Regulatory Sequences Involved in the Promotion and Termination of RNA Transcription

The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter mutations. Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence.

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Compilation and analysis of Escherichia coli promoter DNA sequences.

Fluctuations in rates of gene expression can produce highly erratic time patterns of protein production in individual cells and wide diversity in instantaneous protein concentrations across cell populations. When two independently produced regulatory proteins acting at low cellular concentrations competitively control a switch point in a pathway, stochastic variations in their concentrations can produce probabilistic pathway selection, so that an initially homogeneous cell population partitions into distinct phenotypic subpopula- tions. Many pathogenic organisms, for example, use this mechanism to randomly switch surface features to evade host responses. This coupling between molecular-level fluctuations and macroscopic phenotype selection is analyzed using the phage l lysis-lysogeny decision circuit as a model system. The fraction of infected cells selecting the lysogenic pathway at different phage:cell ratios, predicted using a molecular- level stochastic kinetic model of the genetic regulatory circuit, is consistent with experimental observations. The kinetic model of the decision circuit uses the stochastic formulation of chemical kinetics, stochastic mechanisms of gene expression, and a statistical-thermodynamic model of promoter regulation. Conven- tional deterministic kinetics cannot be used to predict statistics of regulatory systems that produce probabilis- tic outcomes. Rather, a stochastic kinetic analysis must be used to predict statistics of regulatory outcomes for such stochastically regulated systems.

/pdf/stochastic-kinetic-analysis-of-developmental-pathway-545z0j2lmj.pdf

Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda -infected escherichia coli cells

[This corrects the article on p. 116 in vol. 40.].

https://mmbr.asm.org/content/mmbr/40/1/116.full.pdf

Recalibrated linkage map of Escherichia coli K-12.

Intracellular phospholipases A.

ρ factor-mediated transcription termination at the tR1 terminator site of bacteriophage λ is examined. Mutations affecting the termination event are characterised. These mutations define features of the site which seem to be important to terminator function. In addition, other related transcriptional and translational regulatory elements are defined within the region surrounding the termination site. The potential molecular interactions and structural overlaps of these control signals apparently couple the regulation of the decision between lytic and lysogenic growth patterns by phage λ.

The relationship between function and DNA sequence in an intercistronic regulatory region in phage λ

Control of transcription termination: a rho-dependent termination site in bacteriophage lambda.

A role for phospholipid hydrolysis in the lysis of Escherichia coli infected with bacteriophage T4

fabA mutants of Escherichia coli require an appropriate unsaturated fatty acid for growth. The fabA locus has now been mapped at minute 21.5 of the linkage map of E. coli. The locus is cotransduced with pyrD and aroA but not with pyrC, purB, or pdxC. The clockwise order of markers in the region is pdxC, aroA, cmlB, pyrD, fabA, pyrC.

Mapping of the fabA Locus for Unsaturated Fatty Acid Biosynthesis in Escherichia coli

INTRODUCTION mRNA encoding the c I repressor of bacteriophage λ can be initiated at either of two promoters, which function at different stages in the λ life cycle. In the lysogenic state, repressor transcription initiates from the p RM promoter, which lies immediately adjacent to the c I gene (Fig. 1). This promoter is positively regulated by the c I-gene product and both structurally and functionally overlaps with the promoter-operator signals ( p R o R ) controlling the major rightward operon of λ . In contrast, when λ infects a sensitive cell, repressor transcription originates from the p RE promoter, which lies several hundred base pairs upstream of the c I gene in the λ y region (Fig. 1). This promoter structurally overlaps the region encoding the aminoterminal amino acid sequence of the c II gene. Transcription from p RE is also positively regulated and, in this case, the activator is the c II protein. The c II protein also activates transcription from p I , the promoter for the λ integrase gene. Thus, the c II protein coordinately regulates the two transcription units required for the lysogenic response and thereby acts as a major determinant in controlling the balance between lytic and lysogenic development. The c II activity is itself regulated at multiple levels (transcription, translation, processing, stability, and so on), and a variety of phage and host-encoded functions take part in this regulation. In this paper we examine the p RE transcription unit, with particular emphasis on the p RE promoter signal and its mode of activation by c II protein. We examine the c II protein both genetically and biochemically and...

Daniel L. Wulff

Papers

The relationship between function and DNA sequence in an intercistronic regulatory region in phage λ

Control of transcription termination: a rho-dependent termination site in bacteriophage lambda.

A role for phospholipid hydrolysis in the lysis of Escherichia coli infected with bacteriophage T4

Mapping of the fabA Locus for Unsaturated Fatty Acid Biosynthesis in Escherichia coli

Establishment of Repressor Synthesis