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Melrose J. Separation and Identification of Native Proteoglycans by Composite Agarose-Polyacrylamide Gel Electrophoresis and Immunoblotting. Methods Mol Biol 2023; 2619:187-209. [PMID: 36662471 DOI: 10.1007/978-1-0716-2946-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Composite agarose-polyacrylamide gel electrophoresis (CAPAGE) in gels of 1.2% w/v polyacrylamide and 0.6% w/v agarose can be used to examine the heterogeneity of full-length native proteoglycan populations and their fragments in crude tissue extracts, and when used in conjunction with immunoblotting and specific antibodies to proteoglycan core protein and glycosaminoglycan, side chain epitopes can provide significant information on the level of proteoglycan polydispersity/heterogeneity and a number of proteoglycan populations present in tissue samples. This can be a technically difficult technique, but it reveals significant information on proteoglycans from small tissue samples not possible by any other separation methodology. Native full-length and proteoglycan fragments are examined in this technique something which cannot be done in the popular SDS-PAGE format unless the glycosaminoglycan side chains are first removed. Furthermore, since proteoglycans do not require renaturation from SDS-protein complexes, the proteoglycan populations separated by native electrophoresis are highly reactive with antibodies in immunoblotting procedures. Despite the massive sizes of proteoglycans, transfer conditions have been determined which provide close to quantitative transfer to nitrocellulose membranes without exceeding the binding capacity of such membranes, avoiding bleed-through of the transferred proteoglycans. Development of biotinylated hyaluronan and its application in an affinity blotting procedure has also yielded significant information on aggregatable proteoglycan populations separated by CAPAGE from a number of cartilages and vascular tissues in health and disease. While the CAPAGE system can be a technically demanding technique to master particularly in gel preparation, all other steps are straightforward, and the method yields invaluable information on proteoglycan populations extracted from connective tissues in health and disease that cannot be ascertained by any other technique. Further improvements in the detection of proteoglycan features with the development of novel bio-affinity probes or new antibody preparations are expected to further improve the utility of CAPAGE separation methodology.
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Affiliation(s)
- James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, Australia.
- Raymond Purves Bone and Joint Research Laboratories, Kolling Institute of Medical Research, Royal North Shore Hospital and The Faculty of Medicine and Health, The University of Sydney, St. Leonard's, NSW, Australia.
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2
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Martin JE, Le MT, Bhattarai N, Capdevila DA, Shen J, Winkler ME, Giedroc DP. A Mn-sensing riboswitch activates expression of a Mn2+/Ca2+ ATPase transporter in Streptococcus. Nucleic Acids Res 2020; 47:6885-6899. [PMID: 31165873 PMCID: PMC6649816 DOI: 10.1093/nar/gkz494] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/08/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022] Open
Abstract
Maintaining manganese (Mn) homeostasis is important for the virulence of numerous bacteria. In the human respiratory pathogen Streptococcus pneumoniae, the Mn-specific importer PsaBCA, exporter MntE, and transcriptional regulator PsaR establish Mn homeostasis. In other bacteria, Mn homeostasis is controlled by yybP-ykoY family riboswitches. Here, we characterize a yybP-ykoY family riboswitch upstream of the mgtA gene encoding a PII-type ATPase in S. pneumoniae, suggested previously to function in Ca2+ efflux. We show that the mgtA riboswitch aptamer domain adopts a canonical yybP-ykoY structure containing a three-way junction that is compacted in the presence of Ca2+ or Mn2+ at a physiological Mg2+ concentration. Although Ca2+ binds to the RNA aptamer with higher affinity than Mn2+, in vitro activation of transcription read-through of mgtA by Mn2+ is much greater than by Ca2+. Consistent with this result, mgtA mRNA and protein levels increase ≈5-fold during cellular Mn stress, but only in genetic backgrounds of S. pneumoniae and Bacillus subtilis that exhibit Mn2+ sensitivity, revealing that this riboswitch functions as a failsafe ‘on’ signal to prevent Mn2+ toxicity in the presence of high cellular Mn2+. In addition, our results suggest that the S. pneumoniae yybP-ykoY riboswitch functions to regulate Ca2+ efflux under these conditions.
