A strategy for dissecting the kinetics of transcription repression mechanisms

Cristina S. D. Palma; Sofia Startceva; Ramakanth Neeli-Venkata; Marzieh Zare; Nadia S. M. Gonçalves; Jose M. Fonseca; Samuel M. D. Oliveira; Andre S. Ribeiro

doi:10.1007/978-981-10-5122-7_274

A strategy for dissecting the kinetics of transcription repression mechanisms

Cristina S. D. Palma, Sofia Startceva, Ramakanth Neeli-Venkata, Marzieh Zare, Nadia S. M. Gonçalves, Jose M. Fonseca, Samuel M. D. Oliveira, Andre S. Ribeiro

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Citation (Scopus)

Abstract

Promoters in Escherichia coli include an ‘OFF’ state, during which transcription is halted. Here, we propose a novel empirical method for assessing the time-length spent by promoters in this state. It relies on direct measurements of RNA production kinetics at the single molecule level at different induction levels, followed by an estimation of the RNA production rate under infinite induction, which is then compared to this rate under real, maximum induction. We apply it to the LacO3O1 promoter and infer that, under full induction, on average, 15% of the time between successful transcription events is spent in the OFF state. We verify this result by comparing the kinetics of a mutant strain lacking repressor molecules with that of the inferred rate under infinite induction. We expect this strategy of dissecting the kinetics of transcription repression to be applicable to a wide number of promoters in E. coli.

Original language	English
Title of host publication	EMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017
Publisher	Springer Verlag
Pages	1097-1100
Number of pages	4
Volume	65
ISBN (Print)	9789811051210
DOIs	https://doi.org/10.1007/978-981-10-5122-7_274
Publication status	Published - 1 Jan 2017
Event	Joint Conference of the European Medical and Biological Engineering Conference, EMBEC 2017 and Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2107 - Tampere, Finland Duration: 11 Jun 2017 → 15 Jun 2017

Conference

Conference	Joint Conference of the European Medical and Biological Engineering Conference, EMBEC 2017 and Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2107
Country/Territory	Finland
City	Tampere
Period	11/06/17 → 15/06/17

Keywords

Induction
OFF state
Transcription
τ plot

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10.1007/978-981-10-5122-7_274

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Palma, C. S. D., Startceva, S., Neeli-Venkata, R., Zare, M., Gonçalves, N. S. M., Fonseca, J. M., Oliveira, S. M. D., & Ribeiro, A. S. (2017). A strategy for dissecting the kinetics of transcription repression mechanisms. In EMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017 (Vol. 65, pp. 1097-1100). Springer Verlag. https://doi.org/10.1007/978-981-10-5122-7_274

Palma, Cristina S. D. ; Startceva, Sofia ; Neeli-Venkata, Ramakanth et al. / A strategy for dissecting the kinetics of transcription repression mechanisms. EMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017. Vol. 65 Springer Verlag, 2017. pp. 1097-1100

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abstract = "Promoters in Escherichia coli include an {\textquoteleft}OFF{\textquoteright} state, during which transcription is halted. Here, we propose a novel empirical method for assessing the time-length spent by promoters in this state. It relies on direct measurements of RNA production kinetics at the single molecule level at different induction levels, followed by an estimation of the RNA production rate under infinite induction, which is then compared to this rate under real, maximum induction. We apply it to the LacO3O1 promoter and infer that, under full induction, on average, 15% of the time between successful transcription events is spent in the OFF state. We verify this result by comparing the kinetics of a mutant strain lacking repressor molecules with that of the inferred rate under infinite induction. We expect this strategy of dissecting the kinetics of transcription repression to be applicable to a wide number of promoters in E. coli.",

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Palma, CSD, Startceva, S, Neeli-Venkata, R, Zare, M, Gonçalves, NSM, Fonseca, JM, Oliveira, SMD & Ribeiro, AS 2017, A strategy for dissecting the kinetics of transcription repression mechanisms. in EMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017. vol. 65, Springer Verlag, pp. 1097-1100, Joint Conference of the European Medical and Biological Engineering Conference, EMBEC 2017 and Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2107, Tampere, Finland, 11/06/17. https://doi.org/10.1007/978-981-10-5122-7_274

A strategy for dissecting the kinetics of transcription repression mechanisms. / Palma, Cristina S. D.; Startceva, Sofia; Neeli-Venkata, Ramakanth et al.
EMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017. Vol. 65 Springer Verlag, 2017. p. 1097-1100.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - A strategy for dissecting the kinetics of transcription repression mechanisms

AU - Palma, Cristina S. D.

AU - Startceva, Sofia

AU - Neeli-Venkata, Ramakanth

AU - Zare, Marzieh

AU - Gonçalves, Nadia S. M.

AU - Fonseca, Jose M.

AU - Oliveira, Samuel M. D.

AU - Ribeiro, Andre S.

PY - 2017/1/1

Y1 - 2017/1/1

N2 - Promoters in Escherichia coli include an ‘OFF’ state, during which transcription is halted. Here, we propose a novel empirical method for assessing the time-length spent by promoters in this state. It relies on direct measurements of RNA production kinetics at the single molecule level at different induction levels, followed by an estimation of the RNA production rate under infinite induction, which is then compared to this rate under real, maximum induction. We apply it to the LacO3O1 promoter and infer that, under full induction, on average, 15% of the time between successful transcription events is spent in the OFF state. We verify this result by comparing the kinetics of a mutant strain lacking repressor molecules with that of the inferred rate under infinite induction. We expect this strategy of dissecting the kinetics of transcription repression to be applicable to a wide number of promoters in E. coli.

AB - Promoters in Escherichia coli include an ‘OFF’ state, during which transcription is halted. Here, we propose a novel empirical method for assessing the time-length spent by promoters in this state. It relies on direct measurements of RNA production kinetics at the single molecule level at different induction levels, followed by an estimation of the RNA production rate under infinite induction, which is then compared to this rate under real, maximum induction. We apply it to the LacO3O1 promoter and infer that, under full induction, on average, 15% of the time between successful transcription events is spent in the OFF state. We verify this result by comparing the kinetics of a mutant strain lacking repressor molecules with that of the inferred rate under infinite induction. We expect this strategy of dissecting the kinetics of transcription repression to be applicable to a wide number of promoters in E. coli.

KW - Induction

KW - OFF state

KW - Transcription

KW - τ plot

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DO - 10.1007/978-981-10-5122-7_274

M3 - Conference contribution

AN - SCOPUS:85021725472

SN - 9789811051210

VL - 65

SP - 1097

EP - 1100

BT - EMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017

PB - Springer Verlag

T2 - Joint Conference of the European Medical and Biological Engineering Conference, EMBEC 2017 and Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2107

Y2 - 11 June 2017 through 15 June 2017

ER -

Palma CSD, Startceva S, Neeli-Venkata R, Zare M, Gonçalves NSM, Fonseca JM et al. A strategy for dissecting the kinetics of transcription repression mechanisms. In EMBEC and NBC 2017 - Joint Conference of the European Medical and Biological Engineering Conference EMBEC 2017 and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, NBC 2017. Vol. 65. Springer Verlag. 2017. p. 1097-1100 doi: 10.1007/978-981-10-5122-7_274

A strategy for dissecting the kinetics of transcription repression mechanisms

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