Transcriptional Infidelity Promotes Heritable Phenotypic Change in a Bistable Gene Network

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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. Errors in information transfer from DNA to RNA to protein are inevitable and ubiquitous. When errors that occur in DNA are not repaired and become fixed as permanent mutations, they can have heritable phenotypic consequences for cells. In contrast, errors that occur during RNA transcription are considered transient, because the life span of mRNAs and their encoded proteins is thought to be too short to have heritable consequences. Here, we show that transient errors that arise during transcription can cause a heritable phenotypic change within a population of genetically identical Escherichia coli cells growing in the same environment. We used single-cell observation of the bistable lac operon (which allows a cell to have two alternate states) in a stable ON or OFF state. We show that the epigenetic-switch frequency from the OFF to ON state is increased when the fidelity of RNA transcription is altered: bacterial strains that contain error-prone RNA polymerases, “RNA mutators,” and strains deficient in auxiliary RNA fidelity factors exhibit an increased epigenetic-switch frequency compared with wild-type strains. Therefore, like DNA mutation, transient stochastic events can also have long-lived heritable consequences for the cell.