Difference between revisions of "Part:BBa K5246026"
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<center> <b> Fig. 1. </b> Alphafold 3 structure showing </center> | <center> <b> Fig. 1. </b> Alphafold 3 structure showing </center> | ||
| − | ===Protein | + | ===Protein expression=== |
| − | <h2>CB2 strain</h2> | + | <h2>CB2 strain</h2> <!-- Subheading added here --> |
| − | <p> | + | <p>We chose the BL21(DE3) strain for adjustable and efficient expression of target proteins since the system's proteins were best expressed in this strain. Given the lack of time, we went with conditions optimized beforehand in earlier experiments for the whole pathway expression: temperature of 37°C, induction with 0.5 mM IPTG concentration, and expression for 3 hours.</p> |
| − | <p>< | + | <p>After SDS-PAGE gel analysis, we concluded that we successfully expressed all HfsG, HfsH, HfsJ, HfsK, and HfsL proteins from <i>C. crescentus</i> CB2 and CB2A strains. We noticed that HfsJ and HfsL glycosyltransferases were visible in lower quantities compared to the other proteins. Both of these protein expression conditions need to be further investigated and optimized.</p> |
| − | < | + | <p><b>HfsH</b> is visible on the left side of the gel (Fig. 2).</p> |
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| + | .container { | ||
| + | display: flex; | ||
| + | justify-content: center; | ||
| + | align-items: flex-start; | ||
| + | gap: 5px; /* Space between table and figure */ | ||
| + | } | ||
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| + | margin-right: 10px; | ||
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| + | .figure-container { | ||
| + | margin-left: 10px; | ||
| + | } | ||
| + | </style> | ||
| + | </head> | ||
| + | <body> | ||
| + | <div class="container"> | ||
| + | <!-- Table on the left --> | ||
| + | <div class="table-container"> | ||
| + | <h3>Table 1. <i>C. crescentus</i> protein sizes in kDa</h3> | ||
| + | <table border="1"> | ||
| + | <tr> | ||
| + | <th>Protein Name</th> | ||
| + | <th>Size (kDa)</th> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsG</td> | ||
| + | <td>34</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsH</td> | ||
| + | <td>27.9</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsJ</td> | ||
| + | <td>34.7</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsK</td> | ||
| + | <td>43.3</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsL</td> | ||
| + | <td>33.3</td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | </div> | ||
| − | < | + | <!-- Figure on the right --> |
| − | + | <div class="figure-container"> | |
| − | < | + | <figure> |
| − | + | <div class="center"> | |
| − | <figure> | + | <img src="hhttps://static.igem.wiki/teams/5246/results/protein-expression/cb2-expression.webp" style="width:500px;"> |
| − | <div class = "center" > | + | </div> |
| − | + | <figcaption><center><b>Fig. 2.</b> 12% SDS-PAGE analysis of <i>C. crescentus</i> CB2 strain proteins in BL21(DE3) before expression and after induction at 0.5 mM IPTG concentrations for 3 hours at 37°C. M - molecular weight ladder in kDa, Pageruler Unstained Protein Ladder, 26614 (Thermo Scientific). </center></figcaption> | |
| − | <img src = " | + | </figure> |
| − | </div> | + | </div> |
| − | + | </div> | |
| − | <figcaption><center> | + | </body> |
| − | <b>Fig. | + | |
| − | </figure> | + | |
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</html> | </html> | ||
| − | <h2>CB2A strain</h2> | + | <h2>CB2A strain</h2> <!-- Subheading added here --> |
| − | <p> | + | <p>We chose the BL21(DE3) strain for adjustable and efficient expression of target proteins since the system's proteins were best expressed in this strain. Given the lack of time, we went with conditions optimized beforehand in earlier experiments for the whole pathway expression: temperature of 37°C, induction with 0.5 mM IPTG concentration, and expression for 3 hours.</p> |
| − | <p> | + | <p>After SDS-PAGE gel analysis, we concluded that we successfully expressed all HfsG, HfsH, HfsJ, HfsK, and HfsL proteins from <i>C. crescentus</i> CB2 and CB2A strains. We noticed that HfsJ and HfsL glycosyltransferases were visible in lower quantities compared to the other proteins. Both of these protein expression conditions need to be further investigated and optimized.</p> |
