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Genthon A. Analytical cell size distribution: lineage-population bias and parameter inference. J R Soc Interface 2022; 19:20220405. [PMID: 36416039 PMCID: PMC9682439 DOI: 10.1098/rsif.2022.0405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2023] Open
Abstract
We derive analytical steady-state cell size distributions for size-controlled cells in single-lineage experiments, such as the mother machine, which are fundamentally different from batch cultures where populations of cells grow freely. For exponential single-cell growth, characterizing most bacteria, the lineage-population bias is obtained explicitly. In addition, if volume is evenly split between the daughter cells at division, we show that cells are on average smaller in populations than in lineages. For more general power-law growth rates and deterministic volume partitioning, both symmetric and asymmetric, we derive the exact lineage distribution. This solution is in good agreement with Escherichia coli mother machine data and can be used to infer cell cycle parameters such as the strength of the size control and the asymmetry of the division. When introducing stochastic volume partitioning, we derive the large-size and small-size tails of the lineage distribution and show that the lineage-population bias only depends on the single-cell growth rate. These asymptotic behaviours are extended to the adder model of cell size control. When considering noisy single-cell growth rate, we derive the large-size lineage and population distributions. Finally, we show that introducing noise, either on the volume partitioning or on the single-cell growth rate, can cancel the lineage-population bias.
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Affiliation(s)
- Arthur Genthon
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
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2
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Jędrak J, Ochab-Marcinek A. Contributions to the 'noise floor' in gene expression in a population of dividing cells. Sci Rep 2020; 10:13533. [PMID: 32782314 PMCID: PMC7419568 DOI: 10.1038/s41598-020-69217-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/26/2020] [Indexed: 11/14/2022] Open
Abstract
Experiments with cells reveal the existence of a lower bound for protein noise, the noise floor, in highly expressed genes. Its origins are still debated. We propose a minimal model of gene expression in a proliferating bacterial cell population. The model predicts the existence of a noise floor and it semi-quantitatively reproduces the curved shape of the experimental noise vs. mean protein concentration plots. When the cell volume increases in a different manner than does the mean protein copy number, the noise floor level is determined by the cell population’s age structure and by the dependence of the mean protein concentration on cell age. Additionally, the noise floor level may depend on a biological limit for the mean number of bursts in the cell cycle. In that case, the noise floor level depends on the burst size distribution width but it is insensitive to the mean burst size. Our model quantifies the contributions of each of these mechanisms to gene expression noise.
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Affiliation(s)
- Jakub Jędrak
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224, Warsaw, Poland
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3
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Held J, Lorimer T, Pomati F, Stoop R, Albert C. Second-order phase transition in phytoplankton trait dynamics. CHAOS (WOODBURY, N.Y.) 2020; 30:053109. [PMID: 32491890 DOI: 10.1063/1.5141755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
Key traits of unicellular species, such as cell size, often follow scale-free or self-similar distributions, hinting at the possibility of an underlying critical process. However, linking such empirical scaling laws to the critical regime of realistic individual-based model classes is difficult. Here, we reveal new empirical scaling evidence associated with a transition in the population and the chlorophyll dynamics of phytoplankton. We offer a possible explanation for these observations by deriving scaling laws in the vicinity of the critical point of a new universality class of non-local cell growth and division models. This "criticality hypothesis" can be tested through new scaling predictions derived for our model class, for the response of chlorophyll distributions to perturbations. The derived scaling laws may also be generalized to other cellular traits and environmental drivers relevant to phytoplankton ecology.
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Affiliation(s)
- Jenny Held
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Tom Lorimer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Francesco Pomati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Ruedi Stoop
- Institute of Neuroinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Carlo Albert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
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4
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Jędrak J, Kwiatkowski M, Ochab-Marcinek A. Exactly solvable model of gene expression in a proliferating bacterial cell population with stochastic protein bursts and protein partitioning. Phys Rev E 2019; 99:042416. [PMID: 31108597 DOI: 10.1103/physreve.99.042416] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Indexed: 06/09/2023]
Abstract
Many of the existing stochastic models of gene expression contain the first-order decay reaction term that may describe active protein degradation or dilution. If the model variable is interpreted as the molecule number, and not concentration, the decay term may also approximate the loss of protein molecules due to cell division as a continuous degradation process. The seminal model of that kind leads to gamma distributions of protein levels, whose parameters are defined by the mean frequency of protein bursts and mean burst size. However, such models (whether interpreted in terms of molecule numbers or concentrations) do not correctly account for the noise due to protein partitioning between daughter cells. We present an exactly solvable stochastic model of gene expression in cells dividing at random times, where we assume description in terms of molecule numbers with a constant mean protein burst size. The model is based on a population balance equation supplemented with protein production in random bursts. If protein molecules are partitioned equally between daughter cells, we obtain at steady state the analytical expressions for probability distributions similar in shape to gamma distributions, yet with quite different values of mean burst size and mean burst frequency than would result from fitting of the classical continuous-decay model to these distributions. For random partitioning of protein molecules between daughter cells, we obtain the moment equations for the protein number distribution and thus the analytical formulas for the squared coefficient of variation.
