BBa_K1840007 1 Zwf-Device Device: TT-zwf-mCherry 2015-09-17T11:00:00Z 2015-09-18T02:16:57Z The double terminator was already registered in the iGEM catalogue. The zwf promotor comes from the genome of Pseudomonas putida. The mCherry is codon optimized for expression in Pseudomonas. 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 promotor zwf is influenced by it. The zwf promotor (BBa_K1840002) is contained in the genome of Pseudomonas putida and is situated in front of the enzyme zwf (glucose 6-phosphate dehydrogenase). The repressor HexR can bind the zwf promotor sequence and thus prevent the transcription of the zwf gene. In case the glucose derivative 2-Keto-3-deoxy-6-phosphogluconate is present, it binds to the promotor and leads to a subsequent conformational change. Hence, the repressor can no longer bind and the gene(s) 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 As promotor sequence, we assumed all DNA in front of the zwf gene up to the next gene, coding for the repressor HexR. Since it is encoded on the opposite strand, there is the possibility, that zwf functions as a promotor for this gene as well. Therefore the double terminator was needed. false Julia Anna Adrian component2473635 1 BBa_K1840002 component2473634 1 BBa_B0014 component2473636 1 BBa_K1840004 annotation2473634 1 BBa_B0014 range2473634 1 1 95 annotation2473636 1 BBa_K1840004 range2473636 1 312 1025 annotation2473635 1 BBa_K1840002 range2473635 1 104 305 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-&gt;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 annotation1683 1 stem_loop range1683 1 13 35 annotation7019 1 BBa_B0011 range7019 1 1 46 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 annotation7020 1 BBa_B0012 range7020 1 1 41 annotation1687 1 stop range1687 1 34 34 annotation1686 1 T7 TE range1686 1 8 27 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_K1840002 1 BBa_K1840002 Zwf promotor from Pseudomonas putida 2015-09-17T11:00:00Z 2015-09-18T01:47:02Z The part was designed after information from the paper by DADDAOUA, A., KRELL, T. & RAMOS, J.-L. 2009. Regulation of Glucose Metabolism in Pseudomonas: The Phosphorylative Branch and Entner-Doudoroff Enzymes are Regulated by a Repressor Containing a Sugar Iisomerase Domain. Journal of Biological Chemistry, 284, 21360-21368. This basic part is the promotor in front of the gene for zwf (glucose 6-phosphate dehydrogenase) in Pseudomonas putida. Zwf is concerned with the glucose metabolism in P. putida. The zwf promotor is negatively regulated by the repressor called HexR. It has a binding site for glucose derivative 2-keto-3-deoxy-6-phosphogluconate (KDPG) and binding leads to the release 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 KDPG) level in the environment. Note: The promotor edd (BBa_K1840000) is repressed by the same repressor HexR. See biobrick parts BBa_K1840001 and BBa_K1840003 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 zwf gene. We assumed it starts directly after the previous gene. This gene codes for the repressor, HexR, and is situated on the opposite strand. false Julia Anna Adrian 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 annotation939303 1 BBa_B0012 range939303 1 1 41 annotation939311 1 BBa_B0011 range939311 1 50 95 BBa_K1840002_sequence 1 gggtgtgtccttgggtcgggaagacagccggctgtgtgagcagcaggctttttgcacggtcgtctatcgtactgtcggtgcggttgacgtaccacttgtctgtaacacttgtgtgtaatgttgtggtttttactacattatcccttgaaaaccgtgtgtgaaagcggtattcctagaccaactttaggaaagaaccaacatc BBa_B0014_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt BBa_K1840004_sequence 1 atggtttctaaaggtgaagaagacaacatggctatcatcaaagaatttatgcgtttcaaagttcacatggaaggttctgtgaacggtcacgaatttgaaatcgaaggtgaaggtgaaggtcgtccgtatgaaggcacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtctccgcagttcatgtacggttctaaagcgtatgttaaacacccggctgacatcccggactacctgaaactgtctttcccggaaggtttcaaatgggaacgtgttatgaactttgaagacggtggtgttgttaccgttacccaggactcttctctgcaagacggtgaatttatctacaaagttaaactgcgtggcaccaacttcccgtctgacggtccggttatgcagaaaaaaacgatgggttgggaagcgtcttctgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaacagcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacaaagctaaaaagccggttcaactgccgggtgcttacaacgtgaacatcaaactggacatcacctctcacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactctaccggcggtatggacgaactgtataaatgataa BBa_K1840007_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattttactagaggggtgtgtccttgggtcgggaagacagccggctgtgtgagcagcaggctttttgcacggtcgtctatcgtactgtcggtgcggttgacgtaccacttgtctgtaacacttgtgtgtaatgttgtggtttttactacattatcccttgaaaaccgtgtgtgaaagcggtattcctagaccaactttaggaaagaaccaacatctactagatggtttctaaaggtgaagaagacaacatggctatcatcaaagaatttatgcgtttcaaagttcacatggaaggttctgtgaacggtcacgaatttgaaatcgaaggtgaaggtgaaggtcgtccgtatgaaggcacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtctccgcagttcatgtacggttctaaagcgtatgttaaacacccggctgacatcccggactacctgaaactgtctttcccggaaggtttcaaatgggaacgtgttatgaactttgaagacggtggtgttgttaccgttacccaggactcttctctgcaagacggtgaatttatctacaaagttaaactgcgtggcaccaacttcccgtctgacggtccggttatgcagaaaaaaacgatgggttgggaagcgtcttctgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaacagcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacaaagctaaaaagccggttcaactgccgggtgcttacaacgtgaacatcaaactggacatcacctctcacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactctaccggcggtatggacgaactgtataaatgataa 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