Why does RecA protein hydrolyse ATP?

RecA is a DNA-dependent ATPase involved in DNA-strand repair. Most of the ATP hydrolysis that occurs in a RecA nucleoprotein filament is implicitly considered to be irrelevant in many current models for RecA-mediated DNA-strand exchange. However, preventing RecA from hydrolysing ATP alters its behavior, suggesting that ATP hydrolysis by RecA is more than incidental. This review explores recent results detailing the effects and rates of ATP hydrolysis by RecA, and models are proposed that permit us to account quantitatively for ATP consumption by this protein.

Characterization of Holliday structures in FLP protein-promoted site-specific recombination.

Holliday structures are formed in the course of FLP protein-promoted site-specific recombination. Here, we demonstrate that Holliday structures are formed in reactions involving wild-type substrates and that they are kinetically competent with respect to the overall reaction rate. Together with a previous demonstration of chemical competence (L. Meyer-Leon, L.-C. Huang, S. W. Umlauf, M. M. Cox, and R. B. Inman, Mol. Cell. Biol. 8:3784-3796, 1988), Holliday structures therefore meet all criteria necessary to establish that they are obligate reaction intermediates in FLP-mediated site-specific recombination. In addition, kinetic evidence suggests that two distinct forms of the Holliday intermediate are present in the reaction pathway, interconverted in an isomerization process that is rate limiting at 0 degree C.

Holliday intermediates and reaction by-products in FLP protein-promoted site-specific recombination.

Holliday structures are formed and resolved by FLP protein during site-specific recombination. These structures have been isolated and are visualized in both native and partially denatured states by electron microscopy. No single-strand breaks are found within the junction, indicating that the structure results from a reciprocal exchange of strands. These structures have properties consistent with being reaction intermediates. Double-strand cleavage products and "Y structures" are also detected and appear to be by-products of the reaction. The Y structures are three-armed branched molecules with a covalently closed junction located at the FLP recombination target site. Models are discussed, suggesting that both of these novel structures are made by aberrant cleavages during formation and resolution of the Holliday intermediate.

Vaccines in development against avian influenza.

Avian influenza has become a high priority item for all public health authorities. An influenza pandemic is believed to be imminent. The only questions are what will be the causative agent and when will it happen. Recently, most attention has been directed to human cases of avian influenza caused by an H5N1 avian influenza virus. An effective vaccine will be needed to substantially reduce the impact of an influenza pandemic. Despite the fact that the current influenza vaccine manufacturing technology is not adequate to support vaccine production in the event of a pandemic influenza outbreak, most of the ongoing clinical development is occurring with vaccines made in embryonated chicken eggs. It is clear that innovative production technology is required. This review provides an update on the status of avian vaccine development. In addition available manufacturing technologies are presented, some of which could be more suitable to adequately respond to an emergency situation where billions of doses of vaccines would be required within a very short period of time. The review is concluded with some proposed areas of focus for pandemic vaccine preparedness.

Recombinational DNA repair in bacteria and the RecA protein.

In bacteria, the major function of homologous genetic recombination is recombinational DNA repair. This is not a process reserved only for rare double-strand breaks caused by ionizing radiation, nor is it limited to situations in which the SOS response has been induced. Recombinational DNA repair in bacteria is closely tied to the cellular replication systems, and it functions to repair damage at stalled replication forks, Studies with a variety of rec mutants, carried out under normal aerobic growth conditions, consistently suggest that at least 10-30% of all replication forks originating at the bacterial origin of replication are halted by DNA damage and must undergo recombinational DNA repair. The actual frequency may be much higher. Recombinational DNA repair is both the most complex and the least understood of bacterial DNA repair processes. When replication forks encounter a DNA lesion or strand break, repair is mediated by an adaptable set of pathways encompassing most of the enzymes involved in DNA metabolism. There are five separate enzymatic processes involved in these repair events: (1) The replication fork assembled at OriC stalls and/or collapses when encountering DNA damage. (2) Recombination enzymes provide a complementary strand for a lesion isolated in a single-strand gap, or reconstruct a branched DNA at the site of a double-strand break. (3) The phi X174-type primosome (or repair primosome) functions in the origin-independent reassembly of the replication fork. (4) The XerCD site-specific recombination system resolves the dimeric chromosomes that are the inevitable by-product of frequent recombination associated with recombinational DNA repair. (5) DNA excision repair and other repair systems eliminate lesions left behind in double-stranded DNA. The RecA protein plays a central role in the recombination phase of the process. Among its many activities, RecA protein is a motor protein, coupling the hydrolysis of ATP to the movement of DNA branches.

