenesis in a group of human lung cancer samples. Collectively, our results highlight that TARBP2 is a novel tumor angiogenesis regulator that could promote tumor angiogenesis by selectively downregulating antiangiogenic gene expression.
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Affiliation(s)
- Meicen Zhou
- Department of Endocrinology, Beijing Jishuitan Hospital, The 4th Clinical Medical College of Peking University, Beijing, China
| | - Wenbao Lu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bingwei Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xueting Liu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ailing Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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18
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Dystonia 16 (DYT16) mutations in PACT cause dysregulated PKR activation and eIF2α signaling leading to a compromised stress response. Neurobiol Dis 2020; 146:105135. [PMID: 33049316 DOI: 10.1016/j.nbd.2020.105135] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/17/2020] [Accepted: 10/07/2020] [Indexed: 12/17/2022] Open
Abstract
Dystonia 16 (DYT16) is caused by mutations in PACT, the protein activator of interferon-induced double-stranded RNA-activated protein kinase (PKR). PKR regulates the integrated stress response (ISR) via phosphorylation of the translation initiation factor eIF2α. This post-translational modification attenuates general protein synthesis while concomitantly triggering enhanced translation of a few specific transcripts leading either to recovery and homeostasis or cellular apoptosis depending on the intensity and duration of stress signals. PKR plays a regulatory role in determining the cellular response to viral infections, oxidative stress, endoplasmic reticulum (ER) stress, and growth factor deprivation. In the absence of stress, both PACT and PKR are bound by their inhibitor transactivation RNA-binding protein (TRBP) thereby keeping PKR inactive. Under conditions of cellular stress these inhibitory interactions dissociate facilitating PACT-PACT interactions critical for PKR activation. While both PACT-TRBP and PKR-TRBP interactions are pro-survival, PACT-PACT and PACT-PKR interactions are pro-apoptotic. In this study we evaluate if five DYT16 substitution mutations alter PKR activation and ISR. Our results indicate that the mutant DYT16 proteins show stronger PACT-PACT interactions and enhanced PKR activation. In DYT16 patient derived lymphoblasts the enhanced PACT-PKR interactions and heightened PKR activation leads to a dysregulation of ISR and increased apoptosis. More importantly, this enhanced sensitivity to ER stress can be rescued by luteolin, which disrupts PACT-PKR interactions. Our results not only demonstrate the impact of DYT16 mutations on regulation of ISR and DYT16 etiology but indicate that therapeutic interventions could be possible after a further evaluation of such strategies.
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19
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Chen G, Gu H, Fang T, Zhou K, Xu J, Yin X. Hypoxia-induced let-7f-5p/TARBP2 feedback loop regulates osteosarcoma cell proliferation and invasion by inhibiting the Wnt signaling pathway. Aging (Albany NY) 2020; 12:6891-6903. [PMID: 32305960 PMCID: PMC7202494 DOI: 10.18632/aging.103049] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/23/2020] [Indexed: 12/16/2022]
Abstract
Osteosarcoma (OS) is the most common bone tumor in children and adolescents and is characterized by high metastatic and recurrence rates. In the past, it has been shown that microRNAs may play critical roles in hypoxia-related OS proliferation and invasion. However, the mechanisms by which OS cells acquire this malignant phenotype have remained largely unknown. In the present study, we report that let-7f-5p and TARBP2 were expressed in lower amounts in human OS cell lines when compared with the hFOB normal human osteoblastic cell line; however, both types of cells were repressed by hypoxia. let-7f-5p and TARBP2 significantly inhibited the proliferation and invasion of OS cells. Furthermore, TARBP2 as a downstream and functional target of let-7f-5p regulated the expression of let-7f-5p, and there was a regulatory feedback loop between let-7f-5p and TARBP2. This loop reduced the expression of let-7f-5p and TARBP2 in OS cells to a very low level, which was induced by hypoxia. Furthermore, the hypoxia-induced let-7f-5p/TARBP2 feedback loop contributed to activation of the Wnt signaling pathway. Taken together, our data clearly showed that the feedback loop between let-7f-5p and TARBP2 induced by the hypoxia-promoted OS cell malignant phenotype increased with activation of the Wnt signaling pathway.
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Affiliation(s)
- Guangnan Chen
- Department of Orthopaedics, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
| | - Huijie Gu
- Department of Orthopaedics, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
| | - Tingting Fang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 201100, P.R. China
| | - Kaifeng Zhou
- Department of Orthopaedics, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
| | - Jun Xu
- Department of Orthopaedics, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
| | - Xiaofan Yin
- Department of Orthopaedics, Minhang Hospital, Fudan University, Shanghai 201199, P.R. China
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20
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Fang T, Zhao Z, Yuan F, He M, Sun J, Guo M, Huang P, Yang B, Xia J. Actinidia Chinensis Planch Root extract attenuates proliferation and metastasis of hepatocellular carcinoma by inhibiting the DLX2/TARBP2/JNK/AKT pathway. JOURNAL OF ETHNOPHARMACOLOGY 2020; 251:112529. [PMID: 31891797 DOI: 10.1016/j.jep.2019.112529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/18/2019] [Accepted: 12/25/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Many studies have confirmed that traditional Chinese herbs exert potential anti-tumor effects. Actinidia Chinensis Planch root has been used as a traditional Chinese medicine (TCM) for thousands of years. However, the mechanism of anti-tumor effects of Actinidia Chinensis Planch root has not been clearly clarified. AIM OF THE STUDY To explore the molecular biological mechanisms underlying the inhibitory effect of Actinidia Chinensis Planch root extract (acRoots) on hepatocellular carcinoma (HCC). MATERIALS AND METHODS In our previous study, we used mRNA chip analyses to identify genes regulated by acRoots. Further analyses of altered genes led to the identification of a key regulator of genes that responds to acRoots. We explored the effects of acRoots on the proliferation and invasion of HCC cells via cell counting as well as transwell assays, and further explored the molecular mechanisms underlying the effects of acRoots on HCC cells using qRT-PCR, western blot, and Chip-PCR. RESULTS Increasing the concentration of acRoots as well as prolonging its action time enhanced the inhibitory activity of acRoots as well as its cytotoxicity against HCC cells. High TARBP2 expression in HCC cells, which is associated with advanced-stage HCC and poor prognoses in HCC patients, was downregulated by treatment with acRoots. Furthermore, acRoots inhibited proliferation, invasion, and epithelial-to-mesenchymal transition by downregulating TARBP2 expression. HCC cells with higher TARBP2 expression were more sensitive to acRoots. The expression of TARBP2 and DLX2 in HCC patients and HCC cell lines was significantly positively correlated, and DLX2 as a transcription factor may promote TARBP2 expression, thereby further activating the JNK/AKT signaling pathway leading to the inhibition of HCC. CONCLUSIONS acRoots inhibited the malignant behavior of HCC cells by inhibiting TARBP2 expression, which is affected by the transcription factor DLX2, leading to a reduction in JNK/AKT signaling pathway activation.
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Affiliation(s)
- Tingting Fang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China
| | - Zhiying Zhao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China
| | - Feifei Yuan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China
| | - Mingyan He
- Department of gastroenterology, The First Affiliated Hospital of Nanchang university, Jiangxi, 330006, PR China
| | - Jialei Sun
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China
| | - Mengzhou Guo
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China
| | - Peixin Huang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China
| | - Biwei Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China.
| | - Jinglin Xia
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 201100, PR China; Minhang Hospital, Shanghai Medical School of Fudan University, Shanghai, 201100, PR China.
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21
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Takahashi T, Nakano Y, Onomoto K, Yoneyama M, Ui-Tei K. LGP2 virus sensor enhances apoptosis by upregulating apoptosis regulatory genes through TRBP-bound miRNAs during viral infection. Nucleic Acids Res 2020; 48:1494-1507. [PMID: 31799626 PMCID: PMC7026649 DOI: 10.1093/nar/gkz1143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/16/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
During viral infection, viral nucleic acids are detected by virus sensor proteins including toll-like receptor 3 or retinoic acid-inducible gene I-like receptors (RLRs) in mammalian cells. Activation of these virus sensor proteins induces type-I interferon production and represses viral replication. Recently, we reported that an RLR family member, laboratory of genetics and physiology 2 (LGP2), modulates RNA silencing by interacting with an RNA silencing enhancer, TAR-RNA binding protein (TRBP). However, the biological implications remained unclear. Here, we show that LGP2 enhances apoptosis by upregulating apoptosis regulatory genes during viral infection. Sendai virus (SeV) infection increased LGP2 expression approximately 900 times compared to that in non-virus-infected cells. Then, the induced LGP2 interacted with TRBP, resulting in the inhibition of maturation of the TRBP-bound microRNA (miRNA) and its subsequent RNA silencing activity. Gene expression profiling revealed that apoptosis regulatory genes were upregulated during SeV infection: caspases-2, -8, -3 and -7, four cysteine proteases with key roles in apoptosis, were upregulated directly or indirectly through the repression of a typical TRBP-bound miRNA, miR-106b. Our findings may shed light on the mechanism of apoptosis, induced by the TRBP-bound miRNAs through the interaction of TRBP with LGP2, as an antiviral defense system in mammalian cells.
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Affiliation(s)
- Tomoko Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuko Nakano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
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22
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Mutual Regulation of RNA Silencing and the IFN Response as an Antiviral Defense System in Mammalian Cells. Int J Mol Sci 2020; 21:ijms21041348. [PMID: 32079277 PMCID: PMC7072894 DOI: 10.3390/ijms21041348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 12/20/2022] Open
Abstract
RNA silencing is a posttranscriptional gene silencing mechanism directed by endogenous small non-coding RNAs called microRNAs (miRNAs). By contrast, the type-I interferon (IFN) response is an innate immune response induced by exogenous RNAs, such as viral RNAs. Endogenous and exogenous RNAs have typical structural features and are recognized accurately by specific RNA-binding proteins in each pathway. In mammalian cells, both RNA silencing and the IFN response are induced by double-stranded RNAs (dsRNAs) in the cytoplasm, but have long been considered two independent pathways. However, recent reports have shed light on crosstalk between the two pathways, which are mutually regulated by protein–protein interactions triggered by viral infection. This review provides brief overviews of RNA silencing and the IFN response and an outline of the molecular mechanism of their crosstalk and its biological implications. Crosstalk between RNA silencing and the IFN response may reveal a novel antiviral defense system that is regulated by miRNAs in mammalian cells.
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23
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Manning M, Jiang Y, Wang R, Liu L, Rode S, Bonahoom M, Kim S, Yang ZQ. Pan-cancer analysis of RNA methyltransferases identifies FTSJ3 as a potential regulator of breast cancer progression. RNA Biol 2020; 17:474-486. [PMID: 31957540 PMCID: PMC7237164 DOI: 10.1080/15476286.2019.1708549] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
RNA methylation, catalysed by a set of RNA methyltransferases (RNMTs), modulates RNA structures, properties, and biological functions. RNMTs are increasingly documented to be dysregulated in various human diseases, particularly developmental disorders and cancer. However, the genomic and transcriptomic alterations of RNMTs, as well as their functional roles in human cancer, are limited. In this study, we utilized an unbiased approach to examine copy number alterations and mutation rates of 58 RNMTs in more than 10,000 clinical samples across 32 human cancer types. We also investigated these alterations and RNMT expression level as they related to clinical features such as tumour subtype, grade, and survival in a large cohort of tumour samples, focusing on breast cancer. Loss-of-function analysis was performed to examine RNMT candidates with important roles in growth and viability of breast cancer cells. We identified a subset of RNMTs, notably TRMT12, NSUN2, TARBP1, and FTSJ3, that were amplified or mutated in a subset of human cancers. Several RNMTs were significantly associated with breast cancer aggressiveness and poor prognosis. Loss-of-function analysis indicated FTSJ3, a 2'-O-Me methyltransferase, as a candidate RNMT with functional roles in promoting cancer growth and survival. A subset of RNMTs, like FTSJ3, represents promising novel targets for anticancer drug discovery. Our findings provide a framework for further study of the functional consequences of RNMT alterations in human cancer and for developing therapies that target cancer-promoting RNMTs in the future.
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Affiliation(s)
- Morenci Manning
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Rui Wang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Diagnostics of Chinese Medicine, Hebei University of Chinese Medicine, Hebei, China
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Shomita Rode
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Madison Bonahoom
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
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24
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Salem ESB, Vonberg AD, Borra VJ, Gill RK, Nakamura T. RNAs and RNA-Binding Proteins in Immuno-Metabolic Homeostasis and Diseases. Front Cardiovasc Med 2019; 6:106. [PMID: 31482095 PMCID: PMC6710452 DOI: 10.3389/fcvm.2019.00106] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
The increasing prevalence of worldwide obesity has emerged as a major risk factor for type 2 diabetes (T2D), hepatosteatosis, and cardiovascular disease. Accumulating evidence indicates that obesity has strong inflammatory underpinnings tightly linked to the development of metabolic diseases. However, the molecular mechanisms by which obesity induces aberrant inflammation associated with metabolic diseases are not yet clearly defined. Recently, RNAs have emerged as important regulators of stress responses and metabolism. RNAs are subject to changes in modification status, higher-order structure, and cellular localization; all of which could affect the affinity for RNA-binding proteins (RBPs) and thereby modify the RNA-RBP networks. Proper regulation and management of RNA characteristics are fundamental to cellular and organismal homeostasis, as well as paramount to health. Identification of multiple single nucleotide polymorphisms (SNPs) within loci of fat mass- and obesity-associated protein (FTO) gene, an RNA demethylase, through genome-wide association studies (GWAS) of T2D, and functional assessments of FTO in mice, support the concept that disruption in RNA modifications leads to the development of human diseases including obesity and metabolic disorder. In obesity, dynamic alterations in modification and localization of RNAs appear to modulate the RNA-RBP networks and activate proinflammatory RBPs, such as double-stranded RNA (dsRNA)-dependent protein kinase (PKR), Toll-like receptor (TLR) 3 and TLR7, and RNA silencing machinery. These changes induce aberrant inflammation and the development of metabolic diseases. This review will describe the current understanding of the underlying causes of these common and altered characteristics of RNA-RBP networks which will pave the way for developing novel approaches to tackle the pandemic issue of obesity.
