According to Flor's hypothesis a gene interacts with another gene in gene-for-gene manner where an incompatible reaction occurs ultimately providing resistance to plants against microbes. Though many resistance genes have been cloned for a variety of crop plants. But in comparison to resistance genes, corresponding avirulence genes from plant pathogens are scarce. So in order to assay plant-microbe interaction using Bioinformatics approach one need to have both the gene sequence and later on can be assessed for protein-protein interaction. Anyone working in this field can help me?
I am entering the field.
From what I know, oomycetes are common playground in this. For instance, Brad Day from Michigan State has discovered many avirulence genes during Pseudoperonospora cubensis attack on cucumbers, via RNAseq ([email protected]):
mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection
EA Savory, BN Adhikari, JP Hamilton, B Vaillancourt, CR Buell, B Day
PloS one 7 (4), e35796
Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis
BN Adhikari, EA Savory, B Vaillancourt, KL Childs, JP Hamilton, B Day, CR Buell
PloS one 7 (4), e34954
Alternative splicing of a multi-drug transporter from Pseudoperonospora cubensis generates an RXLR effector protein that elicits a rapid cell death
EA Savory, C Zou, BN Adhikari, JP Hamilton, CR Buell, SH Shiu, B Day
PloS one 7 (4), e34701
Dear Dr. Marcin Nowicki,
I really appreciate the way you have explained and have provided the research papers in connection with this.
But mine problem is this in order to study gene-gene for hypothesis at molecular level , I mean at protein-protein level one should look for what kind of interaction. Sir I am really interested in in this aspect where high-throughput computational techniques can be applied to understand the the plant-microbe interaction especially in cereals.
No need to thank me; that's what we're here for!
The answer is: after employment of RNA-seq (and computational data analysis), Day et al. were able to identify potential effectors in their pathosystem, later to be confirmed by for instance by protein-protein interaction assays. Hope this clarifies the issue.
They published several papers on the topic, since the story's rather big ;)
Also,
http://ppg.cfans.umn.edu/presentations/Gao%20et%20al%20PAG%202012.pdf
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology