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Martinez-Zapien D, Legrand P, McEwen AG, Proux F, Cragnolini T, Pasquali S, Dock-Bregeon AC. The crystal structure of the 5΄ functional domain of the transcription riboregulator 7SK. Nucleic Acids Res 2017; 45:3568-3579. [PMID: 28082395 PMCID: PMC5389472 DOI: 10.1093/nar/gkw1351] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/06/2017] [Indexed: 12/22/2022] Open
Abstract
In vertebrates, the 7SK RNA forms the scaffold of a complex, which regulates transcription pausing of RNA-polymerase II. By binding to the HEXIM protein, the complex comprising proteins LARP7 and MePCE captures the positive transcription elongation factor P-TEFb and prevents phosphorylation of pausing factors. The HEXIM-binding site embedded in the 5΄-hairpin of 7SK (HP1) encompasses a short signature sequence, a GAUC repeat framed by single-stranded uridines. The present crystal structure of HP1 shows a remarkably straight helical stack involving several unexpected triples formed at a central region. Surprisingly, two uridines of the signature sequence make triple interactions in the major groove of the (GAUC)2. The third uridine is turned outwards or inward, wedging between the other uridines, thus filling the major groove. A molecular dynamics simulation indicates that these two conformations of the signature sequence represent stable alternatives. Analyses of the interaction with the HEXIM protein confirm the importance of the triple interactions at the signature sequence. Altogether, the present structural analysis of 7SK HP1 highlights an original mechanism of swapping bases, which could represent a possible ‘7SK signature’ and provides new insight into the functional importance of the plasticity of RNA.
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Affiliation(s)
- Denise Martinez-Zapien
- Biotechnologie et signalisation cellulaire, CNRS UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg, F-67412 Illkirch, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, F-91190 Gif-sur-Yvette, France
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Florence Proux
- Department of functional genomics, CNRS UMR 8197, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France.,Department of functional genomics, INSERM-U1024, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France
| | | | - Samuela Pasquali
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR 9080, Université Sorbonne Paris Cite, Paris Diderot, 75005 Paris, France
| | - Anne-Catherine Dock-Bregeon
- Department of functional genomics, CNRS UMR 8197, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France.,Department of functional genomics, INSERM-U1024, Institut de Biologie de l΄Ecole Normale Supérieure F-75005 Paris, France.,Sorbonne Universités UPMC, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France.,CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
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Schroeder SJ. Stack Locally and Act Globally: A Few Nucleotides Make All the Difference in Enterovirus 71 IRES Binding hnRNAP A1 and Infectious Phenotypes: Commentary on "HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation". J Mol Biol 2017; 429:2859-2862. [PMID: 28802871 DOI: 10.1016/j.jmb.2017.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Susan J Schroeder
- Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA.
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3
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Gu X, Park SY, Tonelli M, Cornilescu G, Xia T, Zhong D, Schroeder SJ. NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions. J Phys Chem Lett 2016; 7:3841-3846. [PMID: 27631837 PMCID: PMC5762182 DOI: 10.1021/acs.jpclett.6b01465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Metal ions are critical for RNA structure and enzymatic activity. We present the structure of an asymmetric RNA loop that binds metal ions and has an essential function in a bacteriophage packaging motor. Prohead RNA is a noncoding RNA that is required for genome packaging activity in phi29-like bacteriophage. The loops in GA1 and phi29 bacteriophage share a conserved adenine that forms a base triple, although the structural context for the base triple differs. NMR relaxation studies and femtosecond time-resolved fluorescence spectroscopy reveal the dynamic behavior of the loop in the metal ion bound and unbound forms. The mechanism of metal ion binding appears to be an induced conformational change between two dynamic ensembles rather than a conformational capture mechanism. These results provide experimental benchmarks for computational models of RNA-metal ion interactions.
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Affiliation(s)
- Xiaobo Gu
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sun-Young Park
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Marco Tonelli
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Tianbing Xia
- Department of Molecular and Cell Biology, University of Texas, Dallas, Texas 75080, United States
| | - Dongping Zhong
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Susan J. Schroeder
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Corresponding Author.
