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Team:Groningen/Project/Construct
From 2013.igem.org
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<li>Select the subunits you need</li> | <li>Select the subunits you need</li> | ||
<li>Assemble them together</li></ol> | <li>Assemble them together</li></ol> | ||
| - | At this point the silk product is ready to be produced ( | + | At this point the silk product is ready to be produced (How? see production backbone) and employed for the desired purpose. |
</p> | </p> | ||
<p> | <p> | ||
| - | The Groningen team | + | The Groningen team enriched the iGEM database adding several new <i>Bacillus subtilis</i> BioBricks containing spider silk gene subunits. This provides the iGEM community with a new bunch of parts; which, in the future, will help anyone in assembling its own silk protein and customize it with different features. |
| - | <br>It is important to remember that is the first time that silk-coding BioBricks suitable for <i>Bacillus subtilis</i> are introduced into the database. Therefore this work marks the starting point for further studies about silk within the <i>Bacillus subtilis</i> chassis | + | <br>It is important to remember that is the first time that silk-coding BioBricks suitable for <i>Bacillus subtilis</i> are introduced into the database. Therefore this work marks the starting point for further studies about silk within the <i>Bacillus subtilis</i> chassis inside the iGEM framework. |
</p> | </p> | ||
<p> | <p> | ||
| - | The advantages shown by our collection are several: less cloning steps and compatibility with most of the BioBrick assembly standards. | + | The advantages shown by our collection are several: less cloning steps and compatibility with most of the BioBrick assembly standards. |
| - | <br> | + | <br><h3>Why less cloning steps?</h3> |
| - | <br> | + | <br>Each part has been blablabl are necessary to assemble Indeed the parts are designed in such a way that any subunit is created |
| + | <br><h3>Compatibility with biobrick standards</h3> | ||
| + | <br> | ||
We divided the several silk coding sequences in 3 big groups: | We divided the several silk coding sequences in 3 big groups: | ||
| - | <ul><li> | + | <ul><li>Subunit E1</li> |
| - | <li> | + | <li>Subunit E2</li> |
| - | <li>Tail</li></ul>subunit E1, subunit E2 and Tail. Each of them has been produced and stored into the iGEM submission backbone (pSB1C3). Each of them shows certain features: | + | <li>Tail</li></ul>subunit E1, subunit E2 and Tail. Each of them has been produced and stored into the iGEM submission backbone (pSB1C3). Each of them shows certain features: signal sequences, strep-tag, starting codon and Ribosome Binding Site (RBS). |
</p> | </p> | ||
<p> | <p> | ||
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<p> | <p> | ||
The following parts have been produced, sequenced and are available into the standard BioBrick submission backbone (pSB1C3): | The following parts have been produced, sequenced and are available into the standard BioBrick submission backbone (pSB1C3): | ||
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<br>What kind of spider silk gene is it | <br>What kind of spider silk gene is it | ||
Revision as of 13:48, 2 October 2013
Constructs
An amyE intergrational backbone
To transform B. subtilis with our developed biobricks we have improved the amyE intergrational backbone from Munich's iGEM team 2012 (BBa_K823023) that had no inducible promoter. We've added the HyperSpank IPTG inducible promoter from Rudner's Lab 2004. This promoter is placed right in front of the prefix, so any biobrick can be inserted in this backbone (BBa_K1085014) and can be induced with IPTG.
In figure 1 a close-up of the promoter is shown.
The HyperSpank promoter has a single nucleotide change (G->T) at the -1 position. This increases the expression levels but also causes leaky expression when IPTG is absence[1]. To improve repression, a second lacO operator site has been inserted 71 bp upstream of the first. (David Rudner, Harvard Medical School)
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| Figure 1: The HyperSpank promoter with in orange the lacO operators, in red the -35, -10, +1 signals and in green the prefix. |
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| Figure 2: BBa_K1085014 with: The amp gene for ampicillin resistance in E. coli; The cat gene for chloramphenicol resistance in B. subtilis; The HyperSpank promoter with its repressor lacI; The amyE up- and downstream fragments for intergration in the amyE locus. |
Promoter activity
BBa_K1085014 was constructed with two variants of GFP (one form our group and one from the biobrick system, BBa_E0840). BBa_K1085014-GFPmg and BBa_K1085014-BBa_E0840 were transformed to B. subtilis. Overnight cultivated strains were diluted 1:100 in fresh medium and grown till OD~0.45 and induced with 1mM IPTG. A 1,2 and 3 hour sample was analysed under the microscope, results are shown in figure 3.|
Figure 3 A: |
B: |
C: |
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| Figure 3: In (a) An overlay picture is shown from the phase-contrast and GFP-channel picture. In (b,c) the intensity in of ~40 cells in the GFP-channel, were analyzed from two pictures. The average intensity (AU) from the cells are plotted above with the standard deviation. In (b) a GFP from our group is shown and in (c)a biobricked GFP (BBa_E0840) is shown in a plot. wt=wildtype, T0= before induction, T1,2,3=#h of induction with IPTG. |
Bacillus subtilis silk genes collection derived from Argiope aurantia MaSp2
One of the challenges that the project includes is the production of spider silk. In order to achieve this goal iGEM Groningen designed for you what we call “The Bacillus subtilis silk assembly shop”.
The 'shop' idea follows those conceptual steps:
- Design your own silk protein
- Browse the iGEM Groningen silk subunits collection
- Select the subunits you need
- Assemble them together
The Groningen team enriched the iGEM database adding several new Bacillus subtilis BioBricks containing spider silk gene subunits. This provides the iGEM community with a new bunch of parts; which, in the future, will help anyone in assembling its own silk protein and customize it with different features.
It is important to remember that is the first time that silk-coding BioBricks suitable for Bacillus subtilis are introduced into the database. Therefore this work marks the starting point for further studies about silk within the Bacillus subtilis chassis inside the iGEM framework.
The advantages shown by our collection are several: less cloning steps and compatibility with most of the BioBrick assembly standards.
Why less cloning steps?
Each part has been blablabl are necessary to assemble Indeed the parts are designed in such a way that any subunit is created
Compatibility with biobrick standards
We divided the several silk coding sequences in 3 big groups:
- Subunit E1
- Subunit E2
- Tail
The aim of the molecular genetic design is to create a handy toolbox in order to produce any desired combination of silk-like genes which can be expressed in Bacillus subtilis for several purposes. Everything is designed within the RFC[23] standard framework. This enables the user to join together all the different parts creating in-frame fusion silk-like proteins.
The following parts have been produced, sequenced and are available into the standard BioBrick submission backbone (pSB1C3):
What kind of spider silk gene is it
What are general problems with this gene
Where did we get it from.
Codon optimisation, solved the problems.
Strep-tag
Why this is needed
For what purposes it comes in handy
Signal peptide
Why is it so important.
The use of existing pathway so not lots of trouble
The signal sequences are nice addition to the registry
how the pathway works and how the silk will be secreted
