<p>Many reactions rely on optimal conditions like pH and co-factors. Thus, this subproject aims at optimizingthe optimization of those circumstances through the integration of new membrane proteins, which alter specific properties of the peroxisomal lumen. Such an approach promises to be very useful for metabolic engineering projects as it can help to adjust the pH, provide cofactors to enzymes, or increase or/decrease the concentrations of metabolites inside to peroxisome. In nature, two distinct mechanisms exist, which are used for the integration of membrane proteins into the peroxisomal membrane – a Pex19-<a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> dependent and an ER-dependent one [1,2].</p>
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<h3>Introduction</h3>
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<p>Many reactions rely on optimal conditions like pH and co-factors. Thus, this subproject aims at the optimization of those circumstances through the integration of new membrane proteins, which alter specific properties of the peroxisomal lumen. Such an approach promises to be very useful for metabolic engineering projects as it can help to adjust the pH, provide cofactors to enzymes or increase/decrease the concentrations of metabolites inside to peroxisome. In nature two distinct mechanisms exist, which are used for the integration of membrane proteins into the peroxisomal membrane – a Pex19-<a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> dependent and an ER-dependent one [1,2].</p>
<p>They rely on a so called mPTS sequence, that is used to mark the proteins for transport to and integration in the peroxisomal membrane [3]. We will try to utilize the capability of both mechanisms to incorporate new proteins into the peroxisomal membrane.
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<p>They rely on a so called mPTS sequence, whichthat is used to mark the proteins for transport to and integration in the peroxisomal membrane [3]. We will try to utilize the capability of both mechanisms to incorporate new proteins into the peroxisomal membrane.
However, to test whether yeast can integrate and use the foreign proteins in its peroxisomal membrane, we will design three different constructs, which will hopefully give us insights into the mechanisms and its efficiency to incorporate new proteins into the peroxisomal membrane.</p>
However, to test whether yeast can integrate and use the foreign proteins in its peroxisomal membrane, we will design three different constructs, which will hopefully give us insights into the mechanisms and its efficiency to incorporate new proteins into the peroxisomal membrane.</p>
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<p>The exact mechanisms of mPTS binding, <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>/Pex19 disassembly, mPTS-PMP binding, and release from the <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>/Pex19 mediated mPTS-PMP docking to the full integration into the membrane are yet unknown [4]. However, general principles of the integration of a new peroxisomal membrane protein (PMP) through Pex19 and <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> are studied. Most PMPs feature a membrane targeting signal (mPTS), multiple binding sites for Pex19p, and at least one transmembrane domain (TMD). The mPTS can appear in two different ways, either located in the middle of the primary amino acid sequence, which is the rather complex form, or it can be found at the N-terminal part of the PMP as in Pex25.Pex19p is a cytosolic protein, which recognizes the mPTS of the PMP to be incorporated. In the first step Pex19p attaches to the PMP by binding to the mPTS and acts like a chaperone, guiding it to the peroxisome. Next, Pex19p binds N-terminally to the peroxisomal membrane protein <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>p, which is attached to the peroxisomal membrane through an N-terminal membrane anchor. This will bring the PMP in close proximity to the peroxisomal membrane. Last, Pex19p initiates the membrane integration of the PMP. [3]</p>
<p>The exact mechanisms of mPTS binding, <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>/Pex19 disassembly, mPTS-PMP binding, and release from the <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>/Pex19 mediated mPTS-PMP docking to the full integration into the membrane are yet unknown [4]. However, general principles of the integration of a new peroxisomal membrane protein (PMP) through Pex19 and <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> are studied. Most PMPs feature a membrane targeting signal (mPTS), multiple binding sites for Pex19p, and at least one transmembrane domain (TMD). The mPTS can appear in two different ways, either located in the middle of the primary amino acid sequence, which is the rather complex form, or it can be found at the N-terminal part of the PMP as in Pex25.Pex19p is a cytosolic protein, which recognizes the mPTS of the PMP to be incorporated. In the first step Pex19p attaches to the PMP by binding to the mPTS and acts like a chaperone, guiding it to the peroxisome. Next, Pex19p binds N-terminally to the peroxisomal membrane protein <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>p, which is attached to the peroxisomal membrane through an N-terminal membrane anchor. This will bring the PMP in close proximity to the peroxisomal membrane. Last, Pex19p initiates the membrane integration of the PMP. [3]</p>
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<h3>Experimental Work/Design</h3>
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<p>In order to test our hypothesis we fused the last 59 amino acids of the C-terminus of human <a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a> (AA 246-305) to a red fluorescent protein, called mRuby2, to further elucidate the <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>/Pex19-dependent import. mRuby is generally used as a marker in combination with a fluorescent microscope to visualize the localization of the fusion protein. The C-terminus of <a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a> contains a helical signal-anchor, which serves as both, a mPTS and transmembrane domain. We designed our construct with mRuby2 fused to the N-terminal side of the <a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a>-C-Terminus, this way the mRuby should face the cytosolic side of the peroxisomal membrane.
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Quite similar to our mRuby-<a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a> approach, we designed a construct for the ER-dependent import. Therefore, we fused the mRuby2 fluorescent protein to the N-terminus of <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> (AA 1-39). This construct should be N-terminally anchored in the peroxisomal membrane, with mRuby2 again facing the cellular lumen.</p>
<p>Our main goal is to introduce a rather complex membrane protein to the peroxisome that can alter specific traits. For that we fused the <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> N-terminus (AA 1-39) to a Halobacterium salinarum <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a> protein (AA 16-262), replacing the first 16 amino acids ( <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>-BacR). The original archaeal <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a> acts as a proton pump by capturing light energy to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy.
