Dissecting the Control Mechanisms for DNA Replication and Cell Division in E. coli

Micali, Gabriele; Grilli, Jacopo; Marchi, Jacopo; Osella, Matteo; Lagomarsino, Marco Cosentino

doi:10.1016/j.celrep.2018.09.061

Cited by 54 publications

(81 citation statements)

References 40 publications

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“…However, as can be seen in Figure 2A , we observe that the initiation length L i and birth length L b are clearly correlated in all conditions, rejecting the initiation mass model. The absence of an initiation mass has been noted recently elsewhere ( Micali et al, 2018a). It should be noted, however, that even though the single-cell fluctuations show that initiation is unlikely to be triggered by a critical volume per origin, one may still investigate to what extent the average volume per origin of replication is held constant across different growth conditions ( Si et al, 2017 ).…”

Section: Resultssupporting

confidence: 55%

“…Thanks to experimental techniques like the one used here, models of bacterial cell cycle regulation dating back from the 1960’s have been recently re-examined in detail in several studies Wallden et al (2016); Si et al (2017); Micali et al (2018a); Ho and Amir (2015); Adiciptaningrum et al (2015); Logsdon et al (2017); Eun et al (2018); Tanouchi et al (2015); Campos et al (2014) . As much as these new data have been useful in shedding light on bacterial physiology regulation mechanism such as the adder, they have also revealed that multiple models are capable of reproducing in large parts experimental data, mainly as a consequence of the correlations existing between measurable cell cycle parameters.…”

Section: Discussionmentioning

confidence: 99%

“…Division is often assumed to be set by a timer starting at replication initiation. Alternatively, it was recently proposed that division and replication are independently regulated, and that the slowest process of the two sets the time of division for each replication cycle ( Micali et al, 2018a) . Finally, it is often assumed that the regulation strategy could be different at slow and fast growth where different constraints occur.…”

Section: Introductionmentioning

confidence: 99%

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Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism

Witz

Nimwegen

Julou

2019

Preprint

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Living cells proliferate by completing and coordinating two essential cycles, a division 9 cycle that controls cell size, and a DNA replication cycle that controls the number of chromosomal 10 copies in the cell. Despite lacking dedicated cell cycle control regulators such as cyclins in 11 eukaryotes, bacteria such as E. coli manage to tightly coordinate those two cycles across a wide 12 range of growth conditions, including situations where multiple nested rounds of replication 13 progress simultaneously. Various cell cycle models have been proposed to explain this feat, but it 14 has been impossible to validate them so far due to a lack of experimental tools for systematically 15 testing their different predictions. Recently new insights have been gained on the division cycle 16 through the study of the structure of fluctuations in growth, size, and division in individual cells. In 17 particular, it was found that cell size appears to be controlled by an adder mechanism, i.e. the 18 added volume between divisions is held approximately constant and fluctuates independently of 19 growth rate and cell size at birth. However, how replication initiation is regulated and coupled to 20 cell size control remains unclear, mainly due to scarcity of experimental measurements on 21 replication initiation at the single-cell level. Here, we used time-lapse microscopy in combination 22 with microfluidics to directly measure growth, division and replication in thousands of single E. coli 23 cells growing in both slow and fast growth conditions. In order to compare different 24 phenomenological models of the cell cycle, we introduce a statistical framework which assess their 25 ability to capture the correlation structure observed in the experimental data. Using this in 26 combination with stochastic simulations, our data indicate that, instead of thinking of the cell cycle 27 as running from birth to division, the cell cycle is controlled by two adder mechanisms starting at 28 the initiation of replication: the added volume since the last initiation event controls the timing of 29 both the next division event and the next replication initiation event. Interestingly the double-adder 30 mechanism identified in this study has recently been found to explain the more complex cell cycle 31 of mycobacteria, suggesting shared control strategies across species. 32 33 34 Across all domains of life, cell proliferation requires that the chromosome replication and cell 35 division cycles are coordinated to ensure that every new cell receives one copy of the genetic 36 material. While in eukaryotes this coordination is implemented by a dedicated regulatory system in 37which genome replication and division occur in well-separated stages, no such system has been 38 found in most bacteria. This suggests that the molecular events that control replication initiation 39 1 of 20 and division might be coordinated more directly in bacteria, through molecular interactions that 40 are yet to be elucidated. The contrast between this effi...

