Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression

Startceva, Sofia; Kandavalli, Vinodh; Visa, Ari; Ribeiro, André S.

doi:10.1016/j.bbagrm.2018.12.005

Cited by 9 publications

(9 citation statements)

References 58 publications

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“…In detail, from Fig 8A, ω can change significantly within 10 −2 < k bind ×[R] < 10 s -1 and 10 −2 < k À 1 after < 10 2 s. For these ranges, we expect RNA production rates (k r , Eqs 5A, 5B, 6B, 7 and 9) to vary from ~10 −5 (if d TSS � 35) and ~10 −4 (if d TSS > 35) until 10 s -1 . In agreement, in E. coli, promoters have RNA production rates from ~10 −3 to 10 −1 s -1 when induced [20][21]39,[50][51] and ~10 −4 to 10 −6 s -1 when non-fully active [28]. Thus, ω can differ within realistic intervals of parameter values.…”

Section: Regulatory Parameters Of Promoter Occupancy and Occlusionmentioning

confidence: 62%

Analytical kinetic model of native tandem promoters in E. coli

et al. 2022

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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.

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Section: Regulatory Parameters Of Promoter Occupancy and Occlusionmentioning

confidence: 62%

Analytical kinetic model of native tandem promoters in E. coli

et al. 2022

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“…These limits allowed observing the whole distributions, without cutting their natural tails. The results did not differ widely from using unsupervised gating as in [57,58], if setting α to 0.95.…”

Section: Flow Cytometrymentioning

confidence: 77%

Sequence-dependent model of genes with dual σ factor preference

Baptista

Kandavalli

Chauhan

et al. 2021

Preprint

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Escherichia coli uses the ability of σ factors to recognize specific DNA sequences in order to quickly control large gene cohorts. While most genes respond to only one σ factor, approximately 5% have dual σ factor preference. The ones in significant numbers are ‘σ70+38 genes’, responsive to σ70, which controls housekeeping genes, as well as to σ38, which activates genes during stationary growth and stresses. We show that σ70+38 genes are almost as upregulated in stationary growth as genes responsive to σ38 alone. Also, their response strengths to σ38 are predictable from their promoter sequences. Next, we propose a sequence- and σ38 level-dependent, analytical model of σ70+38 genes applicable in the exponential, stationary, and in the transition period between the two growth phases. Finally, we propose a general model, applicable to other σ factors as well. This model can guide the design of synthetic circuits with sequence-dependent sensitivity and plasticity to transitions between the exponential and stationary growth phases.Author SummaryPresent challenges in Synthetic Biology include the design of genetic circuits that are robust to growth phase transitions and whose responsiveness is sequence-dependent, and, thus predictable prior to design. We present and validate an empirical-based, sequence-dependent analytical model of E. coli genes with dual responsiveness to the regulators σ70 and σ38. These genes, supported by our sequence-dependent model, could become building blocks for synthetic genetic circuits functional in both the exponential and the stationary growth phases.

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“…We used the E. coli strain DH5α-PRO (identical to DH5αZ1, here named "wild type", WT) 13,14,66 . This strain produces the necessary regulatory proteins (LacI, AraC, and TetR) that tightly regulate each of our promoter constructs 13 .…”

Section: Bacterial Strains Growth Conditions Induction and Antibioticsmentioning

confidence: 99%

Transcription attenuation in synthetic promoters in tandem formation

Chauhan,

Baptista,

Jagadeesan

et al. 2023

Preprint

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Closely spaced promoters are ubiquitous in prokaryotic and eukaryotic genomes. How their structure and dynamics relate remains unclear, particularly for tandem formations. To study their transcriptional interference, we engineered two pairs and one trio of synthetic promoters in non-overlapping, tandem formation, in single-copy plasmids. Fromin vivomeasurements inE. colicells, we found that promoters in tandem formation have attenuated transcription rates. The attenuation strength can be widely fine-tuned by the promoters’ positioning, natural regulatory mechanisms, and other factors, including the antibiotic rifampicin, which hampers RNAP promoter escape. From this, and supported by in silico models, we concluded that the attenuation emerges from premature terminations generated by collisions between RNAPs elongating from upstream promoters and RNAPs occupying downstream promoters. Moreover, we found that these collisions can cause one or both RNAPs to fall-off. The broad spectrum of possible, externally regulated, attenuation strengths in synthetic tandem promoters should make these structures valuable internal regulators of future synthetic circuits.

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Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression

Cited by 9 publications

References 58 publications

Analytical kinetic model of native tandem promoters in E. coli

Analytical kinetic model of native tandem promoters in E. coli

Sequence-dependent model of genes with dual σ factor preference

Transcription attenuation in synthetic promoters in tandem formation

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