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Yu X, Tian J, Wang Y, Su N, Luo J, Duan M, Shi N. The pseudogene GBP1P1 suppresses influenza A virus replication by acting as a protein decoy for DHX9. J Virol 2024; 98:e0073824. [PMID: 38940585 PMCID: PMC11264600 DOI: 10.1128/jvi.00738-24] [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: 04/25/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Recently, substantial evidence has demonstrated that pseudogene-derived long noncoding RNAs (lncRNAs) as regulatory RNAs have been implicated in basic physiological processes and disease development through multiple modes of functional interaction with DNA, RNA, and proteins. Here, we report an important role for GBP1P1, the pseudogene of guanylate-binding protein 1, in regulating influenza A virus (IAV) replication in A549 cells. GBP1P1 was dramatically upregulated after IAV infection, which is controlled by JAK/STAT signaling. Functionally, ectopic expression of GBP1P1 in A549 cells resulted in significant suppression of IAV replication. Conversely, silencing GBP1P1 facilitated IAV replication and virus production, suggesting that GBP1P1 is one of the interferon-inducible antiviral effectors. Mechanistically, GBP1P1 is localized in the cytoplasm and functions as a sponge to trap DHX9 (DExH-box helicase 9), which subsequently restricts IAV replication. Together, these studies demonstrate that GBP1P1 plays an important role in antagonizing IAV replication.IMPORTANCELong noncoding RNAs (lncRNAs) are extensively expressed in mammalian cells and play a crucial role as regulators in various biological processes. A growing body of evidence suggests that host-encoded lncRNAs are important regulators involved in host-virus interactions. Here, we define a novel function of GBP1P1 as a decoy to compete with viral mRNAs for DHX9 binding. We demonstrate that GBP1P1 induction by IAV is mediated by JAK/STAT activation. In addition, GBP1P1 has the ability to inhibit IAV replication. Importantly, we reveal that GBP1P1 acts as a decoy to bind and titrate DHX9 away from viral mRNAs, thereby attenuating virus production. This study provides new insight into the role of a previously uncharacterized GBP1P1, a pseudogene-derived lncRNA, in the host antiviral process and a further understanding of the complex GBP network.
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Affiliation(s)
- Xiaohang Yu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Jiaxin Tian
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun, Jilin Province, China
| | - Yihe Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Ning Su
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Jinna Luo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Ming Duan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Ning Shi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
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Heng X, Herrera AP, Song Z, Boris-Lawrie K. Retroviral PBS-segment sequence and structure: Orchestrating early and late replication events. Retrovirology 2024; 21:12. [PMID: 38886829 PMCID: PMC11181671 DOI: 10.1186/s12977-024-00646-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
An essential regulatory hub for retroviral replication events, the 5' untranslated region (UTR) encodes an ensemble of cis-acting replication elements that overlap in a logical manner to carry out divergent RNA activities in cells and in virions. The primer binding site (PBS) and primer activation sequence initiate the reverse transcription process in virions, yet overlap with structural elements that regulate expression of the complex viral proteome. PBS-segment also encompasses the attachment site for Integrase to cut and paste the 3' long terminal repeat into the host chromosome to form the provirus and purine residues necessary to execute the precise stoichiometry of genome-length transcripts and spliced viral RNAs. Recent genetic mapping, cofactor affinity experiments, NMR and SAXS have elucidated that the HIV-1 PBS-segment folds into a three-way junction structure. The three-way junction structure is recognized by the host's nuclear RNA helicase A/DHX9 (RHA). RHA tethers host trimethyl guanosine synthase 1 to the Rev/Rev responsive element (RRE)-containing RNAs for m7-guanosine Cap hyper methylation that bolsters virion infectivity significantly. The HIV-1 trimethylated (TMG) Cap licenses specialized translation of virion proteins under conditions that repress translation of the regulatory proteins. Clearly host-adaption and RNA shapeshifting comprise the fundamental basis for PBS-segment orchestrating both reverse transcription of virion RNA and the nuclear modification of m7G-Cap for biphasic translation of the complex viral proteome. These recent observations, which have exposed even greater complexity of retroviral RNA biology than previously established, are the impetus for this article. Basic research to fully comprehend the marriage of PBS-segment structures and host RNA binding proteins that carry out retroviral early and late replication events is likely to expose an immutable virus-specific therapeutic target to attenuate retrovirus proliferation.
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Affiliation(s)
- Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
| | - Amanda Paz Herrera
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Zhenwei Song
- Department of Veterinary and Biomedical Sciences, Institute for Molecular Virology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, Institute for Molecular Virology, University of Minnesota, Saint Paul, MN, 55108, USA.
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Nikolenko JV, Georgieva SG, Kopytova DV. Diversity of MLE Helicase Functions in the Regulation of Gene Expression in Higher Eukaryotes. Mol Biol 2023. [DOI: 10.1134/s0026893323010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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4
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Sweeney TR, Dhote V, Guca E, Hellen CUT, Hashem Y, Pestova T. Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs. Nucleic Acids Res 2021; 49:12955-12969. [PMID: 34883515 PMCID: PMC8682770 DOI: 10.1093/nar/gkab1192] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Translation initiation on structured mammalian mRNAs requires DHX29, a DExH protein that comprises a unique 534-aa-long N-terminal region (NTR) and a common catalytic DExH core. DHX29 binds to 40S subunits and possesses 40S-stimulated NTPase activity essential for its function. In the cryo-EM structure of DHX29-bound 43S preinitiation complexes, the main DHX29 density resides around the tip of helix 16 of 18S rRNA, from which it extends through a linker to the subunit interface forming an intersubunit domain next to the eIF1A binding site. Although a DExH core model can be fitted to the main density, the correlation between the remaining density and the NTR is unknown. Here, we present a model of 40S-bound DHX29, supported by directed hydroxyl radical cleavage data, showing that the intersubunit domain comprises a dsRNA-binding domain (dsRBD, aa 377-448) whereas linker corresponds to the long α-helix (aa 460-512) that follows the dsRBD. We also demonstrate that the N-terminal α-helix and the following UBA-like domain form a four-helix bundle (aa 90-166) that constitutes a previously unassigned section of the main density and resides between DHX29's C-terminal α-helix and the linker. In vitro reconstitution experiments revealed the critical and specific roles of these NTR elements for DHX29's function.
