Promoter Family Member (U037O11+D038O22)
Promoter Family Member (U073O11+D002O22)
This part is the twin of the non-compatible biobrick BBa_K1486008 rendered compatible by mutating the two illegal restriction sites. However, all experiments were run on the aforementioned biobrick.
Site-directed mutagenesis was used to remove the restriction sites in the sequence.
http://www.addgene.org/browse/article/8177/ which was then mutated by us.
Promoter Family Member (U097NUL+D014O22)
A Double Reporter (LacZ-alpha and RFP) loaded on pSB3C5. For more information please refer to BBa_I732402.
Promoter Family Member (U085O11+D050O22)
Promoter Family Member (U085O11+D062NUL)
Promoter Family Member (U097O11+D038O22)
LasR/LasI Inducible & RHLR/RHLI repressible Promoter
This part is similar to BBa_R0079 but has an added binding site for RHLR/RHLI in between the -35 and -10 region. Thus this promoter is induced by LasR/LasI but repressed by RHLR/RHLI binding.
The natural spacer between the -35 and -10 is 14bp and the natural O1 site for RHLR/RHLI is 20bp long. There was not much over lap of the -35 or the -10 with this sequence, so it was nessicary to chop off some of the binding site sequence in order to maintain the correct spacing and preserve the -35 and -10 sequence. The binding site sequence is missing a tcc on is 5' end and a t on its 3' end.
Rust L. et. al., "Analysis of the Pseudomonas aeruginosa Elastase (lasB) Regulatory Region". Journal of Bacteriology, 1996.
Promoter Family Member (U049O11+D014O22)
Promoter Family Member (U073O26+D062O61)
Vikram Vijayan, Allen Hsu, Lawrence Fomundam
LasR and 3OC12HSL regulated promoter with CI Operator 1 (binding site for lambda cI repressor)
---- This part is in BBb Format. It is flanked by BamHI and BglII sites instead of XbaI and SpeI. More information about the BBb Format is available at: [http://openwetware.org/wiki/Template:AndersonLab:BBb_Standard BBb Standard Description Page]
PCR mv028/mv029 on rrnB native sequence (721bp, EcoRI/BamHI/DpnI) Sub into pBca1256 (EcoRI/BamHI, 2472+910, L) Product is pBca1256-K112118 ----------------------------------------------- mv028 Forward Biobricking of rrnB P1 promoter cgataGAATTCatgAGATCTatgcactaaaacgtatcctacgcccg mv029 Reverse Biobricking of rrnB P1 promoter cgttaGGATCCcgccttcccgctacagagtcaagc
Promoter Family Member (U049O11+D038O22)
Hybrid promoter constisting of two LacI O2 sites at the ends of the promoter and two recognition sites (OR2 and OR1) for the P22 c2 repressor. The promoter should function as a NOR gate.
a small fragment of OR3 remains.
Constantin Ahlmann-Eltze, Charlotte Bunne, Magdalena Büscher, Jan Gleixner, Max Horn, Anna Huhn, Nils Klughammer, Jakob Kreft, Elisabeth Schäfer, Carolin Schmelas, Silvan Schmitz, Max Waldha
This part has the arabinose regulated promoter (AraC/pBAD) upstream of a ribosome binding site. This is ideal for inserting a protein to be expressed downstream of this part as it's expression can be regulated by the presence of the concentration of arabinose in the growing environment/media of the cells. ==What this part actually does== This composite part includes the AraC/pBAD promoter and a strong ribosome binding site designed from the Anderson family of RBS. The AraC/pBAD promoter can be used with prokaryotic chassis to regulate expresion of proteins. When the AraC/pBAD promoter is placed upstream of your canditate translational unit (protein to be expressed) it allows control of the trancription of the said protein. This is done via controlling the concentration of arabinose sugar in the environment/solution of bacterial growth. Controlling the transcription will not ensure translation. The ribosome binding site is ideally placed a small distance away from the promoter site to ensure that the ribosome will bind and start translating the protein coding sequence found downstream.
The part was designed with RFC10 assembly from supplied biobricks of the iGEM2009 distribution.
The AraC promoter can be found naturally at 1.52min of the E.coli genome ([http://ecogene.org/geneinfo.php?eg_id=EG10054 EcoGene number EG10054]. The RBS was taken from the designed sequences of RBS by the Anderson family. For more information visit the original part page [http://partsregistry.org/Part:BBa_J61100 here].
Promoter Family Member (U085O11+D062O22)
(correct) temperature sensitive promoter
This part has two fused proteins downstream of an arabinose-inducible promoter: CpxR-IFP[1] and CpxR-IFP[2]. This construct was made in all orientations: - CpxR-IFP[1] + CpxR-IFP[2] (BBa_K1286008) - IFP[1]-CpxR + CpxR-IFP[2] (BBa_K1486010) - CpxR-IFP[1] + IFP[2]-CpxR (BBa_K1486011)
All orientations were made, so all dimerizations could be tested (see main page for biobrick numbers). Flexible linkers were used for each of the fused proteins, and an RBS was put before each one of them.
This promoter is a modified version of the Mnt promoter that is also responsive to TetR. The promoter should be repressed by Mnt repressor. It should also be repressed by TetR, and in the absence of Mnt repressor, should be induced by aTc.
Mnt repressor binds as a tetramer to two half-operator sites. Introduction of TetR binding sites between the Mnt promoter -10 sequence and the start site for transcription should allow for repression by TetR. Accordingly, the hybrid promoter was designed by 1) Remove all bases of mnt promoter 3??? to -10: gagtcgtattaattt will be replaced by tccctatcagtgata, and 2) truncate the second half of ptet -10 and mutate -35 so that it function to bind tetR (replace ttgaca with actgta), but is not a promoter, and 3) place the tetR1 and tetR2 binding sites 3??? to truncated mnt -10 sequence.
