Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes

The RNA polymerase II (Pol II) is a eukaryotic enzyme that catalyzes the synthesis of the messenger RNA using a DNA template. Despite numerous biochemical and biophysical studies, it remains elusive whether the “secondary channel” is the only route for NTP to reach the active site of the enzyme or if the “main channel” could be an alternative. On this regard, crystallographic structures of Pol II have been extremely useful to understand the structural basis of transcription, however, the conformation of the unpaired non-template DNA part of the full transcription bubble (TB) is still unknown. Since diffusion routes of the nucleoside triphosphate (NTP) substrate through the main channel might overlap with the TB region, gaining structural information of the full TB is critical for a complete understanding of Pol II transcription process. In this study, we have built a structural model of Pol II with a complete transcription bubble based on multiple sources of existing structural data and used Molecular Dynamics (MD) simulations together with structural analysis to shed light on NTP entry pathways. Interestingly, we found that although both channels have enough space to allow NTP loading, the percentage of MD conformations containing enough space for NTP loading through the secondary channel is twice higher than that of the main channel. Further energetic study based on MD simulations with NTP loaded in the channels has revealed that the diffusion of the NTP through the main channel is greatly disfavored by electrostatic repulsion between the NTP and the highly negatively charged backbones of nucleotides in the non-template DNA strand. Taken together, our results suggest that the secondary channel is the major route for NTP entry during Pol II transcription.Author Summary: In eukaryotic cells, the RNA polymerase II (Pol II) is a central enzyme that reads the genetic information encoded in the DNA template to synthetize a messenger RNA. To perform its function, Pol II needs to have the substrate nucleoside triphosphate (NTP) diffuse into its deeply buried active site. Despite numerous efforts, the NTP entry routes remain elusive: NTP could diffuse only through the secondary channel, or also via the main channel. The structural information of the transcription bubble is essential to study this process, however, the unpaired non-template DNA of the transcription bubble is absent in the available X-ray crystal structures. In this regard, we have built a structural model of the Pol II elongation complex with reconstructed transcription bubble using existing experimental data. We then performed Molecular Dynamics (MD) simulations and applied structural analysis to study the routes of NTP diffusion. We found that sterically the probability of NTP loading through the secondary channel is more than twice that of the main channel. Further analysis of the non-bonded energetic contributions to NTP diffusion suggests that NTP diffusion through the main channel is greatly disfavored by the electrostatic repulsion between the substrate and negatively charged backbones of nucleotides in the non-template strand of the transcription bubble. Altogether, our findings suggest that the secondary channel is the more favorable NTP diffusion route for Pol II transcription elongation.