Difference between revisions of "Team:Aix-Marseille/Part Collection"

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{{Aix-Marseille|title=Part Collection|toc=__TOC__}}
 
{{Aix-Marseille|title=Part Collection|toc=__TOC__}}
  
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Our collection of parts is designed to allow the creation of proteins, or phage-like particles, that target a wide range of different Gram-negative bacteria. Each part corresponds to the domains 1 (D1) and 2 (D2) from the p3 protein of filamentous phages targeting the different organisms. The parts in the collection are expected to be used as fusion proteins and so conform to the RFC25 standard. To know more about the design of these parts, and how we used them to make phage-like particles in our project, you can check out our [[Team:Aix-Marseille/M13_Design|design page]].  
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Our collection of parts is designed to allow the creation of proteins, or phage-like particles, that target a wide range of different Gram-negative bacteria. Each part corresponds to the domains 1 (D1) and 2 (D2) from the p3 protein of filamentous phages targeting the different organisms. The parts in the collection are expected to be used as fusion proteins and so conform to the [http://parts.igem.org/Assembly_standard_25 Rfc25] standard. To know more about the design of these parts, and how we used them to make phage-like particles in our project, you can check out our [[Team:Aix-Marseille/M13_Design|design page]].  
  
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This part collection contains the following biobricks all in RFC25 format:
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This part collection contains the following biobricks all in [http://parts.igem.org/Assembly_standard_25 Rfc25] format:
  
 
*p3_E.coli (RFC25) - [http://parts.igem.org/Part:BBa_K2255008 BBa_K2255008]
 
*p3_E.coli (RFC25) - [http://parts.igem.org/Part:BBa_K2255008 BBa_K2255008]
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*p3_X.fastidiosa (RFC25) - [http://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
 
*p3_X.fastidiosa (RFC25) - [http://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
 
*p3_X.fuscans (RFC25) - [http://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]
 
*p3_X.fuscans (RFC25) - [http://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]
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==Design==
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==Design==
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The domain 3 (D3) and the signal sequence are both the best conserved part from the attachment protein. Using a global protein alignment (Needleman-Wunsch and [https://static.igem.org/mediawiki/parts/5/52/T--Aix-Marseille--alignement.pdf MUSCLE alignments]), using two or three sequence at one time, we were eventually able to determinate domain 1 (D1) and domain 2 (D2) from the attachment protein of each phages.
 +
 +
We were able to found these domains because each of them is separated by a flexible sequence composed of Glycine and Serine <ref>Heilpern, A. J. & Waldor, M. K. pIIICTX, a predicted CTXphi minor coat protein, can expand the host range of coliphage fd to include ''Vibrio cholerae''. J. Bacteriol. 185, 1037–1044 (2003).</ref>. Then we retrotranslate this sequence in a nucleotidic sequence and we used iDT to optimise this sequence for ''E.coli'' production.
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{|
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! scope="col" |Pathogene
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! scope="col" |Filamentous phage
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! scope="col" |GI
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! scope="col" |Part ID
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|-
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|''Escherichia coli''
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|M13 (fd,ff)<ref name=Smeal>Smeal, S. W., Schmitt, M. A., Pereira, R. R., Prasad, A. & Fisk, J. D. Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation. Virology 500, 259–274 (2017).</ref>
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|927334
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|BBa K2255008
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|-
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|''Neisseria gonorrheae''
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|NgoΦ6<ref>Piekarowicz, A. et al. Neisseria gonorrhoeae Filamentous Phage NgoΦ6 Is Capable of Infecting a Variety of Gram-Negative Bacteria. J Virol 88, 1002–1010 (2014).</ref>
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|1260906
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|[http://parts.igem.org/Part:BBa_K2255009 BBa_K2255009]
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|-
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|''Pseudomonas aeruginosa''
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|Pf3<ref>Luiten, R. G., Schoenmakers, J. G. & Konings, R. N. The major coat protein gene of the filamentous Pseudomonas aeruginosa phage Pf3: absence of an N-terminal leader signal sequence. Nucleic Acids Res 11, 8073–8085 (1983).</ref>
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|215374
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|[http://parts.igem.org/Part:BBa_K2255010 BBa_K2255010]
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|-
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| rowspan="2" | ''Ralstonia solanacearum''
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|RSM1Φ<ref name="T,K">T, K. et al. Genomic characterization of the filamentous integrative bacteriophages {phi}RSS1 and {phi}RSM1, which infect Ralstonia solanacearum., Genomic Characterization of the Filamentous Integrative Bacteriophages φRSS1 and φRSM1, Which Infect Ralstonia solanacearum. J Bacteriol 189, 189, 5792, 5792–5802 (2007).</ref>
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|5179368
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|[http://parts.igem.org/Part:BBa_K2255011 BBa_K2255011]
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|-
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|RSS1Φ<ref name="T,K">T, K. et al. Genomic characterization of the filamentous integrative bacteriophages {phi}RSS1 and {phi}RSM1, which infect Ralstonia solanacearum., Genomic Characterization of the Filamentous Integrative Bacteriophages φRSS1 and φRSM1, Which Infect Ralstonia solanacearum. J Bacteriol 189, 189, 5792, 5792–5802 (2007).</ref>
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|4525385
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|[http://parts.igem.org/Part:BBa_K2255012 BBa_K2255012]
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|-
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| rowspan="3" | ''Vibrio Cholerea''
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|CTXΦ<ref name="Heilpern">Heilpern, A. J. & Waldor, M. K. pIIICTX, a predicted CTXphi minor coat protein, can expand the host range of coliphage fd to include Vibrio cholerae. J. Bacteriol. 185, 1037–1044 (2003).</ref>
 +
|26673076
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|[http://parts.igem.org/Part:BBa_K2255013 BBa_K2255013]
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|-
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|VFJΦ(fs2)<ref>Ikema, M. & Honma, Y. A novel filamentous phage, fs-2, of Vibrio cholerae O139. Microbiology 144, 1901–1906 (1998).</ref>
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|1261866
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|[http://parts.igem.org/Part:BBa_K2255014 BBa_K2255014]
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|-
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|VGJΦ<ref>Campos, J. et al. VGJφ, a Novel Filamentous Phage of Vibrio cholerae, Integrates into the Same Chromosomal Site as CTXφ. J. Bacteriol. 185, 5685–5696 (2003).</ref>
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|1260523
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|[http://parts.igem.org/Part:BBa_K2255015 BBa_K2255015]
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|-
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|''Xanthomonas campestris''
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|ΦLf<ref>Tseng, Y.-H., Lo, M.-C., Lin, K.-C., Pan, C.-C. & Chang, R.-Y. Characterization of filamentous bacteriophage ΦLf from Xanthomonas campestris pv. campestris. Journal of general virology 71, 1881–1884 (1990).</ref>
 +
|3730653
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|[http://parts.igem.org/Part:BBa_K2255016 BBa_K2255016]
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|-
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|''Xylella fastidiosa''
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|XfasM23<ref>Chen, J. & Civerolo, E. L. Morphological evidence for phages in Xylella fastidiosa. Virology Journal 5, 75 (2008).</ref>
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|6203562
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|[http://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
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|-
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|''Xanthomonas fucans''
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|XacF1<ref>Ahmad, A. A., Askora, A., Kawasaki, T., Fujie, M. & Yamada, T. The filamentous phage XacF1 causes loss of virulence in Xanthomonas axonopodis pv. citri, the causative agent of citrus canker disease. Front. Microbiol. 5, (2014).</ref>
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|17150318
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|[http://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]
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|}
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Table showing the attachment proteins from various filamentous phages.