Acute and long-term beta-adrenergic blockade for patients with neurocardiogenic syncope.

OBJECTIVES: This study was designed to prospectively evaluate the long-term outcome of drug therapy guided by head-up tilt testing for the management of unexplained syncope and near syncope. BACKGROUND: Head-up tilt testing is used to evaluate patients with unexplained syncope. The validity of acute drug testing and the efficacy of long-term oral therapy for prevention of recurrent syncope have not been investigated in large patient groups. METHODS: We studied 296 consecutive patients with unexplained syncope or near syncope who underwent 80 degrees head-up tilt testing with and without isoproterenol challenge. The efficacy of intravenous and oral beta-blocker therapy was evaluated by repeat testing. Patients with both positive and negative responses to therapy were followed up for rates of recurrence of syncope. RESULTS: A total of 193 patients (65%) had a positive tilt test response; 89% of these 193 required isoproterenol challenge to elicit this response. Patients with a positive tilt test result had lower values for heart rate at rest (mean +/- SD 69 +/- 13 vs. 74 +/- 14 beats/min, p = 0.046) and systolic blood pressure (137 +/- 28 vs. 145 +/- 30 mm Hg, p = 0.0018) at baseline than did the patients with a negative tilt test result. Intravenous propranolol blocked the positive response in 163 (90%) of 181 patients retested. Oral beta-blockers were effective by tilt test criteria in 118 (94%) of 125 patients; 12 (10%) had recurrent clinical symptoms while taking beta-blockers. Eight (42%) of 19 patients who had a negative tilt test response during beta-blocker therapy had recurrent symptoms when they stopped therapy. Three (23%) of 13 patients receiving empiric beta-blocker therapy had recurrent symptoms. The follow-up period for the patients with a positive tilt test result was 28 +/- 11 months (range 5 to 48). CONCLUSIONS: Intravenous propranolol is effective in preventing neurocardiogenic syncope diagnosed during head-up tilt testing and predicts the response to oral beta-blocker therapy. Oral beta-blocker therapy prevents recurrent syncope in the majority of patients. Recurrence of syncope is lowest when efficacy of oral beta-blocker therapy is confirmed by repeat head-up tilt testing.

Dissociation pathway for recA nucleoprotein filaments formed on linear duplex DNA.

recA protein forms stable filaments on duplex DNA at low pH. When the pH is shifted above 6.8, recA protein remains stably bound to nicked circular DNA, but not to linear DNA. Dissociation of recA protein from linear duplex DNA proceeds to a non-zero endpoint. The kinetics and final extent of dissociation vary with several experimental parameters. The instability on linear DNA is most readily explained by a progressive unidirectional dissociation of recA protein from one end of the filament. Dissociation of recA protein from random points in the filament is eliminated as a possible mechanism by several observations: (1) the requirement for a free end; (2) the inverse and linear dependence of the rate of dissociation on DNA length (at constant DNA base-pair concentration); and (3) the kinetics of exposure of a restriction endonuclease site in the middle of the DNA. Evidence against another possible mechanism, ATP-mediated translocation of the filament along the DNA, is provided by a novel effect of the non-hydrolyzable ATP analog, ATP gamma S, which generally induces recA protein to bind any DNA tightly and completely inhibits ATP hydrolysis. We find that very low, sub-saturating levels of ATP gamma S completely stabilize the filament, while most of the ATP hydrolysis continues. If these levels of ATP gamma S are introduced after dissociation has commenced, further dissociation is blocked, but re-association does not occur. These observations are inconsistent with movement of recA protein along DNA that is tightly coupled to ATP hydrolysis. The recA nucleoprotein filament is polar and the protein binds the two strands asymmetrically, polymerizing mainly in the 5' to 3' direction on the initiating strand of a single-stranded DNA tailed duplex molecule. A model consistent with these results is presented.