This part comes from the Mnt promoter and the TetR promoter
Double Promoter (cI, negative / LacI, negative)
Promoter Family Member (U073O11+D062O22)
Modified lambda P(RM) promoter: -10 region from P(L) and cooperatively repressed by 434 cI
Lamdba P(RM) promoter modified to be activated by lamda repressor (cI) and repressed by 434 repressor (cI). Two operator sites are used for both activation and repression to enhance cooperativity. Additionally, the -10 region from lambda P(L) was used instead of that from P(RM).
The O-R3 site of lambda (17 nt) was replaced by the O-R1 site of 434 (14 nt) to facilitate repression by 434 cI. The new 434 O-R1 is 5'-justified with the lambda O-R3 it replaced, leaving the -10 sequence intact. The 434 O-R2 site replaces the wildtype labmda promoter starting at -5, thereby preserving the 8 nt between 434 O-R1 and O-R2 in the wildtype. The mRNA transcript will contain an additional 9 nt compared to wildtype lambda phage. This part differs from BBa_I12036 because the -10 region from P(L) was used instead of that from P(RM).
Bushman, F. D. The bacteriophage 434 right operator roles of O-R1, O-R2, and O-R3. J. Mol. Biol. (1993) 230, 28-40. ; 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 Research, 1997, Vol.25, No.6 (1203-1210)
Promoter Family Member (U049O11+D002O22)
Promoter Family Member (U097NUL+D038O22)
Promoter Family Member (U073O11+D050O22)
Daniel Rodriguez, Eduardo Almeyda, Porfirio Quintero
pRM promoter from Lambda phage. It may be positive and negative regulated according to cI protein concentration. It needs OL region in order to achieve better negative regulation. It may be used to establish a biphasic switch which could permit activation and repression of genes transcribed from it.
Analysis of illegal restriction sites was performed, but it does not have them originally.
It comes directly from genomic DNA of Lambda phage. It was extracted by PCR as recommended by the Registry.
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Promoter Family Member (U049O11+D062NUL)
A Double Reporter (LacZ-alpha and GFP-AAV) loaded on pSB3K5. For more information please refer to BBa_I732402.
Right facing promoter (for xylA) controlled by xylR and CRP-cAMP
removed RBS cut out several xylR activation sites
CRP-cAMP transcriptional dual regulator activates transcription
XylR-Xylose transcriptional activator activates transcription
Promoter Family Member (U097NUL+D050O22)
Complex Quorum sensing circuit that receives the signal of PAI+LasR and AI+LuxR to control the production of LuxI and LasI enzymes.
The biobricks BBa_K266006 and BBa_K266000 where used to build this biobrick
promoter for FabA gene - Membrane Damage and Ultrasound Senstitive
According to Vollmer, et. al in their 1998 Applied and Enviormental Microbiology paper, "Bacterial Stress Responses to 1-Megahertz Pulsed Ultrasound in the Presence of Microbubble", the promoter for the fabA gene, a known membrane damage response gene, is upregulated seven fold when cells are exposed to high frequency ultrasound and microbubble cavitation.
Promoter Family Member (U073O11+D062NUL)
Promoter Family Member (U097O11+D050O22)
This part has a fused protein downstream of an arabinose-inducible promoter: IFP[2]-CpxR. Biobrick BBa_K1486014 has IFP[1]-CpxR with an arabinose promoter. This construct was made in both orientations: BBa_K1486013 is CpxR-IFP[2] (with an arabinose promoter).
Both orientations were made, as well as for IFP[1] so all dimerizations could be tested (see main page for biobrick numbers). Flexible linkers were used to fuse both proteins, and an RBS was put before each one of them.
The part contains CpxR with an upstream arabinose-inducible promoter.
The arabinose had to be upstream of the CpxR. Also, the sequence had to be tested because of a mutation, and it works perfectly.
The CpxR comes from the genome of E coli, and the arabinose promoter comes from a biobrick.
Promoter Family Member (U085O11+D038O22)
Hybrid promoter: HSL-LuxR activated, P22 C2 repressed
Hybrid promoter consisting of the Lux box which overlaps partly with -35 box. Binding sites for P22 C2 OR2 and OR1 are located between the -35 and -10 boxes and downstream of them respectively.
-35 box is partly composite. -10 is taken from the P22 phage PR regulatory region
Promoter Family Member (U061O11+D062NUL)
A Double Reporter (LacZ-alpha and GFP-AAV) loaded on pSB3K5. For more information please refer to BBa_I732401.
This part has a fused protein downstream of an arabinose-inducible promoter: CpxR-IFP[2]. Biobrick BBa_K1486012 has CpxR-IFP[1] with an arabinose promoter. This construct was made in both orientations: BBa_K1486015 is IFP[2]-CpxR (with an arabinose promoter).
Double Promoter (cI, negative / TetR, negative)
nhaA promoter, that can be regulated by pH and nhaR protein.
It's E.coli K12 sodium/proton anti-transport promoter. It can be a pH sensor. We test pH senses in different pH value and Sodium concentration.
Promoter Family Member (U037O11+D062NUL)
A Double Reporter (LacZ-alpha and GFP-AAV) loaded on pSB3K5. For more information please refer to BBa_I732403.
The repression of heat shock gene expression (ROSE) element is an RNA element found in the 5' UTR of some heat shock protein's mRNAs. The ROSE element is an RNA thermometer that negatively regulates heat shock gene expression. The secondary structure is thought to be altered by temperature, thus it is an RNA thermometer. This structure blocks access to the ribosome binding site at normal temperatures. During heat shock however, the structure changes freeing the ribosome binding site and allowing expression to occur. RNA Thermometers are the only known single-component regulators of gene expression.(1) RNA Thermometers are thermosensors that regulate gene expression by temperature-induced changes in RNA conformation. Naturally occurring RNA Thermometers exhibit complex secondary structures which are believed to undergo a series of gradual structural changes in response to temperature shifts.(2) RNA Thermometers often regulate genes required during either a heat shock or cold shock response, but have been implicated in other regulatory roles such as in pathogenecity and starvation.(3)
Note that RNA thermometer actually works as an RBS sequence. Therefore, this part does not include an additional ribosome binding site. Also, this part does not contain an terminator sequence, but a simple stop codon. The RFP should be translated continuously.
