IGEM:IMPERIAL/2008/Prototype/Wetlab/parts/Composite

Composite Parts

Seen as how the wiki may soon cause errors due to the size of the previous page (and the affect it was having on us), here is the new parts page, specifically for composite parts...

We'll start looking at these soon and I'll get back to people after the weekend

Expression Related

P43-gsiB (done)

Name: Promoter 43 and RBS gsiB for B. subtilis

Code: K143050

Long: Constitutive promoter 43(<bbpart>BBa_K143013</bbpart>) coupled to the strong Ribosome Binding Site gsiB(<bbpart>BBa_K143020</bbpart>) from B. subtilis.

P43-gsiB can be used in the context of a Polymerases per second (PoPS) output generator

To get the highest level of translation from this Promoter-RBS combination it must be connected to a coding region preceded by a coding region prefix[1]. A standard prefix will increase the distance between the RBS and the start codon, reducing translational efficiency.

Design: The sequence of P43 and RBS-gsiB were obtained from papers[1, 2] and the sequence synthesised by GeneArt

Source: P43-gsiB was synthesised by GeneArt

References

1. Zhang XZ, Cui ZL, Hong Q, and Li SP. High-level expression and secretion of methyl parathion hydrolase in Bacillus subtilis WB800. Appl Environ Microbiol. 2005 Jul;71(7):4101-3. DOI:10.1128/AEM.71.7.4101-4103.2005 |

1. http://partsregistry.org/Assembly:RBS-CDS_issues

2. Jürgen B, Schweder T, and Hecker M. The stability of mRNA from the gsiB gene of Bacillus subtilis is dependent on the presence of a strong ribosome binding site. Mol Gen Genet. 1998 Jun;258(5):538-45. DOI:10.1007/s004380050765 |

P43-spoVG (done)

Name: Promoter 43 and RBS spoVG for B. subtilis

Code: K143051

Long: Constitutive promoter 43(<bbpart>BBa_K143013</bbpart>) coupled to the strong Ribosome Binding Site spoVG(<bbpart>BBa_K143021</bbpart>) from B. subtilis.

P43-spoVG can be used in the context of a Polymerases per seconds (PoPS) output generator

To get the highest level of translation from this Promoter-RBS combination it must be connected to a coding region preceded by a coding region prefix[1]. A standard prefix will increase the distance between the RBS and the start codon, reducing translational efficiency.

Design: The sequence of P43 and RBS-spoVG were obtained from papers[1, 2] and the sequence synthesised by GeneArt

Source: P43-spoVG was synthesised by GeneArt

References

1. Zhang XZ, Cui ZL, Hong Q, and Li SP. High-level expression and secretion of methyl parathion hydrolase in Bacillus subtilis WB800. Appl Environ Microbiol. 2005 Jul;71(7):4101-3. DOI:10.1128/AEM.71.7.4101-4103.2005 |

1. http://partsregistry.org/Assembly:RBS-CDS_issues

2. Jürgen B, Schweder T, and Hecker M. The stability of mRNA from the gsiB gene of Bacillus subtilis is dependent on the presence of a strong ribosome binding site. Mol Gen Genet. 1998 Jun;258(5):538-45. DOI:10.1007/s004380050765 |

Pveg-gsiB (done)

Name: Promoter Pveg and RBS gsiB for B. subtilis

Code: K143052

Long: Constitutive promoter veg(<bbpart>BBa_K143012</bbpart>) coupled to the strong Ribosome Binding Site gsiB(<bbpart>BBa_K143020</bbpart>) from B. subtilis.

Pveg-gsiB can be used in the context of a Polymerases per second (PoPS) output generator

To get the highest level of translation from this Promoter-RBS combination it must be connected to a coding region preceded by a coding region prefix[1]. A standard prefix will increase the distance between the RBS and the start codon, reducing translational efficiency.