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Section: Resultssupporting

confidence: 55%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism

Witz

Nimwegen

Julou

2019

Preprint

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“…Two processes contribute to the determination of individual bacterial cell shape: growth and division. While the relationship between bacterial size control and the timing of cell division is being thoroughly investigated [7, 8, 9], the problem of how single microbial cells achieve shape homeostasis while growing between two successive divisions is comparatively less explored [10, 11, 12, 13], and can be – to some extent – factored out from that of regulation of cell division. In particular, the relationship between cell growth and shape control has to depend on the differential biosynthesis of cellular mass (volume) and surface-specific “building blocks” [14].…”

Section: Introductionmentioning

confidence: 99%

Single rod-shaped cell fluctuations from stochastic surface/volume growth rates

Romano

Lagomarsino

2019

Preprint

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AbstractGrowing rod-shaped bacterial cells need to modulate the production rates of different surface and bulk components. Population data show that the balance between these rates is central for cell physiology, and affects cell shape, but we still know little about these processes in single cells. We study a minimal stochastic model where single cells grow by two fluctuating volume-specific surface and volume growth rates, solving for the steady-state distributions and the correlation functions of the main geometric features. Our predictions allow us to address the detectability of different scenarios for the intrinsic coupling between the allocation of resources to surface and bulk growth.

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“…9, Supplementary Models 6 ). As ‘rate maintenance’ has been used to support the link between chromosome replication and cell division 38 , a more complete model is necessary to take into account the direct influence of chromosome events on cell division 10,11 .…”

mentioning

confidence: 99%

A general quantitative relation linking bacterial cell growth and the cell cycle

Zheng

Bai

Jiang

et al. 2019

Preprint

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The foundation of bacterial cell cycle studies has long resided in two interconnected dogmas between 18 biomass growth, DNA replication, and cell division during exponential growth: the SMK growth law 19 that relates cell mass (a measure of cell size) to growth rate 1 , and Donachie's hypothesis of a growth-20 rate-independent initiation mass 2 . These dogmas have spurred many efforts to understand their 21 molecular bases and physiological consequences 3-12 . Most of these studies focused on fast-growing 22 cells, with doubling times shorter than 60 min. Here, we systematically studied the cell cycle of E. coli 23 for a broad range of doubling times (24 min to over 10 hr), with particular attention on steady-state 24 growth. Surprisingly, we observed that neither dogma held across the range of growth rates examined. 25In their stead, a new linear relation unifying the slow-and fast-growth regimes was revealed between 26 the cell mass and the number of cell divisions it takes to replicate and segregate a newly initiated pair 27 of replication origins. This and other findings in this study suggest a single-cell division model, which 28 not only reproduces the bulk relations observed but also recapitulates the adder phenomenon 29 established recently for stochastically dividing cells 13-15 . These results allowed us to develop 30 quantitative insight into the bacterial cell cycle, providing a firm new foundation for the study of 31 bacterial growth physiology. 32 A fundamental notion in the quantitative study of bacterial physiology is steady state growth 16,17 , where 33the rate of total cell mass growth ( " ) is identical to the rate of cell number growth ( # ). To cover both 34 the slow-and fast-growth regimes, we cultured E. coli K12 MG1655 cells in 32 different growth media 35 with corresponding growth rates ranging from 0.06 to 1.7 h -1 (doubling times ranging from ~700 min to 36 24 min; see Extended Data Table 1). Special care was taken to ensure that all experimental cultures in 37this study lie on the steady-state line " = # , hereafter designated as ; see Extended Data Fig. 1. 38The SMK growth law 1 , long-accepted in the fast-growth regime, states that the population-averaged 39 cellular mass ( ) scales exponentially with growth rate, ~ )* , with a constant parameter ≈ 1 ℎ. 40We examined several measures of , including dry weight, optical density (OD), and cell size (by flow 41 cytometry and microscopic imaging) (Supplementary Methods). For each measure, we found the SMK 42 law to break down for growth rates below 0.7 h -1 ( Fig. 1a-d). Our OD data appear in good agreement 43 with that obtained by Schaechter et al. 1 (green squares in Fig. 1e) for the mostly fast growth rates they 44analyzed, even though they studied a Salmonella strain. We also extracted cell size data from recent 45 studies by Si et al. 3 and Gray et al. 18 , and found their data to be consistent with ours (blue and red symbols, 46 Fig. 1f). Aside from the average cell size, even the size distributions appear to be indistinguishable ...

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Dissecting the Control Mechanisms for DNA Replication and Cell Division in E. coli

Cited by 54 publications

References 40 publications

Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism

Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism

Single rod-shaped cell fluctuations from stochastic surface/volume growth rates

A general quantitative relation linking bacterial cell growth and the cell cycle

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