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Goldstein SI, Fan AC, Wang Z, Naineni SK, Lengqvist J, Chernobrovkin A, Garcia-Gutierrez SB, Cencic R, Patel K, Huang S, Brown LE, Emili A, Porco JA. Proteomic Discovery of RNA-Protein Molecular Clamps Using a Thermal Shift Assay with ATP and RNA (TSAR). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590252. [PMID: 38659867 PMCID: PMC11042367 DOI: 10.1101/2024.04.19.590252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Uncompetitive inhibition is an effective strategy for suppressing dysregulated enzymes and their substrates, but discovery of suitable ligands depends on often-unavailable structural knowledge and serendipity. Hence, despite surging interest in mass spectrometry-based target identification, proteomic studies of substrate-dependent target engagement remain sparse. Herein, we describe the Thermal Shift Assay with ATP and RNA (TSAR) as a template for proteome-wide discovery of substrate-dependent ligand binding. Using proteomic thermal shift assays, we show that simple biochemical additives can facilitate detection of target engagement in native cell lysates. We apply our approach to rocaglates, a family of molecules that specifically clamp RNA to eukaryotic translation initiation factor 4A (eIF4A), DEAD-box helicase 3X (DDX3X), and potentially other members of the DEAD-box (DDX) family of RNA helicases. To identify unexpected interactions, we optimized a target class-specific thermal denaturation window and evaluated ATP analog and RNA probe dependencies for key rocaglate-DDX interactions. We report novel DDX targets of the rocaglate clamping spectrum, confirm that DDX3X is a common target of several widely studied analogs, and provide structural insights into divergent DDX3X affinities between synthetic rocaglates. We independently validate novel targets of high-profile rocaglates, including the clinical candidate Zotatifin (eFT226), using limited proteolysis-mass spectrometry and fluorescence polarization experiments. Taken together, our study provides a model for screening uncompetitive inhibitors using a systematic chemical-proteomics approach to uncover actionable DDX targets, clearing a path towards characterization of novel molecular clamps and associated RNA helicase targets.
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Affiliation(s)
- Stanley I. Goldstein
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
- Department of Pharmacology, Physiology, and Biophysics, Boston University, Boston, MA, USA
| | - Alice C. Fan
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Zihao Wang
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Sai K. Naineni
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | | | | | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Kesha Patel
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | - Andrew Emili
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - John A. Porco
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
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2
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Heaton SM, Gorry PR, Borg NA. DExD/H-box helicases in HIV-1 replication and their inhibition. Trends Microbiol 2023; 31:393-404. [PMID: 36463019 DOI: 10.1016/j.tim.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Antiretroviral therapy (ART) reduces human immunodeficiency virus type 1 (HIV-1) infection, but selection of treatment-refractory variants remains a major challenge. HIV-1 encodes 16 canonical proteins, a small number of which are the singular targets of nearly all antiretrovirals developed to date. Cellular factors are increasingly being explored, which may present more therapeutic targets, more effectively target certain aspects of the viral replication cycle, and/or limit viral escape. Unlike most other positive-sense RNA viruses that encode at least one helicase, retroviruses are limited to the host repertoire. Accordingly, HIV-1 subverts DEAD-box helicase 3X (DDX3X) and numerous other cellular helicases of the Asp-Glu-x-Asp/His (DExD/H)-box family to service multiple aspects of its replication cycle. Here we review DDX3X and other DExD/H-box helicases in HIV-1 replication and their inhibition.
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Affiliation(s)
- Steven M Heaton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Current affiliation: RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, 1-chōme-7-22 Suehirochō, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan.
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Natalie A Borg
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
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3
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DEAD-box ATPases as regulators of biomolecular condensates and membrane-less organelles. Trends Biochem Sci 2023; 48:244-258. [PMID: 36344372 DOI: 10.1016/j.tibs.2022.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
RNA-dependent DEAD-box ATPases (DDXs) are emerging as major regulators of RNA-containing membrane-less organelles (MLOs). On the one hand, oligomerizing DDXs can promote condensate formation 'in cis', often using RNA as a scaffold. On the other hand, DDXs can disrupt RNA-RNA and RNA-protein interactions and thereby 'in trans' remodel the multivalent interactions underlying MLO formation. In this review, we discuss the best studied examples of DDXs modulating MLOs in cis and in trans. Further, we illustrate how this contributes to the dynamic assembly and turnover of MLOs which might help cells to modulate RNA sequestration and processing in a temporal and spatial manner.
