constitutive promoter with (TA)10 between -10 and -35 elements
With 10 TA repeats between the -10 and -35 elements, the distance between the two elements is optimal for the sigma factor to bind to the promoter. Thus, the promoter should be in the 'on' state.
This part was PCR amplified from two synthesized primers that bound to each other.
Anderson Promoter with lacI binding site
Promoters of the Anderson Promoter Collection with lacI binding site derived from [http://parts.igem.org/Part:BBa_R0010 R_0010] to make them [http://openwetware.org/wiki/IPTG IPTG] iducible.
We choosed lacI-binding-site of part BBa_R0010 because we assumed older parts would be more reliable. The part is shipped in backbone [http://parts.igem.org/Part:BBa_J61002 J61002] because the functionality is directly visible by adding IPTG. RFP ([http://parts.igem.org/Part:BBa_E1010 E1010]) should get expressed then.
Assambly of [http://parts.igem.org/Part:BBa_J23106 J23106] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
T7 promoter with an A->T mutation at the -16 position of the consensus sequence
This part is from the bacteriophage M13 genome, bp 3086-3132 in M13K07. It directs transcription of M13 gene VII (BBa_M13507, BBa_M13007). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VII message (BBa_M13007). The part aligns with base pairs 1092-1107 in M13K07 genome. It was identified as the RBS for gene VII message by Wezenbeek et al in Gene (1980) 11: 129-148
strong synthetic E. coli ribosome binding site with SacI site.
This is a strong synthetic E. coli ribosome binding site. It is synthesised as two complementary oligonucleotides rather than being incorporated into a biobrick plasmid. It incorporates a SacI site overlapping the XbaI site, which is preserved when it is added to any other biobrick. This allows easy detection of the RBS after it has been added upstream of a biobrick coding sequence in a plasmid vector.
Note the presence of a SacI site overlapping the XbaI site, which is preserved when this biobrick is added to any other biobrick. At the time of writing, this biobrick is added as a short piece of DNA composed of two complementary oligonucleotides rather than being incorporated into a biobrick cloning vector by itself. It can be added upstream of a biobrick coding sequence, and its presence can easily be detected in miniprep DNA on a gel by using a SacI-SpeI or similar digest.
This part is from the bacteriophage M13 genome, bp 1155-1201 in M13K07. It directs transcription of M13 gene VIII (BBa_M13508, BBa_M13008). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
This part is the natural RBS associated with the invJ protein in Salmonella Typhimurium LT2.
This part was not designed with compliance to biobrick standard assembly in mind.
Weak1 RBS based on Ron Weiss thesis. Strength is considered relative to BBa_B0030, BBa_B0031, BBa_B0033.
Native ribosome binding site for crtZ (beta-carotene hydroxylase) from Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
A virtual part to be added to the coding sequence blunt (without a scar).
Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
optimized (TA) repeat constitutive promoter with 21 bp between -10 and -35 elements
This part is from the bacteriophage M13 genome, bp 786-835 in M13K07. It directs transcription of M13 gene V (BBa_M13505, BBa_M13005). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
Mitochondrial shuttle plasmid carried mtGFP
Mitochondrial expression vector, with initial site ori7, up elements of cox2 gene (including promoter and RBS), and mtGFP.
This part is the natural RBS for the sopB gene in the Salmonella Type III Secretion System.
This part was not designed with consideration for biobrick standard assembly in mind. This RBS hasn't been explicitly tested for expression rate in a Fluorescence or B-Gal assay.
optimized (TA) repeat constitutive promoter with 19 bp between -10 and -35 elements
consensus Kozak sequence and start codon
designed such that fusion using fusion bricks assembly method leads to in frame translation
consensus Kozak and start built from oligonucleotides
Anderson promoter J23117 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
Specialized RBS modified from that of B0036 (Brink et al.)
This RBS has the modified Shine-Dalgarno sequence, it has a reduced secondary structure relative to using the actual Brink sequence with mixed connective sites flanking it. the spacing between the SD and the ATG is the same as that used by Brink et al. even though it is non-optimal for E. coli
Tar receptor under the control of constitutive promoter J23114
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate and exists as a functional homodimer. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23114 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''Tar'' expression affect the chemotaxis of ''E. coli''.
* Genomic sequence was amplified using the following primers. ** Primers PCR: Base pairs in caps represent the respective restriction sites followed by either prefix or suffix. Primers were provided by SIGMA. *** Fwd: Tar for + prefix: 5?? actGAATTCgcggccgctTCTAGAtgattaaccgtatccgcgtagtc 3?? *** Rev: Tar rev + suffix: 5?? tcCTGCAGcggccgctACTAGTcaaaatgtttcccagtttggatc 3?? * One XbaI site was found at position 420. The restriction site was changed from TCTAGt to CCTAGt via QuikChange PCR. ** Primers QuikChange (QC): Primers were provided by SIGMA. *** Fwd: TarQC for: 5?? ACTGATTGATTAcCTAGATTATGGCAATACTGGAG 3?? *** Rev: TarQC rev: 5?? TGCCATAATCTAGgTAATCAATCAGTTCAGTTAAC 3?? (the uncapitalized letter induces the mutation for removal of the XbaI site)
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23114 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
This is the pBAD promoter (BBa_I13453) in the opposite orientation. It can be used to drive transcription in the direction of suffix to prefix.
This is the 1500 bp upstream of the yeast PGK1 coding region. This is a putative constitutive promoter.
Source: Saccharomyces cerevisiae genomic DNA.
This part was obtained from yeast genomic DNA.
optimized (TA) repeat constitutive promoter with 15 bp between -10 and -35 elements
Anderson promoter J23102 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
Native ribosome binding site of crtY (lycopene cyclase) from Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
This is a virtual part to be added, blunt-ended, to the coding sequence.