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Affiliation(s)
- Esam S B Salem
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew D Vonberg
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Vishnupriya J Borra
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Rupinder K Gill
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Takahisa Nakamura
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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25
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Burnett SB, Vaughn LS, Strom JM, Francois A, Patel RC. A truncated PACT protein resulting from a frameshift mutation reported in movement disorder DYT16 triggers caspase activation and apoptosis. J Cell Biochem 2019; 120:19004-19018. [PMID: 31246344 DOI: 10.1002/jcb.29223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/04/2019] [Indexed: 01/21/2023]
Abstract
Protein Activator (PACT) activates the interferon (IFN)-induced double-stranded (ds) RNA-activated protein kinase (PKR) in response to stress signals. Oxidative stress and endoplasmic reticulum (ER) stress causes PACT-mediated PKR activation, which leads to phosphorylation of translation initiation factor eIF2α, inhibition of protein synthesis, and apoptosis. A dominantly inherited form of early-onset dystonia 16 (DYT16) has been identified to arise due to a frameshift (FS) mutation in PACT. To examine the effect of the resulting truncated mutant PACT protein on the PKR pathway, we examined the biochemical properties of the mutant protein and its effect on mammalian cells. Our results indicate that the FS mutant protein loses its ability to bind dsRNA as well as its ability to interact with PKR while surprisingly retaining the ability to interact with PACT and PKR-inhibitory protein TRBP. The truncated FS mutant protein, when expressed as a fusion protein with a N-terminal fluorescent mCherry tag aggregates in mammalian cells to induce apoptosis via activation of caspases both in a PKR- and PACT-dependent as well as independent manner. Our results indicate that interaction of FS mutant protein with PKR inhibitor TRBP can dissociate PACT from the TRBP-PACT complex resulting in PKR activation and consequent apoptosis. These findings are relevant to diseases resulting from protein aggregation especially since the PKR activation is a characteristic of several neurodegenerative conditions.
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Affiliation(s)
- Samuel B Burnett
- Department of Biological Sciences University of South Carolina, University of South Carolina, Columbia, South Carolina
| | - Lauren S Vaughn
- Department of Biological Sciences University of South Carolina, University of South Carolina, Columbia, South Carolina
| | - Joelle M Strom
- Department of Biological Sciences University of South Carolina, University of South Carolina, Columbia, South Carolina
| | - Ashley Francois
- Department of Biological Sciences University of South Carolina, University of South Carolina, Columbia, South Carolina
| | - Rekha C Patel
- Department of Biological Sciences University of South Carolina, University of South Carolina, Columbia, South Carolina
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26
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Lee YS, Kunkeaw N, Lee YS. Protein kinase R and its cellular regulators in cancer: An active player or a surveillant? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1558. [PMID: 31231984 DOI: 10.1002/wrna.1558] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
Protein kinase R (PKR), originally known as an antiviral protein, senses various stresses as well as pathogen-driven double-stranded RNAs. Thereby activated PKR provokes diverse downstream events, including eIF2α phosphorylation and nuclear factor kappa-light-chain-enhancer of activated B cells activation. Consequently, PKR induces apoptosis and inflammation, both of which are highly important in cancer as much as its original antiviral role. Therefore, cellular proteins and RNAs should tightly control PKR activity. PKR and its regulators are often dysregulated in cancer and it is undoubted that such dysregulation contributes to tumorigenesis. However, PKR's precise role in cancer is still in debate, due to incomprehensible and even contradictory data. In this review, we introduce important cellular PKR regulators and discuss about their roles in cancer. Among them, we pay particular attention to nc886, a PKR repressor noncoding RNA that has been identified relatively recently, because its expression pattern in cancer can explain interesting yet obscure oncologic aspects of PKR. Based on nc886 and its regulation of PKR, we have proposed a tumor surveillance model, which reconciles contradictory data about PKR in cancer. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Nawapol Kunkeaw
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Yeon-Su Lee
- Division of Clinical Research, Research Institute, National Cancer Center, Goyang, Korea
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27
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Kuo YP, Ma CP, Chen HW, Chen YT, Lai YH, Liu H, Kuo RL, Chin-Ming Tan B. A novel antisense RNA ASPACT confers multi-level suppression of PACT and associated signalling. RNA Biol 2019; 16:1263-1274. [PMID: 31135270 DOI: 10.1080/15476286.2019.1624471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The innate immune system is the frontline host protection against pathogens. Effective antiviral immunity is elicited upon recognition of viral RNAs by the host pattern recognition receptors. One of the major viral RNA sensors is retinoic acid inducible gene-1, which triggers the production of interferons (IFNs). In turn, this protective response requires another viral sensor and immunity factor interferon-inducible protein kinase RNA activator (PACT/PRKRA). Here, we report the identification and characterization of a novel antisense PACT gene that expresses a non-coding RNA in a convergent and interferon-inducible manner. Publicly available gene structure and expression data revealed that this gene, that we termed ASPACT, overlaps with the 3' -end of the PACT locus and is highly expressed during viral infection. Our results confirm the IFN-β-inducibility of ASPACT, which is dependent on STAT-1/2. We further discovered that downregulation of ASPACT impacts both the expression and localization of the PACT transcript. At the transcription level, ChIP and ChIRP assays demonstrated that the ASPACT non-coding RNA occupies distinct chromatin regions of PACT gene and is important for promoter recruitment of the epigenetic silencer HDAC1. In parallel, ASPACT was also found to mediate nuclear retention of the PACT mRNA via direct RNA-RNA interaction, as revealed by RNA antisense purification assay. In summary, our results support the model that the non-coding RNA ASPACT acts as a negative regulator of PACT at multiple levels, and reveal a novel regulator of the viral counteractive response.
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Affiliation(s)
- Yu-Ping Kuo
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,b Department of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan
| | - Chung-Pei Ma
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,b Department of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan
| | - Hui-Wen Chen
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,b Department of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan
| | - Yi-Tung Chen
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,b Department of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan
| | - Yi-Hsuan Lai
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,b Department of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan
| | - Hsuan Liu
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,c Molecular Medicine Research Center, Chang Gung University , Taoyuan , Taiwan.,d Department of Cell and Molecular Biology, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,e Division of Colon and Rectal Surgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital , Taoyuan , Taiwan
| | - Rei-Lin Kuo
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,f Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,g Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,h Division of Asthma, Allergy, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital , Taoyuan , Taiwan
| | - Bertrand Chin-Ming Tan
- a Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,b Department of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,g Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University , Taoyuan , Taiwan.,i Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital , Taoyuan , Taiwan
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28
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Dzananovic E, McKenna SA, Patel TR. Viral proteins targeting host protein kinase R to evade an innate immune response: a mini review. Biotechnol Genet Eng Rev 2018; 34:33-59. [PMID: 29716441 DOI: 10.1080/02648725.2018.1467151] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The innate immune system offers a first line of defense by neutralizing foreign pathogens such as bacteria, fungi, and viruses. These pathogens express molecules (RNA and proteins) that have discrete structures, known as the pathogen-associated molecular patterns that are recognized by a highly specialized class of host proteins called pattern recognition receptors to facilitate the host's immune response against infection. The RNA-dependent Protein Kinase R (PKR) is one of the host's pattern recognition receptors that is a key component of an innate immune system. PKR recognizes imperfectly double-stranded non-coding viral RNA molecules via its N-terminal double-stranded RNA binding motifs, undergoes phosphorylation of the C-terminal kinase domain, ultimately resulting in inhibition of viral protein translation by inhibiting the guanine nucleotide exchange activity of eukaryotic initiation factor 2α. Not surprisingly, viruses have evolved mechanisms by which viral non-coding RNA or protein molecules inhibit PKR's activation and/or its downstream activity to allow viral replication. In this review, we will highlight the role of viral proteins in inhibiting PKR's activity and summarize currently known mechanisms by which viral proteins execute such inhibitory activity.
