Difference between revisions of "Part:BBa K4129102"

Revision as of 08:36, 11 October 2022

The fungal synthetic transcription factor, FunsTF04 (LexA-LL-Hmox1-B112-SV40)

FunsTF04 is a synthetic transcription factor (sTF). FunsTF04 is designed to function as a transcription factor that can initiate transcription from the 6xLexO minimal promoter (BBa_K4129115). This sTF can be the sensing part of a biosensor.

FunsTF04 is a fusion protein consisting of the DNA-binding domain LexA, the ligand sensing domain Hmox1, transactivation domain B112 and the nuclear localization signal (NLS) SV40. The linker between LexA and Hmox1 is a longer version linker (Ottoz et. al (2014) compared to sBAD, which was the reference sTF (Castaño-Cerezo et. al (2020)). FunsTF05 was codon optimised to A. Niger.

LexA is a repressor that regulates the SOS response in E. coli (Radman. 1975). LexA binds to a specific DNA motif, namely LexO sites (Erill. et al (2003)), and it is the DNA binding domain, which is interacting with LexO, that is used in FunsTF04. Hmox1 is the human heme oxygenase 1, which is the enzyme that initiates cleavage of heme (Tenhunen et al. (1969)). This enzyme was, despite the seemingly unrelated context, computationally shown to bind furfural (Santhakumar et al (2021)).

The transactivation domain B112 is from E. coli, which were experimentally proven to initiate transcription of a synthetic promoter in S. cerevisiae (Ottoz et. al (2014)). The NLS SV40 is a small peptide sequence of PKKKRKV that enables transport og the protein to the nucleus (Garcia-Bustos et. al (1991)).

Characterization

The functionally of FunsTF05 was tested by measuring the fluorescence of an A. niger carring sTF05 and the mCherry reporter (BBa_K4129122). The A. niger is grown on solid media plates. The plates contained either minimal media, minimal media with mM benzoic acid or MM with 0.6 g/L furfural. The fluorescence was assessed using the Vilber Fusion FX imager system to measure fluorescence shown as grey-white intensity.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 945
Illegal BamHI site found at 607
Illegal BamHI site found at 1604
Illegal XhoI site found at 800
Illegal XhoI site found at 1237
Illegal XhoI site found at 1753
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

@@ Line 1: / Line 1: @@
-=== FunsTF04 ===
+__NOTOC__
-FunsTF04 is a synthetic transcription factor (sTF). FunsTF04 should initiate the transcription through the 6xLexO minimal promoter. This sTF is the sensing part of the biosensor.
+<partinfo>BBa_K4129102 short</partinfo>
-FunsTF04 is a fusion protein consisting of the DNA-binding domain: lexA, ligand sensing domain: Hmox1, transactivation domain; B112 and the nuclear localization signal (NLS) SV40. The linker between LexA and Hmox1 was a longer version (Ottoz et. al (2014)
-compared to sBAD (Castaño-Cerezo et. al (2020)).
-LexA is a repressor that regulates the SOS response in E. coli (Radman. 1975). LexA binds to a specific DNA motif, lexO (Erill. et al (2003)), and it is the DNA binding domain that interacts with LexO that is used in FunsTF04. Hmox1 is the human heme oxygenase 1, which can cleave heme. This function is not of our interest, but it was shown that furfural binds to hmox1.
+FunsTF04 is a synthetic transcription factor (sTF).  FunsTF04 is designed to function as a transcription factor that can initiate transcription from the 6xLexO minimal promoter (BBa_K4129115). This sTF can be the sensing part of a biosensor.
-The transactivation domain B112 is from E. coli, which were experimentally proven to initiate transcription of a synthetic promoter in S. cerevisiae (Ottoz et. al (2014)). The NLS SV40 is a small peptide sequence of PKKKRKV that enables transport og the protein to the nucleus (Garcia-Bustos et. al (1991)).
+FunsTF04 is a fusion protein consisting of the DNA-binding domain LexA, the ligand sensing domain Hmox1, transactivation domain B112 and the nuclear localization signal (NLS) SV40. The linker between LexA and Hmox1 is a longer version linker (Ottoz et. al (2014)  compared to sBAD, which was the reference sTF (Castaño-Cerezo et. al (2020)). FunsTF05 was codon optimised to <i>A. Niger</i>.
+LexA is a repressor that regulates the SOS response in <i>E. coli</i> (Radman. 1975). LexA binds to a specific DNA motif, namely LexO sites (Erill. et al (2003)), and it is the DNA binding domain, which is interacting with LexO, that is used in FunsTF04. Hmox1 is the human heme oxygenase 1, which is the enzyme that initiates cleavage of heme (Tenhunen et al. (1969)). This enzyme was, despite the seemingly unrelated context, computationally shown to bind furfural (Santhakumar et al (2021)).
+The transactivation domain B112 is from <i>E. coli</i>, which were experimentally proven to initiate transcription of a synthetic promoter in <i>S. cerevisiae</i> (Ottoz et. al (2014)). The NLS SV40 is a small peptide sequence of PKKKRKV that enables transport og the protein to the nucleus (Garcia-Bustos et. al (1991)).
 === Characterization ===
+The functionally of FunsTF05 was tested by measuring the fluorescence of an <i>A. niger</i> carring sTF05 and the mCherry reporter (BBa_K4129122). The <i>A. niger</i> is grown on solid media plates. The plates contained either minimal media, minimal media with mM benzoic acid or MM with 0.6 g/L furfural.
+The fluorescence was assessed using the Vilber Fusion FX imager system to measure fluorescence shown as grey-white intensity.