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Affiliation(s)
- Julia E Martin
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - My T Le
- Department of Cell Biology, Faculty of Biological Sciences, Vietnam National University, Hanoi, Vietnam
| | - Nabin Bhattarai
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
| | | | - Jiangchuan Shen
- Department of Cellular and Molecular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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3
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Interaction of the tetracyclines with double-stranded RNAs of random base sequence: new perspectives on the target and mechanism of action. J Antibiot (Tokyo) 2016; 69:622-30. [PMID: 26786504 DOI: 10.1038/ja.2015.145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/02/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023]
Abstract
The 16S rRNA binding mechanism proposed for the antibacterial action of the tetracyclines does not explain their mechanism of action against non-bacterial pathogens. In addition, several contradictory base pairs have been proposed as their binding sites on the 16S rRNA. This study investigated the binding of minocycline and doxycycline to short double-stranded RNAs (dsRNAs) of random base sequences. These tetracyclines caused a dose-dependent decrease in the fluorescence intensities of 6-carboxyfluorescein (FAM)-labelled dsRNA and ethidium bromide (EtBr)-stained dsRNA, indicating that both drugs bind to dsRNA of random base sequence in a manner that is competitive with the binding of EtBr and other nucleic acid ligands often used as stains. This effect was observable in the presence of Mg(2+). The binding of the tetracyclines to dsRNA changed features of the fluorescence emission spectra of the drugs and the CD spectra of the RNA, and inhibited RNase III cleavage of the dsRNA. These results indicate that the double-stranded structures of RNAs may have a more important role in their interaction with the tetracyclines than the specific base pairs, which had hitherto been the subject of much investigation. Given the diverse functions of cellular RNAs, the binding of the tetracyclines to their double-stranded helixes may alter the normal processing and functioning of the various biological processes they regulate. This could help to explain the wide range of action of the tetracyclines against various pathogens and disease conditions.
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4
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Eschbach SH, Lafontaine DA. RNA conformational changes analyzed by comparative gel electrophoresis. Methods Mol Biol 2014; 1086:255-64. [PMID: 24136609 DOI: 10.1007/978-1-62703-667-2_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The study of biologically relevant native RNA structures is important to understand their cellular function(s). Native gel electrophoresis provides information about such native structures in solution as a function of experimental conditions. The application of native gel electrophoresis in a comparative manner allows to obtain precise information on relative angles subtended between given pair of stems in an RNA molecule. By adapting this approach, it is possible to obtain very specific structural information such as the amplitude of dihedral angles and helical rotation. As an example, we will describe how native gel electrophoresis can be used to study the folding of the S-adenosylmethionine (SAM) sensing riboswitch.
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Affiliation(s)
- Sébastien H Eschbach
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, QC, Canada
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5
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Heppell B, Blouin S, Dussault AM, Mulhbacher J, Ennifar E, Penedo JC, Lafontaine DA. Molecular insights into the ligand-controlled organization of the SAM-I riboswitch. Nat Chem Biol 2011; 7:384-92. [PMID: 21532599 DOI: 10.1038/nchembio.563] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 02/17/2011] [Indexed: 01/05/2023]
Abstract
S-adenosylmethionine (SAM) riboswitches are widespread in bacteria, and up to five different SAM riboswitch families have been reported, highlighting the relevance of SAM regulation. On the basis of crystallographic and biochemical data, it has been postulated, but never demonstrated, that ligand recognition by SAM riboswitches involves key conformational changes in the RNA architecture. We show here that the aptamer follows a two-step hierarchical folding selectively induced by metal ions and ligand binding, each of them leading to the formation of one of the two helical stacks observed in the crystal structure. Moreover, we find that the anti-antiterminator P1 stem is rotated along its helical axis upon ligand binding, a mechanistic feature that could be common to other riboswitches. We also show that the nonconserved P4 helical domain is used as an auxiliary element to enhance the ligand-binding affinity. This work provides the first comprehensive characterization, to our knowledge, of a ligand-controlled riboswitch folding pathway.