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Affiliation(s)
- Trevor R Sweeney
- Correspondence may also be addressed to Trevor R. Sweeney. Tel: +44 1483232441; Fax: +44 1483232448;
| | | | - Ewelina Guca
- INSERM U1212 Acides nucléiques : Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Yaser Hashem
- Correspondence may also be addressed to Yaser Hashem. Tel: +33 5 40 00 88 22;
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5
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Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Res 2021; 49:5925-5942. [PMID: 33978756 PMCID: PMC8191761 DOI: 10.1093/nar/gkab342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.
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Affiliation(s)
- Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas Gremminger
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Cheng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Jun Li
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Liming Qiu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Juan Ji
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
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6
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Wu C, Shan Y, Wang S, Liu F. Dynamically probing ATP-dependent RNA helicase A-assisted RNA structure conversion using single molecule fluorescence resonance energy transfer. Protein Sci 2021; 30:1157-1168. [PMID: 33837988 DOI: 10.1002/pro.4081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/08/2021] [Indexed: 12/16/2022]
Abstract
RNA helicase A (RHA) as a member of DExH-box subgroup of helicase superfamily II, participates in diverse biological processes involved in RNA metabolism in organisms, and these RNA-mediated biological processes rely on RNA structure conversion. However, how RHA regulate the RNA structure conversion was still unknown. In order to unveil the mechanism of RNA structure conversion mediated by RHA, single molecule fluorescence resonance energy transfer was adopted to in our assay, and substrates RNA were from internal ribosome entry site of foot-and-mouth disease virus genome. We first found that the RNA structure conversion by RHA against thermodynamic equilibrium in vitro, and the process of dsRNA YZ converted to dsRNA XY through a tripartite intermediate state. In addition, the rate of the RNA structure conversion and the distribution of dsRNA YZ and XY were affected by ATP concentrations. Our study provides real-time insight into ATP-dependent RHA-assisted RNA structure conversion at the single molecule level, the mechanism displayed by RHA may help in understand how RHA contributes to many biological functions, and the basic mechanistic features illustrated in our work also underlay more complex protein-assisted RNA structure conversions.
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Affiliation(s)
- Chengcheng Wu
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Yanke Shan
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Shouyu Wang
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China.,Computational Optics Laboratory, Jiangnan University, Wuxi, China
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
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7
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Identification of DHX9 as a cell cycle regulated nucleolar recruitment factor for CIZ1. Sci Rep 2020; 10:18103. [PMID: 33093612 PMCID: PMC7582970 DOI: 10.1038/s41598-020-75160-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/12/2020] [Indexed: 11/15/2022] Open
Abstract
CIP1-interacting zinc finger protein 1 (CIZ1) is a nuclear matrix associated protein that facilitates a number of nuclear functions including initiation of DNA replication, epigenetic maintenance and associates with the inactive X-chromosome. Here, to gain more insight into the protein networks that underpin this diverse functionality, molecular panning and mass spectrometry are used to identify protein interaction partners of CIZ1, and CIZ1 replication domain (CIZ1-RD). STRING analysis of CIZ1 interaction partners identified 2 functional clusters: ribosomal subunits and nucleolar proteins including the DEAD box helicases, DHX9, DDX5 and DDX17. DHX9 shares common functions with CIZ1, including interaction with XIST long-non-coding RNA, epigenetic maintenance and regulation of DNA replication. Functional characterisation of the CIZ1-DHX9 complex showed that CIZ1-DHX9 interact in vitro and dynamically colocalise within the nucleolus from early to mid S-phase. CIZ1-DHX9 nucleolar colocalisation is dependent upon RNA polymerase I activity and is abolished by depletion of DHX9. In addition, depletion of DHX9 reduced cell cycle progression from G1 to S-phase in mouse fibroblasts. The data suggest that DHX9-CIZ1 are required for efficient cell cycle progression at the G1/S transition and that nucleolar recruitment is integral to their mechanism of action.
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8
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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9
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Singh G, Fritz SE, Seufzer B, Boris-Lawrie K. The mRNA encoding the JUND tumor suppressor detains nuclear RNA-binding proteins to assemble polysomes that are unaffected by mTOR. J Biol Chem 2020; 295:7763-7773. [PMID: 32312751 DOI: 10.1074/jbc.ra119.012005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
One long-standing knowledge gap is the role of nuclear proteins in mRNA translation. Nuclear RNA helicase A (DHX9/RHA) is necessary for the translation of the mRNAs of JUND (JunD proto-oncogene AP-1 transcription factor subunit) and HIV-1 genes, and nuclear cap-binding protein 1 (NCBP1)/CBP80 is a component of HIV-1 polysomes. The protein kinase mTOR activates canonical messenger ribonucleoproteins by post-translationally down-regulating the eIF4E inhibitory protein 4E-BP1. We posited here that NCBP1 and DHX9/RHA (RHA) support a translation pathway of JUND RNA that is independent of mTOR. We present evidence from reciprocal immunoprecipitation experiments indicating that NCBP1 and RHA both are components of messenger ribonucleoproteins in several cell types. Moreover, tandem affinity and RT-quantitative PCR results revealed that JUND mRNA is a component of a previously unknown ribonucleoprotein complex. Results from the tandem IP indicated that another component of the JUND-containing ribonucleoprotein complex is NCBP3, a recently identified ortholog of NCBP2/CBP20. We also found that NCBP1, NCBP3, and RHA, but not NCBP2, are components of JUND-containing polysomes. Mutational analysis uncovered two dsRNA-binding domains of RHA that are necessary to tether JUND-NCBP1/NCBP3 to polysomes. We also found that JUND translation is unaffected by inhibition of mTOR, unless RHA was down-regulated by siRNA. These findings uncover a noncanonical cap-binding complex consisting of NCBP1/NCBP3 and RHA substitutes for the eukaryotic translation initiation factors 4E and 4G and activates mTOR-independent translation of the mRNA encoding the tumor suppressor JUND.