This is the -20 to -1 region of T7 gp0.7, which contains the native RBS region for this gene. The physical instantiation of this part does not exist. This part is not compatible with Standard Biobricks assembly methods, as the scar created during assembly would interrupt the spacing between the RBS and the start codon of the CDS. Individuals wishing to use this RBS sequence in their assembles should refer to part XXXXX. (Information forthcoming)
The -20 to -1 region was chosen to be representative of the RBS region of the T7 genes for the following reasons: 1) The Shine-Delgarno region is contained within this defined region for all T7 genes. 2) Current literature suggests that when bound to the Translation Start Site (0), the Ribosome covers positions -20 to +13.
Genome of wild-type bacteriophage T7, positions 2001-2020. Includes the -20 to -1 region of gp0.7.
This is the native ribosome binding site for sam5 (4-coumarate-3-hydroxylase) of the bacterium Saccharothrix espanaensis.
This is a virtual part to be added to coding sequence I742141.
This promoter is active at higher temperatures.
to be used qith t7 polymerase BBa_J34811
Vikram Vijayan, Allen Hsu, Lawrence Fomundam
Anderson promoter J23118 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
This is the weak version of the consensus RBS for Bacillus subtilis. The sequence is present in front of some B. subtilis operons, but is expected to give weaker expression than the consensus sequence. The consensus sequence AAAGGAGG (BBa_K090505) was changed to AGAGGTGG for this part.
The part must be 8 nucleotides away from the first methionine of the coding sequence, and so we added 'TGT' downstream of the actual binding sequence: AGAGGTGG. This, combined with the truncated non-CDS BioBrick prefix scar, gives exactly 8 'spacer bases' between the 3' end of the RBS and the start of the coding sequence.
Promoter sequence for constituitive expression
This version of the T7 0.3 RBS is designed for construction via Heather Keller's alternative assembly plan using XbaI and SapI for RBS/CDS assembly without a mixed site. Contains the -20 to -1 region of gp0.4 from the wild-type T7 genome. Can also be used with Standard BioBricks assembly, although this will add a 7 amino acid fusion to the N-terminus of the resulting protein.
This RBS is designed to be compatible with Heather Keller's RBS assembly scheme for creating RBS/CDS junctions without a mixed site. For use in this scheme, this part should be cut with XbaI and SapI. It must be used with a coding sequence containing the SapI site at the 5' end. This part is not compatible with CDSs that use a GTG site and must be used with CDSs using an ATG start site. The two bp spacer on the 3' end also allows this part to be used in standard biobricks assembly and is necessary to maintain the reading frame of a downstream CDS. Note that Standard Biobricks Assembly with this part results in the creation of a new ATG start site, and a 7 amino acid fusion at the N terminus of the downstream protein. CDSs with alternative start sites are compatible with this part via Standard Assembly. This part was inadvertently constructed without the single base pair (G/C) that separates the XbaI site and the 5' end of the part.
The RBS is taken from the wild-type bacteriophage T7 genome. Please see part B2001 for more information.
Promoter veg a constitutive promoter for B. subtilis
Pveg is a constitutive promoter that constitutively expresses the P43 protein in ''B.subtilis''. Pveg contains binding sites for the ''B.sutbilis'' major sigma factor#1. Pveg in ''B.subtilis'' utilises two binding sites to cause high expression of genes#2, however our Pveg is lacking the upstream site to give a medium level of gene expression. It has been noted that the sporulation master regulatoion factor spoOA interacts with Pveg though it is not known how#3. The context with which we used the promoter Pveg is as a '''Polymerase Per Second''' (PoPS) generator.
The biobrick part was designed to include a single binding site for the ''B.subtilis major sigma factor. In addition the biobrick standard was applied to the promoter Pveg sequence.
The Pveg promoter was suggested to us by Dr. Jan-Willem Veening of Newcastle University. This sequence supplied was compared to that of the DBTBS database#3 then a section containing the binding site synthesised by Geneart.
pENTCUP2 promoter for the constitutive expression of genes in plants.
Amplified from PCR from the pORE E3 plasmid.
Derived from the pORE vector series (see http://2010.igem.org/Team:Harvard).
Promoter of the liaG gene of Bacillus subtilis, weak constitutive
optimized (A) repeat constitutive promoter with 18 bp between -10 and -35 elements
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene XI message (BBa_M13011). The part aligns with base pairs 3900-3915 in M13K07 genome. It was NOT identified as the RBS for gene XI message by Wezenbeek et al in Gene (1980) 11: 129-148
ribosome binding site for creA gene in the E Coli cre operon
Anderson promoter J23106 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
Modified version of B0031 from the Voigt Lab. Not currently available as an independent part (only in a tet inverter).
The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207] although they should be same. We choosed part BBa_R0010 because we assumed older parts would be reliable.
Assambly of [http://parts.igem.org/Part:BBa_J23100 J23100] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010]
T7 promoter with an A->C mutation at the -16 position of the consensus sequence
This is a derivate of BBa_K105027. Due to a point mutation in the TATA box region the efficiency of this minimal promoter is only 16 % of the natural yeast CYC1 promoter.
This BioBrick contains the TATA-box with one point mutation and most of the 5'UTR (-139 to -36, relative to the translational start) of the natural CYC1 promoter. A Kozak sequence is not included and has thus to be added! Even if there isn't any need for this BioBrick to be fusible to other protein domains, we stayed with our design.
Amplification and Mutation from the plasmid pAH3
This is the promoter sequence of g3 which has been separated from g8. It also includes the restriction enzyme EcoRV in front.
This part used in conjunction with BBa_M131520 allows g8 and promoter of g3 to be separate from each other, therefore allowing free regulation of g3 with no consequences on g8.
This is a derivate of BBa_K105027. Due to a point mutation in the TATA box region the efficiency of this minimal promoter is only 28 % of the natural yeast CYC1 promoter.
This part promotes the transcription of TyrRS(aminoacyl tRNA synthetase).
E.coli We synthetized it according to the GeneBank.