Bradyrhizobium japonicum USDA 110 and Registry
This part has a fused protein downstream of an arabinose-inducible promoter: IFP[1]-CpxR. Biobrick BBa_K1486015 has IFP[2]-CpxR with an arabinose promoter. This construct was made in both orientations: BBa_K1486012 is CpxR-IFP[1] (with an arabinose promoter).
Both orientations were made, as well as for IFP[2] so all dimerizations could be tested (see main page for biobrick numbers). Flexible linkers were used to fuse both proteins, and an RBS was put between the promoter and the cds.
Right facing promoter (for xylF) controlled by xylR and CRP-cAMP
potential looping feature possibly removed
removed RBS, left promoter, and several xylR binding sites
This is the hybB promoter, which normally controlls hydrogenase regulation at low temperatures. It turns ON at 30oC and is active as low as 20oC (lower not tested). It is OFF at 37 and higher temperatures. In the literature, it is also active in anaerobic environments. This hasn't been tested.
lizjaneclarke@gmail.com Univerity of California - San Francisco
Modified lamdba Prm promoter (cooperative repression by 434 cI)
Lamdba Prm promoter modified to be activated by lamda repressor (cI) and repressed by 434 repressor (cI). Two operators are used for both activation and repression to enhance cooperativity.
The O-R3 site of lambda (17 nt) was replaced by the O-R1 site of 434 (14 nt) to facilitate repression by 434 cI. The new 434 O-R1 is 5'-justified with the lambda O-R3 it replaced, leaving the -10 sequence intact. The 434 O-R2 site replaces the wildtype labmda promoter starting at -5, thereby preserving the 8 nt between 434 O-R1 and O-R2 in the wildtype. The mRNA transcript will contain an additional 9 nt compared to wildtype lambda phage.
Bushman, F. D. The bacteriophage 434 right operator roles of O-R1, O-R2, and O-R3. J. Mol. Biol. (1993) 230, 28-40.
Promoter Family Member (U037O11+D002O22)
Regulated by the presence of Iron and UV light irradiation
Our microarray experiment showed that this gene was responsive to sound and ultrasound. Therefore, we cloned the promoter region located approximately 250 base pairs before the start codon for the cadB gene.
There was a relatively high basal level of expression of this gene that made this part difficult to incorporate into our lysis device design.
cloned from E. coli MG1655 genome located upstream of CadA and CadB genes
Promoter of flhDC gene from E. coli flagella
''flhDC'' is the only class 1 gene that is part of the construction of the flagella. It is the master regulator of the biosynthesis of the flagella ( ''Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria'' - S. Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M. G. Surette, U. Alon ). The promoter of ''flhDC'' is regulated by many transcription factors, for instance, OmpR* and EnvZ* are two repressors of this gene. '''Work in progress :''' Characterization of the repression by OmpR* and EnvZ*
The PCR on colony to amplify the promoter of ''flhDC'' did not work. We amplified both the promoter and the gene and then we did a specific amplification of the promoter from the full operon. We had a PCR amplicon of the right length this time. The primers used to amplify the promoter and the gene are : * Forward : GTTTCTTCGAATTCGCGGCCGCTTCTAGAGTTGTATGTGCGTGTAGTGACGAGTACAG * Reverse : GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAAACAGCCTGTACTCTCTGTTCATCC Then to amplify only the promoter we used : * Forward : GTTTCTTCGAATTCGCGGCCGCTTCTAGAGTTGTATGTGCGTGTAGTGACGAGTACAG * Reverse : GTTTCTTCCTGCAGCGGCCGCTACTAGTATCCCACCCAGAATAACCAACTTTAT
This part comes from the genome of ''E.coli'' K12 strain MG1655.
Promoter Family Member (U037O11+D026O22)
K091157 is a modified version of the pLux' promoter (BBa_K091156) containing the addition of a LasR binding site between the -35 and -10 regions. This promoter is expected to be activated in the presence of AI-1 and LuxR and repressed in the presence of PAI-1 and LasR.
In order to fit the LasR binding site between the -35 and -10 regions, the last base of the Las Box was cropped and the -35 region was modified to overlap with the first two bases of the Las Box.
The LasR binding site is from the region upstream of the LasI gene in Pseudomonas aeruginosa. The rest of the promoter is the same as BBa_K091156.
Natural Xylose Regulated Bi-Directional Operator
This part contains the operator region controlling transcription for the xyl operon. This regulatory region is dependent upon the binding of CRP-cAMP and XylR bound to xylose for activation. Upon binding, transcription is activated in both directions (xylFGH and xylAB facing). This part has an unscrambled CRP binding site and and unaltered promoter region (unlike BBa_K100001 through BBa_K100003).
Both directions were kept in the sequence of the part even though it is intended to work in the right facing direction because of possible looping that may occur as a transcriptional control.
Taken from E. Coli genome bases 3728830-3729092
Double Promoter (lacI, negative / P22 cII, negative)
Promoter inducible by nitrile and similar agents.
Promoter taken from NCBI (http://www.ncbi.nlm.nih.gov/nucleotide/346420896?report=genbank&log$=nuclalign&blast_rank=1&RID=W0SH1PA7016).
OmpF promoter that is activated or repressesed by OmpR according to osmolarity.
