Difference between revisions of "Part:BBa K5237015"
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− | + | <!-- Part summary --> | |
− | + | <section id="1"> | |
− | + | <h1>Intimin anti-EGFR nanobody</h1> | |
− | + | <p>This part contains the N-terminus of intimin harbouring the anti-EGFR nanobody (wild-type 7D12) and can be used for surface display of anti-EGFR nanobodies on <i>E.coli</i>. With this part, we sought to enhance bacterial binding to mammalian cells and potentially improve the chances of DNA delivery via conjugation by the bacterial Type IV secretion system (T4SS). As part of the PICasSO toolbox, we seek to use anti-EGFR adhesins to promote delivery of large DNA constructs encoding the various protein staples (presented in our parts collection) from bacteria to mammalian cells via conjugation to enable controlled modulation of chromatin organization by the delivered staples.</p> | |
− | + | <div class="toc" id="toc"> | |
− | + | <div id="toctitle"> | |
− | + | <h1>Contents</h1> | |
− | + | </div> | |
− | + | <ul> | |
− | + | <li class="toclevel-1 tocsection-1"><a href="#1"><span class="tocnumber">1</span> <span class="toctext">Sequence | |
− | + | ||
overview</span></a> | overview</span></a> | ||
− | + | </li> | |
− | + | <li class="toclevel-1 tocsection-2"><a href="#2"><span class="tocnumber">2</span> <span class="toctext">Usage and | |
Biology</span></a> | Biology</span></a> | ||
− | + | </li> | |
− | + | <li class="toclevel-1 tocsetction-3"><a href="#3"><span class="tocnumber">3</span> <span class="toctext">Assembly | |
and part evolution</span></a> | and part evolution</span></a> | ||
− | + | </li> | |
− | + | <li class="toclevel-1 tocsection-5"><a href="#4"><span class="tocnumber">4</span> <span class="toctext">Results</span></a> | |
− | + | </li> | |
− | + | <li class="toclevel-1 tocsection-8"><a href="#5"><span class="tocnumber">5</span> <span class="toctext">References</span></a> | |
− | + | </li> | |
− | + | </ul> | |
− | + | </div> | |
− | + | </section> | |
− | + | <section><p><br/><br/></p> | |
− | + | <font size="5"><b>The PICasSO Toolbox </b> </font> | |
− | + | <div class="thumb" style="margin-top:10px;"></div> | |
− | + | <div class="thumbinner" style="width:550px"><img alt="" class="thumbimage" src="https://static.igem.wiki/teams/5237/wetlab-results/registry-part-collection-engineering-cycle-example-overview.svg" style="width:99%;"/> | |
− | + | <div class="thumbcaption"> | |
− | + | <i><b>Figure 1: How our part collection can be used to engineer new staples</b></i> | |
− | + | </div> | |
− | + | </div> | |
− | + | <p> | |
− | + | <br/> | |
− | + | While synthetic biology has in the past focused on engineering the genomic sequence of organisms, the <b>3D | |
− | + | spatial organization</b> of DNA is well-known to be an important layer of information encoding in | |
− | + | particular in eukaryotes, playing a crucial role in | |
− | + | gene regulation and hence | |
− | + | cell fate, disease development, evolution, and more. However, tools to precisely manipulate and control the | |
− | + | genomic spatial | |
− | + | architecture are limited, hampering the exploration of | |
− | + | 3D genome engineering in synthetic biology. We - the iGEM Team Heidelberg 2024 - have developed PICasSO, a | |
− | + | <b>powerful | |
− | + | molecular toolbox for rationally engineering genome 3D architectures</b> in living cells, based on | |
− | + | various DNA-binding proteins. | |
− | 3D genome in synthetic biology. We - iGEM Team Heidelberg 2024 - have developed PICasSO, a | + | |
− | toolbox based on various DNA-binding proteins | + | |
− | + | ||
</p> | </p> | ||
− | + | <p> | |
The <b>PICasSO</b> part collection offers a comprehensive, modular platform for precise manipulation and | The <b>PICasSO</b> part collection offers a comprehensive, modular platform for precise manipulation and | ||
− | re-programming | + | <b>re-programming |
− | + | of DNA-DNA interactions</b> using engineered "protein staples" in living cells. This enables | |
− | interactions, such as enhancer hijacking, or to design entirely new spatial architectures for gene regulation. | + | researchers to recreate naturally occurring alterations of 3D genomic |
− | Beyond its versatility, PICasSO includes robust assay systems to support the engineering, optimization, and | + | interactions, such as enhancer hijacking in cancer, or to design entirely new spatial architectures for |
− | testing of new staples | + | artificial gene regulation and cell function control. |
− | + | Specifically, the fusion of two DNA binding proteins enables to artificially bring otherwise distant genomic | |
+ | loci into | ||
+ | spatial proximity. | ||
+ | To unlock the system's full potential, we introduce versatile <b>chimeric CRISPR/Cas complexes</b>, | ||
+ | connected either at | ||
+ | the protein or - in the case of CRISPR/Cas-based DNA binding moieties - the guide RNA level. These complexes are | ||
+ | referred to as protein- or Cas staples, respectively. Beyond its | ||
+ | versatility with regard to the staple constructs themselves, PICasSO includes <b>robust assay</b> systems to | ||
+ | support the engineering, optimization, and | ||
+ | testing of new staples <i>in vitro</i> and <i>in vivo</i>. Notably, the PICasSO toolbox was developed in a | ||
+ | design-build-test-learn <b>engineering cycle closely intertwining wet lab experiments and computational | ||
+ | modeling</b> and iterated several times, yielding a collection of well-functioning and -characterized | ||
+ | parts. | ||
</p> | </p> | ||
− | + | <p>At its heart, the PICasSO part collection consists of three categories. <br/><b>(i)</b> Our <b>DNA-binding | |
− | + | proteins</b> | |
include our | include our | ||
− | finalized | + | finalized Cas staple experimentally validated using an artificial "enhancer hijacking" system as well as |
