Difference between revisions of "Part:BBa K2560107"
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<p align="justify">This is the Phytobrick version of the connector 5'Con1 Res and was build as a part of the Marburg Collection. Instructions of how to use the Marburg Collection are provided at the bottom of the page. </p>
 
<p align="justify">This is the Phytobrick version of the connector 5'Con1 Res and was build as a part of the Marburg Collection. Instructions of how to use the Marburg Collection are provided at the bottom of the page. </p>
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===Overview===
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One novel key feature of our toolbox are the connectors. They were designed in order to function as insulators to prevent crosstalk between neighboring transcription units <a href="http://2018.igem.org/Team:Marburg/Design">(Design of the Marburg Collection)</a>. Therefore a perfectly insulating connector would prevent the readthrough from backbone sequences that most probably caused the notably high expression that was measured in the promoter experiment for the dummy promoter <a href="https://parts.igem.org/Part:BBa_K2560007#Characterization">(Promoter experiment)</a>. In addition to blocking transcriptional readthrough, a good connector must not possess any cryptic promoter activity.
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===Characterization===
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We focused on characterizing the 5’ Connector because we expect the stronger influence on signal strengths. For characterizing our connector parts, we created 20 test plasmids with the <a href="https://parts.igem.org/Part:BBa_K2560051"><i>lux</i> operon</a> as the reporter. <br>
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In our toolbox we provide five short connectors, which solely possess the fusion sites for LVL2 cloning, and five long connectors which additionally harbor self-designed insulators. Each of these ten connectors were cloned with the constitutive promoter <a href="https://parts.igem.org/Part:BBa_K2560007">K2560007 </a> (J23100), to check for effects on an active promoter, and with the Promoter Dummy to quantify the extent of transcriptional activity that reaches the Promoter Dummy. <br>
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    <div><img src="https://static.igem.org/mediawiki/2018/f/ff/T--Marburg--Connectoren%2BLux.png">A</div>
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    <div><img src="https://static.igem.org/mediawiki/2018/d/d5/T--Marburg--Connectoren%2BDLux.png">B</div>
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            <figcaption><b>Figure 1: <br> Results of Connector measurmenet</b> <br> A) Connector constructs built with J23100 as promoter part <br> B) Connector constructs built with the Dummy Promoter as promoter part
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===Result===
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The acquired data are shown in figure 1. The data were normalized over the test construct J23100, that was used in the promoter experiment and constructed with the connector dummies. For the five constructs with the active promoter and the long connectors we observed extremely varying signals. We measured a range from 0.2 to 2 fold change compared to the reference construct. It has been shown that the sequence directly upstream of small synthetic promoters can greatly impact the transcription efficiency <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176013"><abbr title =" Swati B. Carr, Jacob Beal, Douglas M. Densmore , Reducing DNA context dependence in bacterial promoters (2017)" >( Carr <i>et al.</i>2017)</abbr></a>. In case of the long connectors, the sequence upstream of the promoter forms the terminator and could affect the efficiency of RNA-polymerase binding to the -35 and -10 regions. For the constructs built with small connectors, we also observed varying signals but to a lesser extent compared to the long connectors.
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For all ten connectors that are provided in our toolbox, we show a tenfold range in the measured luminescence/OD600 signal. As a conclusion, we recommend to carefully consider the combination of promoter and 5’ Connector for rationally designing constructs. <br><br>
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Taking a look at the constructs that were built with the Promoter Dummy, we also see a huge difference in the expression signals. For the long connectors we expected a negligibly low reporter expression which we observed for two out of five long 5’ Connectors resulting in a 14 fold signal reduction compared to the “Promoter Dummy” reference. The remarkably strong signal observed for the remaining three connectors could be due to inefficient terminators or cryptic promoters in the pretended “neutral sequence”. <br><br>
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For the remaining five constructs possessing the five short 5’ connectors we observed a range from 0.3 to 5.5 fold compared to the “Promoter Dummy” reference. We are not able to give an experimental explanation for this observation but we could imagine that the LVL2 fusion sites, the only four bases that differ in these constructs, could constitute a weak promoter together with surrounding sequences.<br>
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Summarizing the connector characterization, we found that sequences upstream of short synthetic promoters greatly affect reporter expression, which is in accordance with literature <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176013"><abbr title =" Swati B. Carr, Jacob Beal, Douglas M. Densmore , Reducing DNA context dependence in bacterial promoters (2017)" >( Carr <i>et al.</i>2017)</abbr></a>. Moreover, we demonstrated that two of our five self-designed connectors efficiently reduce the signal resulting from other sources than the actual promoter.
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We additionally conclude that algorithms that predict the “neutrality” of sequences alone are not sufficient to create well functioning insulators.
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Revision as of 23:31, 16 October 2018


Phytobrick version of 5'Con1_L1_Res Connector

This is the Phytobrick version of the connector 5'Con1 Res and was build as a part of the Marburg Collection. Instructions of how to use the Marburg Collection are provided at the bottom of the page.