Promoter for transcribing keys to act on locks based on Isaacs, Collins, et. al: "Engineered riboregulators enable post-transcriptional control of gene expression" KP3 absorbs three nucleotides from mixed site ("TACTAGAG"), so that the key has a 5 nucleotide spacer region (i.e. "TAGAG") between the transcription start site and the first nucleotide of the key. We are still looking into what the optimal size for the spacer region is. See also KP2 (BBa_J01007), and Key1 (BBa_J01008), Key2 (BBa_J01009), Lock1 (BBa_J01010), and Lock2 (BBa_J01011).
promoter of Paenibacillus sp. WLY78 nif gene cluster
The promoter of Paenibacillus sp. WLY78 nif gene cluster, We named it Pnif. Pnif is a σ70-dependent promoter located upstream of nifB. Pnif is in control of all the gene clusters of nitrogen fixation genome. Confirmation of nif promoter We standardized the nif promoter of Paenibacillus sp. WLY78, and linked it to the upstream of 3 reporter genes (RFP reporter: BBa_K1357010, YFP reporter: BBa_E0430;amilCP reporter: BBa_K1357009) to confirm the reliability of this promoter. The results are shown in Figure 2. A B C http://2015.igem.org/wiki/images/b/b2/Confirmation_of_Pnif_AB.png http://2015.igem.org/wiki/images/thumb/3/34/C-confirmation_of_Pnif.jpeg/622px-C-confirmation_of_Pnif.jpeg Fig.4. Confirmation of nif promoter of Paenibacillus sp. WLY78. (A) Pnif+RFP reporter; (B) Pnif+YFP reporter;(C)Pnif+amilCP reporter. The results confirmed the reliability of Pnif. The initiation of Pnif does not require inducement. Thus it is a effective constitutive promoter.
effeciency of the promoter in E.coli for ordinary parts
Pnif is from Paenibacillus sp. WLY78 genome,located upstream of nifB,the first gene of nitrogen fixation cluster.
This is the natural RBS that drives the sipA effector protein in the Salmonella SPI-1 system
This part was not designed with compatibility to biobrick standard assembly in mind. This RBS has not been explicitly tested in an expression assasy such as B-Gal or GFP expression.
This is the native ribosome binding site of ftsK, a DNA-translocating motor protein involved in cell division in Escherichia coli.
Virtual part to be added to coding sequence BBa_I742137.
Overlap extension of synthetic oligonucleotides
RBS.1 (strong) -- modified from R. Weiss
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
Strong RBS based on Ron Weiss thesis. Strength is considered relative to <bb_part>BBa_B0031</bb_part>, <bb_part>BBa_B0032</bb_part>, <bb_part>BBa_B0033</bb_part>.
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("orig" in figure 4-14 of Ron Weiss thesis). 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 Brian Chow
Promoter ctc is a sigma factor B dependent promoter found in ''B.subtilis''. In ''B.subtilis'' endogenous sigma factor B is activated under mild stress. These mild stress conditions can be generally split into nutrient stress response and physical stress response. Nutrient stress response is triggered by low levels of ATP and GTP and physical stress response is triggered by exposure to blue light, salt, heat, acid or ethanol1. The promoter ctc has been used previously as a read out for the activation of sigma factor B 2. *The context with which we used the promoter ctc, was to take blue light as an input and give '''Polymerase Per Second'''(PoPS) as an output. To do this the other potential inputs need to be carefully controlled so that only blue light activated the sigma B and gives a PoPS output. In order to get sufficient sigma B activation by blue light the light receptor YtvA, part...., needs to be over expressed in ''B.subtilis'' 3. ===Reference=== #1 pmid=16267279 #2 pmid=3100810 #3 pmid=17575448
Biobrick standard was applied to the promoter ctc sequence.
The part was designed using the sequence from the ''B.subtilis'' genome and from previously published papers 23. This sequence was then synthesised by Geneart.
Two T7 promoters are reversely overlapping in five base pairs, with the third one mutated from A to G.
It is difficult to make this short DNA by PCR as both sides are T7 promoters, which are very similar. It is highly possible that they form loops before they can be synthesized by PCR. Thus we order two single stranded DNA and then anneal them together by touchdown PCR.
The sequence of T7 promoter is TAATACGACTCACTATA (from 5' to 3').
Tar receptor under the control of constitutive promoter J23105
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate and exists as a functional homodimer. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23105 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''Tar'' expression affect the chemotaxis of ''E. coli''.
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23105 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
The T7 promoter should only produce PoPS when the T7 polymerase is also being expressed.
flhDC operon under the control of constitutive promoter J23112
The ''flhDC'' operon is the master regulator of motility and chemotaxis in ''E. coli''. FlhDC forms heterotetramers and activates class II operons in concert with sigma factor 70. Among the gene products of class II operons are several components of the flagellum and the alternative sigma factor FliA which is essential for the transcription of class III genes. Here we used a set of 8 constitutive Anderson-promoters from the 2006 Berkeley group to test how different levels of constitutive ''flhDC'' expression affect the motility of ''E. coli''.
*The PstI restriction site in the ''flhDC'' sequence was mutated to CTGCGG using the reverse primer. *''flhDC'' was amplified from genomic DNA of ''E. coli'' DH10B via PCR using the following primers: **Fwd: 5'-actgaattcgcggccgcttctagatgcatacctccgagttgctg-3' **Rev: 5'-tcctgcagcggccgctactagttactgcccgggatggcggttgacataagcCgcaggcaaagctgccaacag-3' (the capitalized "C" induces the mutation for removal of the PstI site)
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23112 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
This is the full length ADH1 promoter including the distal and proximal portions and their regulatory elements.
There were three options for the length of the promoter - short, middle, and long. The middle length was chosen.
The part was extracted from S. cerevisiae, YPH500 strain, using colony PCR protocols. It consists of 720 bp upstream of ADH1 gene according to SGD sequence.
flhDC operon under the control of constitutive promoter J23104
The flhDC operon is the master regulator of motility and chemotaxis in E. coli. FlhDC forms heterotetramers and activates class II operons in concert with sigma factor 70. Among the gene products of class II operons are several components of the flagellum and the alternative sigma factor FliA which is essential for the transcription of class III genes. Here we used a set of 8 constitutive Anderson-promoters from the 2006 Berkeley group to test how different levels of constitutive flhDC expression affect the motility of E. coli.
