Difference between revisions of "Part:BBa K2255008"
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This part is sequence coding for the D1 and D2 of the protein 3 of M13. Those domains are required for M13 adsorption and entry.
 
This part is sequence coding for the D1 and D2 of the protein 3 of M13. Those domains are required for M13 adsorption and entry.
  
−
This part was design with Freiburg (RFC[25]) extension. Thus, it contain the restriction site  NgoMIV and AgeI that are compatible and allow the missing of a start and stop codon, which ease the assemble of multiple protein domain.
+
This part was design with Freiburg ([https://parts.igem.org/Assembly_standard_25 Rfc25]) extension. Thus, it contain the restriction site  NgoMIV and AgeI that are compatible and allow the missing of a start and stop codon, which ease the assemble of multiple protein domain.
 +
 
 +
This part is the first one of our collection part for the attachment protein of M13. To test the specificity of our phage-like particle and to target other pathogenic bacterium we design a large scale of attachment protein.  So with protein global alignment (Needleman-Wunsch alignment), from two or three sequence at one time, we were eventually able to determinate D1 and D2.
 +
 
 +
{|
 +
! scope="col" |Pathogene
 +
! scope="col" |Filamentous phage
 +
! scope="col" |Gene ID
 +
! scope="col" |Part ID
 +
|-
 +
|''Escherichia coli''
 +
|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>
 +
|927334
 +
|BBa K2255008
 +
|-
 +
|''Neisseria gonorrheae''
 +
|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>
 +
|1260906
 +
|[https://parts.igem.org/Part:BBa_K2255009 BBa_K2255009]
 +
|-
 +
|''Pseudomonas aeruginosa''
 +
|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>
 +
|1260906
 +
|[https://parts.igem.org/Part:BBa_K2255010 BBa_K2255010]
 +
|-
 +
| rowspan="2" | ''Ralstonia solanacearum''
 +
|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>
 +
|5179368
 +
|[https://parts.igem.org/Part:BBa_K2255011 BBa_K2255011]
 +
|-
 +
|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>
 +
|4525385
 +
|[https://parts.igem.org/Part:BBa_K2255012 BBa_K2255012]
 +
|-
 +
| rowspan="3" | ''Vibrio Cholerea''
 +
|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
 +
|[https://parts.igem.org/Part:BBa_K2255013 BBa_K2255013]
 +
|-
 +
|VFJΦ(fs2)<ref>Ikema, M. & Honma, Y. A novel filamentous phage, fs-2, of Vibrio cholerae O139. Microbiology 144, 1901–1906 (1998).</ref>
 +
|1261866
 +
|[https://parts.igem.org/Part:BBa_K2255014 BBa_K2255014]
 +
|-
 +
|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>
 +
|1260523
 +
|[https://parts.igem.org/Part:BBa_K2255015 BBa_K2255015]
 +
|-
 +
|''Xanthomonas campestris''
 +
|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
 +
|[https://parts.igem.org/Part:BBa_K2255016 BBa_K2255016]
 +
|-
 +
|''Xanthomonas fucans''
 +
|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>
 +
|17150318
 +
|[https://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
 +
|-
 +
|''Xylella fastidiosa''
 +
|XfasM23<ref>Chen, J. & Civerolo, E. L. Morphological evidence for phages in Xylella fastidiosa. Virology Journal 5, 75 (2008).</ref>
 +
|6203562
 +
|[https://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]
 +
|}
 +
 
 +
Table showing the attachment proteins from various filamentous phages.
 +
 
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Revision as of 16:04, 26 September 2017


p3_E.coli (Rfc25)

This part is sequence coding for the D1 and D2 of the protein 3 of M13. Those domains are required for M13 adsorption and entry.

This part was design with Freiburg (Rfc25) extension. Thus, it contain the restriction site NgoMIV and AgeI that are compatible and allow the missing of a start and stop codon, which ease the assemble of multiple protein domain.

This part is the first one of our collection part for the attachment protein of M13. To test the specificity of our phage-like particle and to target other pathogenic bacterium we design a large scale of attachment protein. So with protein global alignment (Needleman-Wunsch alignment), from two or three sequence at one time, we were eventually able to determinate D1 and D2.

Pathogene Filamentous phage Gene ID Part ID
Escherichia coli M13 (fd,ff)[1] 927334 BBa K2255008
Neisseria gonorrheae NgoΦ6[2] 1260906 BBa_K2255009
Pseudomonas aeruginosa Pf3[3] 1260906 BBa_K2255010
Ralstonia solanacearum RSM1Φ[4] 5179368 BBa_K2255011
RSS1Φ[4] 4525385 BBa_K2255012
Vibrio Cholerea CTXΦ[5] 26673076 BBa_K2255013
VFJΦ(fs2)[6] 1261866 BBa_K2255014
VGJΦ[7] 1260523 BBa_K2255015
Xanthomonas campestris ΦLf[8] 3730653 BBa_K2255016
Xanthomonas fucans XacF1[9] 17150318 BBa_K2255017
Xylella fastidiosa XfasM23[10] 6203562 BBa_K2255018

Table showing the attachment proteins from various filamentous phages.


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
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


  1. ↑ 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).
  2. ↑ 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).
  3. ↑ 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).
  4. ↑ 4.0 4.1 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).
  5. ↑ 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).
  6. ↑ Ikema, M. & Honma, Y. A novel filamentous phage, fs-2, of Vibrio cholerae O139. Microbiology 144, 1901–1906 (1998).
  7. ↑ 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).
  8. ↑ 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).
  9. ↑ 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).
  10. ↑ Chen, J. & Civerolo, E. L. Morphological evidence for phages in Xylella fastidiosa. Virology Journal 5, 75 (2008).