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Team:Toulouse/Result/parts
From 2014.igem.org
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<p class="title3"> | <p class="title3"> | ||
| - | <a href="http://parts.igem.org/Part:BBa_K1364000">BBa_K1364000</a>:N-acetylglucosamine based chemotaxis for <i>Bacillus subtilis</i><br></p> | + | - <a href="http://parts.igem.org/Part:BBa_K1364000">BBa_K1364000</a>:N-acetylglucosamine based chemotaxis for <i>Bacillus subtilis</i><br></p> |
<p class="texte">This part is designed to enable a N-acetylglucosamine | <p class="texte">This part is designed to enable a N-acetylglucosamine | ||
based chemotaxis in <i>Bacillus subtilis</i>. | based chemotaxis in <i>Bacillus subtilis</i>. | ||
| Line 129: | Line 129: | ||
<!--à compléter--> | <!--à compléter--> | ||
</p> | </p> | ||
| + | |||
<br> | <br> | ||
<!--K1364004 : Promotor Pveg + Chimio--> | <!--K1364004 : Promotor Pveg + Chimio--> | ||
<p class="title3"> | <p class="title3"> | ||
| - | <a href="http://parts.igem.org/Part:BBa_K1364004">BBa_K1364004</a>: P<sub>veg</sub> + N-acetylatedglucosamine based chemotaxis for <i>B. subtilis</i> | + | - <a href="http://parts.igem.org/Part:BBa_K1364004">BBa_K1364004</a>: P<sub>veg</sub> + N-acetylatedglucosamine based chemotaxis for <i>B. subtilis</i> |
<br> | <br> | ||
<p class="texte">This part is designed to enable a N-acetylglucosamine based chemotaxis in <i>Bacillus subtilis</i>.</p> | <p class="texte">This part is designed to enable a N-acetylglucosamine based chemotaxis in <i>Bacillus subtilis</i>.</p> | ||
| Line 160: | Line 161: | ||
<!--K1364001 : RBS + Binding + Terminator--> | <!--K1364001 : RBS + Binding + Terminator--> | ||
| - | <p class=" | + | <p class="title3"> |
| - | + | <a href="http://parts.igem.org/Part:BBa_K1364005">BBa_K1364005</a>: P<sub>veg</sub> + Chitin Binding Cell Wall protein</p> | |
| - | + | <p class="texte">This part is designed to enable the binding of <i>Bacillus subtilis</i> to the fungi wall made of chitin.<p/> | |
| - | + | <p class="title4">Design:</p> | |
| - | This part is designed to enable the binding of <i>Bacillus subtilis</i> | + | <p class="texte">This part is composed of a Cell Wall Binding (CWB) sequence |
| - | to the fungi wall made of chitin.< | + | |
| - | < | + | |
| - | + | ||
| - | This part is composed of a Cell Wall Binding (CWB) sequence | + | |
and a Chitin Binding Domain (CBD) linked with a 6 amino acids linker.<br> | and a Chitin Binding Domain (CBD) linked with a 6 amino acids linker.<br> | ||
<br> | <br> | ||
| Line 174: | Line 171: | ||
The CBD is composed of the Domain 4 of the GbpA protein of <i>Vibrio cholerae</i>, | The CBD is composed of the Domain 4 of the GbpA protein of <i>Vibrio cholerae</i>, | ||
a protein reported to mediate bacterial attachment to chitin. | a protein reported to mediate bacterial attachment to chitin. | ||
| - | It has been shown that the Domain 4 was essential to bind chitin.< | + | It has been shown that the Domain 4 was essential to bind chitin.</p> |
| - | < | + | <img src="https://static.igem.org/mediawiki/2014/f/f5/BBa_K1364005.png"> |
| - | < | + | <p class="title4">Type</p> |
| - | + | <p class="texte">Generator</p> | |
| - | < | + | <p class="title4">Tests</p> |
| - | < | + | <p class="texte">This part was tested with chitin beeds. (See <a href="https://2014.igem.org/Team:Toulouse/Result/experimental-results">Binding module</a>)</p> |
| - | This part was tested with chitin beeds. | + | <p class="title4">References</p> |
| - | + | <p class="texte">- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br> | |
| - | < | + | |
| - | < | + | |
| - | - Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br> | + | |
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br> | - The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br> | ||
| - | |||
</p> | </p> | ||
| Line 193: | Line 186: | ||
<p class="title2">Fungicides</p> | <p class="title2">Fungicides</p> | ||
| - | <p class=" | + | <p class="title3">GAFP-1</p> |
<br> | <br> | ||
<!--K1364002 : RBS + GAFP-1--> | <!--K1364002 : RBS + GAFP-1--> | ||
| - | <p class=" | + | <p class="title3"> |
| - | + | <a href="http://parts.igem.org/Part:BBa_K1364002">BBa_K1364002</a>: RBS - Antifungal GAFP-1</p> | |
| - | + | <p class="texte">The <i>Gastrodia</i> anti-fungal protein(GAFP-1), also known as gastrodianin, is a mannose and chitin binding lectin | |
| - | + | originating from the Asiatic orchid Gastrodia elata, a traditional Chinese medicinal herb cultured for thousands of years. | |
| - | + | GAFP-1 is composed of 15 amino acids LDSLSFSYNNFEEDD and is able to inhibit the growth of multiples species of plant pathogenic fungi.</p> | |
| - | The <i>Gastrodia</i> anti-fungal protein (GAFP-1) is a mannose | + | <p class="title4">Design:</p> |
| - | + | <p class="texte">This part is composed of a Strong RBS (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a> and | |
| - | < | + | |
| - | + | ||
| - | This part is composed of a Strong RBS (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a> and | + | |
the open reading frame of the <i>Gastrodia</i> anti-fungal protein 1 (GAFP-1) | the open reading frame of the <i>Gastrodia</i> anti-fungal protein 1 (GAFP-1) | ||
optimized for its expression and its secretion in <i>Bacillus subtilis</i>. | optimized for its expression and its secretion in <i>Bacillus subtilis</i>. | ||
| - | The codon optimization was made thanks to the DNA 2.0 software program.< | + | The codon optimization was made thanks to the DNA 2.0 software program.</p> |
| - | < | + | <img src="https://static.igem.org/mediawiki/2014/5/5f/BBa_K1364002.png"> |
| - | < | + | <p class="title4">Type</p> |
| - | + | <p class="texte">Translational unit</p> | |
| - | < | + | <p class="title4">Tests</p> |
| - | < | + | <p class="texte">This part was tested on the fungi <i>Trichoderma reesei</i> (See <a href="https://2014.igem.org/Team:Toulouse/Result/experimental-results">Fungicides module</a>)</p> |
| - | + | <p class="title4">References</p> | |
| - | < | + | <p class="texte">- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br> |
| - | < | + | - The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br></p> |
| - | - Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br> | + | |
| - | - The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br> | + | |
| - | + | ||
| - | </p> | + | |
<br> | <br> | ||
Revision as of 09:32, 10 October 2014
Parts
SubtiTree, a bacterium to save our trees
Results > parts
As the chassis B. subtilis is not as used as E. coli,
it was sometimes hard for us the get or find desired parts.
However, with the collaboration of other iGEM and a synthesis compagny, we managed to obtain or make the following parts:
Submitted parts
We have deposed 16 new BioBrick parts to the Registry.
All of them were cloned into the standard plasmid pSB1C3, tested and sequenced.
Chemotaxis
- BBa_K1364000:N-acetylglucosamine based chemotaxis for Bacillus subtilis
This part is designed to enable a N-acetylglucosamine based chemotaxis in Bacillus subtilis.
Design:
The encoded protein is a chimera of two proteins:
- the methyl accepting Chemotaxis protein (McpA from Bacillus subtilis which is required for taxis towards glucose.
- the N-acetylglucosamine regulated methyl-accepting chemotaxis protein from Vibrio cholerae (VCD).
