Difference between revisions of "Part:BBa K3332043"

Latest revision as of 21:30, 27 October 2020

Formaldehyde_derivative-2 promoter

An improvement of BBa_K1334002 by adding the binding sites to make it be more sensitive to formaldehyde than BBa_K1334002.

Usage and Biology

As a DNA binding protein, hxlR is the transcriptional activator of the hxlAB operon from Bacillus subtilis. The possible mechanism of formaldehyde induced expression is that the formaldehyde changes the conformation of hxlR which can stimulate RNA polymerase to open the transcription.

Therefore, we increased the amount of binding sites to improve the sensitivity of the formaldehyde promoter.There are two BRH1 and two BRH2 in the formaldehyde_derivative-2 promoter, both of which only has one copy in the registry promoter (BBa_K1334002).

Fig 1. Different improvements of formaldehyde promoter

Characterization

We use ECFP as the reporter gene to characterize the improvement.

The agarose gel electrophoresis images are below：

Fig 2. Formaldehyde_derivative-2 promoter_B0034_E0020_B0015_pSB1C3(BBa_K3332091) digested by Xba I and Pst I (about 1557 bp)

Protocol:

1.Culture glycerol bacteria containing the corresponding plasmid in test tube for 12h.

2.Add 4ml of the above bacterial solution into 200 mL LB medium and maintain the culture condition at 37 ℃ and 180 rpm.

3.Add 0.8mM formaldehyde into each group when OD600 increased to 0.6 and the culture condition is the same as before.

4.Then, sampling culture in 96-well plate reader every 3 hours to measure the fluorescence intensity (ECFP) and corresponding OD600, then calculate the fluorescence / OD value of each group.

Here is the result:

Fig 3. The curve of fluorescence intensity (ECFP) /OD by pHCHO (BBa_K1334002) and formaldehyde_derivative-2 promoter

In this figure,by comparing formaldehyde_derivative-2 promoter with the other two derivative promoters and the registry one, we can see that formaldehyde_derivative-2 promoter is more sensitive to formaldehyde than the registry one and formaldehyde_derivative-1 promoter. So increasing the amount of binding sites is a more effective way to improve formaldehyde promoter even than replacing weak promoter with strong promoter.

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]

Reference

[1]Yurimoto, H., Hirai, R., Matsuno, N., Yasueda, H., Kato, N. and Sakai, Y. (2005), HxlR, a member of the DUF24 protein family, is a DNA‐binding protein that acts as a positive regulator of the formaldehyde‐inducible hxlAB operon in Bacillus subtilis. Molecular Microbiology, 57: 511-519. doi:10.1111/j.1365-2958.2005.04702.x

