Difference between revisions of "Part:BBa K2739005:Design"

Latest revision as of 01:18, 18 October 2018

proR-PhaR-proP-PhaP

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
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 858
Illegal SapI.rc site found at 253

Design Notes

This composite part is consisted PhaR and its native promoter + Phasin and its native promoter. This part was further developed based on the BBa K2739000 (ProR-PhaR). This designed to investigate its relation in PHA production through PHA operon with phasin.

Sequence of Phasin was obtained from previous item team, BBa_K390501(LacP-RBS-PhaP-HlyA-Terminator). Our team found that the end of Phasin's sequence contain a stop codon. The stop codon was then removed, however, consider the work of current composite part, the phasin with stop codon from the previous part was still used to current composite part.

Sequence of Phasin's native promoter was isolated from Ralstonia eutropha and not found on iGEM registry. Therefore, this promoter was genereated by IDT.

Sequence of PhaR and its native promoter could be found in iGEM registry, as two separate basic parts (BBa_K108015 and BBa_K108014) and being not available. The source of these sequences were recorded as 1. Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha H16. Microbiology. 2002, 148:2413–2426. and 2. NCBI (with no further information), having no mentioned if the sequence was codon optimised.

We access the online NCBI data and found out the current available phaR sequence is being 4 bp different to BBa_K108015; and the functional promoter is being 134bp shorter. Therefore we have used the new phaR and promoter sequence as our new template. Due to the excessive GC in the phaR sequence, we have it codon optimised to E.coli and generated the part through the IDT company service.

Figure 1. Comparison of phaR sequence from iGEM08_Tsinghua (BBa_K108015) and online NCBI(AM260479.1). Capital letters: NCBI(AM260479.1) and Small letter: iGEM08_Tsinghua (BBa_K108015).

Figure 2. Comparison of phaR sequence before and after codon optimisation. Capital letters: NCBI (AM260479.1) and Small letter: codon optimised version (BBa_K2739001).

Source

BBa_K108015, BBa_K108014 and NCBI (AM260479.1)

ProR and PhaR Sequence selection based on Reference 1 information.

PhaR sequence codon optimised through IDT. (And Phasin sequence optimised by previous team)

References

1. Yamada M, Takahashi S, Okahata Y, Doi Y, Numata K. (2013 ) Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate]. AMB Express. 3(1):6.

@@ Line 10: / Line 10: @@
 Sequence of Phasin was obtained from previous item team, BBa_K390501(LacP-RBS-PhaP-HlyA-Terminator). Our team found that the end of Phasin's sequence contain a stop codon. The stop codon was then removed, however, consider the work of current composite part, the phasin with stop codon from the previous part was still used to current composite part.
 Sequence of Phasin's native promoter was isolated from Ralstonia eutropha and not found on iGEM registry. Therefore, this promoter was genereated by IDT.
@@ Line 15: / Line 16: @@
 Sequence of PhaR and its native promoter could be found in iGEM registry, as two separate basic parts (BBa_K108015 and BBa_K108014) and being not available. The source of these sequences were recorded as 1. Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha H16. Microbiology. 2002, 148:2413–2426. and 2. NCBI (with no further information), having no mentioned if the sequence was codon optimised.
-We access the online NCBI data and found out the current available phaR sequence is being 4 bp different to BBa_K108015; and the functional promoter is being 134bp shorter. Therefore we have used the new phaR and promoter sequence as our new template. Due to the excessive GC in the sequence, we have it codon optimised to E.coli and generated the part through the IDT company service.
+We access the online NCBI data and found out the current available phaR sequence is being 4 bp different to BBa_K108015; and the functional promoter is being 134bp shorter. Therefore we have used the new phaR and promoter sequence as our new template. Due to the excessive GC in the phaR sequence, we have it codon optimised to E.coli and generated the part through the IDT company service.
 https://static.igem.org/mediawiki/parts/c/cd/T--Edinburgh_OG_BBa_K2739000--image_9.jpeg
-Figure 1. Comparison of phaR sequence from  iGEM08_Tsinghua and online NCBI. Capital letters: NCBI and Small letter: iGEM08_Tsinghua.
+Figure 1. Comparison of phaR sequence from  iGEM08_Tsinghua (BBa_K108015) and online NCBI(AM260479.1). Capital letters: NCBI(AM260479.1)  and Small letter: iGEM08_Tsinghua (BBa_K108015).
+https://static.igem.org/mediawiki/parts/9/9a/T--Edinburgh_OG_BBa_K2739000--image_10.jpeg
+Figure 2. Comparison of phaR sequence before and after codon optimisation. Capital letters:  NCBI (AM260479.1) and Small letter: codon optimised version (BBa_K2739001).
@@ Line 28: / Line 34: @@
 ProR and PhaR Sequence selection based on Reference 1 information.
+PhaR sequence codon optimised through IDT. (And Phasin sequence optimised by previous team)
 ===References===
 . Yamada M, Takahashi S, Okahata Y, Doi Y, Numata K. (2013 ) Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate]. AMB Express. 3(1):6.