Difference between revisions of "Part:BBa K5246032"
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===Introduction===
 
===Introduction===
  
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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 - <I> C. crescentus </I> and <I> H. Baltica </I> - harness 12 protein synthesis pathways to produce sugars anchoring them to the surfaces. We aimed to transfer the polysaccharide synthesis pathway to industrially used <I>E. coli</I> bacteria to produce adhesives. Our team concomitantly focused on creating a novel <I>E. coli</I> strain for more efficient production of adhesives.
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===Usage and Biology===
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TBA
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<html>
 
<html>
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<body>
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<p style="font-size: 1em;">
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This protein is part of the Tetrad assembly system <a href="https://parts.igem.org/Part:BBa_K5246043">BBa_K5246043</a> and operon responsible for the addition of N-acetyl-D-glucosamine and deacetylation of the former molecule <a href="https://parts.igem.org/Part:BBa_K5246042">BBa_K5246042</a>. </p>
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<p>
 
<p>
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This part also has a non his-tagged variant <a href="https://parts.igem.org/Part:BBa_K5246007">BBa_K5246007</a>.
+
 
 +
Part was used in Vilnius-Lithuania iGEM 2024 project "Synhesion" <HTML><b><a href="https://2024.igem.wiki/vilnius-lithuania" target="_blank">https://2024.igem.wiki/vilnius-lithuania/</a></b></html>.
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<html>
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<p style="font-size: 1em;">
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This part also has a non his-tagged variant <a href="https://parts.igem.org/Part:BBa_K5246022">BBa_K5246022</a>.
 +
 
 +
 
 
</p>
 
</p>
 
</html>
 
</html>
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 +
===Biology and usage===
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<h2>Biology</h2>
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<html>
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<p style="font-size: 1em;">
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<i>Hirschia baltica</i> is a common marine of the clade <i>Caulobacterales</i>. Its distinguishing feature is its dual lifestyle. Initially, <i>H. baltica</i> 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 a holdfast, allowing them to adhere to surfaces and perform cell division.[1][2]
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</p>
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<p style="font-size: 1em;">
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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].
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</p>
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<p style="font-size: 1em;">
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The <i>H. baltica</i> holdfast is produced via a polysaccharide synthesis and export pathway similar to the group I capsular polysaccharide synthesis Wzy/Wzx-dependent pathway in <i>Escherichia coli</i>.
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</p>
 +
<p style="font-size: 1em;">
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The holdfast synthesis (<i>hfs</i>) genes include those encoding predicted glycosyltransferases, carbohydrate modification factors, and components of a wzy-type polysaccharide assembly pathway[4][5][6][9].
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</p>
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<p style="font-size: 1em;">
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<b>HfsG</b> in particular is responsible for N-acetyl-D-glucosamine transfer to the acceptor molecule.
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</p>
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</html>
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<h3>HfsJ</h3>
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<html>
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"Gene HfsJ from Hirschia baltica encodes a protein of 260 amino acids. HfsJ is one of the glycosyltransferases involved in holdfast synthesis pathway and is structurally very similar to glycosyltransferases that transfer UDP-N-acetyl-D-mannosaminuronic acid. Ir belongs to the WecB/TagA/CpsF family of glycosyltransferases that catalyze the formation of glycosidic bonds and may be involved in the biosynthesis of repeating polysaccharide units found in membrane glycolipids.
 +
It is predicted that this is an intracellular protein."
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</html>
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<h2>Usage</h2>
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<p>
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  Proteins of the holdfast synthesis system assemble a short chain of sugar monomers in a specific sequence on a lipid carrier - a glycolipid.
 +
</p>
 +
 +
<p>
 +
  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.
 +
</p>
 +
<p>
 +
  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.
 +
</p>
 +
 +
<p>
 +
  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 <i>C. crescentus</i> proteins were expressed and purified from <i>E. coli</i>. 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.
 +
</p>
  
 
===Sequence and Features===
 
===Sequence and Features===
 
<partinfo>BBa_K5246032 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K5246032 SequenceAndFeatures</partinfo>
  
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===Functional Parameters===
 
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<partinfo>BBa_K5246032 parameters</partinfo>
 
  
 
===Experimental characterization===
 
===Experimental characterization===
  
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====Bioinformatic analysis====
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===Protein expression===
 +
<h2><i>Hirschia baltica</i></h2>
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<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>
  
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CDD analysis revealed that HfsJ is part of the WecB/TgA/CpsF glycosyltransferase family. This family catalyzes the formation of glycosidic bonds and may be involved in the biosynthesis of repeating polysaccharide units found in membrane glycolipids. It has domains very similar to <i>E. coli</i> WecG glycosyltransferase, which is responsible for UDP-N-acetyl-D-mannosaminuronic acid transfer. Results are supported by the protein BLAST, which showed significant similarities with the same WecG glycosyltransferase from <i>E. coli</i>.
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<p>After SDS-PAGE gel analysis, we concluded that we successfully expressed HfsG, HfsH, HfsK, and HfsL proteins from <i>H. baltica</i>. Unfortunately, HfsJ was not properly expressed  and need more optimization</p>
  
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DeepTMHMM analysis predicted that HfsJ is a globular protein located on the cytoplasmic side of the membrane.  
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<p><b>HfsJ</b> unfortunately is not visible on the gel (Fig. 1).</p>
  
