Analytical kinetic model of native tandem promoters in E. coli

Abstract

Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites ‘dTSS’, pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression dynamics, where RNAP-promoter occupancy times and dTSS are the key regulators of transcription interference due to TSS occlusion by RNAP at one of the promoters (when dTSS ≤ 35 bp) and RNAP occupancy of the downstream promoter (when dTSS > 35 bp). Occlusion and downstream promoter occupancy are modeled as linear functions of occupancy time, while the influence of dTSS is implemented by a continuous step function, fit to in vivo data on mean single-cell protein numbers of 30 natural genes controlled by tandem promoters. The best-fitting step is at 35 bp, matching the length of DNA occupied by RNAP in the open complex formation. This model accurately predicts the squared coefficient of variation and skewness of the natural single-cell protein numbers as a function of dTSS. Additional predictions suggest that promoters in tandem formation can cover a wide range of transcription dynamics within realistic intervals of parameter values. By accurately capturing the dynamics of these promoters, this model can be helpful to predict the dynamics of new promoters and contribute to the expansion of the repertoire of expression dynamics available to synthetic genetic constructs.

Development of a Growth-Dependent System to Regulate Cell Growth and Keratinase Production in B. subtilis

“…Tandem promoters significantly improve gene expression levels. , Herein, the copy number of P aprE was optimized to promote the transcriptional strength of keratinase at the enzyme-producing stage. Recombinant strains harboring single to quadruplex copies of the P aprE promoter were constructed and were selected based on keratinase activity.…”

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

“…We assumed the classification of GR in (67,68) as an input TF that regulates a large number of genes that rarely regulate themselves and participate in metabolic pathways. Meanwhile, we did not account for promoters’ close proximity (e.g., tandem formation), since a recent study (69) showed that, under similar stress, while close proximity causes transcription interference (reducing overall transcription levels), it does not influence if a gene is up- or down-regulated by input TFs.…”

Deep-learning–assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision

“…However, a detailed molecular biological explanation for this phenomenon is still lacking. It is worth mentioning that in E. coli , 831 genes have been found to be under the control of tandem promoters ( 65 ), suggesting the broadness of the regulatory scheme. Hence, in-depth research on modeling molecular events in the transcription process is needed to elucidate the effect of promoter architecture on expression noise.…”