Difference between revisions of "Part:BBa K515107"
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30 ng DNA of BBa_K515107 part was transformed into 50 μl DH10B competent cells by electroporation. The bacteria colonies growing on the selective LB plates were picked and cultured in 250 μl LB broth medium for one hour as the starting culture. Thereafter, 25 μl of the  
 
30 ng DNA of BBa_K515107 part was transformed into 50 μl DH10B competent cells by electroporation. The bacteria colonies growing on the selective LB plates were picked and cultured in 250 μl LB broth medium for one hour as the starting culture. Thereafter, 25 μl of the  
 
srarting culture was transferred into 1 ml LB medium with different pH respectively and continued to culture for 360 mins.  
 
srarting culture was transferred into 1 ml LB medium with different pH respectively and continued to culture for 360 mins.  
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Every 20 mins, we collected 10 μl bacterial culture and measure the green fluorescence and the red fluorescence before and after photoconversion of Dendar2 by using photon stimulation under UV light.
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ImageJ was used to analysize the florescent intensity of Dendar2 fluorescence.
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[[File:Scau-china-2018-7.png|800px|thumb|center| Figure 1 The fluorescent signal of Dendar2 in the time point of 100 min and 300 min, pH 4.5 and pH 9.1.The protein expression of the part works well in DH10B. In addition, we found that the alkaline condition have a negative impact on the expression of Dendar2 in DH10B. ]]
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Revision as of 04:57, 16 October 2018

Composite p(tetR) - Dendra2

Description

This BioBrick comprises the coding sequence BBa_K515007 under the control of the repressible promoter TetR BBa_R0040 with the RBS BBa_B0034. The coding sequence BBa_K515007 codes for Dendra2, a photoconvertible reporter protein. In its natural state, it is excited and emits at 486 and 505 nm, respectively. This appears green and therefore in its natural state Dendra2 can be used as a GFP reporter. However it can be irreversibly converted to be excited at 558 nm and consequently emit at 575 nm. After conversion reporter appears red and can be observed as RFP. Conversion can be efficiently achieved at wavelengths of both 488 and 405 nm [1]. However, the cytotoxic wavelength of 405 nm converts Dendra2 more efficiently (data not shown).



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]

This BioBrick has been sequence verified.

Characterisation

This part (BBa_K515107) has been characterised in a number of aspects to test its properties as a reporter. The tests describe this part in terms of thermostability, photostability and photoconversion.


Thermostability

This test is to show the thermostability of Dendra2, by finding the temperature at which the protein denatures. Stock solutions of Dendra2 were prepared by extracting the protein from cell lysate, and then 50 μl aliquots of the solution were heated in a PCR thermocycler along a temperature gradient.

After two hours, 30 μl was removed from each aliquot and diluted with 170 μl of 20 mM Tris buffer to give 200 μl samples. The fluorescence of the samples was measured on a 96-well plate. The corresponding curve was plotted on a graph (Figure 1).

Figure 1: Results of the heat denaturation experiment. The temperature at which half of the protein is denatured measured by looking at its fluorescence (PTm50) mRFP1: 82.2°C; GFPmut3b: 61.6°C; Dendra2: 89.1°C; sfGFP: 75.0°C (click on graph to enlarge).

The sigmoidal curves that were calculated gave us the following function in order to find K which we also call PTm50 (temperature at which half of the proteins are denatured studied by measuring fluorescence):



Photostability

This test is to show photostability of the Dendra2 protein for green fluorescence without the conversion to red fluorescence. Green (505 nm wavelength) and red (575 nm wavelength) fluorescence emission was measured for Dendra2-expressing cells over time. As control RFP and GFP expressing cells have been used to compare the green and red fluorescence emission. Red and green fluorescence of control LB medium was also measured as a blank that can be subtracted from the readings of the GFP, RFP and Dendra2 expressing cells.

Figure 2:Graph showing the photostability of Dendra2. The excitation wavelength of 486 nm does not cause photoconversion even though the wavelength of 488 nm does (click on graph to enlarge).

