The chemolithotrophic
ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to
starvation conditions. The transcriptional response of N. europaea to
ammonia addition following short- and long-term
starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding
enzymes for
ammonia oxidation (amoCAB operons) and CO(2) fixation (cbbLS), a third, lone copy of amoC (amoC(3)), and two representative housekeeping genes (glyA and rpsJ). Primer extension analysis of
RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two amoCAB operons. The distal
sigma(70) type amoCAB promoter was constitutively active in the presence of
ammonia, but the proximal promoter was only active when cells were recovering from
ammonia starvation. The lone, divergent copy of amoC (amoC(3)) was expressed only during recovery. Both the proximal amoC(1,2) promoter and the amoC(3) promoter are similar to gram-negative sigma(E) promoters, thus implicating sigma(E) in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative
proline substitution in AmoC(3) may modify the activity of the
holoenzyme, characterization of a DeltaamoC(3) strain showed no significant difference in
starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO(2) fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from
starvation likely involving regulation by sigma(E) and the coordinated regulation of catabolic and anabolic genes.