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Affiliation(s)
- Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Sarah E Fritz
- Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
| | - Bradley Seufzer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108 .,Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
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Corley M, Burns MC, Yeo GW. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. Mol Cell 2020; 78:9-29. [PMID: 32243832 PMCID: PMC7202378 DOI: 10.1016/j.molcel.2020.03.011] [Citation(s) in RCA: 362] [Impact Index Per Article: 90.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we take a look at the components of protein-RNA interaction, from the molecular level to multi-component interaction. We first summarize what is known about protein-RNA molecular interactions based on analyses of solved structures. We additionally describe software currently available for predicting protein-RNA interaction and other resources useful for the study of RBPs. We then review the structure and function of seventeen known RNA-binding domains and analyze the hydrogen bonds adopted by protein-RNA structures on a domain-by-domain basis. We conclude with a summary of the higher-level mechanisms that regulate protein-RNA interactions.
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Affiliation(s)
- Meredith Corley
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Margaret C Burns
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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Brady S, Singh G, Bolinger C, Song Z, Boeras I, Weng K, Trent B, Brown WC, Singh K, Boris-Lawrie K, Heng X. Virion-associated, host-derived DHX9/RNA helicase A enhances the processivity of HIV-1 reverse transcriptase on genomic RNA. J Biol Chem 2019; 294:11473-11485. [PMID: 31175158 PMCID: PMC6663884 DOI: 10.1074/jbc.ra119.007679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/04/2019] [Indexed: 02/02/2023] Open
Abstract
DHX9/RNA helicase A (RHA) is a host RNA helicase that participates in many critical steps of the HIV-1 life cycle. It co-assembles with the viral RNA genome into the capsid core. Virions deficient in RHA are less infectious as a result of reduced reverse transcription efficiency, demonstrating that the virion-associated RHA promotes reverse transcription before the virion gains access to the new host's RHA. Here, we quantified reverse-transcription intermediates in HIV-1-infected T cells to clarify the mechanism by which RHA enhances HIV-1 reverse transcription efficiency. Consistently, purified recombinant human RHA promoted reverse transcription efficiency under in vitro conditions that mimic the early reverse transcription steps prior to capsid core uncoating. We did not observe RHA-mediated structural remodeling of the tRNALys3-viral RNA-annealed complex. RHA did not enhance the DNA synthesis rate until incorporation of the first few nucleotides, suggesting that RHA participates primarily in the elongation phase of reverse transcription. Pre-steady-state and steady-state kinetic studies revealed that RHA has little impact on the kinetics of single-nucleotide incorporation. Primer extension assays performed in the presence of trap dsDNA disclosed that RHA enhances the processivity of HIV-1 reverse transcriptase (RT). The biochemical assays used here effectively reflected and explained the low RT activity in HIV-1 virions produced from RHA-depleted cells. Moreover, RT activity in our assays indicated that RHA in HIV-1 virions is required for the efficient catalysis of (-)cDNA synthesis during viral infection before capsid uncoating. Our study identifies RHA as a processivity factor of HIV-1 RT.
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Affiliation(s)
- Samantha Brady
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Cheryl Bolinger
- Department of Veterinary Biosciences, Ohio State University, Columbus, Ohio 432105
| | - Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Ioana Boeras
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Kexin Weng
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Bria Trent
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - William Clay Brown
- Center for Structural Biology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Kamalendra Singh
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65211
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
- Department of Veterinary Biosciences, Ohio State University, Columbus, Ohio 432105
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
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Cellular RNA Helicase DHX9 Interacts with the Essential Epstein-Barr Virus (EBV) Protein SM and Restricts EBV Lytic Replication. J Virol 2019; 93:JVI.01244-18. [PMID: 30541834 DOI: 10.1128/jvi.01244-18] [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: 08/13/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
Epstein-Barr virus (EBV) SM protein is an RNA-binding protein that has multiple posttranscriptional gene regulatory functions essential for EBV lytic replication. In this study, we identified an interaction between SM and DHX9, a DExH-box helicase family member, by mass spectrometry and coimmunoprecipitation. DHX9 participates in many cellular pathways involving RNA, including transcription, processing, transport, and translation. DHX9 enhances virus production or infectivity of a wide variety of DNA and RNA viruses. Surprisingly, an increase in EBV late gene expression and virion production occurred upon knockdown of DHX9. To further characterize the SM-DHX9 interaction, we performed immunofluorescence microscopy of EBV-infected cells and found that DHX9 partially colocalized with SM in nuclear foci during EBV lytic replication. However, the positive effect of DHX9 depletion on EBV lytic gene expression was not confined to SM-dependent genes, indicating that the antiviral effect of DHX9 was not mediated through its effects on SM. DHX9 enhanced activation of innate antiviral pathways comprised of several interferon-stimulated genes that are active against EBV. SM inhibited the transcription-activating function of DHX9, which acts through cAMP response elements (CREs), suggesting that SM may also act to counteract DHX9's antiviral functions during lytic replication.IMPORTANCE This study identifies an interaction between Epstein-Barr virus (EBV) SM protein and cellular helicase DHX9, exploring the roles that this interaction plays in viral infection and host defenses. Whereas most previous studies established DHX9 as a proviral factor, we demonstrate that DHX9 may act as an inhibitor of EBV virion production. DHX9 enhanced innate antiviral pathways active against EBV and was needed for maximal expression of several interferon-induced genes. We show that SM binds to and colocalizes DHX9 and may counteract the antiviral function of DHX9. These data indicate that DHX9 possesses antiviral activity and that SM may suppress the antiviral functions of DHX9 through this association. Our study presents a novel host-pathogen interaction between EBV and the host cell.
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13
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Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS. Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Nat Biotechnol 2019; 37:169-178. [PMID: 30607034 DOI: 10.1038/s41587-018-0001-2] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022]
Abstract
Existing high-throughput methods to identify RNA-binding proteins (RBPs) are based on capture of polyadenylated RNAs and cannot recover proteins that interact with nonadenylated RNAs, including long noncoding RNA, pre-mRNAs and bacterial RNAs. We present orthogonal organic phase separation (OOPS), which does not require molecular tagging or capture of polyadenylated RNA, and apply it to recover cross-linked protein-RNA and free protein, or protein-bound RNA and free RNA, in an unbiased way. We validated OOPS in HEK293, U2OS and MCF10A human cell lines, and show that 96% of proteins recovered were bound to RNA. We show that all long RNAs can be cross-linked to proteins, and recovered 1,838 RBPs, including 926 putative novel RBPs. OOPS is approximately 100-fold more efficient than existing methods and can enable analyses of dynamic RNA-protein interactions. We also characterize dynamic changes in RNA-protein interactions in mammalian cells following nocodazole arrest, and present a bacterial RNA-interactome for Escherichia coli. OOPS is compatible with downstream proteomics and RNA sequencing, and can be applied in any organism.