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Affiliation(s)
- Benoit Heppell
- Groupe ARN/RNA Group, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Affiliation(s)
- Dana A Baum
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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8
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Xu G, Kiselar J, He Q, Chance MR. Secondary reactions and strategies to improve quantitative protein footprinting. Anal Chem 2007; 77:3029-37. [PMID: 15889890 DOI: 10.1021/ac048282z] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxyl radical-mediated footprinting permits detailed examination of structure and dynamic processes of proteins and large biological assemblies, as changes in the rate of reaction of radicals with target peptides are governed by changes in the solvent accessibility of the side-chain probe residues. The precise and accurate determination of peptide reaction rates is essential to successfully probing protein structure using footprinting. In this study, we specifically examine the magnitude and mechanisms of secondary oxidation occurring after radiolytic exposure and prior to mass spectrometric analysis. Secondary oxidation results from hydrogen peroxide and other oxidative species generated during radiolysis, significantly impacting the oxidation of Met and Cys but not aromatic or other reactive residues. Secondary oxidation of Met with formation of sulfoxide degrades data reproducibility and inflates the perceived solvent accessibility of Met-containing peptides. It can be suppressed by adding trace amounts of catalase or millimolar Met-NH2 (or Met-OH) buffer immediately after irradiation; this leads to greatly improved adherence to first-order kinetics and more precise observed oxidation rates. The strategy is shown to suppress secondary oxidation in model peptides and improve data quality in examining the reactivity of peptides within the Arp2/3 protein complex. Cysteine is also subject to secondary oxidation generating disulfide as the principal product. The disulfides can be reduced before mass spectrometric analysis by reducing agents such as TCEP, while methionine sulfoxide is refractory to reduction by this reagent under typical reducing conditions.
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Affiliation(s)
- Guozhong Xu
- Center for Synchrotron Biosciences, Department of Physiology & Biophysics, and Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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9
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Schultes EA, Spasic A, Mohanty U, Bartel DP. Compact and ordered collapse of randomly generated RNA sequences. Nat Struct Mol Biol 2005; 12:1130-6. [PMID: 16273104 DOI: 10.1038/nsmb1014] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 09/21/2005] [Indexed: 11/08/2022]
Abstract
As the raw material for evolution, arbitrary RNA sequences represent the baseline for RNA structure formation and a standard to which evolved structures can be compared. Here, we set out to probe, using physical and chemical methods, the structural properties of RNAs having randomly generated oligonucleotide sequences that were of sufficient length and information content to encode complex, functional folds, yet were unbiased by either genealogical or functional constraints. Typically, these unevolved, nonfunctional RNAs had sequence-specific secondary structure configurations and compact magnesium-dependent conformational states comparable to those of evolved RNA isolates. But unlike evolved sequences, arbitrary sequences were prone to having multiple competing conformations. Thus, for RNAs the size of small ribozymes, natural selection seems necessary to achieve uniquely folding sequences, but not to account for the well-ordered secondary structures and overall compactness observed in nature.