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4
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Rao S, Mahmoudi T. DEAD-ly Affairs: The Roles of DEAD-Box Proteins on HIV-1 Viral RNA Metabolism. Front Cell Dev Biol 2022; 10:917599. [PMID: 35769258 PMCID: PMC9234453 DOI: 10.3389/fcell.2022.917599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In order to ensure viral gene expression, Human Immunodeficiency virus type-1 (HIV-1) recruits numerous host proteins that promote optimal RNA metabolism of the HIV-1 viral RNAs (vRNAs), such as the proteins of the DEAD-box family. The DEAD-box family of RNA helicases regulates multiple steps of RNA metabolism and processing, including transcription, splicing, nucleocytoplasmic export, trafficking, translation and turnover, mediated by their ATP-dependent RNA unwinding ability. In this review, we provide an overview of the functions and role of all DEAD-box family protein members thus far described to influence various aspects of HIV-1 vRNA metabolism. We describe the molecular mechanisms by which HIV-1 hijacks these host proteins to promote its gene expression and we discuss the implications of these interactions during viral infection, their possible roles in the maintenance of viral latency and in inducing cell death. We also speculate on the emerging potential of pharmacological inhibitors of DEAD-box proteins as novel therapeutics to control the HIV-1 pandemic.
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Affiliation(s)
- Shringar Rao
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Centre, Rotterdam, Netherlands
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5
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DDX50 Is a Viral Restriction Factor That Enhances IRF3 Activation. Viruses 2022; 14:v14020316. [PMID: 35215908 PMCID: PMC8875258 DOI: 10.3390/v14020316] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/06/2022] [Accepted: 01/30/2022] [Indexed: 11/24/2022] Open
Abstract
The transcription factors IRF3 and NF-κB are crucial in innate immune signalling in response to many viral and bacterial pathogens. However, mechanisms leading to their activation remain incompletely understood. Viral RNA can be detected by RLR receptors, such as RIG-I and MDA5, and the dsRNA receptor TLR3. Alternatively, the DExD-Box RNA helicases DDX1-DDX21-DHX36 activate IRF3/NF-κB in a TRIF-dependent manner independent of RIG-I, MDA5, or TLR3. Here, we describe DDX50, which shares 55.6% amino acid identity with DDX21, as a non-redundant factor that promotes activation of the IRF3 signalling pathway following its stimulation with viral RNA or infection with RNA and DNA viruses. Deletion of DDX50 in mouse and human cells impaired IRF3 phosphorylation and IRF3-dependent endogenous gene expression and cytokine/chemokine production in response to cytoplasmic dsRNA (polyIC transfection), and infection by RNA and DNA viruses. Mechanistically, whilst DDX50 co-immunoprecipitated TRIF, it acted independently to the previously described TRIF-dependent RNA sensor DDX1. Indeed, shRNA-mediated depletion of DDX1 showed DDX1 was dispensable for signalling in response to RNA virus infection. Importantly, loss of DDX50 resulted in a significant increase in replication and dissemination of virus following infection with vaccinia virus, herpes simplex virus, or Zika virus, highlighting its important role as a broad-ranging viral restriction factor.
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6
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Xie J, Wen M, Zhang J, Wang Z, Wang M, Qiu Y, Zhao W, Zhu F, Yao M, Rong ZX, Hu W, Pei Q, Sun X, Li J, Mao Z, Sun L, Tan R. The roles of RNA helicases in DNA damage repair and tumorigenesis reveal precision therapeutic strategies. Cancer Res 2022; 82:872-884. [PMID: 34987058 DOI: 10.1158/0008-5472.can-21-2187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/04/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
DEAD-box RNA helicases belong to a large group of RNA processing factors and play vital roles unwinding RNA helices and in ribosomal RNA biogenesis. Emerging evidence indicates that RNA helicases are associated with genome stability, yet the mechanisms behind this association remain poorly understood. In this study, we performed a comprehensive analysis of RNA helicases using multiplatform proteogenomic databases. Over 50% (28/49) of detected RNA helicases were highly expressed in multiple tumor tissues, and more than 60% (17/28) of tumor-associated members were directly involved in DNA damage repair (DDR). Analysis of repair dynamics revealed that these RNA helicases are engaged in an extensively broad range of DDR pathways. Among these factors is DDX21, which was prominently upregulated in colorectal cancer. The high expression of DDX21 gave rise to frequent chromosome exchange and increased genome fragmentation. Mechanistically, aberrantly high expression of DDX21 triggered inappropriate repair processes by delaying homologous recombination repair and increasing replication stress, leading to genome instability and tumorigenesis. Treatment with distinct chemotherapeutic drugs caused higher lethality to cancer cells with genome fragility induced by DDX21, providing a perspective for treatment of tumors with high DDX21 expression. This study revealed the role of RNA helicases in DNA damage and their associations with cancer, which could expand therapeutic strategies and improve precision treatments for cancer patients with high expression of RNA helicases.
