The RpoS-Mediated General Stress Response in Escherichia coli

Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ S and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ S and, together, RprA and σ S orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.RprA | sRNA | feedforward control | plasmid conjugation | Hfq

Section: Discussionmentioning

confidence: 99%

Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella

Papenfort

Espinosa

Casadesús

et al. 2015

“…Six other σ factors compete for core polymerase with RpoD and regulate specific genes (3). One such factor is RpoS (σ 38 ), the general stress response σ factor (4,5); another is RpoN (σ 54 ), the nitrogen-stress σ factor (6).…”

mentioning

confidence: 99%

Transcriptional occlusion caused by overlapping promoters

Zafar

Carabetta

Mandel

et al. 2014

RpoS (σ 38 ) is required for cell survival under stress conditions, but it can inhibit growth if produced inappropriately and, consequently, its production and activity are elaborately regulated. Crl, a transcriptional activator that does not bind DNA, enhances RpoS activity by stimulating the interaction between RpoS and the core polymerase. The crl gene has two overlapping promoters, a housekeeping, RpoD-(σ 70 ) dependent promoter, and an RpoN (σ 54 ) promoter that is strongly up-regulated under nitrogen limitation. However, transcription from the RpoN promoter prevents transcription from the RpoD promoter, and the RpoN-dependent transcript lacks a ribosomebinding site. Thus, activation of the RpoN promoter produces a long noncoding RNA that silences crl gene expression simply by being made. This elegant and economical mechanism, which allows a near-instantaneous reduction in Crl synthesis without the need for transacting regulatory factors, restrains the activity of RpoS to allow faster growth under nitrogen-limiting conditions. transcriptional repression | lncRNA

“…Eσ S -dependent transcription is also activated by Crl (7), a small protein that increases expression of many stress response genes and those required for formation of amyloid curli fibers (which accounts for its name) involved in adhesion and biofilm formation (reviewed in refs. 2,6,8).The effect of Crl on σ S -dependent transcription in vivo is most pronounced during the transition into stationary phase (9). It has been proposed that Crl functions by increasing the concentration of Eσ S holoenzyme by facilitating assembly of σ S with core RNAP (10-12) because Crl's effects on transcription are greatest in vitro when the concentration of σ S is lowest, and overexpression of σ S complements a crl deletion in vivo (13).…”

mentioning

confidence: 99%

“…Eσ S -dependent transcription initiation is regulated by σ S , whose concentration is itself regulated at the levels of transcription, translation, and protein stability (reviewed in ref. 6). Eσ S -dependent transcription is also activated by Crl (7), a small protein that increases expression of many stress response genes and those required for formation of amyloid curli fibers (which accounts for its name) involved in adhesion and biofilm formation (reviewed in refs.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Key features of σ ^S required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme

Banta¹,

Chumanov

Yuan

et al. 2013

Bacteria use multiple sigma factors to coordinate gene expression in response to environmental perturbations. In Escherichia coli and other γ-proteobacteria, the transcription factor Crl stimulates σ Sdependent transcription during times of cellular stress by promoting the association of σ S with core RNA polymerase. The molecular basis for specific recognition of σ S by Crl, rather than the homologous and more abundant primary sigma factor σ 70 , is unknown. Here we use bacterial two-hybrid analysis in vivo and p-benzoylphenylalanine cross-linking in vitro to define the features in σ S responsible for specific recognition by Crl. We identify residues in σ S conserved domain 2 (σ S 2 ) that are necessary and sufficient to allow recognition of σ 70 conserved domain 2 by Crl, one near the promoter-melting region and the other at the position where a large nonconserved region interrupts the sequence of σ 70 . We then use luminescence resonance energy transfer to demonstrate directly that Crl promotes holoenzyme assembly using these specificity determinants on σ S . Our results explain how Crl distinguishes between sigma factors that are largely homologous and activates discrete sets of promoters even though it does not bind to promoter DNA.RNAP formation | transcription initiation | bacterial stress response | RpoS | curli fiber T ranscription initiation in bacteria requires the assembly of a sigma factor (σ) with the RNA polymerase (RNAP) catalytic core (E, composed of 2 α-subunits and one each of β, β′, and ω) to form RNAP holoenzyme (Eσ), which in turn recognizes promoter sequences (1) (reviewed in ref. 2). Multiple sigma factors compete for binding to core RNAP (reviewed in refs. 3,4), and each sigma factor controls a specific set of promoters.In Escherichia coli, which has seven sigma factors, σ 70 is the primary sigma, and σ S is important for certain stress responses and during the stationary phase of growth (5). Eσ S -dependent transcription initiation is regulated by σ S , whose concentration is itself regulated at the levels of transcription, translation, and protein stability (reviewed in ref. 6). Eσ S -dependent transcription is also activated by Crl (7), a small protein that increases expression of many stress response genes and those required for formation of amyloid curli fibers (which accounts for its name) involved in adhesion and biofilm formation (reviewed in refs. 2,6,8).The effect of Crl on σ S -dependent transcription in vivo is most pronounced during the transition into stationary phase (9). It has been proposed that Crl functions by increasing the concentration of Eσ S holoenzyme by facilitating assembly of σ S with core RNAP (10-12) because Crl's effects on transcription are greatest in vitro when the concentration of σ S is lowest, and overexpression of σ S complements a crl deletion in vivo (13). Effects of Crl have also been reported on postholoenzyme assembly steps including promoter binding (14) and open complex formation (12).Sigma factors contain several protease-resistant domains, e...