Major conformational changes occur during the transition from an initiation complex to an elongation complex by T7 RNA polymerase

To examine changes that occur during the transition from an initiation complex (IC) to an elongation complex (EC) in T7 RNA polymerase (RNAP), we used nucleic acid-protein cross-linking methods to probe interactions of the RNAP with RNA and DNA in a halted EC. As the RNA is displaced from the RNA-DNA hybrid approximately 9 bp upstream from the active site (at -9) it interacts with a region within the specificity loop (residues 744-750) and is directed toward a positively charged surface that surrounds residues Lys-302 and Lys-303. Surprisingly, the template and non-template strands of the DNA at the upstream edge of the hybrid (near the site where the RNA is displaced) interact with a region in the N-terminal domain of the RNAP (residues 172-191) that is far away from the specificity loop before isomerization (in the IC). To bring these two regions of the RNAP into proximity, major conformational changes must occur during the transition from an IC to an EC. The observed nucleic acid-protein interactions help to explain the behavior of a number of mutant RNAPs that are affected at various stages in the initiation process and in termination.     

Molecular model of a eucaryotic transcription complex: functions and movements of influenza P proteins during capped RNA-primed transcription

We present a model for the functions and movements of the influenza virus P proteins (PB1, PB2, and PA) as they transcribe the virion RNAs (vRNAs) into messenger RNAs (mRNAs). Using ultraviolet-light-induced crosslinking, we show that the P proteins as a complex move from the 3' ends of the vRNA templates down the elongating mRNAs. PB2 binds the cap 1 structure of heterologous RNAs, which are cleaved to generate capped primer fragments. PB1, initially found at the first residue added onto the primer, moves to the 3' ends of the growing mRNA chains, indicating that it most likely catalyzes each nucleotide addition. PA and PB2 move down the growing chains in concert with PB1. PB2 is also associated with the cap during the first 11-15 nucleotides of chain growth, but then dissociates from the cap as the P protein complex moves further down the mRNA chains.