Anatomy of Escherichia coli σ 70 promoters

Shultzaberger, Ryan K.; Chen, Zehua; Lewis, Karen A.; Schneider, Thomas D.

doi:10.1093/nar/gkl956

Cited by 185 publications

(287 citation statements)

References 110 publications

(238 reference statements)

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“…1B; Koo et al 2009a,b). Consistent with this, the information content of the core regions of s 32 promoters (18.3 bits) (Shultzaberger et al 2007). Requiring extensive recognition determinants would limit transcription to a relatively restricted set of promoters, making it important to understand how these ss maintain dependence on all three promoter motifs.…”

supporting

confidence: 57%

Reduced capacity of alternative σs to melt promoters ensures stringent promoter recognition

et al. 2009

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In bacteria, multiple σs direct RNA polymerase to distinct sets of promoters. Housekeeping σs direct transcription from thousands of promoters, whereas most alternative σs are more selective, recognizing more highly conserved promoter motifs. For σ32 and σ28, two Escherichia coli Group 3 σs, altering a few residues in Region 2.3, the portion of σ implicated in promoter melting, to those universally conserved in housekeeping σs relaxed their stringent promoter requirements and significantly enhanced melting of suboptimal promoters. All Group 3 σs and the more divergent Group 4 σs have nonconserved amino acids at these positions and rarely transcribe >100 promoters. We suggest that the balance of “melting” and “recognition” functions of σs is critical to setting the stringency of promoter recognition. Divergent σs may generally use a nonoptimal Region 2.3 to increase promoter stringency, enabling them to mount a focused response to altered conditions.

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confidence: 57%

Reduced capacity of alternative σs to melt promoters ensures stringent promoter recognition

et al. 2009

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“…The rplY promoter is negatively regulated by ppGpp and transcription factor DksA Analysis of the rplY upstream regions in sequenced genomes of E. coli and related bacteria (NCBI Gene database) revealed that the presumable rplY promoter possesses features typical of the σ 70 -dependent promoters (Harley and Reynolds 1987;Schultzaberger et al 2007), including a "good" putative −10 element (TAg/ tAAT) separated from a −35 hexamer (bearing a universally conserved TTG triplet) by an optimal spacer region of 17 bp (Fig. 1A).…”

Section: Resultsmentioning

confidence: 99%

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

Aseev

Bylinkina

Boni

2015

RNA

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Ribosomal protein (r-protein) L25 is one of the three r-proteins (L25, L5, L18) that interact with 5S rRNA in eubacteria. Specific binding of L25 with a certain domain of 5S r-RNA, a so-called loop E, has been studied in detail, but information about regulation of L25 synthesis has remained totally lacking. In contrast to the rplE (L5) and rplR (L18) genes that belong to the polycistronic spc-operon and are regulated at the translation level by r-protein S8, the rplY (L25) gene forms an independent transcription unit. The main goal of this work was to study the regulation of the rplY expression in vivo. We show that the rplY promoter is down-regulated by ppGpp and its cofactor DksA in response to amino acid starvation. At the level of translation, the rplY expression is subjected to the negative feedback control. The 5 ′ -untranslated region of the rplY mRNA comprises specific sequence/structure features, including an atypical SD-like sequence, which are highly conserved in a subset of gammaproteobacterial families. Despite the lack of a canonical SD element, the rplY'-'lacZ single-copy reporter showed unusually high translation efficiency. Expression of the rplY gene in trans decreased the translation yield, indicating the mechanism of autogenous repression. Site-directed mutagenesis of the rplY 5 ′ UTR revealed an important role of the conserved elements in the translation control. Thus, the rplY expression regulation represents one more example of regulatory pathways that control ribosome biogenesis in Escherichia coli and related bacteria.

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“…The results of this work, together with results of previous work, establish that TSS selection involves at least four promoter sequence determinants: (i) position relative to the −10 element (preference for the position 7-bp downstream of the −10 element) (5-11); (ii) sequence of TSS T and TSS-1 T (strong preference for pyrimidine at TSS T and preference for purine at TSS-1 T , which enable initiation with a purine NTP and maximize stacking between DNA bases and the initiating purine NTP) (11,(17)(18)(19)(20); (iii) sequence of the discriminator element (preference for TSS selection at upstream positions for discriminator sequences that disfavor scrunching and preference for TSS selection at downstream positions for discriminator sequences that favor scrunching) (13,14); and (iv) sequence of the CRE (preference for G at TSS+1 NT ). In addition to these sequence determinants, DNA topology and NTP concentrations also influence TSS selection (6,8,9,11,(21)(22)(23)(24)(25)(26).…”

Section: Discussionmentioning

confidence: 99%

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

Vvedenskaya

Vahedian-Movahed

Zhang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein-DNA interactions with the downstream part of the nontemplate strand of the transcription bubble ("core recognition element," CRE). Here, we investigated whether sequence-specific RNAP-CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP-CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP-CRE interactions on TSS selection in vitro and in vivo for a library of 4 7 (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP-CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5′ merodiploid nativeelongating-transcript sequencing, 5′ mNET-seq, we assessed effects of RNAP-CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP-CRE interactions determine TSS selection. Our findings establish RNAP-CRE interactions are a functional determinant of TSS selection. We propose that RNAP-CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).RNA polymerase | transcription start site selection | promoter | transcription bubble | transcription initiation T ranscription initiation consists of a number of biochemical steps leading to formation of a phosphodiester bond between a nucleoside triphosphate (NTP) bound in the RNA polymerase (RNAP) active-center initiating NTP binding site (i site) and an NTP bound in the RNAP active-center extending NTP binding site (i+1 site) (1-3). For bacterial RNAP, promoter-specific initiation requires the RNAP core enzyme (subunit composition α 2 ββ'ω) to associate with a σ factor forming the RNAP holoenzyme (subunit composition α 2 ββ'ωσ). The σ factor contains determinants for sequence-specific protein-DNA interactions with four core promoter elements: the −35 element, the extended −10 element, the −10 element, and the discriminator element (4).During transcription initiation, RNAP holoenzyme unwinds promoter DNA to form an RNAP-promoter open complex (RPo) containing an unwound, single-stranded "transcription bubble." The process of promoter unwinding begins within the promoter −10 element and propagates downstream, enabling single-stranded nucleotides at the downstream end of the transcription bubble template strand to occup...

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Anatomy of Escherichia coli σ 70 promoters

Cited by 185 publications

References 110 publications

Reduced capacity of alternative σs to melt promoters ensures stringent promoter recognition

Reduced capacity of alternative σs to melt promoters ensures stringent promoter recognition

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

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