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Our assumption is that the first transmembrane segment determines the orientation of the following protein and that therefore due to the N-terminal anchoring signal the <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a> will be inserted in reverse orientation, pumping the protons into the peroxisome. This way the pH of the peroxisomal lumen could actively be controlled and adjusted.</p>
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<p>Finally, our project involved combining the work of other subteams to verify the localization of our constructs in the peroxisome and analyze the effects they have on the import. Therefore, we are using the superfolder-gfp protein, another fluorescent marker, which is in our case fused to the peroxisomal import sequence pts1, and a version of Pex11 that is fused to the fluorescent marker Venus. Both markers emit light in the green light spectrum, were as mRuby2 emits light in the red part of the spectrum, giving us a strong contrast and an easy way of differentiating between the two under the fluorescent microscope. </p>
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<p>To physically create our constructs, we researched the DNA sequences of <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a>, <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> and <a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a> via UniProt and pre-designed our fusion constructs with the software tool „Geneious“. We ordered the synthesis of three separate parts ( <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>, <a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a> and <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>-BacR) from IDT. To ease out the process of assembling our plasmids, we used the „Dueber Toolbox“, containing various parts such as promoters and terminators, to tailor the plasmids specific to your needs. Finally, to combine all the selected parts, we used the „Golden Gate” assembly method.</p>
<p>In order to have full control over the amount of expressed protein, we designed our plasmids with the inducible galactose promoter "pGAL1". Not only were we able to see that our fluorescent marked protein anchors from <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> and <a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a> would localize at specific points inside our cells but also to show that it was in deed the peroxisome they were accumulating at. For that we coexpressed each of our fluorescent membrane anchors together with a GFP protein that was fused to a PTS1 sequence and thus imported into the peroxisome. Under the fluorescent microscope the colocalization of both, the green fluorescing GFP and the red fluorescing mRuby is clearly visible, showing that our anchors integrated into the peroxisomal membrane.</p>
Finally we used the same approach to send a mRuby-tagged <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a> to our compartment. In coexpressing it with the same GFP as in the previous steps, we could show that the <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a> as well as <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a> and <a href="http://www.uniprot.org/uniprot/Q7Z412">PEX26</a> were successfully integrated into the membrane of our compartment. Since <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a> is a rather complex protein, we're very optimistic about integrating other proteins into the membrane using the same approach.
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</p>
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<h4>Outlook</h4>
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<p>The ultimate goal of this subproject is, to have a complete set of ready to transform membrane proteins that could be combined with any promoter to create the optimal conditions for each desired situation. Besides <a href="http://www.uniprot.org/uniprot/P02945">Bacteriorhodopsin</a>, we also started to work with sugar translocators, since yeast does not posses the ability to import it into or export it from the peroxisome. This would open up a whole new chapter of peroxisomal usage, from example as a temporary storage compartment.
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</p>
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<h4>Sources/References</h4>
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<p>[1] I.A. Sparkes, C. Hawes, A. Baker, AtPEX2 and AtPEX10 are targeted to peroxisomes independently of known endoplasmic reticulum trafficking routes, Plant Physiol. 139 (2005) 690–700.</p>
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<p>[2] H.F. Tabak, J.L. Murk, I. Braakman, H.J. Geuze, Peroxisomes start their life in the endoplasmic reticulum, Traffic 4 (2003) 512–518. </p>
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<p>[3] 2010, Schueller - The peroxisomal receptor Pex19p forms a helical mPTS recognition domain</p>
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<p>[4] 2016, Liu - Assembly of Peroxisomal Membrane Proteins via the Direct Pex19p- <a href="http://www.uniprot.org/uniprot/P28795">Pex3</a>p Pathway</p>
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<p>[5]2001, Jones - Multiple Distinct Targeting Signals in Integral Peroxisomal Membrane Proteins</p>
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<p>[6]2004, Jones - PEX19 is a predominantly cytosolic chaperone and import receptor for class 1 peroxisomal membrane proteins</p>
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<p>[7]2004, Rottensteiner - Peroxisomal Membrane Proteins Contain Common Pex19p-binding Sites that Are an Integral Part of Their Targeting Signals</p>
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<p>[8]2016, Mayerhofer - Targeting and insertion of peroxisomal membrane proteins ER trafficking versus direct delivery to peroxisomes</p>
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<p>[9]2016, Hua - Multiple paths to peroxisomes Mechanism of peroxisome maintenance in mammals</p>
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<p>[10]2016, Giannopoulou - Towards the molecular mechanism of the integration of peroxisomal membrane proteins</p>
<figcaption> Yeast viability after 24 h in the presence of (+)-valencene, beta-Nootkatol or nootkatone in different concentrations </figcaption>
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<figcaption> Yeast viability after 24 h in the presence of (+)-valencene, beta-Nootkatol or nootkatone in different concentrations
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</figcaption>
</figure>
</figure>
</div>
</div>
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</div>
</div>
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<button class="accordion">
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<h2 id="designrules">Design Rules For Genome Engineering For Customizing Peroxisome Properties</h2>
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<p>In order to reach the ultimate goal of creating a fully controllable artificial compartment, genome engineering can be utilized for customizing the compartment properties, such as membrane permeability, size/number, decoupling of peroxisomes from cytoskeleton, the peroxisomal proteome or metabolome. In our project we used the Crispr Cas9 system for knocking out several genes (<i>PEX9, PEX31&PEX32, INP1, POT1</i>) at the same time for engineering the previously mentioned properties. Furthermore, we designed a yeast strain, with a completely replaced protein-import machinery for controlling the entire peroxisomal lumen.</p>
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<p>For the future one could think of much more radical strategies for peroxisomal engineering with a final goal of a “minimal peroxisome” by redirecting metabolic pathways by changing the protein-localization-signal in the yeast genome. Additionally, endogenous metabolic pathways could be redirected to our novel artificial compartment for creating an artificial compartment with a customized metabolism specifically tailored for your application.</p>
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</button>
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<div class="panel">
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<h3>Introduction</h3>
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<p>In order to get fully controllable artificial compartment, the first step was to design a completely orthogonal import system and the next step was the knockout of endogenous import systems. However, a few proteins are neither imported by the PEX5 nor the PEX7 import machinery. Therefore, specific genome engineering designs, such as knockouts, deleting or redirecting the protein localization could be utilized for the ultimate goal of creating a synthetic organelle.</p>