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4
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Eichhorn CD, Chug R, Feigon J. hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA. Nucleic Acids Res 2016; 44:9977-9989. [PMID: 27679474 PMCID: PMC5175362 DOI: 10.1093/nar/gkw833] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/21/2022] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal La module binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear. We report the solution NMR structure of the hLARP7 CTD and show that this domain contains an xRRM, a class of atypical RRM first identified in the Tetrahymena thermophila telomerase LARP7 protein p65. The xRRM binds the 3' end of 7SK RNA at the top of stem-loop 4 (SL4) and interacts with both unpaired and base-paired nucleotides. This study confirms that the xRRM is general to the LARP7 family of proteins and defines the binding site for hLARP7 on the 7SK RNA, providing insight into function.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Rahul Chug
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
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5
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Krawczyk K, Sim AYL, Knapp B, Deane CM, Minary P. Tertiary Element Interaction in HIV-1 TAR. J Chem Inf Model 2016; 56:1746-54. [DOI: 10.1021/acs.jcim.6b00152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Konrad Krawczyk
- Department of Computer Science, Oxford University, Parks Road, OX1 3QD Oxford, U.K
| | - Adelene Y. L. Sim
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, Singapore 138671
| | - Bernhard Knapp
- Department of Statistics, Oxford University, St Giles, OX1 3LB Oxford, U.K
| | - Charlotte M. Deane
- Department of Statistics, Oxford University, St Giles, OX1 3LB Oxford, U.K
| | - Peter Minary
- Department of Computer Science, Oxford University, Parks Road, OX1 3QD Oxford, U.K
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6
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Scholz B, Kowarz E, Rössler T, Ahmad K, Steinhilber D, Marschalek R. AF4 and AF4N protein complexes: recruitment of P-TEFb kinase, their interactome and potential functions. AMERICAN JOURNAL OF BLOOD RESEARCH 2015; 5:10-24. [PMID: 26171280 PMCID: PMC4497493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 02/16/2015] [Indexed: 06/04/2023]
Abstract
AF4/AFF1 and AF5/AFF4 are the molecular backbone to assemble "super-elongation complexes" (SECs) that have two main functions: (1) control of transcriptional elongation by recruiting the positive transcription elongation factor b (P-TEFb = CyclinT1/CDK9) that is usually stored in inhibitory 7SK RNPs; (2) binding of different histone methyltransferases, like DOT1L, NSD1 and CARM1. This way, transcribed genes obtain specific histone signatures (e.g. H3K79me2/3, H3K36me2) to generate a transcriptional memory system. Here we addressed several questions: how is P-TEFb recruited into SEC, how is the AF4 interactome composed, and what is the function of the naturally occuring AF4N protein variant which exhibits only the first 360 amino acids of the AF4 full-length protein. Noteworthy, shorter protein variants are a specific feature of all AFF protein family members. Here, we demonstrate that full-length AF4 and AF4N are both catalyzing the transition of P-TEFb from 7SK RNP to their N-terminal domain. We have also mapped the protein-protein interaction network within both complexes. In addition, we have first evidence that the AF4N protein also recruits TFIIH and the tumor suppressor MEN1. This indicate that AF4N may have additional functions in transcriptional initiation and in MEN1-dependend transcriptional processes.
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Affiliation(s)
- Bastian Scholz
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Eric Kowarz
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Tanja Rössler
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Khalil Ahmad
- Institute of Pharmaceutical Chemistry, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
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7
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Lu J, Nguyen L, Zhao L, Xia T, Qi X. A Cyclic Mimic of HIV Tat Differentiates Similar TAR RNAs on the Basis of Distinct Dynamic Behaviors. Biochemistry 2015; 54:3687-93. [DOI: 10.1021/acs.biochem.5b00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jia Lu
- Department
of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Larry Nguyen
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Liang Zhao
- Department
of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Tianbing Xia
- Department
of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Xin Qi
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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