Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter

Kandhavelu, Meenakshisundaram; Lihavainen, Eero; Muthukrishnan, Anantha-Barathi; Yli‐Harja, Olli; Ribeiro, André S.

doi:10.1016/j.biosystems.2011.11.001

Cited by 9 publications

(4 citation statements)

References 28 publications

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“…2 . We selected this promoter, since its dynamics has been extensively characterized 2 , 21 , 29 , 63 – 67 and because it has the same logical structure as the lac promoter, with an activator and a repressor. 63 The resulting Lineweaver–Burk plot is shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Dissecting the stochastic transcription initiation process in liveEscherichia coli

Lloyd-Price

Startceva

Kandavalli

et al. 2016

DNA Res

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We investigate the hypothesis that, in Escherichia coli, while the concentration of RNA polymerases differs in different growth conditions, the fraction of RNA polymerases free for transcription remains approximately constant within a certain range of these conditions. After establishing this, we apply a standard model-fitting procedure to fully characterize the in vivo kinetics of the rate-limiting steps in transcription initiation of the Plac/ara-1 promoter from distributions of intervals between transcription events in cells with different RNA polymerase concentrations. We find that, under full induction, the closed complex lasts ∼788 s while subsequent steps last ∼193 s, on average. We then establish that the closed complex formation usually occurs multiple times prior to each successful initiation event. Furthermore, the promoter intermittently switches to an inactive state that, on average, lasts ∼87 s. This is shown to arise from the intermittent repression of the promoter by LacI. The methods employed here should be of use to resolve the rate-limiting steps governing the in vivo dynamics of initiation of prokaryotic promoters, similar to established steady-state assays to resolve the in vitro dynamics.

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Section: Resultsmentioning

confidence: 99%

Dissecting the stochastic transcription initiation process in liveEscherichia coli

Lloyd-Price

Startceva

Kandavalli

et al. 2016

DNA Res

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“…The K d for SesA/Mg 2ϩ dissociation was 10.5 mM (Fig. 4), which is a rather large value and may be similar to the physiological cellular concentration of Mg 2ϩ (43). We previously reported that Mg 2ϩ suppresses the factor SigE activity by promoting the interaction of SigE and the subunit of the magnesium-chelatase ChlH in Synechocystis (44).…”

Section: ) the Combination Of Ms Ms/ms And Ms/ms/ms Definitively Imentioning

confidence: 99%

Cyanobacteriochrome SesA Is a Diguanylate Cyclase That Induces Cell Aggregation in Thermosynechococcus

Enomoto

Nomura

Shimada

et al. 2014

Journal of Biological Chemistry

100

109

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“…However, the durations of other steps, namely the closed complex formation, isomerization, and promoter clearance are also sequence-dependent, differing widely between promoters and in different conditions (31). Environmental factors can also affect this kinetics (32,33). For example, apart from induction (34), factors such as temperature and pH can also affect the “rate-limiting” steps in initiation (30,35).…”

Section: Introductionmentioning

confidence: 99%

Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells

Muthukrishnan

Kandhavelu

Lloyd-Price

et al. 2012

Nucleic Acids Research

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In Escherichia coli , tetracycline prevents translation. When subject to tetracycline, E. coli express TetA to pump it out by a mechanism that is sensitive, while fairly independent of cellular metabolism. We constructed a target gene, P tetA -mRFP1-96BS, with a 96 MS2-GFP binding site array in a single-copy BAC vector, whose expression is controlled by the tetA promoter. We measured the in vivo kinetics of production of individual RNA molecules of the target gene as a function of inducer concentration and temperature. From the distributions of intervals between transcription events, we find that RNA production by P tetA is a sub-Poissonian process. Next, we infer the number and duration of the prominent sequential steps in transcription initiation by maximum likelihood estimation. Under full induction and at optimal temperature, we observe three major steps. We find that the kinetics of RNA production under the control of P tetA , including number and duration of the steps, varies with induction strength and temperature. The results are supported by a set of logical pairwise Kolmogorov-Smirnov tests. We conclude that the expression of TetA is controlled by a sequential mechanism that is robust, whereas sensitive to external signals.

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Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter

Cited by 9 publications

References 28 publications

Dissecting the stochastic transcription initiation process in liveEscherichia coli

Dissecting the stochastic transcription initiation process in liveEscherichia coli

Cyanobacteriochrome SesA Is a Diguanylate Cyclase That Induces Cell Aggregation in Thermosynechococcus

Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells

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