Sequence-specific interaction of a subunit of E. coli RNA polymerase with DNA

Stender, Walter

doi:10.1093/nar/8.15.3459

Cited by 6 publications

(3 citation statements)

References 10 publications

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“…The core polymerase must play a significant role in facilitating and stabilizing these interactions, of course. Sigma alone binds to DNA, but not tightly (30,31), and the region of DNA that interacts with RNA polymerase extends over at least 60bp (23), a larger area than would be covered by sigma alone. Although there is yet no direct evidence for the model, it has been evident for some time that there must be both specific antimelting and melting interactions involved in promoter binding, and these would require sites with properties ascribed to sigma sites I and II (29).…”

Section: Discussionmentioning

confidence: 99%

Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

1981

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RNA polymerase holoenzymes from many bacterial species share a common promoter recognition specificity since they use the same promoter sites on a variety of templates. These promoters generally include sequences homologous to the average sequences -TTGACA- and -TATAATA-, located -35 and -10 base pairs, respectively, upstream of the transcriptional state site. We have isolated a minor form of B. subtilis RNA polymerase in which the normal sigma subunit (sigma 55) is replaced by a smaller polypeptide (sigma 28) and which is highly specific for a class of promoter sites not used by the sigma 55-holoenzyme. Sequencing of two B. subtilis promoter sites used by the sigma 28-holoenzyme reveals identical sequences at -35 and -10 base pairs from the start site, which are -CTAAA- and -CCGATAT-, respectively. These results confirm that sigma subunit plays a major direct role in promoter sequence recognition, and support a model in which sigma interacts sequentially with -35 and -10 regions, respectively.

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Section: Discussionmentioning

confidence: 99%

Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

1981

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“…The complete lack of sequence homology between several u factors which interact with the same core enzyme indicates that this core recognition site is not dependent on a specific amino acid sequence but probably on a conformational property of the u factors. Since free u factor can bind to DNA (72,73,121), it appears that a DNA recognition or binding site is present on the u factors. The presence of this type of site in DNA-binding proteins has been noted (see reference 49 for summary).…”

Section: Sequences and Functionsmentioning

confidence: 99%

Multiple procaryotic ribonucleic acid polymerase sigma factors.

Doi¹,

Wang²

1986

Microbiological Reviews

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“…The isolated IgG fractions exhibited no cross-reactivity, as dcscribed earlier [16,34]. The anti-a and anti-a fractions were further purified by affinity chromatography according to Ratner [35].…”

Section: Methodsmentioning

confidence: 89%

The quaternary structure of Escherichia coli RNA polymerase studied with (scanning) transmission (immuno)electron microscopy

Tichelaar¹,

Schutter²,

Arnberg³

et al. 1983

Eur J Biochem

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A model for the quaternary structure of Escherichiu coli RNA polymerase (nucleosidetriphosphate: RNA nucleotidyltransferase, EC 2.7.7.6) is presented. It is based on results from classification of profiles of enzyme molecules, and from application of immuno electron microscopy.Classification of molecules, prepared with the single carbon layer technique, was first achieved for images recorded in dark field with the scanning transmission electron microscope and later on for images recorded in brightfield transmission electron microscopy. It results in five approximately equally sized groups, containing about 80 "/, of the core enzyme profiles. Holoenzyme profiles can be grouped into the same classes, and have approximately the same dimensions (9nm x 16nm). Based on the shapes and sizes of the classified profiles, a tentative model for core enzyme has been constructed.Correlation of shadow projections of this model, with the distributions of attachment sites of antibodies against CI,/I$' and CT over thc profiles, has led to models for core and holoenzyme in which the subunits are localized.The model is compared with literature data on the quaternary structure of RNA polymerase.Eschuiclziu coli RNA polymerase (nucleosidetriphosphate : RNA nucleotidyl transferase) catalyses RNA synthesis. Functional aspects of the enzyme have been extensively studied; for reviews, see 18, 91. Various biochemical and physical techniques have been used to study the quaternary structure of RNA polymerase; for a review, see [lo].In cross-linking studies, /I-/? was found to be the main product for both core and holoenzyme [ll, 121. Using crosslinkers of different lengths, Hillel and Wu [12] found distances of less than 1.2nm between subunits. They presented a model consisting of spherical subunits in which / I and p' form a tetrahedron-like structure together with the M subunits, which constitute a dimer; in holoenzyme the CT subunit interacts with fl and /Y, and with one CI subunit. Partial proteolysis studies [13 -151 support this model. Stender [I61 compared the accessibility of free subunits with their accessibility in situ, using antibodies raised against isolated subunits. He found the CI subunit in situ to be much less accessible than in the isolated state; for b and /j' this difference is much smaller.On the basis of small-angle neutron scattering data, Stockel et al. [I71 presented a model in which the core enzyme is an extended triangle of elongated C I~, /I, and /Y subunits, of which the latter two are curved. They arrived at an axial ratio of 6.1Abbreviurions. TEM, transmission electron microscope/y ; STEM, Enzyme. Escherichia coli RNA polymerase (EC 2.7.7.6).scanning transmission electron microscope/y. for C I~ and /Y, and of 5.6 for 1. The distances between the centres of mass of these subunits range from 7.0 nm to 8.2 nm. In the holoenzyme the CT subunit, for which they derived the shape of an elongated disc, nestles up to the core enzyme in a spacefilling manner; the centre-of-subunit structure forms a tetrahedron 1181.Us...

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Sequence-specific interaction of a subunit of E. coli RNA polymerase with DNA

Cited by 6 publications

References 10 publications

Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

Multiple procaryotic ribonucleic acid polymerase sigma factors.

The quaternary structure of Escherichia coli RNA polymerase studied with (scanning) transmission (immuno)electron microscopy

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