SynechoNET: integrated protein interaction database of Synechocystis 6th InCoB 2007 HKUST, Hong Kong SynechoNET: integrated protein interaction database of Synechocystis Sungsoo Kang & Jongsoon Choi Korean BioInformation Center, KRIBB Korea Basic Science Institute

Korean BioInformation Center (KOBIC) The national bioinformatics center of Korea Integration of diverse biological information Genome information Biodiversity information Bioresource information International training programs on bioinformatics Collaborative development of bioinformatics tools and resources BioWiki (online knowledge base of biology) BioPipe (BioWorkflow engine)

BioWiki Wiki a web technology that enables anyone to create and update website contents. suited for developing online knowledge bases (e.g., Wikipedia ). BioWiki To adopt the wiki paradigm in biology Collaborative development of biological knowledge bases. BioWiki Contest ( http://biowiki.net )

BioPipe BioWorkflow Engine BioPipe Contest No installation required ‘Drag and drop’ supported BioPipe Contest Open free Web 2.0 Period: Aug 15th ~ Sep 20th Website: http://www.biopipe.net Easy way to do bioinformatics 4

SynechoNET: integrated protein interaction database of Synechocystis 6th InCoB 2007 HKUST, Hong Kong SynechoNET: integrated protein interaction database of Synechocystis Sungsoo Kang & Jongsoon Choi Korean BioInformation Center, KRIBB Korea Basic Science Institute

Cyanobacteria (Synechocystis) Photosynthetic bacteria with multi-layered membranes Photo-autotrophic or photo-heterotrophic growth Ancestor of plant chloroplast

Photosynthesis of Synechocystis Thylakoid membrane contains many phycobilisomes on its surface Phycobilisomes contain accessory pigments absorbing light for photosynthesis

Synechocystis sp. PCC 6803 Model organism of higher plants Plant-like oxygenic photosynthesis High transformation efficiency Light signal transduction mutants Undergoing systems biology pilot study ‘Genome-to-Life’ project of DOE, USA The first complete genome sequence among photosynthetic bacteria (DNA Research 1996) Genome size: 3,573,470 bp, GC content : 47.7% 3167 proteins (92 two-component regulatory proteins)

SynechoNET Provides predicted protein interaction network of Synechocystis sp. PCC 6803 Integrates four complementary and redundant public protein-protein interaction (PPI) databases Generates prediction reliability based on redundancy Provides predicted membrane protein information trans-membrane topology and domain information

Overview of SynechoNET System 1 2 3 4

Web Pages of SynechoNET

1. Integration of Protein Protein Interaction Data structural interaction 1. Integration of Protein Protein Interaction Data interaction from multi-contexts

Display of predicted protein interactions and their evidences

2. Prediction of Membrane Proteins Amino acid sequence Phobius (HMM model) Signal peptide Profile of predicted TM topology and signal peptide PFAM (protein domain DB) Predicted TM topology Transmembrane (TM) topology Localizome (graphic module) Domain structure

Display of predicted transmembrane topology and its evidence

3. External Links from SynechoNET

4-1. Interactive Network Analysis in SynechoNET

4-2. Keyword Search in SynechoNET

4-3. Functional Category Search in SynechoNET

Application of SynechoNET Analysis on highly interacting hub proteins in a specific functional category Finding upstream or downstream interacting proteins in a cellular pathway Functional prediction of unknown genes Analysis on regulatory membrane proteins

Interaction Network of Regulatory Proteins (further analysis in Cytoscape program) No. of found genes: 279 No. of interactions: 2754

Highly-Interacting Regulatory Proteins with a Transmembrane Domain

Experimental Verification of Predicted Interactions for Further Study Real interaction verified by yeast two-hybrid analysis -His P53 T Lam Sll0043 Sll0038 Sll0039

Conclusion SynechoNET: Synechocystis-specific integrated protein-protein interaction (PPI) database with trans-membrane topology and domain information Integrates PPI information from PSIMAP, iPFAM, InterDom, and STRING Transmembrane topology and domain information from Phobius and Localizome Available at http://synechocystis.org or directly at http://bioportal.kobic.re.kr/SynechoNET/