E. coli 6S RNA complexed to RNA polymerase maintains product RNA synthesis at low cellular ATP levels by initiation with noncanonical initiator nucleotides

ssrS promoter structure, E. coli 6S RNA secondary structures, pRNA sequence and potential product RNA initiators. (A) Map of the ssrS gene. P1 refers to σ⁷⁰-dependent Promoter 1, P2 refers to Promoter 2 dependent on both σ³⁸ and σ⁷⁰ (adapted from Kim 2004, by permission of Oxford University Press). (B) 6S RNA in its free state; resembles a DNA transcriptional bubble. “−35” and “−10” refer to DNA-like regions for RNAP interactions. Highly conserved residues present in the γ-proteobacteria are shown in pink (Shephard et al. 2010). The bubbles to the left (LB1; LB2; LB3) and to the right (RB1; RB2; RB3) of the large central bubble (CB) are noted together with the downstream helix (DH). The pRNA transcription start site (TSS, U44) is indicated by the arrow. (C) Expected 13 nt pRNA sequence for E. coli where X represents p (phosphate) for ATP, ⁺N for NAD⁺, HN for NADH, or F for FAD initiator incorporation. (D) The 6S RNA:pRNA complex after release from RNAP:σ⁷⁰ holoenzyme. An intramolecular hairpin (−10:DH hairpin) arises when pRNA elongates by at least 8 nt (Panchapakesan and Unrau 2012); X (shown in red) represents the potential for noncanonical initiation of the release pRNA as shown in panel C. (E) Chemical structures of the known pRNA transcriptional initiator ATP and potential initiators NAD⁺, NADH, and FAD. The adenosine diphosphate shared by all initiators is indicated in black with the differing functional groups shown in red.