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Affiliation(s)
- Edis Dzananovic
- a Plant Pathology, Plant Protection and Molecular Biology , Agriculture and Agri-Food Canada , Saskatoon , Canada
| | - Sean A McKenna
- b Department of Chemistry, Manitoba Institute for Materials, Department of Biochemistry and Medical Genetics , University of Manitoba , Winnipeg , Canada
| | - Trushar R Patel
- c Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada.,d DiscoveryLab, Faculty of Medicine & Dentistry , University of Alberta , Edmonton , Canada.,e Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada
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29
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Paithankar H, Jadhav PV, Naglekar AS, Sharma S, Chugh J. 1H, 13C and 15N resonance assignment of domain 1 of trans-activation response element (TAR) RNA binding protein isoform 1 (TRBP2) and its comparison with that of isoform 2 (TRBP1). BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:189-194. [PMID: 29445910 DOI: 10.1007/s12104-018-9807-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
TAR RNA binding protein (TRBP) is a double-stranded RNA binding protein involved in various biological processes like cell growth, development, death, etc. The protein exists as two isoforms TRBP2 and TRBP1. TRBP2 contains additional 21 amino acids at its N-terminus, which are proposed to be involved in its membrane localization, when compared to TRBP1. The resonance assignment (19-228) of the double-stranded RNA binding domains (dsRBD 1 and 2) of TRBP2 has been reported earlier. Here, we report 1H, 13C and 15N resonance assignment for dsRBD1 of TRBP2 (1-105) containing the additional N-terminal residues. This assignment will provide deeper insights to understand the effect of these residues on the structure and dynamics of TRBP2 and would therefore help in further elucidating the differences in the role of these isoforms.
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Affiliation(s)
- Harshad Paithankar
- Department of Chemistry, Indian Institute of Science Education & Research, Dr Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Pankaj V Jadhav
- Department of Biotechnology, Savitrabai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411007, India
| | - Amit S Naglekar
- Department of Biotechnology, Savitrabai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411007, India
| | - Shilpy Sharma
- Department of Biotechnology, Savitrabai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411007, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education & Research, Dr Homi Bhabha Road, Pashan, Pune, 411008, India.
- Department of Biology, Indian Institute of Science Education & Research, Dr Homi Bhabha Road, Pashan, Pune, 411008, India.
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30
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Radetskyy R, Daher A, Gatignol A. ADAR1 and PKR, interferon stimulated genes with clashing effects on HIV-1 replication. Cytokine Growth Factor Rev 2018; 40:48-58. [PMID: 29625900 DOI: 10.1016/j.cytogfr.2018.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 12/15/2022]
Abstract
The induction of hundreds of Interferon Stimulated Genes (ISGs) subsequent to virus infection generates an antiviral state that functions to restrict virus growth at multiple steps of their replication cycles. In the context of Human Immunodeficiency Virus-1 (HIV-1), ISGs also possess antiviral functions, but some ISGs show proapoptotic or proviral activity. One of the most studied ISGs, the RNA activated Protein Kinase (PKR), shuts down the viral protein synthesis upon activation. HIV-1 has evolved to evade its inhibition by PKR through viral and cellular mechanisms. One of the cellular mechanisms is the induction of another ISG, the Adenosine Deaminase acting on RNA 1 (ADAR1). ADAR1 promotes viral replication by acting as an RNA sensing inhibitor, by editing viral RNA and by inhibiting PKR. This review challenges the orthodox dogma of ISGs as antiviral proteins, by demonstrating that two ISGs have opposing and clashing effects on viral replication.
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Affiliation(s)
- Roman Radetskyy
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada; Department of Medicine, Division of Experimental Medicine, Canada
| | - Aïcha Daher
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada
| | - Anne Gatignol
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada; Department of Medicine, Division of Experimental Medicine, Canada; Department of Medicine, Division of Infectious Diseases, Canada; Department of Microbiology-Immunology, McGill University, Montréal, Québec, Canada.
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31
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Ye J, Wang J, Zhang N, Liu Y, Tan L, Xu L. Expression of TARBP1 protein in human non-small-cell lung cancer and its prognostic significance. Oncol Lett 2018; 15:7182-7190. [PMID: 29731880 PMCID: PMC5920659 DOI: 10.3892/ol.2018.8202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/27/2018] [Indexed: 12/22/2022] Open
Abstract
The aim of the present study was to investigate the expression of transactivation response RNA-binding protein (TARBP)1 and its clinical significance in human non-small-cell lung cancer (NSCLC). TARBP1 expression at the mRNA level was detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in 10 NSCLC tissues and paired adjacent normal tissues. TARBP1 protein expression was analyzed in 90 paraffin-embedded NSCLC tissue samples and paired adjacent normal tissues by immunohistochemistry. Statistical analyses were performed to assess the clinicopathological significance of TARBP1 expression. The expression of TARBP1 mRNA was higher in the 10 NSCLC samples than in the paired adjacent non-tumor tissues (P=0.0017). In the paraffin-embedded tissue samples, the expression level of TARBP1 was higher in the cancer tissues than in the adjacent non-cancerous tissues. TARBP1 expression was detected in 76.67% (69/90) of the NSCLC samples and in 22.22% (20/90) of the adjacent normal lung tissues (P<0.001). The expression of TARBP1 was significantly associated with histological grade (P<0.001), clinical stage (P=0.024) and pathological type (P<0.001), along with a decreased overall survival (OS) rate (P<0.001). On multivariate analysis, the expression of TARBP1 was an independent prognostic factor for hazard ratio (OS, 2.729; 95% confidence interval, 1.471-5.061; P=0.003). TARBP1 is overexpressed in NSCLC, and the expression of TARBP1 is associated with pathological grade, clinical stage and pathological type. Thus, TARBP1 may be an independent prognostic marker in patients with NSCLC.
