Team:UNIPV-Pavia/Parts/Characterization/RebExistingParts

From 2010.igem.org

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m (BBa_K300003 - Phasin (PhaP) - internal domain)
 
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__NOTOC__
<table width="100%" border="0">
<table width="100%" border="0">
<tr>
<tr>
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</table>
</table>
 +
 +
=Improved Parts: list=
 +
 +
* [[Team:UNIPV-Pavia/Parts/Characterization/RebExistingParts #BBa_K300002 - Phasin (PhaP) - head domain|BBa_K300002 - Phasin (PhaP) - head domain - improvement of BBa_K208001]]
 +
* [[Team:UNIPV-Pavia/Parts/Characterization/RebExistingParts #BBa_K300003 - Phasin (PhaP) - internal domain|BBa_K300003 - Phasin (PhaP) - internal domain - improvement of BBa_K208001]]
 +
 +
<br>
 +
----
 +
<br>
</td></tr>
</td></tr>
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=Phasins=
=Phasins=
-
Polyhydroxyalkanoates (PHAs) are polyoxoesters that are produced by diverse bacteria and that accumulate as intracellular granules. Phasins are proteins that can bind these granules.
+
Polyhydroxyalkanoates (PHAs) are polyoxoesters that are produced by several bacteria and that accumulate as intracellular granules. Phasins are proteins that can bind these granules.
-
Following parts are the phaP gene from ''Ralstonia eutropha'', which encodes for a phasin, without stop codon in order to support protein fusions as a head/internal domain.
+
The following parts are derived from the phaP gene of ''Ralstonia eutropha'', which encodes for a phasin, engineered without the stop codon in order to support protein fusions as a head/internal domain.
-
The tagged protein adhere to the surface of the PHA granules via the phasin tag, which enables the target protein purification.
+
 
-
In literature [Banki MR et al.] it has been shown that affinity tags composed by phasins assembled in tandem can increase the affinity with PHA.
+
Phasins can be used as affinity tags for a target protein, which can bind PHA granules allowing this way protein purification.
 +
 
 +
In literature [Banki MR et al., 2005] it has been shown that affinity tags composed by phasins assembled in tandem can increase the affinity with PHA.
 +
 
 +
The aim of our improvement of phasin already present in the Registry (<partinfo>BBa_K208001</partinfo>) was to provide a head and an internal protein domain useful to build fusion proteins.  
==<partinfo>BBa_K300002</partinfo> - Phasin (PhaP) - head domain==
==<partinfo>BBa_K300002</partinfo> - Phasin (PhaP) - head domain==
-
This part can be used as a N-terminal affinity tag for a target protein that has to be fused downstream of the phasin. Together with BBa_K300003 enables the construction of composite tags.
+
This part can be used as a N-terminal affinity tag for a target protein that has to be fused downstream. Together with <partinfo>BBa_K300003</partinfo> enables the construction of composite tags.
Because this part is a head domain, the Prefix is compatible with RFC10 and the Suffix is compatible with RFC23.
Because this part is a head domain, the Prefix is compatible with RFC10 and the Suffix is compatible with RFC23.
-
This part has been tested through <partinfo>BBa_K300086</partinfo> measurement system.
+
===Construction===
 +
It is identical to <partinfo>BBa_K208001</partinfo>, but it lacks the stop codon in order to support protein fusions.
 +
 
 +
It has been designed as a head domain:
 +
 
 +
The Prefix sequence is 5'-GAATTCGCGGCCGCTTCTAG-3' (RFC10 Prefix)
 +
 
 +
The Suffix sequence is 5'-ACTAGTAGCGGCCGCTGCAG-3' (RFC23 Suffix)
 +
 
 +
For these reasons, a tail domain or an internal domain (compatible with RFC23) can be easily assembled downstream to create protein fusions.
 +
 
 +
To obtain this part, BioBrick <partinfo>BBa_K208001</partinfo> (provided by iGEM HQ in pSB3K3 in RFC23 standard) was PCR-amplified/mutagenized with primers:
 +
 
 +
phaP10F 5'-GCTTCTAGATGATCCTCACCCCGGAACA-3'
 +
 
 +
phaPSR: 5'-GCTACTAGTGGCAGCCGTCGTCTTCTTTG-3'
 +
 
 +
in order to delete the stop codon.
 +
 
 +
The PCR product was ran on a 1% agarose gel, gel-extracted, digested with XbaI-SpeI and ligated with <partinfo>pSB1AK3</partinfo> (previously cut with XbaI-SpeI and dephosphorylated).
 +
Positive clones were selected through digestion screening/sequencing.
 +
 
 +
----
 +
This part was used to construct the following synthetic composite affinity tags:
 +
*<partinfo>BBa_K300093</partinfo>
 +
*<partinfo>BBa_K300094</partinfo>
 +
*<partinfo>BBa_K300095</partinfo>
 +
*<partinfo>BBa_K300084</partinfo>
 +
*<partinfo>BBa_K300097</partinfo>
 +
 
