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Gładysz M, Andrałojć W, Czapik T, Gdaniec Z, Kierzek R. Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA. Sci Rep 2019; 9:4385. [PMID: 30867505 PMCID: PMC6416399 DOI: 10.1038/s41598-019-40715-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/21/2019] [Indexed: 12/21/2022] Open
Abstract
Thionucleotides, especially 4-thiouridine and 6-thioguanosine, are photosensitive molecules that photocrosslink to both proteins and nucleic acids, and this feature is a major reason for their application in various investigations. To get insight into the thermodynamic and structural contributions of 6-thioguanosine to the properties of RNA duplexes a systematic study was performed. In a series of RNA duplexes, selected guanosine residues located in G-C base pairs, mismatches (G-G, G-U, and G-A), or 5' and 3'-dangling ends were replaced with 6-thioguanosine. Generally, the presence of 6-thioguanosine diminishes the thermodynamic stability of RNA duplexes. This effect depends on its position within duplexes and the sequence of adjacent base pairs. However, when placed at a dangling end a 6-thioguanosine residue actually exerts a weak stabilizing effect. Furthermore, the structural effect of 6-thioguanosine substitution appears to be minimal based on NMR and Circular Dichroism (CD) data.
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Affiliation(s)
- Michał Gładysz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Tomasz Czapik
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland.
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Vušurović J, Schneeberger E, Breuker K. Interactions of Protonated Guanidine and Guanidine Derivatives with Multiply Deprotonated RNA Probed by Electrospray Ionization and Collisionally Activated Dissociation. ChemistryOpen 2017; 6:739-750. [PMID: 29226062 PMCID: PMC5715244 DOI: 10.1002/open.201700143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/06/2017] [Indexed: 11/25/2022] Open
Abstract
Interactions of ribonucleic acid (RNA) with guanidine and guanidine derivatives are important features in RNA-protein and RNA-drug binding. Here we have investigated noncovalently bound complexes of an 8-nucleotide RNA and six different ligands, all of which have a guanidinium moiety, by using electrospray ionization (ESI) and collisionally activated dissociation (CAD) mass spectrometry (MS). The order of complex stability correlated almost linearly with the number of ligand atoms that can potentially be involved in hydrogen-bond or salt-bridge interactions with the RNA, but not with the proton affinity of the ligands. However, ligand dissociation of the complex ions in CAD was generally accompanied by proton transfer from ligand to RNA, which indicated conversion of salt-bridge into hydrogen-bond interactions. The relative stabilities and dissociation pathways of [RNA+m L-n H] n- complexes with different stoichiometries (m=1-5) and net charge (n= 2-5) revealed both specific and unspecific ligand binding to the RNA.
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Affiliation(s)
- Jovana Vušurović
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Eva‐Maria Schneeberger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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3
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Schneeberger E, Breuker K. Native Top-Down Mass Spectrometry of TAR RNA in Complexes with a Wild-Type tat Peptide for Binding Site Mapping. Angew Chem Int Ed Engl 2017; 56:1254-1258. [PMID: 28000363 PMCID: PMC5299493 DOI: 10.1002/anie.201610836] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Indexed: 12/18/2022]
Abstract
Ribonucleic acids (RNA) frequently associate with proteins in many biological processes to form more or less stable complex structures. The characterization of RNA-protein complex structures and binding interfaces by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, or strategies based on chemical crosslinking, however, can be quite challenging. Herein, we have explored the use of an alternative method, native top-down mass spectrometry (MS), for probing of complex stoichiometry and protein binding sites at the single-residue level of RNA. Our data show that the electrostatic interactions between HIV-1 TAR RNA and a peptide comprising the arginine-rich binding region of tat protein are sufficiently strong in the gas phase to survive phosphodiester backbone cleavage of RNA by collisionally activated dissociation (CAD), thus allowing its use for probing tat binding sites in TAR RNA by top-down MS. Moreover, the MS data reveal time-dependent 1:2 and 1:1 stoichiometries of the TAR-tat complexes and suggest structural rearrangements of TAR RNA induced by binding of tat peptide.
