Difference between revisions of "Part:BBa K581003"

Latest revision as of 02:56, 6 October 2011

SgrS2+Terminator (small RNA regulator, conjugate part of ptsG2)

This is the conjugate part of ptsG2-gfp[1].

Sequence and Features

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.

Background

SgrS is an Hfq-binding small antisense RNA that is induced upon phosphosugar stress (Vanderpool, 2007). It forms a ribonucleoprotein complex with RNase E through Hfq to mediate silencing of the target ptsG mRNA encoding the major glucose transporter (Geissmann and Touati, 2004). A 31-nt-long stretch in the 3’ region of SgrS is partially complementary to the translation initiation region of ptsG mRNA, and a 6 nt region overlapping the Shine-Dalgarno sequence of the target mRNA turns out to be crucial for SgrS’ function, shown as Fig.1 (Kawamoto et al., 2006; Maki et al., 2010).

Fig.1 Sequence alignment of wildtype ptsG/SgrS pair and its mutant complementary pairs. (A) The partial complementary region of ptsG (wt) mRNA and its corresponding sRNA SgrS. (B) The complementary pair site-mutant version of ptsG2 mRNA and corresponding SgrS2.

Teppei Morita et.al’ s work suggests that two mutations (C85G and C87G) in ptsG mRNA could completely impair the ability of SgrS to downregulate its expression, while compensatory mutations of SgrS (G178C and G176C) restore the gene silencing ability. These results indicate that it is the base pairing of the two RNAs rather than particular nucleotides that is important for SgrS action. They have also illustrated that sequence outside this region, even though complementary, is rather dispensable for the efficient silencing (Kawamoto et al., 2006). This makes mutant ptsG/SgrS pairs orthogonal to genetic context of the host cell. By employing two sets of mutant ptsG mRNA as well as its complementary SgrS in the design shown in Fig 1, we set to biologically implement the comparator. In detail, ptsG1 refers to a C85G mutant of ptsG (wt) while ptsG2 is a C87G mutant. SgrS1 (G178C) and SgrS2 (G176C) are the corresponding revertants which could help restore their complementarity. And as a proof-of-concept experiment, we constructed synthetic gene circuits, in which the 5’ untranslated region of ptsG mRNA was translationally fused to the coding sequence of the reporter gfp (Levine et al., 2007),as shown in Fig 2.

Fig.2 The modular experimental subunits of the comparator. (A) Salicylate leads to the transcription of ptsG-gfp mRNA, which is the target of constitutively expressed SgrS. This is how we implement both reporting and repressing outputs as a result of the activation of Psal. When there is more salicylate in the media, the GFP fluorescence intensity is expected to be stronger. (B) Salicylate leads to the transcription of SgrS, while the ptsG-gfp mRNA is downstream a constitutive promoter. In this scenario, as the concentration of salicylate increases, the repression effect SgrS exerts on ptsG would in turn be stronger, so the GFP fluorescence intensity is supposed to be weaker.

Experimental Data

Learn more

To qualitatively and quantitatively characterize the specifity of ptsG2/SgrS interaction, we conducted the following experiments.

Part I. The Orthogonal Silencing Matrix

The repression capacity of each ptsG/SgrS pair was indicated by the ratio of the average fluorescence intensity before to after the trigger of SgrS. What we expected was a significant repression within the cognate pairs (ptsG1/SgrS1, ptsG2/SgrS2, and ptsG (wt)/SgrS (wt)), and a minor repression folds among different pairs. As Figure 3 shows, the highest ratio lie at the diagonal from the upper left to the lower right as expected, which is 5 to 6 folds. As for the ptsG (wt)/SgrS1&2, ptsG1/SgrS (wt), and ptsG2/SgrS (wt), given that these crosses differ at only one base pair, the repression efficacy is around 3 folds. By contrast, the inhibiting effect of on ptsG2 and SgrS2 on ptsG1 is rather unapparent, which can be seen as an appropriate characteristic fitting our competitor requirements(see Fig.3).

Fig.3 A graphical representation of the repression matrix associated with SgrS and its mutants, and ptsG and its mutants. The values represent the repression ratios, defined as the repression capacity of each ptsG/SgrS pair, denoted by the ratio of fluorescence intensity before to after the induction of SgrS, suggesting within-subgroup pairwise specificity.

Part II. Response Curves

The sRNA-mediated gene silencing can be formulated quantitatively via a simple kinetic model. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA (s) and its target mRNA (m):

The parameters are defined as in Table 1.