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Affiliation(s)
- Rayner M L Queiroz
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | | | - Mie Monti
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Dan-Mircea Mirea
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Veronica Dezi
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | | | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
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14
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Staufen1 Interacts with Multiple Components of the Ebola Virus Ribonucleoprotein and Enhances Viral RNA Synthesis. mBio 2018; 9:mBio.01771-18. [PMID: 30301857 PMCID: PMC6178623 DOI: 10.1128/mbio.01771-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Ebola virus (EBOV) is a negative-strand RNA virus with significant public health importance. Currently, no therapeutics are available for Ebola, which imposes an urgent need for a better understanding of EBOV biology. Here we dissected the virus-host interplay between EBOV and host RNA-binding proteins. We identified novel EBOV host factors, including Staufen1, which interacts with multiple viral factors and is required for efficient viral RNA synthesis. Ebola virus (EBOV) genome and mRNAs contain long, structured regions that could hijack host RNA-binding proteins to facilitate infection. We performed RNA affinity chromatography coupled with mass spectrometry to identify host proteins that bind to EBOV RNAs and identified four high-confidence proviral host factors, including Staufen1 (STAU1), which specifically binds both 3′ and 5′ extracistronic regions of the EBOV genome. We confirmed that EBOV infection rate and production of infectious particles were significantly reduced in STAU1-depleted cells. STAU1 was recruited to sites of EBOV RNA synthesis upon infection and enhanced viral RNA synthesis. Furthermore, STAU1 interacts with EBOV nucleoprotein (NP), virion protein 30 (VP30), and VP35; the latter two bridge the viral polymerase to the NP-coated genome, forming the viral ribonucleoprotein (RNP) complex. Our data indicate that STAU1 plays a critical role in EBOV replication by coordinating interactions between the viral genome and RNA synthesis machinery.
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15
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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16
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Lee T, Pelletier J. The biology of DHX9 and its potential as a therapeutic target. Oncotarget 2018; 7:42716-42739. [PMID: 27034008 PMCID: PMC5173168 DOI: 10.18632/oncotarget.8446] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
DHX9 is member of the DExD/H-box family of helicases with a “DEIH” sequence at its eponymous DExH-box motif. Initially purified from human and bovine cells and identified as a homologue of the Drosophila Maleless (MLE) protein, it is an NTP-dependent helicase consisting of a conserved helicase core domain, two double-stranded RNA-binding domains at the N-terminus, and a nuclear transport domain and a single-stranded DNA-binding RGG-box at the C-terminus. With an ability to unwind DNA and RNA duplexes, as well as more complex nucleic acid structures, DHX9 appears to play a central role in many cellular processes. Its functions include regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. Because of its central role in gene regulation and RNA metabolism, there are growing implications for DHX9 in human diseases and their treatment. This review will provide an overview of the structure, biochemistry, and biology of DHX9, its role in cancer and other human diseases, and the possibility of targeting DHX9 in chemotherapy.
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Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
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17
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Fidaleo M, De Paola E, Paronetto MP. The RNA helicase A in malignant transformation. Oncotarget 2017; 7:28711-23. [PMID: 26885691 PMCID: PMC5053757 DOI: 10.18632/oncotarget.7377] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
The RNA helicase A (RHA) is involved in several steps of RNA metabolism, such as RNA processing, cellular transit of viral molecules, ribosome assembly, regulation of transcription and translation of specific mRNAs. RHA is a multifunctional protein whose roles depend on the specific interaction with different molecular partners, which have been extensively characterized in physiological situations. More recently, the functional implication of RHA in human cancer has emerged. Interestingly, RHA was shown to cooperate with both tumor suppressors and oncoproteins in different tumours, indicating that its specific role in cancer is strongly influenced by the cellular context. For instance, silencing of RHA and/or disruption of its interaction with the oncoprotein EWS-FLI1 rendered Ewing sarcoma cells more sensitive to genotoxic stresses and affected tumor growth and maintenance, suggesting possible therapeutic implications. Herein, we review the recent advances in the cellular functions of RHA and discuss its implication in oncogenesis, providing a perspective for future studies and potential translational opportunities in human cancer.
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Affiliation(s)
- Marco Fidaleo
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
| | - Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
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18
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Capitanio JS, Montpetit B, Wozniak RW. Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9. eLife 2017; 6. [PMID: 28221134 PMCID: PMC5338925 DOI: 10.7554/elife.18825] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022] Open
Abstract
Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98, binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, we focused on identifying novel binding partners and understanding the significance of these interactions. Here we report on the identification of the DExH/D-box helicase DHX9 as an intranuclear Nup98 binding partner. Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner. Importantly, binding of Nup98 stimulates the ATPase activity of DHX9, and a transcriptional reporter assay suggests Nup98 supports DHX9-stimulated transcription. Consistent with these observations, our analysis revealed that Nup98 and DHX9 bind interdependently to similar gene loci and their transcripts. Based on our results, we propose that Nup98 functions as a co-factor that regulates DHX9 and, potentially, other RNA helicases.
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Affiliation(s)
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Department of Viticulture and Enology, University of California, Davis, United states
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19
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Singh G, Fritz SM, Ranji A, Singh D, Boris-Lawrie K. Isolation of Cognate RNA-protein Complexes from Cells Using Oligonucleotide-directed Elution. J Vis Exp 2017. [PMID: 28117770 DOI: 10.3791/54391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribonucleoprotein particles direct the biogenesis and post-transcriptional regulation of all mRNAs through distinct combinations of RNA binding proteins. They are composed of position-dependent, cis-acting RNA elements and unique combinations of RNA binding proteins. Defining the composition of a specific RNP is essential to achieving a fundamental understanding of gene regulation. The isolation of a select RNP is akin to finding a needle in a haystack. Here, we demonstrate an approach to isolate RNPs associated at the 5' untranslated region of a select mRNA in asynchronous, transfected cells. This cognate RNP has been demonstrated to be necessary for the translation of select viruses and cellular stress-response genes. The demonstrated RNA-protein co-precipitation protocol is suitable for the downstream analysis of protein components through proteomic analyses, immunoblots, or suitable biochemical identification assays. This experimental protocol demonstrates that DHX9/RNA helicase A is enriched at the 5' terminus of cognate retroviral RNA and provides preliminary information for the identification of its association with cell stress-associated huR and junD cognate mRNAs.