Photoconversion

Purified Dendra2 protein was measured for the red fluorescence emission after photoconversion using single photon stimulation at 405 nm wavelength. It was exposed to the RFP excitation wavelength (558 nm) and at a set time point it was also exposed to 405 nm photoconversion wavelength.

Figure 3: Red flourescence emission of Dendra2 protein upon single photon stimulation at 405 nm wavelength. Red flourescence is very low before photoconversion, however at time point 25 s after the start of the measurement 405 nm photoconverting wavelength was applied. An increase in red flourescence emission can be observed between time point 25 s and 319 s, after which red flourescence emission levels off.


This part has been used as a reporter for observation of bacterial uptake into the roots of the plants. Due to its photoconvertible properties, it allows monitoring of the metabolic activity of bacterial cell once uptaken into the root. Dendra2 was converted from 486 nm excitation and 505 nm emission wavelength, to 558 nm excitation and 575 nm emission wavelength using single photon stimulation. Conversion was achieved after exposure to 405 nm wavelength using laser. Photoconversion was completed after about 15 rounds of bleaching at 50% laser intensity with the pinhole set to 3 airy units.

Figure 4: Dendra2 photoconversion in bacteria taken up inside plant roots. The graph on the top displays averaged fluorescence over the entire photoconverted area and the amount of brightfield light (the background light used to see the outline of the roots) recorded is therefore very high. The graph on the bottom displays emission at green and red fluorescence over the same time span.

Video 1. This video shows the photoconversion of Dendra2 within E. coli cells that have been taken up into the plant roots as a time-lapse of pictures taken after each round of bleaching at 405 nm. The targeted area of cells being photoconverted corresponds to the top graph in Figure 4. There is a single bacterium visible on the right that was not targeted for photoconversion and serves as a control (data and imaging by Imperial College iGEM 2011).

Intensity ROI 1

After exposure with 405 nm wavelength, the cells are observed to steadily decrease fluorescing in green emission spectra over a time period of 140 seconds. In the same time frame the cells are observed to increase fluorescing in the red spectra, with fluorescence in the two emission spectra being equally intense at 20 seconds after the photoconversion. Brightfield emmision is kept at just over 100 units throughout the duration of observation of photoconversion. Brightfield is present for visualisation of the root and bacterial cells without flourescence.

Intensity ROI 2

ROI 2 displays the fluorescence emitted by a single cell while it is being converted from green to red emission. Emission of green spectra fluorescence can be observed to decrease steadily over time period of 140 seconds. In the same time frame the cell can be observed to fluoresce more strongly in the red spectra. The difference between red and green emission is greater in ROI 2 than in ROI 1 due to single cell focus eliminating backround emission which can be seen in ROI 1 that causes the difference between two spectra in ROI 1 to be smaller than in ROI 2. Brightfield emmision is kept at just over 100 units throughout the duration of observation of photoconversion. This is necessary for visual observation of cells within the root.

A single bacterium on the right (visible in the video above) is used as a negative control. It was not targeted for bleaching by the laser and can be observed to remain green through the conversion process.

Method

The bacterial cells within root were visualised using a Zeiss LSM-510 inverted confocal microscope. The induction of photoconversion was performed using a laser at 405 nm wavelength. The bacterial root uptake experiment used the same protocol as previously described by Paungfoo-Lonhienne et al. [2]

Using Dendra2 to trace metabolic activity

To assess whether Dendra2 could be used to track the metabolic activity of E. coli, culture of Dendra2 expressing E. coli were photoconverted with a blue laser and measured fluorescence during incubation at 30°C to see if green fluoresence re-emerged. As expected, green fluorescence decreased after photoconversion and red fluorescence increased. As the sample was left to incubate at 30˚C, green fluorescence re-emerged as the bacteria are producing more Dendra2. This proves that the cells remain metabolically active and that metabolic activity can be tracked using Dendra2. Surprisingly red fluorescence also increased over time without additional photoconversion. We suspect that this may be a delayed response from the initial photoconversion.


Figure 5: Green and red fluorescence emitted by E. coli expressing Dendra2, before and after photoconversion with a blue laser.