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| − | <p><b> | + | <p><b>HfsJ</b> is visible in the center of the gel (Fig. 2).</p> |
<html> | <html> | ||
| − | < | + | <head> |
| − | <figure> | + | <style> |
| − | <div class = " | + | .container { |
| − | < | + | display: flex; |
| − | < | + | justify-content: center; |
| − | </div> | + | align-items: flex-start; |
| + | gap: 5px; /* Space between table and figure */ | ||
| + | } | ||
| + | .table-container { | ||
| + | margin-right: 10px; | ||
| + | } | ||
| + | .figure-container { | ||
| + | margin-left: 10px; | ||
| + | } | ||
| + | </style> | ||
| + | </head> | ||
| + | <body> | ||
| + | <div class="container"> | ||
| + | <!-- Table on the left --> | ||
| + | <div class="table-container"> | ||
| + | <h3>Table 2. <i>C. crescentus</i> protein sizes in kDa</h3> | ||
| + | <table border="1"> | ||
| + | <tr> | ||
| + | <th>Protein Name</th> | ||
| + | <th>Size (kDa)</th> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsG</td> | ||
| + | <td>34</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsH</td> | ||
| + | <td>27.9</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsJ</td> | ||
| + | <td>34.7</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsK</td> | ||
| + | <td>43.3</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>HfsL</td> | ||
| + | <td>33.3</td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | </div> | ||
| − | < | + | <!-- Figure on the right --> |
| − | <b>Fig. | + | <div class="figure-container"> |
| − | </figure> | + | <figure> |
| − | < | + | <div class="center"> |
| + | <img src="https://static.igem.wiki/teams/5246/results/protein-expression/cb2a-expressions.webp" style="width:500px;"> | ||
| + | </div> | ||
| + | <figcaption><center><b>Fig. 3.</b> 12% SDS-PAGE analysis of <i>C. crescentus</i> CB2A strain proteins in BL21(DE3) before expression and after induction at 0.5 mM IPTG concentrations for 3 hours at 37°C. M - molecular weight ladder in kDa, Pageruler Unstained Protein Ladder, 26614 (Thermo Scientific). </center></figcaption> | ||
| + | </figure> | ||
| + | </div> | ||
| + | </div> | ||
| + | </body> | ||
</html> | </html> | ||
Revision as of 09:45, 29 September 2024
CB2/CB2A HfsH Deacetylase, 6xHis tag for purification
Introduction
Vilnius-Lithuania iGEM 2024 project Synhesion aspires to create biodegradable and environmentally friendly adhesives. We were inspired by bacteria, which naturally produce adhesives made from polysaccharides. Two bacteria from aquatic environments - C. crescentus and H. Baltica - harness 12 protein synthesis pathways to produce sugars anchoring them to the surfaces. We aimed to transfer the polysaccharide synthesis pathway to industrially used E. coli bacteria to produce adhesives. Our team concomitantly focused on creating a novel E. coli strain for more efficient production of adhesives.
This protein is part of the Tetrad assembly system BBa_K5246043 and operon responsible for addition of N-acetyl-D-glucosamine to N-acetyl-D-glucosamine and deacetylation of the said molecule BBa_K5246042.
Part was used in Vilnius-Lithuania iGEM 2024 project "Synhesion" https://2024.igem.wiki/vilnius-lithuania/.
This part also has a non 6xhis-tagged variant BBa_K5246008.
Biology and usage
Biology
Caulobacter crescentus is a common freshwater gram-negative oligotrophic bacterium of the clade Caulobacterales. Its distinguishing feature is its dual lifestyle. Initially, C. crescentus daughter cells are in a “swarmer” cell phase, which has a flagellum, enabling them to perform chemotaxis. After the motile phase, they differentiate into “stalked” cells. This phase features a tubular stalk with an adhesive structure called holdfast, allowing them to adhere to surfaces and perform cell division.[1][2]
Caulobacterales synthesize a polysaccharide-based adhesin known as holdfast at one of their cell poles, enabling tight attachment to external surfaces. It is established that holdfast consists of repeating identical units composed of multiple monomers. Current literature agrees that in Caulobacter crescentus, these units form tetrads composed of glucose, an unidentified monosaccharide (either N-mannosamine uronic acid or xylose), N-acetylglucosamine, and N-glucosamine. These units are polymerized and exported to the outer membrane of the cell, where they function as anchors, securing the bacterium to a surface[3][4].
