During infection of Escherichia coli, bacteriophage T4 usurps the host transcriptional machinery, redirecting it to the expression of early, middle, and late phage genes. This machinery is driven by E. coli RNA polymerase, which, like all bacterial polymerases, is composed of a core of subunits (beta, beta', alpha1, alpha2, and omega) that have RNA synthesizing activity and a specificity factor (sigma). The sigma protein identifies the start of transcription by recognizing and binding to sequence elements within promoter DNA. During exponential growth, the primary sigma of E. coli is sigma70, which, like all primary sigmas, is composed of four regions. Sigma70 recognizes DNA elements around positions -10 and -35 of host promoter DNA, using residues in its central portion (regions 2 and 3) and C-terminal portion (region 4), respectively. In addition, residues within region 4 must also interact with a structure within core polymerase, called the beta-flap, to position sigma70 region 4 so it can contact the -35 DNA. T4 takes over E. coli RNA polymerase through the action of phage-encoded factors that interact with polymerase and change its specificity for promoter DNA. Early T4 promoters, which have -10 and -35 elements that are similar to that of the host, are recognized by sigma70 regions 2 and 4, respectively. However, although T4 middle promoters have an excellent match to the sigma70 -10 element, they have a phage element (a MotA box) centered at -30 rather than the sigma70 -35 element. Two T4-encoded proteins, a DNA-binding activator (MotA) and a T4-encoded co-activator (AsiA), are required to activate the middle promoters. AsiA alone inhibits transcription from a large class of E. coli promoters by binding to and structurally remodeling sigma70 region 4, preventing its interaction with the -35 element and with the beta-flap. In addition to its inhibitory activity, the AsiA-induced remodeling allows the N-terminal domain of MotA (MotANTD) to bind to the C-terminus of sigma70 and the C-terminal domain of MotA (MotACTD) to bind to the MotA box. This process is called sigma appropriation. Despite extensive biochemical and genetic analyses and the reported structures of thermophilic RNAP, the structure and structure-model of E. coli RNAP, and the structures of various activators, whole 3D structural pictures of activated transcription complexes have not been obtained. In the case of sigma appropriation, available structures include AsiA in a complex with sigma70 Region 4 and structures of MotACTD and MotANTD. However, there are no structures of full length MotA or structures that include DNA. Using multiple available structures (E. coli RNA polymerase, the Thermus aquaticus RNA polymerase/DNA open complex, AsiA /sigma70 Region 4, MotANTD, and MotACTD), the Molsoft ICM program, and extensive biochemical evidence indicating the position of MotA relative to the DNA, we are developing a structure-based model for sigma appropriation. Our results will visualize how AsiA/MotA redirects sigma, and therefore RNA polymerase activity, to T4 middle promoter DNA, and demonstrate at a molecular level how the interaction of factors with a small portion of RNA polymerase can alter promoter specificity.