General mechanism for RecA protein binding to duplex DNA.

RecA protein binding to duplex DNA occurs by a multi-step process. The tau analysis, originally developed to examine the binding of RNA polymerase to promoter DNA, is adapted here to study two kinetically distinguishable reaction segments of RecA-double stranded (ds) DNA complex formation in greater detail. One, which is probably a rapid preequilibrium in which RecA protein binds weakly to native dsDNA, is found to have the following properties: (1) a sensitivity to pH, involving a net release of approximately one proton; (2) a sensitivity to salts; (3) little or no dependence on temperature; (4) little or no dependence on DNA length. The second reaction segment, the rate-limiting nucleation of nucleoprotein filament formation accompanied by partial DNA unwinding, is found to have the following properties: (1) a sensitivity to pH, involving a net uptake of approximately three protons; (2) a sensitivity to salts; (3) a relatively large dependence on temperature, with an Arrhenius activation energy of 39 kcal mol(-1); (4) a sensitivity to DNA topology; (5) a dependence on DNA length. These results contribute to a general mechanism for RecA protein binding to duplex DNA, which can provide a rationale for the apparent preferential binding to altered DNA structures such as pyrimidine dimers and Z-DNA.

RecA protein dynamics in the interior of RecA nucleoprotein filaments.

We characterize aspects of the conformation and dynamic state of RecA filaments when bound to dsDNA that are specifically linked to the presence of the second of the two bound DNA strands. Filaments bound to dsDNA exhibit a facile exchange between free and bound RecA monomers or oligomers in the filament interior that is not seen on ssDNA. The RecA mutant K72R, which binds but does not hydrolyze ATP, forms mixed filaments with wild type RecA protein under some conditions. In the presence of dATP, mixed filaments are formed on dsDNA or ssDNA in which the RecA K72R content approximately reflects the proportion of the K72R mutant in the total RecA protein present when the filament is formed. In the presence of ATP, mixed filaments are formed on dsDNA, but the mutant protein strongly inhibits the binding of wtRecA protein to single-stranded DNA. When RecA K72R is added to pre-formed filaments containing only wild-type RecA protein on single-stranded DNA, little of the mutant protein exchanges into the filament. Exchange occurs readily, however, when the filament is bound to double-stranded DNA. The presence of a second DNA strand in RecA-dsDNA filaments produces as altered and more dynamic filament state relative to filaments formed on single-stranded DNA. The results point to a substantial alteration in filament state when synapsis occurs during RecA protein-mediated DNA strand exchange.

Extent of duplex DNA underwinding induced by RecA protein binding in the presence of ATP.

A method is described for the accurate determination of the superhelical density (omega) of highly underwound circular DNA molecules. Using this method, duplex DNA bound by RecA protein in the presence of ATP at pH 7.5 is found to be underwound by 39.6% (omega = -0.396), corresponding to a helical periodicity of 17.4 base-pairs per turn. The underwinding is increased to 41% (17.9 base-pairs per turn) in the presence of low levels of ATP gamma S, in good agreement with the 18.6 base-pairs per turn reported previously. In spite of the extensive underwinding, the distribution of DNA topoisomers produced by RecA protein binding is small. This indicates a high degree of structural uniformity among RecA-double-stranded DNA complexes in the presence of ATP.

DNA recognition by the FLP recombinase of the yeast 2 mu plasmid. A mutational analysis of the FLP binding site.

