Literature DB >> 28069947

First-passage time approach to controlling noise in the timing of intracellular events.

Khem Raj Ghusinga1, John J Dennehy2, Abhyudai Singh3,4,5.   

Abstract

In the noisy cellular environment, gene products are subject to inherent random fluctuations in copy numbers over time. How cells ensure precision in the timing of key intracellular events despite such stochasticity is an intriguing fundamental problem. We formulate event timing as a first-passage time problem, where an event is triggered when the level of a protein crosses a critical threshold for the first time. Analytical calculations are performed for the first-passage time distribution in stochastic models of gene expression. Derivation of these formulas motivates an interesting question: Is there an optimal feedback strategy to regulate the synthesis of a protein to ensure that an event will occur at a precise time, while minimizing deviations or noise about the mean? Counterintuitively, results show that for a stable long-lived protein, the optimal strategy is to express the protein at a constant rate without any feedback regulation, and any form of feedback (positive, negative, or any combination of them) will always amplify noise in event timing. In contrast, a positive feedback mechanism provides the highest precision in timing for an unstable protein. These theoretical results explain recent experimental observations of single-cell lysis times in bacteriophage [Formula: see text] Here, lysis of an infected bacterial cell is orchestrated by the expression and accumulation of a stable [Formula: see text] protein up to a threshold, and precision in timing is achieved via feedforward rather than feedback control. Our results have broad implications for diverse cellular processes that rely on precise temporal triggering of events.

Entities:  

Keywords:  event timing; feedback control; first-passage time; single cell; stochastic gene expression

Mesh:

Substances:

Year:  2017        PMID: 28069947      PMCID: PMC5278449          DOI: 10.1073/pnas.1609012114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  45 in total

1.  Intrinsic and extrinsic contributions to stochasticity in gene expression.

Authors:  Peter S Swain; Michael B Elowitz; Eric D Siggia
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-17       Impact factor: 11.205

2.  Ecdysteroid control of cell cycle and cellular commitment in insect wing imaginal discs.

Authors:  Takashi Koyama; Masafumi Iwami; Sho Sakurai
Journal:  Mol Cell Endocrinol       Date:  2004-01-15       Impact factor: 4.102

3.  Stochastic protein expression in individual cells at the single molecule level.

Authors:  Long Cai; Nir Friedman; X Sunney Xie
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

4.  Transient changes in intercellular protein variability identify sources of noise in gene expression.

Authors:  Abhyudai Singh
Journal:  Biophys J       Date:  2014-11-04       Impact factor: 4.033

5.  Coherence and timing of cell cycle start examined at single-cell resolution.

Authors:  James M Bean; Eric D Siggia; Frederick R Cross
Journal:  Mol Cell       Date:  2006-01-06       Impact factor: 17.970

Review 6.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

7.  Bacteriophage adsorption rate and optimal lysis time.

Authors:  Yongping Shao; Ing-Nang Wang
Journal:  Genetics       Date:  2008-08-30       Impact factor: 4.562

8.  Noise in timing and precision of gene activities in a genetic cascade.

Authors:  Amnon Amir; Oren Kobiler; Assaf Rokney; Amos B Oppenheim; Joel Stavans
Journal:  Mol Syst Biol       Date:  2007-02-13       Impact factor: 11.429

9.  Reliable cell cycle commitment in budding yeast is ensured by signal integration.

Authors:  Xili Liu; Xin Wang; Xiaojing Yang; Sen Liu; Lingli Jiang; Yimiao Qu; Lufeng Hu; Qi Ouyang; Chao Tang
Journal:  Elife       Date:  2015-01-14       Impact factor: 8.140

10.  The magnitude and colour of noise in genetic negative feedback systems.

Authors:  Margaritis Voliotis; Clive G Bowsher
Journal:  Nucleic Acids Res       Date:  2012-05-11       Impact factor: 16.971

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  13 in total

1.  The Timing of Transcriptional Regulation in Synthetic Gene Circuits.

Authors:  Yu-Yu Cheng; Andrew J Hirning; Krešimir Josić; Matthew R Bennett
Journal:  ACS Synth Biol       Date:  2017-09-05       Impact factor: 5.110

2.  A Mechanistic Model of the Regulation of Division Timing by the Circadian Clock in Cyanobacteria.

Authors:  Po-Yi Ho; Bruno M C Martins; Ariel Amir
Journal:  Biophys J       Date:  2020-05-20       Impact factor: 4.033

3.  An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time.

Authors:  Katie Abley; Pau Formosa-Jordan; Hugo Tavares; Emily Yt Chan; Mana Afsharinafar; Ottoline Leyser; James Cw Locke
Journal:  Elife       Date:  2021-06-01       Impact factor: 8.140

4.  Relating cellular signaling timescales to single-molecule kinetics: A first-passage time analysis of Ras activation by SOS.

Authors:  William Y C Huang; Steven Alvarez; Yasushi Kondo; John Kuriyan; Jay T Groves
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-09       Impact factor: 12.779

Review 5.  Infection by bacteriophage lambda: an evolving paradigm for cellular individuality.

Authors:  Ido Golding
Journal:  Curr Opin Microbiol       Date:  2017-11-03       Impact factor: 7.934

6.  An Optimal Lysis Time Maximizes Bacteriophage Fitness in Quasi-Continuous Culture.

Authors:  Sherin Kannoly; Abhyudai Singh; John J Dennehy
Journal:  mBio       Date:  2022-04-25       Impact factor: 7.786

7.  Parallel arrangements of positive feedback loops limit cell-to-cell variability in differentiation.

Authors:  Anupam Dey; Debashis Barik
Journal:  PLoS One       Date:  2017-11-29       Impact factor: 3.240

8.  Temporal precision of regulated gene expression.

Authors:  Shivam Gupta; Julien Varennes; Hendrik C Korswagen; Andrew Mugler
Journal:  PLoS Comput Biol       Date:  2018-06-07       Impact factor: 4.475

9.  Molecular noise of innate immunity shapes bacteria-phage ecologies.

Authors:  Jakob Ruess; Maroš Pleška; Cǎlin C Guet; Gašper Tkačik
Journal:  PLoS Comput Biol       Date:  2019-07-02       Impact factor: 4.475

10.  Optimum Threshold Minimizes Noise in Timing of Intracellular Events.

Authors:  Sherin Kannoly; Tianhui Gao; Supravat Dey; Ing-Nang Wang; Abhyudai Singh; John J Dennehy
Journal:  iScience       Date:  2020-05-21
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