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<p>Additionally, knockouts or genome integrations enable customizing the peroxisomal properties, such as membrane permeability, size/number, decoupling of peroxisomes from cytoskeleton and the peroxisomal metabolism.</p>
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<p>All these strategies allow a rational design of an artificial compartmen<t, which is fully engineerable regarding thein the proteome, metabolome and the entire peroxisomal environment.</p>
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<h3>Design of yeast multi -knockout strains</h3>
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<h4>The Crispr Cas9 System</h4>
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<p>The demands on yeast engineering have significantly increased with the design of more complex systems or extensive metabolic pathways. Genetic techniques that have historically relied on marker recycling are not able to keep up with the ambitions of synthetic biologists. In recent years the Crispr Cas9 system has been used for several strain-engineering purposes, including:</p>
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<ul>
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<li>Markerless integration of multiple genetic cassettes into selected genomic loci</li>
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<li>Multiplexed and iterative gene knockouts without the need to recycle a marker</li>
<p>We utilized the Cas9 system as a tool for peroxisomal engineering and have adopted the existing toolbox from <abbr title="Lee, Michael E.; DeLoache, William C.; Cervantes, Bernardo; Dueber, John E. (2015): A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. In: ACS synthetic biology 4 (9), S. 975–986. DOI: 10.1021/sb500366v.">Lee et al. 2015</abbr> and the complete cloning system which also provides the possibilities for genome integration and gene editing by Cas9. Therefore, two oligonucleotides have to be designed for targeting the Cas protein to the gene of interest.</p>
<figcaption>Figure 1: Plasmid construction for the gRNA expression plasmid<br>Two oligos, containing the targeting sequence of the gRNA, have to be annealed and can then be integrated in the gRNA entry Vector by a Golden Gate reaction. Adapted from (<abbr title="Lee, Michael E.; DeLoache, William C.; Cervantes, Bernardo; Dueber, John E. (2015): A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. In: ACS synthetic biology 4 (9), S. 975–986. DOI: 10.1021/sb500366v.">Lee et al. 2015</abbr>)</figcaption>
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</figure>
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<p>Several gRNA vectors can subsequently assembled together with a Cas9 expression cassette into one vector and then be transformed into yeast. The expression of Cas9 together with gene specific gRNA´s leads to double strand break followed by non-homologous end joining repair or homologous recombination, in case of added repair DNA (figure 3).</p>
<figcaption>Figure 2: Plasmid construction for the expression plasmid containing Cas9 and gRNA´s<br>Vector for Cas9 and gRNA expression, assembled by a Golden Gate reaction, containing a URA marker, Cen6 yeast origin and a kanamycin resistance. Adapted from (<abbr title="Lee, Michael E.; DeLoache, William C.; Cervantes, Bernardo; Dueber, John E. (2015): A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. In: ACS synthetic biology 4 (9), S. 975–986. DOI: 10.1021/sb500366v.">Lee et al. 2015</abbr>)</figcaption>
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</figure>
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<p>The combination of the Cas9 system with DNA repair sequences enable not only knockouts of peroxisomal proteins, but also allows redirecting protein localization by changing protein targeting signals or integration of linear DNA into yeast chromosomes. Genome engineering facilitates yeast strain development for customized peroxisomes.</p>
<figcaption>Figure 3: Design of repair DNA sequences for homologous recombination after inducing double strand break by Cas9<br>
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Repair DNA sequences can be used to increase the efficiency for cas9 guided knocking out of specific genes, but would also allow genomic integration of targeting signals or complete genes. Adapted from (<abbr title="Lee, Michael E.; DeLoache, William C.; Cervantes, Bernardo; Dueber, John E. (2015): A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. In: ACS synthetic biology 4 (9), S. 975–986. DOI: 10.1021/sb500366v.">Lee et al. 2015</abbr>)</figcaption>
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</figure>
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<h3>The peroxisomal proteome of yeast (saccharomyces cerevisiae)</h3>
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<p>The peroxisomal proteome is studied extensively for saccharomyces cerevisiae and contains exactly 67 proteins (<abbr title="Kohlwein, Sepp D.; Veenhuis, Marten; van der Klei, Ida J. (2013): Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of fat--store 'em up or burn 'em down. In: Genetics 193 (1), S. 1–50. DOI: 10.1534/genetics.112.143362.">Kohlwein et al. 2013</abbr>). The function is characterized for the most of those proteins and it is known, that yeast peroxisomes are expendable under optimal growth conditions. Nevertheless, some knockouts are lethal under oleate or stress conditions.</p>
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<table>
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<thead>
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<tr>
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<th>Gene</th>
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<th>Required for growth on oleate</th>
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<th>Expression induced by oleate</th>
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<th>Enzyme/activity</th>
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<th>Molecular mass (kDa)</th>
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<th>Isoelectric point</th>
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<th>Molecules per cell </th>
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<th>Localization</th>
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<th>Function</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td colspan=”9”>ß-Oxidation enzymes</td>
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</tr>
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<tr>
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<td>PCS60 (FAT2)</td>
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<td>No</td>
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<td>Yes</td>
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<td>Medium chain fatty acyl-CoA synthetase</td>
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<td>60.5</td>
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<td>9.98</td>
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<td>8.770</td>
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<td>Peripheral peroxisomal membrane and matrix</td>
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<td>Activates fatty acids with a preference for medium chain lengths, C9-C13</td>
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</tr>
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<tr>
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<td>FAT1</td>
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<td>No</td>
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<td>-</td>
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<td> Very long chain fatty acyl-CoA synthetase and long chain fatty acid transporter</td>
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<td>77.1</td>
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<td>8.47</td>
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<td>16,900</td>
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<td>Lipid droplet, ER, peroxisome Three predicted TM</td>
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<td>Activates fatty acids with a preference for very long chain lengths, C20–C26</td>
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</tr>
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<tr>
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<td>POX1</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Acyl-CoA- oxidase</td>
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<td>84.0</td>
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<td>8.73</td>
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<td>ND</td>
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<td>Peroxisomal matrix</td>
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<td>Oxidation of acyl-CoA</td>
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</tr>
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<tr>
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<td>CTA1</td>
