Difference between revisions of "Part:BBa K1329005"

(Created page with "__NOTOC__ <partinfo>BBa_K1329005 short</partinfo> <!-- Add more about the biology of this part here ===Usage and Biology=== <!-- --> <span class='h3bb'>Sequence and Features...")
 
 
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<partinfo>BBa_K1329005 short</partinfo>
 
<partinfo>BBa_K1329005 short</partinfo>
  
 +
<html><h2>Idea</h2></html>
  
 +
Our approach was to realization the advantages of the nonribosomal peptide
 +
synthesis (NRPS) with the ribosomal pathway, i.e. the enormous repertoire of amino acids
 +
combined with the ability of the ribosome to synthesize huge proteins. To reach that aim,
 +
we planned the creation of a fusion protein that has the capability to activate amino acids derived
 +
from NRPSs´ A-domain PheA and tRNA binding capabilities derived from a part of multi aaRSs
 +
complexes Arc1p-C.
 +
 +
 +
<html><h2>Cloning procedure</h2></html>
 +
 +
The PheA domain was amplified from the PheA-Arc1p-C-2x-pET28a construct and inserted into the
 +
linearized pET28a (XhoI, NdeI) cloning vector by Gibson assembly.  To amplify the resulting
 +
plasmid ''Escherichia coli'' Top10 cells were transformed with it.
 +
 +
 +
<html><h2>Test expression of PheA</h2></html>
 +
 +
After cloning procedures were successfully completed, a test expression of PheA was performed.
 +
Therefore ''E. coli'' BL21 (DE3) was transformed with the PheA containing plasmid. For the expression test,
 +
a 60 mL culture was grown to an OD of 0.5 and induced with 100 µM IPTG. Pre-induction (PI),
 +
induction (I) and two elution (E1, E2) fractions from the Ni-NTA were taken and prepared for
 +
SDS-PAGE analysis.
 +
 +
<html><img src="https://static.igem.org/mediawiki/2014/f/f6/BBa_K1329005_1.png" width="50%;" /></html>
 +
 +
Gel analysis reveals that the transformed ''E. coli'' BL21 (DE3) strain produces PheA on a
 +
small scale. Since the protein band appears at the expected size of 65 kDa an
 +
overexpression was conducted anyway.
 +
 +
<html><h2>Production of PheA</h2></html>
 +
 +
Since the expression test was successful, protein expression was scaled up. For that purpose,
 +
an expression culture was inoculated and induced with 100 µM IPTG until an OD of 0.5.
 +
 +
 +
<html><h2>Ni-NTA with anion exchanger and dialysis of PheA</h2></html>
 +
 +
Cells were harvested and the pellet was resuspended in buffer A before lysing the cells using
 +
a french press. After centrifugation the cleared supernatant (Load) was loaded on a column
 +
with Ni-NTA agarose by Qiagen. Gel analysis reveal that a band of the expected size is present
 +
in the elution fraction of the Ni-NTA. The eluted protein was concentrated and further purified
 +
using an anion exchanger. Possible fractions were analysed by SDS-PAGE.
 +
 +
<html><img src="https://static.igem.org/mediawiki/2014/d/da/BBa_K1329005_2.jpg" width="70%;" /></html>
 +
 +
Gel analysis reveal that a band of the expected size is present in fraction 4 and 5.
 +
The eluted protein was concentrated and further purified by dialysis. Fractions containing PheA were
 +
concentrated and stored at -80 °C until further use.
 +
 +
 +
<html><h2>Measurement of aminoacylation levels</h2></html>
 +
 +
tRNA, amino acid and the fusion protein were incubated and the reaction started by the addition
 +
of ATP. The reaction was stopped by the addition of sodium acetate, tRNA was precipitated with
 +
ethanol and purified by size exclusion chromatography. Half of the sample was treated with base,
 +
reacidified and analyzed by LCMS.
 +
 +
<html><img src="https://static.igem.org/mediawiki/2014/a/a9/BBa_K1329004_2.png" width="100%;" /></html>
 +
 +
Measurements showed that all fusion constructs were able to load L- as well as D-phenylalanine
 +
onto tRNAPhe (Figure 2 a). The varying linker length showed a clear influence on the yield levels
 +
with the 2x-GSSG linker showing the highest catalytic activity yielding 11% loaded tRNA after
 +
30 min while the 8x-construct reached only a maximum of 3% loaded tRNA as well as the linker-less
 +
version. The remaining constructs showed intermediate results. Furthermore the linking of the
 +
two domains leading to the increase in reactant concentration and the correct spatial arrangement
 +
is indeed important for the catalytic effect to occur since a mixture of the unlinked domains
 +
showed only background levels of aminoacylation (Figure 2 b). Further negative controls included
 +
testing the reaction without enzyme or ATP. As a positive control to evaluate the method
 +
phenylalanyl-tRNA synthetase (PheRS) was used. A time-dependent measurement of the aminoacylation
 +
level showed that a maximum is reached after 30 min (Figure 2 c). To test if other tRNAs except
 +
for the tRNAPhe can be aminoacylated using our fusion construct we carried out aminoacylation
 +
assays with five additional ''E. coli'' tRNAs (Figure 2 d). The measurements suggest in
 +
agreement with previous studies that all tRNAs were loaded similarly well.
  