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Affiliation(s)
- Eva‐Maria Schneeberger
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80-826020InnsbruckAustria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80-826020InnsbruckAustria
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4
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Schneeberger E, Breuker K. Native Top‐Down Mass Spectrometry of TAR RNA in Complexes with a Wild‐Type tat Peptide for Binding Site Mapping. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Eva‐Maria Schneeberger
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) Universität Innsbruck Innrain 80-82 6020 Innsbruck Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) Universität Innsbruck Innrain 80-82 6020 Innsbruck Austria
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5
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Komodziński K, Lepczyńska J, Gdaniec Z, Bartolotti L, Delley B, Franzen S, Skalski B. Photochemistry of 6-amino-2-azido, 2-amino-6-azido and 2,6-diazido analogues of purine ribonucleosides in aqueous solutions. Photochem Photobiol Sci 2014; 13:563-73. [DOI: 10.1039/c3pp50385b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Prasanthkumar KP, Suresh CH, Aravindakumar CT. Dimer radical cation of 4-thiouracil: a pulse radiolysis and theoretical study. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- K. P. Prasanthkumar
- School of Chemical Sciences; Mahatma Gandhi University; Kottayam 686560 Kerala India
| | - Cherumuttathu H. Suresh
- National Institute for Interdisciplinary Science & Technology; Trivandrum 695019 Kerala India
| | - C. T. Aravindakumar
- School of Environmental Sciences; Mahatma Gandhi University; Kottayam 686560 Kerala India
- Inter University Instrumentation Center; Mahatma Gandhi University; Kottayam 686560 Kerala India
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Fedorova O, Pyle AM. A conserved element that stabilizes the group II intron active site. RNA (NEW YORK, N.Y.) 2008; 14:1048-56. [PMID: 18441048 PMCID: PMC2390790 DOI: 10.1261/rna.942308] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The internal loop at the base of domain 3 (D3) is one of the most conserved and catalytically important elements of a group II intron. However, the location and molecular nature of its tertiary interaction partners has remained unknown. By employing a combination of site-directed photo-cross-linking and nucleotide analog interference suppression (NAIS), we show that the domain 3 internal loop (D3IL) interacts with the epsilon-epsilon' duplex, which is an active-site element located near the 5'-splice site in D1. Our data also suggest that the D3IL may interact with the bulge of D5, which is a critical active site component. The results of this and other recent studies indicate that the D3IL participates in a complex network of tertiary interactions involving epsilon-epsilon', the bulge of D5 and J23, and that it helps to optimize active site architecture by supporting interactions among these catalytic motifs. Our results are consistent with the role of D3 as a catalytic effector that enhances intron reactivity through active site stabilization.
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Affiliation(s)
- Olga Fedorova
- Howard Hughes Medical Institute at Yale, Yale University, New Haven, Connecticut 06520, USA
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8
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Luo MJ, Reed R. Identification of RNA binding proteins by UV cross-linking. ACTA ACUST UNITED AC 2008; Chapter 27:Unit 27.2. [PMID: 18265329 DOI: 10.1002/0471142727.mb2702s63] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
One of the major focuses of modern biology is to understand the dynamics of RNA-protein interactions, including factors that interact with mRNA, rRNA, tRNA, snRNA, hnRNA, siRNA, and viral RNA. Identification the direct interactions between proteins and RNA has greatly advanced our knowledge about the function of RNA-protein machines. UV crosslinking is a straightforward and powerful tool in this endeavor.
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9
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Espel E, Teixé T, Reina M, Vilaró S, Parra JL, Buxadé M. Use of Western blotting filtration to detect UV-cross-linked protein: RNA complexes. Anal Biochem 2006; 353:138-40. [PMID: 16620744 DOI: 10.1016/j.ab.2005.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2005] [Revised: 11/11/2005] [Accepted: 11/17/2005] [Indexed: 10/25/2022]
Affiliation(s)
- Enric Espel
- Departament de Fisiologia, Facultat de Biologia, Universitat de Barcelona, Spain.
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10
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Gopalakrishna S, Gusti V, Nair S, Sahar S, Gaur RK. Template-dependent incorporation of 8-N3AMP into RNA with bacteriophage T7 RNA polymerase. RNA (NEW YORK, N.Y.) 2004; 10:1820-30. [PMID: 15388871 PMCID: PMC1370669 DOI: 10.1261/rna.5222504] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Accepted: 08/12/2004] [Indexed: 05/21/2023]
Abstract
UV-induced photochemical crosslinking is a powerful approach that can be used for the identification of specific interactions involving nucleic acid-protein and nucleic acid-nucleic acid complexes. 8-AzidoATP (8-N(3)ATP) is a photoaffinity-labeling agent which has been widely used to elucidate the ATP binding site of a variety of proteins. However, its true potential as a photoactivatable nucleotide analog could not be exploited due to the lack of 8-azidoadenosine phosphoramidite, a monomer used in the synthesis of RNA, and the inability of 8-N(3)ATP to serve as an efficient substrate for bacteriophage RNA polymerase. In this study, we explored the ability of SP6, T3, and T7 RNA polymerases and metal ion cofactors to catalyze the incorporation of 8-N(3)AMP into RNA. Whereas transcription buffer containing 2.0-2.5 mM Mn(2+) supports T7 RNA polymerase-mediated insertion of 8-N(3)AMP into RNA, a mixture of 2.5 mM Mn(2+) and 2.5 mM Mg(2+) further improves the yield of 8-N(3)AMP-containing transcript. In addition, both RNA transcription and reverse transcription proceed with high fidelity for the incorporation of 8-N(3)AMP and complementary residue, respectively. Finally, we show that a high-affinity MS2 coat protein binding sequence, in which adenosine residues were replaced by 8-azidoadenosine, crosslinks to the coat protein of the Escherichia coli phage MS2.