− | new Cas staples in the future. We also include our | + | "half staples" that can be combined by scientists to compose entirely |
− | and can be further engineered to create alternative, simpler and more compact staples. <br> | + | new Cas staples in the future. We also include our Simple staples comprised of particularly small, simple |
− | + | and robust DNA binding domains well-known to the synthetic biology community, which serve as controls for | |
− | consist of | + | successful stapling |
− | + | and can be further engineered to create alternative, simpler, and more compact staples. <br/> | |
− | + | <b>(ii)</b> As <b>functional elements</b>, we list additional parts that enhance and expand the | |
− | interkingdom conjugation system. <br> | + | functionality of our Cas and |
− | + | Basic staples. These | |
− | systems</b>. These include components of our established FRET-based proximity assay system, enabling users to | + | consist of staples dependent on |
+ | cleavable peptide linkers targeted by cancer-specific proteases or inteins that allow condition-specific, | ||
+ | dynamic stapling <i>in vivo</i>. | ||
+ | We also include several engineered parts that enable the efficient delivery of PICasSO's constructs into | ||
+ | target cells, including mammalian cells, | ||
+ | with our new | ||
+ | interkingdom conjugation system. <br/> | ||
+ | <b>(iii)</b> As the final category of our collection, we provide parts that underlie our <b>custom | ||
+ | readout | ||
+ | systems</b>. These include components of our established FRET-based proximity assay system, enabling | ||
+ | users to | ||
confirm | confirm | ||
− | accurate stapling. Additionally, we offer a complementary, application-oriented testing system | + | accurate stapling. Additionally, we offer a complementary, application-oriented testing system based on a |
− | + | luciferase reporter, which allows for straightforward experimental assessment of functional enhancer | |
+ | hijacking events | ||
+ | in mammalian cells. | ||
</p> | </p> | ||
− | + | <p> | |
− | The following table gives a | + | The following table gives a comprehensive overview of all parts in our PICasSO toolbox. <mark style="background-color: #FFD700; color: black;">The highlighted parts showed |
− | + | exceptional performance as described on our iGEM wiki and can serve as a reference.</mark> The other | |
− | collection are versatile building blocks designed to provide future iGEMers with the flexibility to engineer their | + | parts in |
− | own custom Cas staples, enabling further optimization and innovation.<br> | + | the |
− | + | collection are versatile building blocks designed to provide future iGEMers with the flexibility to engineer | |
− | + | their | |
− | + | own custom Cas staples, enabling further optimization and innovation in the new field of 3D genome | |
− | + | engineering.<br/> | |
− | + | </p> | |
− | + | <p> | |
− | + | <font size="4"><b>Our part collection includes:</b></font><br/> | |
− | + | </p> | |
− | + | <table style="width: 90%; padding-right:10px;"> | |
− | + | <td align="left" colspan="3"><b>DNA-Binding Proteins: </b> | |
− | + | Modular building blocks for engineering of custom staples to mediate defined DNA-DNA interactions <i>in vivo</i></td> | |
− | + | <tbody> | |
− | + | <tr bgcolor="#FFD700"> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237000" target="_blank">BBa_K5237000</a></td> | |
− | + | <td>Fusion Guide RNA Entry Vector MbCas12a-SpCas9</td> | |
− | + | <td>Entry vector for simple fgRNA cloning via SapI</td> | |
− | + | </tr> | |
− | + | <tr bgcolor="#FFD700"> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237001" target="_blank">BBa_K5237001</a></td> | |
− | + | <td>Staple Subunit: dMbCas12a-Nucleoplasmin NLS</td> | |
− | + | <td>Staple subunit that can be combined with crRNA or fgRNA and dSpCas9 to form a functional staple | |
− | + | </td> | |
− | + | </tr> | |
− | + | <tr bgcolor="#FFD700"> | |
+ | <td><a href="https://parts.igem.org/Part:BBa_K5237002" target="_blank">BBa_K5237002</a></td> | ||
+ | <td>Staple Subunit: SV40 NLS-dSpCas9-SV40 NLS</td> | ||
+ | <td>Staple subunit that can be combined with a sgRNA or fgRNA and dMbCas12a to form a functional staple | ||
</td> | </td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237003" target="_blank">BBa_K5237003</a></td> | |
− | + | <td>Cas Staple: SV40 NLS-dMbCas12a-dSpCas9-Nucleoplasmin NLS</td> | |
− | + | <td>Functional Cas staple that can be combined with sgRNA and crRNA or fgRNA to bring two DNA strands into | |
+ | close | ||
+ | proximity | ||
</td> | </td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237004" target="_blank">BBa_K5237004</a></td> | |
− | + | <td>Staple Subunit: Oct1-DBD</td> | |
− | + | <td>Staple subunit that can be combined to form a functional staple, for example with TetR.<br/> | |
Can also be combined with a fluorescent protein as part of the FRET proximity assay</td> | Can also be combined with a fluorescent protein as part of the FRET proximity assay</td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237005" target="_blank">BBa_K5237005</a></td> | |
− | + | <td>Staple Subunit: TetR</td> | |
− | + | <td>Staple subunit that can be combined to form a functional staple, for example with Oct1.<br/> | |
Can also be combined with a fluorescent protein as part of the FRET proximity assay</td> | Can also be combined with a fluorescent protein as part of the FRET proximity assay</td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237006" target="_blank">BBa_K5237006</a></td> | |
− | + | <td>Simple Staple: TetR-Oct1</td> | |
− | + | <td>Functional staple that can be used to bring two DNA strands in close proximity</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237007" target="_blank">BBa_K5237007</a></td> | |
− | + | <td>Staple Subunit: GCN4</td> | |
