RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

Gama-Castro, Socorro; Salgado, Heladia; Peralta-Gil, Martín; Santos-Zavaleta, Alberto; Muñiz-Rascado, Luis; Solano-Lira, Hilda; Jiménez-Jacinto, Verónica; Weiss, Verena; García-Sotelo, Jair Santiago; López-Fuentes, Alejandra; Porrón-Sotelo, Liliana; Alquicira-Hernández, Shirley; Medina-Rivera, Alejandra; Martínez-Flores, Irma; Alquicira-Hernández, Kevin; Martínez-Adame, Ruth; Bonavides-Martínez, César; Miranda-Ríos, Juan; Huerta, A.; Mendoza-Vargas, Alfredo; Collado‐Torres, Leonardo; Taboada, Blanca; Vega‐Alvarado, Leticia; Olvera, Maricela; Olvera, Leticia; Grande, Ricardo; Morett, Enrique; Collado‐Vides, Julio

doi:10.1093/nar/gkq1110

Cited by 332 publications

(402 citation statements)

References 19 publications

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“…In E. coli, the expression of 51% of all genes are under control of seven highly expressed global transcriptional regulators (CRP, FNR, IHF, FIS, ArcA, NarL and Lrp). Among these all but ArcA are employing negative feedback on their own synthesis 6,7 . However, all the six TFs bind weakly to the operators mediating the feedback compared with their binding to other specific sites (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Negative feedback is therefore commonly used to maintain homeostasis and to reduce the fluctuations in intracellular processes such as gene expression [3][4][5] . For example, nearly half of the B300 transcription factors (TFs) in Escherichia coli make use of negative feedback on their own expression 6,7 . However, the chemical noise that makes regulation necessary also limits the accuracy of feedback regulation 8 .…”

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confidence: 99%

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Transcription factor binding kinetics constrain noise suppression via negative feedback

2013

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Negative autoregulation, where a transcription factor regulates its own expression by preventing transcription, is commonly used to suppress fluctuations in gene expression. Recent single molecule in vivo imaging has shown that it takes significant time for a transcription factor molecule to bind its chromosomal binding site. Given the slow association kinetics, transcription factor mediated feedback cannot at the same time be fast and strong. Here we show that with a limited association rate follows an optimal transcription factor binding strength where noise is maximally suppressed. At the optimal binding strength the binding site is free a fixed fraction of the time independent of the transcription factor concentration. One consequence is that high-copy number transcription factors should bind weakly to their operators, which is observed for transcription factors in Escherichia coli. The results demonstrate that a binding site's strength may be uncorrelated to its functional importance.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Transcription factor binding kinetics constrain noise suppression via negative feedback

2013

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“…Similar to this promoter, which was engineered from two native promoters [6], most native promoters in E. coli are regulated by more than one regulatory molecule [35]. We hypothesize that this may be a consequence of a need for plasticity of noise in gene expression, to facilitate survival in fluctuating environments [36].…”

Section: Discussionmentioning

confidence: 99%

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

et al. 2012

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a b s t r a c tThe kinetics of transcription initiation in Escherichia coli depend on the duration of two rate-limiting steps, the closed and the open complex formation. In a lac promoter variant, P lac/ara-1 , the kinetics of these steps is controlled by IPTG and arabinose. From in vivo single-RNA measurements, we find that induction affects the mean and normalized variance of the intervals between consecutive RNA productions. Transcript production is sub-Poissonian in all conditions tested. The kinetics of each step is independently controlled by a different inducer. We conclude that the regulatory mechanism of P lac/ara-1 allows the stochasticity of gene expression to be environment-dependent.

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“…All functional annotations were obtained from publicly available online databases, such as EcoCyc [54], UniProtKB [55] and RegulonDB [56]. …”

Section: Accepted M Manuscriptmentioning

confidence: 99%

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

Wong

Bhandari

Janga

et al. 2017

Journal of Molecular Biology

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Highlights1. RavA-ViaA form a chaperone-like complex interacting with respiratory chains. 2.RavA-ViaA are induced under oxygen-limiting conditions. 3.RavA-ViaA interact with the flavin-containing subunit of fumarate reductase. 4.RavA-ViaA modulate the activity of the fumarate reductase complex. AbstractRavA is a MoxR AAA+ protein that functions together with a partner protein that we termed [187 words]

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RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

Cited by 332 publications

References 19 publications

Transcription factor binding kinetics constrain noise suppression via negative feedback

Transcription factor binding kinetics constrain noise suppression via negative feedback

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

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