Best Basic Part
1-2 sentence abstract
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<p> | <p> | ||
− | <style | + | <div |
− | + | style="background: url(https://cdn.pixabay.com/photo/2016/02/03/08/32/banner-1176676_1280.jpg); width: 1280px; height: 200px; display: flex; align-items: center; justify-content: center"> | |
− | + | <div class="title" style="color: antiquewhite">Best Basic Part</div> | |
− | + | </div> | |
− | + | ||
− | + | <div style="text-align: justify; hyphens: auto; font-size: 20px"> | |
− | + | <p> | |
− | + | <h1>The origin.</h1> | |
− | + | </p> | |
− | + | <p style="font-size: 20px"> | |
− | + | Inspired by the fast progress in synthetic biology and its urgent need for genetic tools that enable the | |
− | + | exploitation of cyanobacteria for research and biotechnological applications, we set out to construct the most | |
− | + | versatile shuttle vector for cyanobacteria based on the modular Golden Gate Assembly method, allowing for flexible | |
− | + | cloning into a reliable self-replicating system.<br> | |
− | + | </p> | |
− | + | <br> | |
− | + | <div style="width: 400px; height: 300px; float: left; margin: 0.5em"> | |
− | + | <figure> | |
− | + | <img style="display: block; margin: 0 auto 0 auto; width:100%" | |
− | + | src="https://lh3.googleusercontent.com/8ko4suiu3NQ_qmRIeZf1k1sg5EUw8g4JXfkGG3xAmRk1dxaVlZQbzC9Uz-6ToGKXaAf5p_yx9MVHhlO3QdMmG_l0ukJ0OVQOWBzcouM-HOTc_ta7LblxiVtTdLKrf9q4bpzP6ZRP" | |
− | + | alt="Lvl1 ori"> | |
− | + | <figcaption> | |
− | + | Fig.1 - Lvl1 ori | |
− | + | </figcaption> | |
− | + | </figure> | |
− | + | </div> | |
− | + | <p style="font-size: 20px"> | |
− | + | Introduction of exogenous DNA can be done in multiple ways and propagated in a strain if it is integrated in the | |
− | + | chromosome or stably expressed on a self-replicating plasmid.<br> For rapid prototyping in cyanobacteria | |
− | + | self-replicating plasmids are of higher interest than genome-integrations, as the latter can be quite | |
− | + | time-consuming in cyanobacterial strains with multiple genome copies (<a | |
− | + | href="https://www.ncbi.nlm.nih.gov/pubmed/22092711">Griese <i>et al.,</i> 2011</a>). Furthermore, genes | |
− | + | introduced in self-replicating vectors have been shown to have higher gene-expression levels than those integrated | |
− | + | in the genome, as copy numbers are typically higher (<a href="https://doi.org/10.1099/mic.0.000377">Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen <i>et | |
− | + | al.,</i> 2016</a>) – a desirable trait, not just for rapid prototyping in research applications, but also for | |
− | + | biotechnological production of valuable compounds.<br> | |
− | + | With our shuttle-vectors encompass a cyanobacterial origin of replication (ori) from <i>Synechococcus | |
− | + | elongatus</i> PCC7942 as well as an <i>E.coli</i> ori, which is perfect for fast cloning processes, as these | |
− | + | vectors can be easily recovered from the cyanobacteria and reintroduced in an <i>E.coli</i> strain.<br> | |
− | + | </p> | |
− | + | <br> | |
− | + | <p style="font-size: 20px"> | |
− | + | Currently existing shuttle vectors for cyanobacteria are still based on standard systems working with multiple | |
− | + | cloning sites (MCS) for expression of homologous genes (<a href="https://doi.org/10.1099/mic.0.000377">Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen <i>et | |
− | + | al.,</i> 2016</a>). A huge downside is that these vectors include either an MCS (e.g. pAM5188) or a | |
− | + | fluorescence reporter (e.g. pAM4787), which is unpractical for easy selection of recombinant clones. Additionally, | |
− | + | an MCS comes with possible sequence constraints due to restriction sites leaving unwanted base pairs in your | |
− | + | constructs.<br> | |
− | + | Facilitating and standardizing the process of engineering biological systems is one of the fundamental goals of | |
− | + | synthetic biology (<a href="https://doi.org/10.1186/1754-1611-2-5">Shetty Titel anhand dieser DOI in Citavi-Projekt übernehmen <i>et al.,</i> 2008</a>), so the | |
− | + | construction of a shuttle-vector based on a modular cloning method significantly improves the genetic toolbox we | |
− | + | created for genetic engineering and synthetic biology approaches in <i>S.elongatus</i> and other | |
− | + | cyanobacteria.<br> | |
− | + | </p> | |
− | + | <br> | |
− | + | <p style="font-size: 20px"> | |
− | + | The commonly used <i>S.elongatus</i> strain PCC7942 carries two endogenous plasmids, the 46,4kb pANL (<a | |
− | + | href="https://www.ncbi.nlm.nih.gov/pubmed/18353436">Chen <i>et al.,</i> 2008</a>) which is essential and the | |
− | + | 7,8kb pANS (<a href="https://www.ncbi.nlm.nih.gov/pubmed/1552863">Van der Plas <i>et al.,</i> 1992</a>) which is | |
− | + | not essential for the strain and can easily be cured.<br> | |
− | + | This small plasmid has already been used for construction of shuttle vectors (<a | |
− | + | href="https://doi.org/10.1016/0076-6879(87)53054-3">Kuhlemeier Titel anhand dieser DOI in Citavi-Projekt übernehmen & van Arkel, 1987</a> ; <a | |
− | + | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC217787/">Golden & Sherman, 1983</a> ; <a | |
− | + | href="https://doi.org/10.1099/mic.0.000377">Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen <i>et al.,</i> 2016</a>). <br> | |
− | + | We followed this lead to create the best shuttle-vector available for cyanobacteria by encompassing the minimal | |
− | + | replication region of pANS and the ColE1 origin of replication into our vectors, allowing for stable | |
− | + | self-replication with high copy numbers in cyanobacteria (<a href="https://doi.org/10.1099/mic.0.000377">Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen | |
− | + | <i>et al.,</i> 2016</a>) and <i>E.coli</i> (<a href="https://doi.org/10.1016/S0065-2660(02)46013-0">Gerhart Titel anhand dieser DOI in Citavi-Projekt übernehmen | |
− | + | <i>et al.,</i>2002</a>). This addition to the genetic toolbox proves invaluable, as it can be easily recovered | |
− | + | from the cyanobacterial strain and reintroduced in <i>E.coli</i> for fast GoldenGate-based cloning processes.<br> | |
− | + | </p> | |
− | + | <br> | |
− | + | <p style="font-size: 20px"> | |
− | + | In order to supply the community with an easy selection system, we equipped our shuttle vector with a fluorescent | |
− | + | reporter that is cut out when introducing new genetic parts:<br> | |
− | + | A mRFP (red fluorescent protein) cassette is flanked by our standardized TypeIIS restriction enzyme recognition | |
− | + | sequences (BsmBI or BsaI depending on what level you want to clone in). In a standard Golden Gate reaction this | |
− | + | cassette will drop out and leave space for the parts that should be introduced, allowing for easy selection on | |
− | + | plate after successful cloning – red colonies are wrong, still harboring the mRFP cassette and white colonies (if | |
− | + | no other fluorescence is introduced) are correct, as the mRFP was switched with the parts of interest.<br> | |
− | + | <br> | |
− | + | This crucial part comes in two variations - one for cloning Lvl1 and one for Lvl2 constructs -, giving the Golden | |
− | + | Gate community everything they need for successful and reliable creation of self-replicating vectors in | |
− | + | cyanobacteria. | |
− | + | </p> | |
− | + | <br> | |
− | + | </p> | |
− | + | </div> | |
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</p> | </p> | ||
<br> | <br> |
With our additional created parts, we expanded the current Marburg Collection.
1-2 sentence abstract
Inspired by the fast progress in synthetic biology and its urgent need for genetic tools that enable the
exploitation of cyanobacteria for research and biotechnological applications, we set out to construct the most
versatile shuttle vector for cyanobacteria based on the modular Golden Gate Assembly method, allowing for flexible
cloning into a reliable self-replicating system.
Introduction of exogenous DNA can be done in multiple ways and propagated in a strain if it is integrated in the
chromosome or stably expressed on a self-replicating plasmid.
For rapid prototyping in cyanobacteria
self-replicating plasmids are of higher interest than genome-integrations, as the latter can be quite
time-consuming in cyanobacterial strains with multiple genome copies (Griese et al., 2011). Furthermore, genes
introduced in self-replicating vectors have been shown to have higher gene-expression levels than those integrated
in the genome, as copy numbers are typically higher (Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen et
al., 2016) – a desirable trait, not just for rapid prototyping in research applications, but also for
biotechnological production of valuable compounds.
With our shuttle-vectors encompass a cyanobacterial origin of replication (ori) from Synechococcus
elongatus PCC7942 as well as an E.coli ori, which is perfect for fast cloning processes, as these
vectors can be easily recovered from the cyanobacteria and reintroduced in an E.coli strain.
Currently existing shuttle vectors for cyanobacteria are still based on standard systems working with multiple
cloning sites (MCS) for expression of homologous genes (Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen et
al., 2016). A huge downside is that these vectors include either an MCS (e.g. pAM5188) or a
fluorescence reporter (e.g. pAM4787), which is unpractical for easy selection of recombinant clones. Additionally,
an MCS comes with possible sequence constraints due to restriction sites leaving unwanted base pairs in your
constructs.
Facilitating and standardizing the process of engineering biological systems is one of the fundamental goals of
synthetic biology (Shetty Titel anhand dieser DOI in Citavi-Projekt übernehmen et al., 2008), so the
construction of a shuttle-vector based on a modular cloning method significantly improves the genetic toolbox we
created for genetic engineering and synthetic biology approaches in S.elongatus and other
cyanobacteria.