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Affiliation(s)
- Sailesh Gopalakrishna
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, 1450 E. Duarte Rd., Duarte, CA 91010, USA
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11
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Borukhov S, Laptenko O, Lee J. Escherichia coli transcript cleavage factors GreA and GreB: functions and mechanisms of action. Methods Enzymol 2002; 342:64-76. [PMID: 11586920 DOI: 10.1016/s0076-6879(01)42536-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- S Borukhov
- Department of Microbiology and Immunology, State University of New York Health Science Center, Brooklyn, New York 11203, USA
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12
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Liu ZR, Sargueil B, Smith CW. Methylene blue-mediated cross-linking of proteins to double-stranded RNA. Methods Enzymol 2001; 318:22-33. [PMID: 10889977 DOI: 10.1016/s0076-6879(00)18041-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- Z R Liu
- Department of Animal and Dairy Science, Auburn University, Alabama 36849-5415, USA
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13
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Costas C, Yuriev E, Meyer KL, Guion TS, Hanna MM. RNA-protein crosslinking to AMP residues at internal positions in RNA with a new photocrosslinking ATP analog. Nucleic Acids Res 2000; 28:1849-58. [PMID: 10756182 PMCID: PMC103291 DOI: 10.1093/nar/28.9.1849] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new photocrosslinking purine analog was synthesized and evaluated as a transcription substrate for Escherichia coli RNA polymerase. This analog, 8-[(4-azidophenacyl)thio]adenosine 5'-triphosphate (8-APAS-ATP) contains an aryl azide photocrosslinking group that is attached to the ATP base via a sulfur-linked arm on the 8 position of the purine ring. This position is not involved in the normal Watson-Crick base pairing needed for specific hybridization. Although 8-APAS-ATP could not replace ATP as a substrate for transcription initiation, once stable elongation complexes were formed, 8-APAS-AMP could be site-specifically incorporated into the RNA, and this transcript could be further elongated, placing the photoreactive analog at internal positions in the RNA. Irradiation of transcription elongation complexes in which the RNA contained the analog exclusively at the 3' end of an RNA 22mer, or a 23mer with the analog 1 nt from the 3' end, produced RNA crosslinks to the RNA polymerase subunits that form the RNA 3' end binding site (beta, beta'). Both 8-APAS-AMP and the related 8-azido-AMP were subjected to conformational modeling as nucleoside monophosphates and in DNA-RNA hybrids. Surprisingly, the lowest energy conformation for 8-APAS-AMP was found to be syn, while that of 8-azido-AMP was anti, suggesting that the conformational properties and transcription substrate properties of 8-azido-ATP should be re-evaluated. Although the azide and linker together are larger in 8-APAS-ATP than in 8-N(3)-ATP, the flexibility of the linker itself allows this analog to adopt several different energetically favorable conformations, making it a good substrate for the RNA polymerase.
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Affiliation(s)
- C Costas
- Designer Genes, Inc., 8281 East Evans Road, Suite 104, Scottsdale, AZ 85260, USA
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14
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Korshunova GA, Topin AN, Sumbatyan NV, Koroleva ON, Drutsa VL. Trifluoromethyldiazirine-Containing dUTP: Synthesis and Application in DNA/Protein Crosslinking. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908041657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Becker HF, Grosjean H, Fourrey JL. Chemical Synthesis of 4-Thiouridine-Containing Substrate Analogues of tRNA:Pseudouridine-55 Synthase: Photocross-Linking Studies. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/07328319808004327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Topin AN, Gritsenko OM, Brevnov MG, Gromova ES, Korshunova GA. Synthesis of a new Photo-Cross-Linking Nucleoside Analogue Containing an Aryl(Trifluoromethyl)Diazirine Group: Application forEcoRII andMvaI Restriction-Modification Enzymes. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/07328319808004229] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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True HL, Celander DW. Protein components contribute to active site architecture for eukaryotic ribonuclease P. J Biol Chem 1998; 273:7193-6. [PMID: 9516409 DOI: 10.1074/jbc.273.13.7193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, ribonuclease P (RNase P) requires both RNA and protein components for catalytic activity. The eukaryotic RNase P RNA, unlike its bacterial counterparts, does not possess intrinsic catalytic activity in the absence of holoenzyme protein components. We have used a sensitive photoreactive cross-linking assay to explore the substrate-binding environment for different eukaryotic RNase P holoenzymes. Protein components from the Tetrahymena thermophila and human RNase P holoenzymes form specific products in photoreactions containing [4-thio]-uridine-labeled pre-tRNAGln. The HeLa RNase P RNA in neither the presence nor the absence of holoenzyme protein components formed cross-link products to the pre-tRNAGln probe. Parallel photo-cross-linking experiments with the Escherichia coli RNase P holoenzyme revealed that only the bacterial RNase P RNA forms specific substrate photoadducts. A protein-rich active site for the eukaryotic RNase P represents one unique feature that distinguishes holoenzyme organization between bacteria and eukaryotes.
