iGEM_2018_Cell1
1
iGEM 2018 Cell DH10B
BBa_R0063
1
lux pL
Promoter (luxR & HSL regulated -- lux pL)<br>
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr
2003-01-31T12:00:00Z
2015-05-08T01:14:15Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
The lux cassette of V. fischeri contains a left and a right promoter. The left promoter gives weak constitutive expression of downstream genes.This expression is down-regulated by the action of the Lux repressor, LuxR. Two molecules of LuxR protein form a complex with two molecules the signalling compound homoserine lactone (HSL). This complex binds to a palindromic site on the promoter, increasing the rate of transcription from Pr, repressing transcription from Pl</p>
<P> <P> This promoter is based on the Vibrio fischeri quorum sensing gene promoters. Two genes LuxI and LuxR and transcribed in opposite directions as shown below. The original sequence from which the parts <bb_part>BBa_R0062</bb_part> and <bb_part>BBa_R0063</bb_part> were derived is shown in the picture below.Includes most of Lux reulatory region, including the LuxR binding site which activates the right promoter. A putative LuxR autorepression binding site is also identified adjacent to the -10 site of the right promoter. This 2nd site has 55% identity with the first site. Putative inverted repeats (of size 18-27 bp) also exist between these two sites (not marked above), which may represent binding sites for other regulatory proteins. <p><img src="<bb_file>Image01.gif</bb_file>" width="614" height="362"><P>Unspecified.
<em>V. fischeri.</em>
true
annotation7071
1
BBa_R0063
range7071
1
1
151
annotation2051
1
LuxR/HSL
range2051
1
1
20
annotation2054
1
start
range2054
1
128
128
annotation2055
1
Putative LuxR/HSL
range2055
1
130
149
annotation2053
1
-35
range2053
1
89
94
annotation2052
1
-10
range2052
1
115
122
BBa_R0062
1
lux pR
Promoter (luxR & HSL regulated -- lux pR)
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr
2003-01-31T12:00:00Z
2015-05-08T01:14:15Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
Promoter activated by LuxR in concert with HSL</p> <p>The lux cassette of V. fischeri contains a left and a right promoter. The right promoter gives weak constitutive expression of downstream genes.This expression is up-regulated by the action of the LuxR activator protein complexed with the autoinducer, 3-oxo-hexanoyl-HSL. Two molecules of LuxR protein form a complex with two molecules of the signalling compound homoserine lactone (HSL). This complex binds to a palindromic site on the promoter, increasing the rate of transcription.
<P> <P>This promoter is based on the <em>Vibrio fischeri </em>quorum sensing gene promoters. Two genes LuxI and LuxR and transcribed in opposite directions as shown below. The original sequence from which the parts <bb_part>BBa_R0062</bb_part> and <bb_part>BBa_R0063</bb_part> were derived is shown in the picture below. <p><img src="<bb_file>Image1.gif</bb_file>" width="614" height="362"><P>
<em>V. fischeri</em>
true
annotation7070
1
BBa_R0062
range7070
1
1
55
annotation2048
1
start
range2048
1
53
53
annotation2047
1
-10
range2047
1
42
47
annotation2046
1
-35
range2046
1
20
25
annotation2045
1
LuxR/HSL
range2045
1
1
20
BBa_B0031
1
BBa_B0031
RBS.2 (weak) -- derivative of BBa_0030
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
false
true
_41_44_48_46_1_
0
24
7
Released HQ 2013
In stock
false
Medium RBS based on Ron Weiss thesis. Strength considered relative to <bb_part>BBa_B0030</bb_part>, <bb_part>BBa_B0032</bb_part>, <bb_part>BBa_B0033</bb_part>.