Promoter OmpF is activated by phosphorylated OmpR at low osmolarity, and is repressesed by phosphorylated OmpR at high osmolarity.In Escherichia coli, osmoregulation is mediated in part by the actions of such a two-component system consisting of EnvZ and OmpR. These proteins act to control the relative levels of the outer membrane porin genes, ompF and ompC. At low osmo larity, OmpF predominates in the outer membrane, while at high osmolarity the OmpF porin is replaced by OmpC.OmpF has a larger pore and a faster ??ow rate than OmpC. Reference: K. Mattison, R. Oropeza, N. Byers, L. J. Kenney, J Mol Biol 315, 497 (Jan 25, 2002).
The osmolarity range of OmpF sensing still have to be confirmed
Promoter OmpF is activated by phosphorylated OmpR at low osmolarity, and is repressesed by phosphorylated OmpR at high osmolarity.In Escherichia coli, osmoregulation is mediated in part by the actions of such a two-component system consisting of EnvZ and OmpR. These proteins act to control the relative levels of the outer membrane porin genes, ompF and ompC. At low osmo larity, OmpF predominates in the outer membrane, while at high osmolarity the OmpF porin is replaced by OmpC.OmpF has a larger pore and a faster ??ow rate than OmpC.
This part has a fused protein downstream of an arabinose-inducible promoter: CpxR-IFP[1]. Biobrick BBa_K1486013 has CpxR-IFP[2] with an arabinose promoter. This construct was made in both orientations: BBa_K1486014 is IFP[1]-CpxR (with an arabinose promoter).
Both orientations were made, as well as for IFP[2] so all dimerizations could be tested (see main page for biobrick numbers). Flexible linkers were used to fuse both proteins, and an RBS was put before each one of them.
CinR, CinL and glucose controlled promotor
This promotor is controlled by cinr, cinl and extrcellular glucose concentration. High extracellular glucose concentration will inhibit this promotor through the action of phosphorylated OmpR. Phosphorylated OmpR will bind the OmpR binding site of the promotor and block the movement of RNA polymerase. In contrast, the combined action of CinR and CinL will turn on the promotor. But only when the extracellular glucose level is low so OmpR dephosphorylate and dissociate from its binding site will this promotor become active. In essence, this promotor function as an AND gate, it will turn on if and only if the extracellular glucose level is low and there are some functional CinR and CinL protein inside the cell.
The key to the function of the promotor is the inhibitory ability of OmpR binding site. To ensure maximum affinity with phosphorylated OmpR, we use all three OmpR binding site.s.
AND-type promoter synergistically activated by cI and CRP
This part is composed of an arabinose-inducible promoter for superfolded GFP attached by a linker to CpxR (on the N terminus of CpxR).
We had to test both attachments, N and C terminus of the CpxR.
The arabinose promoter and the sfGFP were obtained from the registry, while the CpxR was obtained from the E coli genome.
The AraC/pBAD promoter can be used with prokaryotic chassis to regulate expresion of proteins. When the AraC/pBAD promoter is placed upstream of your canditate translational unit (protein to be expressed) it allows control of the expression of the said protein. This is done via controlling the concentration of arabinose sugar in the environment/solution of bacterial growth. This composite part does not have an LVA degradation tag at its end, hence can be used with all prokaryotic assemblies.
The part was designed and assembled from the iGEM2009 kit with standard RFC10 assembly.
The AraC promoter is found naturally in E.Coli at 1.52 min/centisome in the clockwise orientation. More information can be found at [http://ecogene.org/geneinfo.php?eg_id=EG10054 EcoGene].
Zif268-HIV bs + LexA bs + mCYC promoter
The Zif268-HIV and LexA transcription factor binding sites on the mCYC minimal promoter (in that order.) Transcription regulation comes from Zif268-HIV and LexA-binding transcription factors.
Constructed in our lab with parts from Caroline Ajo-Franklin and David Drubin.
This promoter sequence (-80 to +1) is responsive to the transcription enhancer glnG.
Promoter Family Member (U037O11+D014O22)
This is an 'upside-down' version of I14032. It is a strong, constitual promoter. By adding this part, we wish to emphasise the possibility of engineering both DNA strands, and the additional reglatory possibility that this gives. The upstream sequence is non-functional and simply there to faciliate gel analysis or to physically enable the part to be recomineered (see the Edinburgh 2007 project where it is flanked by dif-sites).
When dealing with reverse complements of a locus, suffix and prefix need be fitted in opposite order.
This sequence is part of the E.coli K12 genome.
Promoter Family Member (U085O11+D014O22)
This promoter is repressed by lacI and luxR with HSL. It contains a lux box and a lacI binding site.
R0010 modified with the insertion of a lux box in between -35 and -10.
Biobricking of cadC promoter and cadC gene PCR cadC-F and cadC-R on MG1655 (2336 bp, EcoR1/BamH1) Sub into pBca1256 (EcoR1/BamH1 910+2472bp, L) Product is pBca1256-K112406 ---------------------------- cb10013-cadC-F cgataGAATTCatgAGATCTcaccagcaatttgcgggcatatc cb10012-cad-R cgtagGGATCCtgaccagaccaaactggcg
Promoter Family Member (U073O27+D062NUL)
The universal stress protein A is a response of Escherichia coli cells to growth arrest, and its lacking generates cells with defective growth.This genetic element is dependent to sigma-70 factor. Its regulation is done through the concentration of a specific stationary phase allormone, guanosine-5'-diphosphate-3'-diphosphate (ppGp), as described elsewhere. The ppGp activate the transcription of downstream elements through a positive regulation of the β-subunit of RNA polymerase. In this sense, the PuspA element is considered a stationary phase promoter. However, its behavior is like a constitutive transcription promotion, becoming higher in stress situations. Diverse conditions make the Escherichia coli cell enter to stress state, like heat shocks, starvation, osmotic stress, ultraviolet light and other conditions. In these situations, the RNA polimerase sigma factors (ropS) trigger the expression of chaperones and other stress protector molecules, in order to help the cell survive. In our project we have used this promoter to trigger the expression of limonene synthase after an osmotic shock. Other uses of this part includes the environmental stress detectors making using a reporter system coupled to this promoter.
