BBa_B0034
1
BBa_B0034
RBS (Elowitz 1999) -- defines RBS efficiency
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
Released HQ 2013
RBS based on Elowitz repressilator.
false
true
_1_
0
24
7
In stock
false
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix. <p>No secondary structures are formed in the given RBS region. Users should check for secondary structures induced in the RBS by upstream and downstream elements in the +50 to -50 region, as such structures will greatly affect the strength of the RBS.
Contact info for this part: <a href="mailto:(bchow@media.mit.edu)">Brian Chow</a>
true
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
annotation23325
1
conserved
range23325
1
5
8
BBa_B0010
1
BBa_B0010
T1 from E. coli rrnB
2003-11-19T12:00:00Z
2015-08-31T04:07:20Z
Transcriptional terminator consisting of a 64 bp stem-loop.
false
false
_1_
0
24
7
In stock
false
true
Randy Rettberg
annotation7018
1
BBa_B0010
range7018
1
1
80
annotation4184
1
stem_loop
range4184
1
12
55
BBa_K218017
1
BBa_K218017
LuxO D47E under constitutive expression of TetR repressible promoter
2009-10-17T11:00:00Z
2015-05-08T01:11:30Z
Reference: Waters C.M. and Bassler B.L. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol. 2005;21:319-46.
Jeremy A. Freeman and Bonnie L. Bassler. A genetic analysis of the function of LuxO, a two-component response regulator involved in quorum sensing in Vibrio harveyi. 1999a. Molecular Microbiology. 31(2), 665-677.
Circuit to express LuxOD47, a mutant form of the LuxO protein that binds to the Pqrr4 promoter (BBa_K218011)
false
false
_321_
0
4377
9
It's complicated
true
Blah...
false
Emily Hicks
component2061960
1
BBa_B0010
component2061949
1
BBa_R0040
component2061962
1
BBa_B0012
component2061955
1
BBa_B0034
component2061959
1
BBa_K218015
annotation2061949
1
BBa_R0040
range2061949
1
1
54
annotation2061959
1
BBa_K218015
range2061959
1
81
1442
annotation2061955
1
BBa_B0034
range2061955
1
63
74
annotation2061960
1
BBa_B0010
range2061960
1
1451
1530
annotation2061962
1
BBa_B0012
range2061962
1
1539
1579
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_R0040
1
p(tetR)
TetR repressible promoter
2003-01-31T12:00:00Z
2015-05-08T01:14:14Z
Lutz, R., Bujard, H., <em>Nucleic Acids Research</em> (1997) 25, 1203-1210.
Released HQ 2013
Sequence for pTet inverting regulator driven by the TetR protein.</P>
false
true
_1_
0
24
7
In stock
false
<P> <P>BBa_R0040 TetR-Regulated Promoter is based on a cI promoter. It has been modified to include two TetR binding sites and the BioBrick standard assembly head and tail restriction sites.<P>
true
June Rhee, Connie Tao, Ty Thomson, Louis Waldman
annotation1986784
1
BBa_R0040
range1986784
1
1
54
annotation1986786
1
TetR 2
range1986786
1
26
44
annotation1986785
1
-35
range1986785
1
20
25
annotation1986787
1
-10
range1986787
1
43
48
annotation1986783
1
TetR 1
range1986783
1
1
19
BBa_K218015
1
BBa_K218015
LuxO D47E, Vibrio harveyi
2009-10-17T11:00:00Z
2015-05-08T01:11:30Z
Reference: Waters C.M. and Bassler B.L. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol. 2005;21:319-46.
Jeremy A. Freeman and Bonnie L. Bassler. A genetic analysis of the function of LuxO, a two-component response regulator involved in quorum sensing in Vibrio harveyi. 1999a. Molecular Microbiology. 31(2), 665-677.
