Latest revision as of 03:03, 22 September 2011

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Lysis Selection System

Lysis selection system Main | Lysis Characterization | DNA Recovery | DNA Selection | T7 Promoter Variants

One major challenge in designing new regulatory parts is to determine which combinations of transcription factors and binding sequences match. From previous research and our own MITOMI experiments, we know which DNA sequences TetR binds to, and which residues of TetR participate in binding, but we do not know how changing these residues will affect either binding affinity or specificity. Molecular dynamics simulations and other theoretical approaches have not come any closer to answering these questions. In short, we know too little about protein-DNA interaction to intelligently design transcription factors. To make up for this lack of knowledge, we present an experimental system to select valid binding pairs from many random tetR and pTet mutants, based on an inducible lysis gene.

The system – in a way a "survival of the weakest" – is related to directed evolution. A lysis system based on the K112808 lysis device is indirectly activated by tetR. Therefore, if in a given cell the tetR variant present can bind to the tetR promoter, the cell lyses and releases its DNA into the culture media. From there, DNA can be recovered and amplified, tranformed, or directly sequenced. By design, this DNA codes for a combination of TF and promoter with high mutual affinity, and therefore almost directly yields a valid regulatory part. In this light, it is a useful component of our transcription factor development pipeline.

This is a direct and practical way of solving the problem of selecting high affinity pairs among the millions of possible combinations of transcription factors and promoters. It can be seen as a form of DNA-based information processing, and is therefore also a neat example of a problem more efficiently solved by non-conventional computation.

To develop the system, we began with a simple experiment to check that a lysis cassette in a plasmid could lyse with greater efficiency as a function of IPTG concentration. The next step towards our goal was to demonstrate that plasmid DNA can be adequately recovered and repackaged (PCR amplified, transformed into a different strain, etc...) as a result of lysing. In a more elaborate experiment, we were able to show that not only did the lysing efficiently release plasmids from the cells, but that it could be made to do so selectively in a large culture containing a variety of strains. Finally, cognizant of the fact that a good lysis selection method ought to be flexible with regards to the larger reporter system, we manufactured twelve different T7 promoter variants that exhibit a wide range of strengths and induction efficiencies. The latter will play a crucial role in being able to accomodate the activation time-scales of fragile and complex selection systems.

All the components of the selection machine have been separately tested experimentally and found to work. Therefore we are convinced the system can work, but it would still require a full-circle experiment to demonstrate its usefulness.

