Ichiro Amitani

Direct observation of individual RecA filaments assembling on single DNA molecules

Escherichia coli RecA is essential for the repair of DNA double-strand breaks by homologous recombination. Repair requires the formation of a RecA nucleoprotein filament. Previous studies have indicated a mechanism of filament assembly whereby slow nucleation of RecA protein on DNA is followed by rapid growth. However, many aspects of this process remain unclear, including the rates of nucleation and growth and the involvement of ATP hydrolysis, largely because visualization at the single-filament level is lacking. Here we report the direct observation of filament assembly on individual double-stranded DNA molecules using fluorescently modified RecA. The nucleoprotein filaments saturate the DNA and extend it ∼1.6-fold. At early time points, discrete RecA clusters are seen, permitting analysis of single-filament growth from individual nuclei. Formation of nascent RecA filaments is independent of ATP hydrolysis but is dependent on the type of nucleotide cofactor and the RecA concentration, suggesting that nucleation involves binding of ∼4–5 ATP–RecA monomers to DNA. Individual RecA filaments grow at rates of 3–10 nm s-1. Growth is bidirectional and, in contrast to nucleation, independent of nucleotide cofactor, suggesting addition of ∼2–7 monomers s-1. These results are in accord with extensive genetic and biochemical studies, and indicate that assembly in vivo is controlled at the nucleation step. We anticipate that our approach and conclusions can be extended to the related eukaryotic counterpart, Rad51 (see ref.), and to regulation by assembly mediators.

The BRC Repeats of BRCA2 Modulate the DNA Binding Selectivity of RAD51

The breast cancer susceptibility protein, BRCA2, is essential for recombinational DNA repair. BRCA2 delivers RAD51 to double-stranded DNA (dsDNA) breaks through interaction with eight conserved, approximately 35 amino acid motifs, the BRC repeats. Here we show that the solitary BRC4 promotes assembly of RAD51 onto single-stranded DNA (ssDNA), but not dsDNA, to stimulate DNA strand exchange. BRC4 acts by blocking ATP hydrolysis and thereby maintaining the active ATP-bound form of the RAD51-ssDNA filament. Single-molecule visualization shows that BRC4 does not disassemble RAD51-dsDNA filaments but rather blocks nucleation of RAD51 onto dsDNA. Furthermore, this behavior is manifested by a domain of BRCA2 comprising all eight BRC repeats. These results establish that the BRC repeats modulate RAD51-DNA interaction in two opposing but functionally reinforcing ways: targeting active RAD51 to ssDNA and prohibiting RAD51 nucleation onto dsDNA. Thus, BRCA2 recruits RAD51 to DNA breaks and, we propose, the BRC repeats regulate DNA-binding selectivity.

Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules

Rad51 protein (Rad51) is central to recombinational repair of double-strand DNA breaks. It polymerizes onto DNA and promotes strand exchange between homologous chromosomes. We visualized the real-time assembly and disassembly of human Rad51 nucleoprotein filaments on double-stranded DNA by single-molecule fluorescence microscopy. Rad51 assembly extends the DNA by ≈65%. Nucleoprotein filament formation occurs via rapid nucleation followed by growth from these nuclei. Growth does not continue indefinitely, however, and nucleoprotein filaments terminate when ≈2 μm in length. The dependence of nascent filament formation on Rad51 concentration suggests that 2–3 Rad51 monomers are involved in nucleation. Rad51 nucleoprotein filaments are stable and remain extended when ATP hydrolysis is prevented; however, when permitted, filaments decrease in length as a result of conversion to ADP-bound nucleoprotein complexes and partial protein dissociation. Dissociation of Rad51 from dsDNA is slow and incomplete, thereby rationalizing the need for other proteins that facilitate disassembly.

RecBCD Enzyme Switches Lead Motor Subunits in Response to χ Recognition

RecBCD is a DNA helicase comprising two motor subunits, RecB and RecD. Recognition of the recombination hotspot, chi, causes RecBCD to pause and reduce translocation speed. To understand this control of translocation, we used single-molecule visualization to compare RecBCD to the RecBCD(K177Q) mutant with a defective RecD motor. RecBCD(K177Q) paused at chi but did not change its translocation velocity. RecBCD(K177Q) translocated at the same rate as the wild-type post-chi enzyme, implicating RecB as the lead motor after chi. P1 nuclease treatment eliminated the wild-type enzymes velocity changes, revealing a chi-containing ssDNA loop preceding chi recognition and showing that RecD is the faster motor before chi. We conclude that before chi, RecD is the lead motor but after chi, the slower RecB motor leads, implying a switch in motors at chi. We suggest that degradation of foreign DNA needs fast translocation, whereas DNA repair uses slower translocation to coordinate RecA loading onto ssDNA.

Single Molecule Imaging of Tid1/Rdh54, a Rad54 Homolog That Translocates on Duplex DNA and Can Disrupt Joint Molecules

The Saccharomyces cerevisiae Tid1 protein is important for the recombinational repair of double-stranded DNA breaks during meiosis. Tid1 is a member of Swi2/Snf2 family of chromatin remodeling proteins and shares homology with Rad54. Members of this family hydrolyze ATP and promote 1) chromatin remodeling, 2) DNA topology alterations, and 3) displacement of proteins from DNA. All of these activities are presumed to require translocation of the protein on DNA. Here we use single-molecule visualization to provide direct evidence for the ability of Tid1 to translocate on DNA. Tid1 translocation is ATP-dependent, and the velocities are broadly distributed, with the average being 84 ± 39 base pairs/s. Translocation is processive, with the average molecule traveling ∼10,000 base pairs before pausing or dissociating. Many molecules display simple monotonic unidirectional translocation, but the majority display complex translocation behavior comprising intermittent pauses, direction reversals, and velocity changes. Finally, we demonstrate that translocation by Tid1 on DNA can result in disruption of three-stranded DNA structures. The ability of Tid1 translocation to clear DNA of proteins and to migrate recombination intermediates may be of critical importance for DNA repair and chromosome dynamics.