The 2 mu plasmid of the yeast Saccharomyces cerevisiae encodes a site-specific recombination system consisting of the FLP protein and two inverted recombination sites on the plasmid. The minimal fully functional substrate for in-vitro recombination in this system consists of two FLP protein binding sites separated by an eight base-pair spacer sequence. We have used site-directed mutagenesis to generate every possible mutation (36 in all) within 11 base-pairs of one FLP protein binding site and the base-pair immediately flanking it. The base-pairs within the binding site can be separated into three classes on the basis of these results. Thirty of the 36 sequence changes, including all three at seven different positions (class I) produce a negligible or modest effect on FLP protein-promoted recombination. In particular, most transition mutations are well-tolerated in this system. In only one case do all three possible mutations produce large effects (class II). At three positions, clustered near the site at which DNA is cleaved by FLP protein, one of the two possible transversions produces a large effect on recombination, while the other two changes produce modest effects (class III). For seven mutants for which FLP protein binding was measured, a direct correlation between decreases in recombination activity and in binding was observed. Positive effects on the reaction potential of mutant sites are observed when the other FLP binding site in a single recombination site is unaltered or when the second recombination site in a reaction is wild-type. This suggests a functional interaction between FLP binding sites both in cis and in trans. When two mutant recombination sites (each with 1 altered FLP binding site) are recombined, the relative orientation of the mutations (parallel or antiparallel) has no effect on the result. These results provide an extensive substrate catalog to complement future studies in this system.

Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA.

On linear single-stranded DNA, RecA filaments assemble and disassemble in the 5' to 3' direction. Monomers (or other units) associate at one end and dissociate from the other. ATP hydrolysis occurs throughout the filament. Dissociation can result when ATP is hydrolyzed by the monomer at the disassembly end. We have developed a comprehensive model for the end-dependent filament disassembly process. The model accounts not only for disassembly, but also for the limited reassembly that occurs as DNA is vacated by disassembling filaments. The overall process can be monitored quantitatively by following the resulting decline in DNA-dependent ATP hydrolysis. The rate of disassembly is highly pH dependent, being negligible at pH 6 and reaching a maximum at pH values above 7. 5. The rate of disassembly is not significantly affected by the concentration of free RecA protein within the experimental uncertainty. For filaments on single-stranded DNA, the monomer kcat for ATP hydrolysis is 30 min-1, and disassembly proceeds at a maximum rate of 60-70 monomers per minute per filament end. The latter rate is that predicted if the ATP hydrolytic cycles of adjacent monomers are not coupled in any way.

Characterization of a mutant RecA protein that facilitates homologous genetic recombination but not recombinational DNA repair: RecA423.

A recA mutant (recA423; Arg169-->His), with properties that should help clarify the relationship between the biochemical properties of RecA protein and its two major functions, homologous genetic recombination and recombinational DNA repair, has been isolated. The mutant has been characterized in vivo and the purified RecA423 protein has been studied in vitro. The recA423 cells are nearly as proficient in conjugational recombination, transductional recombination, and recombination of lambda red- gam- phage as wild-type cells. At the same time, the mutant cells are deficient for intra-chromosomal recombination and nearly as sensitive to UV irradiation as a recA deletion strain. The cells are proficient in SOS induction, and results indicate the defect involves the capacity of RecA protein to participate directly in recombinational DNA repair. In vitro, the RecA423 protein binds to single-stranded DNA slowly, with an associated decline in the ATP hydrolytic activity. The RecA423 protein promoted a limited DNA strand exchange reaction when the DNA substrates were homologous, but no bypass of a short heterologous insert in the duplex DNA substrate was observed. These results indicate that poor binding to DNA and low ATP hydrolysis activity can selectively compromise certain functions of RecA protein. The RecA423 protein can promote recombination between homologous DNAs during Hfr crosses, indicating that the biochemical requirements for such genetic exchanges are minimal. However, the deficiencies in recombinational DNA repair suggest that the biochemical requirements for this function are more exacting.

RecA protein filaments: end-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins.

