Establishing the Roles of the DNA Binding Domains of Replication Protein A (RPA)

During DNA metabolic processes such as replication and repair, double-stranded DNA is transiently unwound to expose single-stranded DNA (ssDNA). Such ssDNA intermediates are immediately coated by Replication Protein A (RPA), an essential single-stranded DNA binding protein present in all eukaryotes. RPA binding to ssDNA fulfills four goals: 1. The ssDNA is protected from degradation by endo- and exo-nucleases. 2. A cell-cycle checkpoint signaling cascade is triggered to indicate the presence of ssDNA. 3. RPA recruits other DNA metabolic enzymes on to the ssDNA. 4. Finally, RPA promotes the catalytic activity of the recruited enzyme. The overall objective of my thesis work focuses on deciphering how a single enzyme can coordinate multiple DNA metabolic processes in the cell to protect genomic integrity.RPA is a multi-subunit complex composed of four DNA binding domains (DBDs-A, B, C and D) and two protein interaction domains (PIDs). The DBDs promote high affinity binding to ssDNA and the PIDs interact with more than two dozen proteins to control and coordinate various DNA metabolic processes. The DBDs and PIDs are tethered by flexible disordered linkers that enable RPA to adopt a variety of conformations. A long-standing hypothesis posits that specific RPA-conformations drive a corresponding cellular activity. My thesis work has developed experimental methodologies to visualize and capture the conformational states of RPA. Furthermore, we show how RPA-conformations are modulated by RPA-interacting proteins and post-translational modifications.The major findings of my thesis research are: i) Establishment of DBDs A, B as the flexible unit of RPA, and DBDs C, D with RPA14 as the stable unit of RPA. ii) Existence of four distinct microscopic binding/ dissociation states of DBD-A and DBD-D in context of full-length RPA iii) DNA structures encountered by RPA affect the conformational states and arrangement of RPA-DBDs iv) RPA interacting proteins, such as Rad52, can selectively modify the DNA binding dynamics of a particular DBD. v) Cooperative binding in Rad52 selectively modulates the DNA binding states of DBD-D but not DBA-A and vi) Post-translational modification alters microscopic binding states and conformational arrangement of DBDs on DNA. This alteration can affect both assembly and stability of the RPA-DNA complex alone, or in the presence of proteins seeking to displace RPA from DNA

Monitoring Replication Protein A (RPA) Dynamics in Homologous Recombination Through Site-specific Incorporation of Non-canonical Amino Acids

An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance

Evidence That the P\u3csub\u3ei\u3c/sub\u3e Release Event Is the Rate-Limiting Step in the Nitrogenase Catalytic Cycle

Nitrogenase reduction of dinitrogen (N2) to ammonia (NH3) involves a sequence of events that occur upon the transient association of the reduced Fe protein containing two ATP molecules with the MoFe protein that includes electron transfer, ATP hydrolysis, Pi release, and dissociation of the oxidized, ADP-containing Fe protein from the reduced MoFe protein. Numerous kinetic studies using the nonphysiological electron donor dithionite have suggested that the rate-limiting step in this reaction cycle is the dissociation of the Fe protein from the MoFe protein. Here, we have established the rate constants for each of the key steps in the catalytic cycle using the physiological reductant flavodoxin protein in its hydroquinone state. The findings indicate that with this reductant, the rate-limiting step in the reaction cycle is not protein–protein dissociation or reduction of the oxidized Fe protein, but rather events associated with the Pi release step. Further, it is demonstrated that (i) Fe protein transfers only one electron to MoFe protein in each Fe protein cycle coupled with hydrolysis of two ATP molecules, (ii) the oxidized Fe protein is not reduced when bound to MoFe protein, and (iii) the Fe protein interacts with flavodoxin using the same binding interface that is used with the MoFe protein. These findings allow a revision of the rate-limiting step in the nitrogenase Fe protein cycle

A Force Sensor that Converts Fluorescence Signal into Force Measurement Utilizing Short Looped DNA

A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged by a DNA hairpin and KCl was titrated to change the applied force. After these proof-of-principle measurements, one of the dsDNA constructs was used to maintain the G-quadruplex (GQ) construct formed by thrombin binding aptamer (TBA) under tension while it interacted with a destabilizing protein and stabilizing small molecule. The force required to unfold TBA-GQ was independently investigated with high-resolution optical tweezers (OT) measurements that established the relevant force to be a few pN, which is consistent with the force generated by the looped dsDNA. The proposed method is particularly promising as it enables studying NAS, protein, and small molecule interactions using a highly-parallel FRET-based assay while the NAS is kept under an approximately constant force