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Affiliation(s)
- H L True
- Department of Microbiology, University of Illinois at Urbana-Champaign, Chemical and Life Sciences Laboratory, Urbana, Illinois 61801, USA
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18
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Favre A, Saintomé C, Fourrey JL, Clivio P, Laugâa P. Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1998; 42:109-24. [PMID: 9540218 DOI: 10.1016/s1011-1344(97)00116-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In the past few years thionucleobases have been extensively used as intrinsic photolabels to probe the structure in solution of folded RNA molecules and to identify contacts within nucleic acids and/or between nucleic acids and proteins, in complex nucleoprotein assemblies. These thio residues such as 4-thiouracil found in E. coli tRNA and its non-natural congeners 4-thiothymine, 6-thioguanine and 6-mercaptopurine absorb light at wavelengths longer than 320 nm and, thus, can be selectively photoactivated. Synthetic or enzymatic procedures have been established, allowing the random or site-specific incorporation of thionucleotide(s) within a RNA (DNA) chain which, in most cases, retains unaltered structural and biological properties. Owing to the high photoreactivity of their triplet state (intersystem yield close to unity), 4-thiouracil and 4-thiothymine derivatives exhibit a high photocrosslinking ability towards pyrimidines (particularly thymine) but also purines. From the nature of the photoproducts obtained in base or nucleotide mixtures and in dinucleotides, the main photochemical pathway was identified as a (2 + 2) photoaddition of the excited C-S bond onto the 5, 6 double bond of pyrimidines yielding thietane intermediates whose structure could be characterized. Depending on the mutual orientation of these bonds in the thietanes, their subsequent dark rearrangement yielded, respectively, either the 5-4 or 6-4 bipyrimidine photoadduct. A similar mechanism appears to be involved in the formation of the unique photoadduct formed between 4-thiothymidine and adenosine. The higher reactivity of thymine derived acceptors can be explained by an additional pathway which involves hydrogen abstraction from the thymine methyl group, followed by radical recombination, leading to methylene linked bipyrimidines. The high photocrosslinking potential of thionucleosides inserted in nucleic acid chains has been used to probe RNA-RNA contacts within the ribosome permitting, in particular, the elucidation of the path of mRNA throughout the small ribosomal subunit. Functional interactions between the mRNA spliced sites and U RNAs could be detected within the spliceosome. Analysis of the photocrosslinks obtained within small endonucleolytic ribozymes in solution led to a tertiary folded pseudo-knot structure for the HDV ribozyme and allowed the construction of a Y form of a hammerhead ribozyme, which revealed to be in close agreement with the structure observed in crystals. Thionucleosides incorporated in nucleic acids crosslink efficiently amino-acid residues of proteins in contact with them. Despite the fact that little is known about the nature of the photoadducts formed, this approach has been extensively used to identify protein components interacting at a defined nucleic acid site and applied to various systems (replisome, spliceosome, transcription complexes and ribosomes).
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Affiliation(s)
- A Favre
- Institut Jacques Monod, CNRS-Université Paris VII, France
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19
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Stefanovic B, Hellerbrand C, Holcik M, Briendl M, Aliebhaber S, Brenner DA. Posttranscriptional regulation of collagen alpha1(I) mRNA in hepatic stellate cells. Mol Cell Biol 1997; 17:5201-9. [PMID: 9271398 PMCID: PMC232371 DOI: 10.1128/mcb.17.9.5201] [Citation(s) in RCA: 175] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The hepatic stellate cell (HSC) is the primary cell responsible for the dramatic increase in the synthesis of type I collagen in the cirrhotic liver. Quiescent HSCs contain a low level of collagen alpha1(I) mRNA, while activated HSCs contain about 60- to 70-fold more of this mRNA. The transcription rate of the collagen alpha1(I) gene is only two fold higher in activated HSCs than in quiescent HSCs. In assays using actinomycin D or 5,6-dichlorobenzimidazole riboside collagen alpha1(I) mRNA has estimated half-lives of 1.5 h in quiescent HSCs and 24 h in activated HSCs. Thus, this 16-fold change in mRNA stability is primarily responsible for the increase in collagen alpha1(I) mRNA steady-state level in activated HSCs. We have identified a novel RNA-protein interaction targeted to the C-rich sequence in the collagen alpha1(I) mRNA 3' untranslated region (UTR). This sequence is localized 24 nucleotides 3' to the stop codon. In transient transfection experiments, mutation of this sequence diminished accumulation of an mRNA transcribed from a collagen alpha1(I) minigene and in stable transfections decreased the half-life of collagen alpha1(I) minigene mRNA. Binding to the collagen alpha1(I) 3' UTR is present in cytoplasmic extracts of activated but not quiescent HSCs. It contains as a subunit alphaCP, which is also found in the complex involved in stabilization of alpha-globin mRNA. The auxiliary factors necessary to promote binding of alphaCP to the collagen 3' UTR are distinct from the factors necessary for binding to the alpha-globin sequence. Since alphaCP is expressed in both quiescent and activated HSCs, these auxiliary factors are responsible for the differentially expressed RNA-protein interaction at the collagen alpha1(I) mRNA 3' UTR.
