Difference between revisions of "Part:BBa K3128015"

(Sequence and features)
 
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__NOTOC__
 
 
<partinfo>BBa_K3128015 short</partinfo>
 
<partinfo>BBa_K3128015 short</partinfo>
  
 
==Sequence and features==
 
==Sequence and features==
 
<div style="text-align:justify;">   
 
<div style="text-align:justify;">   
This biobrick is composed of the external membrane OMPx WT protein fused at its N-terminal end with a 54 aa GGS linker (BBa_K3128010) followed by the T18 subunit of the Bordetella Pertussis adenylate cyclase. This biobrick is under plac promoter, thus the expression of the OmpX protein can be activated with IPTG.
+
This biobrick is composed of the external membrane [https://parts.igem.org/Part:BBa_K3128032 Clickabe Outer Membrane Protein X <i>(COMP)</i>]
 +
protein fused at its N-terminal end to a 54 aa [https://parts.igem.org/wiki/index.php?title=Part:BBa_K3128010 Gly-Gly-Ser Linker (GGS)]
 +
followed by the [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1638004 T18 sub-part of the <i>Bordetella Pertussis</i> adenylate cyclase] (AC) .<br>
  
This biobrick has a TAG codon (Y121F' mutation) which can be used to introduce any Non Natural Amino acid outside the cell ([https://parts.igem.org/Part:BBa_K1492000_medium more informations]).
+
<br>
 +
'''COMP''' correspond to '''OmpX-WT''' that has a TAG codon (Y121F' mutation) which can be used to introduce an '''non natural amino acid''' in the primary structure of proteins ([https://parts.igem.org/Part:BBa_K1492002 more informations]). The non natural amino acid allows the click-recation with an DIBO-aptamer on COMP, the aptamer will then  be in external environment of the bacteria and hooked to COMP. The intracellular part constitutes the signalling  cascade of the biomarker detection (BACTH assay).<br>
 +
 +
<br>
 +
'''iGEM Grenoble-Alpes''' designed this biobrick with the '''pUT18''' plasmid present in the '''Euromedex BACTH kit''' (more informations in the design page).<br>
 +
It is an '''intermediate''' because the team want to switch the '''promoter lactose''' already present in pUT18 by a constitutive promoter.<br>
 +
It will allows the bacteria to have a huge quantity of proteins located in the membrane before the target is added to the external environment thus incresing the sensitivity of the NeuroDrop system.<br>
 +
In addition, we chose to have only one gene under cAMP inducible CAP dependant '''PLac promoter''' in its final system: the reporter gene, in order to do a membrane Bacterial Adenylate Cyclase Two Hybrid.<br>
  
iGEM Grenoble-Alpes designed this biobrick thanks to the pUT18 plasmid contained in the Euromedex BACTH kit (more informations in the design page). It is an '''intermediate''' because the team want to change the plac promoter with a constitutive promoter. It allows the bacteria to have a huge quantity of proteins located in the membrane before the target is added to the external environment (thus, before the detection). In addition, the team needs just one gene under cAMP inducible CAP dependant '''plac promoter''' in its final system: the reporter gene, in order to do a membrane Bacterial Adenylate Cyclase Two Hybrid.
+
<br>This BioBrick is intended to opperate with [https://parts.igem.org/wiki/index.php?title=Part:BBa_K3128016 BBa_K3128016].<br>
 +
These two biobricks are the negative condition of the '''mBACTH''' <i>-free sub-parts condition-</i>.<br>
 +
OmpX proteins are fused to the adenylate cyclase sub-parts at their N-terminal ends. The fusion protein '''move freely''' in the bacterial outer membrane,  
 +
but they are not forced to get closer by any mean. <br>
 +
The reconstitution of the adenylate cyclase in this condition is only due to random occurrence between both parts.<br>
 +
The signal measured is considered as background noise.
  
