# The _E. coli_ Global Regulator DksA Reduces Transcription during T4 Infection
## 3 Results
### Deletion of dksA Results in a Shorter Latent Period in a T4 motA\({}^{am}\) Infection  
Similar burst size experiments were also performed with T4_motA\({}^{am}\)_. In this case, we did not observe a significant difference in burst size for T4_motA\({}^{am}\)_ in host wt vs. \(\Delta\)_dksA_ strain (Figure 2a,c). However, in the absence of DksA, there was a 10 min decrease in the latent period, indicating a significantly faster infection (Figure 2a,c). Global Transcriptome of the T4 motA\({}^{am}\) Infection Reveals that Pm's Are Differentially Affected  
To investigate the effect of DksA on gene expression in a T4 wt or T4_motA\({}^{am}\)_ infection, we first collected detailed information on gene expression alterations in a T4_motA\({}^{am}\)_ infection of B606 wt. Although extensive work has established that _motA_ is required for activation of T4 middle promoters, a global transcriptome analysis of the _motA_ regulon has not been reported. It should be noted that  
Figure 2: Absence of DksA increases the burst size of a T4 wt infection and decreases the latent period of a T4_motA\({}^{am}\)_ infection. (**a**) Representative graph of burst size vs. time after infection; (**b**) burst size, and (**c**) latent period for infections of T4 wt/B606 wt (purple), T4 wt/B606 \(\Delta\)_dksA_ (blue), T4_motA\({}^{am}\)_/B606 wt (orange), and T4_motA\({}^{am}\)_/B606 \(\Delta\)_dksA_ (red). Averages with indicated standard deviations were determined as described in Materials and Methods from three independent replicates. (The error bar on _motA\({}^{am}\)_/\(\Delta\)_dksA_ is too small to be visible.) Asterisks (*) indicate significance as determined by an unpaired t test with a \(p\) value \(\leq\) 0.05. The apparent 5 min difference in latent period of the wt/wt and \(\mathrm{wt}\)/\(\Delta\)_dksA_ infection shown in (**a**) is not statistically significant (see panel (**c**)). while a _motA_ deletion is lethal [52], the T4_motA\({}^{am}\)_ mutation is not. Nevertheless, there is a dramatic inhibition of transcription from MotA-dependent promoters and a DNA delay phenotype [40; 42; 52]. We therefore carried out RNA-seq to define the MotA regulon by comparing gene expression in B606 wt cells infected for 5 min at 37 \({}^{\circ}\)C with either T4 wt or T4_motA\({}^{am}\)_. At the 5 min infection point, middle genes were highly expressed, early transcription was ending, and late gene expression had initiated (reviewed in [53; 54]). Genes, whose expression changed \(\geq\)2-fold with a \(p\) value \(\leq\) 0.05, were considered significant. As shown schematically in Figure 3, the T4 genome is generally organized as regions of pre-replicative genes (early and middle) that are transcribed right-to-left and interrupted by regions of late genes that are transcribed left-to-right (reviewed in [53]). In general, early genes encode products needed for middle gene expression and to usurp host processes. However, the functions of many early genes are still unknown. Middle genes encode products needed for the crucial functions of replication, recombination, late gene transcription, and the continuation of host takeover. Late genes mainly encode morphological proteins. Since the majority of the T4 Pe's, Pm's, and Pl's have been identified (reviewed in [23; 53]), we generated a detailed diagram of early, middle, and late transcription along the entire T4 genome (Figure 3). Convention within the field has provided designations for Pe's based on genomic coordinates (e.g., Pe15.0), whereas Pm's and Pl's are indicated by the first gene within the resulting transcript (e.g., Pm_dsbA_ and PI_15_). Previous global analyses of T4 gene expression using hybridization studies or levels of various phage proteins during a T4_motA\({}^{am}\)_ infection have indicated that when MotA-dependent promoters are not activated, expression of some early genes remains high, while late transcription, which is dependent on the middle products gp55, gp33, and gp45, is significantly diminished (reviewed in [54]). However, the expression of middle genes varies.