The C. crescentus holdfast is produced via a polysaccharide synthesis and export pathway similar to the group I capsular polysaccharide synthesis Wzy/Wzx-dependent pathway in Escherichia coli.
The holdfast synthesis (hfs) genes include those encoding predicted glycosyltransferases, carbohydrate modification factors, and components of a wzy-type polysaccharide assembly pathway[4][5][6].
HfsH, in particular, is responsible for deacetylation of N-acetyl-D-glucosamine molecule.
Usage
Proteins of the holdfast synthesis system assemble a short chain of sugar monomers in a specific sequence on a lipid carrier - a glycolipid.
Glycolipids are predominantly located on the extracellular surface of eukaryotic cell membranes and are responsible for various functions such as receptors for viruses and other pathogens, allowing them to enter a specific host cell that has unique glycolipid markers. This feature can let us use said glycolipids as labels for a precise and targeted liposome distribution throughout the body, delivering anything from cancer drugs to gene editing systems directly to the target cells.
To create a liposome labeling system, we had to select specific proteins that could be utilized for this purpose. Following bioinformatics analysis using the Conserved Domain Database, Protein BLAST, DeepTMHMM, and AlphaFold 3, we identified five proteins of interest from each strain: HfsG, HfsH, HfsJ, HfsK, and HfsL.
To utilize these enzymes, it was essential to develop a suitable purification strategy. For efficient cloning, we chose Golden Gate assembly. For efficient purification, we selected immobilized ion affinity chromatography (IMAC) as our purification method, based on recommendations from one of the few available papers where C. crescentus proteins were expressed and purified from E. coli. We opted for conventional 6x histidine tags (his-tag) to facilitate straightforward purification. It was crucial to determine the appropriate terminus for 6xHis-tag insertion to avoid disrupting the protein conformation and lessening purification efficiency.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal EcoRI site found at 10
- 12INCOMPATIBLE WITH RFC[12]Illegal EcoRI site found at 10
- 21INCOMPATIBLE WITH RFC[21]Illegal EcoRI site found at 10
- 23INCOMPATIBLE WITH RFC[23]Illegal EcoRI site found at 10
- 25INCOMPATIBLE WITH RFC[25]Illegal EcoRI site found at 10
Illegal NgoMIV site found at 68
Illegal NgoMIV site found at 92
Illegal NgoMIV site found at 96
Illegal NgoMIV site found at 169
Illegal NgoMIV site found at 295
Illegal NgoMIV site found at 456 - 1000COMPATIBLE WITH RFC[1000]
Experimental characterization
Bioinformatic analysis
CDD and protein BLAST analysis suggest that HfsG is a glucosyltransferase family 2 protein. Proteins of this family are involved in cell wall biosynthesis. HfsG is similar to the WecA protein in E.Coli that catalyzes the transfer of the GlcNAc-1-phosphate moiety from UDP-GlcNAc onto the carrier lipid undecaprenyl phosphate. In the case of HfsG, it catalyzes the transfer of UDP-GlcNAc to the sugar acceptor made earlier in the holdfast synthesis pathway.
Protein topology analysis using DeepTMHMM suggests that HfsG is a globular protein located in the cytoplasm. AlphaFold 3 structures further confirm it. A pTM score above 0.5 suggests that the predicted overall structure may closely resemble the true protein fold, while ipTM indicates the accuracy of the subunit positioning within the complex. Values higher than 0.8 represent confident, high-quality predictions.
