Paris/ConstructionProcess

From 2007.igem.org

(Difference between revisions)

Revision as of 18:55, 23 October 2007

Overview

Through classical molecular biology techniques, we aimed to construct the following genomically inserted cassette

This full construct has yet to be assembled in the genome.

As can be seen on this schematic representation of the SMB genomic backbone cassette, at basal genomic state (in Germ line cells):

-pTet promoter drives the expression of gfp. -The expression of ftsK is controlled by its natural promoter. -ftsK is isolated from pTet promoter by the intercalation of Terminator (B0015 terminator). -dapA gene is in a dormant state since it lacks a promoter to drive its transcription.

Upon G to S differentiation, the following genomic reassembly should take place: constructed. These are termed the UP “upstream construct” & the DP “downstream construct”:

image de recombinaison

Cre mediated lox recombination should lead to:

-excision of ftsK gene from the genome on a circular unreplicative DNA molecule. We ignore how much time such a DNA is stable in a cell. -placing dapA gene under the control of pTet promoter. This should lead to dapA expression, & hopefully to DAP synthesis.

In order to construct this genomic cassette, we have considered two technical solutions:

1) Either the full construct is cloned on a plasmid and inserted in the genome of a dapA-, ftsK-(ts) E.coli strain. This was the initial strategy we adopted then subsequently abandoned (see here why LIEN). 2) Or the cassette is sequentially assembled, in the genome, around the essential gene selected (ftsK in our case).

The second strategy does not require cloning ftsK gene & does not require using an ftsK mutant.

We have chosen the second strategy mentioned above to generate the SMB genomic backbone construct. The different steps of this process are as follow:

2 plasmid born constructs were generated. These are termed the “upstream construct” & the “downstream construct”:

Upstream construct:

Upstream construct:

See here (LIEN vers une page avec la construction de Nico), how this was sequentially assembled on a plasmid.

Downstream construct:

See here (LIEN vers une page avec la construction de Nico), how this was sequentially assembled

As their names indicate, these constructs are to be inserted upstream and downstream of ftsK gene in the genome of a dapA- strain.

We chose to insert these constructs using a strategy described by …. et al. (ref Wanner)

Petite description de la stratégie de Wanner a mettre.

We have yet to insert the constructs in the genome. This will be done sequentially:

In a first step the downstream construct is amplified using oligonucteotides baring sequences homologous to those downstream of ftsK. The PCR product is used to transform a dapA- E.coli strain.

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Paris/ConstructionProcess

From 2007.igem.org

Revision as of 18:55, 23 October 2007

Contents

Overview

Constructs

Upstream construct

Downstream construct

Intermediate construct

Backward construct with DapA E.Coli

Backward construct with DapA Subtilis

Recombinaison rate measurement

@@ Line 7: / Line 7: @@
 [[Image:Paris_FinalConstruct.JPG|400px]]
+This full construct has yet to be assembled in the genome.
-In order to construct this genomic cassette, we have considered 2 solutions:
+As can be seen on this schematic representation of the SMB genomic backbone cassette, at basal genomic state (in Germ line cells):
-* 1. Either the construct is cloned on a plasmid. Then inserted in the genome strain of a dapA-, ftsK-(ts)  E.coli strain. This was the initial strategy we adopted then subsequently abandoned (see here why LIEN).
+-pTet promoter drives the expression of gfp.
-* 2. Or the cassette is sequentially assembled, in the genome, around the essential gene selected (ftsK in our case).
+-The expression of ftsK is controlled by its natural promoter.
+-ftsK is isolated from pTet promoter by the intercalation of Terminator (B0015 terminator).
+-dapA gene is in a dormant state since it lacks a promoter to drive its transcription.
+Upon G to S differentiation, the following genomic reassembly should take place:
+constructed. These are termed the UP “'''upstream construct'''” & the DP “'''downstream construct'''”:
+image de recombinaison
+Cre mediated lox recombination should lead to:
+-excision of ftsK gene from the genome on a circular unreplicative DNA molecule. We ignore how much time such a DNA is stable in a cell.
+-placing dapA gene under the control of pTet promoter. This should lead to dapA expression, & hopefully to DAP synthesis.
+In order to construct this genomic cassette, we have considered two technical solutions:
+)	Either the full construct is cloned on a plasmid and inserted in the genome of a dapA-, ftsK-(ts)  E.coli strain. This was the initial strategy we adopted then subsequently abandoned (see here why LIEN).
+)	Or the cassette is sequentially assembled, in the genome, around the essential gene selected (ftsK in our case).
+The second strategy does not require cloning ftsK gene & does not require using an ftsK mutant.
+We have chosen the second strategy mentioned above to generate the SMB genomic backbone construct. The different steps of this process are as follow:
+plasmid born constructs were generated. These are termed the “upstream construct” & the “downstream construct”:
+Upstream construct:
-We have chosen the second strategy. The different steps of this process are as follow:
-plasmid born constructs were constructed. These are termed the UP “'''upstream construct'''” & the DP “'''downstream construct'''”:
 '''Upstream construct:'''
 [[Image:Paris_UpstreamConstruct.JPG|400px]]
+See here (LIEN vers une page avec la construction de Nico), how this was sequentially assembled on a plasmid.
 '''Downstream construct:'''
 [[Image:Paris_DownstreamConstruct.JPG|400px]]
-As their names indicate, these constructs are to be inserted upstream and downstream of ftsK in the genome. We chose to insert these constructs using a strategy described by Wanner et al.
+See here (LIEN vers une page avec la construction de Nico), how this was sequentially assembled
+As their names indicate, these constructs are to be inserted upstream and downstream of ftsK gene in the genome of a dapA- strain.
+We chose to insert these constructs using a strategy described by …. et al. (ref Wanner)
+Petite description de la stratégie de Wanner a mettre.
+We have yet to insert the constructs in the genome. This will be done sequentially:
-We have yet to insert the constructs in the genome. This will be done sequentially:
+In a first step the downstream construct is amplified using oligonucteotides baring sequences homologous to those downstream of  ftsK. The PCR product is used to transform a dapA- E.coli strain.
 [[Image:Paris_UpstreamInsertion.JPG|400px]]