Difference between revisions of "Part:BBa K801080:Design"

(→‎Design Notes)
(→‎References)
 
(9 intermediate revisions by 2 users not shown)
Line 16: Line 16:
 
<br>'''Keywords:'''
 
<br>'''Keywords:'''
 
<!--These keywords are necessary to find your part using a fulltext sarch.-->
 
<!--These keywords are necessary to find your part using a fulltext sarch.-->
−
<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5-->
+
preprothaumatin, yeast, sweetner
  
 
<br>'''Abbreviations:'''
 
<br>'''Abbreviations:'''
Line 25: Line 25:
  
 
'''Related BioBrick:'''
 
'''Related BioBrick:'''
−
<!--*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part] -->
+
-
−
<!--*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part]
+
  
 
'''Cloning details:'''<br>
 
'''Cloning details:'''<br>
−
<!--*Designed in RFC10/RFC23/RFC25/RFC25_N-part-->
+
* Designed in RFC10
−
<!--*Mutation C889G to delete XbaI restriction site-->
+
−
<!--*Truncation upstream/downstream compared to template, ?explanation?-->
+
  
 
'''Quality control measures:'''<br>
 
'''Quality control measures:'''<br>
−
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
+
* Part was totally sequenced
−
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
+
−
<!--*Part was partly sequenced/Part was totally sequenced-->
+
  
 
'''Backbone:'''<br>
 
'''Backbone:'''<br>
−
<!--*Backbone name: pSB1C3'/?backbone_name?-->
+
* Backbone name: pSB1C3
−
<!--*Resistance: Amp/Cp/Kan/Tet-->
+
* Resistance: Cp
−
<!--*Copynumber: low/medium/high-->
+
* Copynumber: high
  
 
'''Protein coding:'''<br>
 
'''Protein coding:'''<br>
−
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
+
* Protein: Preprothaumatin [Nucleotide 1 to 708]
−
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
+
* The protein encoded is posttranslationally modified: Aa 1-22 and 229-236 are split off
−
<!--*The protein encoded is posttranslationally modified by ???.-->
+
−
<!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other-->
+
  
 
'''Enzymatic activity:'''
 
'''Enzymatic activity:'''
−
<!--none/EC-number ?.?.?.?-->
+
-
  
 
'''Cytotoxicity:'''<br>
 
'''Cytotoxicity:'''<br>
−
This Biobrick leads to the production of thaumatin. We investigated the toxicity of thaumatin and incubated yeast cells (strain INVSc) with 45 mM of thaumatin. We found out, that thaumatin does not show any negative effect on the growth rate of yeast cells.  
+
This Biobrick leads to the production of thaumatin. We investigated the toxicity of thaumatin and incubated yeast cells (strain INVSc) with 45 mM of thaumatin. We found, that thaumatin does not show any negative effect on the growth rate of yeast cells.  
 
<!--none/not known/cytotoxic for ''organism name''-->
 
<!--none/not known/cytotoxic for ''organism name''-->
  
Line 61: Line 54:
  
 
'''Intellectual property:'''
 
'''Intellectual property:'''
−
<!--Information on patent situation.-->
+
Information on patent situation: Preprothaumatin derived from ''Thaumatococcus daniellii''
 
<!--Intellectual property claims made by the authors.-->
 
<!--Intellectual property claims made by the authors.-->
  
Line 74: Line 67:
 
<!--*Preexisting BioBrick ?Bba_number?-->
 
<!--*Preexisting BioBrick ?Bba_number?-->
 
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
 
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
−
<!--*Synthesized by ?company_name?.-->
+
* Synthesized by idt
  
 
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
Line 80: Line 73:
  
 
'''Organism:'''<br>
 
'''Organism:'''<br>
−
<!--*Genesequence derived from ''?organism_name?''-->
+
* Genesequence derived from ''Thaumatococcus daniellii''
−
<!--*Codonoptimized for ''?organism_name?''-->
+
* Codonoptimized for ''S. cerevisiae''
−
<!--*Designed for the following Chassis: ''?organism-name?''-->
+
* Designed for the following Chassis: ''S. cerevisiae''
−
<!--*Statement about functionality in other chassis.-->
+
* Functionality in other chassis: Should work in other chassis as well (although optimized for ''S. cerevisiae'')
−
 
+
  
 
===References===
 
===References===
Line 90: Line 82:
  
