Difference between revisions of "Part:BBa K238013"

Revision as of 21:38, 19 October 2009

Exact promoter of the blue light receptor

This is a promoter which normally lies before the ycgZ gene, a part of an operon consisting of several genes used by E.coli for regulating e.g. biofilm production. It is regulated by the ycgF/E system. This system consists of a receptor, ycgF, which is responsive to blue light. When blue light strikes, the receptor changes conformation and dimerizes. This allows it to bind to the ycgE repressor through its EAL-domain, releasing the repressor from the promoter region. The inverted repeats shown here are expected to represent the binding site for ycgE. YcgE binding results in transcription repression.

after some experimental set ups following considerations need to be made:

The promoter is weak (compared to standard I20260)
aside from light, temperature is a very important influence (if not a bigger one). for instance when working in low copy plasmids temperature will influence the promoter/repressor ratio. Cells are grown at 37°C will have too much promoter resulting in constitutive activity. At 16°C, there will be more repressor and receptor but the low temperature will put the receptor in its active state thus inhibiting the repressor from doing its job. When grown at 25°C the ratio is beter and the receptor/represssor are still in there ground state leading to a good repression of the promoter.

Comparison of the blue light promotor (blue) to a standard promotor strength I20260 (orange). The blue light promotor shows at least half the strenght of the standard promotor in RPU, meaning it can be classified as a weak promotor

Effect of blue light irradiance on promotor strenght. Cells grown in blue light irradiance (blue) show a stronger expression compared to cells grown in the dark (grey)

our experimental set-up:

liquid cultures were ented (and reented in the evening) and grown on two different temperatures: 37° and 25°.
from each of these growth conditions some of the cultures were put in 16° and the other at 25°. each of these groups were then again divided in a group that was lit with blue light and a group that wasn't.
measurements were done at following hours: 0h;0,5h;1,5h;3h;4,5h;6h;8h.
this was done for our ligation of blp with GFP in three different vector (pSB3K3, pBR322 and pSB1A2)
an example of a sample name is: 37/16/NB/LigA, grown at 37°, put in 16°, not lit and in vector pSB1A2
note: enting of the cultures needs to be done in a dark room (red light)and it might be best to use medium that was put at 4°C overnight.

this experiment was repeated some times and variations were done:

only growing cultures on 25°C and lighting them at room temperature

For more info: Natalia Tschowri, Susan Busse and Regine Hengge, The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes and development23: 522-534 (2009)

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

@@ Line 6: / Line 6: @@
 after some experimental set ups following considerations need to be made:
 * The promoter is weak (compared to standard I20260)
-* aside from light, temperature is a very important influence (if not a bigger one). for instance when working in low copy plasmids temperature will influence the promoter/repressor ratio. Cells are grown at 37°C will have too much promoter resulting in constitutive activity. When grown at 25°C the ratio is beter leading to a good repression of the promoter.
+* aside from light, temperature is a very important influence (if not a bigger one). for instance when working in low copy plasmids temperature will influence the promoter/repressor ratio. Cells are grown at 37°C will have too much promoter resulting in constitutive activity. At 16°C, there will be more repressor and receptor but the low temperature will put the receptor in its active state thus inhibiting the repressor from doing its job. When grown at 25°C the ratio is beter and the receptor/represssor are still in there ground state leading to a good repression of the promoter.
@@ Line 13: / Line 13: @@
 | [[Image:Light-dark.png|thumb|365px|Effect of blue light irradiance on promotor strenght. Cells grown in blue light irradiance (blue) show a stronger expression compared to cells grown in the dark (grey)]]
 |}
+our experimental set-up:
+*liquid cultures were ented (and reented in the evening) and grown on two different temperatures: 37° and 25°.
+*from each of these growth conditions some of the cultures were put in 16° and the other at 25°. each of these groups were then again divided in a group that was lit with blue light and a group that wasn't.
+*measurements were done at following hours: 0h;0,5h;1,5h;3h;4,5h;6h;8h.
+*this was done for our ligation of blp with GFP in three different vector (pSB3K3, pBR322 and pSB1A2)
+*an example of a sample name is: 37/16/NB/LigA, grown at 37°, put in 16°, not lit and in vector pSB1A2
+*note: enting of the cultures needs to be done in a dark room (red light)and it might be best to use medium that was put at 4°C overnight.
+this experiment was repeated some times and variations were done:
+* only growing cultures on 25°C and lighting them at room temperature
 For more info: Natalia Tschowri, Susan Busse and Regine Hengge, The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes and development23: 522-534 (2009)