The commonly used S.elongatus strain PCC7942 carries two endogenous plasmids, the 46,4kb pANL (Chen et al., 2008) which is essential and the
7,8kb pANS (Van der Plas et al., 1992) which is
not essential for the strain and can easily be cured.
This small plasmid has already been used for construction of shuttle vectors (Kuhlemeier Titel anhand dieser DOI in Citavi-Projekt übernehmen & van Arkel, 1987 ; Golden & Sherman, 1983 ; Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen et al., 2016).
We followed this lead to create the best shuttle-vector available for cyanobacteria by encompassing the minimal
replication region of pANS and the ColE1 origin of replication into our vectors, allowing for stable
self-replication with high copy numbers in cyanobacteria (Chen Titel anhand dieser DOI in Citavi-Projekt übernehmen
et al., 2016) and E.coli (Gerhart Titel anhand dieser DOI in Citavi-Projekt übernehmen
et al.,2002). This addition to the genetic toolbox proves invaluable, as it can be easily recovered
from the cyanobacterial strain and reintroduced in E.coli for fast GoldenGate-based cloning processes.
In order to supply the community with an easy selection system, we equipped our shuttle vector with a fluorescent
reporter that is cut out when introducing new genetic parts:
A mRFP (red fluorescent protein) cassette is flanked by our standardized TypeIIS restriction enzyme recognition
sequences (BsmBI or BsaI depending on what level you want to clone in). In a standard Golden Gate reaction this
cassette will drop out and leave space for the parts that should be introduced, allowing for easy selection on
plate after successful cloning – red colonies are wrong, still harboring the mRFP cassette and white colonies (if
no other fluorescence is introduced) are correct, as the mRFP was switched with the parts of interest.
This crucial part comes in two variations - one for cloning Lvl1 and one for Lvl2 constructs -, giving the Golden
Gate community everything they need for successful and reliable creation of self-replicating vectors in
cyanobacteria.
1-2 sentence abstract
Hier bitte den für diese Stelle zutreffenden Text einfügen, wenn dieser fertig ist.
1-2 sentence abstract
Parts of the Marburg Collection 2.0
Download the "Marburg Collection 2.0" (als downloadlinkg und symbol zum download dazu)
Download all 5'Connectors (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228000 | aNSo1 integration up |
K3228001 | aNSo2 integration up |
K3228020 | NS1 up |
K3228021 | NS2 up |
K3228022 | NS3 up |
Download all 3'Homology Connectors (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228002 | aNSo1 integration down |
K3228003 | aNSo2 integration down |
K3228023 | NS1 down |
K3228024 | NS2 down |
K3228025 | NS3 down |
Download all Promotors (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228053 | T7 consensus Promotor |
Download all Terminators (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228004 | shortTB0010 |
K3228005 | shortTB0015 |
K3228006 | shortTB1002 |
K3228007 | shortTB1003 |
K3228008 | shortTB1004 |
K3228009 | shortTB1005 |
K3228010 | shortTB1006 |
K3228011 | shortTB1007 |
K3228012 | shortTB1008 |
K3228013 | shortTB1009 |
K3228014 | shortTB1010 |
K3228015 | shortDummy |
Download all Antibiotic Resistances (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228016 | SpecRes_short |
K3228017 | CmlRes_short |
K3228018 | TetRes_short |
K3228019 | KanRes_short |
K3228027 | GenRes_short |
Download all Shuttle Vectors (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228026 | oriT integration |
K3228069 | panS SpecRes LVL1 |
K3228089 | panS KanRes LVL2 |
Download all Coding Sequences (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228040 | NanoLuc-K1159001 |
K3228041 | NanoLuc (S.e.) |
K3228042 | TeLuc (S.e.) |
K3228043 | Antares2 (S.e.) |
K3228044 | eYFP-E0030 |
K3228045 | sYFP2 (S.e.) |
K3228046 | pHlourin2 (S.e.) |
K3228047 | rxYFP (S.e.) |
K3228048 | sfGFP (S.e.) |
K3228049 | mTurquoise2 (S.e.) |
K3228050 | T7-Polymerase (S.e.) |
K3228051 | Limonene Synthase |
K3228052 | Farnesen Synthase |
K3228100 | cpf1 |
Download all Ribosome-Binding Sites (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228054 | riboJ B0034 |
K3228055 | riboJ B0034 noScar |
K3228056 | SarJ B0034 |
K3228057 | PlmJ B0034 |
Download all Spaceholders (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228060 | PRO placeholder. |
K3228061 | RBS placeholder |
K3228062 | CDS placeholder |
K3228063 | TER placeholder |
Download all Standard Measurement Vectors (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228073 | PRO S.e. |
K3228074 | RBS S.e. |
K3228075 | CDS S.e. |
K3228090 | Ter S.e. |
Download the CRISPR-Kit (Download Symbol für Download)
BioBrick | Name |
---|---|
K3228101 | crRNA-GFP dropout |
K3228103 | cpf1+crRNA-GFP dropout |