The original promoter site was shortened and the last three nucleotides were changed to restriction site adjustment.
We have drawn the sequence for an improved PuspA promoter from an analysis of 400bp upstream the Universal Protein A (UspA) gene in E. coli K12 MG16555 genome. After design, the DNA template of part was synthesized by IDT and was amplified from a G-block and assembled using 3A assembly method.
Promoter Family Member (U073O11+D014O22)
Dual-Repressed Promoter for p22 cII and TetR
TetR usually binds to two operator sites, one located upstream from -35 and one located between -35 and -10. However, p22 mnt also has two operator sites, one between -35 and -10 and another downstream from -10. Since each had an operator site in between -35 and -10, we had to eliminate the TetR operator site in order to allow the promoter to work. TetR was picked because it has a stronger binding than p22 mnt, and so would be more able to use only one site to bind.
This part was designed by combining sequences from parts R0040 (TetR promoter) and R0053 (p22 cII promoter).
Promoter Family Member (U061O11+D038O22)
Dual-Repressed Promoter for LacI and LambdacI
This part is a new construct of a promoter that is dually repressed by either LacI or LambdacI proteins.
LambdacI usually binds to two operator sites, one located upstream from -35 and one located between -35 and -10. By itself, LacI binds downstream from -10. This made the part design very straightforward, since the locations of the operator sites do not overlap at all. In order to complete this part, we simply combined the proper sequences and we had a dually-repressed promoter.
This part was made by combining BioBrick parts R0010(LacI promoter) and R0051 (LambdacI promoter), along with intermediate sequence between these operator sites.
Potential and gate. Composed of pCpcG2 promoter which may be inducible by green light, this way it express penI and this represses mnt expression, allowing the transcription of any gene controlled under pMnt promoter. This construction may be used with another one which represses mnt expression with red light and this way it may act as an and-gate.
Search for illegal sites was performed, they were found and removed.
Sequence of pCpcG2 promoter was obtained from pJT122 plasmid of Dr. Jeff Tabor. Rest of the sequences were obtained from the Registry. Complete construction was synthesized.
The promoter region (inclusive of regulator binding sites) of the B. subtilis RocDEF operon
This is the reported promoter region from the Bacillus subtilis RocDEF operon as taken from the DBTBS website (http://dbtbs.hgc.jp/). Base 1 to base 21 contains the binding site for the binding factor, RocR. The sequence, TATGCAAAAGAATTTTGCACT, reportedly contains the consensus sequence for binding of this factor. Base 42 to base 62 contains another binding site for the RocR binding factor, with ATATCAGAATGTTTTTGCACC as the binding consensus for this sequence. Bases 113-135 outline the binding site of the binding factor AhrC (CTTGCATTTATATAAAGGGAAAG). Bases 96 to 135 outline the promoter region for this operon (CTTGATTTGGCACAGAACTTGCATTTATATAAAGGGAAAG).
This sequence only outlines the reported promoter region as ascertained from the online resource described above, and may lack nucleotides not described by the operon analysis used.
Information was obtained from: http://dbtbs.hgc.jp/COG/prom/rocDEF.html.
Promoter Family Member (U049O11+D062O22)
This promoter is a modified version of the Mnt promoter that is also responsive to LacI. The promoter should be repressed by Mnt repressor. It should also be repressed by LacI, and in the absence of Mnt repressor, should be induced by IPTG.
Mnt repressor binds as a tetramer to two half-operator sites. Introduction of a LacI binding site between the Mnt promoter -10 sequence and the start site for transcription should allow for repression by LacI. Accordingly, the hybrid promoter was designed by 1) Remove all bases of mnt promoter 3??? to -10: gagtcgtattaattt will be replaced by tgtgtggaattgtga, and 2) Position lacI binding site (composed of an inverted repeat) from the lacI regulated promoter (R0010) immediately 3??? to truncated mnt promoter.
This part comes from the Mnt promoter and the LacI promoter
OL region form Lambda phage. It is used to allow a construction to be controlled dually by cI protein. cI protein may interact with pRM promoter and OL region in order to form an octameric structure which permits, first the activation of transcription from pRM promoter and then effectively repression from it as well.
Promoter Family Member (U037O11+D062O22)
this hybrid promoter is designed to be consecutively off.It combines with plasR(R0079) and lambda cI OR1(see C0051).Adding P-AI-1 sould activate the promoter, while repressed by lambda cI.
"CI binding of the OR region. It binds OR1 with highest affinity, OR2 with next highest, and OR3 with lowest"(http://www.nonanone.com/qw/files/Biology%204450/test2_lecture8,9.txt)
Promoter Family Member (U097O11+D002O22)
This promoter can be repressed by lacI protein and induced by either IPTG or arabinose.
IPTG has better effect on this promoter than arabinose
FliA is a transcription factor involved in the formation of the flagella in E. coli. The promotor of fliA is induced by FlhDC. FliA seems to have a positive autoregulation on its promotor.