Table 1. Model Parameters: Definitions and Estimated Values

Levine et. al’s work has revealed that in the idealized scenario when binding between sRNA and mRNA occurs extremely rapidly, gene expression is completely silenced if the target transcription rate is below a threshold. Above this threshold, gene expression will increase linearly. Such threshold-linear model is based on the difference of transcription rates between sRNA and mRNA(Levine et al., 2007)(see Fig.4).

Fig.4 Predicted response curve of a target gene. (a) The red line depicts the idealized threshold-linear mode of regulation in which gene expression is completely silenced if the SgrS transcription rate exceeds a threshold set by the transcription rate of the ptsG-gfp mRNA. Under this threshold, gene expression decreases linearly with the difference between the mRNA and sRNA transcription rates. (b) The red line depicts the idealized threshold-linear mode of regulation in which gene expression is completely silenced if the ptsG-gfp mRNA transcription rate is below a threshold set by the transcription rate of the sRNA. Above this threshold, gene expression increases linearly with the difference between the mRNA and sRNA transcription rates. The idealized scenario is expected when binding between sRNA and mRNA occurs extremely rapidly. The blue line is the actual response expected using the estimated parameters of Table 1

Levine et. al’s work has revealed that in the idealized scenario when binding between sRNA and mRNA occurs extremely rapidly, gene expression is completely silenced if the target transcription rate is below a threshold. Above this threshold, gene expression will increase linearly. Such threshold-linear model is based on the difference of transcription rates between sRNA and mRNA(Levine et al., 2007). Our data of ptsG2/SgrS2 interaction fitted into the predicted scenario quite readily, just as Fig.5 shows.

Fig.5 Salicylate-induced SgrS repressing the expression of ptsG-GFP. The promoter activity is defined as the GFP expression of the Psal+gfp strain grown in identical media. Different promoter activities were obtained by varying salicylate concentration in the media. The conjugate pairs fit into dose-response curve with variable Hill slope given as a parameter, and the R^2 is 0.9607.

Methods

Materials: We have constructed two types of plasmids presented in Figure.6.

Fig.6 Plasmids constructed for characterizing ptsG/SgrS orthogonal silencing matrix

References

[1] Geissmann, T.A., and Touati, D. (2004). Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. The EMBO journal 23: 396-405

[2] Kawamoto, H., Koide, Y., Morita, T., and Aiba, H. (2006). Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Molecular microbiology 61: 1013-1022

[3] Levine, E., Zhang, Z., Kuhlman, T., and Hwa, T. (2007). Quantitative characteristics of gene regulation by small RNA. PLoS biology 5: e229