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<td>No</td>
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<td>Yes</td>
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<td>Catalase</td>
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<td>58.6</td>
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<td>7.46</td>
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<td>623</td>
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<td>Peroxisomal matrix</td>
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<td>Degrades hydrogen peroxide produced by Pox1</td>
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</tr>
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<tr>
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<td>FOX2 (POX2)</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Multifunctional enzyme; 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase</td>
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<td>98.7</td>
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<td>9.75</td>
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<td>ND</td>
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<td>Peroxisomal matrix</td>
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<td>-</td>
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</tr>
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<tr>
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<td>POT1 (FOX3, POX3)</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>3-Ketoacyl-CoA thiolase</td>
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<td>44.7</td>
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<td>7.56</td>
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<td>ND</td>
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<td>Peroxisomal matrix</td>
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<td>Cleaves 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA</td>
<td>Involved in retention of peroxisomes in mother cells</td>
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<td>47.3</td>
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<td>8.34</td>
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<td>639</td>
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<td>Peroxisomal membrane</td>
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<td>Recruited to the peroxisome by binding to Pex3</td>
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</tr>
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<tr>
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<td>INP2</td>
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<td>-</td>
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<td>-</td>
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<td>Myo2 receptor, involved in peroxisome inheritance</td>
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<td>81.5</td>
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<td>9.41</td>
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<td>736</td>
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<td>Peroxisomal membrane</td>
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<td>-</td>
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</tr>
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<tr>
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<td>RHO1</td>
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<td>-</td>
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<td>-</td>
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<td>GTP binding protein of the Rho subfamily of Ras like proteins, involved in actin assembly at the peroxisome</td>
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<td>23.2</td>
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<td>6.07</td>
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<td>ND</td>
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<td>-</td>
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<td>Involved in <em>de novo</em> peroxisome formation recruited to peroxisomes by Pex25</td>
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</tr>
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</tbody>
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</table>
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<h3>Knockout designs in our project</h3>
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<h4>Pex 9</h4>
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<p>Pex9 is a recently discovered import receptor for PTS1 proteins, which is induced by oleate
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and is an import receptor for both malate synthase isoenzymes Mls1p and Mls2p. In order to get a completely empty reaction room, a Pex9 knockout was designed to prevent unintended protein import.</p>
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<h4>Pex 31 & Pex 32</h4>
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<p>It has been shown that knockouts of Pex31 and Pex32 leads to an increased Peroxisomal size, but additionally the membrane permeability was affected (<abbr title="Zhou, Yongjin J.; Buijs, Nicolaas A.; Zhu, Zhiwei; Gómez, Diego Orol; Boonsombuti, Akarin; Siewers, Verena; Nielsen, Jens (2016): Harnessing Yeast Peroxisomes for Biosynthesis of Fatty-Acid-Derived Biofuels and Chemicals with Relieved Side-Pathway Competition. In: Journal of the American Chemical Society 138 (47), S. 15368–15377. DOI: 10.1021/jacs.6b07394.">Zhou et al. 2016</abbr>). This effect can be used as a tool for engineering membrane permeability by knocking out or overexpress both genes. A knockout would lead to an increased permeability and one could think of an opposite effect in case of overexpression, but this has not been shown yet.</p>
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<h4>INP1</h4>
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<p>The INP1 knockout was designed after the skype call of Prof Dueber, who recommended us, decoupling of peroxisomes from cytoskeleton in order to improve the secretion efficiency. INP1 is responsible for the tethering of peroxisome, which would inhibit the secretion of peroxisomes.</p>
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<h4>POT1</h4>
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<p>The only protein, which is imported by the PEX7 import machinery in saccharomyces is the 3-ketoacyl-CoA thiolase (POT1). A knockout of POT1 would enable utilizing the PEX7 import for proteins of interest, which cannot be tagged at the C-terminus with pts1, without having unintended import of other enzymes.
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<h3>Genomic integration of our novel Pex5 import receptor</h3>
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<p>After testing our new Pex5 import systems, which is completely orthogonal to the natural import, the next step would be to replace the endogenous system with our artificial import system. Therefore, an integration plasmid was designed with help of the previously described yeast toolbox, containing HO locus homologies and a hygromycin resistance (Figure 4). Afterwards the plasmid was transformed into the yeast strain which was created by our collaboration partner Aachen (double knockout strain PEX5 & PEX7).</p>
<figcaption>Figure 4: Design of integration plasmid for integrating our orthogonal Pex5 import receptor.<br>Therefore, an integration plasmid was designed with help of the previously described yeast toolbox, containing HO locus homologies and a hygromycin resistance</figcaption>
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</figure>
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<p>The resulting yeast strain allows full control over the peroxisomal matrix proteome, by replacing the whole protein import machinery, which is the first step for creating our artificial compartment.</p>
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<h3>Outlook</h3>
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<p>Besides the genome engineering approaches, which were performed in our project one could think of more radical strategies for peroxisomal engineering. A final goal could be a “minimal peroxisome”, which contains only the proteins that are required for the biogenesis of the peroxisome and import of proteins and metabolites. On the one hand peroxisomal pathways could be redirected to cytosol or other organelles and one the other hand endogenous metabolic pathways could be redirected to our novel artificial compartment by changing the protein localization signal in the yeast genome with help of the Cas9 system. All these strategies would allow tremendous improvements for metabolic engineering applications by creating an artificial compartment, which can be rational designed and customized for specific metabolic pathways.</p>
wognizes?? a single new designed peroxisomal import signal. The most promising modified PEX5s variants will be implemented in vivointo the actual peroxisome.
