Transcriptional Infidelity Promotes Heritable Phenotypic Change in a Bistable Gene Network

Abstract

Bistable epigenetic switches are fundamental for cell fate determination in unicellular and multicellular organisms. Regulatory proteins associated with bistable switches are often present in low numbers and subject to molecular noise. It is becoming clear that noise in gene expression can influence cell fate. Although the origins and consequences of noise have been studied, the stochastic and transient nature of RNA errors during transcription has not been considered in the origin or modeling of noise nor has the capacity for such transient errors in information transfer to generate heritable phenotypic change been discussed. We used a classic bistable memory module to monitor and capture transient RNA errors: the lac operon of Escherichia coli comprises an autocatalytic positive feedback loop producing a heritable all-or-none epigenetic switch that is sensitive to molecular noise. Using single-cell analysis, we show that the frequency of epigenetic switching from one expression state to the other is increased when the fidelity of RNA transcription is decreased due to error-prone RNA polymerases or to the absence of auxiliary RNA fidelity factors GreA and GreB (functional analogues of eukaryotic TFIIS). Therefore, transcription infidelity contributes to molecular noise and can effect heritable phenotypic change in genetically identical cells in the same environment. Whereas DNA errors allow genetic space to be explored, RNA errors may allow epigenetic or expression space to be sampled. Thus, RNA infidelity should also be considered in the heritable origin of altered or aberrant cell behaviour.

Rifampin Resistance rpoB Alleles or Multicopy Thioredoxin/Thioredoxin Reductase Suppresses the Lethality of Disruption of the Global Stress Regulator spx in Staphylococcus aureus

“…Additional consideration of rifampin resistance alleles, especially those equivalent to S. aureus RpoB-P519L, uncovered yet further evidence of linkage to a wide variety of changes in RNAP transcription properties and their physiological consequences. These alterations include transcription slippage, sign epistasis, Rho-dependent terminator read-through, attenuation bypass, global transcriptome changes, and alterations in metabolic profiles (64)(65)(66)(67)(68)(69)(70)(71)(72)(73)(74)(75)). It appears that common solutions to confront diverse stress conditions have occurred in various organisms, hinting at a potentially fundamental process.…”

Visualizing high error levels during gene expression in living bacterial cells

“…In vivo measurements of errors in gene expression in bacteria have been estimated to occur at a rate of 10 −4 to 10 −5 per nucleotide during transcription and ≈10 −3 to 10 −4 per codon during translation. These error rates are significantly higher than that attributed to the highfidelity replication process, where the frequency of errors is as low as 10 −8 to 10 −9 per nucleotide (8,9,(12)(13)(14)(15)(16)(17)(18)(19)(20).…”

“…In more general terms, errors arising spontaneously during gene expression may increase protein variety and thereby enable genetically identical cells to display heterogeneous phenotypes. This phenomenon is likely to contribute to the robustness of unicellular organisms, allowing them to respond to fluctuating environments without changing their genotype (6)(7)(8)(9)(10).…”

Isolation and Characterization of RNA Polymerase rpoB Mutations That Alter Transcription Slippage during Elongation in Escherichia coli

“…Point mutations D675Y in the ␤ subunit and N458D/S in the ␤Ј subunit of E. coli RNAP that reduced fidelity in vitro were also described (14,15). Rifampicin-resistant P564L mutation in the ␤ subunit (also known as ack-1 (9)) was reported to decrease transcription fidelity in vivo and was recently shown to increase molecular noise in E. coli cells because of transient RNA errors (16).…”