Difference between revisions of "Part:BBa K5246006"

 
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===Introduction===
 
===Introduction===
 +
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.
  
 +
This part is also a part of the holdfast export and polymerization operon <html><a href="https://parts.igem.org/Part:BBa_K5246045" target="_blank">BBa_K5246045</a></html> and a part of full polymerization and export operon <html><a href="https://parts.igem.org/Part:BBa_K5246046" target="_blank">BBa_K5246046</a></html>.
  
 
===Usage and Biology===
 
===Usage and Biology===
Encodes an integral membrane protein of 480 amino acids with 14 predicted transmembrane helices. Possesses similarities to  Wzx flippases (formerly known as RfbX) that catalyze the translocation of undecaprenol diphosphate-linked K-repeating units formed at the cytoplasmic side of the inner membrane across this membrane.
+
<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]
 +
<p><i>Caulobacterales</i> 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 <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 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>HfsF encodes an integral membrane protein of 480 amino acids with 14 predicted transmembrane helices. Possesses similarities to  Wzx flippases (formerly known as RfbX) that catalyze the translocation of undecaprenol diphosphate-linked K-repeating units formed at the cytoplasmic side of the inner membrane across this membrane.</P></HTML>
  
 
===Sequence and Features===
 
===Sequence and Features===
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====Bioinformatic analysis====
 
====Bioinformatic analysis====
  
HfsF is a flippase with domains, partly similar to some polysaccharide synthesis pathway proteins in bacteria, as it was shown by CDD analysis.
+
HfsF is a flippase with domains, partly similar to some polysaccharide synthesis pathway proteins in bacteria, as CDD analysis showed.
 +
 
 
Protein BLAST indicates high similarities to MOP superfamily flippases involved in peptidoglycan synthesis.
 
Protein BLAST indicates high similarities to MOP superfamily flippases involved in peptidoglycan synthesis.
 
DeepTMHMM predictions suggest that the protein is located in the membrane, spanning it multiple times.
 
DeepTMHMM predictions suggest that the protein is located in the membrane, spanning it multiple times.
Considering high AlphaFold 3 structure confidence scores, it seems probable that hfsF is 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 (Fig.1).
 
  
All in all, HfsF is a flippase located in the membrane that is responsible for oligosaccharide transfer from the cytoplasmic to the periplasmic side of the inner membrane. This flippase is similar to flippases involved in peptidoglycan synthesis. Our results align with prior studies. [1][2][3]
+
Considering high AlphaFold 3 structure confidence scores, it seems probable that HfsF is 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 (Fig.1).
 +
 
 +
All in all, HfsF is a flippase located in the membrane that is responsible for oligosaccharide transfer from the cytoplasmic to the periplasmic side of the inner membrane. This flippase is similar to flippases involved in peptidoglycan synthesis. Our results align with prior studies. [7][8][9]
  
 
<center> https://static.igem.wiki/teams/5246/registry/hfsf.png </center>
 
<center> https://static.igem.wiki/teams/5246/registry/hfsf.png </center>
  
<center> <b> Fig. 1. </b> AlphaFold 3 structure showing  </center>
+
<center> <b> Fig. 1. </b> AlphaFold 3 structure of HfsF. On the left-folded structure with confidence scores above, on the right-predicted aligned error plot of the structure </center>
 +
 
 +
 
 +
<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===
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. 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.  
 
<br>
 
<br>
2. Hardy, G.G. et al. (2018) ‘Mutations in sugar-nucleotide synthesis genes restore holdfast polysaccharide anchoring to Caulobacter crescentus holdfast anchor mutants’, Journal of Bacteriology, 200(3). doi:10.1128/jb.00597-17.  
+
8. Hardy, G.G. et al. (2018) ‘Mutations in sugar-nucleotide synthesis genes restore holdfast polysaccharide anchoring to Caulobacter crescentus holdfast anchor mutants’, Journal of Bacteriology, 200(3). doi:10.1128/jb.00597-17.  
 
<br>
 
<br>
3. 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.
+
9. 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.

Latest revision as of 16:43, 29 September 2024


CB2/CB2A HfsF Flippase

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 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]

HfsF encodes an integral membrane protein of 480 amino acids with 14 predicted transmembrane helices. Possesses similarities to Wzx flippases (formerly known as RfbX) that catalyze the translocation of undecaprenol diphosphate-linked K-repeating units formed at the cytoplasmic side of the inner membrane across this membrane.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 1033
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 1033
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 93
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 1033
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 1033
    Illegal NgoMIV site found at 343
    Illegal NgoMIV site found at 451
    Illegal NgoMIV site found at 733
    Illegal NgoMIV site found at 790
    Illegal NgoMIV site found at 834
    Illegal NgoMIV site found at 865
    Illegal NgoMIV site found at 1089
    Illegal AgeI site found at 151
  • 1000
    COMPATIBLE WITH RFC[1000]


Experimental characterization

Bioinformatic analysis

HfsF is a flippase with domains, partly similar to some polysaccharide synthesis pathway proteins in bacteria, as CDD analysis showed.

Protein BLAST indicates high similarities to MOP superfamily flippases involved in peptidoglycan synthesis. DeepTMHMM predictions suggest that the protein is located in the membrane, spanning it multiple times.

Considering high AlphaFold 3 structure confidence scores, it seems probable that HfsF is 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 (Fig.1).

All in all, HfsF is a flippase located in the membrane that is responsible for oligosaccharide transfer from the cytoplasmic to the periplasmic side of the inner membrane. This flippase is similar to flippases involved in peptidoglycan synthesis. Our results align with prior studies. [7][8][9]

hfsf.png
Fig. 1. AlphaFold 3 structure of HfsF. On the left-folded structure with confidence scores above, on the right-predicted aligned error plot of the structure


--> 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, 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. Hardy, G.G. et al. (2018) ‘Mutations in sugar-nucleotide synthesis genes restore holdfast polysaccharide anchoring to Caulobacter crescentus holdfast anchor mutants’, Journal of Bacteriology, 200(3). doi:10.1128/jb.00597-17.

9. 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.