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Affiliation(s)
- Gatikrushna Singh
- Department of Veterinary & Biomedical Sciences, University of Minnesota
| | - Sarah M Fritz
- Department of Veterinary Biosciences, Ohio State University
| | - Arnaz Ranji
- Department of Veterinary Biosciences, Ohio State University
| | | | - Kathleen Boris-Lawrie
- Department of Veterinary & Biomedical Sciences, University of Minnesota; Department of Veterinary Biosciences, Ohio State University;
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20
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Boeras I, Song Z, Moran A, Franklin J, Brown WC, Johnson M, Boris-Lawrie K, Heng X. DHX9/RHA Binding to the PBS-Segment of the Genomic RNA during HIV-1 Assembly Bolsters Virion Infectivity. J Mol Biol 2016; 428:2418-2429. [PMID: 27107641 DOI: 10.1016/j.jmb.2016.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 12/28/2022]
Abstract
Cellular RNA-binding proteins incorporated into virions during human immunodeficiency virus type 1 (HIV-1) assembly promote the replication efficiency of progeny virions. Despite its critical role in bolstering virion infectivity, the molecular basis for the incorporation of DHX9/RNA helicase A (RHA) to virions remains unclear. Here, cell-based experiments demonstrate that the truncation of segments of the HIV-1 5'-untranslated region (5'-UTR) distinct from the core encapsidation sequence eliminated virion incorporation of RHA, indicating that RHA recruitment is mediated by specific interactions with the HIV-1 5'-UTR. In agreement with biological data, isothermal titration calorimetry determined that the dimer conformation of the 5'-UTR binds one RHA molecule per RNA strand, and the interaction is independent of nucleocapsid protein binding. NMR spectra employing a deuterium-labeling approach enabled resolution of the dimeric 5'-UTR in complex with the RHA N-terminal domain. The structure of the large molecular mass complex was dependent on RHA binding to a double-stranded region of the primer binding site (PBS)-segment of the 5'-UTR. A single A-to-C substitution was sufficient to disrupt biophysical conformation and attenuate virion infectivity in cell-based assays. Taken together, our studies demonstrate the structural basis for HIV-1 genomic RNA to recruit beneficial cellular cofactor to virions. The support of progeny virion infectivity by RHA is attributable to structure-dependent binding at the PBS-segment of the HIV-1 5'-UTR during virus assembly.
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Affiliation(s)
- Ioana Boeras
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Andrew Moran
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Jarryd Franklin
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - William Clay Brown
- Center for Structural Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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21
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Stake M, Singh D, Singh G, Marcela Hernandez J, Kaddis Maldonado R, Parent LJ, Boris-Lawrie K. HIV-1 and two avian retroviral 5' untranslated regions bind orthologous human and chicken RNA binding proteins. Virology 2015; 486:307-20. [PMID: 26584240 DOI: 10.1016/j.virol.2015.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/31/2015] [Accepted: 06/01/2015] [Indexed: 01/12/2023]
Abstract
Essential host cofactors in retrovirus replication bind cis-acting sequences in the 5'untranslated region (UTR). Although host RBPs are crucial to all aspects of virus biology, elucidating their roles in replication remains a challenge to the field. Here RNA affinity-coupled-proteomics generated a comprehensive, unbiased inventory of human and avian RNA binding proteins (RBPs) co-isolating with 5'UTRs of HIV-1, spleen necrosis virus and Rous sarcoma virus. Applying stringent biochemical and statistical criteria, we identified 185 RBP; 122 were previously implicated in retrovirus biology and 63 are new to the 5'UTR proteome. RNA electrophoretic mobility assays investigated paralogs present in the common ancestor of vertebrates and one hnRNP was identified as a central node to the biological process-anchored networks of HIV-1, SNV, and RSV 5' UTR-proteomes. This comprehensive view of the host constituents of retroviral RNPs is broadly applicable to investigation of viral replication and antiviral response in both human and avian cell lineages.
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Affiliation(s)
- Matthew Stake
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Deepali Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India.
| | - Gatikrushna Singh
- Department Veterinary & Biomedical Sciences, University of Minnesota, 205 VSB, 1971 Commonwealth Avenue, Saint Paul, MN 55108.
| | - J Marcela Hernandez
- Department of Veterinary Biosciences, Center for Retrovirus Research, Center for RNA Biology, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA.
| | - Rebecca Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Leslie J Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Department Microbiology & Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Kathleen Boris-Lawrie
- Department Veterinary & Biomedical Sciences, University of Minnesota, 205 VSB, 1971 Commonwealth Avenue, Saint Paul, MN 55108.
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22
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Helicase associated 2 domain is essential for helicase activity of RNA helicase A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1757-64. [DOI: 10.1016/j.bbapap.2014.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 02/04/2023]
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23
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Xing L, Niu M, Kleiman L. Role of the OB-fold of RNA helicase A in the synthesis of HIV-1 RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1069-78. [PMID: 25149208 DOI: 10.1016/j.bbagrm.2014.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 07/25/2014] [Accepted: 08/12/2014] [Indexed: 11/26/2022]
Abstract
RNA helicase A (RHA), a DExD/H protein, contains a stretch of repeated arginine and glycine-glycine (RGG) residues and an oligonucleotide/oligosaccharide-binding fold (OB-fold) at the C-terminus. RHA has been reported to function as a transcriptional cofactor. This study shows the role of RGG and OB-fold domains of RHA in the activation of transcription and splicing of HIV-1 RNA. RHA stimulates HIV-1 transcription by enhancing the occupancy of RNA polymerase II on the proviral DNA. Deletion of RGG or both RGG and OB-fold does not change the transcriptional activity of RHA, nor does the stability of viral RNA. However, deletion of both RGG and OB-fold rather than deletion of RGG only results in less production of multiply spliced 6D RNAs. The results suggest that the OB-fold is involved in modulating HIV-1 RNA splicing in the context of some HIV-1 strains while it is dispensable for the activation of HIV-1 transcription.