[edit] Usage and Biology
Quorum-sensing bacteria produce and release chemical signal molecules termed autoinducers (AIs) whose external concentration increases as a function of increasing cell-population density. Bacteria detect the accumulation of a minimal threshold stimulatory concentration of these autoinducers and alter gene expression, and therefore their behavior. Using these signal-response systems, bacteria synchronize particular behaviors on a population-wide scale and thus function as multicellular organisms. The bioluminescent marine bacterium Vibrio harveyi uses three different AIs???AHL, CAI-1, and AI-2???to control the expression of genes responsible for bioluminescence and numerous other traits. We have designed our System 2 based on V. harveyi AI-2 signaling. V. harveyi AI-2 signal is a furanosyl borate diester, production of which requires the LuxS enzyme. Biosynthesis of AI-2 is dependent on the usage of S-adenosylmethionine (SAM) by the cell in various methylation reactions. For this reason, during periods of exponential growth, there is a very large production of AI-2, thus perhaps signaling to neighbors that a suitable environment for growth (i.e. rich in nutrients) has been found. LuxS catalyzes the formation of the (S)-4,5-dihydroxy-2,3-pentanedione (DPD) intermediate which spontaneously cyclizes and reacts with borate to give AI-2. AI-2 is bound in the periplasm by the protein LuxP, which is constitutively bound to LuxQ, a membrane bound histidine kinase sensor. The binding of AI-2 to LuxP is necessary in regulating the activity of the periplasm-bound LuxQ. At low cell density, in the absence of significant amounts of autoinducers, LuxQ acts as a kinase, autophosphorylates, and subsequently transfers the phosphate to the cytoplasmic protein LuxU. LuxU passes the phosphate to the DNA-binding response regulator protein LuxO. Phospho-LuxO, in conjunction with a transcription factor termed σ54, involved in nitrogen metabolism, activates transcription of the genes encoding five regulatory small RNAs (sRNAs) termed Qrr1???5 (for Quorum Regulatory RNA). The Qrr sRNAs interact with an RNA chaperone termed Hfq, involved in mRNA splicing. The sRNAs, together with Hfq, bind to and destabilize the mRNA encoding the transcriptional activator termed LuxR. LuxR is required to activate transcription of the luciferase operon: luxCDABE. Thus, at low cell density, because the luxR mRNA is degraded, the bacteria do not express the genes necessary for bioluminescence. At high cell density, when the autoinducers accumulate to the level required for detection, the kinase activity of LuxQ is overtaken by its phosphatase activity and thus drains phosphate from LuxO via LuxU. Unphosphorylated LuxO cannot induce expression of the sRNAs. This allows translation of luxR mRNA, production of LuxR, resulting in bioluminescence.
false
false
_321_
0
4377
9
It's complicated
false
The plasmid containing LuxOD47E (pJAF822) was obtained from Bassler lab (Freeman and Bassler, 1999).
Jeremy A. Freeman and Bonnie L. Bassler. A genetic analysis of the function of LuxO, a two-component response regulator involved in quorum sensing in Vibrio harveyi. 1999a. Molecular Microbiology. 31(2), 665-677.
false
Emily Hicks
annotation2061617
1
Start
range2061617
1
1
3
annotation2061618
1
Stop
range2061618
1
1360
1362
