# The _E. coli_ Global Regulator DksA Reduces Transcription during T4 Infection
## 4 Discussion
Increased transcription from specific Pe's in the \(\Delta\)dksA strain also explains the increased growth of T4\(motA^{am}\) (Figure 1b). It has been well established that T4\(motA^{am}\) severely impairs phage infection by depressing middle transcription. We observe that the improved fitness of T4\(motA^{am}\) in the \(\Delta\)dksA strain correlates with a greater abundance of middle RNA. However, this increase in middle transcripts does not arise from Pm's, but rather from increased transcription from Pe's upstream of middle genes required for replication, recombination, and late transcription (Figure 3). Thus, the increase in Pe transcription compensates for the lack of Pm activation. Presently, it is unclear how DksA exerts an effect on specific Pe's. The results of our in vitro transcription analyses argue that this effect is probably indirect. A comparison of the discriminator region [61; 62] of Pe's whose transcripts were down-regulated vs. those whose transcripts were unchanged does not reveal an obvious sequence motif that typically correlates with DksA reduction of promoter activity. We speculate global host changes that arise from deletion of DksA are likely to be responsible for the enhancement of T4 Pe transcription. In fact, global changes in gene expression during exponential growth have been previously reported for \(\Delta\)dksA [21]. It is important to note, however, that we do not observe a major growth defect in B606 \(\Delta\)dksA during early-exponential phase at the time of T4 infection. Instead the growth defect is seen during stationary phase (Figure S3). This is likely due to decreased \(rpoS\) expression in the \(\Delta\)dksA mutant [73], which regulates expression of genes important for the transition into stationary phase. Although the absence of either DksA or ppGpp results in larger T4 plaques (Figure 1a and Figure S2b), the lack of DksA increases burst size by 2-fold (Figure 2b) and has dramatic effects on T4 gene expression, while ppGpp\({}^{0}\) has no significant effect on burst size or latent period (Figure S4) and has only modest effects on gene expression (Table S2). In the host, ppGpp functions predominately at the level of transcription to adjust gene expression as necessary to overcome stress and to minimize processes that have become superfluous by growth inhibition. Cells that are ppGpp deficient for lack of _spoT_ and _relA_ genes become vulnerable to a variety of physiological stress conditions. As a result, ppGpp\({}^{0}\) cells devote all resources to a full complement of biosynthetic capacity including ribosome content regardless of nutritional adequacy [74]. Since T4 phage infection almost instantly pirates cellular biosynthetic functions and components to devote them exclusively to phage production, perhaps it can be expected that phage development would improve in the absence of ppGpp. Deficiency of ppGpp could alter plaque size without altering burst size, latent period, and/or transcription because plaque size is also governed by properties of inner membranes, peptidoglycan and outer membranes, and the activities of pinholins and spanin complexes (reviewed by [75]). In fact, there is evidence of involvement of ppGpp in altered membranes and phospholipid synthesis that can result in membrane fragility [76; 77]. The enigmatic absence of regulatory effects associated with ppGpp might indicate the need for different conditions to detect effects of ppGpp on T4 burst size and latent period. For example, slow growth in minimal medium with a poor carbon source, which elevates the level of ppGpp, might give different results than a rich nutrient broth where the cellular ribosomal content is high and the ppGpp concentration is very low at the onset of infection. It also might be revealing to measure ppGpp levels during phage T4 lytic development to evaluate if ppGpp levels change. Alternatively, ppGpp levels could be artificially elevated to high levels at the onset of T4 infection to ask if development is altered.