## 9 Temporal Expression Patterns of Regulons and Couplons  
Analyses of the growth phase-dependent expression patterns of regulons and couplons (computed as average patterns of all the genes in the given regulon/couplon and normalized to 1.0; for details see legend to Supplementary Figure S6) show that the temporal patterns of the regulons of NAPs (FIS, H-NS and Lrp) and the corresponding NAP/RpoD couplons are highly correlated (Figure 6). Thus, not only the spatial organization, but also the temporal expression patterns of the NAP/RpoD couplons are positively correlated with those of NAP regulons. In contrast, the growth phase-dependent expression patterns of the NAP/ASF couplons correlate with those of the ASF (RpoS and RpoN) regulons (Figure 7). Thus again, both the spatial organization and the temporal expression patterns of the NAP/ASF couplons are positively correlated with those of ASF regulons. However, the temporal patterns of the IHF/ASF, CRP/ASF and Fnr/ASF couplons demonstrate positive correlations with both of the parent regulons (compare Figures 7 and 8), suggesting a joint impact of the latter on cognate couplon patterns. Thus it appears that the regulons have variable impacts on the temporal patterns of couplons. However, in that case, what determines the temporal patterns of regulons in the first place? Are the expression patterns of regulons determined by cognate regulators? Indeed, analyses showed that with notable exception of the _rpoH_ and _rpoE_ genes, in all cases a positive correlation obtains between the expression pattern of the regulatory gene and its cognate regulon (Figure 9). Since the expression of NAP genes is positively correlated with that of the NAP regulons, while the latter in turn appear determinative for the expression patterns of NAP/RpoD (but not the NAP/ASF) couplons (see Figure 6), this suggests that the temporal patterns of the NAP/RpoD couplons are, by and large, determined by expression patterns of the NAP genes. Conversely, the expression pattern of _rpoS_ gene positively correlates with that of the RpoS regulon, whereas this latter appears determinative for the patterns of corresponding NAP/RpoS couplons (Figure 7B), suggesting that temporal expression patterns of these couplons are ultimately determined by the expression pattern of _rpoS_ gene. Similar argument applies to _rpoN_ gene, RpoN regulon and RpoN couplons. By the same token, whenever the temporal patterns of couplons correlate positively with those of both parent regulons, as is the case with the IHF and global TF couplons (compare Figures 7 and 8), the assumption would be that the expression patterns of both regulatory genes jointly contribute to that of the couplons. The dependence of temporal regulon/couplon patterns on the regulating gene expression is corroborated by observed impacts of altered regulator gene expression on the expression of cognate couplons and/or regulons. For example, FIS is a repressor of _rpoS_ gene expression [114] and while inactivation of the _fis_ gene by mutation abolishes the down-regulation of the _rpoS_ gene expression in stationary phase (Figure 10; compare the grey dashed lines in A and B), the RpoS regulon and couplons react accordingly. Similarly, the _fis_ mutation affects the expression of _lrp_ gene and Lrp couplons and that of _lnts_ gene and H-NS couplons in a concerted manner (Figure 11). In all these cases altered regulator gene expression concomitantly alters the expression pattern of cognate couplons and/or regulon. Figure 6: Correlation between the temporal expression of NAP regulons and couplons. **(A)**. Growth phase-dependent expression of the FIS regulon, FIS/RpoD and FIS/ASF couplons. The colored curves were computed as average patterns of all the regulon/couplon genes and normalized to 1.0 (for details see legend to Supplementary Figure S6). Abscissa—time in minutes after inoculation of cells in fresh growth medium; ordinate—relative frequency of each class of genes as indicated in the inset. (**B**).