Difference between revisions of "Part:BBa K4475003"

Latest revision as of 03:53, 14 October 2022

NOTOC__ CTB1 Gene from Cercospora beticola

This is the full exon only (cDNA) coding sequence for the CTB1 enzyme in the fungus cercospora beticola. The enzyme is the first in a multi step pathway for the production of cercosporin, a reactive oxygen species producing toxin in the presence of sunlight. FSU's iGEM team is looking to synthesize CTB1 in yeast as a proof of concept for cercosporin biosynthesis in a non-native and scalable organism, with the goal of producing cercosporin to combat algal blooms. The coding sequence has been codon optimized for Saccharomyces cerevisiae and modified to remove some illegal iGEM assembly cut sites via silent mutations. An HA tag is embedded on the N-terminus for expression verification.

Source: CB0940_00833 CTB1 [Cercospora beticola] https://www.ncbi.nlm.nih.gov/gene/35424645

AlphaFold Structure - https://alphafold.ebi.ac.uk/entry/A0A2G5IC53

CTB1 is a multi-domain fungal polyketide synthase (2) capable of converting acetyl-CoA and 6 x malonyl-CoA into nor-toralactone. This promoter is designed to be constitutively active to produce strong expression. The sequence was taken from genome of C. beticola and inserted into shuttle vectors for cloning in E. coli and episomal expression in S. cerevisiae.

CTB1

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 3532
Illegal BamHI site found at 3441
Illegal BamHI site found at 5614
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 6121
Illegal AgeI site found at 4195
1000
COMPATIBLE WITH RFC[1000]

Modularity of Design

In our project, choices of plasmid copy number and promoter strength were modulated to encourage maximum production of cercosporin intermediates in our chassis, resulting in several combinatorial designs. Molecular cloning was done using NEB HiFi DNA assembly, allowing DNA fragments for coding sequences and regulatory elements to be interchanged by annealing purposefully designed overlaps.

See:
BBa_K4475003
BBa_K4475004
BBa_K4475005

Enzyme and Product Detection

Assays were implemented for enzyme and product detection

Enzyme Characterization

HA epitope tagging was used.

Product Characterization

The analytical chemistry assays proposed for product identification and quantification were inspired by existing literature. (1,2,3)

Results will be added during the wiki melt after the jamboree. We will be including a plot generated using the appropriate analysis technique.

References

(1) Newman AG, Townsend CA. Molecular Characterization of the Cercosporin Biosynthetic Pathway in the Fungal Plant Pathogen Cercospora nicotianae. J Am Chem Soc. 2016 Mar 30;138(12):4219-28. doi: 10.1021/jacs.6b00633. Epub 2016 Mar 16. PMID: 26938470; PMCID: PMC5129747.

(2) Adam G. Newman, Anna L. Vagstad, Philip A. Storm, and Craig A. Townsend. Systematic Domain Swaps of Iterative, Nonreducing Polyketide Synthases Provide a Mechanistic Understanding and Rationale For Catalytic Reprogramming. Journal of the American Chemical Society 2014 136 (20), 7348-7362 DOI: 10.1021/ja5007299

(3) de Jonge R, Ebert MK, Huitt-Roehl CR, Pal P, Suttle JC, Spanner RE, Neubauer JD, Jurick WM 2nd, Stott KA, Secor GA, Thomma BPHJ, Van de Peer Y, Townsend CA, Bolton MD. Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum. Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5459-E5466. doi: 10.1073/pnas.1712798115. Epub 2018 May 29. Erratum in: Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8324. PMID: 29844193; PMCID: PMC6004482.

