<i>Escherichia coli</i>promoter sequences predict<i>in vitro</i>RNA polymerase selectivity

Mulligan, Martin E.; Hawley, Diane K.; Entriken, Robert; McClure, William R.

doi:10.1093/nar/12.1part2.789

Cited by 468 publications

(258 citation statements)

References 12 publications

Supporting

Mentioning

249

Contrasting

Order By: Relevance

“…As summarized in Table 1, part A, this analysis indicates that P~+ is a relatively strong promoter, with high values for KB, the apparent equilibrium constant for initial binding of free polymerase to the promoter, and kf, the rate constant for isomerization of closed complexes to open complexes. Our measurement of overall promoter strength for P~=+ {estimated by the apparent association rate constant, the product KB x kf) is about sixfold lower than that predicted from the sequence of P.~ by the TARGSEARCH program of Mulligan et al (1984). The P..~ $ U7 mutation at position -12 causes a large decrease in the isomerization constant [30-fold) and a small decrease in the initial binding constant (fivefold).…”

Section: Effect Of Psi Down-mutations On Promoter Strength In Vitromentioning

confidence: 71%

Control of gene expression in bacteriophage P22 by a small antisense RNA. II. Characterization of mutants defective in repression.

Liao²,

McClure³

et al. 1987

Genes Dev.

View full text Add to dashboard Cite

In recent years, it has become clear that some biological regulatory mechanisms are mediated by interactions between complementary RNA molecules Ireviewed by Green et al. 1986}. For example, replication of plasmid ColE1 is controlled by pairing between RNA II, the precursor of the primer for DNA replication, and RNA I, a small regulatory RNA that is complementary to the 5' end of RNA II. This interaction, which is facilitated by a protein called Rop or Rom, interferes with the processing of RNA II to form the mature primer RNA Itoh 1981~ Lacatena et al. 1984;Tomizawa and Som 1984}. The expression of genes encoding proreins can also be controlled by the specific interaction of mRNAs and complementary (antisense} RNAs. Naturally occurring regulation by antisense RNAs has been described for several bacterial proteins, including TnlO transposase (Simons and Kleckner 1983}, the replication proteins of plasmids R1 {Light and Molin 1983} and pT181 {Kumar and Novick 1985}, and the OmpF outer membrane protein of Escherichia coli (Mizuno et al. 1984}.In this paper, we present evidence that the synthesis of phage P22 antirepressor is regulated by a small antisense RNA called sar {for small antisense regulatory RNA). P22 antirepressor is a protein that inhibits the specific DNA-binding activity of P22 c2 repressor, phage k cI repressor, and the analogous repressors of other, related phages (for review, see Susskind and Youderian 19831. These repressors, which are structurally and functionally similar but differ in DNA sequence specificity, turn off transcription of lyric phage genes during lysogeny. The antirepressor gene, ant, is expressed from a strong, rightward promoter called Pant, which is regulated by two repressor proteins [see

show abstract

Section: Effect Of Psi Down-mutations On Promoter Strength In Vitromentioning

confidence: 71%

Control of gene expression in bacteriophage P22 by a small antisense RNA. II. Characterization of mutants defective in repression.

Liao²,

McClure³

et al. 1987

Genes Dev.

View full text Add to dashboard Cite

show abstract

“…Flexible patterns have been presented as a method to detect weak structural similarities of protein domains. The sequence targets used in Mulligan et al (1984) Stochastic context-free grammar (Sakakibara, et al 1994) General hidden Markov model Fig. 1.…”

Section: Survey Of Biomolecular Motif Descriptorsmentioning

confidence: 99%

A flexible motif search technique based on generalized profiles

Bücher¹,

Karplus

Moeri

et al. 1996

Computers & Chemistry

286

203

View full text Add to dashboard Cite

Abstract-A flexible motif search technique is presented which has two major components: (1) a generalized profile syntax serving as a motif definition language; and (2) a motif search method specifically adapted to the problem of finding multiple instances of a motif in the same sequence. The new profile structure, which is the core of the generalized profile syntax, combines the functions of a variety of motif descriptors implemented in other methods, including regular expression-like patterns, weight matrices, previously used profiles, and certain types of hidden Markov models (HMMs). The relationship between generalized profiles and other biomolecular motif descriptors is analyzed in detail, with special attention to HMMs. Generalized profiles are shown to be equivalent to a particular class of HMMs, and conversion procedures in both directions are given. The conversion procedures provide an interpretation for local alignment in the framework of stochastic models, allowing for clear, simple significance tests. A mathematical statement of the motif search problem defines the new method exactly without linking it to a specific algorithmic solution. Part of the definition includes a new definition of disjointness of alignments.

show abstract

“…Comparison of the three trajectories with the effective potential landscape in Figure 1a serves to verify that the direction and range of propagation agree for the two methods. Now the σ 70 subunit of E. coli holoenzyme RNAP recognises hexamers located 35 and 10 bases upstream of transcription initiation [51]. Many strong promoters Comparison with the noise parameter, ε plotted in Figure 1c shows that when the motion is strongly deterministic (|ε| > 2) it is invariably towards regions where promoter recognition can occur.…”

Section: Resultsmentioning

confidence: 99%

Salerno's Model of DNA Re-Analysed: Could Breather Solitons have Biological Significance?

Bashford

2006

J Biol Phys

View full text Add to dashboard Cite

Abstract.We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether "breather" solitons could play a role in the facilitated location of promoters by RNA polymerase (RNAP). In an effective potential formalism, we find excellent correlation between potential minima and Escherichia coli promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while "flat" regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein "particle" about a bent DNA axis.

show abstract

Escherichia colipromoter sequences predictin vitroRNA polymerase selectivity

Cited by 468 publications

References 12 publications

Control of gene expression in bacteriophage P22 by a small antisense RNA. II. Characterization of mutants defective in repression.

Control of gene expression in bacteriophage P22 by a small antisense RNA. II. Characterization of mutants defective in repression.

A flexible motif search technique based on generalized profiles

Salerno's Model of DNA Re-Analysed: Could Breather Solitons have Biological Significance?

Contact Info

Product

Resources

About