 
'''Literature references:'''<br>
 
'''Literature references:'''<br>
−
<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
+
*[http://www.ncbi.nlm.nih.gov/pubmed/6327079 '''Pubmed:''' Edens L, Bom I, Ledeboer AM, Maat J, Toonen MY, Visser C, Verrips CT., 1984: Synthesis and processing of the plant protein thaumatin in yeast]
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/19489607 '''Pubmed:''' Ide N, Sato E, Ohta K, Masuda T, Kitabatake N., 2009: Interactions of the sweet-tasting proteins thaumatin and lysozyme with the human sweet-taste receptor]
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/17897626 '''Pubmed:''' Ide N, Masuda T, Kitabatake N., 2007: Effects of pre- and pro-sequence of thaumatin on the secretion by Pichia pastoris]
  
 
'''Database references:'''<br>
 
'''Database references:'''<br>
−
<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
+
*[http://www.ncbi.nlm.nih.gov/nuccore/121945717 '''GenBank AB265690.1: Thaumatococcus daniellii mRNA for preprothaumatin I]
−
<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
+
*[http://http://www.ebi.ac.uk/interpro/IEntry?ac=IPR017949&query=thaumatin '''Interpro''': Thaumatin, conserved site (IPR017949)]
−
<!--*[http://www.uniprot.org/uniprot/?accessNr? '''Uniprot''': ?title?]-->
+
*[http://www.uniprot.org/uniprot/A1IIJ1 '''Uniprot''': Preprothaumatin I]
 
<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 
<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 
<!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->
 
<!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->
 
<!--*[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=?accessNr? '''Branda:''' ?title?]-->
 
<!--*[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=?accessNr? '''Branda:''' ?title?]-->

Latest revision as of 10:52, 15 October 2012

Prepro-Thaumatin, yeast codon optimized


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]


Synthesized by IDT. The part is codon optimized for yeast. 3 forbidden restriction sites have been removed.

Please note, that the pre- and pro-part are split off, thus there is no possibility to add streptags or form other recombinant proteins.


Based on: http://www.ncbi.nlm.nih.gov/nuccore/121945717



Keywords: preprothaumatin, yeast, sweetner


Abbreviations:

Design Notes

Related BioBrick: -

Cloning details:

  • Designed in RFC10

Quality control measures:

  • Part was totally sequenced

Backbone:

  • Backbone name: pSB1C3
  • Resistance: Cp
  • Copynumber: high

Protein coding:

  • Protein: Preprothaumatin [Nucleotide 1 to 708]
  • The protein encoded is posttranslationally modified: Aa 1-22 and 229-236 are split off

Enzymatic activity: -

Cytotoxicity:
This Biobrick leads to the production of thaumatin. We investigated the toxicity of thaumatin and incubated yeast cells (strain INVSc) with 45 mM of thaumatin. We found, that thaumatin does not show any negative effect on the growth rate of yeast cells.

Safety notes:

Intellectual property: Information on patent situation: Preprothaumatin derived from Thaumatococcus daniellii

Corresponding part author/authors:

Source

Source:

  • Synthesized by idt


Organism:

  • Genesequence derived from Thaumatococcus daniellii
  • Codonoptimized for S. cerevisiae
  • Designed for the following Chassis: S. cerevisiae
  • Functionality in other chassis: Should work in other chassis as well (although optimized for S. cerevisiae)

References

Literature references:

  • [http://www.ncbi.nlm.nih.gov/pubmed/6327079 Pubmed: Edens L, Bom I, Ledeboer AM, Maat J, Toonen MY, Visser C, Verrips CT., 1984: Synthesis and processing of the plant protein thaumatin in yeast]
  • [http://www.ncbi.nlm.nih.gov/pubmed/19489607 Pubmed: Ide N, Sato E, Ohta K, Masuda T, Kitabatake N., 2009: Interactions of the sweet-tasting proteins thaumatin and lysozyme with the human sweet-taste receptor]
  • [http://www.ncbi.nlm.nih.gov/pubmed/17897626 Pubmed: Ide N, Masuda T, Kitabatake N., 2007: Effects of pre- and pro-sequence of thaumatin on the secretion by Pichia pastoris]

Database references:

  • [http://www.ncbi.nlm.nih.gov/nuccore/121945717 GenBank AB265690.1: Thaumatococcus daniellii mRNA for preprothaumatin I]
  • [http://http://www.ebi.ac.uk/interpro/IEntry?ac=IPR017949&query=thaumatin Interpro: Thaumatin, conserved site (IPR017949)]
  • [http://www.uniprot.org/uniprot/A1IIJ1 Uniprot: Preprothaumatin I]