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AlphaFold 3 structure, with a high confidence score, shows that HfsJ is most likely a globular protein mostly made of alpha helices. 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.
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<html>
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<head>
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  <style>
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    .container {
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      display: flex;
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      justify-content: center;
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      align-items: flex-start;
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      gap: 5px; /* Space between table and figure */
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    }
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    .table-container {
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      margin-right: 10px;
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    }
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    .figure-container {
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      margin-left: 10px;
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    }
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  </style>
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</head>
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<body>
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  <div class="container">
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    <!-- Table on the left -->
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    <div class="table-container">
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      <h3>Table 1. <i>H. baltica</i> protein sizes in kDa</h3>
 +
      <table border="1">
 +
        <tr>
 +
          <th>Protein Name</th>
 +
          <th>Size (kDa)</th>
 +
        </tr>
 +
        <tr>
 +
          <td>HfsG</td>
 +
          <td>37</td>
 +
        </tr>
 +
        <tr>
 +
          <td>HfsH</td>
 +
          <td>29</td>
 +
        </tr>
 +
        <tr>
 +
          <td>HfsJ</td>
 +
          <td>41</td>
 +
        </tr>
 +
        <tr>
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          <td>HfsK</td>
 +
          <td>28</td>
 +
        </tr>
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        <tr>
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          <td>HfsL</td>
 +
          <td>36</td>
 +
        </tr>
 +
      </table>
 +
    </div>
  
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Based on our findings and prior research, we propose that HfsJ is likely a globular protein responsible for transferring UDP-N-acetyl-D-mannosaminuronic acid and catalyzing the formation of a glycosidic bond. [1][2]
+
    <!-- Figure on the right -->
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    <div class="figure-container">
 +
      <figure>
 +
        <div class="center">
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          <img src="https://static.igem.wiki/teams/5246/results/protein-expression/baltica-expressions.webp" style="width:500px;">
 +
        </div>
 +
        <figcaption><center><b>Fig. 1.</b> 12% SDS-PAGE analysis of <i>H. baltica</i> 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>
  
 
===References===
 
===References===
−
1. 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.  
+
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
 +
<br>
 +
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
 +
<br>
 +
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
 +
<br>
 +
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
 +
<br>
 +
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
 +
<br>
 +
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
 +
<br>
 +
7. Hershey, D.M., Fiebig, A. and Crosson, S. (2019) ‘A genome-wide analysis of adhesion in Caulobacter crescentus identifies new regulatory and biosynthetic components for holdfast assembly’, mBio, 10(1). doi:10.1128/mbio.02273-18.
 +
<br>
 +
8. Chepkwony, N.K., Hardy, G.G. and Brun, Y.V. (2022) ‘HFAE is a component of the holdfast anchor complex that tethers the holdfast adhesin to the cell envelope’, Journal of Bacteriology, 204(11). doi:10.1128/jb.00273-22.  
 
<br>
 
<br>
−
2. 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.
+
9. Chepkwony, N.K., Berne, C. and Brun, Y.V. (2019) ‘Comparative analysis of ionic strength tolerance between freshwater and marine Caulobacterales adhesins’, Journal of Bacteriology, 201(18). doi:10.1128/jb.00061-19.

Latest revision as of 20:58, 1 October 2024


HB HfsJ Glycosyltransferase, 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 the addition of N-acetyl-D-glucosamine and deacetylation of the former 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 his-tagged variant BBa_K5246022.

Biology and usage

Biology

Hirschia baltica is a common marine of the clade Caulobacterales. Its distinguishing feature is its dual lifestyle. Initially, H. baltica 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 a 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 H. baltica 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][9].

HfsG in particular is responsible for N-acetyl-D-glucosamine transfer to the acceptor molecule.

HfsJ

"Gene HfsJ from Hirschia baltica encodes a protein of 260 amino acids. HfsJ is one of the glycosyltransferases involved in holdfast synthesis pathway and is structurally very similar to glycosyltransferases that transfer UDP-N-acetyl-D-mannosaminuronic acid. Ir belongs to the WecB/TagA/CpsF family of glycosyltransferases that catalyze the formation of glycosidic bonds and may be involved in the biosynthesis of repeating polysaccharide units found in membrane glycolipids. It is predicted that this is an intracellular protein."

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


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 188
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 188
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 622
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 188
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 188
  • 1000
    COMPATIBLE WITH RFC[1000]


Experimental characterization

Protein expression

Hirschia baltica

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 HfsG, HfsH, HfsK, and HfsL proteins from H. baltica. Unfortunately, HfsJ was not properly expressed and need more optimization

HfsJ unfortunately is not visible on the gel (Fig. 1).

Table 1. H. baltica protein sizes in kDa

Protein Name Size (kDa)
HfsG 37
HfsH 29
HfsJ 41
HfsK 28
HfsL 36
Fig. 1. 12% SDS-PAGE analysis of H. baltica 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).

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. Hershey, D.M., Fiebig, A. and Crosson, S. (2019) ‘A genome-wide analysis of adhesion in Caulobacter crescentus identifies new regulatory and biosynthetic components for holdfast assembly’, mBio, 10(1). doi:10.1128/mbio.02273-18.
8. Chepkwony, N.K., Hardy, G.G. and Brun, Y.V. (2022) ‘HFAE is a component of the holdfast anchor complex that tethers the holdfast adhesin to the cell envelope’, Journal of Bacteriology, 204(11). doi:10.1128/jb.00273-22.
9. Chepkwony, N.K., Berne, C. and Brun, Y.V. (2019) ‘Comparative analysis of ionic strength tolerance between freshwater and marine Caulobacterales adhesins’, Journal of Bacteriology, 201(18). doi:10.1128/jb.00061-19.