301
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Abstract
RNA helicases comprise a large family of enzymes that are thought to utilize the energy of NTP binding and hydrolysis to remodel RNA or RNA-protein complexes, resulting in RNA duplex strand separation, displacement of proteins from RNA molecules, or both. These functions of RNA helicases are required for all aspects of cellular RNA metabolism, from bacteria to humans. We provide a brief overview of the functions of RNA helicases and highlight some of the recent key advances that have contributed to our current understanding of their biological function and mechanism of action.
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302
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Baguet A, Degot S, Cougot N, Bertrand E, Chenard MP, Wendling C, Kessler P, Le Hir H, Rio MC, Tomasetto C. The exon-junction-complex-component metastatic lymph node 51 functions in stress-granule assembly. J Cell Sci 2007; 120:2774-84. [PMID: 17652158 DOI: 10.1242/jcs.009225] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Metastatic lymph node 51 [MLN51 (also known as CASC3)] is a component of the exon junction complex (EJC), which is assembled on spliced mRNAs and plays important roles in post-splicing events. The four proteins of the EJC core, MLN51, MAGOH, Y14 and EIF4AIII shuttle between the cytoplasm and the nucleus. However, unlike the last three, MLN51 is mainly detected in the cytoplasm, suggesting that it plays an additional function in this compartment. In the present study, we show that MLN51 is recruited into cytoplasmic aggregates known as stress granules (SGs) together with the SG-resident proteins, fragile X mental retardation protein (FMRP), poly(A) binding protein (PABP) and poly(A)+ RNA. MLN51 specifically associates with SGs via its C-terminal region, which is dispensable for its incorporation in the EJC. MLN51 does not promote SG formation but its silencing, or the overexpression of a mutant lacking its C-terminal region, alters SG assembly. Finally, in human breast carcinomas, MLN51 is sometimes present in cytoplasmic foci also positive for FMRP and PABP, suggesting that SGs formation occurs in malignant tumours.
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Affiliation(s)
- Aurélie Baguet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie du Cancer, UMR 7104 CNRS/U596 INSERM/Université Louis Pasteur, BP 10142, 67404 Illkirch, C.U. de Strasbourg, France
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303
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Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 2007; 8:479-90. [PMID: 17473849 PMCID: PMC5507177 DOI: 10.1038/nrm2178] [Citation(s) in RCA: 906] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many RNA-binding proteins have modular structures and are composed of multiple repeats of just a few basic domains that are arranged in various ways to satisfy their diverse functional requirements. Recent studies have investigated how different modules cooperate in regulating the RNA-binding specificity and the biological activity of these proteins. They have also investigated how multiple modules cooperate with enzymatic domains to regulate the catalytic activity of enzymes that act on RNA. These studies have shown how, for many RNA-binding proteins, multiple modules define the fundamental structural unit that is responsible for biological function.
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Affiliation(s)
- Bradley M Lunde
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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304
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Zhang Z, Krainer AR. Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components. Proc Natl Acad Sci U S A 2007; 104:11574-9. [PMID: 17606899 PMCID: PMC1913901 DOI: 10.1073/pnas.0704946104] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pre-mRNA splicing not only removes introns and joins exons to generate spliced mRNA but also results in remodeling of the spliced messenger ribonucleoprotein, influencing various downstream events. This remodeling includes the loading of an exon-exon junction complex (EJC). It is unclear how the spliceosome recruits the EJC onto the mRNA and whether EJC formation or EJC components are required for pre-mRNA splicing. Here we immunodepleted the EJC core component eIF4A3 from HeLa cell nuclear extract and found that eIF4A3 is dispensable for pre-mRNA splicing in vitro. However, eIF4A3 is required for the splicing-dependent loading of the Y14/Magoh heterodimer onto mRNA, and this activity of human eIF4A3 is also present in the Drosophila ortholog. Surprisingly, the loading of six other EJC components was not affected by eIF4A3 depletion, suggesting that their binding to mRNA involves different or redundant pathways. Finally, we found that the assembly of the EJC onto mRNA occurs at the late stages of the splicing reaction and requires the second-step splicing and mRNA-release factor HRH1/hPrp22. The EJC-dependent and -independent recruitment of RNA-binding proteins onto mRNA suggests a role for the EJC in messenger ribonucleoprotein remodeling involving interactions with other proteins already bound to the pre-mRNA, which has implications for nonsense-mediated mRNA decay and other mRNA transactions.