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Affiliation(s)
- B Stefanovic
- Department of Medicine, The University of North Carolina, Chapel Hill 27599-7080, USA
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20
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Hanna MM. Photochemical cross-linking analysis of protein-nucleic acid interactions in Escherichia coli transcription complexes from lambda PR' promoter. Methods Enzymol 1996; 274:403-18. [PMID: 8902821 DOI: 10.1016/s0076-6879(96)74033-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- M M Hanna
- Department of Chemistry, University of Oklahoma, Norman 73109, USA
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Zenkova M, Ehresmann C, Caillet J, Springer M, Karpova G, Ehresmann B, Romby P. A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:726-35. [PMID: 7544283 DOI: 10.1111/j.1432-1033.1995.0726d.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a methodology which allows the introduction of a photoactivatable azido group at specific internal positions of any RNA in order to identify the neighboring elements of an interacting protein. The first step involves site-directed modification of the target RNA with an antisense oligodeoxyribonucleotide bearing, at its 3' or 5' phosphate, a 4-[-N-(2-chloroethyl)-N-methylamino]benzylmethylamino group. Position N7 of a guanine residue located in the close vicinity of the hybrid is the main target for alkylation. The antisense oligodeoxyribonucleotide is then removed by acidic pH treatment and a photoreactive reagent (2,4-dinitro-5-fluorophenylazide) is condensed to the modified nucleotide. This method was used to induce specific cross-links between Escherichia coli threonyl-tRNA synthetase and the leader region of threonyl-tRNA synthetase mRNA, which is involved in translational feedback regulation. Control experiments revealed that the modification affects neither the structure of the mRNA nor the interaction with the enzyme. More than 50% of the modified mRNA complexed with threonyl-tRNA synthetase can be cross-linked to the enzyme, depending on the nucleotide modified.
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Affiliation(s)
- M Zenkova
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences
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23
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Liu K, Hanna MM. NusA interferes with interactions between the nascent RNA and the C-terminal domain of the alpha subunit of RNA polymerase in Escherichia coli transcription complexes. Proc Natl Acad Sci U S A 1995; 92:5012-6. [PMID: 7539140 PMCID: PMC41838 DOI: 10.1073/pnas.92.11.5012] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The effects of NusA on the RNA polymerase contacts made by nucleotides at internal positions in the nascent RNA in Escherichia coli transcription complexes were analyzed by using the photocrosslinking nucleotide analog 5-[(4-azidophenacyl) thio]-UMP. It was placed at nucleotides between +6 and +15 in RNA transcribed from the phage lambda PR' promoter. Crosslinks of analog in these positions in RNAs which contained either 15, 28, 29, or 49 nt were examined. Contacts between the nascent RNA and proteins in the transcription complex were analyzed as the RNA was elongated, by placing the crosslinker nearest the 5' end of the RNA 10, 23, 24, or 44 nt away from the 3' end. The beta or beta' subunit of polymerase, and NusA when added, were contacted by RNA from 15 to 49 nt long. When the upstream crosslinker was 24 nt from the 3" end of the RNA (29-nt RNA), alpha was also contacted in the absence of NusA. The addition of NusA prevented RNA crosslinking to alpha. When the crosslinker was 44 nt from the 3' end (49-nt RNA), alpha crosslinks were still observed, but crosslinks to beta or beta' and NusA were greatly diminished. RNA crosslinking to alpha, and loss of this crosslink when NusA was added, was observed in the presence of NusB, NusE, and NusG and when transcription was carried out in the presence of an E. coli S100 cell extract. Peptide mapping localized the RNA interactions to the C-terminal domain of alpha.
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Affiliation(s)
- K Liu
- Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
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24
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He B, Riggs DL, Hanna MM. Preparation of probe-modified RNA with 5-mercapto-UTP for analysis of protein-RNA interactions. Nucleic Acids Res 1995; 23:1231-8. [PMID: 7537876 PMCID: PMC306836 DOI: 10.1093/nar/23.7.1231] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We report a modified synthesis for 5-mercapto-UTP (5-SH-UTP) and its use for analysis of protein-RNA interactions utilizing Escherichia coli and T7 RNA polymerases and yeast RNA polymerases I and III. 5-SH-UTP did not affect transcriptional pausing, Rho-independent termination or recognition of the E. coli transcription complex by NusA. RNA containing 5-SH-UMP did not crosslink to polymerase when irradiation was 302 or 337 nm. Transcription complexes containing RNA substituted with 5-SH-UMP were post-transcriptionally modified to attach a photocross-linking group to thiol-tagged nucleotides in the RNA on the surface of the polymerase of free in solution. The pKa for 5-SH-UTP was determined to be 5.6, so modification of the thiol groups in the RNA with p-azidophenacyl bromide could be carried out at pH 7. Addition of the transcription termination factor Rho, a RNA binding protein, to E. coli transcription complexes resulted in RNA crosslinking to Rho and to the beta and beta' subunits of polymerase. Using 5-SH-UTP, one can distinguish RNA binding domains on the surface of RNA polymerases or other RNA binding proteins from those buried within the protein.