WATCHING INDIVIDUAL PROTEINS ACTING ON SINGLE MOLECULES OF DNA

In traditional biochemical experiments, the behavior of individual proteins is obscured by ensemble averaging. To better understand the behavior of proteins that bind to and/or translocate on DNA, we have developed instrumentation that uses optical trapping, microfluidic solution delivery, and fluorescent microscopy to visualize either individual proteins or assemblies of proteins acting on single molecules of DNA. The general experimental design involves attaching a single DNA molecule to a polystyrene microsphere that is then used as a microscopic handle to manipulate individual DNA molecules with a laser trap. Visualization is achieved by fluorescently labeling either the DNA or the protein of interest, followed by direct imaging using high-sensitivity fluorescence microscopy. We describe the sample preparation and instrumentation used to visualize the interaction of individual proteins with single molecules of DNA. As examples, we describe the application of these methods to the study of proteins involved in recombination-mediated DNA repair, a process essential for the maintenance of genomic integrity.

Link between the Enzymatic Kinetics and Mechanical Behavior in an Actomyosin Motor

We have attempted to link the solution actomyosin ATPase with the mechanical properties of in vitro actin filament sliding over heavy meromyosin. To accomplish this we perturbed the system by altering the substrate with various NTPs and divalent cations, and by altering ionic strength. A wide variety of enzymatic and mechanical measurements were made under very similar solution conditions. Excellent correlations between the mechanical and enzymatic quantities were revealed. Analysis of these correlations based on a force-balance model led us to two fundamental equations, which can be described approximately as follows: the maximum sliding velocity is proportional to square root of V(max)K(m)(A), where K(m)(A) is the actin concentration at which the substrate turnover rate is half of its maximum (V(max)). The active force generated by a cross-bridge under no external load or under a small external load is proportional to square root of V(max)/K(m)(A). The equations successfully accounted for the correlations observed in the present study and observations in other laboratories.

Single-molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions

Fluorescent fusion proteins are exceedingly useful for monitoring protein localization in situ or visualizing protein behavior at the single molecule level. Unfortunately, some proteins are rendered inactive by the fusion. To circumvent this problem, we fused a hyperactive RecA protein (RecA803 protein) to monomeric red fluorescent protein (mRFP1) to produce a functional protein (RecA-RFP) that is suitable for in vivo and in vitro analysis. In vivo, the RecA-RFP partially restores UV resistance, conjugational recombination, and SOS induction to recA− cells. In vitro, the purified RecA-RFP protein forms a nucleoprotein filament whose kcat for single-stranded DNA-dependent ATPase activity is reduced ∼3-fold relative to wild-type protein, and which is largely inhibited by single-stranded DNA-binding protein. However, RecA protein is also a dATPase; dATP supports RecA-RFP nucleoprotein filament formation in the presence of single-stranded DNA-binding protein. Furthermore, as for the wild-type protein, the activities of RecA-RFP are further enhanced by shifting the pH to 6.2. As a consequence, RecA-RFP is proficient for DNA strand exchange with dATP or at lower pH. Finally, using single molecule visualization, RecA-RFP was seen to assemble into a continuous filament on duplex DNA, and to extend the DNA ∼1.7-fold. Consistent with its attenuated activities, RecA-RFP nucleates onto double-stranded DNA ∼3-fold more slowly than the wild-type protein, but still requires ∼3 monomers to form the rate-limited nucleus needed for filament assembly. Thus, RecA-RFP reveals that its attenuated biological functions correlate with a reduced frequency of nucleoprotein filament nucleation at the single molecule level.

Real-Time Visualization of Assembly and Disassembly of S. Cerevisiae Rad51 on Duplex DNA

DNA double-strand break (DSB) is a lethal type of DNA damage. Homologous recombination is the most accurate method to repair broken DNA. The process of recombinational DNA repair consists of three phases. First, the ends of broken DNA are processed to generate a 3′-ended single-strand DNA (ssDNA) tail on which the DNA strand exchange protein self-assembles. Second, the protein-DNA complex searches for homology on a donor double-strand DNA (dsDNA), and catalyzes the pairing and exchange of DNA strands. Finally, the heteroduplex DNA product is resolved.In S. cerevisiae, DNA strand exchange is catalyzed by Rad51 protein. Rad51 forms a right-handed helical nucleoprotein filament in an ATP-dependent manner. In the filament, Rad51 occupies 3-4 nucleotides and stretches DNA to ∼150% of its B-form length. Interestingly, Rad51 binds to dsDNA with a similar affinity as for ssDNA, even though the functional form of Rad51 requires assembly on ssDNA. Also, since Rad51 filament formation on dsDNA inhibits DNA strand exchange, the turnover of Rad51 from dsDNA is stimulated by a dsDNA translocase, Rad54.We used single-molecule fluorescence microscopy to visualize both the kinetics of assembly and disassembly of Rad51 nucleoprotein filaments. Visualization was achieved either by directly imaging filament formation using fluorescent Rad51 protein, or by measuring the DNA length change due to Rad51 binding by fluorescently tagging the DNA end. We show that the nucleation of Rad51 on dsDNA requires about 3 monomers; that Rad51 assembly occurs through frequent nucleation; and that the Rad51 filament is stabilized by maintaining ATP-bound state.