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Affiliation(s)
- Zuo Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Adrian R. Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- *To whom correspondence should be addressed at:
Cold Spring Harbor Laboratory, P.O. Box 100, Cold Spring Harbor, NY 11724. E-mail:
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305
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Högbom M, Collins R, van den Berg S, Jenvert RM, Karlberg T, Kotenyova T, Flores A, Karlsson Hedestam GB, Schiavone LH. Crystal structure of conserved domains 1 and 2 of the human DEAD-box helicase DDX3X in complex with the mononucleotide AMP. J Mol Biol 2007; 372:150-9. [PMID: 17631897 DOI: 10.1016/j.jmb.2007.06.050] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/12/2007] [Accepted: 06/14/2007] [Indexed: 11/24/2022]
Abstract
DExD-box helicases are involved in all aspects of cellular RNA metabolism. Conserved domains 1 and 2 contain nine signature motifs that are responsible for nucleotide binding, RNA binding and ATP hydrolysis. The human DEAD-box helicase DDX3X has been associated with several different cellular processes, such as cell-growth control, mRNA transport and translation, and is suggested to be essential for the export of unspliced/partially spliced HIV mRNAs from the nucleus to the cytoplasm. Here, the crystal structure of conserved domains 1 and 2 of DDX3X, including a DDX3-specific insertion that is not generally found in human DExD-box helicases, is presented. The N-terminal domain 1 and the C-terminal domain 2 both display RecA-like folds comprising a central beta-sheet flanked by alpha-helices. Interestingly, the DDX3X-specific insertion forms a helical element that extends a highly positively charged sequence in a loop, thus increasing the RNA-binding surface of the protein. Surprisingly, although DDX3X was crystallized in the presence of a large excess of ADP or the slowly hydrolyzable ATP analogue ATPgammaS the contaminant AMP was seen in the structure. A fluorescent-based stability assay showed that the thermal stability of DDX3X was increased by the mononucleotide AMP but not by ADP or ATPgammaS, suggesting that DDX3X is stabilized by AMP and elucidating why AMP was found in the nucleotide-binding pocket.
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Affiliation(s)
- Martin Högbom
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden
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306
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Viegas MH, Gehring NH, Breit S, Hentze MW, Kulozik AE. The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway. Nucleic Acids Res 2007; 35:4542-51. [PMID: 17586820 PMCID: PMC1935013 DOI: 10.1093/nar/gkm461] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a molecular pathway of mRNA surveillance that ensures rapid degradation of mRNAs containing premature translation termination codons (PTCs) in eukaryotes. NMD has been shown to also regulate normal gene expression and thus emerged as one of the key post-transcriptional mechanisms of gene regulation. Recently, NMD efficiency has been shown to vary between cell types and individuals thus implicating NMD as a modulator of genetic disease severity. We have now specifically analysed the molecular mechanism of variable NMD efficiency and first established an assay system for the quantification of NMD efficiency, which is based on carefully validated cellular NMD target transcripts. In a HeLa cell model system, NMD efficiency is shown to be remarkably variable and to represent a stable characteristic of different strains. In one of these strains, low NMD efficiency is shown to be functionally related to the reduced abundance of the exon junction component RNPS1. Furthermore, restoration of functional RNPS1 expression, but not of NMD-inactive mutant proteins, also restores efficient NMD in this model. We conclude that cellular concentrations of RNPS1 can modify NMD efficiency and propose that cell type specific co-factor availability represents a novel principle that controls NMD.
