Difference between revisions of "Part:BBa K5127012"

Latest revision as of 10:25, 2 October 2024

Genome Integration of butyrate production protein (pReplace-Tes4)

Usage and Biology

The pReplace construction is designed for the integration of GOI into the E.coli MG1655 genome, with GFP downstream serving as a reporter gene to visualize successful integration. The two red features in the figure represent LP-2 homologous regions, which are 500bp sites on the genome utilized for integrase λ-Red mediated plasmid integration. Additionally, stringent ORI: R6K is incorporated, requiring a specialized protein for replication that most bacteria do not produce. This ensures that upon entering the host cell, the plasmid either cannot replicate and is eliminated or becomes integrated into the chromosome and replicates alongside it. This approach guarantees successful plasmid integration into the genome.

Team: BNDS-China 2024

In our platform design, Tes4 is intended to produce butyrate in response to the absence of a specific metabolite. We aim to model the expression of Tes4, which in turn leads to an increase in butyrate levels and its eventual impact on the colonization or growth of our probiotic strain. We want to achieve butyrate production without giving the bacteria too much burden, so we decided to try genome integration of the Tes4 enzyme. To achieve this, we utilized the Lambda Red recombination system to integrate Tes4 and a reporter gene, GFP, into the genome of E. coli MG1655. (Yu et al., 2008) This allows us to track the expression of Tes4 through GFP fluorescence and correlate it with butyrate production and its downstream effects on our probiotic growth and colonization.

Design

Our team has replaced the barcode sequence with Tes4 and subsequently linked it with GFP in MG1655. This modification aims to integrate Tes4 into the genome for further characterization and validation of its ability to effectively produce butyrate.

Construction

pReplace was designed to facilitate the integration of the Gene of Interest (GOI) into the genome. This plasmid includes a barcode for colony PCR verification post-integration(Figure 1).

Figure 1. Plasmid design of pReplace-Tes4. Created by biorender.com.

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal PstI site found at 501
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 129
Illegal NheI site found at 152
Illegal PstI site found at 501
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 530
23
INCOMPATIBLE WITH RFC[23]
Illegal PstI site found at 501
25
INCOMPATIBLE WITH RFC[25]
Illegal PstI site found at 501
Illegal AgeI site found at 923
1000
COMPATIBLE WITH RFC[1000]

@@ Line 2: / Line 2: @@
 __NOTOC__
 <partinfo>BBa_K5127012 short</partinfo>
 ===Usage and Biology===
-The pReplace construction is designed for the integration of GOI into the E.coli MG1655 genome, with GFP downstream serving as a reporter gene to visualize successful integration. The two red features in the figure represent LP-2 homologous regions, which are 500bp sites on the genome utilized for integrase &#955;-Red mediated plasmid integration. Additionally, stringent ORI: R6K is incorporated, requiring a specialized protein for replication that most bacteria do not produce. This ensures that upon entering the host cell, the plasmid either cannot replicate and is eliminated or becomes integrated into the chromosome and replicates alongside it. This approach guarantees successful plasmid integration into the genome.
+The pReplace construction is designed for the integration of GOI into the <i>E.coli MG1655</i> genome, with GFP downstream serving as a reporter gene to visualize successful integration. The two red features in the figure represent LP-2 homologous regions, which are 500bp sites on the genome utilized for integrase &#955;-Red mediated plasmid integration. Additionally, stringent ORI: R6K is incorporated, requiring a specialized protein for replication that most bacteria do not produce. This ensures that upon entering the host cell, the plasmid either cannot replicate and is eliminated or becomes integrated into the chromosome and replicates alongside it. This approach guarantees successful plasmid integration into the genome.
 ==Team: BNDS-China 2024==
-In our platform design, Tes4 is intended to produce butyrate in response to the absence of a specific metabolite. We aim to model the expression of Tes4, which in turn leads to an increase in butyrate levels and its eventual impact on the colonization or growth of our probiotic strain. We want to achieve butyrate production without giving the bacteria too much burden, so we decided to try genome integration of the Tes4 enzyme. To achieve this, we utilized the Lambda Red recombination system to integrate Tes4 and a reporter gene, GFP, into the genome of E. coli MG1655. (Yu et al., 2008) This allows us to track the expression of Tes4 through GFP fluorescence and correlate it with butyrate production and its downstream effects on our probiotic growth and colonization.
+In our platform design, Tes4 is intended to produce butyrate in response to the absence of a specific metabolite. We aim to model the expression of Tes4, which in turn leads to an increase in butyrate levels and its eventual impact on the colonization or growth of our probiotic strain. We want to achieve butyrate production without giving the bacteria too much burden, so we decided to try genome integration of the Tes4 enzyme. To achieve this, we utilized the Lambda Red recombination system to integrate Tes4 and a reporter gene, GFP, into the genome of <i>E. coli MG1655</i>. (Yu et al., 2008) This allows us to track the expression of Tes4 through GFP fluorescence and correlate it with butyrate production and its downstream effects on our probiotic growth and colonization.
 ===Design===
-Our team has replaced the barcode sequence with Tes4 and subsequently linked it with GFP in MG1655. This modification aims to integrate Tes4 into the genome for further characterization and validation of its ability to effectively produce butyrate.
+Our team has replaced the barcode sequence with Tes4 and subsequently linked it with GFP in <i>MG1655</i>. This modification aims to integrate Tes4 into the genome for further characterization and validation of its ability to effectively produce butyrate.
 ===Construction===
 pReplace was designed to facilitate the integration of the Gene of Interest (GOI) into the genome. This plasmid includes a barcode for colony PCR verification post-integration(Figure 1).
 <HTML>
 <p style="text-align:center;"><img src="https://static.igem.wiki/teams/5127/parts/partreptes.jpg" width="400" height="auto"/>
 <br>
-Figure 1. Plasmid design of pReplace-Tes4. Created by biorender.com.
+<i>Figure 1. Plasmid design of pReplace-Tes4. Created by biorender.com.</i>
 </p>
 </html>
-===Reference===
-Byung Jo Yu, Kui Hyeon Kang, Jun Hyoung Lee, Bong Hyun Sung, Mi Sun Kim, & Sun Chang Kim. (2008). Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Research, 36(14), e84–e84. https://doi.org/10.1093/nar/gkn359
 ===Sequence and Features===