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Affiliation(s)
- Jinru Xie
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Ming Wen
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Jiao Zhang
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Zheng Wang
- Department of Geriatrics, Central South University
| | - Meng Wang
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Yanfang Qiu
- Center for Molecular Medicine, Central South University
| | - Wenchao Zhao
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Fang Zhu
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Mianfeng Yao
- Department of Stomatology, Xiangya Hospital Central South University
| | - Zhuo-Xian Rong
- Center for Molecular Medicine, Key Laboratory of Molecular Radiation Oncology, Hunan Province, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Wenfeng Hu
- Center for Molecular Medicine, Xiangya Hospital Central South University
| | - Qian Pei
- Xiangya Hospital Central South University
| | - Xiaoxiang Sun
- School of Life Sciences and Technology, Tongji University
| | - Jinchen Li
- Department of Geriatrics, Central South University
| | - Zhiyong Mao
- School of Life Sciences and Technology, Tongji University
| | | | - Rong Tan
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
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7
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Han P, Ye W, Lv X, Ma H, Weng D, Dong Y, Cheng L, Chen H, Zhang L, Xu Z, Lei Y, Zhang F. DDX50 inhibits the replication of dengue virus 2 by upregulating IFN-β production. Arch Virol 2017; 162:1487-1494. [PMID: 28181036 DOI: 10.1007/s00705-017-3250-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/13/2017] [Indexed: 02/03/2023]
Abstract
Dengue virus (DENV) infects approximately 390 million people per year, and each of the four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) is capable of causing infection. At present, there is no antiviral drug available for the treatment of DENV. Several DExD/H-box helicases have been shown to be involved in the antiviral immune response or viral replication. In the present study, we investigated the role of DDX50 in DENV-2 RNA replication. Our data showed that the level of DENV-2 RNA increased in DDX50 knockdown cells during an early stage of viral infection and decreased in DDX50-overexpressing cells. DDX50, in conjunction with RIG-I and MDA5, upregulated the production of IFN-β in infected cells through an additive effect on the IFN-β promoter. Furthermore, transcription of several IFN-stimulated genes was increased in DDX50-overexpressing cells infected with DENV-2. These results provide evidence that DDX50 negatively regulates DENV-2 replication during the early stages of infection by inducing IFN-β production.
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Affiliation(s)
- Peijun Han
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Wei Ye
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Xin Lv
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Hongwei Ma
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Daihui Weng
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Yangchao Dong
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Linfeng Cheng
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Hesong Chen
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Liang Zhang
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Zhikai Xu
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China
| | - Yingfeng Lei
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China.
| | - Fanglin Zhang
- The Department of Microbiology, School of Preclinical Medicine, The Fourth Military Medical University, No.169, Changle West Road, Xian, 710032, Shaanxi, China.
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8
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Rodríguez-Galán O, García-Gómez JJ, de la Cruz J. Yeast and human RNA helicases involved in ribosome biogenesis: current status and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:775-90. [PMID: 23357782 DOI: 10.1016/j.bbagrm.2013.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/15/2013] [Accepted: 01/16/2013] [Indexed: 11/17/2022]
Abstract
Ribosome biogenesis is a fundamental process that is conserved in eukaryotes. Although spectacular progress has been made in understanding mammalian ribosome synthesis in recent years, by far, this process has still been best characterised in the yeast Saccharomyces cerevisiae. In yeast, besides the rRNAs, the ribosomal proteins and the 75 small nucleolar RNAs, more than 250 non-ribosomal proteins, generally referred to as trans-acting factors, are involved in ribosome biogenesis. These factors include nucleases, RNA modifying enzymes, ATPases, GTPases, kinases and RNA helicases. Altogether, they likely confer speed, accuracy and directionality to the ribosome synthesis process, however, the precise functions for most of them are still largely unknown. This review summarises our current knowledge on eukaryotic RNA helicases involved in ribosome biogenesis, particularly focusing on the most recent advances with respect to the molecular roles of these enzymes and their co-factors in yeast and human cells. This article is part of a Special Issue entitled: The Biology of RNA helicases-Modulation for life.
