Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

Abstract

During transcription of protein-coding genes, bacterial RNA polymerase (RNAP) is closely followed by a ribosome that is engaged in translation of the newly synthesized transcript. Here we show that as a result of translation-transcription coupling the overall elongation rate of transcription is tightly controlled by translation. Acceleration and deceleration of a ribosome results in corresponding changes in the speed of RNAP. Consistently, we found an inverse correlation between the number of rare codons in a gene, which delay ribosome progression, and the rate of transcription. We further show that the stimulating effect of a ribosome on RNAP is achieved by preventing RNAP from adopting non-productive states. The moving ribosome inhibits spontaneous backtracking of RNAP, thereby enhancing its pace and also facilitating read-through of roadblocks in vivo. Such a cooperative mechanism ensures the two gene expression machineries match precisely each other rates, so that the transcriptional yield is always adjusted to translational needs at different genes and under various growth conditions.

Evolutionary optimization of speed and accuracy of decoding on the ribosome

“…Following the recognition of the codon by the anticodon of aa-tRNA and GTP hydrolysis by EF-Tu, aa-tRNA is accommodated in the A site of the 50S subunit and takes part in peptide bond formation. The rate of protein elongation in bacteria is between 4 and 22 amino acids per second at 378C [1][2][3][4][5]; thus, a protein of an average length of 330 amino acids [6] is completed in about 10-80 s. The times required for initiation, termination and ribosome recycling (around 1 s each [3]) are short enough to make elongation rate-limiting for protein synthesis [7]. Translation of a particular codon depends on both the nature and abundance of the respective tRNAs, particularly on the non-random use of synonymous codons and the availability of the respective isoacceptor tRNAs [8].…”

“…Translation of a particular codon depends on both the nature and abundance of the respective tRNAs, particularly on the non-random use of synonymous codons and the availability of the respective isoacceptor tRNAs [8]. The overall rate of translation is limited by the codon-specific rates of cognate ternary complex delivery to the A site and is further attenuated by other factors, such as collisions between individual ribosomes in polysomes [3], controlled ribosome stalling (for a recent review, see [9]), or the cooperation between translating ribosomes and the RNA polymerase machinery [4,10].Estimations of error frequencies of translation range between 10 25 and 10 23 , depending on the type of measurement, concentrations and nature of tRNAs that perform misreading, and the mRNA context [11][12][13]. Different approaches were taken to measure these values.…”

Modulation of Rho-Dependent Transcription Termination in Escherichia coli by the H-NS Family of Proteins

“…The maintenance of transcription-translation coupling in a prokaryotic cell would require dynamic inter-regulation between the binding and progression of a pioneer ribosome on the nascent transcript on the one hand and the rate of transcription elongation on the other (9,45); however, the detailed mechanisms by which such regulation is achieved are not known. Furthermore, in bacteria such as Escherichia coli, nascent transcripts that are not simultaneously translated are subject to a mechanism of factor-dependent transcription termination (also referred to as transcriptional polarity) (reviewed in references 1, 6, 15, 40, 44, 47, and 52), so that the occurrence of translation-uncoupled transcription is minimized within the cells (11,43).…”

“…Finally, the polarity defects of rho and nusG mutants were exacerbated by Hha and YdgT deficiency. A model is proposed that invokes a novel role for the polymeric architectural scaffold formed on DNA by H-NS and StpA independent of the gene-silencing functions of these nucleoid proteins, in modulating Rho-dependent transcription termination such that interruption of the scaffold (as obtained by expression either of the H-NS oligomerization variants or of YdgT) is associated with improved termination efficiency in the rho and nusG mutants.Translation is a cotranscriptional process in both eubacteria and archaebacteria (1,9,25,45,50), and it has been proposed that such coupling is a defining characteristic of prokaryotic life (34, 64). The maintenance of transcription-translation coupling in a prokaryotic cell would require dynamic inter-regulation between the binding and progression of a pioneer ribosome on the nascent transcript on the one hand and the rate of transcription elongation on the other (9, 45); however, the detailed mechanisms by which such regulation is achieved are not known.…”

“…Translation is a cotranscriptional process in both eubacteria and archaebacteria (1,9,25,45,50), and it has been proposed that such coupling is a defining characteristic of prokaryotic life (34, 64). The maintenance of transcription-translation coupling in a prokaryotic cell would require dynamic inter-regulation between the binding and progression of a pioneer ribosome on the nascent transcript on the one hand and the rate of transcription elongation on the other (9, 45); however, the detailed mechanisms by which such regulation is achieved are not known.…”