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D M Lilley

Publications and source records attributed to D M Lilley.

At least 19 recordsLinked to original sources
PubMed1999

Sequence and functional-group specificity for cleavage of DNA junctions by RuvC of Escherichia coli.

RuvC is the DNA junction-resolving enzyme of Escherichia coli. While the enzyme binds to DNA junctions independently of base sequence, it exhibits considerable sequence selectivity for the phosphodiester cleavage reaction. We have analyzed the sequence specificity using a panel of DNA junctions, measuring the rate of cleavage of each under single-turnover conditions. We have found that the optimal sequence for cleavage can be described by (A approximately T)TT downward arrow(C>G approximately A), where downward arrow denotes the position of backbone scission. Cleavage is fastest when the cleaved phosphodiester linkage is located at the point of strand exchange. However, cleavage is possible one nucleotide 3' of this position when directed by the sequence, with a rate that is 1 order of magnitude slower than the optimal. The maximum sequence discrimination occurs at the central TT in the tetranucleotide site, where any alteration of sequence results in a rate reduction of at least 100-fold and cleavage is undetectable for some changes. However, certain sequences in the outer nucleotides are strongly inhibitory to cleavage. Introduction of base analogues around the cleavage site reveals a number of important functional groups and suggests that major-groove contacts in the center of the tetranucleotide are important for the cleavage process. Since RuvC binds to all the variant junctions with very similar affinity, any contacts affecting the rate of cleavage must be primarily important in the transition state. Introduction of the optimal cleavage sequence into a three-way DNA junction led to relatively efficient cleavage by RuvC, at a rate only 3-fold slower than the optimal four-way junction. This is consistent with a protein-induced alteration in the conformation of the DNA.

Bacterial Proteins↗
PubMed1999

Folding and catalysis by the hairpin ribozyme.

The hairpin ribozyme undergoes a site-specific transesterification cleavage of the phosphodiester backbone. The natural form of the ribozyme is a four-way helical junction, where two arms contain unpaired loops. This folds by pairwise coaxial stacking of helical arms, and a rotation into an antiparallel conformation in which there is close association between the loops. This probably generates the local conformation required to facilitate the trajectory into an in-line SN2 transition state. Folding is induced by the cooperative binding of at least two divalent metal ions, which are probably distributed between the junction and the loop-loop interface. The junction forms the structural scaffold on which the geometry of the ribozyme is built, and structural perturbation of the junction leads to impaired catalytic activity.

Base Sequence↗
PubMed1999

Binding of U1A protein to the 3' untranslated region of its pre-mRNA.

We have studied the global structure of the U1A 3' untranslated region (UTR) element using fluorescence resonance energy transfer. Comparison of a single UTR-box with a series of oligoadenine bulges indicates that the UTR-box introduces a significant kink into the axis of the RNA, and quantification of the results suggests an included bend angle of approximately 100 degrees (i.e. 80 degrees from linear). The complete 3'-UTR element is also severely kinked by the two UTR-boxes. We can observe binding of U1A protein to the 3'-UTR element by a change in the fluorescence anisotropy of Cy3 attached to one of the helical ends. In parallel with the binding, we observe a marked increase in fluoresence resonance energy transfer efficiency between fluorophores attached at the two 5' termini, indicating a significant change in global conformation induced by the binding of the protein.

3' Untranslated Regions↗
PubMed1999

RNA folding and misfolding of the hammerhead ribozyme.

The hammerhead ribozyme undergoes a well-defined two-stage folding process induced by the sequential binding of two magnesium ions. These probably correspond to the formation of domain 2 (0-500 microM magnesium ions) and domain 1 (1-20 mM magnesium ions), respectively. In this study we have used fluorescence resonance energy transfer (FRET) to analyze the ion-induced folding of a number of variants of the hammerhead ribozyme. We find that both A14G and G8U mutations are highly destabilizing, such that these species are essentially unfolded under all conditions. Thus they appear to be blocked in the first stage of the folding process, and using uranyl-induced photocleavage we show that the core is completely accessible to this probe under these conditions. Changes at G5 do not affect the first transition but appear to provide a blockage at the second stage of folding; this is true of changes in the sugar (removal of the 2'-hydroxyl group) and base (G5C mutation, previously studied by comparative gel electrophoresis). Arrest of folding at this intermediate stage leads to a pattern of uranyl-induced photocleavage that is changed from the wild-type, but suggests a structure less open than the A14G mutant. Specific photocleavage at G5 is found only in the wild-type sequence, suggesting that this ion-binding site is formed late in the folding process. In addition to folding that is blocked at selected stages, we have also observed misfolding. Thus the A13G mutation appears to result in the ion-induced formation of a novel tertiary structure.

