Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact (original) (raw)

2017, Proceedings of the National Academy of Sciences

Significance RNA polymerase (RNAP), like many cellular processors of information in DNA and RNA, is a complex macromolecular machine whose multiple structural modules and domains undergo poorly understood conformational changes that mediate information processing. We investigated the role of one such mobile module, the polymorphous trigger loop (TL) of RNAP, in intrinsic transcription termination by bacterial RNAP. The TL folds into a helical hairpin to promote RNA synthesis, but also is proposed to aid termination. By separating effects of the TL and of TL variants on termination from effects on RNA synthesis, we established that TL flexibility, not the helical hairpin conformation, facilitates rearrangements of RNAP leading to termination. Our results illustrate how kinetic assays can help dissect complex macromolecular machines.