Difference between revisions of "Part:BBa K801074:Design"

(→‎Design Notes)
 
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<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-->
+
caffeine, TEF1, expression cassette
  
 
<br>'''Abbreviations:'''
 
<br>'''Abbreviations:'''
 
<!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
 
<!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
 
<!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
 
<!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
 +
* CaMXMT1 = coffea arabica 7-methylxanthine N-methyltransferase 1
  
 
===Design Notes===
 
===Design Notes===
  
 
'''Related BioBrick:'''
 
'''Related BioBrick:'''
 +
[https://parts.igem.org/Part:BBa_K801074 BBa_K801071]
 
<!--*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part] -->
 
<!--*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]
 
<!--*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
 
<!--*Designed in RFC10/RFC23/RFC25/RFC25_N-part-->
 
<!--*Designed in RFC10/RFC23/RFC25/RFC25_N-part-->
 
<!--*Mutation C889G to delete XbaI restriction site-->
 
<!--*Mutation C889G to delete XbaI restriction site-->
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'''Quality control measures:'''<br>
 
'''Quality control measures:'''<br>
 +
* Test digest has been performed with use of Xba1 and Pst1 (see mainpage)
 
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
 
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
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'''Backbone:'''<br>
 
'''Backbone:'''<br>
−
<!--*Backbone name: pSB1C3'/?backbone_name?-->
+
*Backbone name: pSB1C3'
 +
*Resistance: Cp
 
<!--*Resistance: Amp/Cp/Kan/Tet-->
 
<!--*Resistance: Amp/Cp/Kan/Tet-->
 
<!--*Copynumber: low/medium/high-->
 
<!--*Copynumber: low/medium/high-->
  
 
'''Protein coding:'''<br>
 
'''Protein coding:'''<br>
 +
* Protein: CaMXMT1-Strep-tag
 
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
 
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
 
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
 
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
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'''Enzymatic activity:'''
 
'''Enzymatic activity:'''
 
<!--none/EC-number ?.?.?.?-->
 
<!--none/EC-number ?.?.?.?-->
−
 
+
* EC-number [http://enzyme.expasy.org/EC/2.1.1.160 2.1.1.160] 
 
'''Cytotoxicity:'''<br>
 
'''Cytotoxicity:'''<br>
 
This Biobrick is one part of the pathway, which leads to caffeine (the BioBricks BBa_801073 and BBa_801075 are further needed). We investigated the toxicity of caffeine and found out, that the growth of yeast strains was inhibited at concentrations of 10 mM. Caffeine with a concentration of 100 mM even showed a lethal effect on yeast cells. Lower concentrations of caffeine (range of micro molar) did not show any growth inhibition or effect.
 
This Biobrick is one part of the pathway, which leads to caffeine (the BioBricks BBa_801073 and BBa_801075 are further needed). We investigated the toxicity of caffeine and found out, that the growth of yeast strains was inhibited at concentrations of 10 mM. Caffeine with a concentration of 100 mM even showed a lethal effect on yeast cells. Lower concentrations of caffeine (range of micro molar) did not show any growth inhibition or effect.
Line 63: Line 69:
  
 
'''Source:'''<br>
 
'''Source:'''<br>
 +
*Preexisting BioBrick BBa_K801071
 
<!--*Commercial system: plasmid name, system name, company name-->
 
<!--*Commercial system: plasmid name, system name, company name-->
 
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
 
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
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'''Organism:'''<br>
 
'''Organism:'''<br>
 +
* Genesequence derived from ''Coffea arabica''
 +
* codonoptimized for ''Saccharomyces cerevisiae''
 +
* designed for ''Saccharomyces cerevisiae''
 
<!--*Genesequence derived from ''?organism_name?''-->
 
<!--*Genesequence derived from ''?organism_name?''-->
 
<!--*Codonoptimized for ''?organism_name?''-->
 
<!--*Codonoptimized for ''?organism_name?''-->
 
<!--*Designed for the following Chassis: ''?organism-name?''-->
 
<!--*Designed for the following Chassis: ''?organism-name?''-->
 
<!--*Statement about functionality in other chassis.-->
 
<!--*Statement about functionality in other chassis.-->
−
 
  
 
===References===
 
===References===
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'''Literature references:'''<br>
 
'''Literature references:'''<br>
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/12746542 '''Pubmed:''' Uefuji H., Ogita S., Yamaguchi Y., Koizumi N. and Sano H., 2003: Molecular cloning and functional characterization of three distinct n-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants.]
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/16247553 '''Pubmed:''' Uefuji H., Ogita S., Yamaguchi Y., Koizumi N. and Sano H., 2005: Caffeine production in tobacco plants by simultaneous expression of three coffee N-methyltrasferases and its potential as a pest repellant.]
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/16925551 '''Pubmed:'''  Kuranda K, Leberre V, Sokol S, Palamarczyk G, François J., 2006: Investigating the caffeine effects in the yeast Saccharomyces cerevisiae brings new insights into the connection between TOR, PKC and Ras/cAMP signalling pathways.]
 
<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
 
<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
  
 
'''Database references:'''<br>
 
'''Database references:'''<br>
 +
* NCBI
 
<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
 
<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
 
<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
 
<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->

Latest revision as of 10:30, 24 October 2012

CaMXMT1 expression cassette for yeast


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1433
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 205


Composite part of BBa_K319003, BBa_K801071 and BBa_K801012


Keywords: caffeine, TEF1, expression cassette


Abbreviations:

  • CaMXMT1 = coffea arabica 7-methylxanthine N-methyltransferase 1

Design Notes

Related BioBrick: BBa_K801071

Quality control measures:

  • Test digest has been performed with use of Xba1 and Pst1 (see mainpage)

Backbone:

  • Backbone name: pSB1C3'
  • Resistance: Cp

Protein coding:

  • Protein: CaMXMT1-Strep-tag

Enzymatic activity:

  • EC-number [http://enzyme.expasy.org/EC/2.1.1.160 2.1.1.160]

Cytotoxicity:
This Biobrick is one part of the pathway, which leads to caffeine (the BioBricks BBa_801073 and BBa_801075 are further needed). We investigated the toxicity of caffeine and found out, that the growth of yeast strains was inhibited at concentrations of 10 mM. Caffeine with a concentration of 100 mM even showed a lethal effect on yeast cells. Lower concentrations of caffeine (range of micro molar) did not show any growth inhibition or effect.

Safety notes:

Intellectual property:

Corresponding part author/authors:

Source

Source:

  • Preexisting BioBrick BBa_K801071


Organism:

  • Genesequence derived from Coffea arabica
  • codonoptimized for Saccharomyces cerevisiae
  • designed for Saccharomyces cerevisiae

References

Literature references:

  • [http://www.ncbi.nlm.nih.gov/pubmed/12746542 Pubmed: Uefuji H., Ogita S., Yamaguchi Y., Koizumi N. and Sano H., 2003: Molecular cloning and functional characterization of three distinct n-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants.]
  • [http://www.ncbi.nlm.nih.gov/pubmed/16247553 Pubmed: Uefuji H., Ogita S., Yamaguchi Y., Koizumi N. and Sano H., 2005: Caffeine production in tobacco plants by simultaneous expression of three coffee N-methyltrasferases and its potential as a pest repellant.]
  • [http://www.ncbi.nlm.nih.gov/pubmed/16925551 Pubmed: Kuranda K, Leberre V, Sokol S, Palamarczyk G, François J., 2006: Investigating the caffeine effects in the yeast Saccharomyces cerevisiae brings new insights into the connection between TOR, PKC and Ras/cAMP signalling pathways.]

Database references:

  • NCBI