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Affiliation(s)
- B He
- Department of Botany/Microbiology, University of Oklahoma, Norman 73019, USA
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Abstract
The choice of a 3' splice site in Saccharomyces cerevisiae introns involves recognition of a uridine-rich tract upstream of the AG dinucleotide splice junction. By isolating mutants that eliminate the normal preference for uridine-containing 3' splice sites in a cis-competition, we identified a mutation that is an allele of PRP8, prp8-101. This was unexpected because previous analysis has demonstrated that the U5 snRNP protein encoded by PRP8 is required for spliceosome assembly prior to the first catalytic step of splicing. In contrast, the uridine recognition defect caused by the prp8-101 mutation selectively inhibits the second catalytic step of splicing. This defect is seen not only in 3' splice site cis-competitions but also in the splicing of an unusual intron in the TUB3 gene and in the ACT1 intron when utilization of its 3' splice site is rate limiting for splicing. Consistent with a direct role in 3' splice site selection, Prp8 can be cross-linked to the 3' splice site during the splicing reaction. These data demonstrate a novel function for Prp8 in 3' splice site recognition and utilization.
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Affiliation(s)
- J G Umen
- Department of Biochemistry and Biophysics, University of California at San Francisco 94143, USA
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27
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Bartholomew B, Braun B, Kassavetis G, Geiduschek E. Probing close DNA contacts of RNA polymerase III transcription complexes with the photoactive nucleoside 4-thiodeoxythymidine. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32421-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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28
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Affiliation(s)
- E J Sontheimer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, Howard Hughes Medical Institute, New Haven, CT 06536-0812
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29
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Zhang Y, Hanna MM. NusA changes the conformation of Escherichia coli RNA polymerase at the binding site for the 3' end of the nascent RNA. J Bacteriol 1994; 176:1787-9. [PMID: 7510675 PMCID: PMC205271 DOI: 10.1128/jb.176.6.1787-1789.1994] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A conformational change in Escherichia coli RNA polymerase induced by NusA was detected by utilizing photocrosslinking. A change in the binding site for the 3' end of the RNA occurred, and NusA increased interactions of the RNA with the beta subunit of the polymerase. NusA was not contacted by the 3' end of the RNA.
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Affiliation(s)
- Y Zhang
- Department of Botany-Microbiology, University of Oklahoma, Norman 73019
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30
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Saintomé C, Clivio P, Fourrey JL, Woisard A, Favre A. Development of new nucleic acid photoaffinity probes: Synthesis of 4-thiothymine labelled nucleoside analogues. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)75986-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Sontheimer EJ, Steitz JA. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 1993; 262:1989-96. [PMID: 8266094 DOI: 10.1126/science.8266094] [Citation(s) in RCA: 280] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Five small nuclear RNAs (U1, U2, U4, U5, and U6) participate in precursor messenger RNA (pre-mRNA) splicing. To probe their interactions within the active center of the mammalian spliceosome, substrates containing a single photoactivatable 4-thiouridine residue adjacent to either splice site were synthesized, and crosslinks were induced during the course of in vitro splicing. An invariant loop sequence in U5 small nuclear RNA contacts exon 1 before and after the first step of splicing because a crosslink between U5 and the last residue of exon 1 appeared in the pre-mRNA and then in the cutoff exon 1 intermediate. Both of these crosslinked species could undergo subsequent splicing, indicating that the crosslinks reflect a functional interaction that is maintained through both reaction steps. The same U5 loop aligns the two exons for ligation since the first residue of exon 2 also became crosslinked to U5 in the lariat intermediate. An invariant sequence in U6 RNA became crosslinked to the conserved second position of the intron within both the lariat intermediate and the lariat intron product. On the basis of these results, several conformational arrangements of small nuclear RNAs within the spliceosomal active center can be distinguished, and additional mechanistic parallels between the spliceosome and self-splicing introns can be drawn.