* The PstI restriction site in the flhDC sequence was mutated to CTGCGG using the reverse primer * flhDC was amplified from genomic DNA of E. coli DH10B via PCR using the following primers: ** Fwd: 5'-actgaattcgcggccgcttctagatgcatacctccgagttgctg-3' ** Rev: 5'-tcctgcagcggccgctactagttactgcccgggatggcggttgacataagcCgcaggcaaagctgccaacag-3' (the capitalized "C" induces the mutation for removal of the PstI site)
* The part was amplified from genomic DNA of E. coli str. K-12 substr. DH10B, complete genome (CP000948.1). * J23100 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene IV message (BBa_M13004). The part aligns with base pairs 4204-4219 in M13K07 genome. It was identified as the RBS for gene IV message by Wezenbeek et al in Gene (1980) 11: 129-148
Anderson promoter J23101 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
This is the naturally-occurring RBS found in the regulatory region of the DntA gene.
'''''This does not physically exist as a basic part due to time constraints; it was cloned as part of composite part which incorporates all of the components necessary for expression of a reporter gene under the control of DntR'''''. For this reason, the ends of the supplied sequence may not accurately represent the boundaries of the functional unit.
Cloned from a historical plasmid based on pQF52 carrying genomic sequences from ''Burkholderia cepacia''.
MpEF1a (Marchantia poylmorpha Elongation Factor 1, PlantSyntax Pro+5U)
This RBS is recognized by ribosomes carrying the modified anti-Shine Dalgarno sequence as found in Brink et al. (see below)
Brink MF, Verbeet MP, de Boer HA (1995). Specialized ribosomes: highly specific translation in vivo of a single targetted mRNA species. Gene, 156, pp. 215-222
Yeast CLB1 promoter region, G2/M cell cycle specific
Description of CLB1 (from SGD): B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome. More information found here: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=CLB1
Part contains 500 bases upstream from the CLB1 ORF. Is NOT a minimal promoter, and has not been tested for composability.
Yeast consensus sequence from SGD chrVII:703140..703639
SpoVG ribosome binding site (RBS) for B. subtilis
Description: SpoVG is an endogenous ribosome binding site from B.subtilis. The sequence of the spoVG ribosome binding site is AAAGGUGGUGA which is complementary to the sequence UUUCCUCCACU from the 3' region of the 16s rRNA from B.subtilis. Previous research showed that the predicted binding energy of the 16s rRNA to the RBS is -19kcal 1
In order to ensure that the RBS is functional the actual ribosome binding site was maintained and the distance between the RBS and the start codon maintained. In order to conform to the biobrick standard the sequence flanking the RBS had to be changed but the distance between the promoter and RBS, and start codon and RBS was maintained.
The sequence was taken from a previous research paper [1] and was constructed by Geneart.
This is the natural RBS for the sigE chaperone (BBa_J64025) in Salmonella Typhimurium LT2.
This part was not designed with compatibility to biobrick standard assembly in mind. This RBS has not been explicitly assayed for expression rate.
This part is from the bacteriophage M13 genome, bp 2716-2764 in M13K07. It directs transcription of M13 gene VI (BBa_M13506, BBa_M13006). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
flhDC operon under the control of constitutive promoter J23113
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23113 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
Promoter for cell division genes ftsI and ftsW
BBa_S03331is based on the reguatory region preceding cell division genes in the mra cluster and includes the biobrick head and tail restriction sites.
A promoter for the first nine genes of the Escherichia coli mra cluster of cell division and cell envelope biosynthesis genes, including ftsI and ftsW. Hara H, Yasuda S, Horiuchi K and Park JT. Journal of Bacteriology (1997) 179: 5802-5811
Anderson promoter J23100 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
Natural RBS sequence for Bacillus Subtilis, described in the literature as a strong RBS for this bacteria.
From genomic sequence Bacillus Subtilis.
T7 promoter (strong promoter from T7 bacteriophage)
T7 promoter is very specific promoter which is transcribed only by specific T7 RNA polymerase. Usually this promoter is used in expression systems where T7 promoter is cotransfected with T7 RNA polymerase. That ensures strong transcription of desired genes.
This is the consensus RBS for Bacillus subtilis.
The part must be 8 nucleotides away from the first methionine of the coding sequence, and so we added 'TGT' downstream of the actual binding sequence: AAAGGAGG. This, combined with the truncated non-CDS BioBrick prefix scar, gives exactly 8 'spacer bases' between the 3' end of the RBS and the start of the coding sequence.
flhDC operon under the control of constitutive promoter J23114
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23100 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
a constitutive expression promoter or use in mammalian cells. Ribosome binding site is included.
Tar receptor under the control of constitutive promoter J23112
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate and exists as a functional homodimer. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23112 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''Tar'' expression affect the chemotaxis of ''E. coli''.
Test RBS from T7 that may be used in E.coli
The promoter from the yeast gene CYC1. Activity characterized here: http://dx.doi.org/10.1016/0378-1119(95)00037-7.
From Mumberg, Muller, and Funk p413 pCYC. See ref. above
Strong constitutive promoter for Bacillus subtilis
'host-takover module' from B.subtilis Bacteriophage SPO1
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene IX message (BBa_M13009). The part aligns with base pairs 1190-1205 in M13K07 genome. It was identified as the RBS for gene IX message by Wezenbeek et al in Gene (1980) 11: 129-148
This is a single bp change from B0034. It's strength is approximately 35% that of B0034.
T7 promoter with an T->G mutation at the -17 position of the consensus sequence
RBS specific to dedicated ribosomes. This RBS is a modified version of B0036. The spacing between the SD sequence and the start codon has been increased by 5 bases to give the same spacing as used by Brink et al. The 5 bases are the same as those used by Brink. That means they form the first five bases of an XbaI site and no negative affects of using these bases are known at present.
Tar receptor under the control of constitutive promoter J23109
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate and exists as a functional homodimer. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23109 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''Tar'' expression affect the chemotaxis of ''E. coli''.
