Processive translocation and DNA unwinding by individual RecBCD enzyme molecules.

RecBCD enzyme is a processive DNA helicase and nuclease that participates in the repair of chromosomal DNA through homologous recombination. We have visualized directly the movement of individual RecBCD enzymes on single molecules of double-stranded DNA (dsDNA). Detection involves the optical trapping of solitary, fluorescently tagged dsDNA molecules that are attached to polystyrene beads, and their visualization by fluorescence microscopy. Both helicase translocation and DNA unwinding are monitored by the displacement of fluorescent dye from the DNA by the enzyme. Here we show that unwinding is both continuous and processive, occurring at a maximum rate of 972 +/- 172 base pairs per second (0.30 microm s(-1)), with as many as 42,300 base pairs of dsDNA unwound by a single RecBCD enzyme molecule. The mean behaviour of the individual RecBCD enzyme molecules corresponds to that observed in bulk solution.

Translocation step size and mechanism of the RecBC DNA helicase.

DNA helicases are ubiquitous enzymes that unwind double-stranded DNA. They are a diverse group of proteins that move in a linear fashion along a one-dimensional polymer lattice--DNA--by using a mechanism that couples nucleoside triphosphate hydrolysis to both translocation and double-stranded DNA unwinding to produce separate strands of DNA. The RecBC enzyme is a processive DNA helicase that functions in homologous recombination in Escherichia coli; it unwinds up to 6,250 base pairs per binding event and hydrolyses slightly more than one ATP molecule per base pair unwound. Here we show, by using a series of gapped oligonucleotide substrates, that this enzyme translocates along only one strand of duplex DNA in the 3'-->5' direction. The translocating enzyme will traverse, or 'step' across, single-stranded DNA gaps in defined steps that are 23 (+/-2) nucleotides in length. This step is much larger than the amount of double-stranded DNA that can be unwound using the free energy derived from hydrolysis of one molecule of ATP, implying that translocation and DNA unwinding are separate events. We propose that the RecBC enzyme both translocates and unwinds by a quantized, two-step, inchworm-like mechanism that may have parallels for translocation by other linear motor proteins.

UTP is a cofactor for the DNA strand exchange reaction performed by the RecA protein of Escherichia coli.

The RecA protein of Escherichia coli is required for homologous genetic recombination and induction of the SOS regulon. In order for RecA protein to function in these two roles, a nucleoside triphosphate cofactor, usually ATP or dATP, is required. We have examined the ability of UTP to substitute for (r,d)ATP as nucleoside triphosphate cofactor. We have found that although UTP is hydrolyzed by RecA protein in the presence of long DNA molecules, it is not hydrolyzed in reactions in which the cofactors are oligodeoxyribonucleotides less than approximately 50 nt in length. We show that UTP can efficiently substitute for ATP as nucleoside triphosphate cofactor for the DNA strand exchange reaction in vitro. The RecA1332 protein (Cys129 --> Met), which was originally shown to be defective for homologous recombination in vivo, is able to perform DNA strand exchange in vitro with ATP, but is unable to do so with UTP. These results suggest that UTP may be a cofactor for DNA strand exchange in vivo. The inability of RecA protein to hydrolyze UTP with oligodeoxyribonucleotides as cofactor and the ability of RecA to utilize UTP as cofactor in DNA strand exchange suggest a separation of the functions of RecA protein into those that require exclusively ATP and those which can utilize additional nucleoside triphosphate cofactors.

The reduced levels of chi recognition exhibited by the RecBC1004D enzyme reflect its recombination defect in vivo.

Homologous recombination in Escherichia coli is initiated by the RecBCD enzyme and is stimulated by an 8-nucleotide element known as Chi (chi). We present a detailed biochemical characterization of a mutant RecBCD enzyme, designated RecBC1004D, that displays a reduced level of chi site recognition. Initially characterized genetically as unable to respond to the chi sequence, we provide evidence to indicate that the ability of this mutant enzyme to respond to chi is reduced rather than lost; the mutant displays about 20-fold lower chi recognition than wild-type RecBCD enzyme. Although this enzyme exhibits wild-type levels of double-stranded DNA exonuclease, helicase, and ATPase activity, its ability to degrade single-stranded DNA is enhanced 2-3-fold. The data presented here suggest that the reduced recombination proficiency of the recBC1004D strain observed in vivo results from a basal level of modification of the RecBC1004D enzyme at both chi-specific, as well as nonspecific, DNA sequences.

DNA strand exchange proteins: a biochemical and physical comparison.

Homologous genetic recombination is an essential biological process that involves the pairing and exchange of DNA between two homologous chromosomes or DNA molecules. It is of fundamental importance to the preservation of genomic integrity, the production of genetic diversity, and the proper segregation of chromosomes. In Escherichia coli, the RecA protein is essential to recombination, and biochemical analysis demonstrates that it is responsible for the crucial steps of homologous pairing and DNA strand exchange. The presence of RecA-like proteins, or their functional equivalents, in bacteriophage, other eubacteria, archaea, and eukaryotes, confirms that the mechanism of homologous pairing and DNA strand exchange is conserved throughout all forms of life. This review focuses on the biochemical and physical characteristics of DNA strand exchange proteins from three diverse organisms: RecA protein from E. coli, UvsX protein from Bacteriophage T4, and RAD51 protein from Saccharomyces cerevisiae.

