Structures of the RNA polymerase-σ ⁵⁴ reveal new and conserved regulatory strategies

Abstract

Transcription by RNA polymerase in bacteria requires specific promoter recognition by σ factors. The major variant σ factor (σ54) initially forms a transcriptionally silent complex requiring specialised ATP-dependent activators for initiation. Our crystal structure of the 450 kDa RNAP-σ54 holoenzyme at 3.8 Å reveals molecular details of σ54 and its interactions with RNAP. The structure explains how σ54 targets different regions in RNAP to exert its inhibitory function. Although σ54 and the major σ factor, σ70, have similar functional domains and contact similar regions of RNAP, unanticipated differences are observed in their domain arrangement and interactions with RNAP, explaining their distinct properties. Furthermore, we observe evolutionarily conserved regulatory hotspots in RNAPs that can be targeted by a diverse range of mechanisms to fine tune transcription.

Molecular Mechanisms of Transcription Initiation—Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation

“…Sequence and structural alignments demonstrate that σ 54 and σ 70 are not derived from a common ancestor but have evolved independently in the bacterial domain [7]. There are thus two functionally discrete mechanisms of transcription initiation in bacteria that are either (i) spontaneous (σ 70 ) or (ii) relying on ATP hydrolysis by bacterial enhancer binding proteins (bEBP) of the AAA+ family (σ 54 ).…”

“…-holo RNAP readily forms a CC, while OC formation requires the action of bEBPs and ATP-hydrolysis [7]. Class II transcription activators such as catabolite activator protein (CAP) also regulate transcription by enhancing OC formation [75].…”

The Master Regulators of the Fla1 and Fla2 Flagella of Rhodobacter sphaeroides Control the Expression of Their Cognate CheY Proteins

“…The expression of cheOp1 has yet to be studied. The other chemotaxis operon whose expression has already been analyzed is cheOp2, which is dependent on 70 and 28 (FliA) (27). Therefore, whether cheY4 and cheOp1 are expressed concurrently with fla1 and fla2, respectively, remains to be determined.…”

“…Another important aspect that remains to be determined is the identity of the activator protein that is responsible for interacting with E 54 -3 to promote cheOp3 expression; since E 54 is unable to form open complex by itself, the presence of an activator protein of the bacterial enhancer-binding protein (bEBP) family is compulsory (28). In this context, it should be stressed that most bacteria have a single 54 factor (encoded by rpoN) that interacts with multiple bEBPs that recognize specific binding sites to achieve the transcription of a specific set of genes (29).…”

Bacillus cereus growth and biofilm formation: the impact of substratum, iron sources, and transcriptional regulator Sigma 54

“…An example of specifically targeting a transcription factor has been provided previously for another sigma factor, Sigma B, activity of which could be blocked by using a sulfonamide derivative compound (Palmer et al 2011). Sigma 54 was proposed as a specific target for antibacterial treatments due to its involvement in bacterial defences (Yang et al 2015) and stress responses (Feklístov et al 2014). Although a challenging idea, complexity of the roles that different sigma factors play and their interconnection with other sigma factors and transcriptional regulators can make the effect of such an approach unpredictable and therefore unreliable.…”