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Affiliation(s)
- Li Xing
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
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24
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Xing L, Niu M, Zhao X, Kleiman L. Different activities of the conserved lysine residues in the double-stranded RNA binding domains of RNA helicase A in vitro and in the cell. Biochim Biophys Acta Gen Subj 2014; 1840:2234-43. [PMID: 24726449 DOI: 10.1016/j.bbagen.2014.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 12/25/2022]
Abstract
BACKGROUND RNA helicase A regulates a variety of RNA metabolism processes including HIV-1 replication and contains two double-stranded RNA binding domains (dsRBD1 and dsRBD2) at the N-terminus. Each dsRBD contains two invariant lysine residues critical for the binding of isolated dsRBDs to RNA. However, the role of these conserved lysine residues was not tested in the context of enzymatically active full-length RNA helicase A either in vitro or in the cells. METHODS The conserved lysine residues in each or both of dsRBDs were substituted by alanine in the context of full-length RNA helicase A. The mutant RNA helicase A was purified from mammalian cells. The effects of these mutations were assessed either in vitro upon RNA binding and unwinding or in the cell during HIV-1 production upon RNA helicase A-RNA interaction and RNA helicase A-stimulated viral RNA processes. RESULTS Unexpectedly, the substitution of the lysine residues by alanine in either or both of dsRBDs does not prevent purified full-length RNA helicase A from binding and unwinding duplex RNA in vitro. However, these mutations efficiently inhibit RNA helicase A-stimulated HIV-1 RNA metabolism including the accumulation of viral mRNA and tRNA(Lys3) annealing to viral RNA. Furthermore, these mutations do not prevent RNA helicase A from binding to HIV-1 RNA in vitro as well, but dramatically reduce RNA helicase A-HIV-1 RNA interaction in the cells. CONCLUSIONS The conserved lysine residues of dsRBDs play critical roles in the promotion of HIV-1 production by RNA helicase A. GENERAL SIGNIFICANCE The conserved lysine residues of dsRBDs are key to the interaction of RNA helicase A with substrate RNA in the cell, but not in vitro.
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Affiliation(s)
- Li Xing
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Xia Zhao
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
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25
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Abstract
Superfamily 2 helicase proteins are ubiquitous in RNA biology and have an extraordinarily broad set of functional roles. Central among these roles are the promotion of rearrangements of structured RNAs and the remodeling of ribonucleoprotein complexes (RNPs), allowing formation of native RNA structure or progression through a functional cycle of structures. Although all superfamily 2 helicases share a conserved helicase core, they are divided evolutionarily into several families, and it is principally proteins from three families, the DEAD-box, DEAH/RHA, and Ski2-like families, that function to manipulate structured RNAs and RNPs. Strikingly, there are emerging differences in the mechanisms of these proteins, both between families and within the largest family (DEAD-box), and these differences appear to be tuned to their RNA or RNP substrates and their specific roles. This review outlines basic mechanistic features of the three families and surveys individual proteins and the current understanding of their biological substrates and mechanisms.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712; ,
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26
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Fu Q, Yuan YA. Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9). Nucleic Acids Res 2013; 41:3457-70. [PMID: 23361462 PMCID: PMC3597700 DOI: 10.1093/nar/gkt042] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/18/2012] [Accepted: 01/06/2013] [Indexed: 12/31/2022] Open
Abstract
Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.
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Affiliation(s)
| | - Y. Adam Yuan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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27
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Marintchev A. Roles of helicases in translation initiation: a mechanistic view. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:799-809. [PMID: 23337854 DOI: 10.1016/j.bbagrm.2013.01.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/08/2013] [Accepted: 01/09/2013] [Indexed: 12/12/2022]
Abstract
The goal of this review is to summarize our current knowledge about the helicases involved in translation initiation and their roles in both general and mRNA-specific translation. The main topics covered are the mechanisms of helicase action, with emphasis on the roles of accessory domains and proteins; the functions performed by helicases in translation initiation; and the interplay between direct and indirect effects of helicases that also function in steps preceding translation initiation. Special attention is given to the dynamics of eIF4A binding and dissociation from eIF4F during mRNA unwinding. It is proposed that DHX29, as well as other helicases and translation initiation factors could also cycle on and off the translation initiation complexes, similar to eIF4A. The evidence in favor of this hypothesis and its possible implications for the mechanisms of translation initiation is discussed. This article is part of a Special Issue entitled: The biology of RNA helicases - Modulation for life.
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Affiliation(s)
- Assen Marintchev
- Dept. of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA.
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Kallen AN, Ma J, Huang Y. Does Lin28 Antagonize miRNA-Mediated Repression by Displacing miRISC from Target mRNAs? Front Genet 2012; 3:240. [PMID: 23162570 PMCID: PMC3499807 DOI: 10.3389/fgene.2012.00240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/20/2012] [Indexed: 12/26/2022] Open
Abstract
Lin28 is a developmentally regulated RNA-binding protein that plays important roles in diverse physiological and pathological processes including oncogenesis and brain synaptic function. These pleiotropic roles of Lin28 are mechanistically linked both to its ability to directly stimulate translation of genes involved primarily in cell growth and metabolism and to its ability to block biogenesis of a subset of miRNAs including the let-7 family of miRNAs. In the case of direct stimulation of gene expression, Lin28 binds to targeted mRNAs through recognition of Lin28-responsive elements (LREs) within mRNAs and recruits RNA helicase A (RHA) to promote translation. RHA belongs to the DEAD-box protein family of RNA helicases, which generally catalyze ATP-dependent unwinding of RNA duplexes or remodeling of ribonucleoprotein complexes (RNPs). Since any given mRNA can potentially be inhibited by miRNAs bearing complementary sequences, we hypothesize that binding of Lin28 to LREs not only nucleates the binding of multiple Lin28 molecules to the same mRNA, but also leads to remodeling of RNPs through recruitment of RHA and causes release of inhibitory miRNA-induced silencing complexes bound to the mRNA. This mode of action may contribute to Lin28-mediated stimulation of translation in both tumor and neuronal cells.