− | + | <td>Staple subunit that can be combined to form a functional staple, for example with rGCN4</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237008" target="_blank">BBa_K5237008</a></td> | |
− | + | <td>Staple Subunit: rGCN4</td> | |
− | + | <td>Staple subunit that can be combined to form a functional staple, for example with rGCN4</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237009" target="_blank">BBa_K5237009</a></td> | |
− | + | <td>Mini Staple: bGCN4</td> | |
− | + | <td> | |
Assembled staple with minimal size that can be further engineered</td> | Assembled staple with minimal size that can be further engineered</td> | ||
− | + | </tr> | |
− | + | </tbody> | |
− | + | <td align="left" colspan="3"><b>Functional Elements: </b> | |
− | Protease cleavable peptide linkers and inteins are used to control and modify staples for further optimization | + | Protease-cleavable peptide linkers and inteins are used to control and modify staples for further |
− | for custom applications | + | optimization |
− | + | for custom applications</td> | |
− | + | <tbody> | |
− | + | <tr bgcolor="#FFD700"> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237010" target="_blank">BBa_K5237010</a></td> | |
− | + | <td>Cathepsin B-cleavable Linker: GFLG</td> | |
+ | <td>Cathepsin B-cleavable peptide linker that can be used to combine two staple subunits to make | ||
+ | responsive | ||
staples</td> | staples</td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237011" target="_blank">BBa_K5237011</a></td> | |
− | + | <td>Cathepsin B Expression Cassette</td> | |
− | + | <td>Expression cassette for the overexpression of cathepsin B</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237012" target="_blank">BBa_K5237012</a></td> | |
− | + | <td>Caged NpuN Intein</td> | |
− | + | <td>A caged NpuN split intein fragment that undergoes protein <i>trans</i>-splicing after protease | |
− | + | activation, which can be used to create functionalized staple | |
− | + | subunits</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237013" target="_blank">BBa_K5237013</a></td> | |
− | + | <td>Caged NpuC Intein</td> | |
− | + | <td>A caged NpuC split intein fragment that undergoes protein <i>trans</i>-splicing after protease | |
− | + | activation, which can be used to create functionalized staple | |
− | + | subunits</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237014" target="_blank">BBa_K5237014</a></td> | |
− | + | <td>Fusion Guide RNA Processing Casette</td> | |
− | + | <td>Processing cassette to produce multiple fgRNAs from one transcript, that can be used for | |
− | + | multiplexed 3D | |
− | + | genome reprogramming</td> | |
− | + | </tr> | |
+ | <tr> | ||
+ | <td><a href="https://parts.igem.org/Part:BBa_K5237015" target="_blank">BBa_K5237015</a></td> | ||
+ | <td>Intimin anti-EGFR Nanobody</td> | ||
+ | <td>Interkingdom conjugation between bacteria and mammalian cells, as an alternative delivery tool for | ||
+ | large | ||
constructs</td> | constructs</td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K4643003" target="_blank">BBa_K4643003</a></td> | |
− | FRET and enhancer recruitment to | + | <td>IncP Origin of Transfer</td> |
− | + | <td>Origin of transfer that can be cloned into the plasmid vector and used for conjugation as a | |
− | + | means of | |
− | + | delivery</td> | |
− | + | </tr> | |
− | + | </tbody> | |
− | + | <td align="left" colspan="3"><b>Readout Systems: </b> | |
+ | FRET and enhancer recruitment readout systems to rapidly assess successful DNA stapling in bacterial and | ||
+ | mammalian cells | ||
+ | </td> | ||
+ | <tbody> | ||
+ | <tr bgcolor="#FFD700"> | ||
+ | <td><a href="https://parts.igem.org/Part:BBa_K5237016" target="_blank">BBa_K5237016</a></td> | ||
+ | <td>FRET-Donor: mNeonGreen-Oct1</td> | ||
+ | <td>FRET donor-fluorophore fused to Oct1-DBD that binds to the Oct1 binding cassette, which can be used to | ||
+ | visualize | ||
+ | DNA-DNA | ||
proximity</td> | proximity</td> | ||
− | + | </tr> | |
− | + | <tr bgcolor="#FFD700"> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237017" target="_blank">BBa_K5237017</a></td> | |
− | + | <td>FRET-Acceptor: TetR-mScarlet-I</td> | |
− | + | <td>Acceptor part for the FRET assay binding the TetR binding cassette, which can be used to visualize | |
+ | DNA-DNA | ||
proximity</td> | proximity</td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237018" target="_blank">BBa_K5237018</a></td> | |
− | + | <td>Oct1 Binding Casette</td> | |
− | + | <td>DNA sequence containing 12 Oct1 binding motifs, compatible with various assays such as the FRET | |
proximity assay</td> | proximity assay</td> | ||
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237019" target="_blank">BBa_K5237019</a></td> | |
− | + | <td>TetR Binding Cassette</td> | |
− | + | <td>DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the | |
+ | FRET | ||
proximity assay</td> | proximity assay</td> | ||
− | + | </tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237020" target="_blank">BBa_K5237020</a></td> | |
− | + | <td>Cathepsin B-Cleavable Trans-Activator: NLS-Gal4-GFLG-VP64</td> | |
− | + | <td>Readout system that responds to protease activity, which was used to test cathepsin B-cleavable linker | |
− | </ | + | </td> |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237021" target="_blank">BBa_K5237021</a></td> | |
− | + | <td>NLS-Gal4-VP64</td> | |
− | + | <td>Trans-activating enhancer, that can be used to simulate enhancer hijacking</td> | |
− | + | </tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237022" target="_blank">BBa_K5237022</a></td> | |
− | + | <td>mCherry Expression Cassette: UAS, minimal Promoter, mCherry</td> | |
− | + | <td>Readout system for enhancer binding, which was used to test cathepsin B-cleavable linker</td> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237023" target="_blank">BBa_K5237023</a></td> | |
