Difference between revisions of "Part:BBa K3889021"

Revision as of 15:57, 10 October 2022

Steroid Responsive Transcription Factor1 (SRTF1)

Steroid Responsive Transcription Factor (SRTF1) is a bacterial transcription factor that can respond to progesterone in a concentration-dependent manner. SRTF1 binds to its binding site (BBa_K3889030) resulting in inhibition of gene expression. Now as progesterone enters the system SRTF1 binds to progesterone leaving its binding site free for the transcription machinery to start working. This results in a progesterone inducible gene expression. [1]

T--IISER-Tirupati India--SRTF1 repression.png

Contribution: Waseda_Tokyo 2022

Waseda_Tokyo 2022 used this part in the aim for detecting progesterone in cell-free protein synthesis (CFPS) system in E.coli. We demonstrated that this part did not work in E.coli. We transformed this plasmid into E.coli BL21(DE3)Star strain, and made cell-free extracts enriched with the protein. Fig. 1 shows the result of SDS-PAGE performed with the bacterial extract. SRTF1 optimized for E.coli BBa_K4158012 is shown as a control. As shown in Fig. 1., the molecular mass of the protein optimized for Bacillus subtilis was smaller than that of SRTF1 (22kDa). Thus, we found that SRTF1 gene optimized for Bacillus subtilis was not fully translated in E.coli due to the difference in codon usage in these two organisms.

Fig. 1. The result of SDS-PAGE (SRTF1)

The nucleotide sequence of this part BBa K3889021 (B.subtilis optimized SRTF1 gene) is shown below. Bold letters represent low-usage codons in E.coli [2]

atg/tct/agt/act/gcg/gag/aga/ata/cgg/cca/gga/aga/agc/ggg/att/ctc/gct/gct/gcc/act/cgc/ctc/ttc/gcg/acg/cac/gga/gtg/tct/ggc/aca/tca/tta/caa/caa/ata/gcc/gat/gcc/act/ggt/atc/ aca/aaa/gct/gct/gta/tac/cat/cac/ttc/cct/acc/aaa/gaa/gaa/gtg/gtc/gtc/gct/gtc/ttg/gcg/cct/gcc/ctt/gag/gcc/atc/caa/ggc/atc/gtt/aga/aca/gca/ggg/gct/cac/gaa/gat/cct/cgc/gcc/ gct/acc/gag/gca/gcg/att/att/gga/ctc/gcg/gac/caa/gca/gtc/acg/cat/cgc/cag/cgc/tgg/gct/gtt/ctg/tta/caa/gat/gca/gca/gta/gaa/gaa/tac/gtc/cgt/aac/aat/cca/gac/cac/gat/gag/ttg/ ttc/act/cgt/ctg/aga/tta/ctg/ctt/act/ggc/ccc/gat/ccg/acc/cct/ggg/act/aga/ctg/caa/gtg/tcc/ctc/ttc/ttg/tct/ggt/ctt/ttg/ggg/cca/gca/caa/gat/cct/tct/tgc/gca/gat/ata/gac/gac/gat/gcg/ tta/aga/gcg/gga/atc/gta/cgt/gcg/ggc/cgt/aga/ctg/ctc/ttg/gcg/gat/gac/gac/gct/taa

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]

References

1. Grazon, C., Baer, R. C., Kuzmanović, U., Nguyen, T., Chen, M., Zamani, M., Chern, M., Aquino, P., Zhang, X., Lecommandoux, S., Fan, A., Cabodi, M., Klapperich, C., Grinstaff, M. W., Dennis, A. M., & Galagan, J. E. (2020). A progesterone biosensor derived from microbial screening. In Nature Communications (Vol. 11, Issue 1). Springer Science and Business Media LLC. https://doi.org/10.1038/s41467-020-14942-5

2. Don Lorimer et al. Gene Composer: Database Software for Protein Construct Design, Codon Engineering, and Gene Synthesis. BMC Biotechnology 9(1):36(2009).

