Database Research Summaries2018 NE Soybean Phytophthora root rot disease control by identifying protein interactions of virulence effectors in Phytophthora Sojae to soybean proteins
The focus of this project is to explore the so-far blank research area of protein interactions between P. Sojae virulence effectors and soybean proteins with a statistical model trained from existing protein interaction data.
- Identify the protein physical interactions between putative virulence
effectors in P. Sojae and proteins in soybeans based on a statistical model training with the know protein domain interaction data, which can confirm the computational discovered virulence effectors and discover novel innate immune components in soybean.
- Systematically discover the pathogenic target genes that are enriched in
the plant pathways, which can reveal the mechanism of P. Sojae’s pathogenicity and be used to develop control methods for Phytophthora root rot.
- Based on the designed statistical network model, researchers identified the protein interaction networks between the pathogen and soybean. After the algorithm identified the protein-protein interaction information, researchers could confirm the predicted virulence effectors and understand the functions of these virulence effectors.
- The model predicted the interactions between 596 P. sojae virulence effecters and 18142 soybean proteins. Based the cross-validation evaluation, this new improvement can make the prediction accuracy better than other existing methods, such as methods based on sequence similarity, position weighted matrix (PWM), and hidden Markovmodel (HMM).
- For objective 2, we found that most P. sojae virulence factors are structural constituent of ribosomes (Gene ontology annotation term GO:0003735) and structural molecule activity (Gene ontology annotation term GO:0005198). The results indicate that P. sojae pathogens interfere the genetic information flowing and functions of virulence factor are related to cell signals and DNA binding.
- Understanding the intricate interactions between this pathogen and soybean is important because it is a key step towards disease control.
- The discovered protein interactions between virulence factors and host proteins can lead to the development of disease-resistant soybeans, which can help Nebraska soybean farmers prevent the yield-loss due to Phytophthora root rot.
For more information about this research project, please visit the National Soybean Checkoff Research Database.
Funded in part by the soybean checkoff.