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Affiliation(s)
- Jingmei Ye
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China
| | - Jiani Wang
- Breast Cancer Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Nana Zhang
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Yu Liu
- Breast Cancer Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Li Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China
| | - Lihua Xu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China.,Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China
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32
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Functional Redundancy of DICER Cofactors TARBP2 and PRKRA During Murine Embryogenesis Does Not Involve miRNA Biogenesis. Genetics 2018; 208:1513-1522. [PMID: 29467169 PMCID: PMC5887145 DOI: 10.1534/genetics.118.300791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/10/2018] [Indexed: 12/21/2022] Open
Abstract
Several in vitro studies have suggested that canonical microRNA (miRNA) biogenesis requires the DICER cofactors TARBP2 and PRKRA for processing of pre-miRNAs to mature miRNAs. To investigate the roles of TARBP2 and PRKRA in miRNA biogenesis in vivo, and to determine possible functional redundancy, we first compared the phenotypes of Tarbp2 and Prkra single and double mutants. In contrast to Dicer −/− embryos, which die by embryonic day 7.5 (E7.5), single Tarbp2 −/− and Prkra −/− mice survive beyond E7.5 and either die perinatally or survive and exhibit cranial/facial abnormalities, respectively. In contrast, only a few Tarbp2 −/−; Prkra −/− double mutants survived beyond E12.5, suggesting genetic redundancy between Tarbp2 and Prkra during embryonic development. Sequencing of miRNAs from single-mutant embryos at E15.5 revealed changes in abundance and isomiR type in Tarbp2 −/−, but not Prkra −/−, embryos, demonstrating that TARBP2, but not PRKRA, functions in miRNA biogenesis of a subclass of miRNAs, and suggesting that functional redundancy between TARBP2 and PRKRA does not involve miRNA biogenesis.
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Masliah G, Maris C, König SL, Yulikov M, Aeschimann F, Malinowska AL, Mabille J, Weiler J, Holla A, Hunziker J, Meisner-Kober N, Schuler B, Jeschke G, Allain FHT. Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains. EMBO J 2018; 37:embj.201797089. [PMID: 29449323 PMCID: PMC5852647 DOI: 10.15252/embj.201797089] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 01/10/2018] [Accepted: 01/12/2018] [Indexed: 11/23/2022] Open
Abstract
The accurate cleavage of pre‐micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA‐induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here, we solved the solution structure of the two N‐terminal dsRNA binding domains (dsRBDs) of TRBP in complex with a functionally asymmetric siRNA using NMR, EPR, and single‐molecule spectroscopy. We find that siRNA recognition by the dsRBDs is not sequence‐specific but rather depends on the RNA shape. The two dsRBDs can swap their binding sites, giving rise to two equally populated, pseudo‐symmetrical complexes, showing that TRBP is not a primary sensor of siRNA asymmetry. Using our structure to model a Dicer‐TRBP‐siRNA ternary complex, we show that TRBP's dsRBDs and Dicer's RNase III domains bind a canonical 19 base pair siRNA on opposite sides, supporting a mechanism whereby TRBP influences Dicer‐mediated cleavage accuracy by binding the dsRNA region of the pre‐miRNA during Dicer cleavage.
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Affiliation(s)
- Gregoire Masliah
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | | | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | | | - Anna L Malinowska
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Julie Mabille
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jan Weiler
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Andrea Holla
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Juerg Hunziker
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Benjamin Schuler
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Frederic H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
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Stress-induced TRBP phosphorylation enhances its interaction with PKR to regulate cellular survival. Sci Rep 2018; 8:1020. [PMID: 29348664 PMCID: PMC5773696 DOI: 10.1038/s41598-018-19360-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/29/2017] [Indexed: 12/20/2022] Open
Abstract
Transactivation response element RNA-binding protein (TRBP or TARBP2) initially identified to play an important role in human immunodeficiency virus (HIV) replication also has emerged as a regulator of microRNA biogenesis. In addition, TRBP functions in signaling pathways by negatively regulating the interferon-induced double-stranded RNA (dsRNA)-activated protein kinase (PKR) during viral infections and cell stress. During cellular stress, PKR is activated and phosphorylates the α subunit of the eukaryotic translation factor eIF2, leading to the cessation of general protein synthesis. TRBP inhibits PKR activity by direct interaction as well as by binding to PKR’s two known activators, dsRNA and PACT, thus preventing their interaction with PKR. In this study, we demonstrate for the first time that TRBP is phosphorylated in response to oxidative stress and upon phosphorylation, inhibits PKR more efficiently promoting cell survival. These results establish that PKR regulation through stress-induced TRBP phosphorylation is an important mechanism ensuring cellular recovery and preventing apoptosis due to sustained PKR activation.
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Chukwurah E, Willingham V, Singh M, Castillo-Azofeifa D, Patel RC. Contribution of the two dsRBM motifs to the double-stranded RNA binding and protein interactions of PACT. J Cell Biochem 2018; 119:3598-3607. [PMID: 29231267 DOI: 10.1002/jcb.26561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/01/2017] [Indexed: 11/12/2022]
Abstract
PACT is a stress-modulated activator of protein kinase PKR (protein kinase, RNA activated), which is involved in antiviral innate immune responses and stress-induced apoptosis. Stress-induced phosphorylation of PACT is essential for PACT's increased association with PKR leading to PKR activation, phosphorylation of translation initiation factor eIF2α, inhibition of protein synthesis, and apoptosis. PACT-induced PKR activation is negatively regulated by TRBP (transactivation response element RNA-binding protein), which dissociates from PACT after PACT phosphorylation in response to stress signals. The conserved double-stranded RNA binding motifs (dsRBMs) in PKR, PACT, and TRBP mediate protein-protein interactions, and the stress-dependent phosphorylation of PACT changes the relative strengths of PKR-PACT, PACT-TRBP, and PACT-PACT interactions to bring about a timely and transient PKR activation. This regulates the general kinetics as well as level of eIF2α phosphorylation, thereby influencing the cellular response to stress either as recovery and survival or elimination by apoptosis. In the present study, we evaluated the effect of specific mutations within PACT's two evolutionarily conserved dsRBMs on dsRNA-binding, and protein-protein interactions between PKR, PACT, and TRBP. Our data show that the two motifs contribute to varying extents in dsRNA binding, and protein interactions. These findings indicate that although the dsRBM motifs have high sequence conservation, their functional contribution in the context of the whole proteins needs to be determined by mutational analysis. Furthermore, using a PACT mutant that is deficient in PACT-PACT interaction but competent for PACT-PKR interaction, we demonstrate that PACT-PACT interaction is essential for efficient PKR activation.
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Affiliation(s)
- Evelyn Chukwurah
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Victoria Willingham
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Madhurima Singh
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | | | - Rekha C Patel
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
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Scarborough RJ, Gatignol A. RNA Interference Therapies for an HIV-1 Functional Cure. Viruses 2017; 10:E8. [PMID: 29280961 PMCID: PMC5795421 DOI: 10.3390/v10010008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
HIV-1 drug therapies can prevent disease progression but cannot eliminate HIV-1 viruses from an infected individual. While there is hope that elimination of HIV-1 can be achieved, several approaches to reach a functional cure (control of HIV-1 replication in the absence of drug therapy) are also under investigation. One of these approaches is the transplant of HIV-1 resistant cells expressing anti-HIV-1 RNAs, proteins or peptides. Small RNAs that use RNA interference pathways to target HIV-1 replication have emerged as competitive candidates for cell transplant therapy and have been included in all gene combinations that have so far entered clinical trials. Here, we review RNA interference pathways in mammalian cells and the design of therapeutic small RNAs that use these pathways to target pathogenic RNA sequences. Studies that have been performed to identify anti-HIV-1 RNA interference therapeutics are also reviewed and perspectives on their use in combination gene therapy to functionally cure HIV-1 infection are provided.
