Abstract
BackgroundIn order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar.ResultsQuantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets.ConclusionsIn summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-497) contains supplementary material, which is available to authorized users.
Highlights
In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum)
Overview of differentially expressed genes and changes in protein abundance In order to study stress responses in plant–oomycete interactions, we performed time series analyses of two incompatible interactions (Sarpo Mira and SW93-1015) and one compatible interaction (Desiree) with P. infestans (SE-03058). This was performed at a global level using genome-wide microarrays to determine gene expression changes and short 1D-gel separation followed by MS/ MS analysis on a LC-coupled Orbitrap mass spectrometer to determine quantitative changes in apoplastic protein levels
In our genome-wide array, 17451 transcripts were significantly differentially expressed relative to uninoculated control in at least one time point in one or more clones during the course of P. infestans challenge (Table 1)
Summary
In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). A large number of extracellular and cytoplasmic effectors in the P. infestans genome have been identified [6,7] and increasing evidence for their role in establishing ETS exists. Knowledge about their targets in the plant host is scarce, mainly because of the limited availability of hemibiotrophic pathogens with susceptible interactions with the model species Arabidopsis [8]. Kazal-like extracellular serine protease inhibitors EPI1 and EPI10 inhibit the P69B subtilisinlike serine protease in tomato [9,10], while others such as the cystatin-like protein target cysteine-proteases [11] and EPIC1 and EPIC2B inhibit papain-like cysteine protease RCR3, in the same plant [12]. P. infestans has several xyloglucan-specific endoglucanases while the potato genome includes ten clustered genes for xyloglucans-specific endoglucanase inhibitor proteins (XEGIPs) [15]
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