<P> <P>Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("RBS-1" in figure 4-14 of thesis). <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. <P>
Contact info for this part: <a href="mailto:(bchow@media.mit.edu)">Brian Cho</a>
true
annotation23316
1
conserved
range23316
1
7
10
BBa_J61101
1
BBa_J61101
Ribosome Binding Site Family Member
John Anderson
2007-01-28T12:00:00Z
2015-08-31T02:03:00Z
false
false
_95_
0
483
95
In stock
false
fix
N/A
N/A
true
BBa_C0012
1
lacI
lacI repressor from E. coli (+LVA)
Grace Kenney, Daniel Shen, Neelaksh Varshney, Samantha Sutton
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
Coding region for the LacI protein with an LVA degradation tail and without an RBS. LacI binds to the pLac regulator <bb_part>BBa_R0010</bb_part> and PLlac01 hybrid regulator <bb_part>BBa_R0011</bb_part> and inhibits transcription. IPTG (Isopropylthiogalactoside) binds to LacI and inhibits its operation, therefore promoting transcription.</P> <P>A rapid degredation tail (LVA) has been added to improve the High to Low performance of this part.</P>
References (unparsed) here: <p>Elowitz, M.B., Leibler, S. A synthetic oscillatory network of transcriptional regulators. <em>Nature</em> 403, 335-338 (2000). <a href="http://biobricks.ai.mit.edu/BB_References.htm#ELOW00">[ELOW00]</a><br> <br> </P> <P> References (unparsed) here: <p>Elowitz, M.B., Leibler, S. A synthetic oscillatory network of transcriptional regulators. <em>Nature</em> 403, 335-338 (2000). <a href="http://biobricks.ai.mit.edu/BB_References.htm#ELOW00">[ELOW00]</a><br> <br> </P> <P>Sequence taken from the repressilator of Elowitz and Leibler (2000). The obtained sequence was compared to the wild-type sequence for LacI obtained through a database search. The sequence had been modified from the wild-type in that wild-type GTG start was changed to an ATG start (note, actual ORF in E.coli has several GTG starts it would seem). The LVA tag has been added for quicker degradation.<P> Incompatible with systems containing LacI, lactose, or IPTG.
represillator of Elowitz and Leibler (2000)
true
annotation2213988
1
Help:Barcodes
range2213988
1
1129
1153
annotation7031
1
BBa_C0012
range7031
1
1
1128
annotation1723
1
lacI-LVA
range1723
1
1
1128
annotation1722
1
LVA
range1722
1
1090
1128
BBa_R1062
1
lux pR
Promoter, Standard (luxR and HSL regulated -- lux pR)<br>
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr<br> Drew Endy<br>
2003-01-31T12:00:00Z
2015-05-08T01:14:15Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
[Note: This is the same part as R0062 except that the -10 and -35 sites and spacing have been changed to comply with BBa_S0001].</p> <p>Promoter activated by LuxR in concert with HSL</p> <p>The lux cassette of V. fischeri contains a left and a right promoter. The right promoter gives weak constitutive expression of downstream genes.This expression is up-regulated by the action of the LuxR activator protein complexed with the autoinducer, 3-oxo-hexanoyl-HSL. Two molecules of LuxR protein form a complex with two molecules of the signalling compound homoserine lactone (HSL). This complex binds to a palindromic site on the promoter, increasing the rate of transcription.
<P> <P>This promoter is based on the <em>Vibrio fischeri </em>quorum sensing gene promoters. Two genes LuxI and LuxR and transcribed in opposite directions as shown below. The original sequence from which the parts <bb_part>BBa_R0062</bb_part> and <bb_part>BBa_R0063</bb_part> were derived is shown in the picture below. <p><img src="<bb_file part=BBa_R0062>Image1.gif</bb_file>" width="614" height="362"><br><br> Modified to comply with BBa_S0001:<br> TTGACA-17N-GATACT<br> <P>
<em>V. fischeri</em>
true
annotation2101
1
-35
range2101
1
20
25
annotation2099
1
-10
range2099
1
42
48
annotation7077
1
BBa_R1062
range7077
1
1
56
annotation2100
1
start
range2100
1
54
54
annotation2098
1
LuxR/HSL
range2098
1
1
20
BBa_R0065
1
cI+luxR
Promoter (lambda cI and luxR regulated -- hybrid)
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr
2003-01-31T12:00:00Z
2015-05-08T01:14:15Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
cI repressor negatively regulates this promoter and LuxR activates its transcription.The effect of cI is dominant over LuxR. This part is based on the LuxR and cI repressor regulated hybrid promoter designed and tested by Ron Weiss. It requires the binding of two cI repressor dimers for maximal repression and contains two cI repressor binding sites namely, OR1 and OR2. This promoter is leaky in the sense that 'some' transcription is seen in the absence of both cI and LuxR. </P> <P> </P> <table width="75%" border="1"> <tr> <td><strong>LuxI</strong></td> <td><strong>cI</strong></td> <td><strong>activity of promoter</strong></td> </tr> <tr> <td>+</td> <td>+</td> <td>zero</td> </tr> <tr> <td>+</td> <td>-</td> <td>maximum</td> </tr> <tr> <td>-</td> <td>+</td> <td>zero</td> </tr> <tr> <td>-</td> <td>-</td> <td>leaky (no quantitative information)</td> </tr> </table> <P> </P>
<P> <P>This part was designed based on the LuxR and cI repressor regulated hybrid promoter tested by Ron Weiss and the LuxR-LuxICDABE sequence annotated by Tom Knight <genbank>AF170104</genbank>. <P>
true
annotation1986774
1
BBa_R0065
range1986774
1
1
97
annotation1986780
1
OR1 cI
range1986780
1
81
97
annotation1986775
1
Lux Box
range1986775
1
6
25
annotation1986777
1
OR2 cI
range1986777
1
57
73
annotation1986778
1
lux p(R) start
range1986778
1
58
58
annotation1986779
1
-35
range1986779
1
71
76
annotation1986781
1
-10
range1986781
1
94
97
annotation1986776
1
-10
range1986776
1
47
52
BBa_J61100
1
BBa_J61100
Ribosome Binding Site Family Member
John Anderson
2007-01-28T12:00:00Z
2015-08-31T02:03:00Z
false
true
_95_
0
483
95
In stock
false
{{JCA_Arkin_RBSFamily}}
N/A
N/A
true
BBa_B0011
1
BBa_B0011
LuxICDABEG (+/-)
Reshma Shetty
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
Bidirectional transcriptional terminator consisting of a 22 bp stem-loop.</p>
<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>
Derived from luxICDABEG operon terminator of Vibrio fischeri <genbank>AF170104</genbank>.
true
annotation7019
1
BBa_B0011
range7019
1
1
46
annotation1683
1
stem_loop
range1683
1
13
35
BBa_B0034
1
BBa_B0034
RBS (Elowitz 1999) -- defines RBS efficiency
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
RBS based on Elowitz repressilator.
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
annotation23325
1
conserved
range23325
1
5
8
BBa_C0051
1
cI lam
cI repressor from E. coli phage lambda (+LVA)
Vinay S Mahajan, Brian Chow, Peter Carr, Voichita Marinescu and Alexander D. Wissner-Gross
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
Coding region for the cI repressor based on cI repressor from bacteriophage lambda modified with an LVA tail for rapid degradation of the protein. cI repressor binds to the cI regulator (BBa_R0051).</P>
References (unparsed) here: <p><a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000</P> <P><a href="http://www.genesdev.org/cgi/content/full/15/22/3013">Octamerization of CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. </a>Ian B. Dodd,1 Alison J. Perkins, Daniel Tsemitsidis, and J. Barry Egan , Genes and Development (Vol 15, No. 22) 3013-3022: 2001</P> <p></p> <P> References (unparsed) here: <p><a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000</P> <P><a href="http://www.genesdev.org/cgi/content/full/15/22/3013">Octamerization of CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. </a>Ian B. Dodd,1 Alison J. Perkins, Daniel Tsemitsidis, and J. Barry Egan , Genes and Development (Vol 15, No. 22) 3013-3022: 2001</P> <p></p> <P>BBa_C0051 cI repressor is based on the cI repressor from the Elowitz's repressilator. It has been modified to include a rapid degradation LAA tail, and includes the BioBrick standard assembly head and tail restriction sites. The RBS has been removed. The stop codon has been changed from TAA to a double stop codon TAATAA.<P>
Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999).