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Affiliation(s)
- Amanda N Kallen
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Stem Cell Center, Yale University School of Medicine New Haven, CT, USA
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29
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Zhu Y, Liu S, Yin Q, Xu T, Wu X, Zhuang Y. Generation of Dhx9-deficient clones in T-cell development with a mitotic recombination technique. Genesis 2012; 50:543-51. [PMID: 22988576 DOI: 10.1002/dvg.22005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mitotic recombination is an effective tool for generating mutant clones in somatic tissues. Because of difficulties associated with detecting and quantifying mutant clones in mice, this technique is limited to analysis of growth-related phenotypes induced by loss function of tumor suppressor genes. Here, we used the polymorphic CD45.1/CD45.2 alleles on chromosome 1 as pan-hematopoietic markers to track mosaic clones generated through mitotic recombination in developing T cells. We show that lineage-specific mitotic recombination can be induced and reliably detected as CD45.1 or CD45.2 homozygous clones from the CD45.1/CD45.2 heterozygous background. We have applied this system in the analysis of a lethal mutation in the Dhx9 gene. Mosaic analysis revealed a stage-specific role for Dhx9 during T-cell maturation. Thus, the experimental system described in this study offers a practical means for mosaic analysis of germline mutations in the hematopoietic system.
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Affiliation(s)
- Yi Zhu
- Institute of Developmental Biology and Molecular Medicine, School of Life Science, Fudan University, Shanghai, China
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Roles of individual domains in the function of DHX29, an essential factor required for translation of structured mammalian mRNAs. Proc Natl Acad Sci U S A 2012; 109:E3150-9. [PMID: 23047696 DOI: 10.1073/pnas.1208014109] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
On most eukaryotic mRNAs, initiation codon selection involves base-by-base inspection of 5' UTRs by scanning ribosomal complexes. Although the eukaryotic initiation factors 4A/4B/4G can mediate scanning through medium-stability hairpins, scanning through more stable structures additionally requires DHX29, a member of the superfamily 2 DEAH/RNA helicase A (RHA) helicase family that binds to 40S subunits and possesses 40S-stimulated nucleoside triphosphatase (NTPase) activity. Here, sequence alignment and structural modeling indicated that DHX29 comprises a unique 534-aa-long N-terminal region (NTR), central catalytic RecA1/RecA2 domains containing a large insert in the RecA2 domain, and the C-terminal part, which includes winged-helix, ratchet, and oligonucleotide/oligosaccharide-binding (OB) domains that are characteristic of DEAH/RHA helicases. Functional characterization revealed that specific ribosomal targeting is required for DHX29's activity in initiation and is determined by elements that map to the NTR and to the N-terminal half of the winged-helix domain. The ribosome-binding determinant located in the NTR was identified as a putative double-stranded RNA-binding domain. Mutational analyses of RecA1/RecA2 domains confirmed the essential role of NTP hydrolysis for DHX29's function in initiation and validated the significance of a β-hairpin protruding from RecA2. The large RecA2 insert played an autoinhibitory role in suppressing DHX29's intrinsic NTPase activity but was not essential for its 40S-stimulated NTPase activity and function in initiation. Deletion of the OB domain also increased DHX29's basal NTPase activity, but more importantly, abrogated the responsiveness of the NTPase activity to stimulation, which abolished DHX29's function in initiation. This finding suggests that the OB domain, which is specific for DEAH/RHA helicases, plays an important role in their NTPase cycle.
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31
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In vitro and in vivo analysis of the interaction between RNA helicase A and HIV-1 RNA. J Virol 2012; 86:13272-80. [PMID: 23015696 DOI: 10.1128/jvi.01993-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNA helicase A (RHA) promotes multiple steps of HIV-1 RNA metabolism during viral replication, including transcription, translation, and the annealing of primer tRNA(3)(Lys) to the viral RNA. RHA is a member of the DExH subclass of RNA helicases that uniquely contains two double-stranded RNA binding domains (dsRBDs) at its N terminus. Here, we performed a genome-wide analysis of the interaction of RHA with HIV-1 RNA both in vitro, using fluorescence polarization, and during viral replication, using an RNA-protein coprecipitation assay. In vitro, RHA binds to all the isolated regions of the HIV-1 RNA genome tested, with K(d) (equilibrium dissociation constant) values ranging from 44 to 178 nM. In contrast, during viral replication, RNA-protein coprecipitation assays detected only a major interaction of RHA with the 5'-untranslated region (5'-UTR) and a minor interaction with the Rev response element (RRE) of HIV-1 RNA. Since RHA does not associate well with all the highly structured regions of HIV-1 RNA tested in vivo, the results suggest that other viral or cellular factors not present in vitro may modulate the direct interaction of RHA with HIV-1 RNA during virus replication. Nevertheless, a role for duplex RNA as a target for RHA binding in vivo is suggested by the fact that the deletion of either one or both dsRBDs eliminates the in vivo interaction of RHA with HIV-1 RNA. Furthermore, these mutant RHAs do not promote the in vivo annealing of tRNA(3)(Lys) to viral RNA, nor are they packaged into virions, demonstrating that the dsRBDs are essential for the role of RHA in HIV-1 replication.
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A new framework for understanding IRES-mediated translation. Gene 2012; 502:75-86. [PMID: 22555019 DOI: 10.1016/j.gene.2012.04.039] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 03/23/2012] [Accepted: 04/17/2012] [Indexed: 01/08/2023]
Abstract
Studies over the past 5 or so years have indicated that the traditional clustering of mechanisms for translation initiation in eukaryotes into cap-dependent and cap-independent (or IRES-mediated) is far too narrow. From individual studies of a number of mRNAs encoding proteins that are regulatory in nature (i.e. likely to be needed in small amounts such as transcription factors, protein kinases, etc.), it is now evident that mRNAs exist that blur these boundaries. This review seeks to set the basic ground rules for the analysis of different initiation pathways that are associated with these new mRNAs as well as related to the more traditional mechanisms, especially the cap-dependent translational process that is the major route of initiation of mRNAs for housekeeping proteins and thus, the bulk of protein synthesis in most cells. It will become apparent that a mixture of descriptions is likely to become the norm in the near future (i.e. m(7)G-assisted internal initiation).