The chimeric protein contains the intracellular domains of McpA from Bacillus subtilis to enable the transduction of the signal:
these domains correspond to the amino acids 1-37 and 282-610.
The extracellular domain of VCD is inserted between the intracellular regions of McpA
to sense N-acetylglucosamine and corresponds to the amino acids 31-310.
Type
Translation unit
Tests
This part is not tested yet.
References
Uniprot:
- McpA
- N-acetylglucosamine regulated methyl-accepting chemotaxis protein
- BBa_K1364004: Pveg + N-acetylatedglucosamine based chemotaxis for B. subtilis
This part is designed to enable a N-acetylglucosamine based chemotaxis in Bacillus subtilis.
Design:
This expression cassette is designed for the expression of an antifungal peptide, D4E1 and for its secretion in Bacillus subtilis. It is composed of the strong, constitutive promotor of B. subtilis Pveg (K823003), strong RBS for B. subtilis (K780002), the open reading frame of D4E1 and a double terminator (B0015)
Type
Generator
Tests
This part was not tested yet.
References
Uniprot:
- McpA
- N-acetylglucosamine regulated methyl-accepting chemotaxis protein
Binding
BBa_K1364005: Pveg + Chitin Binding Cell Wall protein
This part is designed to enable the binding of Bacillus subtilis to the fungi wall made of chitin.
Design:
This part is composed of a Cell Wall Binding (CWB) sequence
and a Chitin Binding Domain (CBD) linked with a 6 amino acids linker.
The CWB domain has been extracted from LytC (BBa_K316030) of the iGEM 2010 Imperial College team.
The CBD is composed of the Domain 4 of the GbpA protein of Vibrio cholerae,
a protein reported to mediate bacterial attachment to chitin.
It has been shown that the Domain 4 was essential to bind chitin.
Type
Generator
Tests
This part was tested with chitin beeds. (See Binding module)
References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373
Fungicides
GAFP-1
BBa_K1364002: RBS - Antifungal GAFP-1
The Gastrodia anti-fungal protein(GAFP-1), also known as gastrodianin, is a mannose and chitin binding lectin originating from the Asiatic orchid Gastrodia elata, a traditional Chinese medicinal herb cultured for thousands of years. GAFP-1 is composed of 15 amino acids LDSLSFSYNNFEEDD and is able to inhibit the growth of multiples species of plant pathogenic fungi.
Design:
This part is composed of a Strong RBS (K780002 and the open reading frame of the Gastrodia anti-fungal protein 1 (GAFP-1) optimized for its expression and its secretion in Bacillus subtilis. The codon optimization was made thanks to the DNA 2.0 software program.
Type
Translational unit
Tests
This part was tested on the fungi Trichoderma reesei (See Fungicides module)
References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373
BBa_K1364007: Strong RBS for B. subtilis
(K780002) + GAFP-1 + Double terminator (B0015
GAFP-1: Gastrodia anti-fungal protein
The Gastrodia anti-fungal protein (GAFP-1) is a mannose-binding lectin
which is able to inhibit the growth of multiples species of plant pathogenic fungi.
Design:
This part is composed of a Strong RBS (K780002,
the open reading frame of the Gastrodia anti-fungal protein 1 (GAFP-1)
and a double terminator B0015.
optimized for its expression and its secretion in Bacillus subtilis.
The codon optimization was made thanks to the DNA 2.0 software program.
Type
Composite part
Tests
Link ?
References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373
BBa_K1364008:
Strong, constitutive promoter of Bacillus subtilis Pveg (K823003 +
Strong RBS for B. subtilis
(K780002) +
GAFP-1 +
Double terminator (B0015
GAFP-1: Gastrodia anti-fungal protein
The Gastrodia anti-fungal protein (GAFP-1) is a mannose-binding lectin
which is able to inhibit the growth of multiples species of plant pathogenic fungi.