− | + | <td>Oct1 - 5x UAS Binding Casette</td> | |
− | + | <td>Oct1 and UAS binding cassette, that was used for the simulated enhancer hijacking assay</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td><a href="https://parts.igem.org/Part:BBa_K5237024" target="_blank">BBa_K5237024</a></td> | |
− | + | <td>TRE-minimal Promoter- Firefly Luciferase</td> | |
− | + | <td>Contains firefly luciferase controlled by a minimal promoter, which was used as a luminescence | |
− | + | readout for | |
− | simulated enhancer hijacking | + | simulated enhancer hijacking</td> |
− | + | </tr> | |
− | + | </tbody> | |
− | + | </table></section> | |
− | + | <section id="1"> | |
− | + | <h1>1. Sequence overview</h1> | |
− | + | </section> | |
− | + | ||
− | + | ||
− | + | ||
</body> | </body> | ||
</html> | </html> | ||
− | |||
<!--################################--> | <!--################################--> | ||
− | <span class= | + | <span class="h3bb">Sequence and Features</span> |
<partinfo>BBa_K5237015 SequenceAndFeatures</partinfo> | <partinfo>BBa_K5237015 SequenceAndFeatures</partinfo> | ||
<!--################################--> | <!--################################--> | ||
− | |||
<html> | <html> | ||
<body> | <body> | ||
<section id="2"> | <section id="2"> | ||
− | + | <h1>2. Usage and Biology</h1> | |
− | + | <p>This part contains the N-terminus of intimin harbouring the anti-EGFR (wild-type 7D12) adhesin and can be used for surface display of anti-EGFR nanobodies on <i>E.coli</i>. Salema et al., (2013) showed efficient presentation of nanobodies on the surface of <i>E.coli</i> K-12 cells by fusing them to the β domain of intimin. The β domain of intimin comes from the pNeae2 plasmid (addgene #168300) and encodes an N-terminal signal peptide for Sec-dependent translocation into the periplasm, a LysM domain that interacts with the peptidoglycan and provides anchoring, and a β-barrel that inserts into the outer membrane. The coding sequence of the anti-EGFR nanobody is located in the C-terminus (that is exposed to the extracellular milieu) between the E tag (GAPVPYPDPLEP) and the myc tag (EQKLISEED). These tags can be utilized for purification or detection of the protein.</p> | |
− | + | <p>The idea behind engineering this part was to use it for increasing cell-cell contact between bacteria and mammalian cells and thereby potentially enhancing the chances of inter-kingdom conjugational DNA transfer. The inspiration to test inter-kingdom conjugation came from the fact that all the events leading to DNA transfer by conjugation are driven by the donor bacterium and the protein components are typically plasmid encoded, making it possible for any type of cell to serve as the recipient (Waters, 2001). Furthermore, as the primary trigger for conjugation remains obscure, we hypothesized that cell-cell contact might be one of the main determinants for conjugation to occur efficiently. Robledo <i>et al.</i>(2022) showed that enhanced cell-cell contact mediated by synthetic adhesins led to a 100-fold increase in conjugation efficiency between bacteria in liquid media, where the RP4 conjugative system is particularly ineffective. This combination of knowledge motivated us to engineer conjugation as a generalized DNA delivery tool for large plasmid constructs (around ~100 kb). Figure 2 below presents an illustration of our idea.</p> | |
− | + | <div class="thumb"> | |
− | + | <div class="thumbinner" style="width:60%;"> | |
− | + | <img alt="Inter-kingdom conjugation" class="thumbimage" src="https://static.igem.wiki/teams/5237/figures-corrected/conjugation-mammalian-bacteria.svg" style="width:99%;"/> | |
− | + | <div class="thumbcaption"> | |
− | + | <i><b>Figure 2. Illustration of DNA delivery from bacteria to mammalian cells via conjugation.</b>A conjugative helper plasmid catalyzes transfer of an <i><a href="https://parts.igem.org/Part:BBa_K4643003">oriT</a></i> carrying mobilizable plasmid from bacteria to mammalian cells. Anti-EGFR adhesins are shown to stabilize the mating pair.</i> | |
− | + | </div> | |
− | + | </div> | |
− | + | <p>This part is a member of the PICasSO toolbox and can be used to promote adhesion to mammalian cell surfaces as EGFR is a common mammalian surface receptor. This part finds its application as an alternative DNA delivery tool to mammalian cells for parts in the PICasSO Toolbox such as the dCas-based staples (<a href="https://parts.igem.org/Part:BBa_K5237001" target="_blank"> BBa_K5237001</a>, <a href="https://parts.igem.org/Part:BBa_K5237002" target="_blank"> BBa_K5237002</a>, <a href="https://parts.igem.org/Part:BBa_K5237003" target="_blank">BBa_K5237003</a> ) along with fgRNAs, which are encoded by rather large plasmids. It is known that lipofection efficiency decreases with increasing plasmid size (Kreiss <i>et al.</i>, 1999), so conjugation may be employed as an alternative tool to deliver such large plasmids to mammalian cells <i>in vitro</i>, to not only enable engineering of chromatin conformations, but also to allow for its controlled modulation in a stimulus-responsive manner. Moreover, the anti-EGFR nanobody can easily be swapped with other nanobodies to alter the target specificity or binding affinities.</p> | |
− | + | </div></section> | |
− | + | ||
− | + | ||
− | </section> | + | |
− | + | ||
<section id="3"> | <section id="3"> | ||
− | + | <h1>3. Assembly and part evolution</h1> | |
− | + | <p>The pNeae2 plasmid was obtained from addgene (#168300). Codon optimized DNA sequence of chain L anti-EGFR (7D12) nanobody (Schmitz et al., 2013) for expression in <i>E.coli</i> was procured as a gBlock containing 5' and 3' restriction sites for SfiI and NotI. Attempts at cloning the anti-EGFR nanobody by restriction ligation (using SfiI and NotI) into the coding sequence of intimin in pNeae2 (suggested cloning strategy by Salema et al., (2013)) were unsuccessful as indicated by test digests and Sanger sequencing. To circumvent vector re-ligation issues that we encountered, Gibson assembly shall be attempted in the near future.</p> | |
