Supplementary Material for: Global Gene Expression Profiling of <i>Bacillus subtilis</i> in Response to Ammonium and Tryptophan Starvation as Revealed by Transcriptome and Proteome Analysis

The global gene expression profile of <i>Bacillus subtilis</i> in response to ammonium and tryptophan starvation was analyzed using transcriptomics and proteomics which gained novel insights into these starvation responses. The results demonstrate that both starvation conditions induce specific, overlapping and general starvation responses. The TnrA regulon, the glutamine synthetase (<i>glnA</i>) as well as the σ<sup>L</sup>-dependent <i>bkd</i> and <i>roc</i> operons were most strongly and specifically induced after ammonium starvation. These are involved in the uptake and utilization of ammonium and alternative nitrogen sources such as amino acids, γ-aminobutyrate, nitrate/nitrite, uric acid/urea and oligopeptides. In addition, several carbon catabolite-controlled genes (e.g. <i>acsA</i>, <i>citB</i>), the α-acetolactate synthase/-decarboxylase <i>alsSD </i>operon and several aminotransferase genes were specifically induced after ammonium starvation. The induction of σ<sup>F</sup>- and σ<sup>E</sup>-dependent sporulation proteins at later time points in ammonium-starved cells was accompanied by an increased sporulation frequency. The specific response to tryptophan starvation includes the TRAP-regulated tryptophan biosynthesis genes, some RelA-dependent genes (e.g. <i>adeC, ald</i>) as well as <i>spo0E</i>. Furthermore, we recognized overlapping responses between ammonium and tryptophan starvation (e.g. <i>dat</i>, <i>maeN</i>) as well as the common induction of the CodY and σ<sup>H</sup> general starvation regulons and the RelA-dependent stringent response. Many genes encoding proteins of so far unknown functions could be assigned to specifically or commonly induced genes.