true
annotation23335
1
LVA
range23335
1
712
744
annotation23334
1
cI lambda
range23334
1
4
711
annotation2213991
1
Help:Barcodes
range2213991
1
751
775
BBa_R0051
1
cI lam
promoter (lambda cI regulated)
Vinay S Mahajan, Brian Chow, Peter Carr, Voichita Marinescu and Alexander D. Wissner-Gross
2003-01-31T12:00:00Z
2015-05-08T01:14:14Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
The cI regulated promoter is based on the pR promtoer from bacteriohage lambda. The promoter has two two DNA binding sites for lambda cI repressor <bb_part>BBa_C0051</bb_part>. cI binding results in repression of transcription. The specific sequence used here is based on the cI repressible promoter used in the Elowitz repressilator (and references therein).</P>
<P> <P>In order to address concerns about the promoter transcribing in the reverse direction, we have removed the -35 and -10 signals responsible for the promoter activity in the reverse direction. (<b><font color="red">More details needed here! DE, 2/24/03</font></b>)<P> Incompatible with host expressing cI repressor.
<a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000
true
annotation7067
1
BBa_R0051
range7067
1
1
49
annotation2024
1
OR1
range2024
1
25
41
annotation2023
1
-35
range2023
1
15
20
annotation2022
1
-10
range2022
1
38
43
annotation2025
1
OR2
range2025
1
1
17
BBa_R0053
1
cII p22
Promoter (p22 cII regulated)
Maia Mahoney
2003-01-31T12:00:00Z
2015-05-08T01:14:14Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
The p22 cII regulatory region sequence is a 97 base-pair sequence with the standard BioBrick prefix and suffix sections on its ends. p22 cII repressor protein, BBa_C0053, binds to it.<br> This segment contains O-R1, O-R2, a fragment of O-R3, the -35 of P-RM, and P-R (-10 and -35 from Tom Knight)</p>
<P> <P><P>
Bacteriophage p22.
true
annotation2038
1
-35
range2038
1
18
23
annotation2041
1
-35
range2041
1
8
13
annotation2035
1
OR3
range2035
1
1
3
annotation7069
1
BBa_R0053
range7069
1
1
54
annotation2037
1
OR1
range2037
1
34
51
annotation2042
1
-10
range2042
1
30
35
annotation2036
1
OR2
range2036
1
11
28
BBa_C0062
1
luxr
luxR repressor/activator, (no LVA?)
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
In complex with HSL, LuxR binds to the Lux promoter, activating transcription from Pr <bb_part>BBa_R0062</bb_part>, and repressing transcription from Pl <bb_part>BBa_R0063</bb_part>. <p>The lux cassette of V. fischeri contains a left and a right promoter. The right promoter gives weak constitutive expression of downstream genes.This expression is up-regulated by the action of the Lux activator, LuxR complexed to HSL. Two molecules of LuxR protein form a complex with two molecules the signalling compound homoserine lactone (HSL). This complex binds to a palindromic site on the promoter, increasing the rate of transcription.</p>
<P> <P>2 silent point mutants were introduced in the coding sequence to remove internal XbaI and PstI sites. Mutation sites were chosen to replace codons commonly used in <em>E. coli</em> with codons used at a similar frequency. <P>
<em>V. fischeri</em> <genbank>AF170104</genbank>
true
annotation1762
1
prefix
range1762
1
1
2
annotation1765
1
A
range1765
1
492
492
annotation1766
1
luxR
range1766
1
1
750
annotation1764
1
T
range1764
1
174
174
annotation7039
1
BBa_C0062
range7039
1
1
756
annotation2213986
1
Help:Barcodes
range2213986
1
757
781
BBa_B0032
1
BBa_B0032
RBS.3 (medium) -- derivative of BBa_0030
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
false
true
_41_44_48_46_1_
0
24
7
Released HQ 2013
In stock
false
Weak1 RBS based on Ron Weiss thesis. Strength is considered relative to <bb_part>BBa_B0030</bb_part>, <bb_part>BBa_B0031</bb_part>, <bb_part>BBa_B0033</bb_part>.
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("RBS-2" in figure 4-14 of thesis). <P>
Contact info for this part: <a href="mailto:(bchow@media.mit.edu)">Brian Chow</a>
true
annotation7027
1
BBa_B0032
range7027
1
1
13
annotation1710
1
RBS
range1710
1
7
10
annotation1709
1
RBS-3\Weak
range1709
1
1
13
BBa_C0050
1
cI HK022
cI repressor from phage HK022 (+LVA?)
