Difference between revisions of "Part:BBa K4129100"
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
=== Background for FunsTF01 ===
+
__NOTOC__
 +
<partinfo>BBa_K4129100 short</partinfo>
  
−
FunsTF01 is a synthetic transcription factor (sTF) based on sensor of benzoic acid derivatives (sBAD), which is a sTF in S. cerevisiae (Castaño-Cerezo et. al (2020)). FunsTF01 should initiate the transcription through the 6xLexO minimal promoter. This sTF is the sensing part of the biosensor.
 
  
−
FunsTF01 is a fusion protein consisting of the DNA-binding domain: lexA, ligand sensing domain: HbaR, transactivation domain; B112 and the nuclear localization signal (NLS) SV40. The linker between LexA and HbaR was a longer version (Ottoz et. al (2014 ) compared to sBAD (Castaño-Cerezo et. al (2020)).
+
FunsTF01 is a synthetic transcription factor (sTF) based on a sensor of benzoic acid derivatives (sBAD), which is a sTF in <i>S. cerevisiae</i> (Castaño-Cerezo et. al (2020)). FunsTF01 deviates from sBAD, in that it has a nuclear localization signal (NLS) and is codon optimised to <i>A. niger</i>
 +
FunsTF01 is designed to function as a transcription factor that can initiate transcription from the 6xLexO minimal promoter (BBa_K4129115). This sTF is designed to be the sensing part of a biosensor.
 +
 +
FunsTF01 is a fusion protein consisting of the DNA-binding domain from LexA, the ligand sensing domain from HbaR, transactivation domain B112 and the NLS SV40. The linker between the LexA domain and the HbaR domain is a longer linker (Ottoz et. al (2014) compared to the linker in sBAD, which was the reference sTF (Castaño-Cerezo et. al (2020)).
  
−
LexA is a repressor that regulates the SOS response in <i>E. coli</i> (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 FunsTF01. HbaR is a transcriptional factor from <i>Rhodopseudomonas palustris</i> that initiates transcription in the presence of benzoic acid or in the presence of benzoic acid derivatives (Egland. Et al (2000), Castaño-Cerezo et. al (2020)).The transactivation domain B112 is from <i>E. coli</i>, 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)).
+
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)). HbaR is a transcription factor from <i>Rhodopseudomonas palustris</i> that initiates transcription in the presence of benzoic acid (Egland. et al (2000)) or in the presence of benzoic acid derivatives (Castaño-Cerezo et. al (2020)).
  
−
=== References: ===
+
The transactivation domain B112 is from <i>E. coli</i>, and it was 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 of the protein to the nucleus (Garcia-Bustos et. al (1991)).
−
Garcia-Bustos J, Heitman J, Hall MN. Nuclear protein localization. Biochim Biophys Acta. 1991 Mar 7;1071(1):83-101. doi: 10.1016/0304-4157(91)90013-m. PMID: 2004116.
+
  
−
Ottoz DS, Rudolf F, Stelling J. Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae. Nucleic Acids Res. 2014;42(17):e130. doi: 10.1093/nar/gku616. Epub 2014 Jul 17. PMID: 25034689; PMCID: PMC4176152.
 
−
 
−
Castaño-Cerezo S, Fournié M, Urban P, Faulon JL, Truan G. Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae. Front Bioeng Biotechnol. 2020 Jan 7;7:372. doi: 10.3389/fbioe.2019.00372. PMID: 31970152; PMCID: PMC6959289.
 
−
 
−
Egland PG, Harwood CS. HbaR, a 4-hydroxybenzoate sensor and FNR-CRP superfamily member, regulates anaerobic 4-hydroxybenzoate degradation by Rhodopseudomonas palustris. J Bacteriol. 2000 Jan;182(1):100-6. doi: 10.1128/JB.182.1.100-106.2000. PMID: 10613868; PMCID: PMC94245.
 
−
 
−
Radman M. SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci. 1975;5A:355-67. doi: 10.1007/978-1-4684-2895-7_48. PMID: 1103845.
 
−
 
−
Erill I, Escribano M, Campoy S, Barbé J. In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon. Bioinformatics. 2003 Nov 22;19(17):2225-36. doi: 10.1093/bioinformatics/btg303. PMID: 14630651.
 
  
 
<!-- -->
 
<!-- -->
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
−
<partinfo>BBa_K4129103 SequenceAndFeatures</partinfo>
+
<partinfo>BBa_K4129100 SequenceAndFeatures</partinfo>
  
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
−
<partinfo>BBa_K4129103 parameters</partinfo>
+
<partinfo>BBa_K4129100 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 19:14, 11 October 2022

The fungal synthetic transcription factor, FunsTF01 (LexA-LL-HbaR-B112-SV40)


FunsTF01 is a synthetic transcription factor (sTF) based on a sensor of benzoic acid derivatives (sBAD), which is a sTF in S. cerevisiae (Castaño-Cerezo et. al (2020)). FunsTF01 deviates from sBAD, in that it has a nuclear localization signal (NLS) and is codon optimised to A. niger FunsTF01 is designed to function as a transcription factor that can initiate transcription from the 6xLexO minimal promoter (BBa_K4129115). This sTF is designed to be the sensing part of a biosensor.

FunsTF01 is a fusion protein consisting of the DNA-binding domain from LexA, the ligand sensing domain from HbaR, transactivation domain B112 and the NLS SV40. The linker between the LexA domain and the HbaR domain is a longer linker (Ottoz et. al (2014) compared to the linker in sBAD, which was the reference sTF (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, namely LexO sites (Erill. et al (2003)). HbaR is a transcription factor from Rhodopseudomonas palustris that initiates transcription in the presence of benzoic acid (Egland. et al (2000)) or in the presence of benzoic acid derivatives (Castaño-Cerezo et. al (2020)).

The transactivation domain B112 is from E. coli, and it was 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 of the protein to the nucleus (Garcia-Bustos et. al (1991)).


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 673
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 607
    Illegal BamHI site found at 1199
    Illegal XhoI site found at 1348
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 765
  • 1000
    COMPATIBLE WITH RFC[1000]