Dynamics and Selective Remodeling of the DNA-binding Domains of RPA

Replication protein A (RPA) coordinates important DNA metabolic events by stabilizing single-stranded DNA (ssDNA) intermediates, activating the DNA-damage response and handing off ssDNA to the appropriate downstream players. Six DNA-binding domains (DBDs) in RPA promote high-affinity binding to ssDNA yet also allow RPA displacement by lower affinity proteins. We generated fluorescent versions of Saccharomyces cerevisiae RPA and visualized the conformational dynamics of individual DBDs in the context of the full-length protein. We show that both DBD-A and DBD-D rapidly bind to and dissociate from ssDNA while RPA remains bound to ssDNA. The recombination mediator protein Rad52 selectively modulates the dynamics of DBD-D. These findings reveal how RPA-interacting proteins with lower ssDNA binding affinities can access the occluded ssDNA and remodel individual DBDs to replace RPA

Yeast Rad52 is a homodecamer and possesses BRCA2-like bipartite Rad51 binding modes

Homologous recombination (HR) is an essential double-stranded DNA break repair pathway. In HR, Rad52 facilitates the formation of Rad51 nucleoprotein filaments on RPA-coated ssDNA. Here, we decipher how Rad52 functions using single-particle cryo-electron microscopy and biophysical approaches. We report that Rad52 is a homodecameric ring and each subunit possesses an ordered N-terminal and disordered C-terminal half. An intrinsic structural asymmetry is observed where a few of the C-terminal halves interact with the ordered ring. We describe two conserved charged patches in the C-terminal half that harbor Rad51 and RPA interacting motifs. Interactions between these patches regulate ssDNA binding. Surprisingly, Rad51 interacts with Rad52 at two different bindings sites: one within the positive patch in the disordered C-terminus and the other in the ordered ring. We propose that these features drive Rad51 nucleation onto a single position on the DNA to promote formation of uniform pre-synaptic Rad51 filaments in HR

Phosphate removal and recovery using immobilized phosphate binding proteins

Progress towards a more circular phosphorus economy necessitates development of innovative water treatment systems which can reversibly remove inorganic phosphate (Pi) to ultra-low levels (<100 μg L−1), and subsequently recover the Pi for reuse. In this study, a novel approach using the high-affinity E. coli phosphate binding protein (PBP) as a reusable Pi bio-adsorbent was investigated. PBP was expressed, extracted, purified and immobilized on NHS-activated Sepharose beads. The resultant PBP beads were saturated with Pi and exposed to varying pH (pH 4.7 to 12.5) and temperatures (25–45 °C) to induce Pi release. Increase in temperature from 25 to 45 °C and pH conditions between 4.7 and 8.5 released less than 20% of adsorbed Pi. However, 62% and 86% of the adsorbed Pi was released at pH 11.4 and 12.5, respectively. Kinetic experiments showed that Pi desorption occurred nearly instantaneously (<5 min), regardless of pH conditions, which is advantageous for Pi recovery. Additionally, no loss in Pi adsorption or desorption capacity was observed when the PBP beads were exposed to 10 repeated cycles of adsorption/desorption using neutral and high pH (≥12.5) washes, respectively. The highest average Pi adsorption using the PBP beads was 83 ± 5%, with 89 ± 4.1% average desorption using pH 12.5 washes over 10 wash cycles at room temperature. Thermal shift assay of the PBP showed that the protein was structurally stable after 10 cycles, with statistically similar melting temperatures between pH 4 and 12.5. These results indicate that immobilized high-affinity PBP has the potential to be an effective and reversible bio-adsorbent suitable for Pi recovery from water/wastewater. Keywords: Adsorbent, Phosphorus, Nutrient reuse, pstS, Water, Wastewate

Evidence That the P_i Release Event Is the Rate-Limiting Step in the Nitrogenase Catalytic Cycle

Nitrogenase reduction of dinitrogen (N₂) to ammonia (NH₃) involves a sequence of events that occur upon the transient association of the reduced Fe protein containing two ATP molecules with the MoFe protein that includes electron transfer, ATP hydrolysis, P_i release, and dissociation of the oxidized, ADP-containing Fe protein from the reduced MoFe protein. Numerous kinetic studies using the nonphysiological electron donor dithionite have suggested that the rate-limiting step in this reaction cycle is the dissociation of the Fe protein from the MoFe protein. Here, we have established the rate constants for each of the key steps in the catalytic cycle using the physiological reductant flavodoxin protein in its hydroquinone state. The findings indicate that with this reductant, the rate-limiting step in the reaction cycle is not protein–protein dissociation or reduction of the oxidized Fe protein, but rather events associated with the P_i release step. Further, it is demonstrated that (i) Fe protein transfers only one electron to MoFe protein in each Fe protein cycle coupled with hydrolysis of two ATP molecules, (ii) the oxidized Fe protein is not reduced when bound to MoFe protein, and (iii) the Fe protein interacts with flavodoxin using the same binding interface that is used with the MoFe protein. These findings allow a revision of the rate-limiting step in the nitrogenase Fe protein cycle