Difference between revisions of "Part:BBa K3889021"

Revision as of 05:24, 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

Waeda_Tokyo 2022 performed some experiment with this parts.

We found out that BBa_K3889021 can't express in E. coli by SDS-page

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

SRTF is 22kDa. E. coli codon optimized SRTF1(BBa_K4158012) seems that it expressed finely while B. sub optimized SRTF1(BBa K3889021) doesn't.

It is because BBa K3889021 contains E. coli rare codon, we guess.

The nucleotide sequence of 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 6: / Line 6: @@
 [[File:T--IISER-Tirupati India--SRTF1 repression.png|centre]]
+Waeda_Tokyo 2022 performed some experiment with this parts.
 We found out that BBa_K3889021 can't express in <i>E. coli</i> by SDS-page
@@ Line 12: / Line 14: @@
 SRTF is 22kDa.
-E. coli codon optimized SRTF1(BBa_K4158012) seems that it expressed finely while B. sub optimized SRTF1(BBa K3889021) doesnt't.
+<i>E. coli</i> codon optimized SRTF1(BBa_K4158012) seems that it expressed finely while <i>B. sub</i> optimized SRTF1(BBa K3889021) doesn't.
 It is because BBa K3889021 contains <i>E. coli</i> rare codon, we guess.
-The nucleotide sequence of BBa K3889021(<i>B.subtilis</i> optimized SRTF1 gene [2]) is shown in the below. <b>Bold</b> letters represent low-usage codons in <i>E.coli</i> [3]
+The nucleotide sequence of BBa K3889021(<i>B.subtilis</i> optimized SRTF1 gene) is shown below. <b>Bold</b> letters represent low-usage codons in <i>E.coli</i> [2]
 atg/tct/<b>agt</b>/act/gcg/gag/aga/ata/<b>cgg</b>/cca/<b>gga</b>/aga/agc/<b>ggg</b>/att/ctc/gct/gct/gcc/act/cgc/ctc/ttc/gcg/acg/cac/<b>gga</b>/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/<b>ggg</b>/gct/cac/gaa/gat/cct/cgc/gcc/
@@ Line 41: / Line 42: @@
 ===References===
 . 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
 . Don Lorimer et al. Gene Composer: Database Software for Protein Construct Design, Codon Engineering, and Gene Synthesis. <i>BMC Biotechnology</i> <b>9</b>(1):36(2009).
-. Raymond, A., Lovell, S., Lorimer, D. et al. Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer. <i> BMC Biotechnol</i> <b>9</b>, 37 (2009).