Part:BBa_K731721

biology T7 bacteriophage direction Forward forward_efficiency 0.915 +/- 0.008 with T7 promoter; 0.80 +/- 0.01 with Ptac

T7 terminator wild type terminator from T7 bacteriophage. The characterization of this part was done by the Trento iGEM team 2012 using the new platforms for terminator characterization that they have built and submitted to the Registry BBa_K731700 and BBa_K731710.

Examples of Secondary Structures

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MEASUREMENTS

Our experiments exploited an E. coli lysogen strain carrying T7 RNA polymerase and lacIq. Additionally, the cells, i.e. E. coli BL21(DE3) pLysS, also contained a plasmid encoding T7 lysozyme and chloramphenicol resistance. T7 lysozyme is a natural inhibitor of T7 RNA polymerase activity, thus reducing background expression of the target genes. The T7 RNA polymerase is behind a lacUV5 promoter.

The activity of this part was analyzed both with T7 and E. coli RNA polymerases in vivo and with T7 RNA polymerase in vitro.

The parameters used to analyze the data are:

apparent termination efficiency, calculated with the equation found in literature Nojima,

raw termination efficiency, that does not consider the mCherry contribution

relative increase in the upstream gene expression,

(the last parameter was added as some terminators were found to increase the expression of the upstream gene Abe)

where

-Vs is the A206K Venus peak’s intensity of the construct with the terminator of interest inserted in the prefix-suffix linker

-Vc is the A206K Venus peak’s intensity of the control construct without intervening terminator

-Cs is the mCherry peak’s intensity of the construct with the terminator inserted

-Cc is the mCherry peak’s intensity of the control construct

In vivo measurements:

FIGURE 1. T7 bacteriophage terminator's effect on protein expression with two different RNA polymerases
The data shown in figure 1 were acquired in two different days. For each day 4 different replicates were measured at different times. Briefly, BL21(DE3)pLysS were grown in 10 mL of LB until an OD of 0.6 was reached and induced with 0.5 mM IPTG. After 3 hours of induction, 4 separate aliquots of 1 mL were taken and sonicated 3 times for 10 seconds at intervals of 30 seconds. After sonication the samples were diluted 1:2 with PBS 1X directly into a cuvette and incubated overnight at 4°C. Fluorescence measurements were taken with a Cary Eclipse Varian fluorimeter with a window ranging from 450 nm to 700 nm, a slit of 5nm, a voltage of 570V for the characterization with T7 polymerase and of 520V for the measurements with E. coli RNA polymerase. The following table shows the variations in excitation and emission wavelengths we adopted.

	Standard Excitation (nm)	Standard Emission (nm)	Modified Excitation (nm)	Modified Emission (nm)
mCherry	587	609	587	615
mVenus	515	528	485	528

TABLE 1. Standard and modified excitation and emission wavelengths

It is worth to highlight that the apparent and the raw transcriptional termination efficiencies, shown in figure 1, are essentially different from both a mathematical and a biological point of view. More specifically, raw termination efficiency is determined just by the expression of the downstream gene, while the apparent termination efficiency represents the variations that occur in the expression of both genes up- and down-stream of the terminator. They are in the same chart just for a comparison purpose.

For more information about the protocol we adopted to take these in vivo measurements, see BBa K731700 and BBa K731710 measurements.

In vitro measurements:

We performed the in vitro analysis only with the T7 RNA polymerase.

FIGURE 2. T7 bacteriophage terminator's effect on in vitro protein synthesis with the T7 RNA polymerases
Cell free measurements were done with the PurExpress kit from New England Biolabs, using 250 ng of DNA previously purified by ethanol precipitation, following the protocol suggested by the manufacturer. Measurements were done with a PTI fluorimeter using the same excitation and emission wavelengths used for the in vivo measurements. Note that the in vivo data are the same shown above; they are reported here to aid comparison.

We submitted also this Part inside both BBa_K731700 (T7 promoter backbone) and BBa_K731710 (tac promoter backbone) as, respecitively, BBa_K731701 and BBa_K731702. We hope that this could be helpful for anyone who want to verify and further delve into our results.

More information can be found in the iGEM Trento 2012 wiki page.

References

<biblio>

1. Nojima pmid=16379390
2. Abe pmid=9150882

</biblio>