@@ Line 2: / Line 2: @@
 <partinfo>BBa_K581003 short</partinfo>
-This is the conjugate part of ptsG2-gfp.
+This is the conjugate part of <b>ptsG2-gfp</b>[https://parts.igem.org/wiki/index.php?title=Part:BBa_K581004].
 <!-- Add more about the biology of this part here
@@ Line 25: / Line 25: @@
 <h2>Background</h2>
-<p>SgrS is an Hfq-binding small antisense RNA that is induced upon phosphosugar stress (Vanderpool, 2007). It forms a ribonucleoprotein complex with RNase E through Hfq to mediate silencing of the target ptsG mRNA encoding the major glucose transporter (Geissmann and Touati, 2004). A 31-nt-long stretch in the 3’ region of SgrS is partially complementary to the translation initiation region of ptsG mRNA, and a 6 nt region overlapping the Shine-Dalgarno sequence of the target mRNA turns out to be crucial for SgrS’ function, shown as Fig.1 (Kawamoto et al., 2006; Maki et al., 2010).</p>
+<p><b>SgrS</b> is an Hfq-binding small antisense RNA that is induced upon phosphosugar stress (Vanderpool, 2007). It forms a ribonucleoprotein complex with RNase E through Hfq to mediate silencing of the target ptsG mRNA encoding the major glucose transporter (Geissmann and Touati, 2004). A 31-nt-long stretch in the 3’ region of SgrS is partially complementary to the translation initiation region of ptsG mRNA, and a 6 nt region overlapping the Shine-Dalgarno sequence of the target mRNA turns out to be crucial for SgrS’ function, shown as Fig.1 (Kawamoto et al., 2006; Maki et al., 2010).</p>
+<div class="imgbox" style="width:370px;margin:0 auto;">
+<img class="border" src="http://fmn.rrimg.com/fmn061/20111006/0940/large_q5Ai_544e0000b6ae125e.jpg" width="370px"/>
+</div>
+<br/><br/>
+<div class="imgbox" style="width:390px;margin:0 auto;">
+<img class="border" src="http://fmn.rrimg.com/fmn056/20111006/0945/large_36PR_59610000b6ca1212.jpg" width="390px"/>
+</div>
+<br/>
-<img src="http://fmn.rrimg.com/fmn065/20111006/0735/original_JgIW_49750000b3941215.jpg" width="520px" margin="100" auto/></a></h3>
-             <img src="http://fmn.rrfmn.com/fmn058/20111006/0600/original_Y0mV_61420000b3931211.jpg" width="520px" margin="100" auto/></a></h3>
 <p><i>Fig.1 Sequence alignment of wildtype ptsG/SgrS pair and its mutant complementary pairs.
           (A) The partial complementary region of ptsG (wt) mRNA and its corresponding sRNA SgrS.
@@ Line 36: / Line 47: @@
 Teppei Morita et.al’ s work suggests that two mutations (C85G and C87G) in ptsG mRNA could completely impair the ability of SgrS to downregulate its expression, while compensatory mutations of SgrS (G178C and G176C) restore the gene silencing ability. These results indicate that it is the base pairing of the two RNAs rather than particular nucleotides that is important for SgrS action. They have also illustrated that sequence outside this region, even though complementary, is rather dispensable for the efficient silencing (Kawamoto et al., 2006). This makes mutant ptsG/SgrS pairs orthogonal to genetic context of the host cell.
-By employing two sets of mutant ptsG mRNA as well as its complementary SgrS in the design shown in Fig 1, we set to biologically implement the comparator. In detail, ptsG1 refers to a C85G mutant of ptsG (wt) while ptsG2 is a C87G mutant. SgrS1 (G178C) and SgrS2 (G176C) are the corresponding revertants which could help restore their complementarity. And as a proof-of-concept experiment, we constructed synthetic gene circuits, in which the 5’ untranslated region of ptsG mRNA was translationally fused to the coding sequence of the reporter gfp (Levine et al., 2007),as shown in Fig 2.
+By employing two sets of mutant ptsG mRNA as well as its complementary SgrS in the design shown in Fig 1, we set to biologically implement the comparator. In detail, ptsG1 refers to a C85G mutant of ptsG (wt) while ptsG2 is a C87G mutant. SgrS1 (G178C) and SgrS2 (G176C) are the corresponding revertants which could help restore their complementarity.
-<img src="http://fmn.rrimg.com/fmn056/20111006/0555/original_yJXu_4b940000b3d41213.jpg" width="420px" margin="1000" auto/></a></h3>
+And as a proof-of-concept experiment, we constructed synthetic gene circuits, in which the 5’ untranslated region of ptsG mRNA was translationally fused to the coding sequence of the reporter gfp (Levine et al., 2007),as shown in Fig 2.
+<br/>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<img src="http://fmn.rrimg.com/fmn056/20111006/0555/original_yJXu_4b940000b3d41213.jpg" width="420px" margin="1000" auto/></a></h3>
 <img src="http://fmn.rrimg.com/fmn056/20111006/0555/original_lv2E_45160000b4361267.jpg" width="420px" margin="10000" auto/></a></h3>