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23109 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
This part is from the bacteriophage M13 genome. It directs transcription of M13 gene II (BBa_M13502, BBa_M13002). Promoter identified in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
T7 promoter with an A->T mutation at the -10 position of the consensus sequence
Native rbs from crtI (phytoene dehydrogenase) of Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
Virtual part to be added to the coding sequence.
Assambly of [http://parts.igem.org/Part:BBa_J23116 J23116] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
The ribosomal binding site for gene creC in the E Coli cre operon.
Using this promoter allows for the constant expression of a reporter gene or a selectable antibiotic.
This part was obtained from members of the Weiss Lab.
Full-length stationary phase osmY promoter
osmY's promoter is active in stationary phase and under high osmotic pressure conditions.
Truncated Forward Primer: 5'- GTT TCT TCG AAT TCG CGG CCG CTT CTA GGCT TAT GTT TTC GCT GAT ATC - 3' Total Length: 49 bp Annealing Length: 21 bp GC Content: 38.1% Melting Temperature: 49.5 degrees C hairpin deltaG: -2.66 kcal/mol self dimer deltaG: -99.97 kcal/mol Full Forward Primer: 5'- GTT TCT TCG AAT TCG CGG CCG CTT CTA GCTG GCA CAG GAA CGT TAT C - 3' Total Length: 47 bp Annealing Length: 19 bp GC Content: 52.6% Melting Temperature: 53.4 degrees C hairpin deltaG: -3.99 kcal/mol self dimer deltaG: -98.3 kcal/mol Reverse Primer: 5'-GTT TCT TCC TGC AGC GGC CGC TAC TAG TAT TGT TAA ATA TAG ATC ACA ATT TTG- 3' Total Length: 54 bp Annealing Length: 25 bp GC Content: 20.0% Melting Temperature: 46.4 degrees C hairpin deltaG: -2.86 kcal/mol self dimer deltaG: -99.44 kcal/mol heterodimer deltaG with Forward Primer: -99.44 kcal/mol heterodimer deltaG with Conserved Forward Primer: -99.97 kcal/mol
This part was PCRed out of E. coli's genome.
LacZ constitutive promoter, without including operators.
Mid-expression level constitutive promoter in yeast
Constitutive weak promoter of lacZ which sequence was changed at position 29 (T->G) in order to make it weaker
This part is from the bacteriophage M13 genome, bp 381-428 in M13K07. It directs transcription of M13 gene X (BBa_M13510, BBa_M13010). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
Assambly of [http://parts.igem.org/Part:BBa_J23110 J23110] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene V message (BBa_M13005). The part aligns with base pairs 827-842 in M13K07 genome. It was identified as the RBS for the gene V message by Wezenbeek et al in Gene (1980) 11: 129-148
RBS.4 (weaker) -- derivative of BBa_0030
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). 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: Brian Chow
The expression level of this RBS has not been quantified.
This is the native ribosome binding site of crtE (geranylgeranyl pyrophosphate synthase) from Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321) Accession: D90087.
This is a virtual part to be added, blunt ended, to the coding sequence.
Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321) Accession: D90087.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene II message (BBa_M13002). The part aligns with base pairs 8252-8267 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
This is the natural RBS associated with the sopA effector protein in the Salmonella SPI-1 system.
This part was not designed with compliance to biobrick standard assembly in mind. This RBS hasn't been explicitly tested in an expression assay such as GFP fluorescence or B-Gal expression.
The ribosomal binding site of the creD gene in the E Coli creD operon.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene III message (BBa_M13003). The part aligns with base pairs 1563-1578 in M13K07 genome. It was identified as the RBS for gene III message by Wezenbeek et al in Gene (1980) 11: 129-148 New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban
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>.
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("RBS-1" in figure 4-14 of thesis). 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: Brian Cho
Assambly of [http://parts.igem.org/Part:BBa_J23104 J23104] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
optimized (TA) repeat constitutive promoter with 17 bp between -10 and -35 elements
Strong RBS based on Ron Weiss thesis. Strength is considered relative to BBa_B0031, BBa_B0032, BBa_B0033 and BBa_B0034.
Tar receptor under the control of constitutive promoter J23106
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate and exists as a functional homodimer. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23106 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''Tar'' expression affect the chemotaxis of ''E. coli''.
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23106 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
optimized (TA) repeat constitutive promoter with 13 bp between -10 and -35 elements
The transmembrane receptor Tar of E. coli mediates chemotaxis towards aspartate.
One XbaI site was found at position 420. The restriction site was changed from TCTAGt to CCTAGt via QuikChange PCR.
The part was amplified from genomic DNA of E. coli str. K-12 substr. DH10B chromosome (NC_010473.1).
Tar receptor under the control of constitutive promoter J23104
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate and exists as a functional homodimer. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23100 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''Tar'' expression affect the chemotaxis of ''E. coli''.
Up elements (including promoter and RBS) of cox2 gene from Saccharomyces cerevisiae mitochondrial DNA.
Designed by Qiwu XU, BioBrick restriction enzyme sites added.
Two T7 promoters are reversely overlapping in two base pairs while a point mutation occurs at the 12th base pair, from A-T to T-A.
The spv promoter. ---- 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 <Pspv> basic part K112707 PCR of dv017/dv016 on pBca1037 (499bp, EcoRI/BamHI/DpnI) Sub into pBca1256 (EcoRI/BamHI, 2472+499, L) Product is pBca1256-K112707 ----------------------------------------------- dv017 Forward biobricking of <Pspv> cgataGAATTCatgAGATCTaGATCCTGTGATGTTTGGCG dv016 Reverse biobricking of <Pspv> cgttaGGATCCGATAATGTtTGCAGGGGAATTATTTTG
This is the promoter for molecular chaperone htpG. It is active during the heat shock response.
This is a correction to part [http://parts.igem.org/Part:BBa_J45504 BBa_J45504], also the htpG Heat Shock Promoter. The original part contains a fragment of the coding sequence for molecular chaperone htpG (base pairs >287) which can be confirmed by [http://blast.ncbi.nlm.nih.gov/ BLASTing the sequence]. This part contains only the first 287 bases of the original part which consist solely of the htpG promoter. You can see the difference between the two sequences in the image below.
