Innovation, conservation, and repurposing of gene function in root cell type development Graphical abstract Highlights d Tomato cell type-resolution translatome atlas reveals cell type function d Conservation and repurposing in gene regulation between Arabidopsis and tomato d The tomato exodermis is lignified, suberized, and enriched for nitrogen regulation d The root meristem is molecularly homologous across plant species

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Determining the complete Arabidopsis (Arabidopsis thaliana) protein-protein interaction network is essential for understanding the functional organization of the proteome. Numerous small-scale studies and a couple of large-scale ones have elucidated a fraction of the estimated 300,000 binary protein-protein interactions in Arabidopsis. In this study, we provide evidence that a docking algorithm has the ability to identify real interactions using both experimentally determined and predicted protein structures. We ranked 0.91 million interactions generated by all possible pairwise combinations of 1,346 predicted structure models from an Arabidopsis predicted "structure-ome" and found a significant enrichment of real interactions for the topranking predicted interactions, as shown by cosubcellular enrichment analysis and yeast two-hybrid validation. Our success rate for computationally predicted, structure-based interactions was 63% of the success rate for published interactions naively tested using the yeast two-hybrid system and 2.7 times better than for randomly picked pairs of proteins. This study provides another perspective in interactome exploration and biological network reconstruction using protein structural information. We have made these interactions freely accessible through an improved Arabidopsis Interactions Viewer and have created community tools for accessing these and ;2.8 million other protein-protein and protein-DNA interactions for hypothesis generation by researchers worldwide. The Arabidopsis Interactions Viewer is freely available at http://bar.utoronto.ca/interactions2/. Proteins rarely work alone, and most of the time they function in concert with other proteins or macromolecules. In Arabidopsis (Arabidopsis thaliana), the total number of binary interactions is estimated to be around 300,000 (Arabidopsis Interactome Mapping Consortium, 2011), but so far, only a small fraction of those interactions have been studied. Currently, there are 36,329 experimentally confirmed and 70,944 interolog-predicted protein-protein interactions (PPIs) in the Bio-Analytic Resource (BAR) interactions database (Geisler-Lee et al., 2007) that can be queried through the Arabidopsis Interactions Viewer (AIV). This huge gap indicates there is still a long way to go in elucidating the Arabidopsis interactome, both experimentally and computationally. With the arguable exception of the yeast two-hybrid method (Arabidopsis Interactome Mapping Consortium, 2011) or split ubiquitin method (Chen et al., 2012), traditional experimental methods for determining PPIs, such as mass spectrometry (Van Leene et al., 2007), protein microarrays (Popescu et al., 2007), and others (Zhang et al., 2010; Fukao, 2012), cannot readily be extended to determine the whole Arabidopsis interactome. Interolog-based computational PPI prediction methods (Geisler-Lee et al., 2007) can have a large-scale predictive ability but cannot

Plant species have evolved myriads of solutions to adapt to dynamic environments, 35 including complex cell type development and regulation. To understand this diversity, we profiled tomato root cell type translatomes and chromatin accessibility. Using xylem differentiation in tomato, relative to Arabidopsis, examples of functional innovation, repurposing and conservation of transcription factors are described. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Translatome 40 analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, and that the functions of constitutively expressed genes are more conserved than those of cell 45 Arabidopsis inflorescence stem vascular bundles and is not expressed in primary root xylem 4 (15), and two HD-ZIPIII TFs, SlPHB/PHV (Solyc02g069830) and SlCORONA (Solyc03g120910), whose Arabidopsis orthologs regulate root protoxylem vessel differentiation via positional signals derived from a miR165/166 gradient (2,11,16). Contrary to their function in Arabidopsis, over-expression of SlbZIP11 or SlKNAT1 was sufficient to specify additional protoxylem cell files ( Fig. 2C-D), although these files were often non-contiguous for the 5 SlbZIP11 lines (Fig. 2C) (statistical analyses in Fig. S5, Data S3). The bHLH and MYB overexpression lines had no vascular phenotype. Relative to Arabidopsis, In the case of SlKNAT1, this demonstrates "repurposed" regulation, while in the case of SlbZIP11 it represents innovation in function. miRNA-resistant versions of SlCORONA and SlPHB/PHV were sufficient to regulate protoxylem vessel identity and patterning within the vascular cylinder 10 similar to their Arabidopsis function and are thus conserved regulators (Fig. 2D, E).Cell type/tissue translatomes are likely dynamic over developmental time and in response to the environment. In Arabidopsis, cell type-enriched genes that maintain expression despite stress are also critical regulators of cell fate (3, 17). However, the majority of plant cell type profiles are 15

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