Difference between revisions of "Part:BBa K1065302"

Revision as of 19:04, 23 September 2013

Blue light sensing device without inverter for the production of amilGFP

This part consists of a Blue light sensor device, Bba_k952003 that was improved by 2013 UNITN-Trento iGEM team with an RBS sequence. When blue light (470 nm) is present production of the reporter amilGFP is inhibited. In the dark the device is activated. Everything is under the control of a constitutive promoter pLac.
This part was cloned, improved and successfully characterized by UNITN-Trento 2013 iGEM team in order to test protein transcription and then add an ethylene forming enzyme (EFE) after amilGFP.
Unlike Bba_K1065310, we built this part to have Ethylene production in the dark. The purpose is to demonstrate that the presence of the inverter cassette in Bba_K1065310 could be one of the reasons of the imperfect behavior of the switch.
The part used is from 2012 Columbia-Cooper-NYC iGEM team.

SAFETY NOTES: this part does not have safety concerns.

Usage and Biology

YF1, the blue light sensor, is a fusion protein of the LOV blue light sensor domain of Bacillus subtilis (YtvA) and FixL histidine kinase domain (from Bradyrhizobium japonicum).
In the dark, the autophosphorylated YF1 phosphorylates FixJ, its Response Regulator, which activates the pFixK2 promoter allowing amilGFP transcription.
Under constant illumination with blue light net kinase activity is strongly suppressed, consisting in a consequent inactivation of pFixK2: amilGFP is no longer produced.
The functioning of the device is due to the presence of an RBS inserted after pFixK2, that was missing in the original part. We characterized this part in E. coli using cells NEB10b.

induction test: successful improvement of the part and defined light dependent ON/OFF switch

To understand if inserting an RBS after pFixK2 would actually improve the part we characterized both our new part and the original one, testing them under the same conditions. Infact we saw an impressive difference between the 2 of them: the improved part actually behaved as expected, producing the yellow fluorescent protein at dark and not under illumination. Bba_K952003 instead doesn't work in both cases: that means that the original part doesn't work and we effectively improved it.

Figure 1. improved part and not improved part after induction:we grew one culture of E. coli (strain NEB10b) transformed with Bba_K1065302 and one with Bba_K952003, until they reached an OD = 0.7. Then we splitted each culture in 2 5ml samples ( at dark and under illumination). We let them grow in glass tubes at 37 degrees under shaking O/N. After this time lapse we centrifuged the cultures and obtained pellets to compare. AmilGFP gives a yellow shade to the cells so it was a little difficult to get a difference in color. Nevertheless we could see a different color in the Bba_K1065302-transformed sample that stayed in the dark.

===fluorometer measurements confirms previuos testing=== After the induction time, we took some fluorimetric measurement since amilGFP is a fluorescent reporter that emits at 512 nm and absorbs at 503 nm.

<img src="

" style="width:800px;"/>

Figure 2. Slight yellow shade appears only in the induced sample with RBS: After the culture with <a href="https://parts.igem.org/Part:BBa_K1065302" >Bba_K1065302</a> reached OD= 0.7 we split it into 2 samples of 5ml at 37°: blue light exposed control and induced sample at dark.We also made 2 sample at the same conditions from a culture transformed with the original part missing the RBS, in order to compare the original part to the improved one. From both the image and the plot we can confirm that our part with RBS is undeniably improved and works as expected.

</html> 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
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 770
Illegal NgoMIV site found at 842
Illegal NgoMIV site found at 932
Illegal NgoMIV site found at 950
Illegal NgoMIV site found at 1462
Illegal NgoMIV site found at 1755
Illegal NgoMIV site found at 1849
Illegal AgeI site found at 484
Illegal AgeI site found at 1630
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI site found at 1519
Illegal BsaI.rc site found at 383

@@ Line 20: / Line 20: @@
 We characterized this part in E. coli using cells NEB10b. <BR/></html>
-===induction test: successful improvement of the part and defined ON/OFF switch===
+===induction test: successful improvement of the part and defined light dependent ON/OFF switch===
 To understand if inserting an RBS after pFixK2 would actually improve the part we characterized both our new part and the original one, testing them under the same conditions. Infact we saw an impressive difference between the 2 of them: the improved part actually behaved as expected, producing the yellow fluorescent protein at dark and not under illumination. Bba_K952003 instead doesn't work in both cases: that means that the original part doesn't work and we effectively improved it.
@@ Line 29: / Line 29: @@
 <center><p style="width:600px; margin-bottom:60px; text-align:justify">
-<b>Figure 1. improved part and not improved part after induction:</b>we grew one culture of E. coli (strain NEB10b) transformed with Bba_K1065302 and one with Bba_K952003, until they reached an OD = 0.7. Then we splitted each culture in 2 5ml samples ( at dark and under illumination). We let them grow in these conditions over night. after this time lapse we centrifuged the cultures and obtained pellets to compare. AmilGFP gives a yellow shade to the cells so it was a little difficult to get a difference in color. Nevertheless we succeded in seeing a different color in the sample in the dark transformed with our improved part </p></center>
+<b>Figure 1. improved part and not improved part after induction:</b>we grew one culture of E. coli (strain NEB10b) transformed with Bba_K1065302 and one with Bba_K952003, until they reached an OD = 0.7. Then we splitted each culture in 2 5ml samples ( at dark and under illumination). We let them grow in glass tubes at 37 degrees under shaking O/N. After this time lapse we centrifuged the cultures and obtained pellets to compare. AmilGFP gives a yellow shade to the cells so it was a little difficult to get a difference in color. Nevertheless we could see a different color in the Bba_K1065302-transformed sample that stayed in the dark.</p></center>
+<html>
+===fluorometer measurements confirms previuos testing===
+After the induction time, we took some fluorimetric measurement since amilGFP is a fluorescent reporter that emits at 512 nm and absorbs at 503 nm.
+</html>
 <center><img src="https://static.igem.org/mediawiki/2013/2/22/Tn-2013_part_improvement_plot.jpg" style="width:800px;"/></center><br/>
 <span class="caption">
-			<b>Fig. 1: Slight yellow shad appears only in the induced sample with RBS</b>: After the culture with <a href="https://parts.igem.org/Part:BBa_K1065302" >Bba_K1065302</a> reached OD= 0.7 we split it into 2 samples of 5ml at 37°: blue light exposed control and induced sample at dark.We also made 2 sample at the same conditions from a culture transformed with the original part missing the RBS, in order to compare the original part to the improved one. From both the image and the plot we can confirm that <b>our part with RBS is undeniably improved and works as expected</b>.
+			<b>Figure 2. Slight yellow shade appears only in the induced sample with RBS</b>: After the culture with <a href="https://parts.igem.org/Part:BBa_K1065302" >Bba_K1065302</a> reached OD= 0.7 we split it into 2 samples of 5ml at 37°: blue light exposed control and induced sample at dark.We also made 2 sample at the same conditions from a culture transformed with the original part missing the RBS, in order to compare the original part to the improved one. From both the image and the plot we can confirm that <b>our part with RBS is undeniably improved and works as expected</b>.
 		</span>
 		<br/>