@@ Line 1: / Line 1: @@
-{{:Team:EPF-Lausanne/Templates/Header|title=T7 promoter variants}}
+{{:Team:EPF-Lausanne/Templates/T7lysisHeader|title=Intro}}
-We made two families of T7 promoter variants. One family has mutations on the T7 promoter consensus sequence while the other has the same set of mutations on the consensus sequence but also has a lac operator downstream of the T7 promoter (but upstream of the reporter RFP or Lysis). In each family, we made six designed variants with different predicted promoter strengths compared to the wildtype and also made three sets of randomer variants which we wanted to use to check the overall range of promoter strength.
-=== The Making Of A Variant ===
+One major challenge in designing new regulatory parts is to determine which combinations of transcription factors and binding sequences match.
+From previous research and our own MITOMI experiments, we know which DNA sequences TetR binds to, and which residues of TetR participate in binding, but we do not know how changing these residues will affect either binding affinity or specificity.
+Molecular dynamics simulations and other theoretical approaches have not come any closer to answering these questions.
+In short, we know too little about protein-DNA interaction to intelligently design transcription factors.
+To make up for this lack of knowledge, we present an experimental system to select valid binding pairs from many random tetR and pTet mutants, based on an inducible lysis gene.
-To produce these T7 promoter variants, we used a two-step PCR process. The first PCR, which we call "gene-specific" PCR, is a typical PCR that adds a ribosome-binding site (rbs) in front of either RFP or the Lysis operon and adds a terminator downstream.
+[[File:EPFL-Solange-Lysis.jpg|700px]]
-[[File:rbs_rfp_term.png]]
+The system – in a way a "survival of the weakest" – is related to directed evolution.
+A lysis system based on the K112808 lysis device is indirectly activated by tetR.
+Therefore, if in a given cell the tetR variant present can bind to the tetR promoter, the cell lyses and releases its DNA into the culture media.
+From there, DNA can be recovered and amplified, tranformed, or directly sequenced.
+By design, this DNA codes for a combination of TF and promoter with high mutual affinity, and therefore almost directly yields a valid regulatory part.
+In this light, it is a useful component of our transcription factor development pipeline.
-[[File:rbs_lys_term.png]]
+This is a direct and practical way of solving the problem of selecting high affinity pairs among the millions of possible combinations of transcription factors and promoters.
+It can be seen as a form of DNA-based information processing, and is therefore also a neat example of a problem more efficiently solved by non-conventional computation.
-With this PCR product now serving as the DNA template, we start a second PCR which we call the "extension" PCR. It extends the product by adding the T7 promoter, with or without a lac operator downstream. In these illustrations, we have substituted the lysis operon for the RFP gene but the same process is done for RFP.
+To develop the system, we began with a [[Team:EPF-Lausanne/Our_Project/T7_promoter_variants/lysis|simple experiment]] to check that a lysis cassette in a plasmid could lyse with greater efficiency as a function of IPTG concentration. The next step towards our goal was to demonstrate that [[Team:EPF-Lausanne/Our_Project/T7_promoter_variants/recovery|plasmid DNA can be adequately recovered]] and repackaged (PCR amplified, transformed into a different strain, etc...) as a result of lysing. In a [[Team:EPF-Lausanne/Our_Project/T7_promoter_variants/selection|more elaborate experiment]], we were able to show that not only did the lysing efficiently release plasmids from the cells, but that it could be made to do so selectively in a large culture containing a variety of strains. Finally, cognizant of the fact that a good lysis selection method ought to be flexible with regards to the larger reporter system, we manufactured [[Team:EPF-Lausanne/Our_Project/T7_promoter_variants/t7prom|twelve different T7 promoter variants]] that exhibit a wide range of strengths and induction efficiencies. The latter will play a crucial role in being able to accomodate the activation time-scales of fragile and complex selection systems.
-[[File:t7_rbs_lysis_term.png]]
-[[File:t7_lac_rbs_lysis_term.png]]
-In the last stage, we run another PCR with a set of primers that will add Gibson overhangs for the Gibson assembly that will add this promoter construct into the desired plasmid.
-[[File:gibson_t7_lac_lysis_gibson.png]]
-=== Characterization with RFP ===
-With T7 and T7-lac promoter variants in hand, we want to characterize their relative strengths. To obtain the right set-up, we transform the promoter variant plasmids into a different strain of E. coli called BL21. These cells have a mutation in the promoter for the lacI gene that makes LacI protein. As a result of this mutation, LacI protein is overproduced and is found abundantly in these cells. In this same strain, the gene for the T7 RNA polymerase is preceded by a lac operator. Since LacI is a repressor and LacI is strongly present in BL21 cells, the production of T7 RNA polymerases is severely repressed. With very few T7 RNA polymerases available, there is very little recognition and binding of T7 promoters and consequently very little expression of the gene driven by the T7 promoter. Moreover, the expression of a gene driven by a T7-lac promoter would be even less, since the presence of LacI would block any action of the T7 RNA polymerase.
-With such a system in place, the transformation of our T7 and T7-lac promoter variant plasmids into BL21 cells would produce little to no reporter expression. Now to induce promoter activity, we rely on the fact that the chemical IPTG blocks the production of LacI. Without these LacI proteins, the cell can resume production of T7 RNA polymerases. These in turn can bind to the T7 and T7-lac promoters and express the reporter gene without interruption. So the adding of IPTG to a BL21 cell culture containing these T7 and T7-lac promoter variant plasmids ought to produce high levels of RFP or Lysis expression. Since lysis is a rather binary process (either the cell is lysed or it is not), we use RFP fluorescence as a gauge of promoter strength and efficiency.
-== DNA Recovery with Lysis ==
+All the components of the selection machine have been separately tested experimentally and found to work. Therefore we are convinced the system can work, but it would still require a full-circle experiment to demonstrate its usefulness.
 {{:Team:EPF-Lausanne/Templates/Footer}}

Team:EPF-Lausanne/Our Project/T7 promoter variants

From 2011.igem.org

Latest revision as of 03:03, 22 September 2011

Lysis Selection System