 
</div>
 
</div>
  
  
<partinfo>BBa_K3128011 SequenceAndFeatures</partinfo>
+
<partinfo>BBa_K3128015 SequenceAndFeatures</partinfo>
  
 +
<br>
  
===Usage and Biology===
+
==Usage and Biology==
 
<div style="text-align:justify;">   
 
<div style="text-align:justify;">   
In 1989, Fields and Song demonstrated a new genetic system allowing protein-protein interaction detection <sup>(1)</sup>. At first, it was done in ''Saccharomyces cerevisiae'' yeast and it was called the yeast two-hybrid assay (Y2H). In 1998, Ladant and al. described the system in bacteria <sup>(2)</sup>. Nowadays, this biological technique is mostly used to show and characterize the physical interaction between two cytosolic proteins or internal membrane proteins in vivo <sup>(3)</sup>.  
+
In 1989, Fields and Song demonstrated a new genetic system allowing the detection of protein-protein interaction <sup>(1)</sup>. At first, it was performed in ''Saccharomyces cerevisiae''  
 +
yeast and it was called the yeast two-hybrid assay (Y2H). In 1998, Ladant and al. described the system in bacteria <sup>(2)</sup>. Nowadays, this biological technique is mostly  
 +
used to show and characterize the physical interaction between two cytosolic proteins or internal membrane proteins in vivo <sup>(3)</sup>.  
 +
<br>
  
 +
<br>
 +
===<u>Bacterial Adenylate Cyclase Two-Hybrid</u> (BACTH)===
 +
<div style="text-align:justify;"> 
  
===BACTH Principle===
+
<br>The principle lies on the interaction-mediated reconstitution of a signalling cascade in <i>Escherichia coli</i>. The messenger molecule involved in this cascade is the
 +
cyclic adenosine monophosphate (cAMP) produced by the adenylate cyclase. Adenylate cyclase is an enzyme catalysing the cAMP production from ATP. It
 +
physiologically participates to the cellular transmission. <br>
  
https://static.igem.org/mediawiki/parts/0/0b/BACTH_constructions.gif
+
<br>This system involves the <i>Bordetella pertussis</i> '''adenylate cyclase'''. You might know this bacterium; it is the responsible agent for the pertussis disease.
 +
It adenylates cyclase catalytic domain has the particularity to be splittable in two distinct parts: '''T18''' and '''T25''' sub-parts, <u>unable to work unless they
 +
reassociate.</u> Each sub-part of the enzyme is fused with a protein of interest, either the bait or the prey protein chose beforehand by the experimentator. <br>
  
The BACTH principle lies on the interaction-mediated reconstitution of a signaling cascade in ''Escherichia Coli'' bacteria. The messenger molecule involved in this cascade is the cyclic adenosine monophosphate (cAMP) produced by the adenylate cyclase. The adenylate cyclase is an enzyme catalysing the cAMP production from ATP, it physiologically participates to the cellular transmission.  
+
<span style="margin: 12%;">
 +
https://2019.igem.org/wiki/images/e/ec/T--Grenoble-Alpes--BACTH_classicBACTH.gif
 +
</span>
  
 +
<br>If the proteins interact, then '''T18''' and '''T25''' are bring together and reconstitute a <u>functional adenylate cyclase enzyme</u> thus enabling cAMP production. Using
 +
<i>cya-</i> bacteria<i> – strain for whom the adenylate gene is deleted, involving an absence of this endogenous enzyme – </i> a BACTH could be done with the creation of two
 +
fusion proteins : the first one, fused at its N or C terminal intracellular end with the '''T18 sub-part'''; the second one fused with the '''T25 sub-part'''. <br>
 +
The interaction of these proteins of interest will lead to the adenylate cyclase reconstitution, thus <u>initiating cAMP production</u>. The cAMP produced will act as a
 +
messenger by fixing itself to the transcriptional activator CAP, cAMP form the <u>CAP-cAMP</u> complex, controlling the expression of the promoter lactose by '''initiating transcription of the following gene'''. <br>
 +
This promoter is placed upstream from the chosen reporter gene.<br>
 +
</div>
  
In this system, the Bordetella pertussis adenylate cyclase, responsible agent for the pertussis, is involved. Its catalytical domain has the particularity to may be split in two distinct parts: T18 and T25 fragments, unable to work unless they reassociate. Each part of the enzyme is fused with a protein, either the bait or the prey protein. If the proteins interact, then T18 and T25 get sufficient closer and reconstitute a functional enzyme, thus allowing cAMP production. By using cya- bacteria ''–bacteria for whom the adenylate gene was deleted, involving an absence of this endogenous enzyme –'' a BACTH could be done with the creation of two fusion proteins : the first one, fused at its N or C terminal intracellular end with T18 fragment; the second one fused with T25 fragment.
+
<br>
  