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K3332043 short</partinfo>
-An improvement of BBa_K1334002 by adding the binding sites.It's more sensitive to formaldehyde.We use it to test whether it has any improvement compared with BBa_K1334002.
+An improvement of <partinfo>BBa_K1334002</partinfo> by adding the binding sites to make it be more sensitive to formaldehyde than <partinfo>BBa_K1334002</partinfo>.
 ===Usage and Biology===
-As a DNA binding protein, hxlR is the transcriptional activator of the hxlAB operon from ''Bacillus subtilis''. The possible mechanism of formaldehyde induced expression is that the formaldehyde changes the conformation of hxlR which can stimulate RNA polymerase to start the transcription.
-Therefore, we increased the amount of binding sites to improve the sensitivity of the formaldehyde promoter. There are two BRH1 and two BRH2 in the formaldehyde_derivative-2 promoter, while there is only one BRH1 and one BRH2 in the registry formaldehyde promoter (BBa_ K1334002).
+As a DNA binding protein, hxlR is the transcriptional activator of the hxlAB operon from ''Bacillus subtilis''. The possible mechanism of formaldehyde induced expression is that the formaldehyde changes the conformation of hxlR which can stimulate RNA polymerase to open the transcription.
+Therefore, we increased the amount of binding sites to improve the sensitivity of the formaldehyde promoter.There are two BRH1 and two BRH2 in the formaldehyde_derivative-2 promoter, both of which only has one copy in the registry promoter (<partinfo>BBa_K1334002</partinfo>).
 <html>
      <figure>
@@ Line 18: / Line 20: @@
      </figure>
 </html>
-'''Fig 1.''' Different improvements of formaldehyde promoter.
+'''Fig 1.''' Different improvements of formaldehyde promoter
-To construct this part, we moved formaldehyde_derivative-2 promoter (BBa_K3332043) and RBS-ECFP-T (BBa_E0420) into the expression vector pSB1C3 by standard assembly. Then the ligation mixture was transformed into ''E.coli'' BL21(DE3) to compare the sensitivity of formaldehyde with other promoters (formaldehyde_derivative-1 promoter, formaldehyde_derivative-3, formaldehyde promoter).
 ===Characterization===
+We use ECFP as the reporter gene to characterize the improvement.
 The agarose gel electrophoresis images are below：
 [[File:2043.fig.2.png|none|500px|caption]]
-'''Fig 2.''' Formaldehyde_derivative-2 promoter_B0034_E0020_B0015_pSB1C3 (BBa_K3332093) digested by ''Xba'' I and ''Pst'' I (about 1557 bp).
+'''Fig 2.''' Formaldehyde_derivative-2 promoter_B0034_E0020_B0015_pSB1C3(<partinfo>BBa_K3332091</partinfo>) digested by ''Xba'' I and ''Pst I (about 1557 bp)
 '''Protocol: '''
-.Culture glycerol bacteria containing the corresponding plasmids in test tube for 12h.
+.Culture glycerol bacteria containing the corresponding plasmid in test tube for 12h.
-.Add 4mL of the above bacterial solution into 200 mL LB medium and maintain the culture condition at 37 ℃ and 180 rpm.
+.Add 4ml of the above bacterial solution into 200 mL LB medium and maintain the culture condition at 37 ℃ and 180 rpm.
-.Add 0.8mM formaldehyde into each group when OD<sub>600</sub> increased to 0.6 and the culture condition is the same as before.
+.Add 0.8mM formaldehyde into each group when OD600 increased to 0.6 and the culture condition is the same as before.
-.Then, sampling culture in 96-well plate reader every 3 hours to measure the fluorescence intensity (ECFP) and corresponding OD<sub>600</sub> , then calculate the fluorescence / OD value of each group.
+.Then, sampling culture in 96-well plate reader every 3 hours to measure the fluorescence intensity (ECFP) and corresponding OD600, then calculate the fluorescence / OD value of each group.
 Here is the result:
 [[File:2042.fig.4.png|none|500px|caption]]
-'''Fig 3. ''' The curve of fluorescence intensity (ECFP) /OD of pHCHO (BBa_ K1334002) and formaldehyde_derivative-2 promoter, respectively.
-'''Note:''' Formaldehyde_derivative-2 promoter is equal to pHCHO(modified-2).
+'''Fig 3.''' The curve of fluorescence intensity (ECFP) /OD by pHCHO (<partinfo>BBa_K1334002</partinfo>) and formaldehyde_derivative-2 promoter
-In this figure, we can compare formaldehyde_derivative-2 promoter with the other two derivative promoters and the registry formaldehyde promoter. And we can conclude that formaldehyde_derivative-2 promoter is more sensitive to formaldehyde than the registry formaldehyde promoter and formaldehyde_derivative-1 promoter. So increasing the amount of binding sites is a more effective way to improve formaldehyde promoter even than replacing weak promoter with strong promoter.
+In this figure,by comparing formaldehyde_derivative-2 promoter with the other two derivative promoters and the registry one, we can see
+that formaldehyde_derivative-2 promoter is more sensitive to formaldehyde than the registry one and formaldehyde_derivative-1 promoter. So increasing the amount of binding sites is a more effective way to improve formaldehyde promoter even than replacing weak promoter with strong promoter.