annotation2061646
1
Mutation
range2061646
1
139
141
BBa_B0010_sequence
1
ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc
BBa_B0034_sequence
1
aaagaggagaaa
BBa_R0040_sequence
1
tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac
BBa_K218017_sequence
1
tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcactactagagaaagaggagaaatactagatggtagaagacaccgcatccgttgcggcactttaccgctcttacctcacgccacttggcatcgatatcaatattgttggaacaggcagagacgccattgaaagcctgaaccatcgcattcctgatcttattctgctcgagctccgtctacctgatatgacggggatggacgtattgcacgcggtgaagaaaagccacccagacgtgccaatcatcttcatgacagcccatggttctatcgatactgcggtagaggcgatgcgccacggttctcaagacttcctaatcaaaccatgtgaagcagaccgtttacgtgtcacggtgaacaatgcgatccgtaaagcaaccaaattaaagaatgaagctgacaaccccggtaaccaaaattaccaaggcttcatcggcagtagccaaacgatgcagcaggtttaccgcaccattgactcggcagcgagcagtaaagcgagtattttcatcacgggtgaaagtggtacgggtaaagaagtgtgtgccgaagcgattcacgcagcaagcaaacgcggtgataagccgtttatcgccatcaactgtgcggcaatcccgaaagaccttattgaaagtgagctgtttggtcacgtaaaaggtgcgtttactggtgctgcgaatgaccgacaaggtgcggcagagcttgctgatggcggcaccttgttccttgatgaactctgtgaaatggacttggatcttcaaactaagctattgcgctttatccaaacgggtacattccaaaaagtcggttcttctaaaatgaagagcgtggatgtgcgctttgtgtgtgcaactaaccgagacccttggaaagaagtgcaagaaggccgtttccgtgaagacttgtattaccgtttgtacgtgattcctttgcaccttccgccgctgcgtgagcgtggtaaagacgttattgaaattgcatactcgttgcttggttatatgtctcatgaggaaggtaagagtttcgtccgtttcgcacaagacgtgattgaaagattcaacagctacgaatggccgggtaacgttcgccagttgcaaaacgtattgcgtaatatcgtggtactgaacaatggcaaagagatcacgctggatatgttaccgccaccactgaatcagcctgttgtgcgccaatcggtagcaaaattcattgaacctgacattatgacggtgtcagatattatgccgctttggatgacagagaaaatggctattgagcaggcaattcaagcgtgtgaaggcaacattccacgcgctgctggctatttggatgttagtccatcaacgatttatcgcaagttgcaagcttggaatagcaaggacgaaaaacaaaacgtatgatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
BBa_B0012_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttata
BBa_K218015_sequence
1
atggtagaagacaccgcatccgttgcggcactttaccgctcttacctcacgccacttggcatcgatatcaatattgttggaacaggcagagacgccattgaaagcctgaaccatcgcattcctgatcttattctgctcgagctccgtctacctgatatgacggggatggacgtattgcacgcggtgaagaaaagccacccagacgtgccaatcatcttcatgacagcccatggttctatcgatactgcggtagaggcgatgcgccacggttctcaagacttcctaatcaaaccatgtgaagcagaccgtttacgtgtcacggtgaacaatgcgatccgtaaagcaaccaaattaaagaatgaagctgacaaccccggtaaccaaaattaccaaggcttcatcggcagtagccaaacgatgcagcaggtttaccgcaccattgactcggcagcgagcagtaaagcgagtattttcatcacgggtgaaagtggtacgggtaaagaagtgtgtgccgaagcgattcacgcagcaagcaaacgcggtgataagccgtttatcgccatcaactgtgcggcaatcccgaaagaccttattgaaagtgagctgtttggtcacgtaaaaggtgcgtttactggtgctgcgaatgaccgacaaggtgcggcagagcttgctgatggcggcaccttgttccttgatgaactctgtgaaatggacttggatcttcaaactaagctattgcgctttatccaaacgggtacattccaaaaagtcggttcttctaaaatgaagagcgtggatgtgcgctttgtgtgtgcaactaaccgagacccttggaaagaagtgcaagaaggccgtttccgtgaagacttgtattaccgtttgtacgtgattcctttgcaccttccgccgctgcgtgagcgtggtaaagacgttattgaaattgcatactcgttgcttggttatatgtctcatgaggaaggtaagagtttcgtccgtttcgcacaagacgtgattgaaagattcaacagctacgaatggccgggtaacgttcgccagttgcaaaacgtattgcgtaatatcgtggtactgaacaatggcaaagagatcacgctggatatgttaccgccaccactgaatcagcctgttgtgcgccaatcggtagcaaaattcattgaacctgacattatgacggtgtcagatattatgccgctttggatgacagagaaaatggctattgagcaggcaattcaagcgtgtgaaggcaacattccacgcgctgctggctatttggatgttagtccatcaacgatttatcgcaagttgcaagcttggaatagcaaggacgaaaaacaaaacgtatga
igem2sbol
1
iGEM to SBOL conversion
Conversion of the iGEM parts registry to SBOL2.1
James Alastair McLaughlin
Chris J. Myers
2017-03-06T15:00:00.000Z