Subcellular Localization and Prediction of Qualitative Expression of the Proteome of Sorghum and Maize

Study of the regulation and location of the protein products of genes is essential for understanding the phenotype of the organism. The quantitative and qualitative control of protein production, as well as post-translational modification and subcellular localization of the protein, in part determine the effect of a gene on a biological system. As it becomes more apparent that complex traits are controlled by effects from many loci, it has become more imperative that we seek a proteome-wide understanding of protein regulation and localization. The proteomes of four maize subcellular organelles were characterized by comparison to their source tissues, defining both organelle-enriched and depleted protein sets. High confidence localizations to organelle were obtained for plasma membranes (2154), mitochondria (1079), glyoxysomes (461), and plastids (539). Many cases of localization were novel or revised existing annotations, including that of nearly 40% of localized maize classical genes. Many proteins localized to multiple compartments, including a large overlap between mitochondrial and chloroplast proteins, whereas few proteins were shared between the chloroplast and non-mitochondrial organelles. A machine learning approach was used to identify the expressible gene sets of sorghum and gene set annotations from versions 2 and 4 of the maize genome. These gene sets were identified by a classifier trained using only DNA methylation data as model features. Synteny was leveraged to identify species-specific expressible genes, revealing enrichment of biotic and abiotic stress-associated genes in the species-specific pools. Expressible gene sets also provide evidence for express-ability of gene models absent from the maize version 2 annotated filtered gene set or the maize version 4 annotated gene set.