## 6 Indirect Regulation of Alternative \(\sigma\) Factors by Primary \(\sigma\) Factor Control  
In _E. coli_, \(\sigma^{70}\) has a higher affinity for RNAP than alternative \(\sigma\) factors and is present in excess of RNAP that is not involved in elongation [94; 95; 96]. This generates a competitive environment and raises the question of how alternative \(\sigma\) factors can effectively access RNAP. Under conditions (e.g., nutrient starvation) where the expression of growth-related genes such as rRNA operons is rapidly reduced, the resulting increase in free core RNAP would be expected to lead to a passive rise of alternative holoenzyme forms [97]. An alternative mechanism is to sequester \(\sigma^{70}\), which appears to be the role of Rsd in _E. coli_. Rsd was discovered in a search for an anti-\(\sigma\) factor that might promote \(\sigma^{\text{S}}\) activity during stationary phase [98]. As is the case for other anti-\(\sigma\) factors, Rsd interacts with both \(\sigma^{70}\)\({}_{2}\) and \(\sigma^{70}\)\({}_{4}\) domains [99] with the latter shown to prevent binding both to the \(\beta\)-flap-tip-helix and to \(-\)35 promoter elements [100]. Interestingly, although there is only a two-fold increase in Rsd from exponential to stationary phase, Rsd associates effectively with \(\sigma^{70}\) only during stationary phase [95]. A possible explanation is that Rsd can alternatively bind the non-phosphorylated form of the phosphoenolpyruvate-dependent phosphotransferase system (PTS) control protein HPr, which is the dominant form of HPr when cells are growing exponentially with glucose as carbon source [101]. HPr therefore appears to act through a partner-switching type mechanism with Rsd to control levels of \(\sigma^{70}\) holoenzyme. Nonetheless, the importance of Rsd in _E. coli_ remains enigmatic because null mutants have little discernable phenotype. Whereas Rsd was identified biochemically, its orthologue AlgQ in _Pseudomonas aeruginosa_ was identified genetically as a positive regulator for alginate production, a key virulence factor that contributes to long term persistence of chronic lung infections in cystic fibrosis patients [102]. The key enzyme for alginate production is encoded by _algD_, which is transcribed by the ECF \(\sigma\) factor \(\sigma^{\text{AlgU}}\)[103]. The evolution of mucoid strains that overproduce alginate often occurs as a result of mutations in the downstream encoded anti-sigma factor MucA [104; 105]. The expression of _algD_ additionally relies on AlgQ (also known as AlgR2), which is 55% identical to Rsd and binds to \(\sigma^{70}\) in _Pseudomonas_ spp. [106; 107]. It has therefore been proposed that AlgQ activates \(\sigma^{\text{AlgU}}\) indirectly, by sequestering \(\sigma^{70}\)[107]. Consistent with such an indirect effect, AlgQ also affects the expression of pyoverdine uptake and production genes by \(\sigma^{\text{PvdS}}\) and \(\sigma^{\text{PpvI}}\). AlgQ mutants show reduced levels of pyoverdine, which can be suppressed by the over-expression of \(\sigma^{\text{PvdS}}\) or augmented by the over-expression of \(\sigma^{70}\)[108]. An interesting future question is whether HPr also plays a role in _Pseudomonas aeruginosa_, linking alginate, siderophore and other virulence gene expression to central metabolism.