Real world application
As a proof of concept for our compartimentation strategy we intend to establish the Nootkatone pathway inside the peroxisome. Nootkatone is a natural compound found inside the peel of the grapefruit, which gives it its characteristic taste and smell. In addition, Nootkatone is a natural repellent for mosquitoes and ticks that is already being commercially used and industrially manufactured. Unfortunately, the production costs are extremely high, because it has to either be extracted from the peels of millions of grapefruits or synthesized inside of yeast. The difficulties problem lie in the toxicity ofis that the Nootkatone pathway towardsis toxic for yeast and the resulting low efficiency is rather low. Here our compartmentation comes into play: we plan to translocateimplement the whole pathway into the modified peroxisome to prove, that we have transformed the peroxisome into an independent compartment with all the features we required by us.
PTS1 Import
The vast majority of peroxisomal matrix proteins is imported by the PEX5 importer. PEX5 recognizes the C-terminal PTS1 peptide whose evolutionarily conserved sequence is (S/A/C)-(K/R/H)-(L/M) ( Gould et al., 1989 ). PEX5 is a 612 amino acid protein which contains seven tetratrico peptide repeats (TPR). The TPR is a 34 amino acid motif which forms a structure of alpha-helices separated by one turn. A whole TPR domain consists of three of those structures (Gatto Jr. et al 2000).
TPR domains are often involved in protein−protein interaction. and Aas it can be seen in the following figure, the TPR regions mediate the binding of the peroxisomal targeting signal.
TPR domain of the human PEX5, with a pentapeptide in its binding pocket (Gatto Jr. et al. , 2000)
The following figure depicts the import mechanism of PTS1 tagged proteins via PEX5.
Import mechanism (Erdmann et al., 2005)
Upon recognition of the PTS1 in the cytosol, PEX5 binds to its cargo (i). It docks to the peroxisomal membrane complex, consisting of PEX13, PEX14 and PEX17 (ii). This docking complex is connected to the RING-finger complex, consisting of PEX2, PEX10 and PEX12, via PEX8. This multi-protein complex is known as the importomer. PEX5 and PEX14 form a pore in the membrane, through which the cargo is translocated (iii). Due to competitive binding of PEX8's PTS1 motif, the receptor–cargo complex dissociates at the matrix site of the membrane (iv). The integral PTS1-receptor is either monoubiquitinated by the E2-enzyme PEX4 or polyubiquitinated by Ubc4 or Ubc5. The AAA peroxins PEX1 and PEX6, which are anchored to the peroxisomal membrane by PEX15, dislocate the ubiquitinated PEX5 from the membrane back to the cytosol (v). The polyubiquitinated PTS1-receptors are degraded by the proteasome, whereas the monoubiquitinated receptors are recycled for further rounds of import.
In this subproject we mutated the PEX5 receptor in a way that enables it to recognizes a new signal peptide which does not occur in nature. As PEX5 is responsible for the import of most proteins most of the import, we have complete control over its content once we knock out the wild type receptor and replace it with our newly mutated one.
Corresponding to the new receptor, one needs to design a peroxisomal targeting signal that provides favorable interactions with the residues of the amino acids within the TPR needs to be designed.
Our first approach for the mutation deals with the introduction of site-directed mutagenesis in the TPR of PEX5 followed by computational simulation of the binding affinity between our new designed PEX5 receptor and several peptide variants via Molecular Dynamics. In the model section we explain the molecular dynamics approach in more detail.
Our second approach relies on recently published literature. We designed a receptor similar to what Baker et al. did in the moss Physcomitrella patens in 2017. To understand how and where we set the mutations in the PEX5 receptor following this approach, please proceed with the design section.
PTS2 Import
The peroxisomal import depends on two pathways. A vast majority of the proteins normally found in the peroxisome are imported via the Pex5 importer. In S. cerevisiae only one protein, the 3-Oxoacyl-CoA thiolase Ralf Erdmann(1994), localized in the peroxisome, is instead imported by the receptor Pex7 and some coreceptors instead. Ralf Erdmann (2015).
The targeting signal for this pathway is localized near the N-terminus of each protein. Kunze and colleagues described the PTS2 consensus sequence as the following:
The peroxisomal targeting signal type two consists of nine amino acids. Residue one contains Arginine or Lysine, residue two Leucine, Valine or Isoleucine. The amino acids three toill seven are highly variable. Residue number eight consists of Histidine or Glutamine and the ninth is either Leucine or Alanine. Markus Kunze (2015)
The five amino acids in the center are not conserved and highly variable. In yeast, among other organisms, the protein Pex7 works as a soluble chaperone, which recognizes PTS2 and directs the protein to the import pore at the peroxisomal membrane Ralf Erdmann et al.(2015).
Towards the aim of implementing a valuable import device for our toolbox we created a library of different PTS2 versions showing variable import efficiencies. Subsequently, one can ensure customizabletailormade concentrations of different pathway parts in the peroxisome. MoreoverBesides, proteins which require an unmodified C-terminus can be imported via PTS2 since this sequence is located on the N-terminus of the protein (PTS1 import).
Kunze et al. performed a mutational analysis for the PTS2 containing human thiolase, specifically for the five variable residues in the core region. The wild type sequence of those residues was defined as glutamine, valine, valine, leucine and glycine. These amino acids were substituted by specific amino acids to be able to evaluate the effect of distinct types in the above stated positions within the sequence. The selected amino acids represent different groups to investigate the biochemical effects of different side chains or other factors: aspartate as a negatively charged, tryptophan as an aromatic, arginine as a basic, leucine as a bulky and lysine as a positively charged amino acid. The thiolase import was subsequently measured with immunofluorescence microscopy. The recognition and import of the PTS2 harboring protein of interest by Pex7 worked out with aspartate at position X1, but not on X2 or X3. Lysine on residue X3 lead to a strong decrease of import activity. Kunze et al. concluded that the import of a given protein relies highly on the amino acid groups in the core region of the PTS2 Markus Kunze (2015) .
