Predicting Protein–Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches

Rice blast, caused by the fungus Magnaporthe oryzae, is the most devastating disease affecting rice production. Identification of protein–protein interactions (PPIs) is a critical step toward understanding the molecular mechanisms underlying resistance to blast fungus in rice. In this study, we presented a computational framework for predicting plant–pathogen PPIs based on structural information. Compared with the sequence-based methods, the structure-based approach showed to be more powerful in discovering new PPIs between plants and pathogens. Using the structure-based method, we generated a global PPI network consisted of 2,018 interacting protein pairs involving 1,344 rice proteins and 418 blast fungus proteins. The network analysis showed that blast resistance genes were enriched in the PPI network. The network-based prediction enabled systematic discovery of new blast resistance genes in rice. The network provided a global map to help accelerate the identification of blast resistance genes and advance our understanding of plant–pathogen interactions.

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Genetic studies on resistance of rice plant to blast fungus. (VII). Blast resistance genes of Kuroka.

Japanese Journal of Phytopathology ◽

10.3186/jjphytopath.54.460 ◽

1988 ◽

Vol 54 (4) ◽

pp. 460-465 ◽

Cited By ~ 14

Author(s):

Iwasaburo GOTO

Keyword(s):

Resistance Genes ◽

Rice Plant ◽

Blast Resistance ◽

Genetic Studies ◽

Blast Fungus ◽

Blast Resistance Genes

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Resistance Spectrum Difference between Two Broad-Spectrum Blast Resistance Genes,PigmandPi2, and Their Interaction Effect onPi1

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2013.01927 ◽

2013 ◽

Vol 39 (11) ◽

pp. 1927 ◽

Cited By ~ 5

Author(s):

Miao-Miao YU ◽

Zheng-Yuan DAI ◽

Cun-Hong PAN ◽

Xi-Jun CHEN ◽

Ling YU ◽

...

Keyword(s):

Resistance Genes ◽

Broad Spectrum ◽

Interaction Effect ◽

Blast Resistance ◽

Resistance Spectrum ◽

Blast Resistance Genes

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Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

Current Medicinal Chemistry ◽

10.2174/0929867326666190620101637 ◽

2020 ◽

Vol 27 (37) ◽

pp. 6306-6355 ◽

Cited By ~ 2

Author(s):

Marian Vincenzi ◽

Flavia Anna Mercurio ◽

Marilisa Leone

Keyword(s):

Drug Discovery ◽

Protein Interaction ◽

Protein Interactions ◽

Structural Information ◽

Protein Complexes ◽

Structural Features ◽

Protein Protein Interactions ◽

Modular Architecture ◽

Post Translational Modifications ◽

Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

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Structure, Function, Involvement in Diseases and Targeting of 14-3-3 Proteins: An Update

Current Medicinal Chemistry ◽

10.2174/0929867324666170426095015 ◽

2018 ◽

Vol 25 (1) ◽

pp. 5-21 ◽

Cited By ~ 25

Author(s):

Ylenia Cau ◽

Daniela Valensin ◽

Mattia Mori ◽

Sara Draghi ◽

Maurizio Botta

Keyword(s):

Protein Interactions ◽

Molecular Mechanisms ◽

Physiological Role ◽

Specific Protein ◽

Protein Protein Interactions ◽

Cellular Processes ◽

Protein Partners ◽

High Sequence Homology ◽

Small Molecule Modulators

14-3-3 is a class of proteins able to interact with a multitude of targets by establishing protein-protein interactions (PPIs). They are usually found in all eukaryotes with a conserved secondary structure and high sequence homology among species. 14-3-3 proteins are involved in many physiological and pathological cellular processes either by triggering or interfering with the activity of specific protein partners. In the last years, the scientific community has collected many evidences on the role played by seven human 14-3-3 isoforms in cancer or neurodegenerative diseases. Indeed, these proteins regulate the molecular mechanisms associated to these diseases by interacting with (i) oncogenic and (ii) pro-apoptotic proteins and (iii) with proteins involved in Parkinson and Alzheimer diseases. The discovery of small molecule modulators of 14-3-3 PPIs could facilitate complete understanding of the physiological role of these proteins, and might offer valuable therapeutic approaches for these critical pathological states.

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Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states

eLife ◽

10.7554/elife.12509 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 56

Author(s):

Dan Tan ◽

Qiang Li ◽

Mei-Jun Zhang ◽

Chao Liu ◽

Chengying Ma ◽

...

