E. Colimousine

Overview

This project is destined to generate an E. Coli strain which can transport target protein along a gradient back and forth. The bacteria can bind with the target protein at one place and then, by sensing the gradient of certain amino acid, move to its destination, where it releases the protein with the help from another E. Coli strain. When this is done, it will move back to transport more target protein. In this process, four modules are necessary: binding, releasing, movement and transition.

Binding

We first need to conjugate a binding vehicle directly sensing substrate in the medium. Outer membrane protein A (OmpA)

Src-homology 3 (SH3) domain <div class="div-tip">Src-homology 3 (SH3) domain has high affinity for proline-rich peptides and together they can form a left-handed poly-Pro type II helix, with the minimal consensus Pro-X-X-Pro.</div> which has high affinity for proline-rich peptides, could act like tongs to grab any protein with a proline riich motif. For easy track, fluorescent protein mCherry was the one linked withthe binding motif (Kd=3.67μM).

SH3 binding domain (shown bound to proline-rich peptide)

OmpA transmembrane segment

The binding module eventually comprises of two proteins, namely, OmpA-SH3 protein, which functions as the binding vehicle and proline-rich containing mCherry protein, which functions as the binding substrate.

Releasing

It’s difficult to release the substrate from strong binding, and hence protease is called into play. HIV-protease is readily available and its high efficiency, low molecular weight and high specificity constitutes fine candidate. We only need to add the substrate sequence (HIV-protease site) between OmpA and SH3 sequence and the protease will cut off the binding cassette. In order to segregate the action, we fuse the HIV-protease with OmpA and expressed it in a second E.coli strain which we immobilize at the destination. So, when the E.coli transporter arrives at the destination, the HIV-protease that is located on the outer membrane of the second E.coli strain will help release the substrate (together with SH3 domain) by cut the HIV-protease site.

Protease site between OmpA and SH3 binding domain.

Protease presented outside by OmpA fusion

Movement

Chemotaxis is most frequently used when it comes to the movement of E.coli cells and the regulatory network controlling E.coli chemotaxis is one of the well-studied models of signal transduction. Extracellular signals, aspartate and serine in this case, are sensed by receptors Tar and Tsr respectively. These receptors assemble into large clusters that are predominantly located at the poles of the bacterium. The CheW protein binds to the receptors and acts as a scaffold protein to recruit CheA, whose phosphorylation is stimulated by the receptor. The phosphate is transferred to the cytoplasmic protein CheY, which controls flagellar rotation and in turn, controls the movement of E.coli. Previously, a pair of mutations in CheW* (V108M) and Tsr* (E402A) was shown to produce an orthogonal pair, where the mutated proteins interact with each other but not with wildtype Tsr or CheW. So, this can be used to toggle between activating the serine-responsive Tsr* and aspartate-responsive Tar. When we set up two gradients (serine and aspartate) going in opposite direction, the bacteria can move forth and back.

Transition

We need to shift between two states, the binding state and the releasing state. This molecular device is well-known for its lag in phase change, which is well adapted for our application. The lag during the phase transition is appropriate for movement and transport. λ repressor is used in our project and we can see the two different states and how we shift between them from the two picture below.