PutidaNET :Interactome database service and network analysis of

Pseudomonas putida KT2440 (P. putida KT2440)

Korean BioInformation Center (KOBIC) Seong-Jin, Park

Pseudomonas putida (P. putida)

• A ubiquitous bacterium which can break down

a variety of organic materials for food.

• Plays vital role in recycling of organic wastes and degradation of biogenic and xenobiotic pollutants present in the environment.

• A model organism for genetic and physiological studies and for

the development of biotechnological applications.

Why Protein Interactome is important?

• To provide valuable insights into biological functions and processes in cells.

• To provide important clues about how to interpret metabolic

pathways of enzymes.

• Comprehensive interaction database which provides predicted protein-protein interaction information of P. putida

• A web server that provides various kinds of functional information such

as physico-chemical properties, biological pathways, and gene

ontology of protein.

What is PutidaNET?

Overview of PutidaNET system

Functional annotation

Protein interaction

analysis

PutidaNET

PEIMAP

PSIMAP

iPfam

KEGG

GO

NCBI

P. Putida KT2440

Protein-protein interaction prediction methods

• PSIMAP (Protein Structural Interaction)

The interactions among proteins by using BLASTP algorithm with a common expectation value (0.0001).

• PEIMAP (Protein Experimental Interaction)

Integrating various experimental protein-protein interaction database such as BIND, DIP, MINT, HPRD and BioGrid.

• iPfam

Alignment of Pfam domains of all the P. putida proteins with hmmpfam by the cut-off of expectation value (0.01).

PSIMAP & PEIMAP

• The biological function information using KEGG and GO databases.

• General information about proteins such as hydropathy scores, subcellular- localization, GRAVY score, and protein instability index.

Provides valuable insight into protein functions and help to understand the PPI networks of P.putida

Functional annotation

PutidaNET statistics

• 3,254 proteins for P. putida KT2440, contains 82,019 predicted PPI partners.

• PPIs are ranked by confidence score base on reliability.

Confidence Score = 1- π(1-Ri)3

= 1- (1-RPEIMAP)(1-RPSIMAP)(1-RiPfam) I : Interaction method used

R : Reliability of each method

• We integrated PPI network with experimental 2 DE/MS-MS data.

• We then acquired the protein lists in culture media including succinate and benzoate.

PutidaNET case study (1/2)

-> Benzoate

-> Succinate

-> Intersection set of succinate and benzoate

-> No information

B S

B-S S-BB∩S

66 806 514

PutidaNET case study (2/2)

• We calculated the degree score for the network.

• We found that the main protein network of P.putida is regulated by an intersection set of succinate and benzoate.

Y axis : Degree ScoreX axis : Cultured media in carbon source

Web interface

NP_742815.1

Web interface

Interaction partners

Web interface

Web interface

PutidaNET

• An integration of mutually complementary protein-protein

interactions for the systematic analysis of P. putida.

• Provide the highly predicted PPIs by ranking using confidence score

• Researchers to access and obtain information through an

automatic annotation for queried protein.

• PutidaNET: http://sequenceome.kobic.kr/PutidaNET