Revision as of 22:00, 13 October 2017

Part Collection

Contents


Our collection of parts is designed to allow the creation of proteins, or phage-like particles, that target a wide range of different Gram-negative bacteria. Each part corresponds to the domains 1 (D1) and 2 (D2) from the p3 protein of filamentous phages targeting the different organisms. The parts in the collection are expected to be used as fusion proteins and so conform to the [http://parts.igem.org/Assembly_standard_25 Rfc25] standard. To know more about the design of these parts, and how we used them to make phage-like particles in our project, you can check out our design page.

This part collection contains the following biobricks all in [http://parts.igem.org/Assembly_standard_25 Rfc25] format:

  • p3_E.coli (RFC25) - [http://parts.igem.org/Part:BBa_K2255008 BBa_K2255008]
  • p3_ N.gonorrhoeae (RFC25) - [http://parts.igem.org/Part:BBa_K2255009 BBa_K2255009]
  • p3_P.aeruginosa (RFC25) - [http://parts.igem.org/Part:BBa_K2255010 BBa_K2255010]
  • p3_R.solanacearum_RSM1 (RFC25) - [http://parts.igem.org/Part:BBa_K2255011 BBa_K2255011]
  • p3_R.solanacearum_RSS1 (RFC25) - [http://parts.igem.org/Part:BBa_K2255012 BBa_K2255012]
  • p3_V.Cholerae_CTXΦ (RFC25) - [http://parts.igem.org/Part:BBa_K2255013 BBa_K2255013]
  • p3_V.Cholerae_fs2 (RFC25) - [http://parts.igem.org/Part:BBa_K2255014 BBa_K2255014]
  • p3_V.Cholerea_VGJΦ (RFC25) - [http://parts.igem.org/Part:BBa_K2255015 BBa_K2255015]
  • p3_X.campestris (RFC25) - [http://parts.igem.org/Part:BBa_K2255016 BBa_K2255016]
  • p3_X.fastidiosa (RFC25) - [http://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
  • p3_X.fuscans (RFC25) - [http://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]

Design

Design

The domain 3 (D3) and the signal sequence are both the best conserved part from the attachment protein. Using a global protein alignment (Needleman-Wunsch and MUSCLE alignments), using two or three sequence at one time, we were eventually able to determinate domain 1 (D1) and domain 2 (D2) from the attachment protein of each phages.