 +
===<u>NeuroDrop Project - inter-Membrane BACTH</u> (mBACTH) ===
 +
<div style="text-align:justify;">
 +
<br>
 +
https://static.igem.org/mediawiki/parts/0/0b/BACTH_constructions.gif
 +
<br>
 +
<br>[http://2015.igem.org/Team:TU_Eindhoven Eindhoven-2015] iGEM project’s aim was to develop a “universal membrane sensor platform for biosensors”.<br>
 +
This year, '''Team Grenoble-Alpes''' is designing a new tears biosensor system based on [http://2015.igem.org/Team:TU_Eindhoven Eindhoven-2015]’s project.
 +
Both projects have a common base, the same receptors are used at the external surface of bacteria : '''[https://parts.igem.org/Part:BBa_K1492000 Clickable Outer Membrane Protein called COMP]'''. <br>
  
The interaction of these protein of interest will lead to the adenylate cyclase reconstitution, and the cAMP produced will have a messenger role. By fixing itself to the transcriptional activator CAP, cAMP form the CAP/cAMP complex, controlling the expression of a plac inducible promoter. This promoter is placed upstream the chosen reporter gene.
+
OmpX is an outer membrane protein with the C- and N-termini in the intracellular domain. To be able to use OmpX as a scaffold, a unnatural amino acid needs to be introduced.
 +
This can be done by implementing the amber stop codon TAG in one of the loops of OmpX via a mutation. With a specific tRNA an azide-functionalized amino acid can be built in,
 +
which can be used for the SPAAC click chemistry reaction with DBCO functionalized groups, this modified protein is called '''COMP'''.
 +
The complex '''aptamer''' fixed to a '''COMP''' is then called a '''COMB''' for '''Clickable Outer Membrane Biosensor'''.<br>
  
===NeuroDrop Project - Membrane BACTH ===
+
<br>The Grenoble-Alpes team aims to develop an '''intermembrane Bacterial Adenylate Cyclase Two Hybrid''' <i>(mBACTH)</i>.<br>
 +
In this case, the two adenylate cyclase sub-parts are fused to the N-terminal ends of '''COMPs''' with a [https://parts.igem.org/wiki/index.php?title=Part:BBa_K3128010 Gly-Gly-Ser Linker (GGS)] of 54 amino acids <i>- in order to ensure a sufficient flexibility -</i>.<br>
 +
When '''COMPs''' and the aptamers catch the extracellular target, they get closer, thus allowing the reconstitution of a functional adenylate cyclase due to the physical proximity of
 +
the two sub-parts.<br>
 +
The enzyme is operational again and can produce the production of a high quantity of '''cAMP''' <i>(around 17,000 mmol of cAMP formed per mg of adenylate cyclase per minute)</i>,
 +
<u>the molecule responsible of the signal transduction in the bacterium</u>.<br>
 +
https://static.igem.org/mediawiki/parts/e/ec/BACTH_1.gif <br>
  
iGEM Grenoble-Alpes team have chose to create a membrane bacterial two hybrid by using the OmpX protein, fused with adenylate cyclase subparts.  
+
<br>'''cAMP''' molecules diffuse to the cytoplasm of the bacterium and interact with catabolite activator proteins (CAP). One '''cAMP molecule''' binds to one transcriptional activator CAP;
 
+
then two '''cAMP-CA'''P complexes are needed to activate the <u>expression of the gene under the control of the lactose promoter</u>.<br>
https://static.igem.org/mediawiki/parts/e/ec/BACTH_1.gif
+
Because of the high quantity of cAMP diffusing in the cytoplasm of the bacterium (2), the reporter gene is continually activated as long as cAMP is produced.<br>
https://static.igem.org/mediawiki/parts/f/fd/BACTH_2.gif
+
https://static.igem.org/mediawiki/parts/f/fd/BACTH_2.gif <br>
  
