Difference between revisions of "Part:BBa K3280007"
Line 1: Line 1:
  
 
__NOTOC__
 
__NOTOC__
−
<partinfo>BBa_K3280007 short</partinfo>
+
<partinfo>BBa_K3280001 short</partinfo>
  
−
This is a composite part. We call this part an “Iara alpha*”. This Biobrick has a bidirectional promoter of MerR, a dCBD anchor, a lead binding peptide (MBP), a HlyA tag to secretion and a tDGC to induce biofilm formation.
+
WspR. This part is a protein that has a domain that increases levels of c-di-GMP to induce biofilm formation.
  
 +
===Usage and Biology===
 +
 +
This part is originated from Pseudomonas aeruginosa. In our project we used this Wspr to test biofilm quantification in order to see what diguanylate cyclase is more efficient in biofilm formation. We use this and others diguanylate cyclases (Yddv and YdeH) in pETSUMO plasmid to run the tests. We did experiments with and without agitation, and also testing the efficiency of biofilm adherence in coconut fiber.
  
 
<h2>Characterization</h2>
 
<h2>Characterization</h2>
 
<h3>By Team iGEM19_USP_SaoCarlos-Brazil 2019</h3>
 
<h3>By Team iGEM19_USP_SaoCarlos-Brazil 2019</h3>
−
===Usage and Biology===
 
  
−
This part represent our MermAID systems, which contains our chimera and a diguanylate cyclase. This biobrick has a bidirecional promoter MerR + metal binding peptide that makes our MermAID catches mercury from the contaminate waters. And it also has a di-guanylate cyclase, a gene that contain a GGDEF domain responsible for induce production of biofilm, this biofilm will help to improve captation of mercury. With the HlyA, that is a tag to secretion our protein with mercury and the dCBD is an anchor to connect both into the biofilm. Therefore, if our circuit is properly working.
+
Cyclic di-GMP (c-di-GMP) is recognized as an intracellular signaling molecule that coordinates the “lifestyle transition” from motility to sessility and vice versa (i.e. dispersion). The correlation between high c-di-GMP concentration in the cell and biofilm formation or between low c-di-GMP levels and motility has been demonstrated in several bacterial species [1].
  
−
[[File:T--USP_SaoCarlos-Brazil--MerR-Chimerainv.svg|700px|center|]]
+
Our project include one protein that capture mercury and also produces biofilm to improve the fixation of the heavy metal. So one of our experiments was to characterize several cyclic diguanylate in order to choose the best one for our circuit through quantification of biofilm with crystal violet. To know the specific protocol we used, access https://2019.igem.org/Team:USP_SaoCarlos-Brazil/Experiments
  
−
Our work plan was basically based on combining two biobricks in order to capture mercury (BBa_k3280005 and BBa_k3280006), a double cellulose binding domain (dCBD), which consisted in two cellulose binding domains from Trichoderma reesei cellobiohydrolases completed with linkers (BBa_k3280006) and a protein domain that increases levels of c-di-GMP to induce biofilm formation (BBa_k3280000). We wanted to achieve a system that could capture mercury from contaminated samples and from that, induce biofilm. We also wanted the captured metal to stay attached to a substrate, which was coconut fiber, therefore the cellulose binding domain (BBa_k1321340).
+
[[File:T--USP_SaoCarlos-Brazil--Chimera-vector-bba.svg|500px|center]]
  
−
In addition to our main parts, we also had to use other biobricks to complete the system, such as linkers (BBa_k243005), a terminator (BBa_B0015) and a signal peptide, HlyA, used to target proteins for secretion via the Type I secretion pathway of gram-negative bacteria (BBa_B0015).
+
This part is originated from Pseudomonas aeruginosa. In our project we used this Wspr to test biofilm quantification in order to see what diguanylate cyclases is more efficient in biofilm formation. We use this and others diguanylate cyclases (Yddv and YdeH) in pETSUMO plasmid to run the tests. We did experiments with and without agitation, and also testing the efficiency of biofilm adherence in coconut fiber.  
  
