An integrated RNA-Seq and proteomics profile following Fusarium venenatum elicitation reveals major patterns of gene expression and translational re-programming in maize
Maize is a major staple food crop with important agricultural and agronomic impact worldwide. However, fungi of the genus Fusarium can cause diseases in maize, resulting in significant economic losses. Immunity requires both transcriptional and translational regulation for an effective defense response. To investigate how fungal challenge affects maize, we generated RNA-Seq and proteomics data from plants that had been challenged with heat-killed Fusarium venenatum hyphae over a ten-point time course. Our findings indicated that maize can exhibit different transcriptional and translational responses to fungal elicitation. Weighted gene co-expression network analysis (WGCNA) resulted in identification of a module in which RNA does not change over time and protein abundance increases, providing examples of translational re-programming in maize. GO analysis on the genes in this module revealed enrichment for protein modifications and vesicle-mediated transport. Performing WGCNA on the fold change rank orders yielded four main patterns of RNA and protein expression. In the largest rank-order module, RNA and protein abundance both decreased over time; this module was most enriched for genes involved in plant development, providing evidence for the shift from growth towards defense. The next three largest modules exhibited increasing protein abundance, and were enriched for genes involved in ubiquitination and responses to stimuli, which are all involved in defense. Surprisingly, about 15% of detected genes are in Module 2 and tend to have decreasing RNA expression and increasing protein abundance. Transcriptional and proteomic analyses will promote greater understanding of the complex regulation of the plant response to pathogen challenge.