Team:Heidelberg/Indigoidine

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                        <h1><span style="font-size:170%;color:#0B2161;">Indigoidine.</span><span class="text-muted" style="font-family:Arial, sans-serif; font-size:100%"> Proving Modularity of NRPS by Shuffling Domains.</span></h1>
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                                  <h1>Week 5</h1>
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At the beginning of our wetlab phase, we wanted to transform ''E. coli'' cells with plasmids containing an [[IndPD#ind_synthetase|indigoidine synthetase]] and a [[IndPD#PPTase|4'-Phosphopanthetheinyl-transferase]] (PPTase) to see whether we can observe blue colonies on our plates as this has been reported by groups working with indigoidine synthetases (<bib id="Takahashi2007"/><bib id="Brachmann2012"/>). <br/>
We focused on the work of Marius Müller et. al. in 2012 (<bib id="Muller2012"/>). The group used the [[Gene#bpsA|bpsA]] indigoidine synthetase (''blue pigment synthetase A'') from ''S. lavendulae''  ATCC11924 (<bib id="Takahashi2007"/>) and the PPTase [[Gene#svp|svp]] from ''S. verticillus'' ATCC15003 (<bib id="Sanchez2001"/>) to establish both a fluorescence and a chromophore based reporter assay for mammalian cells by expression of bpsA and svp which results in production of a blue pigment/ fluorophore. The group kindly supported us by sending two of their constructs, namely the pET derived expression vectors [[Plasmids#pMM64|pMM64]] carrying the bpsA indigoidine synthetase with an ampicillin resistance gene and [[Plasmids#pMM65|pMM65]] carrying svp and a kanamycin resistance gene. Both bpsA and svp rom the Fussenegger lab are codon-optimized versions for expression in eukaryotic cell lines. <br/>
We transformed competent [[Strain#TOP10|''E. coli'' TOP10]] with each plasmid to prepare plasmid DNA and perform a cotransformation of an [[Strain#Rosetta|''E. coli'' Rosetta]] strain with both plasmids. Transformed cells which carry both plasmids should produce the blue pigment indigoidine.
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Unfortunately, there were no blue colonies after the co-transformation. We repeated the experiment under various growth conditions; i.e. we used different incubation temperatures, light conditions, shaking and addition of ascorbic acid, which was reported to stabilize indigoidine in liquid cultures (<bib id="Muller2012"/>).
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In order to transfer the gold precipitating NRPS from <i>D. acidovorans</i> to <i>E.coli</i>, the necessary modules will be amplified from the D. acidovorans genome and assembled as plasmids. Due to its large size of 18 Kb, the module DelH will be expressed on a separate plasmid. A strategy was developed, primers designed accordingly and necessary BioBricks obtained from the distribution. The <i>D. acidovorans</i> was obtained from the DSMZ and cultured in Acidovorax complex medium. 
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In order to clone the Delftibactin cluster from D. Acidovorans we decided to use Gibson cloning. Accordingly Gibson Primers were designed to amplify our target backbone pSB4K5 with an overlap to DelA. Furthermore the Gibson Primer designed to join DelOP with DelAF will introduce the ribosome binding site BBa_BNILS. Accordingly the Gibson Primer designed to join DelL with DelOP will introduce the ribosome binding site BBa_BAGAINNILSYOUNOOB.
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                                  <p>At the beginning of the week, we could verify that the Gibson Assembly for Tripeptide I was indeed positive, however, the other Gibson Assemblies did not work properly. Instead of picking new colonies, we decided to optimize the Gibson recipe instead, as backbone religations were the most common problem. With these improved protocols, we used Gibson Assembly for the Dipeptide, Tripeptide II and Tetrapeptide I, later that week, Tetrapeptide II followed. After the Transformation to DH10β cells and screening by restriction digest we could send samples for the Dipeptide and Tetrapeptide I to sequencing and obtained a positive alignment. Hence we transformed BAP I cells with the positive constructs. The same was...

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                                  <p>At the beginning of the week, we could verify that the Gibson Assembly for Tripeptide I was indeed positive, however, the other Gibson Assemblies did not work properly. Instead of picking new colonies, we decided to optimize the Gibson recipe instead, as backbone religations were the most common problem. With these improved protocols, we used Gibson Assembly for the Dipeptide, Tripeptide II and Tetrapeptide I, later that week, Tetrapeptide II followed. After the Transformation to DH10β cells and screening by restriction digest we could send samples for the Dipeptide and Tetrapeptide I to sequencing and obtained a positive alignment. Hence we transformed BAP I cells with the positive constructs. The same was...

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                                  <h1>Week 14</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">At the beginning of the week, we could verify that the Gibson Assembly for Tripeptide I was indeed positive, however, the other Gibson Assemblies did not work properly. Instead of picking new colonies, we decided to optimize the Gibson recipe instead, as backbone religations were the most common problem. With these improved protocols, we used Gibson Assembly for the Dipeptide, Tripeptide II and Tetrapeptide I, later that week, Tetrapeptide II followed.</p>
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                                  <h1>Week 15</h1>
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                                  <h1>Week 16</h1>
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                                  <h1>Week 18</h1>
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                                  <h1>Week 20</h1>
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                                  <h1>Week 21</h1>
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                <h2>Methods:</h2>
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