Besides a biased approach, which relies on substitution of single residues in the amino acid sequence of the PTS2, in a second approach we aim to randomly change the sequence to characterize a huge library of different sequence compositions.
Introduction
Many reactions rely on optimal conditions like pH and co-factors. Thus, this subproject aims at optimizingthe optimization of those circumstances through the integration of new membrane proteins, which alter specific properties of the peroxisomal lumen. Such an approach promises to be very useful for metabolic engineering projects as it can help to adjust the pH, provide cofactors to enzymes, or increase or/decrease the concentrations of metabolites inside to peroxisome. In nature, two distinct mechanisms exist, which are used for the integration of membrane proteins into the peroxisomal membrane – a Pex19-Pex3 dependent and an ER-dependent one [1,2].
They rely on a so called mPTS sequence, whichthat is used to mark the proteins for transport to and integration in the peroxisomal membrane [3]. We will try to utilize the capability of both mechanisms to incorporate new proteins into the peroxisomal membrane.
However, to test whether yeast can integrate and use the foreign proteins in its peroxisomal membrane, we will design three different constructs, which will hopefully give us insights into the mechanisms and its efficiency to incorporate new proteins into the peroxisomal membrane.
As a proof of concept, we will incorporate three proteins through three different approaches into the peroxisomal membrane: (i) mRuby2-PEX26 as a proof for the Pex19-dependent mechanism, (ii) Pex3-mRuby2 itself to showcase the ER-dependent mechanism and (iii) Bacteriorhodopsin, a unidirectional proton pump, fused to the N-terminal anchor of Pex3.
Pex19-dependent Mechanism
The exact mechanisms of mPTS binding, Pex3/Pex19 disassembly, mPTS-PMP binding, and release from the Pex3/Pex19 mediated mPTS-PMP docking to the full integration into the membrane are yet unknown [4]. However, general principles of the integration of a new peroxisomal membrane protein (PMP) through Pex19 and Pex3 are studied. Most PMPs feature a membrane targeting signal (mPTS), multiple binding sites for Pex19p, and at least one transmembrane domain (TMD). The mPTS can appear in two different ways, either located in the middle of the primary amino acid sequence, which is the rather complex form, or it can be found at the N-terminal part of the PMP as in Pex25.Pex19p is a cytosolic protein, which recognizes the mPTS of the PMP to be incorporated. In the first step Pex19p attaches to the PMP by binding to the mPTS and acts like a chaperone, guiding it to the peroxisome. Next, Pex19p binds N-terminally to the peroxisomal membrane protein Pex3p, which is attached to the peroxisomal membrane through an N-terminal membrane anchor. This will bring the PMP in close proximity to the peroxisomal membrane. Last, Pex19p initiates the membrane integration of the PMP. [3]
For the application in S. cerevisiae we designed fusion proteins of the v-SNARE Snc1 with different peroxisomal membrane anchors *needs to be change* .
We tested the constructs using an GUS Assay. The assays were performed using transformants of the strain BY4742.
Our results *needs to be change* indicate, that it is possible to use our approach for secretion. The best efficiency was achieved using Snc1 fused with a linker to the peroxisomal membrane anchor Pex15. Furthermore the deletion of Pex11 did not increase the amount of active Gus secreted to the supernatant
Introduction
Peroxisome Biogenesis and Proliferation
Peroxisomes can be generated in different ways and their size and abundance is controlled by a number of pathways [8]. In yeast, peroxisomes can be generated de novo by budding from the endoplasmatic reticulum (ER) or through division from pre-existing peroxisomes using new proteins and lipids supplied from the ER in the form of vesicles [1]. Both pathways are still being investigated and to date haven’t been fully understood.
Fig.1: Peroxisomes can form through two pathways Nat Rev Mol Cell Biol. 2013 Dec; 14(12): 803–817.
Peroxisomes are extremely sensitive to environmental cues and are able to proliferate or be degraded accordingly [3]. Depending on the growth medium and their extracellular environment, peroxisomes are able to divide and multiply separately from cell division [3]. Their size and number is directly influenced by the presence of e.g. fatty acids, which lead to an increase in both size and number. Furthermore, peroxisome population is regulated by different peroxisomal integral membrane proteins, so called peroxins [2].
Peroxins
The formation of peroxisomes, both by de novo generation as well as growth and fission, is a highly controlled mechanism. Multiple studies have shown that the growth and division of peroxisomes are regulated by protein families specific to peroxisomes, so called peroxins [2]. Since S. cerevisiae naturally contains a very small amount of peroxisomes when growing under glucose-rich conditions, biosynthesis and target yield can be increased by altering peroxisome size and number. A short introduction to the peroxins used in this part of the project is given hereafter.
PEX11
Due to its unique ability to promote peroxisome division and its role in peroxisome biogenesis [11], the first peroxin we chose for our purpose is Pex11, which is located in the inner surface of the peroxisomal membrane [9]. Erdmann and Blobel have shown that the deletion of the PEX11 gene in S. cerevisiae results in cells with fewer, larger peroxisomes, whereas overexpression results in cells with a higher quantity of smaller peroxisomes [2]. Studies conducted by Smith and Aitchison confirmed that Pex11p-deficient cells growing on fatty acids failed to increase the amount of peroxisomes and instead the accumulation of a few giant peroxisomes was observed [1]. Other media, like oleate-containing ones, cause an induction of peroxisomal proliferation, which is due to an oleate responsive element of the PEX11 promoter [12].
In order to find out more about the complexity of peroxisome biogenesis and proliferation and also get constructive feedback on our work, we consulted with Florian David from Biopetrolia in Sweden. Their company specializes in yeast engineering in order to improve production titers, yields and rates for the production of biofuels, pharmaceuticals and other products. He suggested to expand our project to working not only with PEX11, but PEX31,32 and PEX34 as well.