 +
or alone as a head domain; in this case it has been tested through <partinfo>BBa_K300086</partinfo> measurement system.
 +
 
===Methods===
===Methods===
Inoculum (into 5 ml LB+Amp) from glycerol stock of:
Inoculum (into 5 ml LB+Amp) from glycerol stock of:
-
*<partinfo>BBa_K300086</partinfo>
+
*<partinfo>BBa_K300086</partinfo>,
-
*<partinfo>BBa_K173000</partinfo> (positive control)
+
*<partinfo>BBa_K173000</partinfo> (positive control),
-
*<partinfo>BBa_B0031</partinfo> (negative control)
+
*<partinfo>BBa_B0031</partinfo> (negative control).
-
They were let grow ON at +37°C, 220 rpm.
+
ON cultures' growth at 37°C, 220 rpm.
-
The following day cultures were diluted 1:100 and let grow again for about five hours at +37°C, 220 rpm.
+
The following day, cultures were diluted 1:100 and let grown again for about five hours at 37°C, 220 rpm.
-
Optical density (O.D.) of each cell culture was than measured with TECAN Infinte F200. Samples were diluted in order to obtain the same O.D. equal to 0,02.
+
The optical density (O.D.) of each cell culture was than measured with TECAN Infinte F200. Samples were diluted in order to obtain the same O.D. equal to 0,02.
-
Than we performed a 21 hours' experiment with measurements of absorbance and green fluorescence every five minutes with TECAN Infinite F200. Each value shown is the mean of three measurements, from GFP data that of a non-fluorescent culture (negative control) was subtracted; cultures were shaken for 15 seconds every five minutes.
+
Then we performed a 21-hours' experiment with measurements of absorbance and green fluorescence every five minutes using TECAN Infinite F200; cultures were shaken for 15 seconds every five minutes. Each value shown below is the mean of three measurements, from GFP data that of a non-fluorescent culture (negative control) was subtracted.
===Results===
===Results===
Line 71: Line 116:
<table border="1" align="center">
<table border="1" align="center">
<tr align="center">
<tr align="center">
-
<th>Culture</th><th>Doubling time [min.]</th>
+
<th>Culture</th><th>Doubling time [min.] ± std error</th>
</tr>
</tr>
<tr align="center">
<tr align="center">
-
<td><partinfo>BBa_K173000</partinfo></td><td>77</td>
+
<td><partinfo>BBa_K173000</partinfo></td><td>76.3336 ± 1.4362</td>
</tr>
</tr>
<tr align="center">
<tr align="center">
-
<td><partinfo>BBa_K300086</partinfo></td><td>74</td>
+
<td><partinfo>BBa_K300086</partinfo></td><td>73.6685 ± 1.6245</td>
</tr>
</tr>
<tr align="center">
<tr align="center">
-
<td><partinfo>BBa_B0031</partinfo></td><td>69</td>
+
<td><partinfo>BBa_B0031</partinfo></td><td>70.8421 ± 2.2181</td>
</tr>
</tr>
</table>
</table>
===Discussion===
===Discussion===
-
All cell cultures showed a similar growth curve and doubling time was computed as described [[Team:UNIPV-Pavia/Parts/Characterization#Doubling_time_evaluation|here]] in order to have informations about the burden due to synthesis of such fusion proteins. It's possible to see that all doubling time are very similar; it's possible to assert that the expression of these BioBrick parts doesn't cause abnormal stress to the cells.
+
All cell cultures showed a similar growth curve; doubling time was computed as described [[Team:UNIPV-Pavia/Parts/Characterization#Doubling_time_evaluation|here]] in order to have informations about the burden due to the synthesis of such fusion proteins. It's possible to see that all doubling time are very similar; it's possible to assert that the expression of these BioBrick parts doesn't cause abnormal stress to cells.
-
In GFP curve it's possible to appreciate that in <partinfo>BBa_K300086</partinfo> GFP accumulation it's significantly different from that of negative control <partinfo>BBa_B0031</partinfo>. This result shows the right folding of the green fluorescent protein assembled downstream of the genetic circuit.
+
From GFP curve it's possible to appreciate that in <partinfo>BBa_K300086</partinfo> GFP accumulation it's significantly different from that of negative control <partinfo>BBa_B0031</partinfo>. This result shows that the green fluorescent protein assembled downstream of the genetic circuit is correctly folded.
The mean protein synthesis rate was also computed over the growth exponential phase, showing an appreciable GFP production rate that is about a half of the positive control.
The mean protein synthesis rate was also computed over the growth exponential phase, showing an appreciable GFP production rate that is about a half of the positive control.
==<partinfo>BBa_K300003</partinfo> - Phasin (PhaP) - internal domain==
==<partinfo>BBa_K300003</partinfo> - Phasin (PhaP) - internal domain==
-
This part without stop codon and with Prefix and Suffix compatible with RFC23 (Silver Standard) in order to fully support protein fusions as an internal domain. Together with <partinfo>BBa_K300002</partinfo>, enables the construction of synthetic affinity tags based on phasins in tandem, possibly spaced by peptide linkers, as described in [Banki MR et al.].
+
This part without stop codon and with Prefix and Suffix compatible with RFC23 (Silver Standard) was built in order to fully support protein fusions as an internal domain. Together with <partinfo>BBa_K300002</partinfo>, enables the construction of synthetic affinity tags containing phasins in tandem, possibly spaced by peptide linkers, as described in [Banki MR et al., 2005].
===Construction===
===Construction===
 +
It is identical to <partinfo>BBa_K208001</partinfo>, but it lacks the stop codon in order to support protein fusions.
 +
 +
It has been designed as an internal domain:
 +
 +
The Prefix sequence is 5'-GAATTCGCGGCCGCTTCTAG-3' (RFC23 Prefix)
 +
 +
The Suffix sequence is 5'-ACTAGTAGCGGCCGCTGCAG-3' (RFC23 Suffix)
 +
 +
For these reasons, a tail domain or an internal domain (compatible with RFC23) can be easily assembled downstream this BiobBrick to create protein fusions.
 +
 +
To obtain this part, BioBrick <partinfo>BBa_K208001</partinfo> (provided by iGEM HQ in pSB3K3 in RFC23 standard) was PCR-amplified/mutagenized with primers:
 +
 +
phaPSF: 5'-GCTTCTAGAATGATCCTCACCCCGGAACA-3'
 +
 +
phaPSR: 5'-GCTACTAGTGGCAGCCGTCGTCTTCTTTG-3'
 +
 +
in order to delete the stop codon.
 +
 +
The PCR product was ran on a 1% agarose gel, gel-extracted, digested with XbaI-SpeI and ligated with <partinfo>pSB1A3</partinfo> (previously cut with XbaI-SpeI and dephosphorylated).
 +
Positive clones were selected through digestion screening/sequencing.
-
COPIARE DA REGISTRY
+
----
 +
This part was used as an internal domain to construct the following synthetic composite affinity tags:
 +
*<partinfo>BBa_K300093</partinfo>
 +
*<partinfo>BBa_K300094</partinfo>
 +
*<partinfo>BBa_K300084</partinfo>
 +
*<partinfo>BBa_K300097</partinfo>
</td>
</td>
</tr>
</tr>
</table>
</table>

