Abstract Detail

Colloquia: Moss: from deep phylogeny and model organisms.

Schuette, Scott [1], Corley, Aaron [2], Geisler, Matt [3].

How to use the predicted interactome of the moss Physcomitrella patens to answer biological questions.

Complete sequencing of plant genomes has been completed for two mosses, a lycophyte, numerous angiosperms and projects are now outlined for liverworts, ferns, gymnosperms and the algal ancestors to land plants. New genes are now routinely annotated solely by their homology to known genes. Biological activity is often determined by physical interactions between proteins which increases organismal complexity beyond the genome itself. A map of all protein-protein interactions is thus an invaluable tool to elucidate this complexity. We predict these interactions on the basis of orthology to known interacting proteins in reference species, by analysis of co-expression and by detection of co-evolving proteins. Here we present a predicted interactome for Physcomitrella patens. A confidence value is generated from the quantity and type of supporting evidence. Currently we have predicted more than 26,000 unique interactions between over 3000 moss proteins and these numbers are expected to increase as more reference organisms are added. Network topology analysis using MCODE has reconstructed more than 50 clusters of highly interconnected proteins, including the ribosome, proteosome, and several key metabolic and regulatory branches. Predicted interactions add to gene annotation of eukaryotically conserved proteins, which along with domain and global homology allow for prediction of gene function. We describe how a user with no background in bioinformatics can make use of this database to find protein pathways, interacting partners, likely regulators, protein complex members, and make sense of the results. These tools will greatly aid researchers to identify and extend known complexes, pathways and signaling networks in this evolutionarily important plant.

Broader Impacts:
Having a plant interactome is an invaluable tool which can potentially transform systems biology approaches to reconstruction of biological pathways. With the inclusion of moss and several other early sister taxa to the angiosperms we can observe co-evolution of important pathways and protein networks. This might have immediate benefit of finding alternatives to important pathways in crop and environmentally important species. The cross training of biology and computer science students generated by this research opens important doors in the future of bioinformatics.

Related Links:
Arabidopsis predicted interactome

1 - Southern Illinois University, Department of Plant Biology, 1125 Lincoln Drive, Carbondale, Illinois, 62901-6509, USA
2 - Southern Illinois University, Computer Science, 1125 Lincoln Ave., LSII, Carbondale, IL, 62901, USA
3 - Southern Illinois University Carbondale, Plant Biology, 1125 Lincoln Ave., LSII, Rm403, Carbondale, Illinois, 62901, USA

Keywords:
Physcomitrella patens
protein-protein interaction
systems biology
bioinformatics.

Presentation Type: Symposium or Colloquium Presentation
Session: C1
Location: Ballroom D/Convention Center
Date: Monday, August 2nd, 2010
Time: 10:45 AM
Number: C1006
Abstract ID:594