One of the biggest challenges in nanobiotechnology is to engineer a biological component to carry out a specific task. The goal of this application is to engineer the bacteriophage T4 DNA packaging motor to translocate double stranded RNA and RNA:DNA hybrid molecules. The ability to alter the translocation specificity of the motor will greatly enhance its potential as a delivery nanomachine;adapting the existing machinery to transport a therapeutic molecule of interest into cells. The X-ray and cryo-EM structures of the phage T4 packaging motor have been recently determined. The motor protein, gp17, consists of several parts;ATPase (the engine), translocase (the wheel) and arginine finger (the spark plug). The translocation specificity is determined by a DNA binding groove that is well- separated from the rest of the motor. The shape and size of the groove fit a double stranded DNA molecule, and the distribution of positively charged residues lining the groove follows the pitch of the double helix;interacting with the backbone phosphates. These features suggest that the packaging motor is amendable to design novel motors with altered specificity. The translocation groove of gp17 will be mutagenized by error-prone and overlap extension PCR to introduce ~3 mutations per groove. Hundreds, if not thousands, of variants will be screened for the ability to translocate RNA in a high-throughput format. The his-tagged mutants will be overexpressed in E.coli and purified by affinity chromatography using 96-well Ni-Sepharose plates. An established defined in vitro packaging assay consisting of purified proheads, the packaging motor, ATP, and nucleic acid will be used to rapidly screen for RNA translocation mutants. This assay assembles the packaging machine in solution, and translocation into proheads is assessed by the presence of nuclease-protected RNA following agarose gel electrophoresis. The simplicity of this system lends itself well to the high-throughput format, allowing hundreds of mutant proteins and several different nucleic acids to be tested. The gp17 RNA translocation mutants identified in the high-throughput screen will be purified and analyzed for packaging ATPase, efficiency, and substrate specificity. Structural modeling of the mutant translocation grooves will be guided by the already determined crystal structures of the motor protein and its domains. Single molecule studies will be performed using optical tweezers to analyze motor dynamics;force, power, and rate, as well as frequency of slips or pauses;identifying subtle mechanistic differences between DNA and RNA translocation. Together, these findings will establish the design principles for further engineering of the motor to improve specificity and/or efficiency of RNA translocation. The proof of principle data generated from this application will provide a broader foundation for the application of the phage T4 packaging motor as a versatile nanomachine.
A major challenge in nanobiotechnology is the ability to engineer new or improved biological devices for a specific purpose. The current application aims to use an established scheme of mutagenesis, biochemistry, structural analysis, and biophysical measurements and apply it to the design of a novel nanomachine from a well-defined viral packaging motor. This project will provide proof of principle data for the development of this system into a versatile delivery vehicle, delivering DNA, RNA, peptide, or drug therapy into the cell.
| Feiss, Michael; Rao, Venigalla B (2012) The bacteriophage DNA packaging machine. Adv Exp Med Biol 726:489-509 |
| Zhang, Zhihong; Kottadiel, Vishal I; Vafabakhsh, Reza et al. (2011) A promiscuous DNA packaging machine from bacteriophage T4. PLoS Biol 9:e1000592 |
| Ghosh-Kumar, Manjira; Alam, Tanfis I; Draper, Bonnie et al. (2011) Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4. Nucleic Acids Res 39:2742-55 |