Latest revision as of 03:25, 28 October 2010

IMPROVED PARTS


Return to Characterization

New Parts

Improved Parts

Existing Parts from the Registry


Improved Parts: list




Phasins

Polyhydroxyalkanoates (PHAs) are polyoxoesters that are produced by several bacteria and that accumulate as intracellular granules. Phasins are proteins that can bind these granules. The following parts are derived from the phaP gene of Ralstonia eutropha, which encodes for a phasin, engineered without the stop codon in order to support protein fusions as a head/internal domain.

Phasins can be used as affinity tags for a target protein, which can bind PHA granules allowing this way protein purification.

In literature [Banki MR et al., 2005] it has been shown that affinity tags composed by phasins assembled in tandem can increase the affinity with PHA.

The aim of our improvement of phasin already present in the Registry (<partinfo>BBa_K208001</partinfo>) was to provide a head and an internal protein domain useful to build fusion proteins.

<partinfo>BBa_K300002</partinfo> - Phasin (PhaP) - head domain

This part can be used as a N-terminal affinity tag for a target protein that has to be fused downstream. Together with <partinfo>BBa_K300003</partinfo> enables the construction of composite tags.

Because this part is a head domain, the Prefix is compatible with RFC10 and the Suffix is compatible with RFC23.

Construction

It is identical to <partinfo>BBa_K208001</partinfo>, but it lacks the stop codon in order to support protein fusions.

It has been designed as a head domain:

The Prefix sequence is 5'-GAATTCGCGGCCGCTTCTAG-3' (RFC10 Prefix)

The Suffix sequence is 5'-ACTAGTAGCGGCCGCTGCAG-3' (RFC23 Suffix)

For these reasons, a tail domain or an internal domain (compatible with RFC23) can be easily assembled downstream to create protein fusions.

To obtain this part, BioBrick <partinfo>BBa_K208001</partinfo> (provided by iGEM HQ in pSB3K3 in RFC23 standard) was PCR-amplified/mutagenized with primers:

phaP10F 5'-GCTTCTAGATGATCCTCACCCCGGAACA-3'

phaPSR: 5'-GCTACTAGTGGCAGCCGTCGTCTTCTTTG-3'

in order to delete the stop codon.