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Affiliation(s)
- Marcelo H. Viegas
- Department of Pediatric Oncology, Hematology and Immunology, Children's Hospital, University of Heidelberg, Im Neuenheimer Feld 150, 69120 Heidelberg, Germany, Molecular Medicine Partnership Unit (University of Heidelberg and European Molecular Biology Laboratory) and European Molecular Biology Laboratory, Gene Expression Unit, Meyerhofstr 1, 69117 Heidelberg, Germany
| | - Niels H. Gehring
- Department of Pediatric Oncology, Hematology and Immunology, Children's Hospital, University of Heidelberg, Im Neuenheimer Feld 150, 69120 Heidelberg, Germany, Molecular Medicine Partnership Unit (University of Heidelberg and European Molecular Biology Laboratory) and European Molecular Biology Laboratory, Gene Expression Unit, Meyerhofstr 1, 69117 Heidelberg, Germany
| | - Stephen Breit
- Department of Pediatric Oncology, Hematology and Immunology, Children's Hospital, University of Heidelberg, Im Neuenheimer Feld 150, 69120 Heidelberg, Germany, Molecular Medicine Partnership Unit (University of Heidelberg and European Molecular Biology Laboratory) and European Molecular Biology Laboratory, Gene Expression Unit, Meyerhofstr 1, 69117 Heidelberg, Germany
| | - Matthias W. Hentze
- Department of Pediatric Oncology, Hematology and Immunology, Children's Hospital, University of Heidelberg, Im Neuenheimer Feld 150, 69120 Heidelberg, Germany, Molecular Medicine Partnership Unit (University of Heidelberg and European Molecular Biology Laboratory) and European Molecular Biology Laboratory, Gene Expression Unit, Meyerhofstr 1, 69117 Heidelberg, Germany
| | - Andreas E. Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Children's Hospital, University of Heidelberg, Im Neuenheimer Feld 150, 69120 Heidelberg, Germany, Molecular Medicine Partnership Unit (University of Heidelberg and European Molecular Biology Laboratory) and European Molecular Biology Laboratory, Gene Expression Unit, Meyerhofstr 1, 69117 Heidelberg, Germany
- *To whom correspondence should be addressed. +49 6221 56 2303+49 6221 56 4559 Correspondence may also be addressed to Matthias W. Hentze. +49 6221 387 501+49 6221 387 518
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307
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Jankowsky E, Fairman ME. RNA helicases--one fold for many functions. Curr Opin Struct Biol 2007; 17:316-24. [PMID: 17574830 DOI: 10.1016/j.sbi.2007.05.007] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Revised: 03/27/2007] [Accepted: 05/29/2007] [Indexed: 12/25/2022]
Abstract
RNA helicases are a large group of enzymes that function in virtually all aspects of RNA metabolism. Although RNA helicases share a highly conserved structure, different enzymes display a wide array of biochemical activities, including RNA duplex unwinding, protein displacement from RNA and strand annealing. Recent structural and functional studies have started to illuminate the mechanisms by which this remarkable diversity of functions can be conducted by the conserved helicase fold.
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Affiliation(s)
- Eckhard Jankowsky
- Department of Biochemistry and Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
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308
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Parma DH, Bennett PE, Boswell RE. Mago Nashi and Tsunagi/Y14, respectively, regulate Drosophila germline stem cell differentiation and oocyte specification. Dev Biol 2007; 308:507-19. [PMID: 17628520 PMCID: PMC3010412 DOI: 10.1016/j.ydbio.2007.06.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 05/21/2007] [Accepted: 06/07/2007] [Indexed: 12/27/2022]
Abstract
A protein complex consisting of Mago Nashi and Tsunagi/Y14 is required to establish the major body axes and for the localization of primordial germ cell determinants during Drosophila melanogaster oogenesis. The Mago Nashi:Tsunagi/Y14 heterodimer also serves as the core of the exon junction complex (EJC), a multiprotein complex assembled on spliced mRNAs. In previous studies, reduced function alleles of mago nashi and tsunagi/Y14 were used to characterize the roles of the genes in oogenesis. Here, we investigated mago nashi and tsunagi/Y14 using null alleles and clonal analysis. Germline clones lacking mago nashi function divide but fail to differentiate. The mago nashi null germline stem cells produce clones over a period of at least 11 days, suggesting that mago nashi is not necessary for stem cell self-renewal. However, germline stem cells lacking tsunagi/Y14 function are indistinguishable from wild type. Additionally, in tsunagi/Y14 null germline cysts, centrosomes and oocyte-specific components fail to concentrate within a single cell and oocyte fate is not restricted to a single cell. Together, our results suggest not only that mago nashi is required for germline stem cell differentiation but that surprisingly mago nashi functions independently of tsunagi/Y14 in this process. On the other hand, Tsunagi/Y14 is essential for restricting oocyte fate to a single cell and may function with mago nashi in this process.