Reshma Shetty
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
Coding region for the HK022 bacteriophage cI protein. cI binds to the HK022 pR regulator (BBa_R0050). It represses transcription of the protein encoded by the sequence 3' to the pR region. This coding sequence does not contain a RBS.</P>
References (unparsed) here: <p>Carlson NG, Little JW. Highly cooperative DNA binding by the coliphage HK022 repressor. J Mol Biol. 1993 Apr 20;230(4):1108-30.<br> PMID: 8487297.</P> <P> Mao C, Little JW. Mutations affecting cooperative DNA binding of phage HK022 CI repressor.<br> J Mol Biol. 1998 May 29;279(1):31-48. PMID: 9636698.</P> <p></p> <p></p> <P> References (unparsed) here: <p>Carlson NG, Little JW. Highly cooperative DNA binding by the coliphage HK022 repressor. J Mol Biol. 1993 Apr 20;230(4):1108-30.<br> PMID: 8487297.</P> <P> Mao C, Little JW. Mutations affecting cooperative DNA binding of phage HK022 CI repressor.<br> J Mol Biol. 1998 May 29;279(1):31-48. PMID: 9636698.</P> <p></p> <p></p> <P>Derived from <genbank>STHK022N</genbank>.<br> <br> Response from John Little (Arizona) regarding the start of HK022 cI<br> <br> From: <jlittle@email.arizona.edu> <br> Date: Tue Jan 21, 2003 4:39:21 PM US/Eastern <br> To: "Drew Endy" <endy@MIT.EDU><br> Subject: RE: hk022 cI start (naive question)? <br> Hello Drew and Michael, I seriously doubt that the extra 27 aa are part of CI. It doesn't make sense in terms of the biology, for sure. In any case, the protein we characterized starts where Carlson and Little stated; as I recall, oR3 partially overlaps the start of cI. I have a vague memory of some possibly interesting biology, having to do with multicopy plasmids. I don't recall the findings themselves. Anyway, one possible explanation was that this extra N-terminal addition was made (e.g. from the pRE promoter, or from a message that arose from transcription around the entire plasmid), making a protein with altered functions. We never followed it up. <br> Good luck <br> John<br> <br> -- Original Message -- <br> Date: Sun, 19 Jan 2003 15:26:26 -0500 <br> Subject: hk022 cI start (naive question)? <br> Cc: elowitm@rockefeller.edu <br> To: jlittle@u.arizona.edu <br> From: Drew Endy <endy@MIT.EDU> <br> Hi John, I'm sitting here with Michael Elowitz and we're working through the sequence for HK022 cI. We noticed that the annotation from NC_002166 includes an "extra" 81 base pairs upstream of what we thought of as the actual start. It looks like this extra DNA extends into the PR regulatory region. We're wondering what's going on here? I'm guessing this is well documented somewhere. Thanks for any pointers/info! <br> Drew<P> It is unknown whether there is cross-talk between this repressor and Lambda cI regulatory region, 434 cI regulatory region and P22 regulatory region.
Bacteriophage HK022.
true
annotation7033
1
BBa_C0050
range7033
1
1
744
annotation1737
1
OR3 partial
range1737
1
1
8
annotation1734
1
2
range1734
1
739
744
annotation2213990
1
Help:Barcodes
range2213990
1
745
769
annotation1735
1
cI HK022
range1735
1
1
744
annotation1736
1
SsrA
range1736
1
706
738
BBa_B0033
1
BBa_B0033
RBS.4 (weaker) -- derivative of BBa_0030
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
false
true
_41_44_48_46_1_
0
24
7
Released HQ 2013
In stock
false
Weaker RBS based on Ron Weiss thesis. Strengths relative to <bb_part>BBa_B0030</bb_part>, <bb_part>BBa_B0031</bb_part>, <bb_part>BBa_B0032</bb_part>.