Adenine↗
PubMed1999

Transcription-induced hypersupercoiling of plasmid DNA.

Transcription can induce high levels of negative supercoiling into plasmid DNA under some circumstances. This is especially true when the plasmid carries a functional tetracycline-resistance gene tetA, and is borne in a topA strain of Escherichia coli or Salmonella typhimurium. An important mechanism in transcription-induced supercoiling is believed to be the twin supercoiled-domain effect resulting from hindered rotation of the transcriptional complex, and this is very much more efficient where there is coupled transcription, translation and membrane insertion of the gene product. However, we have noted that strong promoters inserted into tetA-carrying plasmids can greatly increase the fraction of hypersupercoiled DNA. We show here that this effect is clearly present when the inserted promoter transcribes a very short segment of DNA (down to transcript lengths of approximately 45 nt), and where there is no possibility of translation of the RNA transcript. We suggest that the repeated helical opening due to transcriptional initiation is a significant contributor to the induction of high levels of supercoiling.

Base Sequence↗
PubMed1999

Catalytic and binding mutants of the junction-resolving enzyme endonuclease I of bacteriophage t7: role of acidic residues.

Endonuclease I is a 149 amino acid protein of bacteriophage T7 that is a Holliday junction-resolving enzyme, i.e. a four-way junction-selective nuclease. We have performed a systematic mutagenesis study of this protein, whereby all acidic amino acids have been individually replaced by other residues, mainly alanine. Out of 21 acidic residues, five (Glu20, Glu35, Glu65, Asp55 and Asp74) are essential. Replacement of these residues by other amino acids leads to a protein that is inactive in the cleavage of DNA junctions, but which nevertheless binds selectively to DNA junctions. The remaining 16 acidic residues can be replaced without loss of activity. The five critical amino acids are located within one section of the primary sequence. It is rather likely that their function is to bind one or more metal ions that coordinate the water molecule that brings about hydrolysis of the phosphodiester bond. We have also constructed a mutant of endonuclease I that lacks nine amino acids (six of which are arginine or lysine) at the C-terminus. Unlike the acidic point mutants, the C-terminal truncation is unable to bind to DNA junctions. It is therefore likely that the basic C-terminus is an important element in binding to the DNA junction.

Alanine↗
PubMed1999

Structure, folding and catalysis of the small nucleolytic ribozymes.

The small nucleolytic ribozymes are largely (but not exclusively) found in the RNA of plant pathogens and are involved in the self-catalysed processing of the concatameric RNA resulting from rolling circle replication. They catalyse a site-specific transesterification reaction in which their 2' hydroxyl attacks the 3' phosphate, with the exclusion of the 5' oxyanion. This requires an in-line geometry, which is not present in normal RNA structure. A significant part of the activation is probably provided by a distortion of the local conformation in order to facilitate the trajectory into the transition state and, thus, RNA folding and catalysis are intimately connected. A second element of the catalysis is provided by bound metal ions; however, a number of recent experiments cast doubt on the direct role of metal ions in the catalytic chemistry.

Catalysis↗
PubMed1999

The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form.