PEX30-32
According to Zhou et al., the genes of the PEX30 – 32 family have been shown to influence peroxisome proliferation [2]. Their deletion resulted in the production of a higher quantity of large peroxisomes. Zhou et al. further investigated the effect of a PEX31,32 knockout, showing both number and size increase, also leading to a higher metabolic yield. However, a PEX31,32 knockout has been proven to attribute to a change in the membrane structure, resulting in higher permeability of the peroxisome membrane for fatty aldehydes and other intermediates and byproducts [2]. Due to these side effects we decided to discard working with a PEX31,32 knockout for now.
PEX34
Similar to Pex11, Pex34p is another peroxisomal integral membrane protein that can act both, independently and in combination with Pex11p, Pex25p, and Pex27p to control the peroxisome morphology and population. Pex34p is suggested to directly influence peroxisome proliferation as well as constitutive peroxisome division. Specifically, Pex34p overexpression positively affects peroxisome numbers in wild type and pex34 cells, whereas Pex34 deletion results in cells with fewer peroxisomes [6, 2]. In their studies Zhou et al. targeted synthetic pathways to peroxisomes in order to increase the production of fatty-acid-derived fatty alcohols, alkanes and olefins. By harnessing peroxisomes to produce fatty-acid-derived chemicals and biofuels they were able to show that peroxisome increases the production of target molecules while decreasing byproduct formation. Additionally, analyzing the effect of peroxin knockouts and overexpression, their research revealed that PEX34 overexpression significantly increased their yield [2]. The main advantage of working with Pex34p over Pex31,32 is the effect on the peroxisomal membrane. While Pex31,32 significantly increases membrane permeability, Pex34 has less effects on the membrane structure [2].
Fig. 2: Regulation of peroxisome quantity and morphology by different peroxins
Our Project
One step towards achieving the creation of a fully controllable artificial compartment is the regulation of and control over its morphology. In our case we are aiming at achieving the exact regulation of the size and number of the peroxisome. As a first approach we have chosen to control the PEX11 concentration in the cell. Furthermore PEX11 is to be designed as a 3b toolbox part so it can be combined and its effects tested with different promoters. For that purpose we are working with two constitutive promoters of varying strength as well as two inducible promoters which increase gene expression when grown in varying concentrations of galactose or copper sulfate. To control the range from a few giant peroxisomes to a high quantity of small ones we are working in a Pex11-$\Delta$ knockout strain. Secondly, following the advice of Florian David from Biopetrolia, we intend to increase both, the size and quantity of peroxisomes in the cell via a PEX34 overexpression. By working with PEX34 we will not only be able to control the peroxisome morphology, but also positively influence production yields.
How does it integrate into the overall project?
Controlling the size and number of peroxisomes is one of the multiple functions we plan to integrate into our artificial compartment toolbox so that it can be utilized for various projects. However, even though the exact control of proliferation can help understand the complex matter of peroxisome dynamics, the advantages of these findings exceed mere foundational research.
Integrating synthetic pathways into cells is often impeded by competing pathways and accruing intermediates or undesired byproducts that negatively influence biosynthesis. In order to achieve feasible results from microbial production, respective pathways need to be isolated into a suitable environment. Compartmentation provides microenvironments for metabolic functions of cells shielding them from the interference of simultaneously occurring reactions and therefore favoring biosynthesis. Going one step further, establishing synthetic pathways into a fully controlled compartment has the potential to increase the efficiency and productivity of these pathways resulting in higher yields of target products [2,6]. In our case, we change the peroxisome’s morphology by knocking out or over expressing PEX11 and PEX34 to obtain either a large amount of smaller peroxisomes or a high amount of enlarged ones. Especially the overexpression of PEX34 which results in a high quantity of large peroxisomes has been shown to actively regulate metabolic processes [1] and increase the production of target molecules while decreasing byproduct formation [2]. Furthermore, evidence indicates that changing the morphology of a compartment, including both, its shape and size, influences the amount of chemical reactions embedded in that compartment [1], a trait that can be used to increase the yield of otherwise inefficient reactions. Ultimately, even though we decided to discard our work on a PEX31,32 knockout, the effects this knockout has on membrane permeability and structure could potentially be used for further pathways within the peroxisome.
Overall goal of this subproject
In our subproject we want to achieve full control over peroxin concentrations in the yeast cell, in order to establish a simple method to regulate the peroxisome morphology and quantity.
pH Sensor
The activity of enzymatic Proteins is mostly pH-dependent. Therefore, it is of high interest to understand the pH-regulating mechanism of the peroxisome and the effects on the imported pathways. Literature has not agreed whether there is a common peroxisomal pH nor whether there is a regulating mechanismen or not. For our measurements, we use pH Lourin2 a GFP variant with a bimodal excitation spectrum with peaks at 395 and 475 nm and an emission maximum at 509 nm. Upon acidification excitation spectrum shifts from 395 to 475 nm Mahon et al. (2011)
pHLuorin2 emission at 509 nm, excited at wavelengths between 350 nm and 500 nm . Five different pH values, ranging from 5.8 to 7.8 are shown Mahon et al. (2011) .
roGFP2 Sensor
To maintain thermodynamic driving forces and electron fluxes which are needed at steady state, the intact chemeostasis of the redox machinery is very important (2016, Schwarzländer) . Glutathione is considered to be inside the peroxisomal lumen (Elbaz-Alon, Y., et al. 2014) . We therefore wanted to monitor glutathione redox potentials inside the peroxisomal lumen using the GFP variant roGFP2, which is able to precisely detect redox changes of glutathione. Two cysteines in the beta barrel structure can either form two thiols or one dDisulfide bondage dependent on whether they are reduced or oxidized. This influences the proton transfer of the chromophore and ultimately leads to a ratiometric shift in excitation. Excitation at 488 nm of the reduced form of roGFP exceeds the of the oxidized form and excitation at 405 nm behaves vise verse (Morgan, B. and M. Schwarzländer 2016) .