Characterization of RecA1332 in vivo and in vitro. A role for alpha-helix E as a liaison between the subunit-subunit interface and the DNA and ATP binding domains of RecA protein.

BACKGROUND: The RecA protein of Escherichia coli is essential for homologous recombination and induction of the SOS response. RecA has three cysteines located at positions 90, 116 and 129. Chemical modification of these residues abolishes ATP hydrolysis and repressor cleavage, and causes a reduction in the DNA strand exchange and DNA strand annealing activities. Several mutants at each of these positions were isolated and partially characterized. One of these, recA1332, replaces cysteine 129 with methionine. Although this is a relatively conservative mutation based on hydrophobicity, recA1332 was completely defective for DNA repair but the purified protein was active for ATPase in vitro. RESULTS: In vivo, strains containing this mutant allele were shown to be defective when assayed for all RecA-dependent activities. In vitro, RecA1332 protein possessed DNA-dependent ATP hydrolysis activity that showed an increased sensitivity to inhibition by monovalent cations, and whose k(cat) was reduced 3- to 12-fold. In addition, RecA1332 was unable to use oligodeoxyribonulceotides as ssDNA cofactors in the ATPase reaction. RecA1332 showed altered binding to single- and double-stranded DNA and, although it was able to perform DNA strand exchange, it was slowed in its ability to both form joint molecule intermediates and to convert these species to product. CONCLUSIONS: Our results are consistent with a defect in intermolecular interactions between RecA monomers. We propose that alpha-helix E (which includes C129M) is a liaison that connects the subunit-subunit interactions to DNA and ATP binding, thereby creating filament stability and cooperativity.

The recombination hotspot Chi is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5'-GCTGGTGG-3'.

The RecBCD enzyme of Escherichia coli functions in the seemingly disparate roles of homologous recombination and the degradation of DNA. Which of these two roles it assumes is regulated by the 8-base recombination hotspot, Chi. Using double-stranded DNA substrates that are heteroduplex at the Chi locus we have established the determinants for Chi recognition. Our results show that an actively translocating RecBCD enzyme requires only the sequence information in the 5'-GCTGGTGG-3'-containing strand to recognize and to be regulated by Chi. Furthermore, the RecBCD enzyme can translocate through DNA heteroduplex bubbles as large as 22 bases, and still recognize a Chi sequence embedded in this region. This implies that recognition of Chi occurs following the unwinding of the DNA.

Interaction of the RecA protein of Escherichia coli with single-stranded oligodeoxyribonucleotides.

The RecA protein of Escherichia coli performs a number of ATP-dependent, in vitro reactions and is a DNA-dependent ATPase. Small oligodeoxyribonucleotides were used as DNA cofactors in a kinetic analysis of the ATPase reaction. Polymers of deoxythymidilic acid as well as oligonucleotides of mixed base composition stimulated the RecA ATPase activity in a length-dependent fashion. Both the initial rate and the extent of the reaction were affected by chain length. Full activity was seen with chain lengths > or = 30 nt. Partial activity was seen with chain lengths of 15-30 nt. The lower activity of shorter oligonucleotides was not simply due to a reduced affinity for DNA, since effects of chain length on KmATP and the Hill coefficient for ATP hydrolysis were also observed. The results also suggested that single-stranded DNA secondary structure frequently affects the ATPase activity of RecA protein with oligodeoxyribonucleotides.

Automated determination of beta-galactosidase specific activity.

We describe a modification of an automated kinetic assay for beta-galactosidase (beta-gal) activity. This modification includes an assay to quantitate the amount of protein added to each assay. The determination of specific activity includes the amount of protein in the calculation which produces a specific activity with units of pmol product produced/minute/mg protein. In addition to this modification, we present a series of macros written in Microsoft Excel for either the Macintosh or Windows on the PC. These macros decrease the amount of time required to analyze the data from beta-gal assays.

Update of 156 episodes of central nervous system bleeding in hemophiliacs.

Between 1960 and 1991, 156 episodes of central nervous system (CNS) bleeding were documented in 106 patients from a total population of 1,410 hemophiliacs (7.5%). Ninety-one hemophilia A patients presented 131 bleeding episodes; 15 hemophilia B patients had 25 episodes. 32% of these episodes took place in patients less than 5 years of age. 46% were age 10 or less, and 72% were age 20 or less. The mean age was 14.8 years in hemophilia A and 9 years in hemophilia B patients. A significant increase in the mean age of hemophilia A patients has been observed over the last 10 years; this may be related to HIV infection. A history of recent trauma was documented in 39.7% of the episodes. Spontaneous CNS bleeding was predominant in severe hemophilia (85.2%). One hundred and fifty-four CNS bleeding episodes were intracranial and 2 intraspinal. Of the intracranial episodes, 37.7% were subarachnoid, 29.8 subdural, and 22.7% intracerebral. Factor VIII or IX inhibitors were present in 11.3% of the patients; this figure is slightly lower than that observed in our total hemophilic population. Over 50% of the patients had psychoneurological sequelae; the most frequent were seizure disorders and motor impairment. The overall mortality rate was 29.2%. The mortality was more closely related to the CNS bleeding site than to the severity of hemophilia. Treatment should be based on prompt and prolonged replacement therapy to ensure hemostatic levels of antihemophilia factors.