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Nagata T, Tsuda K, Kobayashi N, Shirouzu M, Kigawa T, Güntert P, Yokoyama S, Muto Y. Solution structures of the double-stranded RNA-binding domains from RNA helicase A. Proteins 2012; 80:1699-706. [PMID: 22454253 DOI: 10.1002/prot.24059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/03/2012] [Accepted: 02/07/2012] [Indexed: 12/21/2022]
Abstract
RNA helicase A (RHA) is a highly conserved protein with multifaceted functions in the gene expression of cellular and viral mRNAs. RHA recognizes highly structured nucleotides and catalytically rearranges the various interactions between RNA, DNA, and protein molecules to provide a platform for the ribonucleoprotein complex. We present the first solution structures of the double-stranded RNA-binding domains (dsRBDs), dsRBD1 and dsRBD2, from mouse RHA. We discuss the binding mode of the dsRBDs of RHA, in comparison with the known dsRBD structures in their complexes. Our structural data provide important information for the elucidation of the molecular reassembly mediated by RHA.
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Affiliation(s)
- Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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Abstract
RNA helicases are encoded by all eukaryotic and prokaryotic cells and a minority of viruses. Activity of RNA helicases is necessary for all steps in the expression of cells and viruses and the host innate response to virus infection. Their vast functional repertoire is attributable to the core ATP-dependent helicase domain in conjunction with flanking domains that are interchangeable and engage viral and cellular cofactors. Here, we address the important issue of host RNA helicases that are necessary for replication of a virus. This chapter covers approaches to identification and characterization of candidate helicases and methods to define the biochemical and biophysical parameters of specificity and functional activity of the enzymes. We discuss the context of cellular RNA helicase activity and virion-associated RNA helicases. The methodology and choice of controls fosters the assessment of the virologic scope of RNA helicases across divergent cell lineages and viral replication cycles.
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Affiliation(s)
- Amit Sharma
- Department of Veterinary Biosciences, Ohio State University, Columbus, Ohio, USA,Center for Retrovirus Research, Ohio State University, Columbus, Ohio, USA,Center for RNA Biology, Ohio State University, Columbus, Ohio, USA,Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary Biosciences, Ohio State University, Columbus, Ohio, USA,Center for Retrovirus Research, Ohio State University, Columbus, Ohio, USA,Center for RNA Biology, Ohio State University, Columbus, Ohio, USA,Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
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Miki T, Kamikawa Y, Kurono S, Kaneko Y, Katahira J, Yoneda Y. Cell type-dependent gene regulation by Staufen2 in conjunction with Upf1. BMC Mol Biol 2011; 12:48. [PMID: 22087843 PMCID: PMC3226675 DOI: 10.1186/1471-2199-12-48] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 11/16/2011] [Indexed: 12/01/2022] Open
Abstract
Background Staufen2 (Stau2), a double-stranded RNA-binding protein, is a component of neuronal RNA granules, which are dendritic mRNA transport machines. Although Stau2 is thought to be involved in the dendritic targeting of several mRNAs in neurons, the mechanism whereby Stau2 regulates these mRNAs is unknown. To elucidate the functions of Stau2, we screened for novel binding partners by affinity purification of GST-tagged Stau2 from 293F cells. Results Three RNA helicases, RNA helicase A, Upf1 and Mov10, were identified in Stau2-containing complexes. We focused our studies on Upf1, a key player in nonsense-mediated mRNA decay. Stau2 was found to bind directly to Upf1 in an RNA-independent manner in vitro. Tethering Stau2 to the 3'-untranslated region (UTR) of a reporter gene had little effect on its expression in HeLa cells. In contrast, when the same tethering assay was performed in 293F cells, we observed an increase in reporter protein levels. This upregulation of protein expression by Stau2 turned out to be dependent on Upf1. Moreover, we found that in 293F cells, Stau2 upregulates the reporter mRNA level in an Upf1-independent manner. Conclusions These results indicate that the recruitment of Stau2 alone or in combination with Upf1 differentially affects the fate of mRNAs. Moreover, the results suggest that Stau2-mediated fate determination could be executed in a cell type-specific manner.
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Affiliation(s)
- Takashi Miki
- Department of Frontier Bioscience, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
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Abstract
The translation initiation step in eukaryotes is highly regulated and rate-limiting. During this process, the 40S ribosomal subunit is usually recruited to the 5' terminus of the mRNA. It then migrates towards the initiation codon, where it is joined by the 60S ribosomal subunit to form the 80S initiation complex. Secondary structures in the 5' untranslated region (UTR) can impede binding and movement of the 40S ribosome. The canonical eukaryotic translation initiation factor eIF4A (also known as DDX2), together with its accessory proteins eIF4B and eIF4H, is thought to act as a helicase that unwinds secondary structures in the mRNA 5' UTR. Growing evidence suggests that other helicases are also important for translation initiation and may promote the scanning processivity of the 40S subunit, synergize with eIF4A to 'melt' secondary structures or facilitate translation of a subset of mRNAs.
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Ranji A, Boris-Lawrie K. RNA helicases: emerging roles in viral replication and the host innate response. RNA Biol 2010; 7:775-87. [PMID: 21173576 DOI: 10.4161/rna.7.6.14249] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RNA helicases serve multiple roles at the virus-host interface. In some situations, RNA helicases are essential host factors to promote viral replication; however, in other cases they serve as a cellular sensor to trigger the antiviral state in response to viral infection. All family members share the conserved ATP-dependent catalytic core linked to different substrate recognition and protein-protein interaction domains. These flanking domains can be shuffled between different helicases to achieve functional diversity. This review summarizes recent studies, which have revealed two types of activity by RNA helicases. First, RNA helicases are catalysts of progressive RNA-protein rearrangements that begin at gene transcription and culminate in mRNA translation. Second, RNA helicases can act as a scaffold for alternative protein-protein interactions that can defeat the antiviral state. The mounting fundamental understanding of RNA helicases is being used to develop selective and efficacious drugs against human and animal pathogens. The analysis of RNA helicases in virus model systems continues to provide insights into virology, cell biology and immunology, and has provided fresh perspective to continue unraveling the complexity of virus-host interactions.
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Affiliation(s)
- Arnaz Ranji
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
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