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Affiliation(s)
- Robert J Scarborough
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A0G4, Canada.
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A0G4, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC H3A0G4, Canada.
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KSHV inhibits stress granule formation by viral ORF57 blocking PKR activation. PLoS Pathog 2017; 13:e1006677. [PMID: 29084250 PMCID: PMC5679657 DOI: 10.1371/journal.ppat.1006677] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/09/2017] [Accepted: 10/03/2017] [Indexed: 11/18/2022] Open
Abstract
TIA-1 positive stress granules (SG) represent the storage sites of stalled mRNAs and are often associated with the cellular antiviral response. In this report, we provide evidence that Kaposi's sarcoma-associated herpesvirus (KSHV) overcomes the host antiviral response by inhibition of SG formation via a viral lytic protein ORF57. By immunofluorescence analysis, we found that B lymphocytes with KSHV lytic infection are refractory to SG induction. KSHV ORF57, an essential post-transcriptional regulator of viral gene expression and the production of new viral progeny, inhibits SG formation induced experimentally by arsenite and poly I:C, but not by heat stress. KSHV ORF37 (vSOX) bearing intrinsic endoribonuclease activity also inhibits arsenite-induced SG formation, but KSHV RTA, vIRF-2, ORF45, ORF59 and LANA exert no such function. ORF57 binds both PKR-activating protein (PACT) and protein kinase R (PKR) through their RNA-binding motifs and prevents PACT-PKR interaction in the PKR pathway which inhibits KSHV production. Consistently, knocking down PKR expression significantly promotes KSHV virion production. ORF57 interacts with PKR to inhibit PKR binding dsRNA and its autophosphorylation, leading to inhibition of eIF2α phosphorylation and SG formation. Homologous protein HSV-1 ICP27, but not EBV EB2, resembles KSHV ORF57 in the ability to block the PKR/eIF2α/SG pathway. In addition, KSHV ORF57 inhibits poly I:C-induced TLR3 phosphorylation. Altogether, our data provide the first evidence that KSHV ORF57 plays a role in modulating PKR/eIF2α/SG axis and enhances virus production during virus lytic infection.
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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ADAR1 and PACT contribute to efficient translation of transcripts containing HIV-1 trans-activating response (TAR) element. Biochem J 2017; 474:1241-1257. [PMID: 28167698 PMCID: PMC5363390 DOI: 10.1042/bcj20160964] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/30/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) has evolved various measures to counter the host cell's innate antiviral response during the course of infection. Interferon (IFN)-stimulated gene products are produced following HIV-1 infection to limit viral replication, but viral proteins and RNAs counteract their effect. One such mechanism is specifically directed against the IFN-induced Protein Kinase PKR, which is centrally important to the cellular antiviral response. In the presence of viral RNAs, PKR is activated and phosphorylates the translation initiation factor eIF2α. This shuts down the synthesis of both host and viral proteins, allowing the cell to mount an effective antiviral response. PACT (protein activator of PKR) is a cellular protein activator of PKR, primarily functioning to activate PKR in response to cellular stress. Recent studies have indicated that during HIV-1 infection, PACT's normal cellular function is compromised and that PACT is unable to activate PKR. Using various reporter systems and in vitro kinase assays, we establish in this report that interactions between PACT, ADAR1 and HIV-1-encoded Tat protein diminish the activation of PKR in response to HIV-1 infection. Our results highlight an important pathway by which HIV-1 transcripts subvert the host cell's antiviral activities to enhance their translation.
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40
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Byun SH, Kim J, Han D, Kwon M, Cho JY, Ng HX, Pleasure SJ, Yoon K. TRBP maintains mammalian embryonic neural stem cell properties by acting as a novel transcriptional coactivator of the Notch signaling pathway. Development 2017; 144:778-783. [PMID: 28174252 DOI: 10.1242/dev.139493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 01/16/2017] [Indexed: 12/19/2022]
Abstract
Transactivation response element RNA-binding protein (TRBP; TARBP2) is known to play important roles in human immunodeficiency virus (HIV) replication and microRNA biogenesis. However, recent studies implicate TRBP in a variety of biological processes as a mediator of cross-talk between signal transduction pathways. Here, we provide the first evidence that TRBP is required for efficient neurosphere formation and for the expression of neural stem cell markers and Notch target genes in primary neural progenitor cells in vitro Consistent with this, introduction of TRBP into the mouse embryonic brain in utero increased the fraction of cells expressing Sox2 in the ventricular zone. We also show that TRBP physically interacts with the Notch transcriptional coactivation complex through C promoter-binding factor 1 (CBF1; RBPJ) and strengthens the association between the Notch intracellular domain (NICD) and CBF1, resulting in increased NICD recruitment to the promoter region of a Notch target gene. Our data indicate that TRBP is a novel transcriptional coactivator of the Notch signaling pathway, playing an important role in neural stem cell regulation during mammalian brain development.
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Affiliation(s)
- Sung-Hyun Byun
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, South Korea
| | - Juwan Kim
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, South Korea
| | - Dasol Han
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, South Korea
| | - Mookwang Kwon
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, South Korea
| | - Jae Youl Cho
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, South Korea
| | - Hui Xuan Ng
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Samuel J Pleasure
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Keejung Yoon
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, South Korea
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41
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TRBP ensures efficient Dicer processing of precursor microRNA in RNA-crowded environments. Nat Commun 2016; 7:13694. [PMID: 27934859 PMCID: PMC5155159 DOI: 10.1038/ncomms13694] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 01/03/2023] Open
Abstract
The RNA-binding protein TRBP is a central component of the Dicer complex. Despite a decade of biochemical and structural studies, the essential functionality of TRBP in microRNA (miRNA) biogenesis remains unknown. Here we show that TRBP is an integral cofactor for time-efficient Dicer processing in RNA-crowded environments. We competed for Dicer processing of pre-miRNA with a large amount of cellular RNA species and found that Dicer-TRBP, but not Dicer alone, remains resilient. To apprehend the mechanism of this substrate selectivity, we use single-molecule fluorescence. The real-time observation reveals that TRBP acts as a gatekeeper, precluding Dicer from engaging with pre-miRNA-like substrates. TRBP acquires the selectivity using the PAZ domain of Dicer, whereas Dicer moderates the RNA-binding affinity of TRBP for fast turnover. This coordinated action between TRBP and Dicer accomplishes an efficient way of discarding pre-miRNA-like substrates. The RNA binding protein TRBP is a component of the Dicer complex but its role in microRNA biogenesis remains poorly understood. Here the authors use a crowded RNA environment and single-molecule imaging to show that TRBP acts as a gatekeeper to prevent Dicer engagement with pre miRNA-like substrates.