Keyword(s):

Protein Interactions ◽

Structural Information ◽

Affinity Purification ◽

Protein Protein Interactions ◽

C Elegans ◽

Protein Protein Interaction ◽

Lysine Residues ◽

Spacer Arm ◽

Cross Linker ◽

Protein Nucleic Acid

To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation. By locating the flexible proteins on the surface of 70S ribosome, we show that this trifunctional cross-linker is effective at attaining structural information not easily attainable by crystallography and electron microscopy. From a crude Rrp46 immunoprecipitate, it helped identify two direct binding partners of Rrp46 and 15 protein-protein interactions (PPIs) among the co-immunoprecipitated exosome subunits. Applying it to E. coli and C. elegans lysates, we identified 3130 and 893 inter-linked lysine pairs, representing 677 and 121 PPIs. Using a quantitative CXMS workflow we demonstrate that it can reveal changes in the reactivity of lysine residues due to protein-nucleic acid interaction.

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Improvement of Upland Rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable Rice Production

Rice Science ◽

10.1016/j.rsci.2021.07.009 ◽

2021 ◽

Vol 28 (5) ◽

pp. 493-500

Author(s):

Vishalakshi Balija ◽

Umakanth Bangale ◽

Senguttuvel Ponnuvel ◽

Kalyani Makarand Barbadikar ◽

Srinivas Prasad Madamshetty ◽

...

Keyword(s):

Drought Tolerance ◽

Resistance Genes ◽

Upland Rice ◽

Blast Resistance ◽

Rice Variety ◽

Rice Production ◽

Blast Resistance Genes

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Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis

Jurnal Teknologi ◽

10.11113/jt.v63.1226 ◽

2013 ◽

Vol 63 (1) ◽

Cited By ~ 1

Author(s):

Geok Wei Leong ◽

Sheau Chen Lee ◽

Cher Chien Lau ◽

Peter Klappa ◽

Mohd Shahir Shamsir Omar

Keyword(s):

Protein Interactions ◽

Network Visualization ◽

Database Integration ◽

File Format ◽

Output File ◽

Ppi Network ◽

Protein Protein Interactions ◽

Computational Tools ◽

Protein Protein Interaction ◽

Visualization Tools

Several visualization tools for the mapping of protein-protein interactions have been developed in recent years. However, a systematic comparison of the virtues and limitations of different PPI visualization tools has not been carried out so far. In this study, we compare seven commonly used visualization tools, based on input and output file format, layout algorithm, database integration, Gene Ontology annotation and accessibility of each tool. The assessment was carried out based on brain disease datasets. Our suggested tools, NAViGaTOR, Cytoscape and Gephi perform competitively as PPI network visualization tools, can be a reference for future researches on PPI mapping and analysis.

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Expression-based genotyping of the rice blast resistance genes in the elite maintainer line Yixiang1B

European Journal of Plant Pathology ◽

10.1007/s10658-017-1149-1 ◽

2017 ◽

Vol 148 (4) ◽

pp. 955-965 ◽

Cited By ~ 1

Author(s):

Li Wang ◽

Xiao-Hong Hu ◽

Gang Lin ◽

De-Ming Zhao ◽

Jun Shi ◽

...

Keyword(s):

Resistance Genes ◽

Rice Blast ◽

Blast Resistance ◽

Maintainer Line ◽

Rice Blast Resistance ◽

Blast Resistance Genes

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Activation and assembly of the NADPH oxidase: a structural perspective

Biochemical Journal ◽

10.1042/bj20041835 ◽

2005 ◽

Vol 386 (3) ◽

pp. 401-416 ◽

Cited By ~ 369

Author(s):

Yvonne GROEMPING ◽

Katrin RITTINGER

Keyword(s):

Nadph Oxidase ◽

Protein Interactions ◽

Structural Information ◽

Three Dimensional ◽

Protein Protein Interactions ◽

Crucial Component ◽

Enzyme Subunits ◽

Membrane Components ◽

Inhibitory Interactions ◽

Encompassing Model

The NADPH oxidase of professional phagocytes is a crucial component of the innate immune response due to its fundamental role in the production of reactive oxygen species that act as powerful microbicidal agents. The activity of this multi-protein enzyme is dependent on the regulated assembly of the six enzyme subunits at the membrane where oxygen is reduced to superoxide anions. In the resting state, four of the enzyme subunits are maintained in the cytosol, either through auto-inhibitory interactions or through complex formation with accessory proteins that are not part of the active enzyme complex. Multiple inputs are required to disrupt these inhibitory interactions and allow translocation to the membrane and association with the integral membrane components. Protein interaction modules are key regulators of NADPH oxidase assembly, and the protein–protein interactions mediated via these domains have been the target of numerous studies. Many models have been put forward to describe the intricate network of reversible protein interactions that regulate the activity of this enzyme, but an all-encompassing model has so far been elusive. An important step towards an understanding of the molecular basis of NADPH oxidase assembly and activity has been the recent solution of the three-dimensional structures of some of the oxidase components. We will discuss these structures in the present review and attempt to reconcile some of the conflicting models on the basis of the structural information available.

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