−
In order to verify if our part really worked, we performed two different tests: growth curve and Hg difusion disc test. With these we hoped to demonstrate that cells containing our biological circuit were more fit to survive in and medium containing Hg, and therefore prove that not only our protein was being expressed, but also that it was properly exerting its function.  
+
[[File:T--USP_SaoCarlos-Brazil--Parts-DGC24.png|500px|center|Figure 1: Each column is the mean value of a sample with 5 identical experiments made in the same 24-well plate, with the exception of the static SOC medium which had 1 of its results masked due to their dissonance from the rest, implying external contamination.
 +
]]
  
−
<h4>Growth Curve</h4>
+
As it can be seen from  figure 1, the bacteria transformed with WspR did not show a higher biofilm production in a non-static condition, which was coherent with other biofilm growth experiments made with E. coli.
−
In order to evaluate if the expression of our chimera confers resistance to mercury and determining which are the most appropriate mercury concentrations to the other experiments, we made growth curves of the transformed bacteria in culture medium containing different concentrations of mercury and compare with the results obtained for the unmodified strain.
+
It’s interesting to note that a certain quantity of biofilm was expected for the control, pETSUMO without DGC insert, since our bacteria naturally produces low rates of biofilm.
  
−
For the experiment, we transformed into E. Coli DH5-the metal pickup chimera (Iara-) and the GGDEF domain-containing protein (Q9X2A8), both regulated by same Mer promoter. The insert was into the pBS1K3 vector.
 
−
We started the test with a low optical density and keep measuring it every 30 minutes within 8 hours (for the transformed bacteria) and within 6 hours (for the unmodified strain).  The bacteria was growth in culture medium Luria-Bertani (LB) containing different concentrations of mercury such as 0, 7.5, and 20 µg/ml. For the transformated strain we also made the experiment with high mercury concentrations such as 200 and 2000 µg/ml. The results are shown in the figure 1 below.
 
  
−
[[File:T--USP_SaoCarlos-Brazil--groww0.jpg|300px|]][[File:T--USP_SaoCarlos-Brazil--groww7.5.jpg|300px|]][[File:T--USP_SaoCarlos-Brazil--groww20.jpg|300px|]][[File:T--USP_SaoCarlos-Brazil--groww200.jpg|300px|]][[File:T--USP_SaoCarlos-Brazil--groww2000.jpg|300px|]]
+
[[File:T--USP_SaoCarlos-Brazil--Parts-DGC24.png|500px|center|Figure 2: Once again, 5 replicates were made, with dissonant results masked]]
  
−
<p style="text-align: center">Figure 1: Growth curve of the bacteria expressing Iara-α and the unmodified strain in culture medium containing 0, 7.5, 20, 200 and 2000 µg/ml of mercury.</p>
+
The 48h static plate showed lower biofilm formation if compared to the 24h static plate. This could indicate a natural tendency for the E. coli to not maintain the small amount of biofilm that they produced under static conditions, since forming this matrix it’s a costly metabolic function.  
 +
As for the 48h agitated plate, the absorption rate didn’t change significantly for the bacteria transformed with WspR, even though we can see a small increase in the absorption bar, which could indicate a preference for a longer period of incubation under agitated conditions. Also, the agitated WspR showed a very heterogeneous growth in the 24 hour plate. We can infer that this is a form of response from this DGC and that these bacterias would reach a higher level of absorbance if a longer incubation time was tested.  
  
−
As can be seen on the graphs above, in the experiment performed with 0 µg/ml the insert-containing bacteria had a slower growth compared to the unmodified strain. This behavior may be due to increased metabolic expenses of  transformed bacteria to express the synthetic proteins. Moreover, the transformed bactéria was able to grow in culture medium containing 7.5 µg/ml while the unmodified strain failed to grow in this concentration. Thus we can infer that our metal pickup chimera, Iara-α, gave to the bacteria a greater resistance to mercury, making it able to survive in environments with the concentration of Hg tested. Also, this is an evidence that Iara-α is been expressed and it is working as desired.  In higher concentrations neither the engineered bacteria nor the unmodified one survived, since mercury ions are highly toxic this result was expected.
+
The same results can be presented in a different manner, In order to evaluate the changes happening from 24h to 48h, we plotted the change in absorption against time:
  
  
−
<h4>Hg Difusion Disc Test</h4>
+
[[File:T--USP_SaoCarlos-Brazil--Parts-DGCest.png|500px|center|Figure 3
 +
]]
  
−
[[File:T--USP SaoCarlos-Brazil--difusion.jpg|700px|center|]]
+
[[File:T--USP_SaoCarlos-Brazil--Parts-DGCagit.png|500px|center|Figure 4
 +
]]
  
−
In order to properly analyse the relation between Hg presence and cell growth the halos were measured using ImageJ, to maximize measurements precision the area of each halo was characterized 5 times, we then took its average value and compared obtained values in each replicate. The next step is to plot histograms with the average values of our experiment replicates vs. the control culture, comparing cell behaviour around the Hg contaminated zones. We expect to find smaller halos, i.e. smaller radii of death zones, in transformed cells due to their capacity to capture Hg which is believed to enhance cells chance to survive in the hostile environment. The table below shows the measured radii for each plate and then the average values for each concentration.
 
