Difference between revisions of "Part:BBa K801076:Design"

Latest revision as of 10:32, 24 October 2012

Yeast expression cassette for CaXMT1 and CaMXMT1

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 3613
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 138
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 2385

Composite part of BBa_K801010, BBa_K801070, BBa_K801012, BBa_K319003, BBa_K801071 and BBa_K801012

Keywords: caffeine, TEF1, TEF2, ADH1, expression cassette

Abbreviations:

CaXMT1 = coffea arabica xanthosine N-methyltransferase 1
CaMXMT1 = coffea arabica 7-methylxanthine N-methyltransferase 1

Design Notes

Related BioBrick: BBa_K801070 BBa_K801071 BBa_K801077

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: CaXMT1-Strep-tag and CaMXMT1-Strep-tag

Enzymatic activity: EC-number [http://enzyme.expasy.org/EC/2.1.1.158 2.1.1.158] 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 BioBrick BBa_K801075 is 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_K801070 and 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

@@ Line 8: / Line 8: @@
 <br>'''Keywords:'''
 <!--These keywords are necessary to find your part using a fulltext sarch.-->
-caffeine, TEF1, expression cassette
+caffeine, TEF1, TEF2, ADH1, expression cassette
 <br>'''Abbreviations:'''
 <!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
 <!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
+* CaXMT1 = coffea arabica xanthosine N-methyltransferase 1
+* CaMXMT1 = coffea arabica 7-methylxanthine N-methyltransferase 1
 ===Design Notes===
 '''Related BioBrick:'''
+[https://parts.igem.org/Part:BBa_K801073 BBa_K801070]
+[https://parts.igem.org/Part:BBa_K801076 BBa_K801071]
+[https://parts.igem.org/Part:BBa_K801073 BBa_K801077]
 <!--*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>
+* Desigend in RFC 10
 <!--*Designed in RFC10/RFC23/RFC25/RFC25_N-part-->
 <!--*Mutation C889G to delete XbaI restriction site-->
@@ Line 26: / Line 31: @@
 '''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-->
 <!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
@@ Line 32: / Line 38: @@
 '''Backbone:'''<br>
 *Backbone name: pSB1C3'
+* Resistance: Cp
 <!--*Resistance: Amp/Cp/Kan/Tet-->
 <!--*Copynumber: low/medium/high-->
 '''Protein coding:'''<br>
+* Protein: CaXMT1-Strep-tag and CaMXMT1-Strep-tag
 <!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
 <!--*The protein has the amino acid replacements ???99??? to ???99???.-->
@@ Line 42: / Line 51: @@
 '''Enzymatic activity:'''
+EC-number [http://enzyme.expasy.org/EC/2.1.1.158 2.1.1.158]
+EC-number [http://enzyme.expasy.org/EC/2.1.1.160 2.1.1.160]
 <!--none/EC-number ?.?.?.?-->
@@ Line 62: / Line 74: @@
 '''Source:'''<br>
+* Preexisting BioBrick BBa_K801070 and BBa_K801071
 <!--*Commercial system: plasmid name, system name, company name-->
 <!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
@@ Line 72: / Line 85: @@
 '''Organism:'''<br>
+* Genesequence derived from ''Coffea arabica''
+* codonoptimized for ''Saccharomyces cerevisiae''
+* designed for ''Saccharomyces cerevisiae''
 <!--*Genesequence derived from ''citrus limonen''-->
 <!--*Codonoptimized for ''?organism_name?''-->
@@ Line 81: / Line 98: @@
 '''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?]-->
 '''Database references:'''<br>
+* NCBI
 <!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
 <!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->