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Affiliation(s)
- Takahisa Nakamura
- Divisions of Endocrinology and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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43
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Warner MJ, Bridge KS, Hewitson JP, Hodgkinson MR, Heyam A, Massa BC, Haslam JC, Chatzifrangkeskou M, Evans GJO, Plevin MJ, Sharp TV, Lagos D. S6K2-mediated regulation of TRBP as a determinant of miRNA expression in human primary lymphatic endothelial cells. Nucleic Acids Res 2016; 44:9942-9955. [PMID: 27407113 PMCID: PMC5175334 DOI: 10.1093/nar/gkw631] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/16/2016] [Accepted: 07/02/2016] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that silence mRNAs. They are generated following transcription and cleavage by the DROSHA/DGCR8 and DICER/TRBP/PACT complexes. Although it is known that components of the miRNA biogenesis machinery can be phosphorylated, it remains poorly understood how these events become engaged during physiological cellular activation. We demonstrate that S6 kinases can phosphorylate the extended C-terminal domain of TRBP and interact with TRBP in situ in primary cells. TRBP serines 283/286 are essential for S6K-mediated TRBP phosphorylation, optimal expression of TRBP, and the S6K-TRBP interaction in human primary cells. We demonstrate the functional relevance of this interaction in primary human dermal lymphatic endothelial cells (HDLECs). Angiopoietin-1 (ANG1) can augment miRNA biogenesis in HDLECs through enhancing TRBP phosphorylation and expression in an S6K2-dependent manner. We propose that the S6K2/TRBP node controls miRNA biogenesis in HDLECs and provides a molecular link between the mTOR pathway and the miRNA biogenesis machinery.
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Affiliation(s)
- Matthew J Warner
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Katherine S Bridge
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, EC1M 6BQ, UK
| | - James P Hewitson
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, Wentworth Way, York, YO10 5DD, UK
| | | | - Alex Heyam
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Bailey C Massa
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jessica C Haslam
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Maria Chatzifrangkeskou
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Gareth J O Evans
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Michael J Plevin
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Tyson V Sharp
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, EC1M 6BQ, UK
| | - Dimitris Lagos
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, Wentworth Way, York, YO10 5DD, UK
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Kalantari R, Hicks JA, Li L, Gagnon KT, Sridhara V, Lemoff A, Mirzaei H, Corey DR. Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (NEW YORK, N.Y.) 2016; 22:1085-98. [PMID: 27198507 PMCID: PMC4911916 DOI: 10.1261/rna.056499.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/25/2016] [Indexed: 05/25/2023]
Abstract
Argonaute 2 (AGO2), the catalytic engine of RNAi, is typically associated with inhibition of translation in the cytoplasm. AGO2 has also been implicated in nuclear processes including transcription and splicing. There has been little insight into AGO2's nuclear interactions or how they might differ relative to cytoplasm. Here we investigate the interactions of cytoplasmic and nuclear AGO2 using semi-quantitative mass spectrometry. Mass spectrometry often reveals long lists of candidate proteins, complicating efforts to rigorously discriminate true interacting partners from artifacts. We prioritized candidates using orthogonal analytical strategies that compare replicate mass spectra of proteins associated with Flag-tagged and endogenous AGO2. Interactions with TRNC6A, TRNC6B, TNRC6C, and AGO3 are conserved between nuclei and cytoplasm. TAR binding protein interacted stably with cytoplasmic AGO2 but not nuclear AGO2, consistent with strand loading in the cytoplasm. Our data suggest that interactions between functionally important components of RNAi machinery are conserved between the nucleus and cytoplasm but that accessory proteins differ. Orthogonal analysis of mass spectra is a powerful approach to streamlining identification of protein partners.
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Affiliation(s)
- Roya Kalantari
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jessica A Hicks
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Liande Li
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Viswanadham Sridhara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Trbp Is Required for Differentiation of Myoblasts and Normal Regeneration of Skeletal Muscle. PLoS One 2016; 11:e0155349. [PMID: 27159388 PMCID: PMC4861269 DOI: 10.1371/journal.pone.0155349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/27/2016] [Indexed: 12/19/2022] Open
Abstract
Global inactivation of Trbp, a regulator of miRNA pathways, resulted in developmental defects and postnatal lethality in mice. Recently, we showed that cardiac-specific deletion of Trbp caused heart failure. However, its functional role(s) in skeletal muscle has not been characterized. Using a conditional knockout model, we generated mice lacking Trbp in the skeletal muscle. Unexpectedly, skeletal muscle specific Trbp mutant mice appear to be phenotypically normal under normal physiological conditions. However, these mice exhibited impaired muscle regeneration and increased fibrosis in response to cardiotoxin-induced muscle injury, suggesting that Trbp is required for muscle repair. Using cultured myoblast cells we further showed that inhibition of Trbp repressed myoblast differentiation in vitro. The impaired myogenesis is associated with reduced expression of muscle-specific miRNAs, miR-1a and miR-133a. Together, our study demonstrated that Trbp participates in the regulation of muscle differentiation and regeneration.
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46
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Svobodova E, Kubikova J, Svoboda P. Production of small RNAs by mammalian Dicer. Pflugers Arch 2016; 468:1089-102. [PMID: 27048428 PMCID: PMC4893058 DOI: 10.1007/s00424-016-1817-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/20/2016] [Accepted: 03/24/2016] [Indexed: 01/16/2023]
Abstract
MicroRNA (miRNA) and RNA interference (RNAi) pathways employ RNase III Dicer for the biogenesis of small RNAs guiding post-transcriptional repression. Requirements for Dicer activity differ in the two pathways. The biogenesis of miRNAs requires a single Dicer cleavage of a short hairpin precursor to produce a small RNA with a precisely defined sequence, while small RNAs in RNAi come from a processive cleavage of a long double-stranded RNA (dsRNA) into a pool of small RNAs with different sequences. While Dicer is generally conserved among eukaryotes, its substrate recognition, cleavage, and biological roles differ. In Metazoa, a single Dicer can function as a universal factor for RNAi and miRNA pathways or as a factor adapted specifically for one of the pathways. In this review, we focus on the structure, function, and evolution of mammalian Dicer. We discuss key structural features of Dicer and other factors defining Dicer substrate repertoire and biological functions in mammals in comparison with invertebrate models. The key for adaptation of Dicer for miRNA or RNAi pathways is the N-terminal helicase, a dynamically evolving Dicer domain. Its functionality differs between mammals and invertebrates: the mammalian Dicer is well adapted to produce miRNAs while its ability to support RNAi is limited.
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Affiliation(s)
- Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Jana Kubikova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic.