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Affiliation(s)
- E J Sontheimer
- Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, CT 06536-0812
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32
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Eichler DC, Liberatore JA, Shumard CM. Selection of a preribosomal RNA processing site by a nucleolar endoribonuclease involves formation of a stable complex. Nucleic Acids Res 1993; 21:5775-81. [PMID: 8284228 PMCID: PMC310548 DOI: 10.1093/nar/21.24.5775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A nucleolar endoribonuclease from mouse Ehrlich ascites tumor cells, that has been implicated in the endonucleolytic cleavage of mouse precursor ribosomal RNA, specifically and stably binds an in vitro-derived rRNA transcript containing the +650 early processing site. The specificity of binding was demonstrated by mobility shift analysis, glycerol gradient velocity sedimentation analysis, and UV-crosslinking studies. Binding did not require Mg2+ and therefore was not dependent on cleavage; however, binding was dependent on the presence of the early +650 processing site since a pre-rRNA transcript with the +650 processing site deleted failed to compete in binding. A small nucleolar RNA component was not required for the formation of this stable complex or for the specific cleavage of a processing competent pre-rRNA transcript. UV crosslinking studies using 32P-labeled 5-azidouridine-substituted pre-rRNA with bound nucleolar endoribonuclease identified three closely sized polypeptides of approximately 50, approximately 48, and approximately 45 kDa, respectively, that specifically crosslinked to the processing competent rRNA transcript. These three polypeptides species were identified following ribonuclease digestion and electrophoresis on a SDS-polyacrylamide gel. An identical pattern of labeled polypeptides was also identified from gel mobility shift analysis where the specifically shifted material was U.V. crosslinked. The largest of these polypeptides corresponded to the estimated size of the nucleolar endoribonuclease, while the lower molecular weight species may represent partially proteolyzed enzyme. Overall, these results suggest that the unique specificity of the nucleolar endoribonuclease may, in part, be attributed to the formation of a stable complex at the +650 processing site for mouse preribosomal RNA, and that formation of this unique stable complex affords a means to specifically label the limited amount of available partially purified enzyme for sequence analysis.
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Affiliation(s)
- D C Eichler
- Department of Biochemistry and Molecular Biology, University of South Florida, College of Medicine, Tampa 33612-4799
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Hanna MM, Zhang Y, Reidling JC, Thomas MJ, Jou J. Synthesis and characterization of a new photocrosslinking CTP analog and its use in photoaffinity labeling E. coli and T7 RNA polymerases. Nucleic Acids Res 1993; 21:2073-9. [PMID: 7684833 PMCID: PMC309467 DOI: 10.1093/nar/21.9.2073] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A new photocrosslinking CTP analog that functioned as a substrate during transcription was synthesized and used to photoaffinity label E. coli and bacteriophage T7 RNA polymerases. This analog, 5-((4-azidophenacyl)thio) cytidine-5'-triphosphate (5-APAS-CTP) contains an aryl azide group approximately 10 A from the nucleotide base and specifically replaced CTP during synthesis of RNA by both polymerases. Analog was placed at the 3' end or internally within RNA. Both polymerases inefficiently incorporated two 5-APAS-CMP molecules sequentially, as was found for the related 5-APAS-UMP. Analog was placed at the 3' end of RNA in transcription complexes paused at the site of Q-modification of E. coli RNA polymerase, downstream of the lambda PR' promoter (+16), a pause that requires specific DNA sequences but no apparent RNA hairpin. Crosslinking was examined in the presence and absence of the NusA protein, which enhances the transcriptional pause at this site and is required for Q modification of the polymerase. Crosslinking of the 3' end of the RNA to NusA was not observed, consistent with our earlier results involving a NusA-enhanced pause site downstream from an RNA hairpin.
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Affiliation(s)
- M M Hanna
- Department of Botany and Microbiology, University of Oklahoma, Norman 73019
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Cremer G, Kalbas M, Fasold H, Prochnow D. Covalent attachment of ribonucleic acids to proteins. JOURNAL OF PROTEIN CHEMISTRY 1992; 11:553-60. [PMID: 1280439 DOI: 10.1007/bf01025033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As a prerequisite for the synthesis of affinity labels, we describe methods to couple histones to ribonucleic acids. For the synthesis of these covalent hybrid molecules, we used a population of histones H1, H2A, H2B, H3, and H4 from calf thymus and polyadenylic acid with an average chain length of up to 260-280 bases, representing the size of poly(A)-tails from mature mRNAs. Three methods were investigated. (a) Poly(A) containing an 8-N3-A residue was cross-linked to histones by ultraviolet irradiation. (b) The 3'-end of the polynucleotide was connected to a mononucleotide containing an aliphatic amino group, and the resulting poly(A)-derivative was coupled to histones via derivation with a bromoacetyl group. (c) The 3'-end of the polynucleotide was oxidized with sodium periodate and bound covalently to an amino group of the polypeptide. To demonstrate the RNA content of the hybrid molecule, the poly(A) was removed with RNase T2.