HfsG is family 2 glycosyltransferase similar to WecA of E.Coli. This globular protein transfers UDP-GlcNAc to the acceptor molecule, our conclusions are in agreement with existing research. [1][2][3]
Protein expression
CB2 strain
We chose the BL21(DE3) strain for adjustable and efficient expression of target proteins since the system's proteins were best expressed in this strain. Given the lack of time, we went with conditions optimized beforehand in earlier experiments for the whole pathway expression: temperature of 37°C, induction with 0.5 mM IPTG concentration, and expression for 3 hours.
After SDS-PAGE gel analysis, we concluded that we successfully expressed all HfsG, HfsH, HfsJ, HfsK, and HfsL proteins from C. crescentus CB2 and CB2A strains. We noticed that HfsJ and HfsL glycosyltransferases were visible in lower quantities compared to the other proteins. Both of these protein expression conditions need to be further investigated and optimized.
HfsH is visible on the left side of the gel (Fig. 2).
Table 1. C. crescentus protein sizes in kDa
| Protein Name | Size (kDa) |
|---|---|
| HfsG | 34 |
| HfsH | 27.9 |
| HfsJ | 34.7 |
| HfsK | 43.3 |
| HfsL | 33.3 |
CB2A strain
We chose the BL21(DE3) strain for adjustable and efficient expression of target proteins since the system's proteins were best expressed in this strain. Given the lack of time, we went with conditions optimized beforehand in earlier experiments for the whole pathway expression: temperature of 37°C, induction with 0.5 mM IPTG concentration, and expression for 3 hours.
After SDS-PAGE gel analysis, we concluded that we successfully expressed all HfsG, HfsH, HfsJ, HfsK, and HfsL proteins from C. crescentus CB2 and CB2A strains. We noticed that HfsJ and HfsL glycosyltransferases were visible in lower quantities compared to the other proteins. Both of these protein expression conditions need to be further investigated and optimized.
HfsJ is visible in the center of the gel (Fig. 2).
Table 2. C. crescentus protein sizes in kDa
| Protein Name | Size (kDa) |
|---|---|
| HfsG | 34 |
| HfsH | 27.9 |
| HfsJ | 34.7 |
| HfsK | 43.3 |
| HfsL | 33.3 |
References
1. Hendrickson, H., & Lawrence, J. G. (2000). Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. FEMS Microbiology Reviews, 24(2), 177–183. https://doi.org/10.1111/j.1574-6976.2000.tb00539.x
2. Andrews, S. C., Robinson, A. K., & Rodríguez-Quiñones, F. (2004). Bacterial iron homeostasis. Journal of Bacteriology, 186(5), 1438–1447. https://doi.org/10.1128/jb.186.5.1438-1447.2004
3.Rabah, A., & Hanchi, S. (2023). Experimental and modeling study of the rheological and thermophysical properties of molybdenum disulfide-based nanofluids. Journal of Molecular Liquids, 384, 123335. https://doi.org/10.1016/j.molliq.2023.123335
4. Boutte, C. C., & Crosson, S. (2009). Bacterial lifestyle shapes stringent response activation. Journal of Bacteriology, 191(9), 2904-2912. https://doi.org/10.1128/jb.01003-08
5. Mackie, J., Liu, Y. C., & DiBartolo, G. (2019). The C-terminal region of the Caulobacter crescentus CtrA protein inhibits stalk synthesis during the G1-to-S transition. mBio, 10(2), e02273-18. https://doi.org/10.1128/mbio.02273-18
6.Thanbichler, M., & Shapiro, L. (2003). MipZ, a spatial regulator coordinating chromosome segregation with cell division in Caulobacter. Journal of Bacteriology, 185(4), 1432-1442. https://doi.org/10.1128/jb.185.4.1432-1442.2003
7. Toh, E., Kurtz, Harry D. and Brun, Y.V. (2008) ‘Characterization of the Caulobacter crescentus holdfast polysaccharide biosynthesis pathway reveals significant redundancy in the initiating glycosyltransferase and polymerase steps’, Journal of Bacteriology, 190(21), pp. 7219–7231. doi:10.1128/jb.01003-08.
8. Chepkwony, N.K., Berne, C. and Brun, Y.V. (2019b) ‘Comparative analysis of ionic strength tolerance between freshwater and marine Caulobacterales adhesins’, Journal of Bacteriology, 201(18). doi:10.1128/jb.00061-19.