In the natural form of the hairpin ribozyme the two loop-carrying duplexes that comprise the majority of essential bases for activity form two adjacent helical arms of a four-way RNA junction. In the present work we have manipulated the sequence around the junction in a way known to perturb the global folding properties. We find that replacement of the junction by a different sequence that has the same conformational properties as the natural sequence gives closely similar reaction rate and Arrhenius activation energy for the substrate cleavage reaction. By comparison, rotation of the natural sequence in order to alter the three-dimensional folding of the ribozyme leads to a tenfold reduction in the kinetics of cleavage. Replacement with the U1 four-way junction that is resistant to rotation into the antiparallel structure required to allow interaction between the loops also gives a tenfold reduction in cleavage rate. The results indicate that the conformation of the junction has a major influence on the catalytic activity of the ribozyme. The results are all consistent with a role for the junction in the provision of a framework by which the loops are presented for interaction in order to create the active form of the ribozyme.

Base Sequence↗
PubMed1998

Folding of the four-way RNA junction of the hairpin ribozyme.

The hairpin ribozyme consists of two loop-carrying duplexes (called A and B) that are adjacent arms of a four-way junction in its natural context in the viral RNA. We have shown previously that the activity of the ribozyme is strongly influenced by the structure adopted by the junction. In this study, we have used fluorescence resonance energy transfer to analyze the conformation and folding of the isolated four-way junction. Like other four-way RNA junctions, in the absence of added metal ions this junction adopts a square configuration of coaxially stacked arms, based on A on D and B on C stacking. Upon addition of magnesium ions, the junction undergoes an ion-induced transition to an antiparallel conformation. The data are consistent with folding induced by the binding of a single ion, with an apparent association constant in the range of 2000 M-1. Other divalent metal ions (calcium or manganese) can also induce this change in structure; however, sodium ions are unable to substitute for these ions, and are slightly inhibitory with respect to the transition. The loop-free hairpin junction adopts the same stacking conformer as the full ribozyme, but forms a more symmetrical X-shaped structure. In addition, the apparent stoichiometry of structural ion binding is lower for the isolated junction, and the affinity is considerably lower.

Calcium↗
PubMed1998

Interaction of the resolving enzyme YDC2 with the four-way DNA junction.

Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in particular a high structure specificity for binding and metal-dependent, (frequently) sequence-specific cleavage activity. In Saccharomyces cerevisiae, the enzyme CCE1 is necessary for the resolution of recombining mitochondrial genomes, and in Schizosaccharomyces pombe the homologous protein YDC2 is thought to have a similar function. We have generated an inactive mutant of YDC2, D226N, that retains structure-specific junction binding and have analysed the interaction of this protein with the four-way DNA junction. YDC2 binds the four-way junction in two specific complexes (I and II), unfolding the stacked X-structure into a conformation where the arms extend to the four corners of a square. This structure is reminiscent of that of the free junction in the absence of metal ions and of the structures imposed on the Holliday junction by CCE1 and RuvA. DNase I probing reveals footprints specific for complexes I and II which extend from the junction centre on all four arms. No protection is observed with the small, hydrophobic probe DMS.

Binding Sites↗
PubMed1998

Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions.

The natural form of the hairpin ribozyme consists of a four-way RNA junction of which the single-stranded loop-carrying helices are adjacent arms. The junction can be regarded as providing a framework for constructing the active ribozyme, and the rate of cleavage can be modulated by changing the conformation of the junction. We find that the junction-based form of the hairpin ribozyme is active in magnesium, calcium, or strontium ions, but not in manganese, cadmium, or sodium ions. Using fluorescence resonance energy transfer experiments, we have investigated the global structure of the ribozyme. The basic folding of the construct is based on pairwise helical stacking, so that the two loop-carrying arms are located on opposite stacked helical pairs. In the presence of magnesium, calcium, or strontium ions, the junction of the ribozyme undergoes a rotation into a distorted antiparallel geometry, creating close physical contact between the two loops. Manganese ions induce the same global folding, but no catalytic activity; this change in global conformation is therefore necessary but not sufficient for catalytic activity. Fitting the dependence of the conformation on ionic concentration to a two-state model suggests that cooperative binding of two ions is required to bring about the folding. However, further ion binding is required for cleavage activity. Cobalt hexammine ions also bring about global folding, while spermidine generates a more symmetrical form of the antiparallel structure. Cadmium ions generate a different folded form, interpreted in terms of close loop-loop association while the junction is unfolded. Sodium ions were unable to induce any folding of the ribozyme, which remained slightly parallel. These results are consistent with a folding process induced by the binding of two group IIA metal ions, distributed between the junction and the loop interface.