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Affiliation(s)
- Erik A Schultes
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Liu J, Déclais AC, Lilley DMJ. Electrostatic Interactions and the Folding of the Four-way DNA Junction: Analysis by Selective Methyl Phosphonate Substitution. J Mol Biol 2004; 343:851-64. [PMID: 15476805 DOI: 10.1016/j.jmb.2004.08.079] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 08/24/2004] [Accepted: 08/25/2004] [Indexed: 11/16/2022]
Abstract
The structure and dynamics of the four-way (Holliday) junction are strongly dependent on the presence of metal ions. In this study, the importance of phosphate charge in and around the point of strand exchange has been explored by selective replacement with electrically neutral methyl phosphonate groups, guided by crystal structures of the junction in the folded, stacked X conformation. Junction conformation has been analysed by comparative gel electrophoresis and fluorescence resonance energy transfer (FRET). Three of sets of phosphate groups on the exchanging strands have been analysed; those at the point of strand exchange and those to their 3' and 5' sides. The exchanging and 3' phosphate groups form a box of negatively charged groups on the minor groove face of the junction, while the 5' phosphate groups face each other on the major groove side, with their proR oxygen atoms directed at one another. The largest effects are observed on substitution of the exchanging phosphate groups; replacement of both groups leads to the loss of the requirement for addition of metal ions to allow junction folding. When the equivalent phosphate groups on the continuous strands were substituted, a proportion of the junction folded into the alternative conformer so as to bring these phosphate groups onto the exchanging strands. These species did not interconvert, and thus this is likely to result from the alternative diasteromeric forms of the methyl phosphonate group. This shows that some of the conformational effects result from more than purely electrostatic interactions. Smaller but significant effects were observed on substitution of the flanking phosphate groups. All methyl phosphonate substitutions at these positions allowed folding to proceed at a reduced concentration of magnesium ions, with double substitutions more effective than single substitutions. Substitution of 5' phosphates resulted in a greater degree of folding at a given ionic concentration compared to the corresponding 3' phosphate substitutions. These results show that the phosphate groups at the point of strand exchange exert the largest electrostatic effect on junction folding, but a number of phosphate groups in the vicinity of the exchange region contribute to the overall effects.
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Affiliation(s)
- Jia Liu
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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11
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Guan JQ, Almo SC, Chance MR. Synchrotron radiolysis and mass spectrometry: a new approach to research on the actin cytoskeleton. Acc Chem Res 2004; 37:221-9. [PMID: 15096059 DOI: 10.1021/ar0302235] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxyl radicals generated from millisecond exposure of aqueous solutions to synchrotron X-rays react with proteins to yield stable oxidative modifications of solvent-accessible amino acid side chains. Following proteolysis, HPLC/MS analysis is performed to quantitate the side chain reactivities, and MS/MS analysis is used to identify the modification site(s). Side chain reactivity is shown to be correlated with solvent accessibility; thus the method provides detailed site-specific information about protein structure. The application of these techniques to the study of the actin cytoskeleton is described in detail, including defining the binding sites of monomeric actin with gelsolin segment-1, the actin monomer binding surface on cofilin, the divalent cation-dependent structure changes of monomeric actin, and the conformational changes associated with actin filamentous assembly.
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Affiliation(s)
- Jing-Qu Guan
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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12
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Melcher SE, Wilson TJ, Lilley DMJ. The dynamic nature of the four-way junction of the hepatitis C virus IRES. RNA (NEW YORK, N.Y.) 2003; 9:809-20. [PMID: 12810915 PMCID: PMC1370448 DOI: 10.1261/rna.5130703] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Accepted: 03/26/2003] [Indexed: 05/19/2023]
Abstract
Translation is initiated within the RNA of the hepatitis C virus at the internal ribosome entry site (IRES). The IRES is a 341-nucleotide element that contains a four-way helical junction (IIIabc) as a functionally important element of the secondary structure. The junction has three additional, nonpaired nucleotides at the point of strand exchange on one diagonal. We have studied the global conformation and folding of this junction in solution, using comparative gel electrophoresis and steady-state and time-resolved fluorescence resonance energy transfer. In the absence of divalent metal ions, the junction adopts an extended-square structure, in contrast to perfect four-way RNA junctions, which retain coaxial helical stacking under all conditions. The IIIabc junction is induced to fold on addition of Mg(2+), by pairwise coaxial stacking of arms, into the conformer in which the unpaired bases are located on the exchanging strands. Fluorescence lifetime measurements indicate that in the presence of Mg(2+) ions, the IIIabc junction exists in a dynamic equilibrium comprising approximately equal populations of antiparallel and parallel species. These dynamic properties may be important in mediating interactions between the IRES and the ribosome and initiation factors.
