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. Lower concentrations of caffeine (range of mikro 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.
 
<!--none/not known/cytotoxic for ''organism name''-->
 
<!--none/not known/cytotoxic for ''organism name''-->
  
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'''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