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. 2009 Sep 18;4(9):e7073. doi: 10.1371/journal.pone.0007073

Figure 2. Rapidly AA-responsive Genes.

Figure 2

(A) Venn diagrams about the number of rapidly Val-, Glu-, and Gln-responding genes: all three-fold responsive genes at 5 min; the three-fold induced genes at 5 min; the three-fold repressed genes at 5 min; There are four genes (yhgD, pel, cydA, and cydB) showing converse expression between Val and Glu; one gene ilvB, showing converse expression between Val and Gln. (B) Classification of all amino acid-responsive genes: All valine-(Val), glutamate-(Glu), and glutamine-(Gln) responsive genes with known-function were classified according Subtilist Database (http://genolist.pasteur.fr/SubtiList/). 1, Cell wall; 2, Transport/binding proteins and lipoproteins; 3, Sensors (signal transduction); 4, Membrane bioenergetics; 5, Mobility and chemotaxis; 6, Protein secretion; 7, Cell division; 8, Sporulation; 9, Germination; 10, Specific pathways; 11, Main glycolytic pathways; 12, TCA cycle; 13, Metabolism of amino acids and related molecules; 14, Metabolism of nucleotides and nucleic acids; 15 Metabolism of lipids; 16, Metabolism of coenzymes and prosthetic groups; 17, Metabolism of phosphate; 18, Metabolism of sulfur; 19, DNA recombination; 20, RNA synthesis; 21, Protein synthesis; 22, Adaptation to atypical conditions; 23, Detoxification; 24, Antibiotic production; 25, Phage-related functions; 26, Transposon and IS. (C) Three expression categories of rapidly responsive genes: In category 2 of valine (Val-Cat 2), cydBC genes, encoding cytochrome bd ubiquinol oxidase and ABC membrane transporter, were upregulated at 5 min, whereas downregulated after 30 min.