Design: The sequence of Pveg was obtained from the DBTBS[1] and RBS-gsiB were obtained from papers[2] and the sequence synthesised by GeneArt

Source: Pveg-gsiB was synthesised by GeneArt

References

1. Sierro N, Makita Y, de Hoon M, and Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 2008 Jan;36(Database issue):D93-6. DOI:10.1093/nar/gkm910 |

1. http://partsregistry.org/Assembly:RBS-CDS_issues

2. Jürgen B, Schweder T, and Hecker M. The stability of mRNA from the gsiB gene of Bacillus subtilis is dependent on the presence of a strong ribosome binding site. Mol Gen Genet. 1998 Jun;258(5):538-45. DOI:10.1007/s004380050765 |

Pveg-spoVG (Ready for Upload)

Name: Promoter Pveg and RBS spoVG for B. subtilis

Code: K143053

Long: Constitutive promoter veg(<bbpart>BBa_K143012</bbpart>) coupled to the strong Ribosome Binding Site spoVG(<bbpart>BBa_K143021</bbpart>) from B. subtilis.

Pveg-spoVG can be used in the context of a Polymerases per second (PoPS) output generator

To get the highest level of translation from this Promoter-RBS combination it must be connected to a coding region preceded by a coding region prefix[1]. A standard prefix will increase the distance between the RBS and the start codon, reducing translational efficiency.

Design: The sequence of Pveg was obtained from the DBTBS[1] and RBS-spoVG were obtained from papers[2] and the sequence synthesised by GeneArt

Source: Pveg-spoVG was synthesised by GeneArt

References

1. Sierro N, Makita Y, de Hoon M, and Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 2008 Jan;36(Database issue):D93-6. DOI:10.1093/nar/gkm910 |

1. http://partsregistry.org/Assembly:RBS-CDS_issues

2. Jürgen B, Schweder T, and Hecker M. The stability of mRNA from the gsiB gene of Bacillus subtilis is dependent on the presence of a strong ribosome binding site. Mol Gen Genet. 1998 Jun;258(5):538-45. DOI:10.1007/s004380050765 |

Phyper-spank-gsiB (Ready for Upload)

Name: Promoter hyper-spank and RBS gsiB for B. subtilis

Code: K143054

Long: Inducible promoter hyper-spank(<bbpart>BBa_K143015</bbpart>) coupled to the strong Ribosome Binding Site gsiB(<bbpart>BBa_K143020</bbpart>) from B. subtilis.

Phyperspank-gsiB can be used to take an intake of IPTG and give a Ribosomes per second (RiPS) output generator.

IPTG does not directly induce the expression of the promoter hyper-spank, but requires the transcriptional regulator LacI, (<bbpart>BBa_K413035</bbpart>). This means that LacI must be constitutively expressed in B.subtilis in order to use the promoter hyper-spank as an inducible promoter.

To get the highest level of translation from this Promoter-RBS combination it must be connected to a coding region preceded by a coding region prefix[1]. A standard prefix will increase the distance between the RBS and the start codon, reducing translational efficiency.

Design: The sequence of promoter hyperspank was obtained form the B. subtilis integration vector pDR111 and RBS-gsiB were obtained from papers[1] and the sequence synthesised by GeneArt

Source: Phyperspank-gsiB was synthesised by GeneArt

References

1. Jürgen B, Schweder T, and Hecker M. The stability of mRNA from the gsiB gene of Bacillus subtilis is dependent on the presence of a strong ribosome binding site. Mol Gen Genet. 1998 Jun;258(5):538-45. DOI:10.1007/s004380050765 |

1. http://partsregistry.org/Assembly:RBS-CDS_issues

Phyper-spank-spoVG

Name:

Code: K143055

Long:

Design:

Source:

Pxyl-gsiB

Name:

Code: K143056

Long:

Design:

Source:

Pxyl-spoVG

Name:

Code: K143057

Long:

Design:

Source:

Pctc-gsiB

Name:

Code: K143058

Long:

Design:

Source:

Pctc-spoVG

Name:

Code: K143059

Long:

Design:

Source:

PgsiB-gsiB

Name:

Code: K143060

Long:

Design:

Source:

PgsiB-spoVG

Name:

Code: K143061

Long:

Design:

Source:

LacI-Terminator (done)

Name: LacI repressor protein - Terminator

Code: K143062

Long: LacI transcriptional repressor protein (<bbpart>BBa_K143033</bbpart>) coupled to the double terminator (<bbpart>BBa_B0015</bbpart>.