This part comes from the genome of E. coli K12 strain MG1655.
pSB1A30: High copy BioBrick cloning/expression backbone carrying Amp resitance
Constantin Ahlmann-Eltze, Charlotte Bunne, Magdalena B??scher, Jan Gleixner, Max Horn, Anna Huhn, Nils Klughammer, Jakob Kreft, Elisabeth Sch??fer, Carolin Schmelas, Silvan Schmitz, Max Waldha
Promoter Family Member (U097O11+D062O22)
This part has two fused proteins downstream of an arabinose-inducible promoter: CpxR-IFP[1] and CpxR-IFP[2]. This construct was made in all orientations: - IFP[1]-CpxR + IFP[2]-CpxR (BBa_K1286009) - IFP[1]-CpxR + CpxR-IFP[2] (BBa_K1486010) - CpxR-IFP[1] + IFP[2]-CpxR (BBa_K1486011)
Tir1 promoter, Saccharomyces cerevisiae cold shock promoter
used to induce the expression of SrUCP under low temperature
cloned from genomic DNA of Saccharomyces cerevisiae
bolA promoter is a promoter where levels of expression are inversely proportional to the growth rate. To read more, go to following link [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=402084&blobtype=pdf] This part is actually in BBb format. ---- This part is in BBb Format. It is flanked by BamHI and BglII sites instead of XbaI and SpeI. More information about the BBb Format is available at: [http://openwetware.org/wiki/Template:AndersonLab:BBb_Standard BBb Standard Description Page]
PCR al0017/al0018 on MG1655 (467bp, EcoRI/BamHI/DpnI) Sub into pBca1256 (EcoRI/BamHI, 2472+910, L) Product is pBca1256-K112318 ----------------------------------------------- al0017 Forward Biobricking of bolA promoter CCATAGAATTCatgAGATCTtgctgtggcagtgtaatcgtc al0018 Reverse Biobricking of bolA promoter CGttaGGATCCcttctatccgctcacgtatc
Pdps promoter. This part is actually in BBb format. ---- This part is in BBb Format. It is flanked by BamHI and BglII sites instead of XbaI and SpeI. More information about the BBb Format is available at: [http://openwetware.org/wiki/Template:AndersonLab:BBb_Standard BBb Standard Description Page]
PCR JH089F/JH089R on Salmonella L2. (379 bp, EcoRI/BamHI/DpnI) Sub into pBjh1601CK (EcoRI/BamHI, 3134+910, L) Product is pBjh1601CK-K112322 ----------------------------------------------- JH089F Forward biobricking of {Pdps} cgataGAATTCatgAGATCTaacgattcgacgcgaaccgc JH089R Reverse biobricking of {Pdps} cgttaGGATCCaatctcatatcctcttgatg
Promoter Family Member (U061O11+D026O22)
Biphasic switch is a composite part which permits positive and negative regulation of a gene set through pRM promoter and OL region from Lambda phage.
Distance between pRM and OL must be longer than 1.6 kb due to necessity of loop formation for more effiecient repression state of the switch.
Extracted directly from Lambda genome by separate as pRM and OL parts, constructed by classic BioBricks system.
LasR and 3OC12HSL regulated promoter with a single Tet Operator (binding site for TetR repressor)
Promoter Family Member (U073O11+D026O22)
This hybrid promoter uses the LsrA promoter that is capable of being repressed by LsrR - induction can occur with phospho-AI-2. Binding sites for cI repressor also occur. As a result the promoter is off in the absence of AI-2 and on in the presence of AI-2, but always off in the presence of cI.
The promoter region for LsrA should remain unaltered while cI binding sites (OR1 and OR2) are introduced downstream. The OR2 sites with cI bound should not allow transcription. The cI binding sites have a natural 6 bp spacer between them. It would be desirable to position the cI binding sites immediately downstream of the -10 region of the LsrA promoter. However, experimental evidence for the transciption start (+1) appears to be lacking.
The Missouri Western/Davidson team designed primers for LsrA and extracted the DNA from E. coli MG1655. The CI portion was pulled from the registry as part number R0051.
Zif268-HIV binding sites + TEF constitutive yeast promoter
This hybrid promoter is designed to respond to activation by LuxR when it is bound to AHL and to repression by the phage lambda cI repressor. The repression needs to win over activation.
This part is based on the idea of replacing the region of the Lux promoter downstream of the -35 with the OR2 cI half-operator, added LuxR-10 region. Based on what we have found up to now, promoters which are constructed just by inserting OR1/2 downstream of Lux are all very leaky.
this part comes from LuxR promoter and cI lambda promoter.
Modified lamdba Prm promoter (repressed by 434 cI)
Lamdba Prm promoter modified to be activated by lamda repressor (cI) and repressed by 434 repressor (cI)
The O-R1 region of 434 contained 14 base pairs as opposed to the 17 base pairs of the O-R3 site of lambda. Also, it was noticed that the O-R3 site of the lambda included part of the -10 site. Hence, to preserve the spacing and the -10 site, the three nucleotides that were in both the -10 site and the lambda O-R3 site were retained. The 14 nucleotides that were in the O-R3 site and not in the -10 site were replaced with the O-R1 site of the 434.
Double Promoter (LuxR/HSL, positive / cI, negative)
Double Promoter (TetR, negative / P22 cII, negative)
A part used to quantify the AraC-RBS construct K259007 created by the BCCS-Bristol iGEM'09 team.
This part was designed with the specified biobricks from the parts registry. AraC occurs naturally in E.coli. GFP occurs in jellyfish species, RBS designed by the Anderson family and Terminator by Resma Shetty.
Promoter Family Member (U097O11+D014O22)
PAI+LasR -> LasI+GFP & AI+LuxR --| LasI+GFP
BBa_K091146 promoter (PAI+LasR inducible & AI+LuxR repressible) controls the policistronic expresion of LasI enzyme and GFP, double terminator
The biobricks BBa_K266005 and BBa_E0840 where used to build this biobrick.
Promoter Family Member (U097NUL+D062O22)
sense TWO INPUTS, activation by AHL and repression by LacI.
Compared with existing BioBrick hybrid promoter R0065, this promoter is different in that its sequence is much shorter with lux box and -35 region overlapping, and that it is repressed by LacI, not cI. Also, the output is clearly detected as shown in Fig. 3.