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Affiliation(s)
- Jakub Jędrak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | | | - Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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5
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Abstract
Microbial cells go through repeated cycles of growth and division. These cycles are not perfect: the time and size at division can fluctuate from one cycle to the next. Still, cell size is kept tightly controlled, and fluctuations do not accumulate to large deviations. How this control is implemented in single cells is still not fully understood. We performed experiments that follow individual bacteria in microfluidic traps for hundreds of generations. This enables us to identify distinct individual dynamic properties that are maintained over many cycles of growth and division. Surprisingly, we find that each cell suppresses fluctuations with a different strength; this variability defines an “individual” behavior for each cell, which is inherited along many generations. Microbial growth and division are fundamental processes relevant to many areas of life science. Of particular interest are homeostasis mechanisms, which buffer growth and division from accumulating fluctuations over multiple cycles. These mechanisms operate within single cells, possibly extending over several division cycles. However, all experimental studies to date have relied on measurements pooled from many distinct cells. Here, we disentangle long-term measured traces of individual cells from one another, revealing subtle differences between temporal and pooled statistics. By analyzing correlations along up to hundreds of generations, we find that the parameter describing effective cell size homeostasis strength varies significantly among cells. At the same time, we find an invariant cell size, which acts as an attractor to all individual traces, albeit with different effective attractive forces. Despite the common attractor, each cell maintains a distinct average size over its finite lifetime with suppressed temporal fluctuations around it, and equilibration to the global average size is surprisingly slow (>150 cell cycles). To show a possible source of variable homeostasis strength, we construct a mathematical model relying on intracellular interactions, which integrates measured properties of cell size with those of highly expressed proteins. Effective homeostasis strength is then influenced by interactions and by noise levels and generally varies among cells. A predictable and measurable consequence of variable homeostasis strength appears as distinct oscillatory patterns in cell size and protein content over many generations. We discuss implications of our results to understanding mechanisms controlling division in single cells and their characteristic timescales.
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Sheldon spectrum and the plankton paradox: two sides of the same coin—a trait-based plankton size-spectrum model. J Math Biol 2017; 76:67-96. [PMID: 28547211 PMCID: PMC5754429 DOI: 10.1007/s00285-017-1132-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 04/18/2017] [Indexed: 01/25/2023]
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Intrinsic limits to gene regulation by global crosstalk. Nat Commun 2016; 7:12307. [PMID: 27489144 PMCID: PMC4976215 DOI: 10.1038/ncomms12307] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/21/2016] [Indexed: 01/21/2023] Open
Abstract
Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements. Limited specificity of transcription factor-DNA interactions leads to crosstalk in gene regulation. Here the authors consider global crosstalk in regulatory networks of growing size and complexity, and show that it imposes constraints on gene regulation and on the evolution of regulatory networks.
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Brenner N, Newman CM, Osmanović D, Rabin Y, Salman H, Stein DL. Universal protein distributions in a model of cell growth and division. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042713. [PMID: 26565278 DOI: 10.1103/physreve.92.042713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 06/05/2023]
Abstract
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal measurements of protein content, showing accumulation and division across generations. Here we present a stochastic growth-and-division model with feedback which captures these observed properties. The limiting copy number distribution is calculated exactly, and a single parameter is found to determine the distribution shape and the variance-to-mean relation. Estimating this parameter from bacterial temporal data reproduces the measured distribution shape with high accuracy and leads to predictions for future experiments.
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Affiliation(s)
- Naama Brenner
- Department of Chemical Engineering and Laboratory of Network Biology, Technion, Haifa 32000, Israel
| | - C M Newman
- Courant Institute of Mathematical Sciences, New York, New York 10012 USA and NYU-ECNU Institute of Mathematical Sciences at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Dino Osmanović
- Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yitzhak Rabin
- Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hanna Salman
- Department of Physics and Astronomy, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - D L Stein
- Department of Physics and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 USA and NYU-ECNU Institutes of Physics and Mathematical Sciences at NYU Shanghai, 3663 Zhongshan Road North, Shanghai, 200062, China
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Schwabe A, Bruggeman FJ. Contributions of cell growth and biochemical reactions to nongenetic variability of cells. Biophys J 2015; 107:301-313. [PMID: 25028872 DOI: 10.1016/j.bpj.2014.05.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/29/2014] [Accepted: 05/06/2014] [Indexed: 11/25/2022] Open
Abstract
Cell-to-cell variability in the molecular composition of isogenic, steady-state growing cells arises spontaneously from the inherent stochasticity of intracellular biochemical reactions and cell growth. Here, we present a general decomposition of the total variance in the copy number per cell of a particular molecule. It quantifies the individual contributions made by processes associated with cell growth, biochemical reactions, and their control. We decompose the growth contribution further into variance contributions of random partitioning of molecules at cell division, mother-cell heterogeneity, and variation in cell-cycle progression. The contribution made by biochemical reactions is expressed in variance generated by molecule synthesis, degradation, and their regulation. We use this theory to study the influence of different growth and reaction-related processes, such as DNA replication, variable molecule-partitioning probability, and synthesis bursts, on stochastic cell-to-cell variability. Using simulations, we characterize the impact of noise in the generation-time on cell-to-cell variability. This article offers a widely-applicable theory on the influence of biochemical reactions and cellular growth on the phenotypic variability of growing, isogenic cells. The theory aids the design and interpretation of experiments involving single-molecule counting or real-time imaging of fluorescent reporter constructs.