Figure 6: Re-emergence of green fluorescence over time as cells produce new Dendra2 protein that has not been photoconverted.

NEW SINCE EUROPE JAMBOREE

To assess whether E. coli remain metabolically active inside Arabidopsis roots, Dendra2 was photoconverted inside Arabidopsis roots and left in cygel over night so that they could be re-imaged after 24 hours. The roots were imaged four days after infection with Dendra2 expressing E. coli. The bacteria were shown to continue expressing green Dendra2 protein, proving that they are metabolically active inside the roots (Video 7).


Video 7. Photoconversion of Dendra2 in Arabidopsis thaliana roots. After 24 hours, the bacteria were re-imaged at the same settings. Expression of green Dendra2 had increased, showing that the bacteria are metabolically active inside the roots (Imaging by Mark Scott for Imperial College iGEM 2011).


ImageJ was used to analyse the relative fluorescence intensities in the different samples. By determining the percentage change in green fluorescence after photoconversion and 24 hours incubation in relation to the initial level of green fluorescence (Figure 7), we can clearly see that green fluorescence decreased dramatically after photoconversion (as expected by the properties of Dendra2). Additionally, after 24 hours the initial green fluorescence level was re-established and slightly surpassed due to production of new Dendra2 protein by the metabolically active bacteria. No red fluorescence was re-converted to green fluorescence because Dendra2 irreversibly changes from fluorescing green to red. There was a high background fluorescence in the red spectrum as roots are highly autofluorescent in the same spectrum.

Figure 7: Relative fluorescence of Dendra2-expressing bacteria inside Arabidopsis roots. The roots incubated with bacteria were imaged on the confocal microscope, photoconverted and imaged again, and left overnight to be imaged after 24 hours. This graph shows the percentage change of green fluorescence after photoconversion and 24 hours incubation in relation to the initial green fluorescence.

Dendra2 has therefore been shown as a useful reporter protein for accurately tracking metabolic activity of bacteria. These results suggest that Dendra2 could be utilised as a very useful tool for assessing cell metabolic activity in synthetic biology.

References:

[1] Gurskaya N et al. (2006) Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nature Biotechnology 24: 461-465.

[2] Paungfoo-Lonhienne et al. (2010) Turning the table: plants consume microbes as a source of nutrients. PLoS ONE 5(7):, e11915. http://www.nih.gov/science/models/arabidopsis/index.html

Team SCAU-China 2018 : Suitable culture condition for the expression of Dendar2

The main goal of this characterization is to find out which pH value is the most effective among the 6 pH values in order to obtain a suitable culture condition for the expression of Dendar2.We further found that the part which expressed the protein Dendar2 worked well in E.coli strain DH10B, like in the DH5 alpha. Experiment To figure out the best cultural pH for protein expression, we have tested 6 different sets of pH that including: 4.5, 5.8, 6.2, 7.2, 8.2, 9.1, We also performed a time-lapse culture for 360 mins to find out the best time point for harvesting DH10B that expresses Dendar2. The competent cells of DH10B were prepared from the bacterial stock stored in the deep freezer in the lab. 30 ng DNA of BBa_K515107 part was transformed into 50 μl DH10B competent cells by electroporation. The bacteria colonies growing on the selective LB plates were picked and cultured in 250 μl LB broth medium for one hour as the starting culture. Thereafter, 25 μl of the srarting culture was transferred into 1 ml LB medium with different pH respectively and continued to culture for 360 mins. Every 20 mins, we collected 10 μl bacterial culture and measure the green fluorescence and the red fluorescence before and after photoconversion of Dendar2 by using photon stimulation under UV light. ImageJ was used to analysize the florescent intensity of Dendar2 fluorescence. [[File:Scau-china-2018-7.png|800px|thumb|center| Figure 1 The fluorescent signal of Dendar2 in the time point of 100 min and 300 min, pH 4.5 and pH 9.1.The protein expression of the part works well in DH10B. In addition, we found that the alkaline condition have a negative impact on the expression of Dendar2 in DH10B. ]] |};