Analysis of the Transcriptome Dynamics of 

Virus-Infected Brachypodium distachyon

To identify molecular pathways affected by PMV/SPMV complex, we performed genome-wide expression analysis of PMV/SPMV infected Brachypodium distachyon plants at 7 day post-infection stage.  A custom-designed Affymetrix tiling array was utilized that covered all predicted exons and introns in ~27,000 genes with multiple probes.  In summary, we found expression of approximately 621 and 433 genes significantly up- and down-regulated in PMV/SPMV co-infection, respectively (Figure 1) (Mandadi and Scholthof, 2012). PMV alone infection resulted in 464 up- and 326 down-regulated genes.

Preliminary functional annotation of the mis-expressed genes revealed that PMV and PMV/SPMV infection affected genes in primary metabolism, metabolite transport, defense, and cell-wall remodeling, etc and suggests an altered metabolic fate of the infected cells (Figure 2).  Among the induced genes, detoxification and stress-responsive transcripts corresponding to Glutahione-S-transferaseCytochrome P450, Heat-shock proteins, etc were over-represented.  In the down regulated genes, photosynthesis related transcripts corresponding to Chlorophyll A/B binding and Photosystem-related proteins were predominant.  The latter result may explain the chlorosis symptoms and lowered Chlorophyll A and Chlorophyll B levels (Mandadi and Scholthof, 2012) in the infected plants.  Importantly, we identified several proteins involved in signal transduction and transcription factors that were mis-regulated by PMV/SPMV.  Ongoing work in the lab is aimed to characterize these candidate proteins and determine their biological significance in PMV/SPMV infection.