Team:TU Delft/Modeling/interaction-mapping


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Revision as of 19:00, 16 September 2010

Homolog Interaction Mapping (HIM)

Part of our project was development of an application that can generate a list of putative interactions for genes in a new host organism. In our project, the clearest example of this is the insertion of a prefoldin (phPFDα + phPFDβ) coding plasmid into E. coli. Using this application it was possible to get a list of putative interactions with the prefoldin proteins, and therefore give some hints about how these proteins are actually working.

Problems with introducing new genes

In our project, we are taking genes from various organisms and putting them as a biobrick plasmid into E. coli. This may cause various unexpected problems in the newly designed biological system:

  • The protein in the original organism may need some other functional partners (proteins or RNAs) in order to behave correctly (I.A.W. a part of the imported system is missing)
  • The introduced protein can interact with local proteins that are not ment to interact.

Searching for interactions

To get an idea of which interactions may occur, interactions within the original organisms where mapped to their E. coli homologs: IGEMTUDelft Interactiongraph.PNG

In more detail:

  • The sequence of every introduced protein (See the coding biobricks) was blasted against the STRING protein database. This resulted in a number of proteins that are either the correct proteins, or homologs of the introduced proteins.
Biobrick Short name STRING Database ID
BBa_K398000 LadA 420246.GTNG_3499
BBa_K398001 AlkB 101510.RHA1_ro02534
BBa_K398002 RubA3 246196.MSMEG_1840
BBa_K398003 RubA4 350058.Mvan_1744
BBa_K398004 Rubredoxin reductase 101510.RHA1_ro02537
BBa_K398005 Bt-ADH 235909.GK0984
BBa_K398006 Bt-ALDH 235909.GK2772
BBa_K398100 bbc1 Dropped: Not in STRING database, and

protein sequence blast only resulted in eukaryotic homologs

BBa_K398200 AlnA 62977.ACIAD0697
BBa_K398201 OprG 160488.PP_0504
BBa_K398300 AlkS 399739.Pmen_0429
BBa_K398400 Prefoldin-alpha 70601.PH0527
BBa_K398401 Prefoldin-beta 70601.PH0532
  • For each protein, the interactions stored in STRING where gathered.
  • For each found interacting protein, E. coli homologs where gathered.
  • This results in a combination of interactions with their E. coli homologs. The likelyness of this being a true interaction depends on the STRING interaction score (Data from publication text mining, microarrays and other sources) and the BLAST score (The homolog mapping step).

Software development

An application was developed that can run these queries on a PostgreSQL server running the STRING database. This database can be downloaded for free for academic use. Unfortunately, the STRING API does not provide enough functionality to do the homolog mapping, so a PostgreSQL database with the STRING data is always needed.

Source code is available in a github repository, or by directly downloading the code in zip format


Prefoldin interaction mapping

The network below shows the putative interactions of the prefoldin biobricks, and any interacting proteins that do not have homologs in E. coli.

  • Green: E. coli homologs of a Pyrococcus protein that is interacting with prefoldin, according to the STRING database.
  • Red: Missing homolog.

As prefoldin is working in E. coli, one could argue that this is because it is interacting with the green proteins. This could be a hint for more research into the Pyrococcus prefoldin proteins.

Alkane degradation pathway interaction mapping

Additionally, the alkane degradation proteins where also entered into the mapping tool, as shown below. However, we already know how this system works. The STRING interactions probably just show parts of the pathway proteins that are expressed together, hence this analysis is a lot less useful.