Endy:Chassis engineering/Orthogonal protein synthesis: Difference between revisions

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==Dedicated systems==
==Motivation==
[[Image:DedicatedTubesW852.jpg|thumb|right|300px|An independent protein production channel, dedicated to the synthesis of engineered system proteins would contribute to decoupling the operation of systems and their cellular chassis]].
[[Image:DedicatedTubesW852.jpg|thumb|right|300px|Two orthogonal protein synthesis channels, one specific for engineered biological systems and one specific for normal cellular function.]]
Engineered biological systems use host cells as a power supply and chassis.  In an ideal chassis-system relationship, the operation of the chassis should be decoupled from the operation of the system and vice versa.  This is not the case for today's engineered biological systems.  For example, today's engineered systems use the same transcription and translation machinery as the cellular chassis.  The engineered system and the chassis also share a pool of nucleotides, amino acids, and tRNAs. Variations in machinery and material levels affect the operation of the engineered system and high demands for machinery and materials by the system perturb the function of the chassis.


A solution to this problem of the coupled function of the engineered system and chassis is to construct a second protein production system inside the chassis, which is independent from, or orthogonal to, the endogenous protein production system.  Ideally, this dedicated system channel would use transcription, translation machinery that is orthogonal from that of the cellular chassis and also draw from a different material pool than the chassis.  The levels and regulation of the components of the dedicated system channel could be modified independent from the levels and regulation of the protein production system of the chassis itself.
We are working to reduce the coupling between engineered biological systems and their cellular chassis.  This coupling leads to unexpected system behavior and perturbed cellular function.  A major source of the coupling between system and chassis is that both share the same transcription and translation processes.  We are working to implement an orthogonal protein synthesis channel that is solely used by an engineered biological system and does not perturb cellular function.


If this dedicated system channel could be standardized and designed to be able function in multiple cell types, then the dedicated systems could form the basis of a [[Endy:Dedicated systems/Virtual machines| biological virtual machine]]
 
If this orthogonal channel can be standardized and designed to function in multiple cell types, then it forms the basis of a [[Endy:Dedicated systems/Virtual machines| biological virtual machine]]([[Endy:Dedicated systems/Virtual machines|1.0]], [[Endy:Chassis engineering/VM2.0|2.0]]).
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*[[Endy:Dedicated systems/Transcription|Dedicated Transcription]]
*[[Endy:Dedicated systems/Transcription|Dedicated Transcription]]
*[[Endy:Dedicated systems/Translation|Dedicated Translation]]
*[[Endy:Dedicated systems/Translation|Dedicated Translation]]
==Demonstrating the usefulness of dedicated systems==
#'''Measure specificity of combined dedicated systems'''
#'''Demonstrate decoupled function of the system and the cellular chassis'''
#*GFP accumulation as chassis make the transition from log to stationary phase should indicate whether system performance is less affected by the change in the chassis state.
#*Suddenly turning on the high level protein expression of a system should reduce growth rate of the chassis when the system uses dedicated systems than when it does not.  Initial experiments have suggested that this might only be true in a minimal media such as M9.


==First generation reporter devices for the dedicated transcription/translation systems==
==First generation reporter devices for the dedicated transcription/translation systems==
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==Demonstrating the usefulness of dedicated systems==
#'''Measure specificity of combined dedicated systems'''
#'''Demonstrate decoupled function of the system and the cellular chassis'''
#*GFP accumulation as chassis make the transition from log to stationary phase should indicate whether system performance is less affected by the change in the chassis state.
#*Suddenly turning on the high level protein expression of a system should reduce growth rate of the chassis when the system uses dedicated systems than when it does not.  Initial experiments have suggested that this might only be true in a minimal media such as M9.

Latest revision as of 14:44, 7 March 2007

Motivation

Two orthogonal protein synthesis channels, one specific for engineered biological systems and one specific for normal cellular function.

We are working to reduce the coupling between engineered biological systems and their cellular chassis. This coupling leads to unexpected system behavior and perturbed cellular function. A major source of the coupling between system and chassis is that both share the same transcription and translation processes. We are working to implement an orthogonal protein synthesis channel that is solely used by an engineered biological system and does not perturb cellular function.


If this orthogonal channel can be standardized and designed to function in multiple cell types, then it forms the basis of a biological virtual machine(1.0, 2.0).

Currently, we are working to enable dedicated transcription and dedicated translation in an E. coli strain MG1655 chassis. Details on this work can be found on the following pages -

Demonstrating the usefulness of dedicated systems

  1. Measure specificity of combined dedicated systems
  2. Demonstrate decoupled function of the system and the cellular chassis
    • GFP accumulation as chassis make the transition from log to stationary phase should indicate whether system performance is less affected by the change in the chassis state.
    • Suddenly turning on the high level protein expression of a system should reduce growth rate of the chassis when the system uses dedicated systems than when it does not. Initial experiments have suggested that this might only be true in a minimal media such as M9.

First generation reporter devices for the dedicated transcription/translation systems

General Translation VM Translation
General Transcription I7101
 I7102
VM Transcription E7104
 E7103
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