RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes

Biochemistry ◽  
1989 ◽  
Vol 28 (19) ◽  
pp. 7829-7842 ◽  
Author(s):  
Barbara Krummel ◽  
Michael J. Chamberlin
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Ternary Complexes ◽  
Structural Transitions ◽  
Chain Initiation

scholarly journals Mechanism of transcription initiation and promoter escape byE.coliRNA polymerase

2017 ◽  
Vol 114 (15) ◽  
pp. E3032-E3040 ◽  
Author(s):  
Kate L. Henderson ◽  
Lindsey C. Felth ◽  
Cristen M. Molzahn ◽  
Irina Shkel ◽  
Si Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Free Energy ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
Initial Phase ◽  
Rna Synthesis ◽  
Quantitative Model ◽  
Ternary Complexes ◽  
Promoter Escape ◽  
Abortive Cycling

To investigate roles of the discriminator and open complex (OC) lifetime in transcription initiation byEscherichia coliRNA polymerase (RNAP; α2ββ’ωσ70), we compare productive and abortive initiation rates, short RNA distributions, and OC lifetime for the λPRand T7A1 promoters and variants with exchanged discriminators, all with the same transcribed region. The discriminator determines the OC lifetime of these promoters. Permanganate reactivity of thymines reveals that strand backbones in open regions of long-lived λPR-discriminator OCs are much more tightly held than for shorter-lived T7A1-discriminator OCs. Initiation from these OCs exhibits two kinetic phases and at least two subpopulations of ternary complexes. Long RNA synthesis (constrained to be single round) occurs only in the initial phase (<10 s), at similar rates for all promoters. Less than half of OCs synthesize a full-length RNA; the majority stall after synthesizing a short RNA. Most abortive cycling occurs in the slower phase (>10 s), when stalled complexes release their short RNA and make another without escaping. In both kinetic phases, significant amounts of 8-nt and 10-nt transcripts are produced by longer-lived, λPR-discriminator OCs, whereas no RNA longer than 7 nt is produced by shorter-lived T7A1-discriminator OCs. These observations and the lack of abortive RNA in initiation from short-lived ribosomal promoter OCs are well described by a quantitative model in which ∼1.0 kcal/mol of scrunching free energy is generated per translocation step of RNA synthesis to overcome OC stability and drive escape. The different length-distributions of abortive RNAs released from OCs with different lifetimes likely play regulatory roles.

scholarly journals Regulatory state of ribosomal genes and physiological changes in the concentration of free ribonucleic acid polymerase in Escherichia coli

1975 ◽  
Vol 150 (1) ◽  
pp. 9-12 ◽  
Author(s):  
H Bremer ◽  
D G Dalbow
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Fold Increase ◽  
Ribosomal Genes ◽  
Physiological Changes ◽  
Regulatory State ◽  
Chain Initiation ◽  
State Growth

The concept of promoter efficiency is introduced as frequency of RNA chain initiation at a given promoter normalized to the intracellular concentration of free (but functional) RNA polymerase. Previous observations from this laboratory on the synthesis of ribosomes and β-galactosidase are used to show that during a nutritional shift-up from succinate minimal to glucose-amino acids medium (3-fold increase in steady-state growth rate) the concentration of free (active) RNA polymerase decreases to one-quarter of the pre-shift value and the promoter efficiencies of the genes for ribosomal RNA and ribosomal proteins increase 9- and 6-fold respectively. This extent of control of ribosomal genes is much greater than expected on the basis of the increase in the rate of ribosome synthesis (3-fold).

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