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309
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Shen J, Zhang L, Zhao R. Biochemical characterization of the ATPase and helicase activity of UAP56, an essential pre-mRNA splicing and mRNA export factor. J Biol Chem 2007; 282:22544-50. [PMID: 17562711 DOI: 10.1074/jbc.m702304200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DEXD/H-box protein UAP56 is an essential pre-mRNA splicing factor required for the first ATP-dependent spliceosome assembly step. UAP56 is also essential for the export of the majority of mRNAs from the nucleus to the cytoplasm. We performed biochemical characterization of UAP56's ATPase and helicase activity, which is important for further understanding the role of these activities in UAP56's function. We showed that UAP56 is an RNA-stimulated ATPase that can only hydrolyze ATP. We demonstrated that UAP56 is an ATP-dependent RNA helicase that can unwind substrates with 5' or 3' overhangs or blunt ends in vitro. We showed that U2AF(65) and Aly, two proteins known to interact with UAP56, do not influence UAP56's ATPase or helicase activity. We also demonstrated that several mutants in the conserved helicase motifs I, II, and III abolish UAP56's ATPase and/or helicase activity, providing tools for future investigation of the role of UAP56's ATPase and helicase activity in spliceosome assembly and mRNA export.
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Affiliation(s)
- Jingping Shen
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA
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310
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Büttner K, Nehring S, Hopfner KP. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat Struct Mol Biol 2007; 14:647-52. [PMID: 17558417 DOI: 10.1038/nsmb1246] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 04/06/2007] [Indexed: 11/08/2022]
Abstract
To reveal the mechanism of processive strand separation by superfamily-2 (SF2) 3'-->5' helicases, we determined apo and DNA-bound crystal structures of archaeal Hel308, a helicase that unwinds lagging strands and is related to human DNA polymerase theta. Our structure captures the duplex-unwinding reaction, shows that initial strand separation does not require ATP and identifies a prominent beta-hairpin loop as the unwinding element. Similar loops in hepatitis C virus NS3 helicase and RNA-decay factors support the idea that this duplex-unwinding mechanism is applicable to a broad subset of SF2 helicases. Comparison with ATP-bound SF2 enzymes suggests that ATP promotes processive unwinding of 1 base pair by ratchet-like transport of the 3' product strand. Our results provide a first structural framework for strand separation by processive SF2 3'-->5' helicases and reveal important mechanistic differences from SF1 helicases.
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Affiliation(s)
- Katharina Büttner
- Center for Integrated Protein Science, Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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311
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Stewart M. Ratcheting mRNA out of the nucleus. Mol Cell 2007; 25:327-30. [PMID: 17289581 DOI: 10.1016/j.molcel.2007.01.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 12/05/2006] [Accepted: 01/12/2007] [Indexed: 01/18/2023]
Abstract
Export of mature mRNA to the cytoplasm is the culmination of the nuclear portion of eukaryotic gene expression. After transport-competent mature mRNP export complexes are formed in the nucleus, their passage through nuclear pore complexes (NPCs) is facilitated by the Mex67:Mtr2 heterodimer. At the NPC cytoplasmic face, mRNP remodeling prevents its return to the nucleus and so functions as a molecular ratchet imposing directionality on transport. In budding yeast, recent work suggests that the DEAD-box helicase Dbp5 remodels mRNPs at the NPC cytoplasmic face by removing Mex67 and that the Dbp5 ATPase is activated by Gle1 and inositol hexaphosphate (IP(6)).
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Affiliation(s)
- Murray Stewart
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK.
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312
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Noble CG, Song H. MLN51 stimulates the RNA-helicase activity of eIF4AIII. PLoS One 2007; 2:e303. [PMID: 17375189 PMCID: PMC1810427 DOI: 10.1371/journal.pone.0000303] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 02/17/2007] [Indexed: 11/30/2022] Open
Abstract
The core of the exon-junction complex consists of Y14, Magoh, MLN51 and eIF4AIII, a DEAD-box RNA helicase. MLN51 stimulates the ATPase activity of eIF4AIII, whilst the Y14-Magoh complex inhibits it. We show that the MLN51-dependent stimulation increases both the affinity of eIF4AIII for ATP and the rate of enzyme turnover; the KM is decreased by an order of magnitude and kcat increases 30 fold. Y14-Magoh do inhibit the MLN51-stimulated ATPase activity, but not back to background levels. The ATP-bound form of the eIF4AIII-MLN51 complex has a 100-fold higher affinity for RNA than the unbound form and ATP hydrolysis reduces this affinity. MLN51 stimulates the RNA-helicase activity of eIF4AIII, suggesting that this activity may be functionally important.