  
 +
We observed a substantial increase in biofilm formation for plates incubated under agitation, as well as for longer periods of time. We also noted that under static conditions, cells tend to considerably decrease biofilm production. Moreover, the DGC that showed the fastest response in the matter of biofilm production was YddV, which managed to saturate the acetic acid solution with biofilm in at least 24 hours. The second fastest response was from the DGC YdeH, reaching the maximum absorbance level in 48 hours. The agitated wells containing wspR manage to increase its biofilm production in the span of 24 hours, but did not reach the same high levels as YdeH and YddV, a longer timespan is necessary to evaluate wspR biofilm production.
  
  
−
[[File:T--USP SaoCarlos-Brazil--difusiong1.jpg|500px|center|]]
+
In the end of our experiments, we came to the conclusion that Wspr is the less efficient diguanylate cyclase when compared to YdeH and YddV.  
  
−
The graph displayed above exhibits the constructed histogram of average radii vs. control culture. In this case, the culture was incubated for 12h and the results indicate that transformed cells were able to survive in Hg contaminated zones better than non transformed cells, in particular for higher Hg concentrations which cells were not expected to survive at all.
 
  
  
 +
<h2>References</h2>
 +
[1]. Ha DG, O'Toole GA. c-di-GMP and its Effects on Biofilm Formation and Dispersion: a Pseudomonas Aeruginosa Review. Microbiol Spectr. 2015;3(2):10.1128/microbiolspec.MB-0003-2014. doi:10.1128/microbiolspec.MB-0003-2014
  
−
[[File:T--USP SaoCarlos-Brazil--difusiong2.jpg|500px|center|]]
+
[2] Valentini M, Filloux A. Biofilms and Cyclic di-GMP (c-di-GMP) Signaling: Lessons from Pseudomonas aeruginosa and Other Bacteria. J Biol Chem. 2016;291(24):12547–12555. doi:10.1074/jbc.R115.711507
  
−
When comparing replicates behaviour, we are able to identify that transformed cells might have an optimal Hg concentration to outgrow non transformed cells around 1000 ug/mL. The results shown above indicate that the are cells are suitable for our projects interest due to the results obtained for concentrations above 20 000 ug/mL.
 
  
  
  
−
===References===
 
−
 
−
[1] Ha DG, O'Toole GA. c-di-GMP and its Effects on Biofilm Formation and Dispersion: a Pseudomonas Aeruginosa Review. Microbiol Spectr. 2015;3(2):10.1128/microbiolspec.MB-0003-2014. doi:10.1128/microbiolspec.MB-0003-2014
 
−
 
−
[2] Valentini M, Filloux A. Biofilms and Cyclic di-GMP (c-di-GMP) Signaling: Lessons from Pseudomonas aeruginosa and Other Bacteria. J Biol Chem. 2016;291(24):12547–12555. doi:10.1074/jbc.R115.711507
 
−
 
−
<!-- -->
 
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
−
<partinfo>BBa_K3280007 SequenceAndFeatures</partinfo>
+
<partinfo>BBa_K3280001 SequenceAndFeatures</partinfo>
  
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
−
<partinfo>BBa_K3280007 parameters</partinfo>
+
<partinfo>BBa_K3280001 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Revision as of 20:52, 21 October 2019


WspR Diguanylate Cyclase

WspR. This part is a protein that has a domain that increases levels of c-di-GMP to induce biofilm formation.

Usage and Biology

This part is originated from Pseudomonas aeruginosa. In our project we used this Wspr to test biofilm quantification in order to see what diguanylate cyclase is more efficient in biofilm formation. We use this and others diguanylate cyclases (Yddv and YdeH) in pETSUMO plasmid to run the tests. We did experiments with and without agitation, and also testing the efficiency of biofilm adherence in coconut fiber.