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("RBS-3" in figure 4-14 of thesis). <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
annotation7028
1
BBa_B0033
range7028
1
1
11
annotation1713
1
RBS-4\Weaker
range1713
1
1
11
annotation1714
1
RBS
range1714
1
7
10
BBa_C0053
1
c2 P22
c2 repressor from Salmonella phage P22 (+LVA)
Maia Mahoney
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
The P22 c2 repressor protein coding sequence is a 720 base-pair sequence with the standard RBS-compatible BioBrick prefix and the standard BioBrick suffix sections on its ends. It binds to the P22 c2 regulatory sequence, BBa_R0053. The sequence contains a LVA tag for faster degredation.</p>
References (unparsed) here: <p>Vander Byl,C. and Kropinski,A.M. <em>Sequence of the genome of Salmonella bacteriophage P22</em><br> J. Bacteriol. 182 (22), 6472-6481 (2000) <P> References (unparsed) here: <p>Vander Byl,C. and Kropinski,A.M. <em>Sequence of the genome of Salmonella bacteriophage P22</em><br> J. Bacteriol. 182 (22), 6472-6481 (2000) <P><P>
Bacteriophage P22
true
annotation1751
1
stop
range1751
1
682
687
annotation1747
1
cII p22
range1747
1
1
648
annotation7036
1
BBa_C0053
range7036
1
1
687
annotation2213993
1
Help:Barcodes
range2213993
1
688
712
annotation1750
1
LVA
range1750
1
649
681
BBa_C0061
1
luxI
autoinducer synthetase for AHL
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
Synthesizes 3OC<sub>6</sub>HSL, which binds to LuxR.</p> <p>The lux cassette of V. fischeri contains a left and a right promoter. The right promoter gives weak constitutive expression of downstream genes.This expression is up-regulated by the action of the Lux repressor, LuxR. Two molecules of LuxR protein form a complex with two molecules the signalling compound HSL. This complex binds to a palindromic site on the promoter, increasing the rate of transcription.</p>
<P> <P>An LVA tail (sequence: AANDENYALVA) was added to increase protein degradation. . <P>
<em>V. fischeri</em> <genbank>AF170104</genbank>
true
annotation1760
1
LVA
range1760
1
580
611
annotation7038
1
BBa_C0061
range7038
1
1
618
annotation2213985
1
Help:Barcodes
range2213985
1
619
643
annotation1761
1
luxI
range1761
1
1
579
BBa_C0052
1
cI 434
cI repressor from phage 434 (+LVA)
Maia Mahoney
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
The 434 cI repressor protein coding sequence is a 710 base-pair sequence with the standard RBS-compatible BioBrick prefix and the standard BioBrick suffix sections on its ends. It binds to the 434 regulatory sequence, BBa_R0052. The sequence contains a LVA tag for faster degredation and has no RBS.</p>
References (unparsed) here: <p>Nikolnikov,S., Posfai,G. and Sain,B. <em>The construction of a versatile plasmid vector that allows direct<br> selection of fragments cloned into six unique sites of the cI gene of coliphage 434</em>. Gene 30 (1-3), 261-265 (1984)<P> References (unparsed) here: <p>Nikolnikov,S., Posfai,G. and Sain,B. <em>The construction of a versatile plasmid vector that allows direct<br> selection of fragments cloned into six unique sites of the cI gene of coliphage 434</em>. Gene 30 (1-3), 261-265 (1984)<P><P>
Bacteriophage 434
true
annotation7035
1
BBa_C0052
range7035
1
1
669
annotation1743
1
cI 434
range1743
1
1
669
annotation2213992
1
Help:Barcodes
range2213992
1
670
694
annotation1745
1
LVA
range1745
1
631
669
BBa_R0011
1
lacI+pL
Promoter (lacI regulated, lambda pL hybrid)
Neelaksh Varshney, Grace Kenney, Daniel Shen, Samantha Sutton
2003-01-31T12:00:00Z
2015-05-08T01:14:14Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
Inverting regulatory region controlled by LacI (<bb_part>BBa_C0010</bb_part>, <bb_part>BBa_C0011</bb_part>, etc.) <p> The PLlac 0-1 promoter is a hybrid regulatory region consisting of the promoter P(L) of phage lambda with the cI binding sites replaced with lacO1. The hybrid design allows for strong promotion that can nevertheless be tightly repressed by LacI, the Lac inhibitor (i.e. repressor) (<bb_part>BBa_C0010</bb_part>) ([LUTZ97]). The activity of the promoter can be regulated over a >600-fold range by IPTG in E.Coli DH5-alpha-Z1 (same paper reference).
