The global gene expression profile of Bacillus subtilis 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 (glnA) as well as the sigma(L)-dependent bkd and roc 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, gamma-aminobutyrate,
nitrate/
nitrite,
uric acid/
urea and
oligopeptides. In addition, several
carbon catabolite-controlled genes (e.g. acsA, citB), the
alpha-acetolactate synthase/-
decarboxylase alsSD operon and several
aminotransferase genes were specifically induced after
ammonium starvation. The induction of sigma(F)- and sigma(E)-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. adeC, ald) as well as spo0E. Furthermore, we recognized overlapping responses between
ammonium and
tryptophan starvation (e.g. dat, maeN) as well as the common induction of the CodY and sigma(H) 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.