</section> | </section> | ||
− | |||
<section id="4"> | <section id="4"> | ||
− | + | <h1>4. Results</h1> | |
− | + | <h2><b>Successful expression of myc-tagged intimin by <i>E.coli</i> 10-beta</b></h2> | |
− | + | <p>Despite unsuccessful cloning of anti-EGFR adhesin into the coding sequence of intimin, protein expression was tested in <i>E.coli</i> 10-beta since they will be utilized as the donor strain in our upcoming conjugation tests - due to their ability to stably maintain and tolerate large plasmid constructs. Since <i>E.coli</i> 10-beta is not a typical strain used for protein expression, it was important to test their ability to overexpress outer membrane proteins and its potential toxicity to the cells. | |
− | <p><i>E.coli</i> 10-beta were transformed with pNeae2, and protein expression was induced with 50 µM IPTG. A Western Blot against the myc epitope on the C-terminus of intimin revealed expression of myc-tagged intimin of the expected size (~76 kDa) after induction (Figure 3). However, a smear of several bands was noted which could be a consequence of several factors included but not limited to protein degradation, expression of truncated proteins or high SDS-PAGE protein load. Nevertheless, this result still suggests that <i>E.coli</i> 10-beta could be used as the donor strain for our future conjugation assays owing to their ability to express full-length intimin.</p> | + | <p><i>E.coli</i> 10-beta were transformed with pNeae2, and protein expression was induced with 50 µM IPTG. A Western Blot against the myc epitope on the C-terminus of intimin revealed expression of myc-tagged intimin of the expected size (~76 kDa) after induction (Figure 3). However, a smear of several bands was noted which could be a consequence of several factors included but not limited to protein degradation, expression of truncated proteins or high SDS-PAGE protein load. Nevertheless, this result still suggests that <i>E.coli</i> 10-beta could be used as the donor strain for our future conjugation assays owing to their ability to express full-length intimin.</p> |
− | + | <div class="thumb"> | |
− | + | <div class="thumbinner" style="width:30%;"> | |
− | + | <img alt="Anti-myc Western Blot" class="thumbimage" src="https://static.igem.wiki/teams/5237/wetlab-results/anti-myc-wb-intimin-myc2.png" style="width:99%;"/> | |
− | + | <div class="thumbcaption"> | |
− | + | <i><b>Figure 3: Fluorescence western blot scan showing expression of myc-tagged intimin by <i>E.coli</i> 10-beta after IPTG induction.</b> <i>E.coli</i> 10-beta were transformed with pNeae2, induced with 50 µM IPTG and lysed. Lane 1 was loaded with 30 µg of total protein from the <i>E.coli</i> lysate after IPTG induction and Lane 2 was loaded with 30 µg of total protein from the uninduced <i>E.coli</i> lysate. The blue arrow indicates the position of the myc-tagged intimin (~76 kDa)</i> | |
− | + | </div> | |
− | + | </div> | |
− | + | </div> | |
− | + | <h2><b>Outlook</b></h2> | |
− | + | <p>Upcoming experiments shall address the interaction between the anti-EGFR adhesin and EGFR <i>in vitro</i> and also examine the increased localization of adhesin-expressing bacteria on the surface of mammalian cells. Ultimately, this part shall be used in conjugation assays between bacteria and mammalian cells to delineate the role of cell-cell contact in promoting inter-kingdom conjugation.</p> | |
− | + | </p></section> | |
− | </section> | + | |
− | + | ||
<section id="5"> | <section id="5"> | ||
− | + | <h1>5. References</h1> | |
− | + | <p>Kreiss, P., Cameron, B., Rangara, R., Mailhe, P., Aguerre-Charriol, O., Airiau, M., Scherman, D., Crouzet, J., & Pitard, B. (1999). Plasmid DNA size does not affect the physicochemical properties of lipoplexes but modulates gene transfer efficiency. Nucleic Acids Research, 27(19). https://doi.org/10.1093/nar/27.19.3792</p> | |
− | + | <p>Robledo, M., Álvarez, B., Cuevas, A., González, S., Ruano-Gallego, D., Fernández, L. Á., & De La Cruz, F. (2022). Targeted bacterial conjugation mediated by synthetic cell-to-cell adhesions. Nucleic Acids Research, 50(22). https://doi.org/10.1093/nar/gkac1164</p> | |
− | + | <p>Salema, V., Marín, E., Martínez-Arteaga, R., Ruano-Gallego, D., Fraile, S., Margolles, Y., Teira, X., Gutierrez, C., Bodelón, G., & Fernández, L. Á. (2013). Selection of Single Domain Antibodies from Immune Libraries Displayed on the Surface of E. coli Cells with Two β-Domains of Opposite Topologies. PLoS ONE, 8(9). https://doi.org/10.1371/journal.pone.0075126</p> | |
− | + | <p>Schmitz, K. R., Bagchi, A., Roovers, R. C., Van Bergen En Henegouwen, P. M. P., & Ferguson, K. M. (2013). Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure, 21(7).https://doi.org/10.1016/j.str.2013.05.008</p> | |
− | + | <p>Waters, V. L. (2001). Conjugation between bacterial and mammalian cells. Nature Genetics, 29(4). https://doi.org/10.1038/ng779</p> | |
</section> | </section> | ||
− | |||
</body> | </body> | ||
</html> | </html> |
Revision as of 07:27, 2 October 2024
Intimin anti-EGFR nanobody
This part contains the N-terminus of intimin harbouring the anti-EGFR nanobody (wild-type 7D12) and can be used for surface display of anti-EGFR nanobodies on E.coli. With this part, we sought to enhance bacterial binding to mammalian cells and potentially improve the chances of DNA delivery via conjugation by the bacterial Type IV secretion system (T4SS). As part of the PICasSO toolbox, we seek to use anti-EGFR adhesins to promote delivery of large DNA constructs encoding the various protein staples (presented in our parts collection) from bacteria to mammalian cells via conjugation to enable controlled modulation of chromatin organization by the delivered staples.