The LacI does not possess a LVA degradation tag and gas a short (3 amino acid) N-terminal deletion consistent with LacI used in conjunction with B. subtilis.

LacI can be used in conjunction with the lac operon promoter (<bbpart>BBa_K143015</bbpart>), where the LacI will act as a receiver for an IPTG input to result in a Polymerases per second (PoPS) output.

The double terminator is the most commonly used terminator and is a combination of parts <bbpart>BBa_B0010</bbpart> and <bbpart>BBa_B0012</bbpart>.

The double terminator allows the LacI to be easily incorporated into a closed transcriptional unit.

Design: LacI was identified from the pDR111 B. subtilis integration vector. The double terminator is the most commonly used registry terminator.

Source: LacI was produced by PCR cloning using Pfu form the B. subtilis integration vector and cloned into a BioBrick with the registry double terminator

XylR-Terminator

Name:

Code: K143063

Long:

Design:

Source:

Antibiotic Related

Chloraphemicol Resistance Protein - Terminator (Ready for Upload)

Name: Chloraphemicol resistance protein - Terminator

Code: K143064

Long: Chloraphemicol acetyltransferase protein(<bbpart>BBa_J31005</bbpart>) coupled to the double terminator (<bbpart>BBa_B0015</bbpart>).

Chloraphemicol acetyltransferase confers resistance to Chloraphemicol

The double terminator is the most commonly used terminator and is a combination of parts <bbpart>BBa_B0010</bbpart> and <bbpart>BBa_B0012</bbpart>.

The double terminator allows the CAT to be incorporated into a closed transcriptional unit.

Design: Chloraphemicol acetyltransferase is an exisiting registry protein. The double terminator is the most commonly used registry termiantor

Source: The Chloraphemicol acetyltransferase and double terminator were taken both taken from the registry.

Spectinomycin Resistance Protein (Aad9) - Terminator

Name: Spectinomycin Resistance Protein (Aad9) - Terminator

Code: K143065

Long: protein(<bbpart>BBa_</bbpart>) coupled to the double terminator (<bbpart>BBa_B0015</bbpart>).

confers resistance to 

The double terminator is the most commonly used terminator and is a combination of parts <bbpart>BBa_B0010</bbpart> and <bbpart>BBa_B0012</bbpart>.

The double terminator allows the Spectinomycin resistance gene to be incorporated into a closed transcriptional unit.

Design: The double terminator is the most commonly used registry termiantor

Source: The double terminator was taken both taken from the registry.

Codes and associated parts

Note

• Aad9 is the Spectinomycin resistance gene
• RI - Resistance Integration Brick, P - Promoter, Pi - chemically inducible promoter, Pl - light inducible promoter, Bs - B.subtilis, PTC - Promoter Testing Construct, Rep - Repressor protein

Code	Part	Code	Part	Code	Part	Code	Part	Code	Part
K143050	P43-gsiB	K143051	P43-spoVG	K143052	Pveg-gsiB	K143053	Pveg-spoVG	K143054	Phyperspank-gsiB
K143055	Phyper-spank-spoVG	K143056	Pxyl-gsiB	K143057	Pxyl-spoVG	K143058	Pctc-gsiB	K143059	Pctc-spoVG
K143060	PgsiB-gsiB	K143061	PgsiB-spoVG	K143062	LacI - Terminator	K143063	XylR - Terminator	K143064	CAT - Terminator
K143065	Aad9 - Terminator	K143066	Int Open	K143067	RI Brick	K143068	RI-Rep-Pi Brick	K143069	RI-Ytva-Pl Brick
K143070	Bs-PTC	K143071	Int Close	K143072		K143073		K143074
K143075		K143076		K143077		K143078		K143079
K143080		K143081		K143082		K143083		K143084
K143085		K143086		K143087		K143088		K143089