RNA thermometer assay

1. Introduction

Temperature increase is required for an RNA thermometer in the enhanced expression of BBa_K1333309 (J23119_K115002_E1010) constructed by iGEM 2014 SYSU-China. The RNA thermometers are located in the 5’-untranslated region (5’-UTR) and block the Shine-Dalgarno (SD) sequence by base pairing. Translation initiating temperature allows the disconnection of the coupling of the hydrogen bonds, which block the SD sequence at low temperature. Therefore, RNA thermometers change their conformations to the open state so that the ribosome could access the SD sequence and to initiate translation.

We thus improved characterization of BBa_K1333309 by (1) measuring the function of the part at 42 ºC, (2) explicating the way to deal with the background derived from Negative control, (3) measuring with the flow cytometer.

We think that this experiment is meets Gold medal criteria.Description

2. Summary of the Experiment

Our purpose is to confirm the behavior of the RNA thermometer by setting Positive control and Negative control and to characterize the temperature dependence of the RNA thermometer at 30ºC, 37ºC and 42ºC by using the flow cytometer. We prepared the samples as shown below.

BBa_K1333309: Pcon_RNA thermometer_rfp(pSB1C3)

Positive control: Plac_rfp_TT(pSB1C3)

Negative control: RNA thermometer_rfp(pSB1C3)


Fig. 3-7-2-1. Parts that we used

3. Results

We measured each sample at 30ºC, 37ºC and 42ºC. 37ºC is the translation initiating temperature. Little does the background from the medium affects results for the flow cytometer. Although iGEM 2014 SYSU-China confirmed the function of Pcon_RNA thermometer_rfp at these temperatures, we measured each sample at 42ºC, which is higher than the translation initiating temperature.

3.1. The fluorescence intensities of RFP

We found that the fluorescence intensities of both Pcon_RNA thermometer_rfp and Plac_rfp increased along with the rise of the temperature (Fig. 3-7-3-1.).


Fig. 3-7-3-1. RAW data

The error bar represents the standard deviation for each sample calculated from the two values of all two colonies.

3.2. The standardized fluorescence intensities of RFP

3.2.1. The standardized fluorescence intensities of RFP

We got the increasing ratios of fluorescence intensities at 37ºC and at 42ºC by dividing the each of the raw fluorescence intensities (Fig. 3-7-3-1.) by those at 30ºC. The increasing ratios of the Plac_rfp at 37ºC and at 42ºC show that the fluorescence intensities increased dependent on temperature. We evaluated the increasing ratios of Pcon_RNA thermometer_rfp at 37ºC and at 42ºC. Compared to the increasing ratios of Plac_rfp, those of the Pcon_RNA thermometer_rfp were higher at respective temperature. We observed not only the increase in the fluorescence intensities dependent on temperature but also the increase in the fluorescence intensities due to the function of the RNA thermometer (Table. 3-7-3-1.). The increasing ratio of Pcon_RNA thermometer_rfp was 1.3 times higher than that of Plac_rfp at 37ºC. Furthermore, the increasing ratio of Pcon_RNA thermometer_rfp was 3.2 times higher than that of Plac_rfp at 42ºC. These differences of the increasing ratios were dependent on the function of the RNA thermometer. We concluded that the RNA thermometer shows higher function at 42ºC compared to 37ºC.

Table. 3-7-3-1. The increasing ratios

3.2.2. The standardized fluorescence intensities of RFP
after subtracting the background derived from the Negative control cell

By subtracting the fluorescence intensity of the RNA thermometer_rfp (Fig. 3-7-3-1.) from both the fluorescence intensities of Plac_rfp and Pcon_RNA thermometer_rfp (Fig. 3-7-3-1.), each at the same temperature, we processed the background derived from the Negative control. We followed the increasing ratios with background subtraction as the section of the standardized fluorescence intensities of RFP, except this time we subtracted the backgrounds of all the fluorescence intensities. The increasing ratios of the Plac_rfp with background subtraction at 37ºC and at 42ºC show that the fluorescence intensities increased dependent on temperature. We evaluated the increasing ratios of Pcon_RNA thermometer_rfp with background subtraction at 37ºC and at 42ºC. Compared to the increasing ratios of Plac_rfp with background subtraction, those of the Pcon_RNA thermometer_rfp were higher at respective temperature. We observed not only the increase in the fluorescence intensities dependent on temperature but also the increase in the fluorescence intensities due to the function of the RNA thermometer (Table. 3-7-3-2.). The increasing ratio of Pcon_RNA thermometer_rfp with background subtraction was 2.7 times higher than that of Plac_rfp at 37ºC. Furthermore, the increasing ratio of Pcon_RNA thermometer_rfp with background subtraction was 6.8 times higher than that of Plac_rfp at 42ºC. These differences in the increasing ratios were dependent on the function of the RNA thermometer. We concluded that the RNA thermometer shows higher function at 42ºC compared to 37ºC.

Table. 3-7-3-2. The increasing ratios with background subtraction

4. Discussion

We examined that the reason the function of the RNA thermometer was worse at 37ºC than at 42ºC was that the amount of hydrogen bonds forming RNA thermometer was not enough to change in the structure of the RNA thermometer at 37ºC.
Furthermore, differences between the increasing ratios with and without background subtraction disclose the importance of background treatment. At 30ºC, Pcon_RNA thermometer_rfp wasn’t translated enough and showed little expression of RFP. Since the fluorescence intensity of Pcon_RNA thermometer_rfp at 30 ℃ was small, the increasing ratios of the Pcon_RNA thermometer with and without background subtraction greatly differ in both 37ºC and 42ºC (Table. 3-7-4-1.). Therefore, it is important to clarify whether the background derived from Negative control was processed or not.

Table. 3-7-4-1. The difference the increasing ratios with and without background subtraction

5. Materials and Methods

5.1. Construction

-Strain

All the samples were DH5alpha strain.

-Plasmids

(1)BBa_K1333309: Pcon_RNA thermometer_rfp(pSB1C3)


Fig. 3-7-5-1.

(2) Positive control: Plac_rfp_TT(pSB1C3)


Fig. 3-7-5-2.

(3) Negative Control:RNA thermometer_rfp(pSB1C3)


Fig. 3-7-5-3.

5.2. Assay Protocol

1. Prepare 2 over night cultures for each sample in 3 mL LB medium containing chloramphenicol (25 microg / mL) at 37ºC for 12 h.
2. Dilute the overnight cultures to 1/100 in fresh LB medium (3 mL) containing chloramphenicol (25 microg / mL ) in triplicate (fresh culture).
3. Incubate the triplicated fresh cultures each at 30ºC, 37ºC and 42ºC for each sample for 8 h.
4. Centrifuge the samples at 9000x g, 1 min , 4ºC.
5. Remove the supernatants by using P100 pipette and suspend the samples with 1 mL of filtered PBS (phosphate-buffered saline).
6. Dispense all of each suspension into a disposable tube through a cell strainer.
7. Measure fluorescence intensity with flow cytometer.

6. Reference

1. Stassen, Oscar MJA, et al., Toward tunable RNA thermo-switches for temperature dependent gene expression. arXiv preprint arXiv:1109.5402 (2011).

2. SYSU-China 2014

Team:Tokyo Tech/Experiment/RNA thermometer assay

RNA thermometer assay

contents

1. Introduction

2. Summary of the Experiment