While synthetic biology has in the past focused on engineering the genomic sequence of organisms, the 3D
spatial organization of DNA is well-known to be an important layer of information encoding in
particular in eukaryotes, playing a crucial role in
gene regulation and hence
cell fate, disease development, evolution, and more. However, tools to precisely manipulate and control the
genomic spatial
architecture are limited, hampering the exploration of
3D genome engineering in synthetic biology. We - the iGEM Team Heidelberg 2024 - have developed PICasSO, a
powerful
molecular toolbox for rationally engineering genome 3D architectures in living cells, based on
various DNA-binding proteins.
The PICasSO part collection offers a comprehensive, modular platform for precise manipulation and re-programming of DNA-DNA interactions using engineered "protein staples" in living cells. This enables researchers to recreate naturally occurring alterations of 3D genomic interactions, such as enhancer hijacking in cancer, or to design entirely new spatial architectures for artificial gene regulation and cell function control. Specifically, the fusion of two DNA binding proteins enables to artificially bring otherwise distant genomic loci into spatial proximity. To unlock the system's full potential, we introduce versatile chimeric CRISPR/Cas complexes, connected either at the protein or - in the case of CRISPR/Cas-based DNA binding moieties - the guide RNA level. These complexes are referred to as protein- or Cas staples, respectively. Beyond its versatility with regard to the staple constructs themselves, PICasSO includes robust assay systems to support the engineering, optimization, and testing of new staples in vitro and in vivo. Notably, the PICasSO toolbox was developed in a design-build-test-learn engineering cycle closely intertwining wet lab experiments and computational modeling and iterated several times, yielding a collection of well-functioning and -characterized parts.
At its heart, the PICasSO part collection consists of three categories.
(i) Our DNA-binding
proteins
include our
finalized Cas staple experimentally validated using an artificial "enhancer hijacking" system as well as
"half staples" that can be combined by scientists to compose entirely
new Cas staples in the future. We also include our Simple staples comprised of particularly small, simple
and robust DNA binding domains well-known to the synthetic biology community, which serve as controls for
successful stapling
and can be further engineered to create alternative, simpler, and more compact staples.
(ii) As functional elements, we list additional parts that enhance and expand the
functionality of our Cas and
Basic staples. These
consist of staples dependent on
cleavable peptide linkers targeted by cancer-specific proteases or inteins that allow condition-specific,
dynamic stapling in vivo.
We also include several engineered parts that enable the efficient delivery of PICasSO's constructs into
target cells, including mammalian cells,
with our new
interkingdom conjugation system.
(iii) As the final category of our collection, we provide parts that underlie our custom
readout
systems. These include components of our established FRET-based proximity assay system, enabling
users to
confirm
accurate stapling. Additionally, we offer a complementary, application-oriented testing system based on a
luciferase reporter, which allows for straightforward experimental assessment of functional enhancer
hijacking events
in mammalian cells.
The following table gives a comprehensive overview of all parts in our PICasSO toolbox. The highlighted parts showed
exceptional performance as described on our iGEM wiki and can serve as a reference. The other
parts in
the
collection are versatile building blocks designed to provide future iGEMers with the flexibility to engineer
their
own custom Cas staples, enabling further optimization and innovation in the new field of 3D genome
engineering.