Overview

One novel key feature of our toolbox are the connectors. They were designed in order to function as insulators to prevent crosstalk between neighboring transcription units (Design of the Marburg Collection). Therefore a perfectly insulating connector would prevent the readthrough from backbone sequences that most probably caused the notably high expression that was measured in the promoter experiment for the dummy promoter (Promoter experiment). In addition to blocking transcriptional readthrough, a good connector must not possess any cryptic promoter activity.

Characterization

We focused on characterizing the 5’ Connector because we expect the stronger influence on signal strengths. For characterizing our connector parts, we created 20 test plasmids with the lux operon as the reporter.
In our toolbox we provide five short connectors, which solely possess the fusion sites for LVL2 cloning, and five long connectors which additionally harbor self-designed insulators. Each of these ten connectors were cloned with the constitutive promoter K2560007 (J23100), to check for effects on an active promoter, and with the Promoter Dummy to quantify the extent of transcriptional activity that reaches the Promoter Dummy.

A
B
Figure 1:
Results of Connector measurmenet
A) Connector constructs built with J23100 as promoter part
B) Connector constructs built with the Dummy Promoter as promoter part

Result

The acquired data are shown in figure 1. The data were normalized over the test construct J23100, that was used in the promoter experiment and constructed with the connector dummies. For the five constructs with the active promoter and the long connectors we observed extremely varying signals. We measured a range from 0.2 to 2 fold change compared to the reference construct. It has been shown that the sequence directly upstream of small synthetic promoters can greatly impact the transcription efficiency ( Carr et al.2017). In case of the long connectors, the sequence upstream of the promoter forms the terminator and could affect the efficiency of RNA-polymerase binding to the -35 and -10 regions. For the constructs built with small connectors, we also observed varying signals but to a lesser extent compared to the long connectors. For all ten connectors that are provided in our toolbox, we show a tenfold range in the measured luminescence/OD600 signal. As a conclusion, we recommend to carefully consider the combination of promoter and 5’ Connector for rationally designing constructs.

Taking a look at the constructs that were built with the Promoter Dummy, we also see a huge difference in the expression signals. For the long connectors we expected a negligibly low reporter expression which we observed for two out of five long 5’ Connectors resulting in a 14 fold signal reduction compared to the “Promoter Dummy” reference. The remarkably strong signal observed for the remaining three connectors could be due to inefficient terminators or cryptic promoters in the pretended “neutral sequence”.

For the remaining five constructs possessing the five short 5’ connectors we observed a range from 0.3 to 5.5 fold compared to the “Promoter Dummy” reference. We are not able to give an experimental explanation for this observation but we could imagine that the LVL2 fusion sites, the only four bases that differ in these constructs, could constitute a weak promoter together with surrounding sequences.
Summarizing the connector characterization, we found that sequences upstream of short synthetic promoters greatly affect reporter expression, which is in accordance with literature ( Carr et al.2017). Moreover, we demonstrated that two of our five self-designed connectors efficiently reduce the signal resulting from other sources than the actual promoter. We additionally conclude that algorithms that predict the “neutrality” of sequences alone are not sufficient to create well functioning insulators.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Marburg Toolbox

We proudly present the Marburg Collection, a novel golden-gate-based toolbox containing various parts that are compatible with the PhytoBrick system and MoClo. Compared to other bacterial toolboxes, the Marburg Collection shines with superior flexibility. We overcame the rigid paradigm of plasmid construction - thinking in fixed backbone and insert categories - by achieving complete de novo assembly of plasmids.

36 connectors facilitate flexible cloning of multigene constructs and even allow for the inversion of individual transcription units. Additionally, our connectors function as insulators to avoid undesired crosstalk.

The Marburg Collection contains 123 parts in total, including:
inducible promoters, reporters, fluorescence and epitope tags, oris, resistance cassettes and genome engineering tools. To increase the value of the Marburg Collection, we additionally provide detailed experimental characterization for V. natriegens and a supportive software. We aspire availability of our toolbox for future iGEM teams to empower accelerated progression in their ambitious projects.


Figure 3: Hierarchical cloning is facilitated by subsequent Golden Gate reactions.
Basic building blocks like promoters or terminators are stored in level 0 plasmids. Parts from each category of our collection can be chosen to built level 1 plasmids harboring a single transcription unit. Up to five transcription units can be assembled into a level 2 plasmid.
Figure 4: Additional bases and fusion sites ensure correct spacing and allow tags.
Between some parts, additional base pairs were integrated to ensure correct spacing and to maintain the triplet code. We expanded our toolbox by providing N- and C- terminal tags by creating novel fusions and splitting the CDS and terminator part, respectively.


Parts of the Marburg Toolbox




Tags and Entry Vectors




  • K2560001 (Entry Vector with RFP dropout)
  • K2560002 (Entry Vector with GFP dropout)
  • K2560005 (Resistance Entry Vector with RFP Dropout)
  • K2560006 (Resistance Entry Vector with GFP Dropout)
  • K2560305 (gRNA Entry Vector with GFP Dropout)