RecA protein filaments formed on circular (ssDNA) in the presence of ssDNA binding protein (SSB) are generally stable as long as ATP is regenerated. On linear ssDNA, stable RecA filaments are believed to be formed by nucleation at random sites on the DNA followed by filament extension in the 5' to 3' direction. This view must now be enlarged as we demonstrate that RecA filaments formed on linear ssDNA are subject to a previously undetected end-dependent disassembly process. RecA protein slowly dissociates from one filament end and is replaced by SSB. The results are most consistent with disassembly from the filament end nearest the 5' end of the DNA. The bound SSB prevents re-formation of the RecA filaments, rendering the dissociation largely irreversible. The dissociation requires ATP hydrolysis. Disassembly is not observed when the pH is lowered to 6.3 or when dATP replaces ATP. Disassembly is not observed even with ATP when both the RecO and RecR proteins are present in the initial reaction mixture. When the RecO and RecR proteins are added after most of the RecA protein has already dissociated, RecA protein filaments re-form after a short lag. The newly formed filaments contain an amount of RecA protein and exhibit an ATP hydrolysis rate comparable to that observed when the RecO and RecR proteins are included in the initial reaction mixture. The RecO and RecR proteins thereby stabilize RecA filaments even at the 5' ends of ssDNA, a fact which should affect the recombination potential of 5' ends relative to 3' ends. The location and length of RecA filaments involved in recombinational DNA repair is dictated by both the assembly and disassembly processes, as well as by the presence or absence of a variety of other proteins that can modulate either process.

The deduced Vibrio cholerae RecA amino-acid sequence.

The nucleotide sequence of the recA gene of Vibrio cholerae (Vc) has been determined. The amino acid (aa) sequence of the protein product is very similar to other known RecA aa sequences. However, this sequence does not agree with a previously reported Vc RecA aa sequence [Ghosh et al., Nucleic Acids Res. 20 (1992) 372].

Cycling of inducibility of paroxysmal supraventricular tachycardia in women and its implications for timing of electrophysiologic procedures.

Arrhythmias in women may be affected by phases of the menstrual cycle. This study was designed to determine the prevalence of perimenstrual clustering of spontaneous episodes of paroxysmal supraventricular tachycardia (SVT) in women. It also tested the hypothesis that women with this temporal pattern of events have an altered probability of induction of paroxysmal SVT during electrophysiologic testing at higher estrogen states (midcycle or with estrogen replacement therapy) than at low estrogen states (perimenstrual or without estrogen replacement). A structured history of the relation of spontaneous paroxysmal SVTs to phases of the menstrual cycle was obtained prospectively among 42 women referred during a 3-year period. Patients with cyclical patterns of spontaneous tachycardias, who had had negative electrophysiologic studies at midcycle or while receiving estrogen replacement therapy, had repeat procedures (1) when premenstrual or at the onset of menses, or (2) after stopping estrogen replacement therapy. Seventeen of 42 consecutive female patients (40%) had histories of perimenstrual clustering of arrhythmias. Six women (4 with normal menstrual cycles, 2 on estrogen replacement therapy), who qualified for paired electrophysiologic studies because of a negative initial electrophysiologic study that included provocation with isoproterenol, had inducibility into SVTs during the second study. All 6 had dual atrioventricular (AV) nodal pathway physiology, 4 had AV nodal reentrant tachycardia (AVNRT) induced, 1 had both AVNRT and reciprocating AV tachycardias, and 1 had nonsustained AVNRT and an atrial tachycardia induced. Successful ablation procedures were performed in 5 of the 6 patients. Thus, among women with a history of perimenstrual clustering of paroxysmal SVT and among those receiving estrogen replacement therapy, scheduling of elective electrophysiologic procedures at times of low estrogen levels (premenstrual or off estrogen replacement therapy) may facilitate the probability of a successful procedure.

A shared pathway in atrioventricular nodal reentrant tachycardia and atrial flutter: implications for pathophysiology and therapy.

