Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service.

BMC Bioinformatics
Jeong-Gu KimJong Bhak

Abstract

Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysaccharides production, toxins release, iron acquisition, and effector proteins secretion. Many such mechanisms involve some kind of protein-protein interaction in hosts. Our first aim was to predict the whole protein interaction pairs (interactome) of Xanthomonas oryzae pathovar oryzae (Xoo) that is an important pathogenic bacterium that causes bacterial blight (BB) in rice. We developed a detection protocol to find possibly interacting proteins in its host using whole genome PPI prediction algorithms. The second aim was to build a DB server and a bioinformatic procedure for finding target proteins in Xoo for developing pesticides that block host-pathogen protein interactions within critical biochemical pathways. A PPI network in Xoo proteome was predicted by bioinformatics algorithms: PSIMAP, PEIMAP, and iPfam. We present the resultant species specific interaction network and host-pathogen interaction, XooNET. It is a compre...Continue Reading

References

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Citations

May 2, 2008·Nucleic Acids Research·Daeui ParkSunghoon Lee
Nov 11, 2008·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Myoung-Ki HongLin-Woo Kang
Nov 11, 2008·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Phuong-Thuy Ho NgoLin-Woo Kang
Oct 22, 2010·BMC Bioinformatics·Ranjit Kumar, Bindu Nanduri
Jan 22, 2013·Annual Review of Plant Biology·Pascal BraunClaire Lurin
May 16, 2009·Journal of Dermatological Science·Zhi-Rong LüFei Zou
Oct 1, 2008·Journal of Dermatological Science·Zhi-Rong LüJun-Mo Yang
Mar 12, 2015·Frontiers in Microbiology·Esmaeil NouraniSaliha Durmuş
Apr 4, 2017·Database : the Journal of Biological Databases and Curation·Junyang YueYongsheng Liu
Sep 12, 2014·Integrative Biology : Quantitative Biosciences From Nano to Macro·Edson Luiz FoladorVasco Azevedo
May 29, 2021·Frontiers in Microbiology·Padhmanand SudhakarSéverine Vermeire

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Methods Mentioned

BETA
two-hybrid
interaction predictions

Software Mentioned

XooNET
IntAct
PEIMAP Experimental Interactome MAP
BLAST
PEIMAP
BLASTP
Integrator
GO
iPfam
PSIMAP

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