biomolbioandco

Science, discussed.

Resource allocation in Synthetic Biology [review]

What do you do to improve the efficiency of a system in which a key component P is used by multiple ‘effector’ mechanisms Si?
At first, one might be tempted to modulate the number (or availability) of P so that it is never rate-limiting. However, it might actually be better to find an alternative component P, say PT7, that does the job equally well, but is specific to the Si elements that need boosting. This way, the core processes will not be affected, and fine-tuning of the system becomes feasible

This is the approach exploited in Molecular Biology for protein (over-)expression: the T7 RNA Polymerase from the T7 Bacteriophage has been engineered in the chromosome of E. coli so that any heterologous plasmids bearing a gene under the control of the T7Pol promoter can be transcribed (T7 Polymerase image, courtesy of Wikipedia). The orthogonality of the system allows the implementation of additional switches, most importantly the ability to control the onset of protein expression. Although other polymerases have been implemented to build analogous systems, this is by far the most widely used method for protein production in E. coli (see review1, review2 and review3 for a sample of available literature).

Then Synthetic Biology came around to make a mess of everything. Many genes, multiple regulatory elements, all within a living cell. A synthetic system has a high energetic burden, and still ends up being underused.

But let’s take a step back. Transcription in E. coli is a good example of the ideal complex mentioned above:  different pools of genes have to be transcribed at different times, on top of a set of constantly-expressed housekeeping genes. The way bacterial cells deal with this is by implementing modularity: instead of a single polymerase enzyme P, there is a protein complex Paσ  in which catalytic activity and specificity determinants are uncoupled: in E. coli, the Pa apoenzyme provides the catalytic machinery, while different sigma factors σi are responsible for the docking of the RNA Pol apoenzyme to selected promoters, and hence drive the expression of subsets of genes under different conditions.

figure2

(image credits: left – composition of the RNA Pol ; right – role of sigma factors in directing transcription)

 

So, and I finally get to the real point of this post, one might ask: why not implementing modularity in synthetic systems? That’s precisely the idea of the authors of the following paper:


A ‘resource allocator’ for transcription based on a highly fragmented T7 RNA polymerase
Thomas H Segall‐Shapiro, Adam J Meyer, Andrew D Ellington, Eduardo D Sontag, Christopher A Voigt
Molecular Systems Biology
http://dx.doi.org/10.15252/msb.20145299

graphic-1


I’ve basically already described their ideas in the first part of the post, but I’d like to stress the following:

  • By introducing modularity, the authors optimise resource allocation, i.e. improve performance and minimise waste (or, to be more accurate, implemented the possibility to do all of the above)
  • This paper is a very nice piece of protein/enzyme engineering as the splitting of the T7Pol is anything but trivial. I understand that the Synthetic Biology part of the work is more fashionable, but this part should not be overlooked either.

Not surprisingly, a patent has been filed by the authors. Nevertheless, open access publication means everyone can read about this.

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About Pietro Gatti

Interested in discussing (good) Science Lover of coffee & good films. Ideas all & only my own.

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