 +
<br>The high enzymatic activity (1) of <i>Bordetella pertussis</i> Adenylate Cyclase involves a high production of '''cAMP''' in presence of ATP in the bacterium
 +
thus <u>activating the signaling cascade with the CAP-cAMP dependant promoter</u>.<br>
 +
Hence this system is promising because it might have a great sensitivity and may give a great signal amplification for a low amount of target detected.<br>
 
</div>
 
</div>
  
==References==
+
<br>
<sup>(1)</sup> Fields S, Song O. A novel genetic system to detect protein–protein interactions. Nature [Internet]. 1989
+
  
<sup>(2)</sup> Karimova G, Pidoux J, Ullmann A, Ladant D. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. PNAS [Internet]. 1998
+
==References==
 
+
<i>
<sup>(3)</sup> Karimova G, Gauliard E, Davi M, P.Ouellette S, Ladant D. Protein–Protein Interaction: Bacterial Two-Hybrid. 2017
+
<sup>(1)</sup> Fields S, Song O. A novel genetic system to detect protein–protein interactions. Nature [Internet]. 1989<br>
 +
<sup>(2)</sup> Karimova G, Pidoux J, Ullmann A, Ladant D. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. PNAS [Internet]. 1998<br>
 +
<sup>(3)</sup> Karimova G, Gauliard E, Davi M, P.Ouellette S, Ladant D. Protein–Protein Interaction: Bacterial Two-Hybrid. 2017<br>
 +
</i>

Latest revision as of 11:57, 21 October 2019

COMP fused with T18 subpart of Bordetella Pertussis adenylate cyclase under lactose promoter

Sequence and features

This biobrick is composed of the external membrane Clickabe Outer Membrane Protein X (COMP) protein fused at its N-terminal end to a 54 aa Gly-Gly-Ser Linker (GGS) followed by the T18 sub-part of the Bordetella Pertussis adenylate cyclase (AC) .


COMP correspond to OmpX-WT that has a TAG codon (Y121F' mutation) which can be used to introduce an non natural amino acid in the primary structure of proteins (more informations). The non natural amino acid allows the click-recation with an DIBO-aptamer on COMP, the aptamer will then be in external environment of the bacteria and hooked to COMP. The intracellular part constitutes the signalling cascade of the biomarker detection (BACTH assay).


iGEM Grenoble-Alpes designed this biobrick with the pUT18 plasmid present in the Euromedex BACTH kit (more informations in the design page).
It is an intermediate because the team want to switch the promoter lactose already present in pUT18 by a constitutive promoter.
It will allows the bacteria to have a huge quantity of proteins located in the membrane before the target is added to the external environment thus incresing the sensitivity of the NeuroDrop system.
In addition, we chose to have only one gene under cAMP inducible CAP dependant PLac promoter in its final system: the reporter gene, in order to do a membrane Bacterial Adenylate Cyclase Two Hybrid.


This BioBrick is intended to opperate with BBa_K3128016.
These two biobricks are the negative condition of the mBACTH -free sub-parts condition-.
OmpX proteins are fused to the adenylate cyclase sub-parts at their N-terminal ends. The fusion protein move freely in the bacterial outer membrane, but they are not forced to get closer by any mean.
The reconstitution of the adenylate cyclase in this condition is only due to random occurrence between both parts.
The signal measured is considered as background noise.



Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 1465
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 1006
    Illegal NgoMIV site found at 1416
    Illegal AgeI site found at 1222
  • 1000
    COMPATIBLE WITH RFC[1000]


Usage and Biology

In 1989, Fields and Song demonstrated a new genetic system allowing the detection of protein-protein interaction (1). At first, it was performed in Saccharomyces cerevisiae yeast and it was called the yeast two-hybrid assay (Y2H). In 1998, Ladant and al. described the system in bacteria (2). Nowadays, this biological technique is mostly used to show and characterize the physical interaction between two cytosolic proteins or internal membrane proteins in vivo (3).


Bacterial Adenylate Cyclase Two-Hybrid (BACTH)


The principle lies on the interaction-mediated reconstitution of a signalling cascade in Escherichia coli. The messenger molecule involved in this cascade is the cyclic adenosine monophosphate (cAMP) produced by the adenylate cyclase. Adenylate cyclase is an enzyme catalysing the cAMP production from ATP. It physiologically participates to the cellular transmission.