Base Sequence↗
PubMed1998

Dissection of the sequence specificity of the Holliday junction endonuclease CCE1.

CCE1 is a Holliday (four-way DNA) junction-specific endonuclease which resolves mitochondrial DNA recombination intermediates in Saccharomycescerevisiae. The junction-resolving enzymes are a diverse class, widely distributed in nature from viruses to higher eukaryotes. In common with most other junction-resolving enzymes, the cleavage activity of CCE1 is nucleotide sequence-dependent. We have undertaken a systematic study of the sequence specificity of CCE1, using a single-turnover kinetic assay and a panel of synthetic four-way DNA junction substrates. A tetranucleotide consensus cleavage sequence 5'-ACT downward arrowA has been identified, with specificity residing mainly at the central CT dinucleotide. Equilibrium constants for CCE1 binding to four-way junctions are unaffected by sequence variations, suggesting that substrate discrimination occurs predominantly in the transition state complex. CCE1 cuts most efficiently at the junction center, but can also cleave the DNA backbone at positions one nucleotide 3' or 5' of the point of strand exchange, suggesting a significant degree of conformational flexibility in the CCE1:junction complex. Introduction of base analogues at single sites in four-way junctions has allowed investigation of the sequence specificity of CCE1 in finer detail. In particular, the N7 moiety of the guanine base-pairing with the cytosine of the consensus sequence appears to be crucial for catalysis. The functional significance of sequence specificity in junction-resolving enzymes is discussed.

Adenine↗
PubMed1998

Structural recognition and distortion by the DNA junction-resolving enzyme RusA.

RusA is a relatively small DNA junction-resolving enzyme of lambdoid phage-origin. Many of the physical characteristics of this enzyme are similar to those of junction-resolving enzymes of different origins. RusA binds to DNA junctions as a dimer, with a dissociation constant of 2 to 7 nM. RusA also exists in dimeric form in free solution, with a half time for subunit exchange of 4.2 minutes. We find that RusA can cleave both fixed junctions and those that can undergo a number of steps of branch migration, and confirm that the enzyme exhibits a strong preference for cleavage 5' to a CpC sequence. We have isolated a mutant protein, RusA D70N, that is completely inactive in cleavage while binding normally to DNA junctions, suggesting a role for aspartate 70 in the cleavage reaction. Constraining the conformation of the junction by means of tethering the helical ends leads to a marked reduction in cleavage rate by RusA, suggesting that the structure must be altered for cleavage. Using comparative gel electrophoresis we find that the global structure of the DNA junction is altered on RusA binding, into a structure that is different from any that is formed by the free junction. Moreover, the structure of the complex is the same irrespective of the presence or absence of magnesium ions. Thus, like all the junction-resolving enzymes, RusA both recognises and distorts the structure of DNA junctions.

Catalysis↗
PubMed1998

Two superhelix density-dependent DNA transitions detected by changes in DNA adsorption/desorption behavior.

The adsorption behavior of covalently closed circular plasmid DNA at the mercury/water interface was studied by means of AC impedance measurements. The dependence of the differential capacitance (C) of the electrode double layer on the potential (E) was measured in the presence of adsorbed DNA. It was found that the C-E curves of supercoiled DNA at native and highly negative superhelix densities (sigma), relaxed covalently closed circular DNA, and nicked DNA differed from each other. A detailed study of topoisomer distributions ranging from -sigma of 0 to 0.11 revealed two supercoiling-dependent transitions, at about -sigma = 0.04 (transition TI) and 0.07 (transition TII). Transition TI was detected by measuring the height of the adsorption/desorption peak 1 (at about -1.2 V against the saturated calomel electrode) and the decrease of capacitance (DeltaC) at -0.35 V. This transition may be due to a sudden change in the ability of the DNA to respond to the alternating voltage, probably caused by changes in the DNA tertiary and/or secondary structure. Transition TII was detected by measuring peak 3* (at about -1.3 V), which was absent in topoisomers with -sigma less than 0.05. This transition is due to changes in the DNA adsorption/desorption behavior related to increased accessibility of bases at elevated negative superhelix density. Opening of the duplex at highly negative superhelix density was also detected by the single-strand selective probe of DNA structure, osmium tetroxide, 2, 2'-bipyridine. Our results suggest that electrochemical techniques provide sensitive experimental analysis of changes in DNA structure.