Atrioventricular (AV) nodal reentrant tachycardia and atrial flutter are considered 2 distinct supraventricular tachycardias. Recent clinical and experimental data suggest that both these tachycardias include an area in the lower right atrial septum in their reentrant pathways. This study was designed to test the hypothesis that there is an association between the mechanisms of AV nodal reentrant tachycardia and atrial flutter because of a shared pathway of reentry. Consecutive patients referred for evaluation and management of supraventricular tachycardia, thought to be due to AV nodal reentry, underwent electrophysiologic testing protocols designed to induce both AV nodal reentrant tachycardia and atrial flutter, if present. Fifteen of 29 patients (52%) had both AV nodal reentrant tachycardia and atrial flutter induced during electrophysiologic testing. Seven of these 15 patients (47%) underwent transcatheter radiofrequency current application (mean power 34 +/- 4 W) against the tricuspid annulus above the coronary sinus. In each patient, neither AV nodal reentrant tachycardia nor atrial flutter could be induced after the procedure. Repeat study after successful ablation (mean 6 days) showed no inducible supraventricular arrhythmia of either type at baseline study or during isoproterenol infusion. Atrial flutter occurs frequently (15 of 29 patients; 52%) in patients with AV nodal reentrant tachycardia, because of a shared pathway in their reentry circuits. Because of this shared pathway, both arrhythmias can be ablated at the same site. These observations promote new insights into the mechanism and therapeutics of supraventricular tachycardias.

Mechanisms and dynamics of episodes of progression of 2:1 atrioventricular block in patients with documented two-level conduction disturbances.

Twenty episodes of progression of 2:1 atrioventricular (AV) block were identified during incremental atrial stimulation in 7 patients with documented (2-level) block in the AV node and His-Purkinje system. All occurred at cycle lengths shorter than those at which stable 2:1 HV block had been detected. Thirteen episodes were typical since 2:1 increased to 3:1 AV block when an atrio-His (AH) Wenckebach period was completed with an atrial impulse that otherwise would have been conducted. These episodes occurred with dynamic A(M): V(N) ratios similar to those seen at the AV node. Seven atypical episodes were identified (while AH Wenckebach periods were occurring): (1) 2:1 increasing to 3:1 AV block and then to 4:1 AV block resulting from prolonged refractoriness in the His-Purkinje system subsequently followed by concealed conduction in the latter structure; (2) conversion of 3:2 directly into 3:1 AV block due to block of the next-to-last atrial impulse in the His-Purkinje system with completion of AH Wenckebach period with the following atrial impulse; and (3) 4:2 AV block presumably due to supernormal conduction in a transversely dissociated His-Purkinje system. These episodes occurred with A(M): V(N) ratios, which in other structures would have been indicative of different degrees of AV block. In conclusion, progression of 2:1 AV block during documented 2 level conduction disturbances (1) can be explained by mechanisms different than those currently known, and (2) has rich, but different dynamics from those observed exclusively in the AV node and exclusively in the His-Purkinje system.

Gonococcal endocarditis complicating pregnancy: a case report and literature review.

The incidence of gonorrhea has decreased substantially in the past decade. Disseminated gonorrhea is more common in women than in men, although gonococcal endocarditis is more common in men. Disseminated gonorrhea is most commonly described in women during menses or pregnancy. Only two cases of gonococcal endocarditis during pregnancy have been reported in the literature since 1942. We report a patient who experienced sudden hemodynamic decompensation at 30 weeks' gestation, resulting in fetal death. Aortic valve replacement was performed, but extensive involvement of the aortic root made complete eradication of infection impossible and eventually resulted in maternal death.

Resection of right atrial lymphoma in a patient with AIDS.

Although cardiac problems are common in acquired immunodeficiency syndrome, there is limited experience with heart surgery in this group of patients. We report a case in which a right atrial lymphoma was resected to alleviate tricuspid valve obstruction in a patient with AIDS. The patient did well for approximately 7 months. At that time, he developed multiple complications of AIDS and deteriorated rapidly; he died 8 months after operation. Cardiac surgery can be successfully performed in AIDS patients. However, the late outcome is compromised by the nature of the underlying viral infection.