  

Latest revision as of 17:09, 17 October 2014

NRPS: Amino acid activation domain

Idea

Our approach was to realization the advantages of the nonribosomal peptide synthesis (NRPS) with the ribosomal pathway, i.e. the enormous repertoire of amino acids combined with the ability of the ribosome to synthesize huge proteins. To reach that aim, we planned the creation of a fusion protein that has the capability to activate amino acids derived from NRPSs´ A-domain PheA and tRNA binding capabilities derived from a part of multi aaRSs complexes Arc1p-C.


Cloning procedure

The PheA domain was amplified from the PheA-Arc1p-C-2x-pET28a construct and inserted into the linearized pET28a (XhoI, NdeI) cloning vector by Gibson assembly. To amplify the resulting plasmid Escherichia coli Top10 cells were transformed with it.


Test expression of PheA

After cloning procedures were successfully completed, a test expression of PheA was performed. Therefore E. coli BL21 (DE3) was transformed with the PheA containing plasmid. For the expression test, a 60 mL culture was grown to an OD of 0.5 and induced with 100 µM IPTG. Pre-induction (PI), induction (I) and two elution (E1, E2) fractions from the Ni-NTA were taken and prepared for SDS-PAGE analysis.

Gel analysis reveals that the transformed E. coli BL21 (DE3) strain produces PheA on a small scale. Since the protein band appears at the expected size of 65 kDa an overexpression was conducted anyway.

Production of PheA

Since the expression test was successful, protein expression was scaled up. For that purpose, an expression culture was inoculated and induced with 100 µM IPTG until an OD of 0.5.


Ni-NTA with anion exchanger and dialysis of PheA

Cells were harvested and the pellet was resuspended in buffer A before lysing the cells using a french press. After centrifugation the cleared supernatant (Load) was loaded on a column with Ni-NTA agarose by Qiagen. Gel analysis reveal that a band of the expected size is present in the elution fraction of the Ni-NTA. The eluted protein was concentrated and further purified using an anion exchanger. Possible fractions were analysed by SDS-PAGE.

Gel analysis reveal that a band of the expected size is present in fraction 4 and 5. The eluted protein was concentrated and further purified by dialysis. Fractions containing PheA were concentrated and stored at -80 °C until further use.


Measurement of aminoacylation levels

tRNA, amino acid and the fusion protein were incubated and the reaction started by the addition of ATP. The reaction was stopped by the addition of sodium acetate, tRNA was precipitated with ethanol and purified by size exclusion chromatography. Half of the sample was treated with base, reacidified and analyzed by LCMS.

Measurements showed that all fusion constructs were able to load L- as well as D-phenylalanine onto tRNAPhe (Figure 2 a). The varying linker length showed a clear influence on the yield levels with the 2x-GSSG linker showing the highest catalytic activity yielding 11% loaded tRNA after 30 min while the 8x-construct reached only a maximum of 3% loaded tRNA as well as the linker-less version. The remaining constructs showed intermediate results. Furthermore the linking of the two domains leading to the increase in reactant concentration and the correct spatial arrangement is indeed important for the catalytic effect to occur since a mixture of the unlinked domains showed only background levels of aminoacylation (Figure 2 b). Further negative controls included testing the reaction without enzyme or ATP. As a positive control to evaluate the method phenylalanyl-tRNA synthetase (PheRS) was used. A time-dependent measurement of the aminoacylation level showed that a maximum is reached after 30 min (Figure 2 c). To test if other tRNAs except for the tRNAPhe can be aminoacylated using our fusion construct we carried out aminoacylation assays with five additional E. coli tRNAs (Figure 2 d). The measurements suggest in agreement with previous studies that all tRNAs were loaded similarly well.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 577
    Illegal AgeI site found at 736
    Illegal AgeI site found at 1228
  • 1000
    COMPATIBLE WITH RFC[1000]