-<p><i>Fig. 2 The modular experimental subunits of the comparator. (A) Salicylate leads to the transcription of ptsG-gfp mRNA, which is the target of constitutively expressed SgrS. This is how we implement both reporting and repressing outputs as a result of the activation of Psal. When there is more salicylate in the media, the GFP fluorescence intensity is expected to be stronger. (B) Salicylate leads to the transcription of SgrS, while the ptsG-gfp mRNA is downstream a constitutive promoter. In this scenario, as the concentration of salicylate increases, the repression effect SgrS exerts on ptsG would in turn be stronger, so the GFP fluorescence intensity is supposed to be weaker.</i></p>
+<p><i>Fig.2 The modular experimental subunits of the comparator. (A) Salicylate leads to the transcription of ptsG-gfp mRNA, which is the target of constitutively expressed SgrS. This is how we implement both reporting and repressing outputs as a result of the activation of Psal. When there is more salicylate in the media, the GFP fluorescence intensity is expected to be stronger. (B) Salicylate leads to the transcription of SgrS, while the ptsG-gfp mRNA is downstream a constitutive promoter. In this scenario, as the concentration of salicylate increases, the repression effect SgrS exerts on ptsG would in turn be stronger, so the GFP fluorescence intensity is supposed to be weaker.</i></p>
 <h2>Experimental Data</h2>
-<h4>To qualitatively and quantitatively characterize the performance of our competitor, we conducted the following experiments.</h4>
+<br/>
+<a href="http://2011.igem.org/Team:Peking_S/project/nonb/comparator" target="_blank">Learn more</a>
+<h4>To qualitatively and quantitatively characterize the specifity of ptsG2/SgrS interaction, we conducted the following experiments. </h4>
 <h3>Part I. The Orthogonal Silencing Matrix</h3>
 The repression capacity of each ptsG/SgrS pair was indicated by the ratio of the average fluorescence intensity before to after the trigger of SgrS. What we expected was a significant repression within the cognate pairs (ptsG1/SgrS1, ptsG2/SgrS2, and ptsG (wt)/SgrS (wt)), and a minor repression folds among different pairs.
-As Figure 3 shows, the highest ratio lie at the diagonal from the upper left to the lower right as expected, which is 5 to 6 folds. As for the ptsG (wt)/SgrS1&2, ptsG1/SgrS (wt), and ptsG2/SgrS (wt), given that these crosses differ at only one base pair, the repression efficacy is around 3 folds. By contrast, the inhibiting effect of on ptsG2 and SgrS2 on ptsG1 is rather unapparent, which can be seen as an appropriate characteristic fitting our competitor requirements.
+As Figure 3 shows, the highest ratio lie at the diagonal from the upper left to the lower right as expected, which is 5 to 6 folds. As for the ptsG (wt)/SgrS1&2, ptsG1/SgrS (wt), and ptsG2/SgrS (wt), given that these crosses differ at only one base pair, the repression efficacy is around 3 folds. By contrast, the inhibiting effect of on ptsG2 and SgrS2 on ptsG1 is rather unapparent, which can be seen as an appropriate characteristic fitting our competitor requirements(see Fig.3).
-The original data also provided below (Fig.3).
-<img src="http://fmn.rrfmn.com/fmn058/20111006/0700/original_423z_544b0000b4fc1265.jpg" width="540px" margin="0" auto/></a>
+<div class="imgbox" style="width:370px;margin:0 auto;">
+<img class="border" src="http://fmn.rrfmn.com/fmn058/20111006/0700/original_423z_544b0000b4fc1265.jpg" width="370px"/>
 <p><i>Fig.3 A graphical representation of the repression matrix associated with SgrS and its mutants, and ptsG and its mutants. The values represent the repression ratios, defined as the repression capacity of each ptsG/SgrS pair, denoted by the ratio of fluorescence intensity before to after the induction of SgrS, suggesting within-subgroup pairwise specificity.</i></p>
+</div>
 <h3>Part II. Response Curves</h3>
+</html>
 The sRNA-mediated gene silencing can be formulated quantitatively via a simple kinetic model. The model is cast in terms of two mass-action equations for the cellular concentrations of the sRNA (s) and its target mRNA (m):
+<html>
+<div class="imgbox" style="width:240px;margin:0 auto;">
+<img class="border" src="https://static.igem.org/mediawiki/2011/5/58/M_model.png" width="240px"/>
+<br/></div>
+</html>
+The parameters are defined as in Table 1.
-<img src="http://fmn.rrimg.com/fmn063/20111006/0555/original_f2u6_5a440000b6cb126a.jpg" width="540px" margin="0" auto/></a>
+<center>''Table 1. Model Parameters: Definitions and Estimated Values''</center>
+<html>
-<p>To verify this, we performed experiments to get the dose-response curve. The result is shown in Figure 4.</p>