Promoter Family Member (U037O11+D050O22)
This is the same sequence as STE2 promotor(BBa_K110008), but with suffix and prefix switched
Binary signal generator, RBS(reverse) - attB - Promoter - attP - RBS
Dual phase protein generator promoter reversed, RBS(reverse) - attB - Promoter(reverse) - attP - RBS This part is composed of 3 elements. 1. RBS: BBa_B0034, upsteam one is reversed 2. Promoter: BBa_J23119, Bacterial constitutive promoter 3. att site: Recognition site for Mycobacteriophage Bxb1 integrase/excisionase We designed this part to generate two different proteins one at a time. At the first state, this device promotes transcription and translation of downstream gene because its promoter orientation. When Mycobacteriophage Bxb1 integrase recognizes and inverts sequence flanking with attB and attP sequence, promoter orientation reversed. Then this device promotes transcription and translation of upstream gene(must be reversed at the construction step). This device is tested by GFP and mRFP attached construct. See BBa_K090700N and BBa_K090700N
Promoter and RBS are derived from BBa_J23119 and BBa_B0034, respectively. Whole construct was de novo synthesized by Bioneer.
Zif268-HIV binding sites + MET25 constitutive yeast promoter
RHLR/RHLI Inducible & LasR/LasI repressible Promoter
There is a 17bp spacer between the -35 and -10 regions and the binding site for RHLR/RHLI is 20bp long. I was able to fit the whole binding site in the spacer region because the last three base pairs of the -35 region and the first three base pairs of the RHLR/RHLI binding site are the same.
Promoter Family Member (U073O26+D062NUL)
Promoter Family Member (U061O11+D014O22)
Promoter Family Member (U097NUL+D002O22)
A Double Reporter (LacZ-alpha and GFP-AAV) loaded on pSB3C5. For more information please refer to BBa_I732401.
Promoter Family Member (U085O11+D026O22)
Promoter Family Member (U061O11+D050O22)
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr
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 homoserine lactone (HSL). This complex binds to a palindromic site on the promoter, increasing the rate of transcription.In thisversion, a binding site for cI dimer has been added: binding to this site dominantly represses transcription.
V. fishceri and phage lambda (courtesy of Ron Weiss)
IPTG inducible AHL generator, LasI device.
pConstitutive: J23100 LasI device: K772005
The IbpB thermometer is an RNA thermometer element found in the ibpAB operon. The operon contains two heat-shock genes, encoding inclusion body binding proteins A and B (IbpA/B), and is the most drastically upregulated operon under heat-shock in Escherichia coli. IbpA is regulated by a ROSE element found in its 5' UTR, while IbpB has its own heat-sensitive cis-regulatory element. The activity of this thermoregulator was confirmed in vitro but was not found in vivo, suggesting more complicated operon regulation exists in bacterial cells. In this part, red fluorescent protein (RFP) is added in the downstream region to measure the activity of RNA thermometer. You check our Experience page for further information about our characterization and experiments. For the inner elements in the part design; check out the Part Design page. RNA Thermometers are the only known single-component regulators of gene expression.(1) RNA Thermometers are thermosensors that regulate gene expression by temperature-induced changes in RNA conformation. Naturally occurring RNA Thermometers exhibit complex secondary structures which are believed to undergo a series of gradual structural changes in response to temperature shifts.(2) RNA Thermometers often regulate genes required during either a heat shock or cold shock response, but have been implicated in other regulatory roles such as in pathogenecity and starvation.(3)
Escherichia coli, NCBI GeneBank Other elements are obtained from Registry.
Promoter Family Member (U097O11+D062NUL)
Promoter Family Member (U073O11+D038O22)
panas promoter with a rbs. The panas promoter is hypoxia inducible.
The panas promoter is self-designed The rbs is from the registry
This part is composed of an arabinose-inducible promoter for superfolded GFP attached by a linker to CpxR (on the C terminus of CpxR).
This is identical to BBa_R0051 exept that some base has been modifed to alow for additional ZFP repressors to bind
Promoter Family Member (U049O11+D026O22)
Promoter Family Member (U049O11+D050O22)
BBa_K091146 promoter (PAI+LasR inducible & AI+LuxR repressible) controls the expresion of LasI enzyme, no terminator
The biobricks BBa_K091146 and BBa_S03154 where used to build this biobrick
Promoter Family Member (U061O11+D002O22)
Promoter Family Member (U097NUL+D026O22)
A Double Reporter (LacZ-alpha and GFP) loaded on pSB3C5. For more information please refer to BBa_I732403.
Dual-Repressed Promoter for p22 mnt and TetR
This part is a promoter that is repressed by both p22 mnt and TetR. It can be used to control the response of any gene that follows this promoter. It will be repressed by the presence of either p22 mnt or TetR.
This part was designed by combining sequences from parts C0040 (TetR promoter) and C0072 (p22 mnt promoter).
OmpR-P strong binding, regulatory region for Team Challenge03-2007
Contains the F1 consensus site from the OmpF regulator. Contains a LacI repressor consensus binding site between the -35 and -10 portions of a T7 core promoter region, and a TetR consensus binding site upstream of the -35 site.
The weaker binding repressor binds upstream of the core promoter (upstream of -35), while the stronger binds inbetween the -35 and -10.
Information for creation of this construct came from the following sorces: Yoshida et al. JBC 2006 Frank et al. JMB 1997 Rong et al. PNAS 1998 Merabet et al. Biochemistry 1995 Su et al. JBC 1998 Kedracka-Krok et al. JPC 1999 Kleinschmidt et al. Biochemistry 1988 Butler et al. JBC 1982 Jorgensen et al. JBC 1991 Hillen et al. JMB 1984 Head et al. JMB 1998
Promoter (lambda cI and luxR regulated -- hybrid)
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. LuxI cI activity of promoter + + zero + - maximum - + zero - - leaky (no quantitative information)
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 AF170104 .