<P> <P>hybrid promoter design to create strong promoter that is, at the same time, highly repressible. note that the upstream operator installed in this hybrid is slightly different than the one in the original source (Lutz and Bujard, 1997). the most upstream operator region is slightly truncated in the represillator version, so that both operators in the hybrid are the same sequence. see references for details. also, the sequence has been truncated after the transcriptional start site.<P>LacI binds to this regulator. This part is incompatible with species containing active LacI coding regions. Lactose and IPTG disable the operation of LacI and increase transcription. This part is incompatible with environments containing lactose or lactose analogs.
represillator of Elowitz and Leibler (2000)
true
annotation2000
1
-35
range2000
1
20
25
annotation7064
1
BBa_R0011
range7064
1
1
54
annotation1999
1
lac O1
range1999
1
3
19
annotation2002
1
-10
range2002
1
43
48
annotation2001
1
lac O1
range2001
1
26
42
BBa_C0060
1
aiiA
autoinducer inactivation enzyme from Bacillus; hydrolyzes acetyl homoserine lactone
Vinay S Mahajan, Brian Chow, Peter Carr, Voichita D. Marinescu and Alexander D. Wissner-Gross
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
Coding region for the autoinducer inactivation enzyme A (<em>aiiA</em>) LVA tagged. The gene was originally isolated from <em>Bacillus</em> sp. 240B1 and it encodes an enzyme that catalyzes the degradation of N-acyl homoserine lactones (AHLs)--quorum sensing autoinducers.</P>
References (unparsed) here: <p>Dong,Y.H., Xu,J.L., Li,X.Z. and Zhang,L.H.: AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of <em>Erwinia<br> carotovora</em>, Proc. Natl. Acad. Sci. U.S.A. 97 (7), 3526-3531 (2000). <a href="#">http://www.pnas.org/cgi/content/full/97/7/3526</a></P> <P>Lee SJ, Park SY, Lee JJ, Yum DY, Koo BT, Lee JK.: Genes encoding the N-acyl homoserine lactone-degrading enzyme are widespread in many subspecies of Bacillus thuringiensis, Appl Environ Microbiol 2002 Aug;68(8):3919-24. <a href="#">http://aem.asm.org/cgi/content/full/68/8/3919?view=full&pmid=12147491</a><br> <br> </P> <P> References (unparsed) here: <p>Dong,Y.H., Xu,J.L., Li,X.Z. and Zhang,L.H.: AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of <em>Erwinia<br> carotovora</em>, Proc. Natl. Acad. Sci. U.S.A. 97 (7), 3526-3531 (2000). <a href="#">http://www.pnas.org/cgi/content/full/97/7/3526</a></P> <P>Lee SJ, Park SY, Lee JJ, Yum DY, Koo BT, Lee JK.: Genes encoding the N-acyl homoserine lactone-degrading enzyme are widespread in many subspecies of Bacillus thuringiensis, Appl Environ Microbiol 2002 Aug;68(8):3919-24. <a href="#">http://aem.asm.org/cgi/content/full/68/8/3919?view=full&pmid=12147491</a><br> <br> </P> <P>BBa_C0060 insert contains open reading frame (nucleotides 49-801) of the GeneBank sequence AF196486 followed by the LVA tag and two double stop codons inserted in the BioBrick prefix and suffix flanking regions. The original stop codon was TAG and in the present sequence it was substituted by TAATAA.<P>
<genbank>AF196486</genbank> from <em>Bacillus</em> sp. 240B1 putative metallohydrolase (<em>aiiA</em>) gene. <BR> Dong,Y.H., Xu,J.L., Li,X.Z. and Zhang,L.H.: AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of <em>Erwinia<br> carotovora</em>, Proc. Natl. Acad. Sci. U.S.A. 97 (7), 3526-3531 (2000).<br>
true
annotation7037
1
BBa_C0060
range7037
1
1
789
annotation1756
1
LVA
range1756
1
751
783
annotation1757
1
aiiA
range1757
1
1
750
annotation1754
1
start
range1754
1
1
3
annotation1755
1
2
range1755
1
784
789
annotation2213987
1
Help:Barcodes
range2213987
1
790
814
BBa_R0040
1
p(tetR)
TetR repressible promoter
June Rhee, Connie Tao, Ty Thomson, Louis Waldman
2003-01-31T12:00:00Z
2015-05-08T01:14:14Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
Sequence for pTet inverting regulator driven by the TetR protein.</P>
<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>
Lutz, R., Bujard, H., <em>Nucleic Acids Research</em> (1997) 25, 1203-1210.
