BBa_B0014
1
BBa_B0014
double terminator (B0012-B0011)
2003-07-15T11:00:00Z
2015-08-31T04:07:20Z
Released HQ 2013
Double terminator consisting of BBa_B0012 and BBa_B0011
false
true
_1_
0
24
7
In stock
false
true
Reshma Shetty
component939303
1
BBa_B0012
component939311
1
BBa_B0011
annotation939311
1
BBa_B0011
range939311
1
50
95
annotation939303
1
BBa_B0012
range939303
1
1
41
BBa_K1840003
1
BBa_K1840003
Gad promotor from Pseudomonas
2015-09-17T11:00:00Z
2015-09-18T01:53:30Z
This part was designed after information from the paper by DADDAOUA, A., KRELL, T., ALFONSO, C., MOREL, B. & RAMOS, J.-L. 2010. Compartmentalized Glucose Metabolism in Pseudomonas putida Is Controlled by the PtxS Repressor. Journal of Bacteriology, 192, 4357-4366.
This basic part is the promotor in front of the gene for gad (gluconate dehydrogenase) in Pseudomonas putida. Gad is concerned with the glucose metabolism in P. putida. The gad promotor is negatively regulated by the repressor called PtxS. The glucose derivative 2-Ketogluconate can bind to it and this leads to subsequent release of PtxS from the promotor.
For our project (NTNU Trondheim 2015) we integrated the promotor in front of the mCherry gene. Hence we built a glucose detection device, that expresses mCherry according to the glucose (and therefore 2-Ketogluconate) level in the environment (see BBa_K1840008).
Note: The promotor kgu (BBa_K1840001) is repressed by the same repressor PtxS. See biobrick parts BBa_K1840000 and BBa_K1840002 for other promotors on operons regulated by glucose derivatives.
false
false
_2266_
26543
26543
9
false
The considerations we made regarded the starting and endpoint of the promotor. We only know that it has to be in front of the gad gene. We assumed it starts directly after the previous gene, which is encoded on the opposite strand.
false
Julia Anna Adrian
BBa_K1840008
1
Gad-Device
Device: TT-gad-mCherry
2015-09-17T11:00:00Z
2015-09-18T02:29:30Z
The double terminator was already registered in the iGEM catalogue. The kgu promotor comes from the genome of Pseudomonas putida. The mCherry is codon optimized for expression in Pseudomonas. The whole device was synthesized by IDT.
This device acts as a detector for glucose (and certain derivatives of it). The double transcription terminator ensures, that only the gene downstream of the gad promotor is influenced by it. The promotor (BBa_K1840003) is contained in the genome of Pseudomonas putida and is situated in front of the enzyme gad (gluconate oxidase). The repressor PtxS can bind the gad promotor sequence and thus prevent the transcription of the gad gene. In case the glucose derivative 2-ketogluconate is present, it binds the promotor and leads to a subsequent conformational change. Hence, the repressor can no longer bind and the gene downstream can be transcribed. In our device, the downstream gene is mCherry, codon optimized for Pseudomonas (BBa_K1840004). Therefore, in the presence of glucose, mCherry is expressed. In various experiments, we could see that this device is in deed working.
false
false
_2266_
26543
26543
9
false
Considerations were made regarding the actual start of the promotor. As promotor sequence we assumed all DNA between the gad gene and the previous gene (upstream). Since this gene is encoded on the opposite strand, the terminator was needed.
false
Julia Anna Adrian
component2473657
1
BBa_K1840003
component2473656
1
BBa_B0014
component2473658
1
BBa_K1840004
annotation2473658
1
BBa_K1840004
range2473658
1
460
1173
annotation2473656
1
BBa_B0014
range2473656
1
1
95
annotation2473657
1
BBa_K1840003
range2473657
1
104
453
BBa_B0011
1
BBa_B0011
LuxICDABEG (+/-)
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
Derived from luxICDABEG operon terminator of Vibrio fischeri <genbank>AF170104</genbank>.
Released HQ 2013
Bidirectional transcriptional terminator consisting of a 22 bp stem-loop.</p>
false
false
_1_
0
24
7
In stock
false
<P> <P>In the naturally-occuring sequence there is a mismatch in the stem of the stem loop. This can be corrected via an A->G mutation (at position 40 -- sequence coordinate/not MFOLD coordinate). The above sequence does not reflect this mutation (but the MFOLD image does). This terminator's location cannot be found using some inverted repeat detectors like PALINDROME because it is too short and contains a mismatch. This one was found with the help of Tom Knight. It lies between two coding regions that point towards eachother.<P>
true
Reshma Shetty
annotation7019
1
BBa_B0011
range7019
1
1
46
annotation1683
1
stem_loop
range1683
1
13
35
BBa_K1840004
1
BBa_K1840004
mCherry for Pseudomonas
2015-09-17T11:00:00Z
2015-09-18T11:02:21Z
It comes from the standard mCherry sequence and was condon optimized.
