The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa

Abstract

Summary Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α‐helix with unstructured N‐ and C‐terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70) and the stress sigma factor holoenzyme (EσS) in vitro, but has a greater impact on EσS. In both cases, SutA appears to affect intermediates in the open complex formation and its N‐terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.

Bacterial transcription during growth arrest

“…Also in P. aeruginosa , a small, acidic, and largely unstructured protein named SutA was recently shown to be upregulated in stationary phase and anoxia [ 80 ]. SutA binds to the β1 domain (or protrusion) of RNAP, and modestly enhances transcription of hundreds of mostly housekeeping genes, including the rRNA genes [ 112 ]. This finding was initially counterintuitive, but if low levels of new protein synthesis are required during growth arrest to respond to threats or transient opportunities, factor(s) that modulate the energy landscapes of these promoters to counter the negative influences of growth arrest-induced changes to DNA conformation and nucleoid environment might be required.…”

Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding

“…SutA has no sequence homology to any other characterized proteins. Previous NMR study and secondary structural prediction suggested that SutA comprises a middle α-helix, a N-terminal D/E-rich region, and a C-terminal disordered tail 2 . Both the middle and N-terminal regions are required for its transcription activation activity on the promoter of ribosomal RNA rrn 2 .…”

“…Recent studies discovered SutA as a new binding partner of Pseudomonas aeruginosa ( Pae ) RNAP 1 , 2 . The expression of SutA is induced under anaerobic survival conditions to help maintaining minimal transcription activity of Pae RNAP.…”

“…RNAP-β protrusion is likely the primary anchor site of SutA 2 . SutA interacts with both RNAP-σ A and RNAP-σ S holoenzymes and has greater effect on increasing transcription activity of the RNAP-σ S holoenzyme compared with RNAP-σ A holoenzyme 2 .…”

“…RNAP-β protrusion is likely the primary anchor site of SutA 2 . SutA interacts with both RNAP-σ A and RNAP-σ S holoenzymes and has greater effect on increasing transcription activity of the RNAP-σ S holoenzyme compared with RNAP-σ A holoenzyme 2 . Previous results of cross-linking and FeBABE cleavage assays suggested that SutA first associates with RNAP-σ S , subsequently undergoes conformational change upon promoter dsDNA loading and unwinding, and eventually dissociates upon formation of the RNAP-promoter DNA open complex (RPo) 2 .…”