Team:MIT phage design

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Phage
hairy cells and polymerizing phage - design

OVERVIEW
When designing the system we had to consider two critical aspects: linkage creation and circuitry. We decided to use an M13 bacteriophage-based system. By knocking out pIII production we could get the infected cells to create polyphage "hairs". To make this easy, instead of using wild-type M13, we used a product called Hyperphage, which comes with a truncated gene for pIII. For linkage, we decided to use phage-display of leucine zippers, fusing them to the pVIII coat protein. The circuitry used is similar to the circuitry for the RFP output: our fusion protein is controlled by the toggle, allowing UV input to begin fusion protein production and hopefully polymerization (amongst a heterogeneous population with matching linkers). Additionally, we wanted to have the exterior of the UV pattern have no polymerization, so we designed an inverter to be ON where UV is OFF. See below for further details.

PHAGE-RELEVANT CIRCUITRY DESIGN


  1. Toggle - The toggle-switch works by mutual repression. Through addition of IPTG, it can be set to “off”, and UV, “on”. The “on” state lets RecA cleave cI, allowing for leaky transcription from the hybrid luxR/cI-regulated promoters. For full transcription, the LuxR-AHL complex must bind. AHL can thus be added to induce transcription while LuxR is produced constitutively. This toggle was donated from the Collins lab. It has been biobricked as K415300 (a low-power version is K415301).

  2. & 3. Pattern Formation - Constitutive LuxR allows for expression of mCherry and pVIII fusion proteins where there is no cI (i.e., where there is UV induction). Two distinct pVIII phage proteins are expressed in two populations of cells which then should bind together via leucine zipper interactions to allow for polymerization in the UV-induced area. Part (2) is K415010, Part (3) combined with Part (2) creates our K415147-152 parts.

  3. Inverter - In order to inhibit phage polymerization outside of the UV-induced region, an inverter allows for transcription only in areas where UV has not been introduced. pIII production then prohibits polyphage from forming which precludes leucine zipper interactions and polymerization. This part is currently in the construction phase and has not been incorporated into existing circuitry. (There's also another inverter being developed using the CymR system.)


HYPERPHAGE
Hyperphage is a plasmid with the gene for pIII truncated. The pIII protein is required for phage exit from the host cell membrane; phage without a proper pIII grow into long fibril-like structures called polyphage. The goal is to crosslink these polyphage. Hyperphage can be obtained from Progen in Germany.

P8-FUSION DESIGN


The above shows the RBS + p8-fusion genetic design. We chose p8 because of the large number of copies, increasing the potential for incorporation, and hopefully allowing for large-scale polymerization instead of small-scale clumping which might happen with p9 (due to the small number of p9 produced). This genetic fusion is designed to allow the expression of a leucine zipper (coil in the diagram) on the p8 phage coat protein. There are six total p8 fusions for the six different zippers. To assist in proper cellular trafficking to the membrane, a leader sequence was introduced. Additionally, HA and Myc tags were introduced (one for each half of a zipper pair), which were used in western blotting experiments to test for the expression of the p8-fusion genes. A special version of p8 has been used, called opti-p8, which displays proteins better (see Weiss et al. Mutational analysis of the major coat protein of M13 identifies residues that control protein display. 2000.)

P8-FUSION DESIGN IN DETAIL Below is a PDF document detailing all aspects of the fusion designs, including some design notes and references.
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