Our part collection includes:
DNA-Binding Proteins: Modular building blocks for engineering of custom staples to mediate defined DNA-DNA interactions in vivo | ||
BBa_K5237000 | Fusion Guide RNA Entry Vector MbCas12a-SpCas9 | Entry vector for simple fgRNA cloning via SapI |
BBa_K5237001 | Staple Subunit: dMbCas12a-Nucleoplasmin NLS | Staple subunit that can be combined with crRNA or fgRNA and dSpCas9 to form a functional staple |
BBa_K5237002 | Staple Subunit: SV40 NLS-dSpCas9-SV40 NLS | Staple subunit that can be combined with a sgRNA or fgRNA and dMbCas12a to form a functional staple |
BBa_K5237003 | Cas Staple: SV40 NLS-dMbCas12a-dSpCas9-Nucleoplasmin NLS | Functional Cas staple that can be combined with sgRNA and crRNA or fgRNA to bring two DNA strands into close proximity |
BBa_K5237004 | Staple Subunit: Oct1-DBD | Staple subunit that can be combined to form a functional staple, for example with TetR. Can also be combined with a fluorescent protein as part of the FRET proximity assay |
BBa_K5237005 | Staple Subunit: TetR | Staple subunit that can be combined to form a functional staple, for example with Oct1. Can also be combined with a fluorescent protein as part of the FRET proximity assay |
BBa_K5237006 | Simple Staple: TetR-Oct1 | Functional staple that can be used to bring two DNA strands in close proximity |
BBa_K5237007 | Staple Subunit: GCN4 | Staple subunit that can be combined to form a functional staple, for example with rGCN4 |
BBa_K5237008 | Staple Subunit: rGCN4 | Staple subunit that can be combined to form a functional staple, for example with rGCN4 |
BBa_K5237009 | Mini Staple: bGCN4 | Assembled staple with minimal size that can be further engineered | Functional Elements: Protease-cleavable peptide linkers and inteins are used to control and modify staples for further optimization for custom applications |
BBa_K5237010 | Cathepsin B-cleavable Linker: GFLG | Cathepsin B-cleavable peptide linker that can be used to combine two staple subunits to make responsive staples |
BBa_K5237011 | Cathepsin B Expression Cassette | Expression cassette for the overexpression of cathepsin B |
BBa_K5237012 | Caged NpuN Intein | A caged NpuN split intein fragment that undergoes protein trans-splicing after protease activation, which can be used to create functionalized staple subunits |
BBa_K5237013 | Caged NpuC Intein | A caged NpuC split intein fragment that undergoes protein trans-splicing after protease activation, which can be used to create functionalized staple subunits |
BBa_K5237014 | Fusion Guide RNA Processing Casette | Processing cassette to produce multiple fgRNAs from one transcript, that can be used for multiplexed 3D genome reprogramming |
BBa_K5237015 | Intimin anti-EGFR Nanobody | Interkingdom conjugation between bacteria and mammalian cells, as an alternative delivery tool for large constructs |
BBa_K4643003 | IncP Origin of Transfer | Origin of transfer that can be cloned into the plasmid vector and used for conjugation as a means of delivery | Readout Systems: FRET and enhancer recruitment readout systems to rapidly assess successful DNA stapling in bacterial and mammalian cells |
BBa_K5237016 | FRET-Donor: mNeonGreen-Oct1 | FRET donor-fluorophore fused to Oct1-DBD that binds to the Oct1 binding cassette, which can be used to visualize DNA-DNA proximity |
BBa_K5237017 | FRET-Acceptor: TetR-mScarlet-I | Acceptor part for the FRET assay binding the TetR binding cassette, which can be used to visualize DNA-DNA proximity |
BBa_K5237018 | Oct1 Binding Casette | DNA sequence containing 12 Oct1 binding motifs, compatible with various assays such as the FRET proximity assay |
BBa_K5237019 | TetR Binding Cassette | DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the FRET proximity assay | BBa_K5237020 | Cathepsin B-Cleavable Trans-Activator: NLS-Gal4-GFLG-VP64 | Readout system that responds to protease activity, which was used to test cathepsin B-cleavable linker |
BBa_K5237021 | NLS-Gal4-VP64 | Trans-activating enhancer, that can be used to simulate enhancer hijacking | BBa_K5237022 | mCherry Expression Cassette: UAS, minimal Promoter, mCherry | Readout system for enhancer binding, which was used to test cathepsin B-cleavable linker |
BBa_K5237023 | Oct1 - 5x UAS Binding Casette | Oct1 and UAS binding cassette, that was used for the simulated enhancer hijacking assay |
BBa_K5237024 | TRE-minimal Promoter- Firefly Luciferase | Contains firefly luciferase controlled by a minimal promoter, which was used as a luminescence readout for simulated enhancer hijacking |
1. Sequence overview
- 10INCOMPATIBLE WITH RFC[10]Illegal EcoRI site found at 105
Illegal EcoRI site found at 2259
Illegal PstI site found at 401
Illegal PstI site found at 649
Illegal PstI site found at 1096 - 12INCOMPATIBLE WITH RFC[12]Illegal EcoRI site found at 105
Illegal EcoRI site found at 2259
Illegal PstI site found at 401
Illegal PstI site found at 649
Illegal PstI site found at 1096
Illegal NotI site found at 2410 - 21INCOMPATIBLE WITH RFC[21]Illegal EcoRI site found at 105
Illegal EcoRI site found at 2259
Illegal BamHI site found at 1983 - 23INCOMPATIBLE WITH RFC[23]Illegal EcoRI site found at 105
Illegal EcoRI site found at 2259
Illegal PstI site found at 401
Illegal PstI site found at 649
Illegal PstI site found at 1096 - 25INCOMPATIBLE WITH RFC[25]Illegal EcoRI site found at 105
Illegal EcoRI site found at 2259
Illegal PstI site found at 401
Illegal PstI site found at 649
Illegal PstI site found at 1096
Illegal NgoMIV site found at 2004 - 1000COMPATIBLE WITH RFC[1000]
2. Usage and Biology
This part contains the N-terminus of intimin harbouring the anti-EGFR (wild-type 7D12) adhesin and can be used for surface display of anti-EGFR nanobodies on E.coli. Salema et al., (2013) showed efficient presentation of nanobodies on the surface of E.coli K-12 cells by fusing them to the β domain of intimin. The β domain of intimin comes from the pNeae2 plasmid (addgene #168300) and encodes an N-terminal signal peptide for Sec-dependent translocation into the periplasm, a LysM domain that interacts with the peptidoglycan and provides anchoring, and a β-barrel that inserts into the outer membrane. The coding sequence of the anti-EGFR nanobody is located in the C-terminus (that is exposed to the extracellular milieu) between the E tag (GAPVPYPDPLEP) and the myc tag (EQKLISEED). These tags can be utilized for purification or detection of the protein.
