E-GEOD-43648 - Examining gene expression of the fungus Magnaporthe oryzae during challenge with the bacterium Lysobacter enzymogenes

Released on 1 October 2013, last updated on 25 November 2013
Magnaporthe oryzae
Samples (12)
Protocols (3)
Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While basal defenses in these organisms are well studied, there is almost a complete lack of understanding of such systems in fungal species, and more specifically, how they are able to detect and mount a defense response upon pathogen attack. Hence, the goal of the present study was to understand how fungi respond to biotic stress by assessing the transcriptional profile of the rice blast pathogen, Magnaporthe oryzae, when challenged with the bacterial antagonist Lysobacter enzymogenes. Based on microscopic observations of interactions between M. oryzae and wild-type L. enzymogenes strain C3, we selected early and intermediate stages represented by time-points of 3 and 9 hours post-inoculation, respectively, to evaluate the fungal transcriptome using RNA-seq. For comparative purposes, we also challenged the fungus with L. enzymogenes mutant strain DCA, previously demonstrated to be devoid of antifungal activity. A comparison of transcriptional data from fungal interactions with the wild-type bacterial strain C3 and the mutant strain DCA revealed 463 fungal genes that were down-regulated during attack by C3; of these genes, 100 were also found to be up-regulated during the interaction with DCA. Functional categorization of genes in this suite included those with roles in carbohydrate metabolism, cellular transport and stress response. One gene in this suite belongs to the CFEM-domain class of fungal proteins. Another CFEM class protein called PTH11 has been previously characterized, and we found that a deletion in this gene caused advanced lesion development by C3 compared to its growth on the wild-type fungus. We discuss the characterization of this suite of 100 genes with respect to their role in the fungal defense response. Included in the analysis are two biological replicates each of the fungus in buffer alone (control), the fungus challenged with wild type bacterium at 3 and 9 hours post-inoculation (hpi) and the fungus challeged with the mutant bacterium (mutated for ability to secrete antibiotics and enzymes) at 3 and 9 hpi.
Experiment type
RNA-seq of coding RNA 
Sridhara G Kunjeti <sridhara@udel.edu>, Bianca Riddick, Donald Y Kobayashi, James A Sweigard, Jeffrey L Caplan, Kirk J Czymmek, Nicole M Donofrio, Nrupali Patel, Sandra M Mathioni, Saritha Kunjeti, Vidhyavathi Raman
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-43648.idf.txt
Sample and data relationshipE-GEOD-43648.sdrf.txt
Additional data (1)E-GEOD-43648.additional.1.zip