This is the naturally-occurring RBS found in the regulatory region of the DntR gene.
Anderson promoter J23113 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
Sequence comes from the natural gene 5 RBS. Using gene 5 as a strong RBS is from initial results from experiments characterizing all natural T7 RBSs.
PlepA is the promoter of the PlepA gene of Bacillus subtilis. It is a constitutive promoter and does not contain a ribosome binding site.
Assambly of [http://parts.igem.org/Part:BBa_J23103 J23103] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
Parts J23100 through J23119 are a family of constitutive promoter parts isolated from a small combinatorial library. B0030 is a strong RBS based on Ron Weiss thesis
Pveg is a strong, constitutive promoter of Bacillus subtilis
A constitutive plant actin promoter followed by two copies of the Lac operator. This allows control of promoter activity by LacI.
MAS is a plant specific promoter which is constitutively expressed. This part is compatible with the GoldenGate MoClo Assembly Standard as it is free from BsaI and BpiI recognition sequences.
Domestication for GoldenGate by removal of BsaI and BpiI recognition sequences.
NikR promoter, a protein of the ribbon helix-helix family of trancription factors that repress expre
Nickel responsive transcriptional regulator
Complete sMMO of Methylococcus capsulatus
The part consists of the six subunits of methane monooxygenase (MMO). Gene order: mmoX, mmoY, mmoB, mmoZ, mmoD, mmoC The expression is under control of lac+pl. MMO converts methane to methanol.
Part is designed considering the RFC10 standard.
b0034 derived RBS to match spacing of J01122
RBS spacing modification to [RBS] such that the spacing between the shine-delgarno and the ORF is the same as it is in J01122.
Template for Building Primer Family Member
This part is from the bacteriophage M13 genome, bp 1500-1547 in M13K07. It directs transcription of M13 gene III (BBa_M13503, BBa_M13003). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
Constitutive Promoter, Medium Transcription
This is the natural RBS for the sptP gene in Salmonella Type III Secretion
This part was designed without consideration for biobrick standard assembly. This RBS has not been explicitly tested for expression rate.
Anderson promoter J23114 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
Anderson promoter J23107 (with one nucleotide different to the original Anderson promoter sequence) without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
Assambly of [http://parts.igem.org/Part:BBa_J23102 J23102] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
Native ribosome binding site of sam8 (tyrosine ammonia lyase) from the bacterium Saccharothrix espanaensis DSM 44229.
Virtual part to be added to coding sequence I742142.
Anderson promoter J23103 without RFP in backbone vector pSB1C3 to easily fuse the promoter with other reporters e.g. the lux operon.
E. Coli CreABCD phosphate sensing operon promoter
CreABCD phosphate sensing operon promoter taken from RegulonDB.
Reverse RBS (RBSrev) -- corresponds to BBa_B0030
Repeats in oligos caused unusual products during cloning
Sequence comes from the natural B0030. Using B0030 as a medium strength RBS is from initial results from experiments characterizing all natural T7 RBSs.
constitutive promoter which outputs .3 TIPs point mutants of wild type rrnB promoter P1
This part is the natural invI RBS from Salmonella Typhimurium LT2.
This part was not designed with consideration for biobrick standard assembly in mind. This RBS has not been explicitly tested for expression level in a fluorescence or B-Gal assay.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene X message (BBa_M13010). The part aligns with base pairs 480-495 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
Infrared signal reporter (J23119:IFP:J23119:HO1)
Gene sequence is obtained directly from Tsien's lab.
(correct) temperature sensitive promoter
This part is just for upload test. It is meaningless
RBS (Elowitz 1999) -- defines RBS efficiency
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix. 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: Brian Chow
GsiB ribosome binding site (RBS) for B. subtilis
GsiB is an endogenous ribosome binding site from ''B.subtilis''. The sequence of the gsiB ribosome binding site is '''AAAGGAGG''' which is complementary to the sequence '''UUUCCUCC''' from the 3' region of the 16s rRNA from ''B.subtilis''. GsiB is an endogenous ribosome binding site (RBS) from ''B.subtilis''. The sequence of the gsiB ribosome binding site is '''AAAGGAGG''' which is complementary to the sequence '''UUUCCUCC''' from the 3' region of the 16s rRNA from ''B.subtilis''. Previous research showed that the predicted binding energy of the 16s rRNA to the RBS is -9.3kcal.
This part is the natural RBS from the sipC protein in Salmonella Type III Secretion.
This part was not designed with biobrick standard assembly in mind. This RBS has not been explicitly measured for expression rate using fluorescence or B-Gal assay.
Synthetic ribosome binding site added by Son of Babel procedure
This is a 4bp synthetic ribosome binding site which can be added by fusion PCR using a reverse primer and the Son of Babel cloning system.
The part can be added by fusion PCR using a Son of Babel reverse primer.
Truncated Forward Primer: 5'- GTT TCT TCG AAT TCG CGG CCG CTT CTA GGCT TAT GTT TTC GCT GAT ATC - 3' Total Length: 49 bp Annealing Length: 21 bp GC Content: 38.1% Melting Temperature: 49.5 degrees C hairpin deltaG: -2.66 kcal/mol self dimer deltaG: -99.97 kcal/mol Reverse Primer: 5'-GTT TCT TCC TGC AGC GGC CGC TAC TAG TAT TGT TAA ATA TAG ATC ACA ATT TTG- 3' Total Length: 54 bp Annealing Length: 25 bp GC Content: 20.0% Melting Temperature: 46.4 degrees C hairpin deltaG: -2.86 kcal/mol self dimer deltaG: -99.44 kcal/mol heterodimer deltaG with Conserved Forward Primer: -99.97 kcal/mol
Regulatory region spanning 680 bp upstream of the start codon of the GPD1 gene in yeast. Very strong constitutive promoter.
ribosome binding site for transcription initiation
Promoter gsiB is a sigma factor B dependent promoter found in ''B.subtilis''. In ''B.subtilis'' endogenous sigma factor B is activated under mild stress. These mild stress conditions can be generally split into nutrient stress response and physical stress response. Nutrient stress response is triggered by low levels of ATP and GTP and physical stress response is triggered by exposure to blue light, salt, heat, acid or ethanol1. The promoter gsiB has been used previously as a read out for the activation of sigma factor B 2. The context with which we used the promoter gsiB, was to take blue light as an input and give '''Polymerase Per Second'''(PoPS) as an output. To do this the other potential inputs need to be carefully controlled so that only blue light activated the sigma B and gives a PoPS output. In order to get sufficient sigma B activation by blue light the light receptor YtvA, part...., needs to be over expressed in ''B.subtilis'' 3.
Biobrick standard was applied to the promoter gsiB sequence.
flhDC operon under the control of constitutive promoter J23109
This is the -20 to -1 region of T7 gp0.5, which contains the native RBS region for this gene. The physical instantiation of this part does not exist. This part is not compatible with Standard Biobricks assembly methods, as the scar created during assembly would interrupt the spacing between the RBS and the start codon of the CDS. Individuals wishing to use this RBS sequence in their assembles should refer to part B2103.
The -20 to -1 region was chosen to be representative of the RBS region of the T7 genes for the following reasons: 1) The Shine-Delgarno region is contained within this defined region for all T7 genes. 2) Current literature suggests that when bound to the Translation Start Site (0), the Ribosome covers positions -20 to +13 of the gene.
Genome of wild-type bacteriophage T7, positions 1476-1495. Includes the -20 to -1 region of gp0.5.
This is the natural RBS from the sicA chaperone (BBa_J6021) in the Salmonella Type III Secretion System.
This part was not designed with standard biobrick assembly in mind.
This is a derivate of BBa_K105027. Due to a point mutation in the TATA box region the efficiency of this minimal promoter is only 43 % of the natural yeast CYC1 promoter.
This is the core of the CYC1 promoter of ''S. cerevisiae''. This promoter element allows basal transcription. The transcription signal can be modulated by adding operator sites upstream of this BioBrick. In that way activators or repressors can act on the transcription machinery. <br<
This BioBrick contains the TATA-box and most of the 5'UTR (-139 to -36, relative to the translational start)of the natural CYC1 promoter. A Kozak sequence is not included and has thus to be added!
Tar receptor under the control of constitutive promoter J23100
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23100 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''flhDC'' expression affect the motility of ''E. coli''.
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
RFC10 compatible strong RBS derived from the T7 phage gene 10a (major capsid protein)[1]. When assembled to a coding part with the A of the start codon being part of the XbaI site, the RBS will be shifted one bp downstream compared to the native sequence. The sequence was successfully used by the iGEM team Heidelberg 2014 for the expression of many proteins in E.coli. 1. Olinss, P. & Rangwala, S. H. Derived from Bacteriophage T7 mRNA Acts ELS an Enhancer of Translation of the lac2 Gene in. 16973???16976 (1989).
The 18 bp including the XbaI that can be found upstream of the presumably important part of the RBS were included into the sequence just to make sure it works. However to fully comply with RFC10 a G was inserted behind the XbaI site.
synthesized as found in the T7 genome and several commercial expression plasmids.
Assambly of [http://parts.igem.org/Part:BBa_J23118 J23118] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
flhDC operon under the control of constitutive promoter J23100
The flhDC operon is the master regulator of motility and chemotaxis in E. coli. FlhDC forms heterotetramers and activates class II operons in concert with sigma factor 70. Among the gene products of class II operons are several components of the flagellum and the alternative sigma factor FliA which is essential for the transcription of class III genes. Here we used a set of 8 constitutive promoters from the 2006 Berkeley group to test how different levels of constitutive ''flhDC'' expression affect motility in ''E. coli''.
*The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). *J23100 information was from partsregistry and physical DNA from the 2012 distribution kit.
The spv2 promoter. ---- 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 <Pspv2> basic part K112706 PCR of dv015/dv016 on pBca1037 (500bp, EcoRI/BamHI/DpnI) Sub into pBca1256 (EcoRI/BamHI, 2472+ 500, L) Product is pBca1256-K112706 ----------------------------------------------- dv015 Forward biobricking of <Pspv2> cgataGAATTCatgAGATCTccttatgcagcgtaagggccgcaac dv016 Reverse biobricking of <Pspv2> cgttaGGATCCGATAATGTtTGCAGGGGAATTATTTTG
RBS.3 (medium) -- derivative of BBa_0030
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). Contact info for this part: Brian Chow
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VIII message (BBa_M13008). The part aligns with base pairs 1285-1300 in M13K07 genome. It was identified as the RBS for gene VIII message by Wezenbeek et al in Gene (1980) 11: 129-148
optimized (A) repeat constitutive promoter with 17 bp between -10 and -35 elements
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene I message (BBa_M13001). The part aligns with base pairs 8252-8267 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
Promoter 43 a constitutive promoter for B. subtilis
Promoter 43 is a constitutive promoter that constitutively expresses the P43 protein in ''B.subtilis''. This promoter has been shown to be recognized and active during the exponential and lag phases of growth. It has been hypothesized that the ability to recognize the promoter in exponential and lag phase of growth is due to the recognition of the promoter by both sigma factor 55 (the major sigma factor) and sigma factor 37 (the lag phase sigma factor) 1. The P43 promoter has been previously used for constitutive expression of exogenous genes within ''B.subtilis'' vectors 2. The context with which we used the promoter P43 is as a '''Polymerase Per Second''' (PoPS) generator.
The biobrick part was designed to include the binding sites for both the sigma factor A and B. In addition the biobrick standard was applied to the promoter P43 sequence.
The part was designed using the sequence from the ''B.subtilis'' genome and from previously published papers 2. This sequence was then synthesised by Geneart.
The kozak sequence acts as a eukaryotic RBS. It is cloned directly between a promoter and coding region.