This system involves the Bordetella pertussis adenylate cyclase. You might know this bacterium; it is the responsible agent for the pertussis disease. It adenylates cyclase catalytic domain has the particularity to be splittable in two distinct parts: T18 and T25 sub-parts, unable to work unless they reassociate. Each sub-part of the enzyme is fused with a protein of interest, either the bait or the prey protein chose beforehand by the experimentator.

T--Grenoble-Alpes--BACTH_classicBACTH.gif


If the proteins interact, then T18 and T25 are bring together and reconstitute a functional adenylate cyclase enzyme thus enabling cAMP production. Using cya- bacteria – strain for whom the adenylate gene is deleted, involving an absence of this endogenous enzyme – a BACTH could be done with the creation of two fusion proteins : the first one, fused at its N or C terminal intracellular end with the T18 sub-part; the second one fused with the T25 sub-part.
The interaction of these proteins of interest will lead to the adenylate cyclase reconstitution, thus initiating cAMP production. The cAMP produced will act as a messenger by fixing itself to the transcriptional activator CAP, cAMP form the CAP-cAMP complex, controlling the expression of the promoter lactose by initiating transcription of the following gene.
This promoter is placed upstream from the chosen reporter gene.


NeuroDrop Project - inter-Membrane BACTH (mBACTH)


BACTH_constructions.gif

[http://2015.igem.org/Team:TU_Eindhoven Eindhoven-2015] iGEM project’s aim was to develop a “universal membrane sensor platform for biosensors”.
This year, Team Grenoble-Alpes is designing a new tears biosensor system based on [http://2015.igem.org/Team:TU_Eindhoven Eindhoven-2015]’s project. Both projects have a common base, the same receptors are used at the external surface of bacteria : Clickable Outer Membrane Protein called COMP.

OmpX is an outer membrane protein with the C- and N-termini in the intracellular domain. To be able to use OmpX as a scaffold, a unnatural amino acid needs to be introduced. This can be done by implementing the amber stop codon TAG in one of the loops of OmpX via a mutation. With a specific tRNA an azide-functionalized amino acid can be built in, which can be used for the SPAAC click chemistry reaction with DBCO functionalized groups, this modified protein is called COMP. The complex aptamer fixed to a COMP is then called a COMB for Clickable Outer Membrane Biosensor.


The Grenoble-Alpes team aims to develop an intermembrane Bacterial Adenylate Cyclase Two Hybrid (mBACTH).
In this case, the two adenylate cyclase sub-parts are fused to the N-terminal ends of COMPs with a Gly-Gly-Ser Linker (GGS) of 54 amino acids - in order to ensure a sufficient flexibility -.
When COMPs and the aptamers catch the extracellular target, they get closer, thus allowing the reconstitution of a functional adenylate cyclase due to the physical proximity of the two sub-parts.
The enzyme is operational again and can produce the production of a high quantity of cAMP (around 17,000 mmol of cAMP formed per mg of adenylate cyclase per minute), the molecule responsible of the signal transduction in the bacterium.
BACTH_1.gif


cAMP molecules diffuse to the cytoplasm of the bacterium and interact with catabolite activator proteins (CAP). One cAMP molecule binds to one transcriptional activator CAP; then two cAMP-CAP complexes are needed to activate the expression of the gene under the control of the lactose promoter.
Because of the high quantity of cAMP diffusing in the cytoplasm of the bacterium (2), the reporter gene is continually activated as long as cAMP is produced.
BACTH_2.gif


The high enzymatic activity (1) of Bordetella pertussis Adenylate Cyclase involves a high production of cAMP in presence of ATP in the bacterium thus activating the signaling cascade with the CAP-cAMP dependant promoter.
Hence this system is promising because it might have a great sensitivity and may give a great signal amplification for a low amount of target detected.


References

(1) Fields S, Song O. A novel genetic system to detect protein–protein interactions. Nature [Internet]. 1989
(2) Karimova G, Pidoux J, Ullmann A, Ladant D. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. PNAS [Internet]. 1998
(3) Karimova G, Gauliard E, Davi M, P.Ouellette S, Ladant D. Protein–Protein Interaction: Bacterial Two-Hybrid. 2017