Difference between revisions of "Part:BBa K1045004:Experience"
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[[File:YdaO_complete2.jpg|1000px|center|thumb|'''Fig. 1.''' ''E. coli'' cells transformed with '''BBa_K1045002''' were cultivated under different conditions and analyzed by fluorescence microscopy. ''Left'': in absence of c-di-AMP, ''center'': in presence of c-di-AMP (1 µg/ml), ''right'': in presence of c-di-AMP (1 µg/ml) and polyamines. All pictures represent merges of a bright field image and a CFP fluorescence image. The exposure time used to record CFP fluorescence was in all cases 1 second.]] | [[File:YdaO_complete2.jpg|1000px|center|thumb|'''Fig. 1.''' ''E. coli'' cells transformed with '''BBa_K1045002''' were cultivated under different conditions and analyzed by fluorescence microscopy. ''Left'': in absence of c-di-AMP, ''center'': in presence of c-di-AMP (1 µg/ml), ''right'': in presence of c-di-AMP (1 µg/ml) and polyamines. All pictures represent merges of a bright field image and a CFP fluorescence image. The exposure time used to record CFP fluorescence was in all cases 1 second.]] | ||
− | Ideally, in the presence of c-di-AMP, ''cfp'' expression should be prevented by the riboswitch. However, we saw no difference between cells grown with or without c-di-AMP. Nevertheless, the strong fluorescence indicated that the ''ydaO'' promoter from ''B. subtilis'' driving the expression of the riboswitch reporter system is highly active. The high promoter activity might even explain why we saw no difference between the different growth conditions: The strong promoter could lead to high RNA levels. Compared to the high RNA levels, the c-di-AMP amounts entering the cells might have been too low. Thus, the expected premature transcripional termination mediated by c-di-AMP and the ''ydaO'' riboswitch could not have been visible. '''In order to achieve premature termination of transcription (e.g. in order to use this biobrick as a "negative inductor"), we suggest our shorter version of the riboswitch ([https://parts.igem.org/wiki/index.php?title=Part:BBa_K1045005 BBa_K1045005, the riboswitch without its native promoter]) combined with a weaker promoter.''' Alternatively, the c-di-AMP amounts could be increased. | + | Ideally, in the presence of c-di-AMP, ''cfp'' expression should be prevented by the riboswitch. However, we saw no difference between cells grown with or without c-di-AMP. Nevertheless, the strong fluorescence indicated that the ''ydaO'' promoter from ''B. subtilis'' driving the expression of the riboswitch reporter system is highly active. The high promoter activity might even explain why we saw no difference between the different growth conditions: The strong promoter could lead to high RNA levels. Compared to the high RNA levels, the c-di-AMP amounts entering the cells might have been too low. Thus, the expected premature transcripional termination mediated by c-di-AMP and the ''ydaO'' riboswitch could not have been visible. '''In order to achieve premature termination of transcription (e.g. in order to use this biobrick as a "negative inductor"), we suggest our shorter version of the riboswitch ([https://parts.igem.org/wiki/index.php?title=Part:BBa_K1045005 BBa_K1045005, the riboswitch without its native promoter]) combined with a weaker promoter.''' Alternatively, the c-di-AMP amounts could be increased. Itt could be possible, as well, that'' E. coli'' is unable to take up c-di-AMP. Hence, one should analyze ''E. coli'' regarding its ability to take up c-di-AMP. |
==Plate reader data== | ==Plate reader data== |
Revision as of 10:27, 27 October 2013
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how you used this part and how it worked out.
Applications of BBa_K1045004
We used this part in our riboswitch reporter system BBa_K1045002. E. coli cells carrying this system were viable. The reporter gene cfp was expressed from BBa_K1045004. However, it could not be regulated by c-di-AMP. For experimental data, see our characterization experiments for BBa_K1045002, which are described in the following sections:
Microscope Data
E. coli cells transformed with BBa_K1045002 were characterized by fluorescence microscopy (Fig. 1). We grew the cells under different conditions: without and with 1 µg/ml c-di-AMP and with c-di-AMP (1 µg/ml) plus polyamines. Polyamines served to allow the uptake of c-di-AMP (Oppenheimer-Shaaman et al., 2011).