Design:
This part is composed of the strong, constitutive promoter of Bacillus subtilis Pveg (K823003,
strong RBS (K780002,
the open reading frame of the Gastrodia anti-fungal protein 1 (GAFP-1)
and a double terminator B0015.
optimized for its expression and its secretion in Bacillus subtilis.
The codon optimization was made thanks to the DNA 2.0 software program.
Type
Expression cassette
Tests
Link ?
References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373
D4E1
BBa_K1364003: Strong RBS for B. subtilis
(K780002) + D4E1
+ Double terminator (B0015
D4E1
D4E1 is a linear synthetic peptide of 17 amino acids
which has shown to have antifungal activities
by complexing with a sterol present in conodial wall of a varety of fungi.
Design:
This part is composed of a Strong RBS (K780002,
the open reading frame of D4E1 and
a Double terminator (B0015)
optimized for its expression and its secretion in Bacillus subtilis.
This part was optimized for the expression and its secretion in Bacillus subtilis
thanks to the DNA 2.0 software program.
Type
Translation unit
Tests
Link ?
References
- De Lucca AJ, Bland JM, Grimm C, Jacks TJ, Cary JW, Jaynes JM, Cleveland TE, Walsh TJ. Fungicidal properties, sterol binding, and proteolytic resistance of the synthetic peptide D4E1.
- Can J Microbiol. 1998 Jun;44(6):514-20.
BBa_K1364009: Strong, constitutive promotor of B. subtilis
Pveg (K823003)
+ RBS, D4E1 code and Double terminator (K1364003)
D4E1
D4E1 is a linear synthetic peptide of 17 amino acids
which has shown to have antifungal activities
by complexing with a sterol present in conodial wall of a varety of fungi.
Design:
This part is composed of the strong, constitutive promotor of B. subtilis
Pveg (K823003),
a strong RBS (K780002),
the open reading frame of D4E1 and
a double terminator (B0015).
This part was optimized for the expression and its secretion in Bacillus subtilis
thanks to the DNA 2.0 software program.
Type
Expression cassette
Tests
Link ?
References
- De Lucca AJ, Bland JM, Grimm C, Jacks TJ, Cary JW, Jaynes JM, Cleveland TE, Walsh TJ. Fungicidal properties, sterol binding, and proteolytic resistance of the synthetic peptide D4E1.
- Can J Microbiol. 1998 Jun;44(6):514-20.
EcAMP-1
BBa_K1364010: Constitutive promoter Pveg and
strong RBS for B. subtilis
(K733013)
+ EcAMP-1 (K1162001)
EcAMP-1
EcAMP-1 is an antimicrobial peptide of 37 amino acids
originated from the specie Echinochloa crus-galli,
a type of wild grass.
This peptide has a particular structure : it is helical because of two disulfide bonds.
EcAMP-1 has shown to have antifungal activities. Its mode of action may be the prevention of hyphae elongation.
This part was added to the Registry by the iGEM Utah State team in 2013.
Design:
This part is composed of the constitutive promoter Pveg and
strong RBS for B. subtilis
(K733013) and
the open reading frame of EcAMP-1.
The EcAMP-1 part was codon optimized for E. coli by the iGEM Utah State team
and thanks to the Life Technologies GeneArt software program.
Type
Composite part
Tests
The electrophoresis and PCR tests were OK.
References
BBa_K1364011: Constitutive promoter Pveg and
strong RBS for B. subtilis
(K733013)
+ EcAMP-1 (K1162001)
+ Double terminator (B0015)
EcAMP-1
EcAMP-1 is an antimicrobial peptide of 37 amino acids
originated from the specie Echinochloa crus-galli,
a type of wild grass.
This peptide has a particular structure : it is helical because of two disulfide bonds.
EcAMP-1 has shown to have antifungal activities. Its mode of action may be the prevention of hyphae elongation.
This part was added to the Registry by the iGEM Utah State team in 2013.
Design:
This part is composed of the constitutive promoter Pveg and
strong RBS for B. subtilis
(K733013),
the open reading frame of EcAMP-1 and
a double terminator (B0015).