We were able to found these domains because each of them is separated by a flexible sequence composed of Glycine and Serine [1]. Then we retrotranslate this sequence in a nucleotidic sequence and we used iDT to optimise this sequence for E.coli production.

Pathogene Filamentous phage GI Part ID
Escherichia coli M13 (fd,ff)[2] 927334 BBa K2255008
Neisseria gonorrheae NgoΦ6[3] 1260906 [http://parts.igem.org/Part:BBa_K2255009 BBa_K2255009]
Pseudomonas aeruginosa Pf3[4] 215374 [http://parts.igem.org/Part:BBa_K2255010 BBa_K2255010]
Ralstonia solanacearum RSM1Φ[5] 5179368 [http://parts.igem.org/Part:BBa_K2255011 BBa_K2255011]
RSS1Φ[5] 4525385 [http://parts.igem.org/Part:BBa_K2255012 BBa_K2255012]
Vibrio Cholerea CTXΦ[6] 26673076 [http://parts.igem.org/Part:BBa_K2255013 BBa_K2255013]
VFJΦ(fs2)[7] 1261866 [http://parts.igem.org/Part:BBa_K2255014 BBa_K2255014]
VGJΦ[8] 1260523 [http://parts.igem.org/Part:BBa_K2255015 BBa_K2255015]
Xanthomonas campestris ΦLf[9] 3730653 [http://parts.igem.org/Part:BBa_K2255016 BBa_K2255016]
Xylella fastidiosa XfasM23[10] 6203562 [http://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
Xanthomonas fucans XacF1[11] 17150318 [http://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]
Table showing the attachment proteins from various filamentous phages.
  1. ↑ Heilpern, A. J. & Waldor, M. K. pIIICTX, a predicted CTXphi minor coat protein, can expand the host range of coliphage fd to include Vibrio cholerae. J. Bacteriol. 185, 1037–1044 (2003).
  2. ↑ Smeal, S. W., Schmitt, M. A., Pereira, R. R., Prasad, A. & Fisk, J. D. Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation. Virology 500, 259–274 (2017).
  3. ↑ Piekarowicz, A. et al. Neisseria gonorrhoeae Filamentous Phage NgoΦ6 Is Capable of Infecting a Variety of Gram-Negative Bacteria. J Virol 88, 1002–1010 (2014).
  4. ↑ Luiten, R. G., Schoenmakers, J. G. & Konings, R. N. The major coat protein gene of the filamentous Pseudomonas aeruginosa phage Pf3: absence of an N-terminal leader signal sequence. Nucleic Acids Res 11, 8073–8085 (1983).
  5. ↑ 5.0 5.1 T, K. et al. Genomic characterization of the filamentous integrative bacteriophages {phi}RSS1 and {phi}RSM1, which infect Ralstonia solanacearum., Genomic Characterization of the Filamentous Integrative Bacteriophages φRSS1 and φRSM1, Which Infect Ralstonia solanacearum. J Bacteriol 189, 189, 5792, 5792–5802 (2007).
  6. ↑ Heilpern, A. J. & Waldor, M. K. pIIICTX, a predicted CTXphi minor coat protein, can expand the host range of coliphage fd to include Vibrio cholerae. J. Bacteriol. 185, 1037–1044 (2003).
  7. ↑ Ikema, M. & Honma, Y. A novel filamentous phage, fs-2, of Vibrio cholerae O139. Microbiology 144, 1901–1906 (1998).
  8. ↑ Campos, J. et al. VGJφ, a Novel Filamentous Phage of Vibrio cholerae, Integrates into the Same Chromosomal Site as CTXφ. J. Bacteriol. 185, 5685–5696 (2003).
  9. ↑ Tseng, Y.-H., Lo, M.-C., Lin, K.-C., Pan, C.-C. & Chang, R.-Y. Characterization of filamentous bacteriophage ΦLf from Xanthomonas campestris pv. campestris. Journal of general virology 71, 1881–1884 (1990).
  10. ↑ Chen, J. & Civerolo, E. L. Morphological evidence for phages in Xylella fastidiosa. Virology Journal 5, 75 (2008).
  11. ↑ Ahmad, A. A., Askora, A., Kawasaki, T., Fujie, M. & Yamada, T. The filamentous phage XacF1 causes loss of virulence in Xanthomonas axonopodis pv. citri, the causative agent of citrus canker disease. Front. Microbiol. 5, (2014).