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Affiliation(s)
- Sonya E Melcher
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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Déclais AC, Fogg JM, Freeman AD, Coste F, Hadden JM, Phillips SE, Lilley DM. The complex between a four-way DNA junction and T7 endonuclease I. EMBO J 2003; 22:1398-409. [PMID: 12628932 PMCID: PMC151070 DOI: 10.1093/emboj/cdg132] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The junction-resolving enzyme endonuclease I is selective for the structure of the DNA four-way (Holliday) junction. The enzyme binds to a four-way junction in two possible orientations, with a 4:1 ratio, opening the DNA structure at the centre and changing the global structure into a 90 degrees cross of approximately coaxial helices. The nuclease cleaves the continuous strands of the junction in each orientation. Binding leads to pronounced regions of protection of the DNA against hydroxyl radical attack. Using all this information together with the known structure of the enzyme and the structure of the BglI-DNA complex, we have constructed a model of the complex of endonuclease I and a DNA junction. This shows how the enzyme is selective for the structure of a four-way junction, such that both continuous strands can be accommodated into the two active sites so that a productive resolution event is possible.
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Affiliation(s)
| | | | | | | | - Jonathan M. Hadden
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH and
Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK Corresponding author e-mail:
| | - Simon E.V. Phillips
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH and
Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK Corresponding author e-mail:
| | - David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH and
Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK Corresponding author e-mail:
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Abstract
The VS ribozyme comprises five helical segments (II-VI) in a formal H shape, organized by two three-way junctions. It interacts with its stem-loop substrate (I) by tertiary interactions. We have determined the global shape of the 3-4-5 junction (relating helices III-V) by electrophoresis and FRET. Estimation of the dihedral angle between helices II and V electrophoretically has allowed us to build a model for the global structure of the complete ribozyme. We propose that the substrate is docked into a cleft between helices II and VI, with its loop making a tertiary interaction with that of helix V. This is consistent with the dependence of activity on the length of helix III. The scissile phosphate is well placed to interact with the probable active site of the ribozyme, the loop containing A730.
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Affiliation(s)
| | | | - David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
Corresponding author e-mail:
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Lafontaine DA, Wilson TJ, Norman DG, Lilley DM. The A730 loop is an important component of the active site of the VS ribozyme. J Mol Biol 2001; 312:663-74. [PMID: 11575922 DOI: 10.1006/jmbi.2001.4996] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The core of the VS ribozyme comprises five helices, that act either in cis or in trans on a stem-loop substrate to catalyse site-specific cleavage. The structure of the 2-3-6 helical junction indicates that a cleft is formed between helices II and VI that is likely to serve as a receptor for the substrate. Detailed analysis of sequence variants suggests that the base bulges of helices II and VI play an architectural role. By contrast, the identity of the nucleotides in the A730 loop is very important for ribozyme activity. The base of A756 is particularly vital, and substitution by any other nucleotide or ablation of the base leads to a major reduction in cleavage rate. However, variants of A756 bind substrate efficiently, and are not defective in global folding. These results suggest that the A730 loop is an important component of the active site of the ribozyme, and that A756 could play a key role in catalysis.
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Affiliation(s)
- D A Lafontaine
- CRC Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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Lafontaine DA, Norman DG, Lilley DM. Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction. EMBO J 2001; 20:1415-24. [PMID: 11250907 PMCID: PMC145516 DOI: 10.1093/emboj/20.6.1415] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The VS nucleolytic ribozyme has a core comprising five helices organized by two three-way junctions. The ribozyme can act in trans on a hairpin-loop substrate, with which it interacts via tertiary contacts. We have determined that one of the junctions (2-3-6) undergoes two-stage ion-dependent folding into a stable conformation, and have determined the global structure of the folded junction using long-range distance restraints derived from fluorescence resonance energy transfer. A number of sequence variants in the junction are severely impaired in ribozyme cleavage, and there is good correlation between changes in activity and alteration in the folding of junction 2-3-6. These studies point to a special importance of G and A nucleotides immediately adjacent to helix II, and comparison with a similar junction of known structure indicates that this could adopt a guanine-wedge structure. We propose that the 2-3-6 junction organizes important aspects of the structure of the ribozyme to facilitate productive association with the substrate, and suggest that this results in an interaction between the substrate and the A730 loop to create the active complex.
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Affiliation(s)
| | | | - David M.J. Lilley
- CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 4HN, UK
Corresponding author e-mail:
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