@@ Line 1: / Line 1: @@
-__NOTOC__
+NOTOC__
-<partinfo>BBa_K4475003 short</partinfo>
+<partinfo>BBa_K4475000 short</partinfo>
+This is the full exon only (cDNA) coding sequence for the CTB1 enzyme in the fungus cercospora beticola. The enzyme is the first in a multi step pathway for the production of cercosporin, a reactive oxygen species producing toxin in the presence of sunlight. FSU's iGEM team is looking to synthesize CTB1 in yeast as a proof of concept for cercosporin biosynthesis in a non-native and scalable organism, with the goal of producing cercosporin to combat algal blooms. The coding sequence has been codon optimized for Saccharomyces cerevisiae and modified to remove some illegal iGEM assembly cut sites via silent mutations. An HA tag is embedded on the N-terminus for expression verification.
+Source:
+CB0940_00833 CTB1 [Cercospora beticola]
+https://www.ncbi.nlm.nih.gov/gene/35424645
+AlphaFold Structure - https://alphafold.ebi.ac.uk/entry/A0A2G5IC53
-Construct designed for strong expression of the fungal enzyme CTB1 in saccharomyces cerevisiae, utilizing the Yeast GPD (TDH3) Promoter and CYC100 Terminator.
 ===Usage and Biology===
-This protein generator was created to serve as a strong constitutive version of for CTB1.
+CTB1 is a multi-domain fungal polyketide synthase (2) capable of converting acetyl-CoA and 6 x malonyl-CoA into nor-toralactone. This promoter is designed to be constitutively active to produce strong expression.
+The sequence was taken from genome of C. beticola and inserted into shuttle vectors for cloning in E. coli and episomal expression in S. cerevisiae.
+[[Image:CTB1.jpeg|400px|thumb|]]
+===CTB1===
+<!-- -->
+<span class='h3bb'>Sequence and Features</span>
+<partinfo>BBa_K4475000 SequenceAndFeatures</partinfo>
+===Modularity of Design===
+In our project, choices of plasmid copy number and promoter strength were modulated to encourage maximum production of cercosporin intermediates in our chassis, resulting in several combinatorial designs. Molecular cloning was done using NEB HiFi DNA assembly, allowing DNA fragments for coding sequences and regulatory elements to be interchanged by annealing purposefully designed overlaps.
+See: <br>
+BBa_K4475003 <br>
+BBa_K4475004 <br>
+BBa_K4475005 <br>
+===Enzyme and Product Detection===
+Assays were implemented for enzyme and product detection
+'''Enzyme Characterization'''
+HA epitope tagging was used.
+'''Product Characterization'''
+The analytical chemistry assays proposed for product identification and quantification were inspired by existing literature. (1,2,3) <br>
+<P><b>Results will be added during the wiki melt after the jamboree. We will be including a plot generated using the appropriate analysis technique. </b></P>
+===References===
+(1) Newman AG, Townsend CA. Molecular Characterization of the Cercosporin Biosynthetic Pathway in the Fungal Plant Pathogen Cercospora nicotianae. J Am Chem Soc. 2016 Mar 30;138(12):4219-28. doi: 10.1021/jacs.6b00633. Epub 2016 Mar 16. PMID: 26938470; PMCID: PMC5129747.
+(2) Adam G. Newman, Anna L. Vagstad, Philip A. Storm, and Craig A. Townsend. Systematic Domain Swaps of Iterative, Nonreducing Polyketide Synthases Provide a Mechanistic Understanding and Rationale For Catalytic Reprogramming. Journal of the American Chemical Society 2014 136 (20), 7348-7362 DOI: 10.1021/ja5007299
+(3) de Jonge R, Ebert MK, Huitt-Roehl CR, Pal P, Suttle JC, Spanner RE, Neubauer JD, Jurick WM 2nd, Stott KA, Secor GA, Thomma BPHJ, Van de Peer Y, Townsend CA, Bolton MD. Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum. Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5459-E5466. doi: 10.1073/pnas.1712798115. Epub 2018 May 29. Erratum in: Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8324. PMID: 29844193; PMCID: PMC6004482.
-===Features===
-This biological part has two key features-constitutive and strong. The constitutive aspect means that it is constantly "on". This part is considered to be strong because its own sequence closely resembles that of the consensus sequence.
@@ Line 17: / Line 64: @@
 <!-- Uncomment this to enable Functional Parameter display
 ===Functional Parameters===
-<partinfo>BBa_K4475003 parameters</partinfo>
+<partinfo>BBa_K4475000 parameters</partinfo>
 <!-- -->