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9
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Martin R, Straub AU, Doebele C, Bohnsack MT. DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol 2012; 10:4-18. [PMID: 22922795 DOI: 10.4161/rna.21879] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Ribosome synthesis requires a multitude of cofactors, among them DExD/H-box RNA helicases. Bacterial RNA helicases involved in ribosome assembly are not essential, while eukaryotes strictly require multiple DExD/H-box proteins that are involved in the much more complex ribosome biogenesis pathway. Here, RNA helicases are thought to act in structural remodeling of the RNPs including the modulation of protein binding, and they are required for allowing access or the release of specific snoRNPs from pre-ribosomes. Interestingly, helicase action is modulated by specific cofactors that can regulate recruitment and enzymatic activity. This review summarizes the current knowledge and focuses on recent findings and open questions on RNA helicase function and regulation in ribosome synthesis.
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Affiliation(s)
- Roman Martin
- Centre for Biochemistry and Molecular Cell Biology, Göttingen University, Göttingen, Germany
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10
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Hickey JG, Myers SM, Tian X, Zhu SJ, V. Shaw JL, Andrew SD, Richardson DS, Brettschneider J, Mulligan LM. RET-mediated gene expression pattern is affected by isoform but not oncogenic mutation. Genes Chromosomes Cancer 2009; 48:429-40. [DOI: 10.1002/gcc.20653] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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11
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Ohnishi S, Pääkkönen K, Koshiba S, Tochio N, Sato M, Kobayashi N, Harada T, Watanabe S, Muto Y, Güntert P, Tanaka A, Kigawa T, Yokoyama S. Solution structure of the GUCT domain from human RNA helicase II/Guβ reveals the RRM fold, but implausible RNA interactions. Proteins 2009; 74:133-44. [DOI: 10.1002/prot.22138] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Abstract
Direct localization of specific genes, RNAs, and proteins has allowed the dissection of individual nuclear speckles in relation to the molecular biology of gene expression. Nuclear speckles (aka SC35 domains) are essentially ubiquitous structures enriched for most pre-mRNA metabolic factors, yet their relationship to gene expression has been poorly understood. Analyses of specific genes and their spliced or mature mRNA strongly support that SC35 domains are hubs of activity, not stores of inert factors detached from gene expression. We propose that SC35 domains are hubs that spatially link expression of specific pre-mRNAs to rapid recycling of copious RNA metabolic complexes, thereby facilitating expression of many highly active genes. In addition to increasing the efficiency of each step, sequential steps in gene expression are structurally integrated at each SC35 domain, consistent with other evidence that the biochemical machineries for transcription, splicing, and mRNA export are coupled. Transcription and splicing are subcompartmentalized at the periphery, with largely spliced mRNA entering the domain prior to export. In addition, new findings presented here begin to illuminate the structural underpinnings of a speckle by defining specific perturbations of phosphorylation that promote disassembly or assembly of an SC35 domain in relation to other components. Results thus far are consistent with the SC35 spliceosome assembly factor as an integral structural component. Conditions that disperse SC35 also disperse poly(A) RNA, whereas the splicing factor ASF/SF2 can be dispersed under conditions in which SC35 or SRm300 remain as intact components of a core domain.
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Affiliation(s)
- Lisa L Hall
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, 01655, USA
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13
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Linder P. Dead-box proteins: a family affair--active and passive players in RNP-remodeling. Nucleic Acids Res 2006; 34:4168-80. [PMID: 16936318 PMCID: PMC1616962 DOI: 10.1093/nar/gkl468] [Citation(s) in RCA: 341] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/19/2006] [Accepted: 06/20/2006] [Indexed: 11/23/2022] Open
Abstract
DEAD-box proteins are characterized by nine conserved motifs. According to these criteria, several hundreds of these proteins can be identified in databases. Many different DEAD-box proteins can be found in eukaryotes, whereas prokaryotes have small numbers of different DEAD-box proteins. DEAD-box proteins play important roles in RNA metabolism, and they are very specific and cannot mutually be replaced. In vitro, many DEAD-box proteins have been shown to have RNA-dependent ATPase and ATP-dependent RNA helicase activities. From the genetic and biochemical data obtained mainly in yeast, it has become clear that these proteins play important roles in remodeling RNP complexes in a temporally controlled fashion. Here, I shall give a general overview of the DEAD-box protein family.
