Figure 2

Two modes of regulation of the translation apparatus. (A) We examined changes in transcript levels (top) and in translation efficiency (TE; bottom), in each condition relative to control proliferating cells, of two functional modules of the translational apparatus: ribogenesis genes (left) and ribosomal protein genes (right). P-values were calculated for each condition by comparing changes observed for the test gene-set and for a background set containing all the other transcripts in the dataset; Wilcoxon test. The figure shows that while the ribosomal protein genes were strikingly and exclusively regulated at the layer of mRNA translation, regulation of ribogenesis genes was enforced at the transcriptional level, and to a lesser extent, in some conditions also at the level of translation. (B) A comprehensive map of the translational apparatus generated using the SPIKE knowledgebase of signaling pathways. The map contains five types of nodes (violet nodes represent genes/proteins; green, protein complexes; yellow, gene families; pink, biological functions or states (for example, 'translation elongation'); and orange, signaling molecules (for example, AMP)), and two types of edges (blue edges represent regulatory relationship between nodes; arrow for activation and T-shaped edges for inhibition; green edges represent associations between gene families or protein complexes and their members). Genes that were repressed in response to energy stress (quiescence state) in our dataset at the transcriptional or the translational levels are colored, respectively, by orange or brown bars to the left of their nodes. (Red and green dots within nodes indicate that the nodes have additional regulation and association relationships in the in SPIKE database that are not displayed in the map to reduce clutter).