Strong Expression level Constitutive promoter in yeast
Endogenous promoter for Alcohol Dehydrogenase
constitutive promoter with (TA)9 between -10 and -35 elements
With 9 TA repeats between the -10 and -35 elements, the distance between the two elements is not optimal for the sigma factor to bind to the promoter. Thus, the promoter should be in the 'off' state.
constitutive promoter with (C)10 between -10 and -35 elements
With 10 C repeats between the -10 and -35 elements, the distance between the two elements is optimal for the sigma factor to bind to the promoter. Thus, the promoter should be in the 'on' state.
constitutive promoter with (C)12 between -10 and -35 elements
With 12 C repeats between the -10 and -35 elements, the distance between the two elements is optimal for the sigma factor to bind to the promoter. Thus, the promoter should be in the 'on' state.
Two T7 promoters are reversely overlapping.
The sequence of T7 promoter is TAATACGACTCACTATA.
Double terminator + Constitutive promoter + Strong RBS
This part contains a double terminator and a constitutive prokaryotic promoter and a strong RBS (BBa_B0014 + BBa_J23100 + BBa_B0030). It is a simple promoter in the goals to begin gene transcription. For Sup???biotech-Paris (2009) team this part is used when adding to a recombinant lambda phage and to begin the transcription of synthetic genes inside the Lambda phage genome.
BBa_B0014 : Designed by Reshma Shetty Group: Registry (2003-07-16). BBa_J23100 : Designed by John Anderson Group: iGEM2006_Berkeley (2006-08-04.) BBa_B0030 : Designed by Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003. Group: NCBS, Prather Lab.
low expression, constitutive promoter in yeast
constitutive promoter which outputs .4 TIPs point mutants of wild type rrnB promoter P1
35S is a plant specific promoter obtained from Cauliflower Mosaic Virus. The part is intended for use as a constitutive promoter for gene expression experiments. The part is compatible with GoldenGate MoClo Assembly Standard (free from BsaI and BpiI recognition sequences).
Domestication for GoldenGate (Removal of internal BsaI and BpiI recognition sequences).
This part is from the bacteriophage M13 genome, bp 4055-4103 in M13K07. It directs transcription of M13 gene IV (BBa_M13504, BBa_M13004). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
This is the naturally-occurring RBS found in the regulatory region of the DntR gene. gataaaaacaagaggaaaacaa
This is a mid-high level constitutive promoter from the yeast gene TEF2.
Assambly of [http://parts.igem.org/Part:BBa_J23119 J23119] and lacI-binding-site of [http://parts.igem.org/Part:BBa_R0010 R_0010] The "lacI binding site" of Part [http://parts.igem.org/Part:BBa_R0010 R_0010] differs from lacO from Part [http://parts.igem.org/Part:BBa_J33207 BBa_J33207].
Restriction sites of Sal I, Bam HI, Bgl II, and Mlu I in front of strong RBS
We designed new prefix(Sal I and Bam HI) and suffix(Bgl II and Mul I) for insertions of promoters and regulator binding sites in front of RBS.
Predicted by Lon Chubiz to be RBS sequence with strongest affinity for T7 ribosomes.
This is an exact 'upside down' version of BBa_R0051. The promoter has two DNA binding sites for lambda cI repressor BBa_C0051. By adding this part, we wish to emphasise the possibility of engineering both DNA strands, and the additional regulatory potential that it gives.
Any 'upside down' (reverse complementary) sequences made by PCR amplification need be made with suffix and prefix is opposite order with respect to the original default sequence.
Double terminator + constitutive promoter
This part contains a double terminator and a constitutive prokaryotic promoter. It is a simple promoter to begin gene transcription. For Sup???biotech-Paris (2009) team this part is used after to be added to a recombinant lambda phage to begin the transcription of synthetic genes inside the Lambda phage genome.
BBa_B0014 : Designed by Reshma Shetty Group: Registry (2003-07-16) BBa_J23100 : Designed by John Anderson Group: iGEM2006_Berkeley (2006-08-04)
Tar receptor under the control of constitutive promoter J23113
The transmembrane chemoreceptor Tar of E. coli mediates chemotaxis towards aspartate and exists as a functional homodimer. Here we used a set of 8 constitutive [http://partsregistry.org/Part:BBa_J23113 Anderson promoters] from the 2006 Berkeley group to test how different levels of constitutive ''Tar'' expression affect the chemotaxis of ''E. coli''.
flhDC operon under the control of constitutive promoter J23106
* The PstI restriction site in the ''flhDC'' sequence was mutated to CTGCGG using the reverse primer * ''flhDC'' was amplified from genomic DNA of ''E. coli'' DH10B via PCR using the following primers: ** Fwd: 5'-actgaattcgcggccgcttctagatgcatacctccgagttgctg-3' ** Rev: 5'-tcctgcagcggccgctactagttactgcccgggatggcggttgacataagcCgcaggcaaagctgccaacag-3' (the capitalized "C" induces the mutation for removal of the PstI site)
* The part was amplified from genomic DNA of ''E. coli'' str. K-12 substr. DH10B, complete genome (CP000948.1). * J23106 information was taken from the partsregistry and physical DNA from the 2012 distribution kit.
DNA is double-stranded. To translate genes of both strands, you need RBSs in both strands.
Please refer to the original (BB_B0034).
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VI message (BBa_M13006). The part aligns with base pairs 2840-2855 in M13K07 genome. It was identified as the RBS for gene VI message by Wezenbeek et al in Gene (1980) 11: 129-148
Annexin V is member of the annexin family of Ca dependent proteins. Its function is not yet known. It binds to phosphatidylserine in a Ca-dependen fashion.
In combination with RBS B0032 there is no detectable expression of annexin V.
This is the natural RBS from the sopD gene in Salmonella Type III Secretion.
This RBS has the modified Shine-Dalgarno sequence, it has a reduced secondary structure relative to using the actual Brink sequence with mixed connective sites flanking it. This RBS is modified from B0071 by reducing the 3' sequence so that the SD to ATG spacing is closer to that which is optimal for E. coli.
This is a derivate of BBa_K105027. Due to a point mutation in the TATA box region the efficiency of this minimal promoter is only 70 % of the natural yeast CYC1 promoter.
T7 promoter for expression of functional RNA