Difference between revisions of "Part:BBa K5246009"
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===Usage and Biology=== | ===Usage and Biology=== | ||
| − | <i>Caulobacter crescentus</i> is a common freshwater gram-negative oligotrophic bacterium of the clade <i>Caulobacterales</i>. Its distinguishing feature is its dual lifestyle. Initially, <i>C. crescentus</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 holdfast, allowing them to adhere to surfaces and perform cell division.[1][2] | + | <i>Caulobacter crescentus</i> is a common freshwater gram-negative oligotrophic bacterium of the clade <i>Caulobacterales</i>. Its distinguishing feature is its dual lifestyle. Initially, <i>C. crescentus</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] |
| − | <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] | + | <p><i>Caulobacterales synthesize</i> 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 <i>Caulobacter crescentus</i>, 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 <i>C. crescentus</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>. | The <i>C. crescentus</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>. | ||
| − | The holdfast synthesis (<i> | + | 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] |
| − | <HTML><P>Gene from <I>Caulobacter crescentus</I> that codes a paralogous protein of 440 amino acids of HfsC polysaccharide polymerase. HfsI that polymerases repeat of monomers into a mature holdfast polymer, deletion of polysaccharide polymerase gene | + | <HTML><P>Gene from <I>Caulobacter crescentus</I> that codes a paralogous protein of 440 amino acids of HfsC polysaccharide polymerase. HfsI that polymerases repeat of monomers into a mature holdfast polymer, deletion of polysaccharide polymerase gene HfsI in <I>C. crescentus</I> didn't cause holdfast synthesis defects because of its paralogue - <HTML><b><a href="https://parts.igem.org/Part:BBa_K5246003" target="_blank">HfsC</a></b></html>. Double mutants of HfsI and HfsC had severe holdfast synthesis defects [7].</P> |
===Sequence and Features=== | ===Sequence and Features=== | ||
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====Bioinformatic analysis==== | ====Bioinformatic analysis==== | ||
| − | CDD analysis showed that HfsI, | + | CDD analysis showed that HfsI, paralogous to HfsC, has a domain similar to that of O-antigen ligase family proteins. Proteins of this family are responsible for outer membrane lipopolysaccharide synthesis in <i>E. coli</i>. |
| − | Protein BLAST also showed partial similarities with E. | + | Protein BLAST also showed partial similarities with <i>E. coli</i> O-antigen ligases suggested by the CDD analysis. |
DeepTMHMM predicted that the protein is embedded in the membrane, crossing it approximately 12 times. This prediction is supported by structural evidence from AlphaFold3, which shows 12 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 (Fig.1). | DeepTMHMM predicted that the protein is embedded in the membrane, crossing it approximately 12 times. This prediction is supported by structural evidence from AlphaFold3, which shows 12 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 (Fig.1). | ||
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<center> https://static.igem.wiki/teams/5246/registry/hfsi.png </center> | <center> https://static.igem.wiki/teams/5246/registry/hfsi.png </center> | ||
| − | <center> <b> Fig. 1. </b> AlphaFold 3 structure showing structure of | + | <center> <b> Fig. 1. </b> AlphaFold 3 structure showing structure of HfsI. On the left-folded structure with confidence scores above, on the right-predicted aligned error plot of the structure </center> |
| − | --> More about this part's functionality as a part of a system you can see in this composite part <html><a href="https://parts.igem.org/Part:BBa_K5246046" target="_blank">BBa_K5246046</a></html>. | + | <b>--> More about this part's functionality as a part of a system you can see in this composite part <html><a href="https://parts.igem.org/Part:BBa_K5246046" target="_blank">BBa_K5246046</a></html>. </b> |
===References=== | ===References=== | ||
Latest revision as of 18:33, 29 September 2024
CB2/CB2A HfsI Polysaccharide polymerase
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 part is also a part of the holdfast export and polymerization operon BBa_K5246045 and a part of full polymerization and export operon BBa_K5246046.
Usage and 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 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 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]
Gene from Caulobacter crescentus that codes a paralogous protein of 440 amino acids of HfsC polysaccharide polymerase. HfsI that polymerases repeat of monomers into a mature holdfast polymer, deletion of polysaccharide polymerase gene HfsI in C. crescentus didn't cause holdfast synthesis defects because of its paralogue - HfsC. Double mutants of HfsI and HfsC had severe holdfast synthesis defects [7].
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 1034
Illegal XhoI site found at 448 - 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 513
Illegal AgeI site found at 228 - 1000COMPATIBLE WITH RFC[1000]
Experimental characterization
Bioinformatic analysis
CDD analysis showed that HfsI, paralogous to HfsC, has a domain similar to that of O-antigen ligase family proteins. Proteins of this family are responsible for outer membrane lipopolysaccharide synthesis in E. coli.
Protein BLAST also showed partial similarities with E. coli O-antigen ligases suggested by the CDD analysis.
DeepTMHMM predicted that the protein is embedded in the membrane, crossing it approximately 12 times. This prediction is supported by structural evidence from AlphaFold3, which shows 12 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 (Fig.1).
Considering our findings with information present in the literature. We predict that HfsI is a paralogous gene to HfsC and has the same functionality in the organism. [8][9][10]
--> More about this part's functionality as a part of a system you can see in this composite part BBa_K5246046.
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, H. D., & 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), 7219–7231. https://doi.org/10.1128/jb.01003-08
8. 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.
9. 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.
10. 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.