Difference between revisions of "Part:BBa K5246020"

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===Introduction===
 
===Introduction===
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Vilnius-Lithuania iGEM 2024 project <HTML><b><a href="https://2024.igem.wiki/vilnius-lithuania" target="_blank">Synhesion</a></b></html> 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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  <title>Waving Rainbow Text</title>
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    /* Container to center the text */
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    /* Waving and rainbow animation for the word */
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    .rainbow-wave {
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      font-family: Arial, sans-serif;
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      animation: wave 2s infinite ease-in-out, rainbow 3s infinite linear;
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    /* Keyframes for waving effect */
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    @keyframes wave {
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      0%  { transform: rotate(0deg) translateX(0px); }
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      25%  { transform: rotate(15deg) translateX(10px); }
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      50%  { transform: rotate(0deg) translateX(0px); }
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      75%  { transform: rotate(-15deg) translateX(-10px); }
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      100% { transform: rotate(0deg) translateX(0px); }
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    /* Keyframes for rainbow color change */
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    @keyframes rainbow {
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      0% { color: red; }
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      14% { color: orange; }
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      28% { color: yellow; }
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      42% { color: green; }
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      57% { color: blue; }
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      71% { color: indigo; }
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      85% { color: violet; }
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<body>
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  <div class="container">
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    <span class="rainbow-wave">holdfast</span>
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  </div>
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===Usage and Biology===
 
===Usage and Biology===
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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>
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<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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The polysaccharide deacetylase HfsH is required for H. baltica adhesion. Holdfast polysaccharides in H. baltica HfsH mutants lack cohesive and adhesive properties.
 
The polysaccharide deacetylase HfsH is required for H. baltica adhesion. Holdfast polysaccharides in H. baltica HfsH mutants lack cohesive and adhesive properties.
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Research instigating the Hirschia baltica genome found that hfsH is in the hfs locus while hfsK and its paralogs are outside the hfs locus. Color coding corresponds to homologs and paralogs. Hash marks indicate genes found in a different location in the genome. [1]
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Research instigating the Hirschia baltica genome found that hfsH is in the hfs locus while hfsK and its paralogs are outside the hfs locus. Color coding corresponds to homologs and paralogs. Hash marks indicate genes found in a different location in the genome. [10]
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HfsH expression correlates positively with holdfast binding in high ionic strength. HfsH is an important factor for adherence in high ionic-strength environments, adhesion and biofilm formation. It is also crucial for the retention of holdfast thiols and galactose monosaccharides. [1]
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HfsH expression correlates positively with holdfast binding in high ionic strength. HfsH is an important factor for adherence in high ionic-strength environments, adhesion and biofilm formation. It is also crucial for the retention of holdfast thiols and galactose monosaccharides. [10]
  
 
<html>
 
<html>
 
<body>
 
<body>
 
<p>
 
<p>
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This part also has a non his-tagged variant <a href="https://parts.igem.org/Part:BBa_K5246031">BBa_K5246031</a>.
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This part also has a his-tagged variant <a href="https://parts.igem.org/Part:BBa_K5246031">BBa_K5246031</a>.
 
</p>
 
</p>
 
</html>
 
</html>
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===Experimental characterization===
 
===Experimental characterization===
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<html>
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<body>
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<p>
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This part also has a his-tagged variant <a href="https://parts.igem.org/Part:BBa_K5246031">BBa_K5246031</a>.
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</p>
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</html>
  
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====Bioinformatic analysis====
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This part needs more characterization.
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Conserved domain database analysis suggests that HfsH is part of the carbohydrate esterase 4 superfamily and polysaccharide deacetylase family. Proteins of this family may catalyze the N- or O- deacetylation of a substrate. Protein BLAST results show high similarity to peptidoglycan N-acetylglucosamine deacetylase and other polysaccharide deacetylases.
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Topology analysis with DeepTMHMM and AlphaFold3 structure showed that HfsH is most probably a globular protein located in the cytoplasm. 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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HfsH is a globular polysaccharide deacetylase that catalyses the deacetylation of N-acetylglucosamine in the holdfast synthesis pathway, previous research supports our conclusions. [1][2][3]
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===References===
 
===References===
−
1. Wan, Z. et al. (2013a) ‘The adhesive and cohesive properties of a bacterial polysaccharide adhesin are modulated by a deacetylase’, Molecular Microbiology, 88(3), pp. 486–500. doi:10.1111/mmi.12199.  
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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
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<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
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<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
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<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
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<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>
 +
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.
 
<br>
 
<br>
−
2. 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.  
+
10. Wan, Z. et al. (2013a) ‘The adhesive and cohesive properties of a bacterial polysaccharide adhesin are modulated by a deacetylase’, Molecular Microbiology, 88(3), pp. 486–500. doi:10.1111/mmi.12199.  
 
<br>
 
<br>
−
3. Liu, Q. et al. (2022) ‘The screening and expression of polysaccharide deacetylase from caulobacter crescentus and its function analysis’, Biotechnology and Applied Biochemistry, 70(2), pp. 688–696. doi:10.1002/bab.2390.
 

Latest revision as of 17:38, 1 October 2024


HB HfsH Deacetylase

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.

Usage and 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] </p>

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]. The polysaccharide deacetylase HfsH is required for H. baltica adhesion. Holdfast polysaccharides in H. baltica HfsH mutants lack cohesive and adhesive properties. Research instigating the Hirschia baltica genome found that hfsH is in the hfs locus while hfsK and its paralogs are outside the hfs locus. Color coding corresponds to homologs and paralogs. Hash marks indicate genes found in a different location in the genome. [10] HfsH expression correlates positively with holdfast binding in high ionic strength. HfsH is an important factor for adherence in high ionic-strength environments, adhesion and biofilm formation. It is also crucial for the retention of holdfast thiols and galactose monosaccharides. [10]

This part also has a his-tagged variant BBa_K5246031.

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
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 385
  • 1000
    COMPATIBLE WITH RFC[1000]


Experimental characterization

This part also has a his-tagged variant BBa_K5246031.

This part needs more characterization.

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.
10. Wan, Z. et al. (2013a) ‘The adhesive and cohesive properties of a bacterial polysaccharide adhesin are modulated by a deacetylase’, Molecular Microbiology, 88(3), pp. 486–500. doi:10.1111/mmi.12199.