# The _E. coli_ Global Regulator DksA Reduces Transcription during T4 Infection
## 1 Introduction  
The integrity and regulation of gene expression is essential for proper cellular function and adaptation. Bacteria have evolved myriad mechanisms to tightly regulate gene expression to ensure that genes are expressed under the correct environmental conditions [1]. Bacteriophages have simultaneously evolved mechanisms for altering gene expression in their host to optimize the expression of genes required for viral proliferation [2; 3; 4]. Bacterial transcription is performed by an RNA polymerase (RNAP), which consists of five core factors (\(\alpha\)I, \(\alpha\)II, \(\beta\), \(\beta^{\prime}\), and \(\omega\)), along with a \(\sigma\) subunit that specifies the transcription start site (reviewed in [5; 6]). In _Escherichia coli_ (_E. coli_), the primary \(\sigma\) factor, \(\sigma^{70}\), recognizes specific \(-10\) and \(-35\) elements within the promoter sequence and is essential for the transcription of genes needed for exponential growth under nutrient-rich conditions. Efficient transcription requires the interaction of RNAP with promoter DNA to create an \"open complex\" with a single-stranded region at the transcription startsite, initiation of RNA synthesis, promoter clearance, processive transcription elongation, and accurate termination (reviewed in [7]). _E. coli_ promoters use specific activators, repressors, and/or other transcriptional regulators to control initiation, elongation, and termination. While activators and repressors typically interact with specific DNA sequence motifs, DksA is a member of a growing class of global transcription regulators, called secondary (2\({}^{\circ}\)) channel proteins, that interact with just RNAP. These proteins, which also include GreA and GreB, all share two superimposable structural domains: a coiled-coil domain that penetrates the 2\({}^{\circ}\) channel of RNAP and a globular domain that binds the rim helices of RNAP atop the 2\({}^{\circ}\) channel [8]. The acidic residues at the tip of the coiled-coil have protein-specified, DNA context-determined effects on catalysis during transcription initiation as well as elongation and fidelity [9]. These features culminate in activation/inhibition of RNA synthesis (diester formation) as well as diesterase cleavage of backtracked mRNA to rescue transcription arrest [10]. The interaction of DksA with RNAP generates one of two binding sites for the small molecule ppGpp on polymerase [11; 12], and in most cases, DksA activity is dependent on ppGpp. While the level of DksA is relatively constant in exponentially growing cells, the concentration of ppGpp increases dramatically under nutrient-poor conditions or other stresses [13; 14]. The physiological roles of DksA and ppGpp in _E. coli_ gene expression are complicated. DksA/ppGpp inhibition of RNAP initiation from the ribosomal promoter \(PrrnB1\) is the most widely studied example, where DksA and ppGpp act synergistically to further destabilize already unstable open complexes [12; 14; 15; 16]. In contrast, ppGpp without the help of DksA can inhibit the strong phage lambda pR promoter that forms stable open complexes, not by destabilizing the open complex but rather by inhibiting promoter escape [17]. In other instances, identical, independent, or even opposing regulatory roles have been reported for the two regulators in _E. coli_ cells [18]. In addition, ppGpp can bind a variety of proteins with regulatory effects independent of transcription [19]. Furthermore, DksA has a cysteine zinc-finger motif that acts independently of ppGpp to sense oxidative stress [20]. It is noteworthy that GreA and GreB are competitive with DksA in binding to RNAP in order to rescue backtracked, arrested, or paused RNAP, primarily during transcription elongation [21; 22]. In a bacteriophage T4 infection, there are three types of T4 promoters (early (Pe), middle (Pm), and late (PI)) based on the stage of development in which they are active (reviewed in [23]).