The idea behind engineering this part was to use it for increasing cell-cell contact between bacteria and mammalian cells and thereby potentially enhancing the chances of inter-kingdom conjugational DNA transfer. The inspiration to test inter-kingdom conjugation came from the fact that all the events leading to DNA transfer by conjugation are driven by the donor bacterium and the protein components are typically plasmid encoded, making it possible for any type of cell to serve as the recipient (Waters, 2001). Furthermore, as the primary trigger for conjugation remains obscure, we hypothesized that cell-cell contact might be one of the main determinants for conjugation to occur efficiently. Robledo et al.(2022) showed that enhanced cell-cell contact mediated by synthetic adhesins led to a 100-fold increase in conjugation efficiency between bacteria in liquid media, where the RP4 conjugative system is particularly ineffective. This combination of knowledge motivated us to engineer conjugation as a generalized DNA delivery tool for large plasmid constructs (around ~100 kb). Figure 2 below presents an illustration of our idea.
This part is a member of the PICasSO toolbox and can be used to promote adhesion to mammalian cell surfaces as EGFR is a common mammalian surface receptor. This part finds its application as an alternative DNA delivery tool to mammalian cells for parts in the PICasSO Toolbox such as the dCas-based staples ( BBa_K5237001, BBa_K5237002, BBa_K5237003 ) along with fgRNAs, which are encoded by rather large plasmids. It is known that lipofection efficiency decreases with increasing plasmid size (Kreiss et al., 1999), so conjugation may be employed as an alternative tool to deliver such large plasmids to mammalian cells in vitro, to not only enable engineering of chromatin conformations, but also to allow for its controlled modulation in a stimulus-responsive manner. Moreover, the anti-EGFR nanobody can easily be swapped with other nanobodies to alter the target specificity or binding affinities.
3. Assembly and part evolution
The pNeae2 plasmid was obtained from addgene (#168300). Codon optimized DNA sequence of chain L anti-EGFR (7D12) nanobody (Schmitz et al., 2013) for expression in E.coli was procured as a gBlock containing 5' and 3' restriction sites for SfiI and NotI. Attempts at cloning the anti-EGFR nanobody by restriction ligation (using SfiI and NotI) into the coding sequence of intimin in pNeae2 (suggested cloning strategy by Salema et al., (2013)) were unsuccessful as indicated by test digests and Sanger sequencing. To circumvent vector re-ligation issues that we encountered, Gibson assembly shall be attempted in the near future.
4. Results
Successful expression of myc-tagged intimin by E.coli 10-beta
Despite unsuccessful cloning of anti-EGFR adhesin into the coding sequence of intimin, protein expression was tested in E.coli 10-beta since they will be utilized as the donor strain in our upcoming conjugation tests - due to their ability to stably maintain and tolerate large plasmid constructs. Since E.coli 10-beta is not a typical strain used for protein expression, it was important to test their ability to overexpress outer membrane proteins and its potential toxicity to the cells.
E.coli 10-beta were transformed with pNeae2, and protein expression was induced with 50 µM IPTG. A Western Blot against the myc epitope on the C-terminus of intimin revealed expression of myc-tagged intimin of the expected size (~76 kDa) after induction (Figure 3). However, a smear of several bands was noted which could be a consequence of several factors included but not limited to protein degradation, expression of truncated proteins or high SDS-PAGE protein load. Nevertheless, this result still suggests that E.coli 10-beta could be used as the donor strain for our future conjugation assays owing to their ability to express full-length intimin.
Outlook
Upcoming experiments shall address the interaction between the anti-EGFR adhesin and EGFR in vitro and also examine the increased localization of adhesin-expressing bacteria on the surface of mammalian cells. Ultimately, this part shall be used in conjugation assays between bacteria and mammalian cells to delineate the role of cell-cell contact in promoting inter-kingdom conjugation.
5. References
Kreiss, P., Cameron, B., Rangara, R., Mailhe, P., Aguerre-Charriol, O., Airiau, M., Scherman, D., Crouzet, J., & Pitard, B. (1999). Plasmid DNA size does not affect the physicochemical properties of lipoplexes but modulates gene transfer efficiency. Nucleic Acids Research, 27(19). https://doi.org/10.1093/nar/27.19.3792
Robledo, M., Álvarez, B., Cuevas, A., González, S., Ruano-Gallego, D., Fernández, L. Á., & De La Cruz, F. (2022). Targeted bacterial conjugation mediated by synthetic cell-to-cell adhesions. Nucleic Acids Research, 50(22). https://doi.org/10.1093/nar/gkac1164
Salema, V., Marín, E., Martínez-Arteaga, R., Ruano-Gallego, D., Fraile, S., Margolles, Y., Teira, X., Gutierrez, C., Bodelón, G., & Fernández, L. Á. (2013). Selection of Single Domain Antibodies from Immune Libraries Displayed on the Surface of E. coli Cells with Two β-Domains of Opposite Topologies. PLoS ONE, 8(9). https://doi.org/10.1371/journal.pone.0075126
Schmitz, K. R., Bagchi, A., Roovers, R. C., Van Bergen En Henegouwen, P. M. P., & Ferguson, K. M. (2013). Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure, 21(7).https://doi.org/10.1016/j.str.2013.05.008
Waters, V. L. (2001). Conjugation between bacterial and mammalian cells. Nature Genetics, 29(4). https://doi.org/10.1038/ng779