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

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{{Aix-Marseille|title=Part Collection|toc=__NOTOC__}}
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<!-- With any luck you will be able to add a testing paragraph or link  -->
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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 have more detail 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 [http://parts.igem.org/Assembly_standard_25 Rfc25] format:
  
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<div class="column full_size judges-will-not-evaluate">
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*p3_E.coli - [http://parts.igem.org/Part:BBa_K2255008 BBa_K2255008]
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<h3>★  ALERT! </h3>
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*p3_N.gonorrhoeae - [http://parts.igem.org/Part:BBa_K2255009 BBa_K2255009]
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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*p3_P.aeruginosa - [http://parts.igem.org/Part:BBa_K2255010 BBa_K2255010]
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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*p3_R.solanacearum_RSM1 - [http://parts.igem.org/Part:BBa_K2255011 BBa_K2255011]
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</div>
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*p3_R.solanacearum_RSS1 - [http://parts.igem.org/Part:BBa_K2255012 BBa_K2255012]
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<div class="clear"></div>
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*p3_V.Cholerae_CTXΦ - [http://parts.igem.org/Part:BBa_K2255013 BBa_K2255013]
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*p3_V.Cholerae_fs2 - [http://parts.igem.org/Part:BBa_K2255014 BBa_K2255014]
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*p3_V.Cholerea_VGJΦ - [http://parts.igem.org/Part:BBa_K2255015 BBa_K2255015]
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*p3_X.campestris - [http://parts.igem.org/Part:BBa_K2255016 BBa_K2255016]
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*p3_X.fastidiosa - [http://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
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*p3_X.fuscans - [http://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]
  
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==Usage==
  
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These biobricks will be used to engineer phage-like particles targeting different bacteria.
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Check out our [[Team:Aix-Marseille/M13_Design|design page]] to know more about their design.
  
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==Design==
  
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The domain 3 (D3) and the signal sequence are the best conserved parts of the innophage attachment protein p3.
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Using a global protein sequence 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 a time, we were able create a good alignment.
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We used this to determine the domain 1 (D1) and domain 2 (D2) sequence for the attachment proteins of each phages.
  
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<div class="column full_size">
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We were able to find these domains because they are separated by flexible sequences, often 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>.
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Then we then retrotranslated these protein sequences to obtain gene sequences and we used the iDT tool to optimise this for production in ''E.coli''.
  
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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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|[http://parts.igem.org/Part:BBa_K2255008 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>
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|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>
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|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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<h1> Part Collection </h1>
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Table showing the attachment proteins from various filamentous phages.
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<p>Did your team make a lot of great parts? Is there a theme that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection, or a collection of awesome pigment parts? Describe your parts collection on this page, so the judges can evaluate you for the Best Part Collection award.</p>
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<p>
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While you should put all the characterization information for your parts on the Registry, you are encouraged to explain how all your parts form a collection on this page.
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</p>
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<br>
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<h3>Best Part Collection Special Prize</h3>
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<p>Did your team make a lot of great parts? Is there a team that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection or a collection of awesome pigment parts? Tell the judges you should be evaluated for the Best Parts Collection award! To be eligible for this award, these parts must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts.
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<br><br>
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If you have a collection of parts you wish to nominate your team for this <a href="https://2017.igem.org/Judging/Awards">special prize</a>, make sure you add your part numbers to your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.</p>
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<div class="highlight">
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<h4>Note</h4>
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<p>This page should list all the parts in the collection your team made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page.</p>
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Latest revision as of 02:42, 2 November 2017

Part Collection


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 have more detail 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 - [http://parts.igem.org/Part:BBa_K2255008 BBa_K2255008]
  • p3_N.gonorrhoeae - [http://parts.igem.org/Part:BBa_K2255009 BBa_K2255009]
  • p3_P.aeruginosa - [http://parts.igem.org/Part:BBa_K2255010 BBa_K2255010]
  • p3_R.solanacearum_RSM1 - [http://parts.igem.org/Part:BBa_K2255011 BBa_K2255011]
  • p3_R.solanacearum_RSS1 - [http://parts.igem.org/Part:BBa_K2255012 BBa_K2255012]
  • p3_V.Cholerae_CTXΦ - [http://parts.igem.org/Part:BBa_K2255013 BBa_K2255013]
  • p3_V.Cholerae_fs2 - [http://parts.igem.org/Part:BBa_K2255014 BBa_K2255014]
  • p3_V.Cholerea_VGJΦ - [http://parts.igem.org/Part:BBa_K2255015 BBa_K2255015]
  • p3_X.campestris - [http://parts.igem.org/Part:BBa_K2255016 BBa_K2255016]
  • p3_X.fastidiosa - [http://parts.igem.org/Part:BBa_K2255017 BBa_K2255017]
  • p3_X.fuscans - [http://parts.igem.org/Part:BBa_K2255018 BBa_K2255018]

Usage

These biobricks will be used to engineer phage-like particles targeting different bacteria. Check out our design page to know more about their design.

Design

The domain 3 (D3) and the signal sequence are the best conserved parts of the innophage attachment protein p3. Using a global protein sequence alignment (Needleman-Wunsch and MUSCLE alignments), using two or three sequence at a time, we were able create a good alignment. We used this to determine the domain 1 (D1) and domain 2 (D2) sequence for the attachment proteins of each phages.

We were able to find these domains because they are separated by flexible sequences, often composed of Glycine and Serine [1]. Then we then retrotranslated these protein sequences to obtain gene sequences and we used the iDT tool to optimise this for production in E.coli.

Pathogene Filamentous phage GI Part ID
Escherichia coli M13 (fd,ff)[2] 927334 [http://parts.igem.org/Part:BBa_K2255008 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).