Specificity mechanisms in the control of transcription

Abstract

In this overview we analyze and illustrate the principles underlying some of the specificity mechanisms that control the initiation, elongation, and termination phases of transcription. Thermodynamic mechanisms dominate in the first steps of initiation, where promoters at various levels of activation can be considered to be in competition for a limiting supply of core RNA polymerase. In the later stages of initiation, as well as in elongation and termination, the regulatory mechanisms that control specificity are largely kinetic, involving rate competition between branching reaction pathways where the outcome depends on the rates (and equilibria) of reaction and interconversion of different forms of the transcription complex. Elongation complexes are very stable at most positions along the DNA template, meaning that only RNA chain elongation (and editing) can occur at these positions. However, the stability of transcription complexes decreases abruptly when termination sequences are encountered, and here the outcome can be easily switched between elongation and termination (RNA release) by minor changes in the relative rates of these competing processes. Cis effecters, defined as sites at which regulatory proteins bind to upstream activation loci on either the DNA or the nascent RNA, play important roles in the control of both initiation and of the elongation-termination decision. Examples, drawn from studies of phage A N-dependent antitermination and E. coli rho-dependent termination processes, illustrate the flexibility and additivity of regulatory components within control mechanisms in transcription that involve multiple determinants. The generality of such regulatory principles are stressed.

In Vivo Expression from the RpoS-Dependent P1 Promoter of the Osmotically Regulated proU Operon in Escherichia coli and Salmonella enterica Serovar Typhimurium: Activation by rho and hns Mutations and by Cold Stress

“…Although the mechanism by which P1 activation occurs in the rho mutants is not known, two lines of evidence suggest that it may be related to the relief of attenuation of transcripts initiated from P1. First, such a mechanism will be consistent with the previously characterized activities and functions of the Rho protein (21,44,56). Second, the rho mutant effect is considerably diminished for S. enterica P1⌬att (plasmid pHYD374), which bears the deletion of a 22-base C-rich segment (on the coding strand) and which has previously been shown (42) to be defective in attenuation.…”

Structural Confirmation of a Bent and Open Model for the Initiation Complex of T7 RNA Polymerase

“…Combine this wash with the first eluate and evaporate them using a Speed-Vac. Add 1ml of NH 4 OH to the column, flush it back and forth and allow it to stand for 1 hour. Add this NH 4 OH eluate to the corresponding DBU/acetonitryl eluate pellet (from the speed vac) and heat it for 14 hrs at 55°C.…”

A Model of Sequence-Dependent Protein Diffusion Along DNA

“…To this respect, we remark that each match will stabilize the complex, while mismatches will act as to destabilize the protein, which will tend therefore to move away from the "wrong" positions [6,7]. For each position n along the chain we can therefore define an energy E(n), simply by counting the number of matches and mismatches, and adding a corresponding negative or positive amount of energy, respectively (empty sites in the recognition pattern do not contribute to the energy).…”

“…This hypothesis can be justified on the basis of some known protein-DNA complex features. The stability of the protein-DNA nonspecific complex is mainly due to electrostatic interaction with the backbone phosphate of DNA [7] and to the entropic release of cations [19][20][21]. Besides these stabilizing factors, sequencedependent interaction allows the protein to test the DNA during the target search [17].…”

“…It is believed that during the sliding motion, the activation barrier for the translocation of the protein to continuous nonspecific positions is high enough to randomize the protein motion through collisions with the solvent molecules, but appropriately small compared to the thermal energy, in order to allow the protein to move [6]. This has induced some authors to propose a model where protein freely slides along DNA under the effect of the thermal fluctuations without any sequence dependent interaction, i.e., the DNA is seen as an homogeneous cylinder on which the protein can diffuse until the specific site is reached [6][7][8]. During sliding, however, the protein must be able to distinguish the specific region from nonspecific DNA so that a recognition mechanism must be involved.…”