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Affiliation(s)
- Anne Schwabe
- Systems Bioinformatics, VU University, Amsterdam, The Netherlands
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Braun E. The unforeseen challenge: from genotype-to-phenotype in cell populations. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:036602. [PMID: 25719211 DOI: 10.1088/0034-4885/78/3/036602] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biological cells present a paradox, in that they show simultaneous stability and flexibility, allowing them to adapt to new environments and to evolve over time. The emergence of stable cell states depends on genotype-to-phenotype associations, which essentially reflect the organization of gene regulatory modes. The view taken here is that cell-state organization is a dynamical process in which the molecular disorder manifests itself in a macroscopic order. The genome does not determine the ordered cell state; rather, it participates in this process by providing a set of constraints on the spectrum of regulatory modes, analogous to boundary conditions in physical dynamical systems. We have developed an experimental framework, in which cell populations are exposed to unforeseen challenges; novel perturbations they had not encountered before along their evolutionary history. This approach allows an unbiased view of cell dynamics, uncovering the potential of cells to evolve and develop adapted stable states. In the last decade, our experiments have revealed a coherent set of observations within this framework, painting a picture of the living cell that in many ways is not aligned with the conventional one. Of particular importance here, is our finding that adaptation of cell-state organization is essentially an efficient exploratory dynamical process rather than one founded on random mutations. Based on our framework, a set of concepts underlying cell-state organization-exploration evolving by global, non-specific, dynamics of gene activity-is presented here. These concepts have significant consequences for our understanding of the emergence and stabilization of a cell phenotype in diverse biological contexts. Their implications are discussed for three major areas of biological inquiry: evolution, cell differentiation and cancer. There is currently no unified theoretical framework encompassing the emergence of order, a stable state, in the living cell. Hopefully, the integrated picture described here will provide a modest contribution towards a physics theory of the cell.
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Affiliation(s)
- Erez Braun
- Department of Physics and Network Biology Research Laboratories, Technion, Haifa 32000, Israel
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11
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Abstract
Biological cells in a population are variable in practically every property. Much is known about how variability of single cells is reflected in the statistical properties of infinitely large populations; however, many biologically relevant situations entail finite times and intermediate-sized populations. The statistical properties of an ensemble of finite populations then come into focus, raising questions concerning inter-population variability and dependence on initial conditions. Recent technologies of microfluidic and microdroplet-based population growth realize these situations and make them immediately relevant for experiments and biotechnological application. We here study the statistical properties, arising from metabolic variability of single cells, in an ensemble of micro-populations grown to saturation in a finite environment such as a micro-droplet. We develop a discrete stochastic model for this growth process, describing the possible histories as a random walk in a phenotypic space with an absorbing boundary. Using a mapping to Polya’s Urn, a classic problem of probability theory, we find that distributions approach a limiting inoculum-dependent form after a large number of divisions. Thus, population size and structure are random variables whose mean, variance and in general their distribution can reflect initial conditions after many generations of growth. Implications of our results to experiments and to biotechnology are discussed.
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Affiliation(s)
- Yuval Elhanati
- Department of Physics, Technion, Haifa, Israel
- Network Biology Research Lab, Technion, Haifa, Israel
| | - Naama Brenner
- Department of Chemical Engineering, Technion, Haifa, Israel
- Network Biology Research Lab, Technion, Haifa, Israel
- * E-mail:
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12
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Salman H, Brenner N, Tung CK, Elyahu N, Stolovicki E, Moore L, Libchaber A, Braun E. Universal protein fluctuations in populations of microorganisms. PHYSICAL REVIEW LETTERS 2012; 108:238105. [PMID: 23003996 DOI: 10.1103/physrevlett.108.238105] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Indexed: 05/12/2023]
Abstract
The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. We show here that protein distributions measured under a broad range of biological realizations collapse to a single non-gaussian curve under scaling by the first two moments. Moreover, in all experiments the variance is found to depend quadratically on the mean, showing that a single degree of freedom determines the entire distribution. Our results imply that protein fluctuations do not reflect any specific molecular or cellular mechanism, and suggest that some buffering process masks these details and induces universality.
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Affiliation(s)
- Hanna Salman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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