Nootkatone is an oxidized sesquiterpene, which is highly valuable for industrial and pharmaceutical application. We will focus on its repellent effect towards insects
Zhu et al. (2001)
.
Also, therapeutic activities of nootkatone have been reported, such as anti-platelet effects in rats
Seo et al. (2011)
,
anti-proliferative activity towards cancer cell lines
Gliszczyńska et al. (2011)
and enhancement of energy metabolism through AMP-activated protein kinase activation in skeletal muscle and liver
Murase et al. (2010)
.
Nootkatone can be extracted from grapefruits, but the organic material is limited and the yield is very low. So far, industrial production of nootkatone requires toxic substances such as heavy metals and strong oxidants like tert-butyl hydroperoxide which is known to be carcinogenic
Cankar et al. (2010)
.
Conversion of valencene to Nootkatol and Nootkatone
The synthesis of nootkatone starts from the precursor farnesyl pyrophosphate (FPP) and requires at least two enzymes. The initial step is the formation of valencene from FPP by a valencene synthase (ValS) followed by the production of nootkatol, nootkatone and other by-products by a P450 BM3 monooxygenase (BM3). The co-expression of an alcohol dehydrogenase (ADH) with ValS improves nootkatone production by favoring the conversion from nootkatol into nootkatone.
Schulz et al. (2015)
.
Previous approaches of nootkatone synthesis in yeast often failed due to toxic intermediates. A specific problem is the toxicity of beta-nootkatol and nootkatone itself for Saccharomyces cerevisiae at concentration higher than 100 mg/L
Gavira et al. (2013)
.
For an efficient industrial production, concentrations need to be in the range of g/L, which is lethal for yeast cells. Beta-nootkatol seems to accumulate in membranes because of its hydrophobic characteristics, resulting in changes of the membrane permeability, integrity and the function of membrane proteins.
Gavira et al. (2013)
.
It is presumed that the toxicity is partly caused by this effect. As one of the original purposes of the peroxisome is to reduce hydrogen peroxide, which is harmful to the cell and also alters the membrane composition
Cooper et al. (2000)
Block et al. (1991)
, we assume that beta-nootkatol does not affect the peroxisomal membrane either. But to be fully sure if this hypothesis is true, we have to collect and evaluate our own data on how beta-nootkatol affects the peroxisome membrane and thus the yield of nootkatone.
Yeast viability after 24 h in the presence of (+)-valencene, beta-Nootkatol or nootkatone in different concentrations
Our goal is the successful integration of the nootkatone pathway into our compartment and to bypass the problem of high concentration toxicity of beta-nootkatol and nootkatone for the yeast cell. This would not only be a more efficient but also a more environmentally friendly method to satisfy the great interest of this sesquiterpene by the industry. It would also facilitate the access to a high performing insect repellent in less developed regions of the world and therefore decrease the spread of diseases like malaria, dengue or the Zika virus.
Violacein (C20H13N3O3), a bisindole, is a violet pigment, formed by condensation of two tryptophan molecules. It can naturally be found in numerous bacterial strains, for example in the gram-negative Chromobacterium violaceum. Due to its wide range of biological properties, violacein is useful for different industrial applications in pharmaceuticals and cosmetics.
Violacein is known to have a variety of different biological activities, including an antitumor
(Bromberg N et al, 2010),
antifungal
(Brucker RM et al., 2008)
and antiviral
(Andrighetti-Fröhner CR et al., 2003)
function. Furthermore, it has been shown that violacein enhances the effect of most commercial antibiotics by working synergistically with them
(Subramaniam S et al., 2014).
This is especially of high interest in the fight against recent antibiotic-resistant strains of pathogenic bacteria such as MRSA (multi resistant Staphylococcus aureus). Violacein’s antibacterial action against S. aureus has been proven by
Cazoto LL et al. (2011)
.
It is of high medical interest that toxic effects of Violacein on cultured cancer cells were shown within in vitro tests. Furthermore, the Ehrlich ascites tumor (EAT) mouse model gives the prove as a in vivo test: daily injection of violacein ($0.1\,\mu g/kg$ up to $1\,mg/kg$) led to a significant increased survival rate of the mice
(Seong Yeol Choi et al., 2015)
. The ability to weaken cancer growth draws more attention to violacein as a possible cancer therapeutic.
de Carvalho DD et al. (2006)
showed that violacein is capable to induce apoptosis in various cancer cells by inducing the production of oxygen radicals.
A main focus also lies in violacein’s antimalarial activity, which was tested in vitro and in vivo on human and murine blood stage forms of Plasmodium parasites
(Stefanie C. P. Lopes et al., 2009)
. P. falciparum is known to be the deadliest Plasmodium species that causes malaria in humans
(Stephen M. Rich et al., 2009)
. Violacein acted effectively against diseases caused by both, young and mature parasite strains, of P. falciparum , and parasite growth was reduced significantly compared to non-treated animals. Moreover, it has a protective effect as mice infected with a lethal strain (P. chabaudi chabaudi) died within 10 days, whereas the majority (80 %) treated with violacein survived the infection
(Stefanie C. P. Lopes et al., 2009)
. Not at least because the emerge resistance to other plant-based malaria drugs becomes more frequent, it is time to look out for further possibilities in the worldwide battle against malaria
(Peplow M, 2016)
.
As the commercial production of violacein is rather difficult and limited for low productivity
(Hongnian Sun et al., 2016)
, researchers are working on improving the fermentative titers by metabolic engineering.
Here we want to make use of the existing potential violacein has and even try to promote this potential. With the great advantages a peroxisomal import has to offer, we want to develop a solid mechanism to not only prove the concept of our project, but also take advantage of violacein’s biological opportunities. By relocalization of the violacein pathway into yeast peroxisomes we want to create a space with optimized conditions for the production of violacein to achieve a high yield of the bisindole.