The EcAMP-1 part was codon optimized for E. coli by the iGEM Utah State team
and thanks to the Life Technologies GeneArt software program.
Type
Expression cassette
Tests
The test does not work yet.
References
Fungicide operons
BBa_K1364012:
RBS and GAFP-1 (K1364002) + RBS, D4E1 and double terminator (K1364003)
Design:
This part is designed for the co-expression of two different peptides
with anti-fungal activities : D4E1 and GAFP-1.
It is composed of the translation unit with D4E1 (BBa_K1364002)
and the composite part with GAFP-1 (BBa_K1364003).
Type
Translation unit
Tests
References
See BBa_K1364002 and BBa_K1364003.
BBa_K1364013:
Strong, constitutive promotor of B. subtilis
Pveg (K823003)
+ RBS, GAFP-1, RBS, D4E1 and double terminator (K1364012).
Design:
This part is designed for the co-expression of two different peptides
with anti-fungal activities : D4E1 and GAFP-1.
It is composed of the strong, constitutive promotor of B. subtilis
Pveg (K823003)
and the translation unit with GAFP-1 and D4E1 (BBa_K1364012).
Type
Expression cassette
Tests
References
See BBa_K1364002 and BBa_K1364003.
BBa_K1364014:
Promotor Pveg RBS spoVG, EcAMP-1 (BBa_K1364010)
+ RBS, GAFP-1, RBS, D4E1 and double terminator (BBa_K1364012)
Design:
This part contains the three fungicides on the same operon.
It is composed of the composite part with EcAMP--1 (BBa_K1364010)
and the translation unit with GAFP-1 and D4E1 (BBa_K1364012).
Type
??
Tests
References
See BBa_K1364010, BBa_K1364002 and BBa_K1364003.
Used parts
| BioBrick | Description | Origine | Module(s) |
| K733013 | Pveg (K316001) + RBS-SpoVG (K143021) : Constitutive promotor Pveg and strong RBS for B. subtilis | 2014 Kit plate 1, 7H | Fungicides (EcAMP) |
| K823003 | Pveg : strong, constitutive promotor of B. subtilis | 2014 Kit plate 1, 20G | Fungicides (D4E1 GAFP-1) Chemotaxis Binding |
| K823002 | PlepA : constitutive promotor of B. subtilis.
It is the promotor of the lepA gene of B. subtilis |
2014 Kit plate 1, 20E | Fungicides (D4E1) Chemotaxis Binding |
| K606061 | SpoVG RBS for B. subtilis
Strong ribosome binding site from subtilis. Works fine in E. coli |
2014 Kit plate 1, 15A | Optional |
| K316027 | B. subtilis transformation vector with LacI, targets amyE locus. | 2014 Kit plate 1, 2N | Fungicides Chemotaxis Binding |
| B0015 | Double terminator (BBa_B0010 + BBa_B0012) | 2014 Kit plate 3, 3F | Fungicides (GAFP-1, EcAMP-1) |
| K780000 | Terminator for B. subtilis | Sent by the Warsaw iGEM team | |
| K780001 | Strong RBS for B. subtilis | Sent by the Warsaw iGEM team | |
| K780002 | Strong RBS for B. subtilis | Sent by the Warsaw iGEM team | |
| K780003 | Strong constitutive promotor for B. subtilis | Sent by the Warsaw iGEM team | Fungicides Chemotaxis Binding |
| K1162001 | EcAMP-1 | Sent by the Utah State iGEM team | Fungicides (EcAMP-1) |
| K823023 | Empty backbone vector pSBBS1C for integration into B. subtilis
It integrates in the amyE locus |
Sent by the Munich iGEM team | Fungicides Chemotaxis Binding |
| K823022 | Empty backbone vector pSBBS4S for integration intoB. subtilis
It integrates in the thrC locus |
Sent by the Munich iGEM team | Fungicides Chemotaxis Binding |
| K823021 | Reporter vector pSBBS1C-lacZ for B. subtilis | Sent by the Munich iGEM team | Fungicides Chemotaxis Binding |
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