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Affiliation(s)
- Patrick Linder
- Department of Microbiology and Molecular Medicine, CMU 1, rue Michel Servet, CH-1211 Genève 4, Switzerland.
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14
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Xu M, Wells KS, Emeson RB. Substrate-dependent contribution of double-stranded RNA-binding motifs to ADAR2 function. Mol Biol Cell 2006; 17:3211-20. [PMID: 16672376 PMCID: PMC1552048 DOI: 10.1091/mbc.e06-02-0162] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 03/31/2006] [Accepted: 04/21/2006] [Indexed: 01/01/2023] Open
Abstract
ADAR2 is a double-stranded RNA-specific adenosine deaminase involved in the editing of mammalian RNAs by the site-specific conversion of adenosine to inosine (A-to-I). ADAR2 contains two tandem double-stranded RNA-binding motifs (dsRBMs) that are not only important for efficient editing of RNA substrates but also necessary for localizing ADAR2 to nucleoli. The sequence and structural similarity of these motifs have raised questions regarding the role(s) that each dsRBM plays in ADAR2 function. Here, we demonstrate that the dsRBMs of ADAR2 differ in both their ability to modulate subnuclear localization as well as to promote site-selective A-to-I conversion. Surprisingly, dsRBM1 contributes to editing activity in a substrate-dependent manner, indicating that dsRBMs recognize distinct structural determinants in each RNA substrate. Although dsRBM2 is essential for the editing of all substrates examined, a point mutation in this motif affects editing for only a subset of RNAs, suggesting that dsRBM2 uses unique sets of amino acid(s) for functional interactions with different RNA targets. The dsRBMs of ADAR2 are interchangeable for subnuclear targeting, yet such motif alterations do not support site-selective editing, indicating that the unique binding preferences of each dsRBM differentially contribute to their pleiotropic function.
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Affiliation(s)
- Ming Xu
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232-8548, USA
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15
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Cordin O, Banroques J, Tanner NK, Linder P. The DEAD-box protein family of RNA helicases. Gene 2005; 367:17-37. [PMID: 16337753 DOI: 10.1016/j.gene.2005.10.019] [Citation(s) in RCA: 729] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Revised: 10/11/2005] [Accepted: 10/15/2005] [Indexed: 11/24/2022]
Abstract
RNA helicases of the DEAD-box protein family have been shown to participate in every aspect of RNA metabolism. They are present in most organisms where they work as RNA helicases or RNPases. The properties of these enzymes in vivo remains poorly described, however some were extensively characterized in vitro, and the solved crystal structures of a few are now available. Taken together, this information gives insight into the regulation of ATP and RNA binding as well as in the ATPase and helicase activities. This review will focus on the description of the molecular characteristics of members of the DEAD-box protein family and on the enzymatic activities they possess.
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Affiliation(s)
- Olivier Cordin
- Département de Microbiologie et Médecine Moléculaire, Centre Médical Universitaire, 1 rue Michel Servet, 1211, Genève 4, Switzerland
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16
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Yang H, Henning D, Valdez BC. Functional interaction between RNA helicase II/Gu(alpha) and ribosomal protein L4. FEBS J 2005; 272:3788-802. [PMID: 16045751 DOI: 10.1111/j.1742-4658.2005.04811.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA helicase II/Gu(alpha) is a multifunctional nucleolar protein involved in ribosomal RNA processing in Xenopus laevis oocytes and mammalian cells. Downregulation of Gu(alpha) using small interfering RNA (siRNA) in HeLa cells resulted in 80% inhibition of both 18S and 28S rRNA production. The mechanisms underlying this effect remain unclear. Here we show that in mammalian cells, Gu(alpha) physically interacts with ribosomal protein L4 (RPL4), a component of 60S ribosome large subunit. The ATPase activity of Gu(alpha) is important for this interaction and is also necessary for the function of Gu(alpha) in the production of both 18S and 28S rRNAs. Knocking down RPL4 expression using siRNA in mouse LAP3 cells inhibits the production of 47/45S, 32S, 28S, and 18S rRNAs. This inhibition is reversed by exogenous expression of wild-type human RPL4 protein but not the mutant form lacking Gu(alpha)-interacting motif. These observations have suggested that the function of Gu(alpha) in rRNA processing is at least partially dependent on its ability to interact with RPL4.
