Topography of intermediates in transcription initiation of E.coli.

Schickor, Peter; Metzger, Willi; Werel, W.; Lederer, Hermann; Heumann, Hermann

doi:10.1002/j.1460-2075.1990.tb07391.x

Cited by 144 publications

(162 citation statements)

References 36 publications

Supporting

Mentioning

140

Contrasting

Order By: Relevance

“…To our knowledge, the conserved sequence TCCC in both species has not been previously identified in any other a7O promoter (i.e., other than rRNA promoters and some tRNA promoters), and its presence raises the possibility of an additional regulatory determinant that may be important for these by the heat shock sigma factor cr32 (9). These nucleotides are in close contact with the RNA polymerase during open complex formation at the start of transcription (41), which is why this conserved sequence might be important in some aspect of the regulation which is similar in the trmA and rrn promoters. Dickson et al (12) and Gaal et al (15) have changed two of the four bases in the TCCC sequence of rrnB P1, resulting in TTCC (C-17T) and CCCC (T-18C).…”

Section: Discussionmentioning

confidence: 87%

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

et al. 1991

View full text Add to dashboard Cite

The tRNA(m5U54)methyltransferase, whose structural gene is designated trmA, catalyzes the formation of 5-methyluridine in position 54 of all tRNA species in Escherichia coli. The synthesis of this enzyme has previously been shown to be both growth rate dependent and stringently regulated, suggesting regulatory features similar to those of rRNA. We have determined the complete nucleotide sequence of the trmA operon in E. coli and the sequence of the trmA promoter region in SalmoneUa typhimurium and also analyzed the transcriptional regulation of the gene. The trmA and the btuB (encoding the vitamin B12 outer membrane receptor protein) promoters are divergent promoters separated by 102 bp between the transcriptional start sites. The trmA promoters of both E. coli and S. typhimurium share promoter elements with the rRNA P1 promoter. The sequence downstream from the -10 region of the trmA promoter is homologous to the discriminatory region found in stringently regulated promoters. Next to and upstream from the -10 region is a sequence, TCCC, in the trmA promoter that is present in all of the seven rRNA P1 promoters and in some tRNA promoters but not in any other Co70 promoter. However, a similar motif is also found in promoters transcribed by the heat shock sigma factor CJ32. The trmA gene is transcribed as a monocistronic operon, and the 3' end of the transcript is shown to be located downstream from a dyad symmetry region not followed by a poly(U) stretch. Using a trmA-cat operon fusion, we show that the growth rate-dependent regulation of trmA resembles that of rRNA and operates at the level of transcription.

show abstract

Section: Discussionmentioning

confidence: 87%

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

et al. 1991

View full text Add to dashboard Cite

show abstract

“…1). The RPc, which is usually unstable and competitor sensitive, gives an abbreviated protection footprint that does not include DNA downstream of the transcription start site (7,9,10). Creation of the stable polymerase/promoter open complex (Rpo) requires bending and unwinding of the DNA (11) and major conformational changes (isomerization) of the polymerase (Fig.…”

mentioning

confidence: 99%

“…1 A) (12)(13)(14). The result of these changes generates a complex in which the promoter is unwound from Ϫ11 to around ϩ3, and the protection footprint extends to around ϩ25 (9,11,(15)(16)(17)(18)(19)(20)(21). In addition, RPo is normally competitor resistant, although RPo at the very strong ribosomal promoters does not follow this rule (22,23).…”

mentioning

confidence: 99%

The promoter spacer influences transcription initiation via σ ⁷⁰ region 1.1 of Escherichia coli RNA polymerase

Hook-Barnard

Hinton

2009

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

View full text Add to dashboard Cite

Transcription initiation is a dynamic process in which RNA polymerase (RNAP) and promoter DNA act as partners, changing in response to one another, to produce a polymerase/promoter open complex (RPo) competent for transcription. In Escherichia coli RNAP, region 1.1, the N-terminal 100 residues of 70 , is thought to occupy the channel that will hold the DNA downstream of the transcription start site; thus, region 1.1 must move from this channel as RPo is formed. Previous work has also shown that region 1.1 can modulate RPo formation depending on the promoter. For some promoters region 1.1 stimulates the formation of open complexes; at the P minor promoter, region 1.1 inhibits this formation. We demonstrate here that the AT-rich P minor spacer sequence, rather than promoter recognition elements or downstream DNA, determines the effect of region 1.1 on promoter activity. Using a P minor derivative that contains good 70 -dependent DNA elements, we find that the presence of a more GC-rich spacer or a spacer with the complement of the P minor sequence results in a promoter that is no longer inhibited by region 1.1. Furthermore, the presence of the Pminor spacer, the GC-rich spacer, or the complement spacer results in different mobilities of promoter DNA during gel electrophoresis, suggesting that the spacer regions impart differing conformations or curvatures to the DNA. We speculate that the spacer can influence the trajectory or flexibility of DNA as it enters the RNAP channel and that region 1.1 acts as a ''gatekeeper'' to monitor channel entry.

