Transcription of rRNAs in Escherichia coli is directed from seven redundant rRNA operons, which are mainly regulated by their P1 promoters. Here we demonstrate by in vivo measurements that the amounts of individual rRNAs transcribed from the different operons under normal growth vary noticeably although the structures of all the P1 promoters are very similar. Moreover, we show that starvation for amino acids does not affect the seven P1 promoters in the same way. Notably, reduction of transcription from rrnD P1 was significantly lower compared to the other P1 promoters. The presence of DksA was shown to be crucial for the ppGpp-dependent downregulation of all P1 promoters. Because rrnD P1 is the only rrn promoter starting with GTP instead of ATP, we performed studies with a mutant rrnD promoter, where the initiating G+1 is replaced by A+1. These analyses demonstrated that the ppGpp sensitivity of rrn P1 promoters depends on the nature and concentration of initiating nucleoside triphosphates (iNTPs). Our results support the notion that the seven rRNA operons are differentially regulated and underline the importance of a concerted activity between ppGpp, DksA and an adequate concentration of the respective iNTP.
INTRODUCTIONThe rapid adaptation of cell growth in response to changing environmental conditions is central for the fitness and survival of bacteria. Bacterial growth rate is largely determined by the number of ribosomes. Hence, regulation of the translational components plays a central role in adaptation. The biogenesis of ribosomes, representing one of the cell's most energy-intensive activities, is governed by a complex network of regulation (Schneider et al., 2003;Wagner, 2009). The key molecules in this network are rRNAs. In contrast, the synthesis of ribosomal proteins, despite having similar regulatory mechanisms to those for rRNA, is largely linked to rRNA transcription by a translational feedback mechanism, which couples ribosomal protein translation to the amount of available rRNAs (Keener & Nomura, 1996;Lemke et al., 2009;Nomura et al., 1984). Therefore, the precise adjustment of rRNA synthesis rate to the nutritional quality and supply from the environment ensures that an appropriate number of ribosomes will be produced and energy resources are not wasted (Condon et al., 1995b;Wagner, 1994Wagner, , 2009).In Escherichia coli, rRNA genes (16S, 23S and 5S rRNA), together with at least one tRNA gene, are organized in a redundant fashion in seven different transcriptional units (the rrnA, rrnB, rrnC, rrnD, rrnE, rrnG and rrnH operons). Although the seven ribosomal operons exhibit a high structural similarity, there are several striking sequence micro-heterogeneities, which could potentially contribute to functionally different ribosome populations (Wagner, 2009). Evidence for such specialized ribosomes in various organisms has been presented (Gunderson et al., 1987;Kim et al., 2007; Ló pez-Ló pez et al., 2007). If the different rRNA operons encode functionally distinct molecules one would expect tha...