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Affiliation(s)
- Hushan Yang
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
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Liu Y, Cheng J, Yang Q, Wang JJ, Ji D, Wang CH, Dang XY, Xu ZQ. Cloning of genes differentially expressed in Jurkat cells treated with glycyrrhizin using cDNA microarray. Shijie Huaren Xiaohua Zazhi 2004; 12:70-73. [DOI: 10.11569/wcjd.v12.i1.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To study the difference in gene expression profile in human lymphoma cell line Jurkat cells treated with glycyrrhizin (GL), and to further elucidate the molecular immune mechanism of glycyrrhizin against T lymphocyte.
METHODS: cDNA microarray technology was employed to detect the mRNA from Jurkat cells treated with GL and 0.9 percent sodium chloride, respectively.
RESULTS: The results indicated that among 1 152 genes which were obtained from gene expression profile analysis, there were 30 genes different from those in GenBank in which 12 genes were up-regulated and 18 genes were down-regulated in Jurkat cells treated with GL, compared to those treated with 0.9 percent sodium chloride. These genes differentially regulated by GL included human genes encoding proteins involved in immune regulation, cell signal transduction, cell proliferation and differentiation.
CONCLUSION: cDNA microarray technology is successfully used to screen the genes differentially expressed in Jurkat cells treated with GL, which brings some new clues for studying the immune regulation mechanism of GL.
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Henning D, So RB, Jin R, Lau LF, Valdez BC. Silencing of RNA helicase II/Gualpha inhibits mammalian ribosomal RNA production. J Biol Chem 2003; 278:52307-14. [PMID: 14559904 DOI: 10.1074/jbc.m310846200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The intricate production of ribosomal RNA is well defined in yeast, but its complexity in higher organisms is barely understood. We recently showed that down-regulation of nucleolar protein RNA helicase II/Gualpha (RH-II/Gualpha or DDX21) in Xenopus oocytes inhibited processing of 20 S rRNA to 18 S and contributed to degradation of 28 S rRNA (Yang, H., Zhou, J., Ochs, R. L., Henning, D., Jin, R., and Valdez, B. C. (2003) J. Biol. Chem. 278, 38847-38859). Since no nucleolar RNA helicase has been functionally characterized in mammalian cells, we used short interfering RNA to search for functions for RH-II/Gualpha and its paralogue RH-II/Gubeta in rRNA production. Silencing of RH-II/Gualpha by more than 80% in HeLa cells resulted in an almost 80% inhibition of 18 and 28 S rRNA production. This inhibition could be reversed by exogenous expression of wild type RH-II/Gualpha. A helicase-deficient mutant form having ATPase activity was able to rescue the production of 28 S but not 18 S rRNA. A phenotype exhibiting inhibition of 18 S and 28 S rRNA production was also observed when the paralogue RH-II/Gubeta was overexpressed. Both down-regulation of RH-II/Gualpha and overexpression of RH-II/Gubeta slowed cell proliferation. The opposite effects of the two paralogues suggest antagonistic functions.
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Affiliation(s)
- Dale Henning
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA
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Abstract
Nucleic acid helicases are characterized by the presence of the helicase domain containing eight motifs. The sequence of the helicase domain is used to classify helicases into families. To identify members of the DEAD and DEAH families of human RNA helicases, we used the helicase domain sequences to search the nonredundant peptide sequence database. We report the identification of 36 and 14 members of the DEAD and DEAH families of putative RNA helicases, including several novel genes. The gene symbol DDX had been used previously for both DEAD- and DEAH-box families. We have now adopted DDX and DHX symbols to denote DEAD- and DEAH-box families, respectively. Members of human DDX and DHX families of putative RNA helicases play roles in differentiation and carcinogenesis.
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Affiliation(s)
- Mohamed Abdelhaleem
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8.
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