The PCR product was ran on a 1% agarose gel, gel-extracted, digested with XbaI-SpeI and ligated with <partinfo>pSB1AK3</partinfo> (previously cut with XbaI-SpeI and dephosphorylated). Positive clones were selected through digestion screening/sequencing.


This part was used to construct the following synthetic composite affinity tags:

  • <partinfo>BBa_K300093</partinfo>
  • <partinfo>BBa_K300094</partinfo>
  • <partinfo>BBa_K300095</partinfo>
  • <partinfo>BBa_K300084</partinfo>
  • <partinfo>BBa_K300097</partinfo>

or alone as a head domain; in this case it has been tested through <partinfo>BBa_K300086</partinfo> measurement system.

Methods

Inoculum (into 5 ml LB+Amp) from glycerol stock of:

  • <partinfo>BBa_K300086</partinfo>,
  • <partinfo>BBa_K173000</partinfo> (positive control),
  • <partinfo>BBa_B0031</partinfo> (negative control).

ON cultures' growth at 37°C, 220 rpm.

The following day, cultures were diluted 1:100 and let grown again for about five hours at 37°C, 220 rpm.

The optical density (O.D.) of each cell culture was than measured with TECAN Infinte F200. Samples were diluted in order to obtain the same O.D. equal to 0,02.

Then we performed a 21-hours' experiment with measurements of absorbance and green fluorescence every five minutes using TECAN Infinite F200; cultures were shaken for 15 seconds every five minutes. Each value shown below is the mean of three measurements, from GFP data that of a non-fluorescent culture (negative control) was subtracted.

Results

Raw growth curve
Raw GFP curve
Mean (dGFP/dt)/O.D. over the exponential phase (under the hypothesis that GFP half-life in fusion contructs is similar to the original one - <partinfo>BBa_E0040</partinfo>)
CultureDoubling time [min.] ± std error
<partinfo>BBa_K173000</partinfo>76.3336 ± 1.4362
<partinfo>BBa_K300086</partinfo>73.6685 ± 1.6245
<partinfo>BBa_B0031</partinfo>70.8421 ± 2.2181

Discussion

All cell cultures showed a similar growth curve; doubling time was computed as described here in order to have informations about the burden due to the synthesis of such fusion proteins. It's possible to see that all doubling time are very similar; it's possible to assert that the expression of these BioBrick parts doesn't cause abnormal stress to cells.

From GFP curve it's possible to appreciate that in <partinfo>BBa_K300086</partinfo> GFP accumulation it's significantly different from that of negative control <partinfo>BBa_B0031</partinfo>. This result shows that the green fluorescent protein assembled downstream of the genetic circuit is correctly folded.

The mean protein synthesis rate was also computed over the growth exponential phase, showing an appreciable GFP production rate that is about a half of the positive control.

<partinfo>BBa_K300003</partinfo> - Phasin (PhaP) - internal domain

This part without stop codon and with Prefix and Suffix compatible with RFC23 (Silver Standard) was built in order to fully support protein fusions as an internal domain. Together with <partinfo>BBa_K300002</partinfo>, enables the construction of synthetic affinity tags containing phasins in tandem, possibly spaced by peptide linkers, as described in [Banki MR et al., 2005].

Construction

It is identical to <partinfo>BBa_K208001</partinfo>, but it lacks the stop codon in order to support protein fusions.

It has been designed as an internal domain:

The Prefix sequence is 5'-GAATTCGCGGCCGCTTCTAG-3' (RFC23 Prefix)

The Suffix sequence is 5'-ACTAGTAGCGGCCGCTGCAG-3' (RFC23 Suffix)

For these reasons, a tail domain or an internal domain (compatible with RFC23) can be easily assembled downstream this BiobBrick to create protein fusions.

To obtain this part, BioBrick <partinfo>BBa_K208001</partinfo> (provided by iGEM HQ in pSB3K3 in RFC23 standard) was PCR-amplified/mutagenized with primers:

phaPSF: 5'-GCTTCTAGAATGATCCTCACCCCGGAACA-3'

phaPSR: 5'-GCTACTAGTGGCAGCCGTCGTCTTCTTTG-3'

in order to delete the stop codon.

The PCR product was ran on a 1% agarose gel, gel-extracted, digested with XbaI-SpeI and ligated with <partinfo>pSB1A3</partinfo> (previously cut with XbaI-SpeI and dephosphorylated). Positive clones were selected through digestion screening/sequencing.


This part was used as an internal domain to construct the following synthetic composite affinity tags:

  • <partinfo>BBa_K300093</partinfo>
  • <partinfo>BBa_K300094</partinfo>
  • <partinfo>BBa_K300084</partinfo>
  • <partinfo>BBa_K300097</partinfo>