Difference between revisions of "Part:BBa K3889021"
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[[File:T--IISER-Tirupati India--SRTF1 repression.png|centre]]
 
[[File:T--IISER-Tirupati India--SRTF1 repression.png|centre]]
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We found out that BBa_K3889021 can't express in <i>E. coli</i> by SDS-page
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[[File:Waseda Tokyo result of SDS-PAGE SRTF1.png|1500px|thumb|center|Fig. 1. result of SDS-PAGE (SRTF1)]]
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SRTF is 22kDa.
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 +
E. coli codon optimized SRTF1(BBa_K4158012) seems that it expressed finely while B. sub optimized SRTF1(BBa K3889021) doesnt'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]
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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/
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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/
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gct/acc/gag/gca/gcg/att/att/<b>gga</b>/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/
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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/
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tta/aga/gcg/<b>gga</b>/atc/gta/cgt/gcg/ggc/cgt/aga/ctg/ctc/ttg/gcg/gat/gac/gac/gct/taa
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<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
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===Usage and Biology===
 
===Usage and Biology===
  
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===References===
 
===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
 
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
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2. 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).
 +
3. 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).

Revision as of 05:10, 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

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) doesnt't.


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

The nucleotide sequence of BBa K3889021(B.subtilis optimized SRTF1 gene [2]) is shown in the below. Bold letters represent low-usage codons in E.coli [3]

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). 3. Raymond, A., Lovell, S., Lorimer, D. et al. Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer. BMC Biotechnol 9, 37 (2009).