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Affiliation(s)
- G Cremer
- Institut für Biochemie, Johann Wolfgang Goethe Universität, Frankfurt, Germany
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35
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Bradley DH, Hanna MM. Synthesis and utility of 5-Thiocyanato deoxyuridine and uridine phosphoramidites as masked synthons. Tetrahedron Lett 1992. [DOI: 10.1016/s0040-4039(00)60938-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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37
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Khanna NC, Lakhani S, Tewari KK. Photoaffinity labelling of the pea chloroplast transcriptional complex by nascent RNA in vitro. Nucleic Acids Res 1991; 19:4849-55. [PMID: 1717936 PMCID: PMC328778 DOI: 10.1093/nar/19.18.4849] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have used photoaffinity labelling to examine the chloroplast RNA polymerase components which come into contact with nascent transcripts during the in vitro transcription of plastid DNA. The transcripts were synthesized in the presence of a photoactive analogue (4-thio UTP) and alpha-32P-ATP, using enriched pea chloroplast RNA polymerase preparation and a recombinant plasmid containing the plastid 16S rRNA promoter. Brief irradiation of the transcriptional complex crosslinked the photoactive nascent RNA to proximal proteins. Labelling of the transcriptional complex was dependent on 4-thio UTP and template DNA. Two polypeptides of 51 and 54 kDa were consistently crosslinked to the nascent transcripts; about 60% of the total radioactivity of the crosslinked RNA was associated with these polypeptides. In some experiments, two additional polypeptides of 38 and 75 kDa were also found to be associated with about 13% and 17% of the total crosslinked RNA radioactivity, respectively. The UV-crosslinked transcriptional complexes were stable to either DNase or S1 nuclease hydrolysis but partially sensitive to RNase T1. Insensitivity of the complex to hydrolysis with RNase H suggested that the nascent transcripts were not crosslinked to the template. The complexes could also be hydrolysed by proteinase K and thermolysin. No crosslinkage was observed when labelled RNA molecules containing 4-thio UMP residues were added after synthesis to the polymerase preparation. This suggested that the method identified only those polypeptides which came into close contact with the transcript during its synthesis. Antibodies raised against the RNA-protein complex confirmed the presence of the polypeptides in the chloroplast RNA polymerase preparation on Western blots. Preincubation of these antibodies with the chloroplast RNA polymerase inhibited plastid DNA transcription. These data showed that the transcript-binding polypeptides were functional components of the chloroplast transcriptional complex.
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Affiliation(s)
- N C Khanna
- International Centre for Genetic Engineering and Biotechnology, Shaheedjit Singh Marg, New Delhi, India
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38
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Gott JM, Willis MC, Koch TH, Uhlenbeck OC. A specific, UV-induced RNA-protein cross-link using 5-bromouridine-substituted RNA. Biochemistry 1991; 30:6290-5. [PMID: 1711897 DOI: 10.1021/bi00239a030] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The well-characterized RNA binding site of the bacteriophage R17 coat protein has been used to investigate the cross-linking of protein to 5-bromouridine (BrU)-substituted RNA using medium-wavelength UV light. We have demonstrated a specific RNA-protein cross-link and identified the site on the RNA of protein attachment. Formation of the covalent complex is dependent upon the presence of BrU at position -5 of the RNA and specific binding of the RNA by coat protein. The amount of cross-linking increases with time and depends on the light source and conditions used. Irradiations using a broad-spectrum UV transilluminator (peak at 312 nm) or monochromatic XeCl excimer laser (308 nm) gave levels of cross-linking exceeding 20 and 50%, respectively. The quantum yield of photo-cross-linking, determined with 308-nm excitation, was 0.003. While little strand breakage or debromination of the RNA occurred, significant protein photodamage was observed.
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Affiliation(s)
- J M Gott
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215
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39
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Dissinger S, Hanna MM. RNA-protein interactions in a Nus A-containing Escherichia coli transcription complex paused at an RNA hairpin. J Mol Biol 1991; 219:11-25. [PMID: 1708833 DOI: 10.1016/0022-2836(91)90853-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have isolated Escherichia coli transcription complexes, paused in the presence and absence of Nus A, which contain RNA substituted at every UMP residue with a photocrosslinking nucleotide analog. The pause site is immediately downstream from an RNA stem-loop structure, and although pausing occurs in the absence of Nus A, it is substantially enhanced in the presence of Nus A. We have analyzed the secondary structure of this RNA and show that the analog does not interfere with the formation of the normal stem-loop structures. Additionally, the analog substrate does not alter transcriptional pausing, in the presence or absence of Nus A, indicating that Nus A recognition of the transcription complex is not affected by the presence of the crosslinking groups in the RNA. Ribonuclease digestion of the RNA in paused complexes identifies two accessible regions, two nucleotides in the loop and one near the base of the upstream side of the stem-loop. Cleavage at one loop nucleotide is enhanced by Nus A, while the nucleotide near the base of the stem-loop is partially protected. Upon irradiation of the transcription complex, Nus A is not photoaffinity labeled by the RNA, even at a high molar ration to RNA polymerase (250:1). Both the beta and beta' subunits are labeled, however, indicating that the putative stem-loop binding domain on the core polymerase involves both subunits. Because the nucleotide protected from ribonuclease by Nus A is very near two analogs, yet Nus A is not crosslinked to the RNA, it is unlikely that Nus A could be protecting this position through direct contact. Furthermore, analog is substituted at positions in both the loop and at several positions in the stem, and again, no crosslinking to Nus A is observed. We conclude that enhancement of pausing by Nus A probably does not require direct interaction with the bases in the RNA stem-loop.
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Affiliation(s)
- S Dissinger
- Department of Biological Chemistry, California College of Medicine, University of California, Irvine 92717
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40
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Active site labeling of Escherichia coli transcription elongation complexes with 5-[4-azidophenacyl)thio)uridine 5'-triphosphate. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39165-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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