The regulation of host translation initiation in plant-pathogen interactions
Pathogens dramatically alter plant mRNA transcript levels by activating and repressing a variety of signaling pathways. However, the effects of plant pathogens on host mRNA translation have not been explored on a genome-wide scale. To assess pathogen-induced changes in host mRNA transcription and translation, we conducted DNA microarray analysis of total and polyribosomal RNA fractions in the Arabidopsis thaliana–Turnip mosaic virus (TuMV) and barley-powdery mildew (Hordeum vulgare–Blumeria graminis f.sp. hordei (Bgh)) interactions. The ratios of mRNA transcript abundance in total versus polyribosomal RNA fractions were compared between inoculated and non-inoculated sample types to identify mRNAs that were differentially regulated at the level of translation. The majority of mRNA transcripts had ratios that were consistent for the non-inoculated and inoculated treatments indicating that they were not differentially translated. However, infection did alter the mRNA transcript abundance of a subset of genes in polyribosomal RNA independent of the abundance of these transcripts in total RNA in both Arabidopsis and barley. In both hosts, approximately one-half of these mRNAs had enhanced association with polyribosomal RNA in response to inoculation while the other half had reduced association with polyribosomal RNA. These results suggest that pathogen infection can cause either enhanced or reduced translation of select sets of plant mRNAs. Analysis of the sequence features of mRNAs that were differentially associated with polyribosomal RNA suggest that TuMV infection leads to a decreased ability to translate mRNAs containing upstream AUG sequences and an increased ability to translate mRNAs with short 5' and 3' UTRs. Sequence analyses of the selectively translated mRNAs identified in barley (using rice orthologs as a surrogate) showed that the compatible interaction was strongly correlated with decreased length and significant mono– and di–nucleotide frequencies. Analysis of overrepresented gene function categories among selectively translated mRNAs identified related sets of genes that were unique to each interaction as well as gene sets that were identified in common to the interactions. In both host-pathogen interactions, a comparison of induced and repressed transcripts of the total and polyribosomal RNA fractions indicated that approximately 10% of interesting mRNA transcripts would be misidentified or not identified if expression profiling was only performed on the total RNA fraction. This work establishes that many host mRNAs are selectively translated in response to pathogen inoculation. Furthermore, many of these mRNAs are overrepresented among groups of genes with specific biological functions, and mRNA sequence features are strongly correlated with particular patterns of selective translation.