true
annotation1986787
1
-10
range1986787
1
43
48
annotation1986784
1
BBa_R0040
range1986784
1
1
54
annotation1986785
1
-35
range1986785
1
20
25
annotation1986783
1
TetR 1
range1986783
1
1
19
annotation1986786
1
TetR 2
range1986786
1
26
44
BBa_R1051
1
cI lam
Promoter, Standard (lambda cI regulated)<br>
Vinay S Mahajan, Brian Chow, Peter Carr, Voichita Marinescu and Alexander D. Wissner-Gross<br> Drew Endy<br>
2003-01-31T12:00:00Z
2015-05-08T01:14:15Z
false
false
_1_
0
24
7
Released HQ 2013
In stock
false
[Note: This is the same part as R0051 except that the -10 and -35 sites and spacing have been changed to comply with BBa_S0001].<br><br>The cI regulated promoter is based on the pR promtoer from bacteriohage lambda. The promoter has two two DNA binding sites for lambda cI repressor <bb_part>BBa_C0051</bb_part>. cI binding results in repression of transcription. The specific sequence used here is based on the cI repressible promoter used in the Elowitz repressilator (and references therein).</P>
<P> <P>In order to address concerns about the promoter transcribing in the reverse direction, we have removed the -35 and -10 signals responsible for the promoter activity in the reverse direction. (<b><font color="red">More details needed here! DE, 2/24/03</font></b>)<br><br> Modified to comply with BBa_S0001:<br> TTGACA-17N-GATACT<br><P> Incompatible with host expressing cI repressor.
<a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000
true
annotation2078
1
-10
range2078
1
38
43
annotation7074
1
BBa_R1051
range7074
1
1
49
annotation2075
1
-35
range2075
1
15
20
annotation2077
1
OR2
range2077
1
1
17
annotation2076
1
OR1
range2076
1
25
41
BBa_C0040
1
tetR
tetracycline repressor from transposon Tn10 (+LVA)
June Rhee, Connie Tao, Ty Thomson, Louis Waldman.
2003-01-31T12:00:00Z
2015-08-31T04:07:23Z
false
true
_1_
0
24
7
Released HQ 2013
In stock
false
Coding region for the TetR protein without the Ribosome Binding Site. Modified with an LVA tail for rapid degradation of the protein and faster fall time for the emission. TetR binds to the pTet regulator (BBa_R0040). aTc (anhydrotetracycline) binds to TetR and inhibits its operation.</P>
References (unparsed) here: <p>Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999). </P> <p> Lutz R, Bujard H., Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997 Mar 15;25(6):1203-10. PMID: 9092630 </p> <P> References (unparsed) here: <p>Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999). </P> <p> Lutz R, Bujard H., Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997 Mar 15;25(6):1203-10. PMID: 9092630 </p> <P>BBa_C0040 TetR Protein is based on the TetR sequence from Elowitz's repressilator. It has been modified to include a rapid degradation LVA tail, and includes the BioBrick standard assembly head and tail restriction sites. The RBS has been removed. The stop codon has been changed from TAA to a double stop codon TAATAA. <P>
Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999)
true
annotation2213989
1
Help:Barcodes
range2213989
1
661
685
annotation23329
1
tetR
range23329
1
4
620
annotation23330
1
SsrA
range23330
1
621
654