show abstract

“…Kinetic studies on the formation of an RNA polymerasepromoter complex revealed the presence of a sequence of isomerization steps leading to the formation of an open complex (16)(17)(18). Furthermore, by decreasing the isomerization rates at lower temperatures, one or more intermediates in the pathway from the initial closed complex to the final open complex were isolated and characterized (19)(20)(21)(22). However, the large, and sometimes nonlinear, temperature dependence of some of the steps in this pathway (16,18,23) and the occurrence of intermediates at low temperatures that were not detected on the normal kinetic pathway (21) suggest that the structure of intermediates and͞or the mechanism of promoter recognition and DNA opening could differ at low temperatures compared with normal physiological conditions.…”

mentioning

confidence: 99%

Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter

Sclavi

Zaychikov

Rogozina

et al. 2005

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

125

View full text Add to dashboard Cite

We have used time-resolved x-ray-generated hydroxyl radical footprinting to directly characterize, at single-nucleotide resolution, several intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase on the T7A1 promoter at 37°C. Three sets of intermediates, corresponding to two major conformational changes, are resolved as a function of time; multiple conformations equilibrate amongst each other before the next large structural change. Analysis of these data in the context of published structural models indicates that initial recognition involves interaction of the UP element with the ␣-subunit Cterminal domain and binding of the subunit to the ؊35 sequence. In the subsequent isomerization step, two complexes with footprints extending into the ؊10 region can be differentiated as the DNA becomes distorted during nucleation of strand separation. During the final isomerization step, the downstream double helix becomes embedded in the ␤͞␤ jaws, leading to a transcriptionally active complex.DNA-protein interactions ͉ time-resolved footprinting ͉ transcription ͉ hydroxyl radicals D e novo RNA synthesis during DNA transcription is a highly regulated cellular process carried out by RNA polymerase. RNA polymerase binds to DNA and diffuses one-dimensionally to the promoter region (1-4); it then must make a number of interactions within the promoter as a prerequisite to forming a relatively stable complex. This complex is then in a state that favors isomerization, leading to strand separation from approximately Ϫ12 to ϩ3 with respect to the site of transcription initiation (5). Each of these steps is a possible site for regulation of the transcription levels. Extensive studies have been conducted on the structure of RNA polymerase-DNA complexes at equilibrium resulting in the characterization of the interaction of each of the enzyme's subunits with specific promoter elements (6, 7). However a direct characterization of the interactions formed at each step of the recognition process is still lacking.The T7A1 promoter used for the studies described here is one of the strongest known prokaryotic promoters (8). Its Ϫ35 sequence, TTGACT, is very close to the consensus (TTGACA), and its Ϫ10 sequence, GATACT, deviates from consensus (TATAAT). In addition, this promoter contains, from Ϫ42 to Ϫ80, a sequence rich in adenine and thymine residues, also known as an UP element (9-11). On other promoters this sequence has been shown to both increase the rate of promoter binding and stimulate isomerization to the open complex (12)(13)(14)(15). Kinetic studies on the formation of an RNA polymerasepromoter complex revealed the presence of a sequence of isomerization steps leading to the formation of an open complex (16-18). Furthermore, by decreasing the isomerization rates at lower temperatures, one or more intermediates in the pathway from the initial closed complex to the final open complex were isolated and characterized (19-22). However, the large, and sometimes nonlinear, temperature dependence of some ...

show abstract

Topography of intermediates in transcription initiation of E.coli.

Cited by 144 publications

References 36 publications

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

The promoter spacer influences transcription initiation via σ ⁷⁰ region 1.1 of Escherichia coli RNA polymerase

Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter

Contact Info

Product

Resources

About

Topography of intermediates in transcription initiation of E.coli.

Cited by 144 publications

References 36 publications

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

The promoter spacer influences transcription initiation via σ 70 region 1.1 of Escherichia coli RNA polymerase

Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter

Contact Info

Product

Resources

About

The promoter spacer influences transcription initiation via σ ⁷⁰ region 1.1 of Escherichia coli RNA polymerase