The standard fluorescent protein mCherry is not efficiently expressed in Pseudomonas spp. Therefore this biobrick part is a codon optimized mCherry for the expression in Pseudomonas. We used it in our project (NTNU Trondheim 2015) in a device as reporter.
Note: See biobrick parts BBa_K1840005 to BBa_K1840008 for the characterization of the devices.
false
false
_2266_
26543
26543
9
false
The expression mechanism in Pseudomonas had to be considered to be able to codon optimize it.
false
Julia Anna Adrian
BBa_B0012
1
BBa_B0012
TE from coliphageT7
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
Derived from the TE terminator of T7 bacteriophage between Genes 1.3 and 1.4 <genbank>V01146</genbank>.
Released HQ 2013
Transcription terminator for the <i>E.coli</i> RNA polymerase.
false
false
_1_
0
24
7
In stock
false
<P> <P>Suggested by Sri Kosuri and Drew Endy as a high efficiency terminator. The 5' end cutoff was placed immediately after the TAA stop codon and the 3' end cutoff was placed just prior to the RBS of Gene 1.4 (before AAGGAG).<P> Use anywhere transcription should be stopped when the gene of interest is upstream of this terminator.
false
Reshma Shetty
annotation1690
1
polya
range1690
1
28
41
annotation1686
1
T7 TE
range1686
1
8
27
annotation1687
1
stop
range1687
1
34
34
annotation7020
1
BBa_B0012
range7020
1
1
41
BBa_K1840008_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattttactagagccttgatcctcgtctcttggcaggtcaaacactcgcagtgcacctacttccatgcggccgggcgcaagcatttgcgaaagtttgaagcctaacgaggaatcaatttttgagacagattgaaacttcctaatgcgttgtaagaagtttcgctaaaagttgtttttaagtgtttcttgtcaaaaaaatgatgttttgtacaggtagggaaggcaaagcatgaaaccggtttcaaaacctttctgaacgcgctagattattcggctgtctcttgatggcctatcaagatcacctctcaattgaaaatcagatggcgcttatcaaggccgccccacagccgatgaggattcgcatactagatggtttctaaaggtgaagaagacaacatggctatcatcaaagaatttatgcgtttcaaagttcacatggaaggttctgtgaacggtcacgaatttgaaatcgaaggtgaaggtgaaggtcgtccgtatgaaggcacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtctccgcagttcatgtacggttctaaagcgtatgttaaacacccggctgacatcccggactacctgaaactgtctttcccggaaggtttcaaatgggaacgtgttatgaactttgaagacggtggtgttgttaccgttacccaggactcttctctgcaagacggtgaatttatctacaaagttaaactgcgtggcaccaacttcccgtctgacggtccggttatgcagaaaaaaacgatgggttgggaagcgtcttctgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaacagcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacaaagctaaaaagccggttcaactgccgggtgcttacaacgtgaacatcaaactggacatcacctctcacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactctaccggcggtatggacgaactgtataaatgataa
BBa_B0014_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt
BBa_K1840004_sequence
1
atggtttctaaaggtgaagaagacaacatggctatcatcaaagaatttatgcgtttcaaagttcacatggaaggttctgtgaacggtcacgaatttgaaatcgaaggtgaaggtgaaggtcgtccgtatgaaggcacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtctccgcagttcatgtacggttctaaagcgtatgttaaacacccggctgacatcccggactacctgaaactgtctttcccggaaggtttcaaatgggaacgtgttatgaactttgaagacggtggtgttgttaccgttacccaggactcttctctgcaagacggtgaatttatctacaaagttaaactgcgtggcaccaacttcccgtctgacggtccggttatgcagaaaaaaacgatgggttgggaagcgtcttctgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaacagcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacaaagctaaaaagccggttcaactgccgggtgcttacaacgtgaacatcaaactggacatcacctctcacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactctaccggcggtatggacgaactgtataaatgataa
BBa_K1840003_sequence
1
ccttgatcctcgtctcttggcaggtcaaacactcgcagtgcacctacttccatgcggccgggcgcaagcatttgcgaaagtttgaagcctaacgaggaatcaatttttgagacagattgaaacttcctaatgcgttgtaagaagtttcgctaaaagttgtttttaagtgtttcttgtcaaaaaaatgatgttttgtacaggtagggaaggcaaagcatgaaaccggtttcaaaacctttctgaacgcgctagattattcggctgtctcttgatggcctatcaagatcacctctcaattgaaaatcagatggcgcttatcaaggccgccccacagccgatgaggattcgca
BBa_B0011_sequence
1
agagaatataaaaagccagattattaatccggcttttttattattt
BBa_B0012_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttata
igem2sbol
1
iGEM to SBOL conversion
Conversion of the iGEM parts registry to SBOL2.1
Chris J. Myers
James Alastair McLaughlin
2017-03-06T15:00:00.000Z