Difference between revisions of "Part:BBa K2052015"

Latest revision as of 00:32, 20 October 2016

ButCoat with strong RBS

Usage & Biology ( Description )

This composite part consists of RBS , a coding region ( ButCoAT ) and enables E.coli to secrete ButCoAT.

ButCoAT is an enzyme (Butyryl-CoA:acetate CoA-transferase) (EC 2.8.3.8) (Uniprot:C7GB37) which converts Acetyl-CoA (Acetyl-CoA is readily present in the cytosol and it can be directly converted into Butyrate) into Butyrate and can be found in Roseburia intestinalis L1-82. The equation of the reaction (acyl-CoA:acetate CoA-transferase) is given down below :

Figure 1: Butanoyl-CoA + Acetate <=> Butanoic acid + Acetyl-CoA

Figure 2: Crystal Structures of Acetobacter aceti Succinyl (Butyryl)-CoA:Acetate CoA-Transferase Reveal Specificity Determinants and Illustrate the Mechanism Used by Class I CoA-Transferases.(Mullins, E.A. et al., 2012)

RBS and our protein coding region (ButCoaT) are digested from our whole construct with the enzymes SpeI, Sall, Xbal.

Cloning

Gel Results

Figure 3. We have loaded an uncut version of K2052015 next to an EcoRI single digested one. In the third lane RBS ligated ButCoat (K2052018) was loaded with its single digested version. Digested ones gave a sharp lane at 3600 bp as we expected.

Characterization

Ligated Parts Transformation Results

Figure 4. After ligating ButcoaT and RFP, we have obtain colonies 2:1 (insert:vector) ratio, and transform them into E.coli BL21.

Confirmational PCR Result

Figure 5. Constitutive promoter-RBS-ButCoaT-GFP-Double terminator cloned into pSB1C3 and after ligation we have transformed into E.coli BL21. Colony PCR results here you can see; one primer stick on insert and another stick on vector. The expected lenght of product is around 850 bp.

Flowcytometry Result

After checking with confirmational PCR we have tried to validate RFP fluoresence experimenttaly through Fluorescence Microscope, Here you can see the analysis.

Figure 6. After measuring RFP signals with channel FL3 we have obtained these graphs. Here again upper triplet stand for Mock(reference point) analysis that is the bacterial culture transformed with only ButCoaT. Middle triplet stand for only RFP expressed bacterial culture analysis which gave a peak that could be used as a control group. The bottom triplet was RFP tagged ButCoaT expressed bacterial group and as we have shown there is any signal depend on RFP activity.

Since ButCoAT was tagged with RFP, to test whether it is functional or not, we have used fluoresence microscopy technique to show its expression is properly done or not. However, because ButCoAT doesn’t have a stop codon at the end it fused with RFP and they both become unfunctional from this fusion. Therefore, we could not see any peak.

Modelling

Molecule versus second

Figure 7.The figure above shows the increase in ButCoAT molecules over a time span of 10 seconds.

Molecule versus second

Figure 8.The figure above shows the molar increase in Butyrate concentration over a time span of 10 seconds.