Adsorption↗
PubMed1998

HMG box proteins bind to four-way DNA junctions in their open conformation.

The HMG box is an 80 amino acid domain found in a variety of eukaryotic chromosomal proteins and transcription factors. Binding to DNA is associated with recognition of structural distortion or manipulation of DNA structure. All the HMG box domains bind to four-way DNA junctions, which must therefore present some feature that is common to the binding targets of this wide variety of proteins. Since the four-way junction can itself adopt a variety of structures depending upon conditions, it is important to determine in which form it exists in complexes with HMG boxes. We find that a single HMG box domain is bound exclusively to the open square form of the junction and that conditions that stabilize the stacked X structure significantly lower affinity for the HMG box. We suggest that the HMG domain binds to one arm of the junction in the minor groove at the point of strand exchange and we present a model for the structure of the complex.

Animals↗
PubMed1998

Exchange between stacking conformers in a four-Way DNA junction.

Four-way DNA junctions undergo metal ion-induced folding by means of pairwise coaxial stacking of helical arms in one of two possible conformers that depend on the choice of stacking partners. For most such junctions there is a significant bias toward one conformer over the other. In this study we have characterized a four-way DNA junction in which there is rapid exchange between equal populations of the two possible stacking conformers. Analysis of the global conformation using comparative gel electrophoresis gives results consistent with either a tetrahedral disposition of the four arms or an equilibrium between equal populations of the two alternative stacked X-structures. Protection of bases at the center of the junction against attack by osmium tetroxide indicates that base stacking is preserved through the point of strand exchange. Cleavage across the point of strand exchange by the restriction enzyme MboII is consistent with pairwise coaxial stacking of helical arms. Taken together, these indicate that the junction adopts the stacked X-structure, but unusually there appears to be little bias for one stacking conformer over the other. Complete digestion of junctions by MboII demonstrates that all the molecules in solution pass through a given conformer during the time of incubation, demonstrating that exchange between conformers must occur. This is true even for minor stacking conformers in strongly biased junctions. Comparative gel electrophoresis shows that sequence changes at the third position out from the point of strand exchange can have a marked influence on the relative stability of the stacking conformers.

Cations, Divalent↗
PubMed1998

Activation of the leu-500 promoter by a reversed polarity tetA gene. Response to global plasmid supercoiling.

The leu-500 promoter is inactivated by a mutation in the -10 region but can be activated in topA Escherichia coli and Salmonella strains. We have found that the tetA gene plays a vital role in the topA-dependent activation of a plasmid-borne leu-500 promoter. In previous studies, the leu-500 promoter and tetA gene have been arranged divergently. In this study we have reversed the polarity of the tetA gene, thus locating the leu-500 promoter at the 3' end of tetA. Despite being formally located in the downstream region of tetA, the leu-500 promoter is equally well activated in a topA strain in this environment, even though it is 1.6 kilobase pairs away from the promoter of the reversed tetA gene. Activation of the leu-500 promoter depends on transcription and translation of tetA but is largely insensitive to the function of other transcription units on the plasmid. These results require a change in viewpoint of the role of tetA, from local to global supercoiling. We conclude that transcription of the tetA gene is the main generator of transcription-induced supercoiling that activates the leu-500 promoter. Unbalanced relaxation of this supercoiling leads to a net increase in the negative linking difference of the plasmid globally, and there is a linear correlation between the change in global plasmid topology and the activation of the leu-500 promoter. Thus the leu-500 promoter appears to respond to the negative supercoiling of the plasmid overall.

Antiporters↗