K091146 is a modified version of the pLas' promoter (BBa_K091117) containing the addition of a luxR binding site between the -35 and -10 regions. This promoter is expected to be activated in the presence of PAI-1 and LasR and repressed in the presence of AI-1 and LuxR.
The Lux box was placed adjacent to the LasR binding site with the aim of minimizing cross-talk in the presence of both PAI-1 and AI-1; since the LasR site should have a higher affinity, we hope that the binding of PAI-1 will competitively exclude the binding of AI-1.
The LuxR binding site is from BBa_R0062 and the pLas' promoter is from the region upstream of the LasI gene in Pseudomonas aeruginosa.
Promoter Family Member (U097NUL+D062NUL)
P_template1 serves as the truss for PCR cloning. By respectively applying 7 different primers upstream and downstream, that is, 49 pairs of primers in total, we have got 49 different promoters. Then we made them digsted and loaded into a vector that has already possessed a lacZ-alpha fragment. In this way, we can read from the color of the clones on the plate whether the inserted promoter works or not. By this means, We can try seven different positions for Operator A and seven for Operator B, thus constructing 7*7 kinds of promoters which have actually constituted a specific promoter family. After transformed into the four test plasmids (pCR00, pCR01, pCR10, pCR11) together with a downstream double-reporter system, we will get to know the solo-repression and co-repression effects of the two repressors on the specific promoter.
nir promoter from Synechocystis sp. PCC6803
The ''nir'' promoter is nitrate inducible.
The ''nirA'' promoter originates from ''Synechocystis'' sp. PCC6803.
Promoter Family Member (U097O11+D026O22)
This is identical to BBa_I12007 exept that some base has been modifed to allow for additional ZFP repressors to bind.
Phns in BBb1 format. ---- This part is in BBb Format. It is flanked by BamHI and BglII sites instead of XbaI and SpeI. More information about the BBb Format is available at: [http://openwetware.org/wiki/Template:AndersonLab:BBb_Standard BBb Standard Description Page]
Construction of [<Phns>] Basic Part K112701 PCR dv001/dv006 on Phns from E. coli K12 MG1655 (~342 bp, gp = A) PCR dv005/dv003 on Phns from E. coli K12 MG1655 (225 bp, gp = B) PCR dv004/dv002 on Phns from E. coli K12 MG1655 (~149 bp, gp = C) --------------------------------------------------- PCR dv001/dv003 on A+B (355 bp, gp = D) --------------------------------------------------- PCR dv001/dv002 on C+D (697bp, EcoRI/BamHI/DpnI) Sub into pBca1256 (EcoRI/BamHI, 2472+697) Product is pBca1256-K112701 ----------------------------------------------- dv001 Forward Biobricking of [<Phns>] CgATAgaattcATGagatctGAAATATAGCTGTGCCATCAGCC dv002 Reverse Biobricking of [<Phns>] cagtcggatccGCACGAAGAGTACGGATG dv003 Removing the 2nd EcoRI site in [<Phns>] (R) GCCAGGAATGTAAGGgATTCAAAATTGTTC dv004 Removing the 2ND EcoRI site in [<Phns>] (F) GAACAATTTTGAATcCCTTACATTCCTGGC dv005 Removing the FIRST EcoRI site in [<Phns>] (F)CGCTTAATAGGGgATTCTCGTAAACAC dv006 Removing the FIRST EcoRI site in [<Phns>] (R)GTGTTTACGAGAATcCCCTATTAAGCG
Promoter Family Member (U085O11+D002O22)
Promoter Family Member (U061O11+D062O22)
This promoter is repressed by tetR and lacI; it contains two binding sites for TetR and one LacI binding site. this part is an AND-gate since transcription occurs only in the presence of both ATC and IPTG.
Also designed by Pallavi Penumetcha and Robert Cool.
This part consists of the R0040 tetR promoter with the addition of the R0010 lacI binding site.
To edit. Pense ?? rajouter les linkers, je ne sais pas s'ils sont de igem ou s'il faut ajouter la s??quence ?? la registry. Check pour tous tes biobricks et dis-moi, please.
Double Promoter (LuxR/HSL, positive / P22 cII, negative)
Repression of heat shock gene expression (ROSE) element The repression of heat shock gene expression (ROSE) element is an RNA element found in the 5' UTR of some heat shock protein's mRNAs. The ROSE element is an RNA thermometer that negatively regulates heat shock gene expression. The secondary structure is thought to be altered by temperature, thus it is an RNA thermometer. This structure blocks access to the ribosome binding site at normal temperatures. During heat shock however, the structure changes freeing the ribosome binding site and allowing expression to occur.[2][3] A partial structure of this RNA element has been determined using NMR.[1] ROSE1 and ROSEAT2 are specific examples of ROSE elements.[4] ROSE1 is found in Bradyrhizobium japonicum whereas ROSEAT2 is a closely related element from Agrobacterium tumefaciens. The two RNA elements have similar secondary structures with ROSE1 having an extra hairpin.[4] All ROSE elements contain a characteristic 'bulged G' opposite the Shine-Dalgarno sequence binding site, without this nucleotide the RNA thermometer loses its temperature-sensitivity.[5]
Based on the AHL regulated BioBrick part R0062 and the previous work on LacI regulated promoter (ref. 1), we designed a new promoter regulated by AHL and LacI. Since this promoter is a kind of a "HYBRID" of the two, we call it HYBRID PROMOTER. Compared with existing BioBrick hybrid promoter R0065, this promoter is different in that its sequence is much shorter with lux box and -35 region overlapping, and that it is repressed by LacI, not cI. Also, the output is clearly detected as shown in Fig. 3.