Characterization

By Team iGEM19_USP_SaoCarlos-Brazil 2019

Cyclic di-GMP (c-di-GMP) is recognized as an intracellular signaling molecule that coordinates the “lifestyle transition” from motility to sessility and vice versa (i.e. dispersion). The correlation between high c-di-GMP concentration in the cell and biofilm formation or between low c-di-GMP levels and motility has been demonstrated in several bacterial species [1].

Our project include one protein that capture mercury and also produces biofilm to improve the fixation of the heavy metal. So one of our experiments was to characterize several cyclic diguanylate in order to choose the best one for our circuit through quantification of biofilm with crystal violet. To know the specific protocol we used, access https://2019.igem.org/Team:USP_SaoCarlos-Brazil/Experiments

500px

This part is originated from Pseudomonas aeruginosa. In our project we used this Wspr to test biofilm quantification in order to see what diguanylate cyclases is more efficient in biofilm formation. We use this and others diguanylate cyclases (Yddv and YdeH) in pETSUMO plasmid to run the tests. We did experiments with and without agitation, and also testing the efficiency of biofilm adherence in coconut fiber.

Figure 1: Each column is the mean value of a sample with 5 identical experiments made in the same 24-well plate, with the exception of the static SOC medium which had 1 of its results masked due to their dissonance from the rest, implying external contamination.

As it can be seen from figure 1, the bacteria transformed with WspR did not show a higher biofilm production in a non-static condition, which was coherent with other biofilm growth experiments made with E. coli. It’s interesting to note that a certain quantity of biofilm was expected for the control, pETSUMO without DGC insert, since our bacteria naturally produces low rates of biofilm.


Figure 2: Once again, 5 replicates were made, with dissonant results masked

The 48h static plate showed lower biofilm formation if compared to the 24h static plate. This could indicate a natural tendency for the E. coli to not maintain the small amount of biofilm that they produced under static conditions, since forming this matrix it’s a costly metabolic function. As for the 48h agitated plate, the absorption rate didn’t change significantly for the bacteria transformed with WspR, even though we can see a small increase in the absorption bar, which could indicate a preference for a longer period of incubation under agitated conditions. Also, the agitated WspR showed a very heterogeneous growth in the 24 hour plate. We can infer that this is a form of response from this DGC and that these bacterias would reach a higher level of absorbance if a longer incubation time was tested.

The same results can be presented in a different manner, In order to evaluate the changes happening from 24h to 48h, we plotted the change in absorption against time:


Figure 3
Figure 4


We observed a substantial increase in biofilm formation for plates incubated under agitation, as well as for longer periods of time. We also noted that under static conditions, cells tend to considerably decrease biofilm production. Moreover, the DGC that showed the fastest response in the matter of biofilm production was YddV, which managed to saturate the acetic acid solution with biofilm in at least 24 hours. The second fastest response was from the DGC YdeH, reaching the maximum absorbance level in 48 hours. The agitated wells containing wspR manage to increase its biofilm production in the span of 24 hours, but did not reach the same high levels as YdeH and YddV, a longer timespan is necessary to evaluate wspR biofilm production.


In the end of our experiments, we came to the conclusion that Wspr is the less efficient diguanylate cyclase when compared to YdeH and YddV.


References

[1]. Ha DG, O'Toole GA. c-di-GMP and its Effects on Biofilm Formation and Dispersion: a Pseudomonas Aeruginosa Review. Microbiol Spectr. 2015;3(2):10.1128/microbiolspec.MB-0003-2014. doi:10.1128/microbiolspec.MB-0003-2014

[2] Valentini M, Filloux A. Biofilms and Cyclic di-GMP (c-di-GMP) Signaling: Lessons from Pseudomonas aeruginosa and Other Bacteria. J Biol Chem. 2016;291(24):12547–12555. doi:10.1074/jbc.R115.711507



Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 393
    Illegal PstI site found at 465
    Illegal PstI site found at 683
    Illegal PstI site found at 807
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 393
    Illegal PstI site found at 465
    Illegal PstI site found at 683
    Illegal PstI site found at 807
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 361
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 393
    Illegal PstI site found at 465
    Illegal PstI site found at 683
    Illegal PstI site found at 807
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 393
    Illegal PstI site found at 465
    Illegal PstI site found at 683
    Illegal PstI site found at 807
    Illegal NgoMIV site found at 306
    Illegal NgoMIV site found at 636
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 450
    Illegal SapI.rc site found at 273
    Illegal SapI.rc site found at 287