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Added value of autoregulation and multi-step kinetics of transcription initiation

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Added value of autoregulation and multi-step kinetics of transcription initiation. / Prajapat, Mahendra Kumar; Ribeiro, Andre S.

julkaisussa: Royal Society Open Science, Vuosikerta 5, Nro 11, 181170, 01.11.2018.

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Prajapat, Mahendra Kumar ; Ribeiro, Andre S. / Added value of autoregulation and multi-step kinetics of transcription initiation. Julkaisussa: Royal Society Open Science. 2018 ; Vuosikerta 5, Nro 11.

Bibtex - Lataa

@article{af3c483ed64b4dc7864f40aea5dffbab,
title = "Added value of autoregulation and multi-step kinetics of transcription initiation",
abstract = "Bacterial gene expression regulation occurs mostly during transcription, which has two main rate-limiting steps: the close complex formation, when the RNA polymerase binds to an active promoter, and the subsequent open complex formation, after which it follows elongation. Tuning these steps’ kinetics by the action of e.g. transcription factors, allows for a wide diversity of dynamics. For example, adding autoregulation generates single-gene circuits able to perform more complex tasks. Using stochastic models of transcription kinetics with empirically validated parameter values, we investigate how autoregulation and the multi-step transcription initiation kinetics of single-gene autoregulated circuits can be combined to fine-tune steady state mean and cell-to-cell variability in protein expression levels, as well as response times. Next, we investigate how they can be jointly tuned to control complex behaviours, namely, time counting, switching dynamics and memory storage. Overall, our finding suggests that, in bacteria, jointly regulating a single-gene circuit’s topology and the transcription initiation multi-step dynamics allows enhancing complex task performance.",
keywords = "Autoregulation mechanisms, Cell-to-cell variability, Rate-limiting steps, Transcription initiation",
author = "Prajapat, {Mahendra Kumar} and Ribeiro, {Andre S.}",
year = "2018",
month = "11",
day = "1",
doi = "10.1098/rsos.181170",
language = "English",
volume = "5",
journal = "Royal Society Open Science",
issn = "2054-5703",
publisher = "Royal Society, The",
number = "11",

}

RIS (suitable for import to EndNote) - Lataa

TY - JOUR

T1 - Added value of autoregulation and multi-step kinetics of transcription initiation

AU - Prajapat, Mahendra Kumar

AU - Ribeiro, Andre S.

PY - 2018/11/1

Y1 - 2018/11/1

N2 - Bacterial gene expression regulation occurs mostly during transcription, which has two main rate-limiting steps: the close complex formation, when the RNA polymerase binds to an active promoter, and the subsequent open complex formation, after which it follows elongation. Tuning these steps’ kinetics by the action of e.g. transcription factors, allows for a wide diversity of dynamics. For example, adding autoregulation generates single-gene circuits able to perform more complex tasks. Using stochastic models of transcription kinetics with empirically validated parameter values, we investigate how autoregulation and the multi-step transcription initiation kinetics of single-gene autoregulated circuits can be combined to fine-tune steady state mean and cell-to-cell variability in protein expression levels, as well as response times. Next, we investigate how they can be jointly tuned to control complex behaviours, namely, time counting, switching dynamics and memory storage. Overall, our finding suggests that, in bacteria, jointly regulating a single-gene circuit’s topology and the transcription initiation multi-step dynamics allows enhancing complex task performance.

AB - Bacterial gene expression regulation occurs mostly during transcription, which has two main rate-limiting steps: the close complex formation, when the RNA polymerase binds to an active promoter, and the subsequent open complex formation, after which it follows elongation. Tuning these steps’ kinetics by the action of e.g. transcription factors, allows for a wide diversity of dynamics. For example, adding autoregulation generates single-gene circuits able to perform more complex tasks. Using stochastic models of transcription kinetics with empirically validated parameter values, we investigate how autoregulation and the multi-step transcription initiation kinetics of single-gene autoregulated circuits can be combined to fine-tune steady state mean and cell-to-cell variability in protein expression levels, as well as response times. Next, we investigate how they can be jointly tuned to control complex behaviours, namely, time counting, switching dynamics and memory storage. Overall, our finding suggests that, in bacteria, jointly regulating a single-gene circuit’s topology and the transcription initiation multi-step dynamics allows enhancing complex task performance.

KW - Autoregulation mechanisms

KW - Cell-to-cell variability

KW - Rate-limiting steps

KW - Transcription initiation

U2 - 10.1098/rsos.181170

DO - 10.1098/rsos.181170

M3 - Article

VL - 5

JO - Royal Society Open Science

JF - Royal Society Open Science

SN - 2054-5703

IS - 11

M1 - 181170

ER -