@@ Line 24: / Line 24: @@
 ttc/act/cgt/ctg/aga/tta/ctg/ctt/act/ggc/<b>ccc</b>/gat/ccg/acc/cct/<b>ggg</b>/act/aga/ctg/caa/gtg/tcc/ctc/ttc/ttg/tct/ggt/ctt/ttg/<b>ggg</b>/cca/gca/caa/gat/cct/tct/tgc/gca/gat/ata/gac/gac/gat/gcg/
 tta/aga/gcg/<b>gga</b>/atc/gta/cgt/gcg/ggc/cgt/aga/ctg/ctc/ttg/gcg/gat/gac/gac/gct/taa
-<big><b>Parts Improvement: Waseda_Tokyo 2022</b></big>
-<partinfo>BBa_K4158012 short</partinfo>
-This part contains RBS and SRTF1-SSGSSG-TEV-His coding site.
-<u><b>SRTF1 sequence is optimized to <i>E. coli</i> codon.
-This part is the improvement of <partinfo>BBa_K3889021</partinfo>(<i>B. sub</i> optimized SRTF1)</b></u>.
-[[File:Waseda Tokyo progesterone detector gene circuit.png|500px|thumb|center|Fig. 1. progesterone detector gene circuit]]
-<b>Design</b>
-SRTF1 amino acid sequence was cited from a previous paper[1].
-We designed this part by
-<ul>
-<li>optimizing SRTF1 amino sequences to <i>E.coli</i> codon by using GeneArt(Thermo).</li>
-<li>optimizing the 5'UTR by using RBS calculator and RNA fold.</li>
-</ul>
-Then, we inserted the fragment into pET26b(+) vector.
-<b>Results</b>
-In order to detect progesterone <i>in vitro</i>, we transformed this part into <i>BL21(DE3)Star</i> strain and prepared crude extracts which were pre-enriched with the transcription factor, SRTF1.
-[[File:Waseda Tokyo Preparation of SRTF1-enriched extract.png|500px|thumb|center|Fig. 2. Preparation of SRTF1-enriched extract]]
-We also prepared cell-free extract enriched with the <i>B. subtilis</i> optimized SRTF1, using <partinfo>BBa_K3889021</partinfo>.
-Then, we performed SDS-PAGE to compare the expression of the protein in E. coli with both of the parts.
-From <b>Fig. 3.</b>, we could confirm that SRTF1(22kDa) codon-optimized for <i>E.coli</i> was successfully expressed in <i>E. coli</i>.
-On the other hand, the molecular mass of the protein optimized for <i>Bacillus subtilis</i>was smaller than that of SRTF1 (22kDa). Thus, we found that SRTF1 gene optimized for <i>Bacillus subtilis</i> was not fully translated in<i>E.coli</i> due to the difference in codon usage in these two organisms.
-[[File:Waseda Tokyo result of SDS-PAGE SRTF1.png|500px|thumb|center|Fig. 3. The result of SDS-PAGE (SRTF1)]]
-We also performed cell-free protein synthesis reaction with the extracts, using <partinfo>BBa_K4158010</partinfo> as the reporter plasmid.
-<b>Fig. 4.</b> shows the result of the experiment. We added 100uM of progesterone in the final concentration.
-We demonstrated that this part could detect progesterone in the cell-free protein synthesis system.
-[[File:Waseda Tokyo comparison of result of progesterone sensing by SRTF1.png|500px|thumb|center|Fig. 4. comparison of result of progesterone sensing by SRTF1]]
-The shaded result represents SRTF1(E. coli)(<partinfo>BBa_K4158012</partinfo>) and the plain result represents SRTF1(B. sub)(<partinfo>BBa_K3889021</partinfo>).
-We could confirm below from <b>Fig. 4.</b>.
-<ul>
-<li>When progesterone was added in the absence of the reporter plasmid, an increase in GFP fluorescence was not observed (left).</li>
-<li>When only the plasmid was added in the absence of progesterone, an increase in GFP fluorescence was slightly observed, due to the leak expression (middle).</li>
-<li>When progesterone was added to the condition above, an increase in GFP fluorescence was observed (right).</li>
-</ul>
-Thus, we succeeded in engineering SRTF1-expressing plasmid which works in <i>E.coli</i>, as a part improvement of <partinfo>BBa_K3889021</partinfo>.