In Ensembl release 109, we introduce a new display that integrates experimentally verified interactions between genes, proteins, mRNA or other small molecules onto our gene pages. This adds an additional layer of data that enables deeper analysis into the ways species interact in a variety of contexts. So far, we have imported curated interactions from PHI-base, HPIDB, and PlasticDB for which we could find exact protein matches in Ensembl.

The image below shows interactions between Phaeosphaeria nodorum (a major fungal pathogen of wheat) gene and proteins in Triticum aestivium (wheat). These interactions have been identified in the literature and imported from PHI-base, our collaborators at Rothamsted Research. Two of these have a target protein in the host identified through experimentation, and a third one has been confirmed but remains to be determined. In cases where several experiments are described in the same paper for the same interaction, we will link to the original databases for further information.

Here we have another example of molecular interactions between Arabidopsis thaliana gene FLS2 and Pseudomonas aeruginosa reported by both intAct and DIP.

Molecular interaction between Arabidopsis thaliana gene FLS2 and Pseudomonas aeruginosa

You can also view molecular interactions between different species and synthetic molecules. We are showing below the interaction between Saccharomonospora viridis protein SAMN02982918_2340 and different types of polymers; imported from PlasticDB.

Molecular interactions between SAMN02982918_2340 and synthetic molecules sourced from PlasticDB.

Our data model has captured interactions from multiple resources and used a number of ontologies to describe the experiments and the associated metadata. We have imported 13,648 interactions for a total of 470 species across the six Ensembl sites. 

Number of INTERACTIONS per division (filtered by source_db):

Input data resource	TOTAL	Bacteria	Fungi	Metazoa	Plants	Protists	Vertebrates
PHI-base	3729	2007	1624	360	1842	126	1499
HPIDB/HPIDBcurated	111	111	0	0	2	0	109
HPIDB/INTACTcurated	9175	7484	1675	14	69	16	9092
HPIDB/MINTcurated	387	278	107	8	7	2	372
HPIDB/DIPcurated	278	170	99	11	29	9	238
PlasticDB	68	68	0	0	0	0	0
TOTAL	13.648	10118	3505	393	1949	153	11310

A set of REST endpoints have been made available to allow this information to be queried programmatically. More documentation on these endpoints can be found on interactions.rest.ensembl.org. 

Unravelling molecular interactions within species has become increasingly important. The unprecedented rate of emergence of microbial pathogens that are resistant to existing chemistries has led to concerns over the possible collapse of our healthcare and food systems [Fisher et al., 2018]. Careful stewardship of antimicrobial therapies and an urgent effort to discover novel intervention techniques, including alternative strategies such as biological control agents and RNA interference will be crucial to solving this issue. Furthermore, the poleward migration of certain microorganisms due to climate change exposes a set of previously uninvolved hosts to their infection mechanisms. Tools that enable a deeper understanding and extrapolation of this data from known, well-studied species to novel hosts and emerging pathogens, will help researchers develop preventive interventions.

This work has been funded by the BBSRC. We would also like to thank our collaborators at Rothamsted Research for all their support.

References:

• Fisher M.C, Hawkins N.J, Sanglard D, Gurr S.J. Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science. 2018, 18;360(6390):739–42.