Experimental details: E. coli cells were grown in LB medium. A culture aliquot was prepared on slides covered with 1 % agarose (in water) and the cells observed under the fluorescence microscope. For all images, the same exposure time was used. Microscope: Axioskop 40 FL fluorescence microscope; Camera: digital camera AxioCam MRm; Software for image processing: AxioVision Rel version 4.8 (Carl Zeiss, Göttingen, Germany); Objective: Neofluar series objective (×100 primary magnification); Filter set: Filter set 47 (BP 436/20, FT 455, and LP 480/40; Carl Zeiss) for CFP detection.
Ideally, in the presence of c-di-AMP, cfp expression should be prevented by the riboswitch. However, we saw no difference between cells grown with or without c-di-AMP. Nevertheless, the strong fluorescence indicated that the ydaO promoter from B. subtilis driving the expression of the riboswitch reporter system is highly active. The high promoter activity might even explain why we saw no difference between the different growth conditions: The strong promoter could lead to high RNA levels. Compared to the high RNA levels, the c-di-AMP amounts entering the cells might have been too low. Thus, the expected premature transcripional termination mediated by c-di-AMP and the ydaO riboswitch could not have been visible. In order to achieve premature termination of transcription (e.g. in order to use this biobrick as a "negative inductor"), we suggest our shorter version of the riboswitch (BBa_K1045005, the riboswitch without its native promoter) combined with a weaker promoter. Alternatively, the c-di-AMP amounts could be increased. Itt could be possible, as well, that E. coli is unable to take up c-di-AMP. Hence, one should analyze E. coli regarding its ability to take up c-di-AMP.
Plate reader data
We furthermore produced quantitative data characterizing the growth and the fluorescence over time of the BL21 E. colis we transformed with the riboswitch reporter system BBa_K1045002. As a control, we employed E. coli cells transformed with the plasmid carrying the cfp gene, but lacking the control elements for CFP expression (BBa_E0020).
The plate reader was used to quantify the strength of the ydaO riboswitch construct. In this setup, a dilution series of c-di-AMP ranging from 0 to 10000 nmol was used to test how strong the affinity of the riboswitch is. In addition to the c-di-AMP, polyamines (1 µl/ml, 1000x stock solution) were added to series of samples to test if the uptake of c-di-AMP into E. coli could be enhanced by this additive. The graphs show the mean values with the standard deviation of two technical replicates of one biological replicate.
Fig. 2 shows the growth curves recorded via the OD at 600 nm. The CFP fluorescence was measured at 480 nm and normalized to the cell density (Fig. 3).
Experimental setup: total time 21 h; 15 min measurement interval; 37°C, medium shaking; 96-well titer plate; Synergy Mx Monochromator-Based Multi-Mode Microplate Reader; Gen5 V2.01
It was observed that the polyamines did not influence the uptake of c-di-AMP into the cells in one way or the other. The concentrations of c-di-AMP tested had no measurable effect on the riboswitch either. The single riboswitch replicate, that showed lower fluorescence (highest concentration) might not be significant as the error bars indicate. We assume this to be an artifact or a pipetting mistake.
There are three possible explanations why we saw no effect of c-di-AMP on cfp expression: (1) the ydaO promoter is too active leading to very high amounts of riboswitch compared to the c-di-AMP amounts used; (2) the c-di-AMP amounts were too low; (3) E. coli is unable to take up c-di-AMP even with polyamines. Thus, future experiments have to involve (1) a riboswitch reporter system expressed from a weaker promoter; (2) higher c-di-AMP concentrations; and (3) analysis of c-di-AMP uptake by E. coli.
In conlusion, we showed that the E. coli cells expressed the CFP reporter over exponential and stationary phase under a promoter from B. subtilis ydaO gene. We also showed, that E. coli was not harmed or hindered in its growth, allowing the reporter system to be used without the danger of killing our host.
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