# The _E. coli_ Global Regulator DksA Reduces Transcription during T4 Infection
## 3 Results
### Reduction of Early Promoter Activity during T4 wt Infection in the Presence of DksA  
Having established that the RNA analyses of T4 wt vs. T4_motA_m_ infections yielded expected results, we investigated gene expression in T4 infections of B606 wt or B606 \(\Delta\)_dksA_ to ask whether DksA reduction of T4 progeny is related to T4 gene expression. In a T4 wt infection at 5 min, the absence of DksA resulted in a 2-fold or greater increase in expression of genes downstream of several Pe's: Pe11.5, Pe12.8, Pe15.0, Pe40.4, Pe57954, Pe57.9, Pe69.9, and Pe69.4 (Figure 3). Only a small subset of the genes in these regions have been functionally characterized. The genes that have been characterized to date have been implicated in host takeover through modification of transcriptional machinery (_modA_, _modB_, _srh_, _mrh_) or degradation of host nucleic acid (_mobD_, _mudE_) [53]. RNA-seq was performed for the 5 min samples and RT-qPCR was used to independently assess the differential expression of 49 selected genes. The fold changes determined by RT-qPCR demonstrated a strong correlation with those determined by RNA-seq, thus confirming results of the RNA-seq analysis (Figure S5b). In addition, primer extension analyses were performed for RNA isolated at 1, 5, and 12 min post-infection. Primer extension analyses also revealed a significant increase in transcription from Pe35.3, Pe40.4, and Pe41 (Figure S6b). In contrast, transcription from Pm's was unaffected or only very modestly affected (Pm45, Pm45.2) by the absence of DksA (Figure S6a). The increase in Pe transcription was not general. For example, no significant increase was observed for Pe148.6 (Figure S6b) and Pe144.6 (Figure S7), two Pe's whose downstream gene expression levels also did not increase in the RNA-seq analysis (Figure 3). Somewhat surprisingly, the expression level of several late genes (Figure 3) and the level of transcription from the corresponding Pl's (Figure S7a) was significantly less at 5 min post-infection in the absence of DksA. Since this result is not compatible with an increase in burst size, we asked whether this decrease in late transcription was reversed at 12 min post-infection, when the level of late transcription in a wt infection is high. Primer extension analyses revealed that the level of RNA from these and other selected late promoters recovered well by this time point (Figure S7b). Taken together, our results are consistent with a role of DksA in lowering the burst of T4 wt phage in a wt infection by decreasing the level of transcription from many Pe's. As mentioned above, the function of many early genes remains unknown. However, these early genes are predicted to be involved in host takeover and transition to middle gene expression [53]. It is plausible that a fitness gain early in infection will cascade to increased progeny production as the infection progresses. Middle Gene Expression is Partially Restored in a T4 motA\({}^{am}\) Infection of B606 \(\Delta\)dksA  
The absence of DksA alleviated the poor growth of T4_motA\({}^{am}\)_ by significantly decreasing the latent period (Figure 2). To determine if DksA affects gene expression in the T4_motA\({}^{am}\)_ infection, RNA-seq, RT-qPCR, and primer extension analyses were performed after isolating RNA from T4_motA\({}^{am}\)_ infections in the presence (B606 wt) or absence (B606 \(\Delta\)dksA) of DksA. The overall result of these analyses is that the DksA deletion partially ameliorates the poor expression of many T4 middle genes through the increase in transcription from certain Pe's. This result is most easily seen in Figure 3, in which expression levels of T4 genes are color coded to designate the extent of increase (shades of red) or decrease (shades of green).