Sequence and Features

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]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K2052015 short</partinfo>
-...............Enter şkjmlkjlıa long description of the part so that users of your part know what it is, what it does, and how to use it in their projects.
 ==Usage & Biology ( Description )==
-This composite part consists of RBS , our coding region ( ButCoaT ) and enables  E.coli to secrete ButCoaT.
-ButCoaT is an enzyme (Butyryl-CoA:acetate CoA-transferase) (EC 2.8.3.8) (Uniprot: C7GB37) which converts Acetyl-CoA to Butyrate and can be found in Roseburia intestinalis L1-82.
+This composite part consists of RBS , a coding region ( ButCoAT ) and enables  E.coli to secrete ButCoAT.
-The equation of the reaction (acyl-CoA:acetate CoA-transferase) (KEGG Reaction No. : R01179)  is given down below :
-Butanoyl-CoA + Acetate <=> Butanoic acid + Acetyl-CoA
+ButCoAT is an enzyme (Butyryl-CoA:acetate CoA-transferase) (EC 2.8.3.8) (Uniprot:C7GB37) which converts Acetyl-CoA (Acetyl-CoA is readily present in the cytosol and it can be directly converted into Butyrate) into Butyrate and can be found in Roseburia intestinalis L1-82. The equation of the reaction (acyl-CoA:acetate CoA-transferase) is given down below :
+[[File:Pathwayson.png|none|frame|700px|]]
+Figure 1: Butanoyl-CoA + Acetate <=> Butanoic acid + Acetyl-CoA
+[[File:ButCoaTStructure.gif|center|none|frame|500px]]
+Figure 2: Crystal Structures of Acetobacter aceti Succinyl (Butyryl)-CoA:Acetate CoA-Transferase Reveal Specificity Determinants and Illustrate the Mechanism Used by Class I CoA-Transferases.(Mullins, E.A. et al., 2012)
+RBS and our protein coding region (ButCoaT) are digested from our whole construct with the enzymes SpeI, Sall, Xbal.
+==Cloning==
+====Gel Results====
+[[File:METU_HS_DENEME8.jpeg|center|400px]]
+Figure 3. We have loaded an uncut version of K2052015 next to an EcoRI single digested one. In the third lane RBS ligated ButCoat (K2052018) was loaded with its single digested version. Digested ones gave a sharp lane at 3600 bp as we expected.
+==Characterization==
+===Ligated Parts Transformation Results===
+[[File:METU HS DENEME9.jpeg|center|250px]]
+Figure 4. After ligating ButcoaT and RFP, we have  obtain colonies 2:1 (insert:vector) ratio, and transform them into E.coli BL21.
+===Confirmational PCR Result===
+[[File:METU_HS_DENEME6888.jpeg|center|500px]]
+Figure 5. Constitutive promoter-RBS-ButCoaT-GFP-Double terminator cloned into pSB1C3 and after ligation we have transformed into E.coli BL21. Colony PCR results here you can see; one primer stick on insert and another stick on vector. The expected  lenght of product is around 850 bp.
+==Flowcytometry Result==
+After checking with confirmational PCR we have tried to validate RFP fluoresence experimenttaly through Fluorescence Microscope, Here you can see the analysis.
-==Characterization==
+[[File:METU_HS_DENEME3luolan.jpeg|center|800px]]
-==Design Notes==
+Figure 6. After measuring RFP signals with channel FL3 we have obtained these graphs. Here again upper triplet stand for Mock(reference point) analysis that is the bacterial culture transformed with only ButCoaT. Middle triplet stand  for only RFP expressed bacterial culture analysis which gave a peak that could be used as a control group. The bottom triplet was RFP tagged ButCoaT expressed bacterial group and as we have shown there is any signal depend on RFP activity.
-RBS and our protein coding region (ButCoaT) are digested from our whole construct with the enzymes SpeI, Sall, Xbal.
-For ButCoaT ;
-E.Coli is synthesised suitable for Codon Bias.
+Since ButCoAT was tagged with RFP, to test whether it is functional or not, we have used fluoresence microscopy technique to show its expression is properly done or not. However, because ButCoAT doesn’t have a stop codon at the end it fused  with RFP and they both become unfunctional from this fusion. Therefore,  we could not see any peak.
-In the expression of pet28a (expression vector) , stop codon is removed in order to add HisTag.
-==Source==
-The ribosome binding site (B0034) that we’ve used is gotten from iGEM part library.
-Source of ButCoaT : Roseburia intestinalis L1-82
-References
-Hassig, C.A., Tong, J.K., Schreiber, S.L. (1997). Fiber-derived Butyrate and the Prevention of Colon Cancer
-Roberto Berni Canani, Margherita Di Costanzo, Ludovica Leone, Monica Pedata, Rosaria Meli, Antonio Calignano. (2011). Potential beneficial affects of butyrate in intestinal and extraintestinal diseases
+==Modelling==
-Duncan,S. H., Barcenilla, A., Stewart, C. S., Pryde, S. E., Flint, H. J. (2002). Acetate Utilization and Butyryl Coenzyme A (CoA):Acetate-CoA Transferase in ButyrateProducing Bacteria from the Human Large Intestine
+Molecule versus second
-Sequence : http://www.uniprot.org/uniprot/C7GB37?sort=score
+[[File:ButCoAT_graph.jpeg|900px]]
-Pathway : http://www.genome.jp/dbget-bin/www_bget?reaction+R00393+R01179+R01359+R07832
+Figure 7.The figure above shows the increase in ButCoAT molecules over a time span of 10 seconds.
-Picture : http://www.brenda-enzymes.org/structure.php?show=reaction&id=360609&type=S&displayType=marvin
+Molecule versus second
+[[File:Butyrate graph.jpeg|900px]]
+Figure 8.The figure above shows the molar increase in Butyrate concentration over a time span of 10 seconds.