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Daniels SM, Sinck L, Ward NJ, Melendez-Peña CE, Scarborough RJ, Azar I, Rance E, Daher A, Pang KM, Rossi JJ, Gatignol A. HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs. RNA Biol 2015; 12:123-35. [PMID: 25668122 DOI: 10.1080/15476286.2015.1014759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Several proteins and RNAs expressed by mammalian viruses have been reported to interfere with RNA interference (RNAi) activity. We investigated the ability of the HIV-1-encoded RNA elements Trans-Activation Response (TAR) and Rev-Response Element (RRE) to alter RNAi. MicroRNA let7-based assays showed that RRE is a potent suppressor of RNAi activity, while TAR displayed moderate RNAi suppression. We demonstrate that RRE binds to TAR-RNA Binding Protein (TRBP), an essential component of the RNA Induced Silencing Complex (RISC). The binding of TAR and RRE to TRBP displaces small interfering (si)RNAs from binding to TRBP. Several stem-deleted RRE mutants lost their ability to suppress RNAi activity, which correlated with a reduced ability to compete with siRNA-TRBP binding. A lentiviral vector expressing TAR and RRE restricted RNAi, but RNAi was restored when Rev or GagPol were coexpressed. Adenoviruses are restricted by RNAi and encode their own suppressors of RNAi, the Virus-Associated (VA) RNA elements. RRE enhanced the replication of wild-type and VA-deficient adenovirus. Our work describes RRE as a novel suppressor of RNAi that acts by competing with siRNAs rather than by disrupting the RISC. This function is masked in lentiviral vectors co-expressed with viral proteins and thus will not affect their use in gene therapy. The potent RNAi suppressive effects of RRE identified in this study could be used to enhance the expression of RNAi restricted viruses used in oncolysis such as adenoviruses.
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Key Words
- Ago2, Argonaute-2
- EGFP, enhanced green fluorescent protein
- EMSA, electrophoresis mobility shift assay
- FL, firefly luciferase
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- HIV, human immunodeficiency virus
- HIV-1
- IP, immunoprecipitation
- NC, nucleocapsid
- PAGE, polyacrylamide gel electrophoresis
- RISC, RNA-Induced Silencing Complex
- RL, Renilla luciferase
- RNA interference
- RNA silencing suppressor
- RNAi, RNA interference
- RRE, Rev Response Element
- RSS, RNA silencing suppressor
- RT, reverse transcription
- Rev-Response Element RNA
- TAR RNA Binding Protein (TRBP)
- TAR, trans-activation responsive element
- TRBP, TAR RNA Binding Protein
- Trans-Activation Response Element
- UTR, untranslated region
- VA, virus-associated
- WT, wild-type
- adenovirus
- ds, double-stranded
- lentiviral vectors
- miRNA, micro RNA
- pre-miRNA, precursor miRNA
- siRNA, small interfering RNA
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Affiliation(s)
- Sylvanne M Daniels
- a Virus-Cell Interactions Laboratory ; Lady Davis Institute for Medical Research ; Montréal , Québec , Canada
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Romero-Cordoba SL, Salido-Guadarrama I, Rodriguez-Dorantes M, Hidalgo-Miranda A. miRNA biogenesis: biological impact in the development of cancer. Cancer Biol Ther 2015; 15:1444-55. [PMID: 25482951 PMCID: PMC4622859 DOI: 10.4161/15384047.2014.955442] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
microRNAs (miRNAs) are non coding RNAs with different biological functions and pathological implications. Given their role as post-transcriptional gene expression regulators, they are involved in several important physiological processes like development, cell differentiation and cell signaling. miRNAs act as modulators of gene expression programs in different diseases, particularly in cancer, where they act through the repression of genes which are critical for carcinogenesis. The expression level of mature miRNAs is the result of a fine mechanism of biogenesis, carried out by different enzymatic complexes that exert their function at transcriptional and post-transcriptional levels. In this review, we will focus our discussion on the alterations in the miRNA biogenesis machinery, and its impact on the establishment and development of cancer programs.
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Key Words
- Ago2, Argonaute 2 protein
- Ars2, Arsenic Resistance protein 2
- DGCR8, DiGeorge syndrome Critical Region 8 protein
- EMT, epithelial–mesenchymal transition
- KSRP, KH-type splicing regulatory protein
- MK2, MAPK-activated protein kinase 2
- PABP, poly(A)-binding protein
- PACT, kinase R–activating protein
- PRC2, Polycomb repressor complex
- RISC, RNA-induced silencing complex
- TRBP, TAR RNA binding protein
- TUT4, terminal uridine transferase-4
- XPO5, exportin 5
- cancer
- cellular signaling
- circRNA, circular RNA
- hnRNPs, heterogeneous nuclear ribonucleoproteins
- miRNA biogenesis
- miRNAs, microRNAs
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Matsui M, Li L, Janowski BA, Corey DR. Reduced Expression of Argonaute 1, Argonaute 2, and TRBP Changes Levels and Intracellular Distribution of RNAi Factors. Sci Rep 2015; 5:12855. [PMID: 26242502 PMCID: PMC4525381 DOI: 10.1038/srep12855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
Until recently, Argonaute 2 (AGO2) and other RNA factors were believed to be restricted to the cytoplasm of mammalian somatic cells. It is now becoming appreciated that RNAi factors can also be found in cell nuclei, but much remains to be learned about their transport, molecular recognition, and function. We find that siRNA-mediated reduction of AGO1 or AGO2 increases the proportion of AGO1 or AGO2 in cell nuclei. Inhibition of AGO1 expression led to increased AGO2 levels, while knockdown of AGO2 led to increased levels of AGO1. Blocking AGO1, AGO2, or TRBP expression changed expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182), and TRBP. These data reveal the expression of RNAi proteins is mutually dependent and that perturbation can affect subcellular distribution of those factors inside cells.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Liande Li
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Bethany A Janowski
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - David R Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
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Ye J, Wang J, Tan L, Yang S, Xu L, Wu X, Deng H, Tan H. Expression of protein TARBP1 in human hepatocellular carcinoma and its prognostic significance. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:9089-9096. [PMID: 26464651 PMCID: PMC4583883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/24/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE The objective of this study was to analyze the expression of TARBP1 and its clinical significance in hepatocellular carcinoma (HCC). MATERIALS AND METHODS 90 patients with primary hepatocellular carcinoma were included in this study. The tumor and paired adjacent non-tumor tissues were collected. TARBP1 expression was assessed by quantitative real-time polymerase chain reaction and immunohistochemistry. Associations of TARBP1 expression with the clinicopathological features were analyzed, and prognosis of HCC patients was evaluated. RESULTS The result show the expression of TARBP1 mRNA in liver cancer tissues were higher than in the adjacent normal liver tissues in 10 paired samples (P=0.0015). Compared with adjacent normal liver tissues, overexpression of TARBP1 was detected in 61.1% (55/90) HCC patients. TARBP1 expression was associated with the AJCC tumor stage (P=0.004) and clinical stage (P=0.005), and decreased overall survival (P=0.002). In multivariate analysis, TARBP1 expression was an independent prognostic factor for overall survival (Hazard ratio [HR]=2.773, 95% confidence interval [CI] 1.542-4.985; P=0.019). CONCLUSIONS TARBP1 is up-regulated in HCC, and the expression of TARBP1 was associated with the pathological grading and clinical stage. TARBP1 maybe is an independent prognostic marker of HCC patients.
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Affiliation(s)
- Jingmei Ye
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Jiani Wang
- Breast Cancer Center, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| | - Li Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Shaojiang Yang
- Department of Hematology, The First People’s Hospital of FoshanFoshan 528000, China
| | - Lihua Xu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Xiaohong Wu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Huaifu Deng
- PET/CT Center, Department of Nuclear Medicine, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Huo Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
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