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Affiliation(s)
- Christian G. Noble
- Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Haiwei Song
- Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, Singapore, Singapore
- * To whom correspondence should be addressed. E-mail:
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313
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Chandran V, Poljak L, Vanzo NF, Leroy A, Miguel RN, Fernandez-Recio J, Parkinson J, Burns C, Carpousis AJ, Luisi BF. Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. J Mol Biol 2006; 367:113-32. [PMID: 17234211 PMCID: PMC7610992 DOI: 10.1016/j.jmb.2006.12.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2006] [Revised: 11/26/2006] [Accepted: 12/07/2006] [Indexed: 12/21/2022]
Abstract
The Escherichia coli protein RhlB is an ATP-dependent motor that unfolds structured RNA for destruction by partner ribonucleases. In E. coli, and probably many other related gamma-proteobacteria, RhlB associates with the essential endoribonuclease RNase E as part of the multi-enzyme RNA degradosome assembly. The interaction with RNase E boosts RhlB's ATPase activity by an order of magnitude. Here, we examine the origins and implications of this effect. The location of the interaction sites on both RNase E and RhlB are refined and analysed using limited protease digestion, domain cross-linking and homology modelling. These data indicate that RhlB's carboxy-terminal RecA-like domain engages a segment of RNase E that is no greater than 64 residues. The interaction between RhlB and RNase E has two important consequences: first, the interaction itself stimulates the unwinding and ATPase activities of RhlB; second, RhlB gains proximity to two RNA-binding sites on RNase E, with which it cooperates to unwind RNA. Our homology model identifies a pattern of residues in RhlB that may be key for recognition of RNase E and which may communicate the activating effects. Our data also suggest that the association with RNase E may partially repress the RNA-binding activity of RhlB. This repression may in fact permit the interplay of the helicase and adjacent RNA binding segments as part of a process that steers substrates to either processing or destruction, depending on context, within the RNA degradosome assembly.
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Affiliation(s)
- Vidya Chandran
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Leonora Poljak
- Laboratoire de Microbiologie et Génétique Moléculaires, Unité Mixte de Recherche 5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Nathalie F. Vanzo
- Laboratoire de Microbiologie et Génétique Moléculaires, Unité Mixte de Recherche 5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Anne Leroy
- Laboratoire de Microbiologie et Génétique Moléculaires, Unité Mixte de Recherche 5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Ricardo Núñez Miguel
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Juan Fernandez-Recio
- Molecular Modelling and Bioinformatics Unit, Institute of Biomedical Research, Parc Cientific de Barcelona (IRB-PCB), C/Josep Samitier 1–5, 08028 Barcelona, Spain
| | - James Parkinson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Christopher Burns
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, 1120 15th Street, Augusta, GA 30912, USA
| | - Agamemnon J. Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, Unité Mixte de Recherche 5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
- Corresponding authors: ;
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
- Corresponding authors: ;
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314
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Hopfner KP, Michaelis J. Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics. Curr Opin Struct Biol 2006; 17:87-95. [PMID: 17157498 DOI: 10.1016/j.sbi.2006.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 10/18/2006] [Accepted: 11/27/2006] [Indexed: 10/23/2022]
Abstract
Enzymes that translocate nucleic acids using ATP hydrolysis include DNA and RNA helicases, viral genome packaging motors and chromatin remodeling ATPases. Recent structural analysis, in conjunction with single-molecule studies, has revealed a wealth of new insights into how these enzymes use ATP-driven conformational changes to move on nucleic acids.
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315
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Yang Q, Jankowsky E. The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases. Nat Struct Mol Biol 2006; 13:981-6. [PMID: 17072313 DOI: 10.1038/nsmb1165] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 10/04/2006] [Indexed: 11/08/2022]
Abstract
Helicases unwind RNA or DNA duplexes and displace proteins from nucleic acids in an ATP-dependent fashion. To unwind duplexes, helicases typically load onto one of the two nucleic acid strands, usually at a single-stranded region, and then translocate on this strand in a unidirectional fashion, thereby displacing the complementary DNA or RNA. Here we show that the DEAD-box RNA helicase Ded1 unwinds duplexes in a different manner. Ded1 uses the single-stranded region to gain access to the duplex. Strand separation is directly initiated from the duplex region and no covalent connection between the single strand and the duplex region is required. This new type of helicase activity explains observations with other DEAD-box proteins and may be the prototype for duplex-unwinding reactions in RNA metabolism.
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Affiliation(s)
- Quansheng Yang
- Department of Biochemistry and Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, USA
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316
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Welded on the spot. Nat Rev Mol Cell Biol 2006. [DOI: 10.1038/nrm2033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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