+<div class="imgbox" style="width:370px;margin:0 auto;">
-<p><i>Fig.4 The dose-response curve of SgrS/ptsG-gfp interaction. Salicylate-induced SgrS repressing the expression of ptsG-GFP. The promoter activity is defined as the GFP expression of the Psal+gfp strain grown in identical media. Different promoter activities were obtained by varying salicylate concentration in the media. The conjugate pairs fit into dose-response curve with variable Hill slope given as a parameter, and the R^2 0.9607 corresponding to salicylate-induced, a dose-response curve is also fitted with an R2 of 0.9301.</i></p>
+<img class="border" src="https://static.igem.org/mediawiki/2011/thumb/e/e1/M_Parameters.png/680px-M_Parameters.png" width="370px"/></div>
+<br/>
+</html>
+Levine et. al’s work has revealed that in the idealized scenario when binding between sRNA and mRNA occurs extremely rapidly, gene expression is completely silenced if the target transcription rate is below a threshold. Above this threshold, gene expression will increase linearly. Such threshold-linear model is based on the difference of transcription rates between sRNA and mRNA(Levine et al., 2007)(see Fig.4).
+<center>[[Image:x.png|600px]]</center>
+<center>[[Image:y.png|600px]]</center>
+''Fig.4 Predicted response curve of a target gene. (a) The red line depicts the idealized threshold-linear mode of regulation in which gene expression is completely silenced if the SgrS transcription rate exceeds a threshold set by the transcription rate of the ptsG-gfp mRNA. Under this threshold, gene expression decreases linearly with the difference between the mRNA and sRNA transcription rates. (b) The red line depicts the idealized threshold-linear mode of regulation in which gene expression is completely silenced if the ptsG-gfp mRNA transcription rate is below a threshold set by the transcription rate of the sRNA. Above this threshold, gene expression increases linearly with the difference between the mRNA and sRNA transcription rates. The idealized scenario is expected when binding between sRNA and mRNA occurs extremely rapidly. The blue line is the actual response expected using the estimated parameters of Table 1''
+<html>
+Levine et. al’s work has revealed that in the idealized scenario when binding between sRNA and mRNA occurs extremely rapidly, gene expression is completely silenced if the target transcription rate is below a threshold. Above this threshold, gene expression will increase linearly. Such threshold-linear model is based on the difference of transcription rates between sRNA and mRNA(Levine et al., 2007).
+Our data of ptsG2/SgrS2 interaction fitted into the predicted scenario quite readily, just as Fig.5 shows.
+ <br/><br/><br/>
+<div class="imgbox" style="width:480px;margin:0 auto;">
+<img class="border" src="http://fmn.rrimg.com/fmn063/20111006/0555/original_f2u6_5a440000b6cb126a.jpg" width="480px"/>
+</div>
+<p><i>Fig.5 Salicylate-induced SgrS repressing the expression of ptsG-GFP. The promoter activity is defined as the GFP expression of the Psal+gfp strain grown in identical media. Different promoter activities were obtained by varying salicylate concentration in the media. The conjugate pairs fit into dose-response curve with variable Hill slope given as a parameter, and the R^2 is 0.9607.</i></p>
@@ Line 77: / Line 131: @@
-<h3>Methods<a href="http://2011.igem.org/Team:Peking_S/lab/protocol"><img src="http://fmn.rrimg.com/fmn061/20111006/0545/original_5I0Y_31c40000b5241210.jpg" width="240px" align="right"/></a></h3>
+<h3>Methods<a href="http://2011.igem.org/Team:Peking_S/lab/protocol"><img src="http://fmn.rrimg.com/fmn056/20111006/1020/original_9rNC_4cb60000b84f1261.jpg" width="240px" align="right"/></a></h3>
-<P>Materials:
+<br/>
-We have constructed two types of plasmids presented in Figure 5.<P>
+<P><b>Materials<b>:
+We have constructed two types of plasmids presented in Figure.6.<P>
+<img src="http://fmn.rrimg.com/fmn056/20111006/0555/original_H8gX_552a0000b554125e.jpg" width="300px" align="left"/></a>
+<img src="http://fmn.rrimg.com/fmn059/20111006/0555/original_r0y8_4bbc0000b3d81213.jpg" width="300px" align="left"/></a>
+<br/><br/><br/><br/><br/><br/><br/><br/> <br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
-<img src="http://fmn.rrimg.com/fmn056/20111006/0555/original_H8gX_552a0000b554125e.jpg" width="260px" align="right"/></a>
+<p><i>Fig.6 Plasmids constructed for characterizing ptsG/SgrS orthogonal silencing matrix</i></p>
+<br/><br/><br/>
-<img src="http://fmn.rrimg.com/fmn059/20111006/0555/original_r0y8_4bbc0000b3d81213.jpg" width="260px" align="right"/></a>
-<p><i>Fig.5 Plasmids constructed for characterizing ptsG/SgrS orthogonal silencing matrix</i></p>