Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

Gray, William T.; Govers, Sander K.; Xiang, Yingjie; Parry, Bradley R.; Campos, Manuel; Kim, Sang-Jin; Jacobs‐Wagner, Christine

doi:10.1016/j.cell.2019.05.017

Cited by 117 publications

(118 citation statements)

References 125 publications

(136 reference statements)

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“…), and 4.7 ± 0.05 µm and 2.6 ± 0.05 µm, respectively, for cells grown at 30 ºC. At both temperatures, we found a linear dependence between the nucleoid length and the cell contour length, similar to other studies 16,18 (Fig. 2h).…”

Section: Replisomes Load Near the Middle Of The Cell And Then Move Awsupporting

confidence: 91%

Direct observation of independently moving replisomes in Escherichia coli

Japaridze

Gogou

Kerssemakers

et al. 2019

Preprint

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The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in E. coli cells with an increased width. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move independently from the origin to the terminus of replication along each of the two arms of the circular chromosome, providing direct support for the so-called train-track model, and against a factory model for replisomes. The origin of replication duplicates near midcell, initially splitting to random directions and subsequently towards the poles. The probability of successful segregation of chromosomes significantly decreases with increasing cell width, indicating that chromosome confinement by the cell boundary is an important driver of DNA segregation. Our findings resolve long standing questions in bacterial chromosome organization.

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Section: Replisomes Load Near the Middle Of The Cell And Then Move Awsupporting

confidence: 91%

Direct observation of independently moving replisomes in Escherichia coli

Japaridze

Gogou

Kerssemakers

et al. 2019

Preprint

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“…1e) for the mostly fast growth rates they analyzed, even though they studied a Salmonella strain. We also extracted cell size data from recent studies by Si et al 3 and Gray et al 18 , and found their data to be consistent with ours (blue and red symbols, Fig. 1f).…”

supporting

confidence: 85%

“…1f). Aside from the average cell size, even the size distributions appear to be indistinguishable for a variety of growth media 18 (Extended Data Fig. 2a).…”

mentioning

confidence: 99%

“…e , Comparison between the optical density data from panel b (gray filled circles) and the original data from Schaechter et al 1 . f , Comparison between the cell volume data from panel d (gray filled circles) and the data sets extracted from recent reports, Gray et al 18 (red triangles, 1 st right y-axis) or Si et al 3 (blue dots, 2 nd right y-axis). The data of Gray et al show a clear transition at growth rate ~0.7 h −1 as in the current study.…”

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confidence: 99%

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

Zheng

Bai

Jiang

et al. 2019

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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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“…Despite being about a thousand times longer than the dimensions of the cell, it is confined to a fraction of the cytosolic volume, which is referred to as the nucleoid (Wang et al, 2013). The cytosolic volume fraction occupied by a nucleoid has been estimated to be in the range of 20%-75% in E. coli (Woldringh, 2002, Sherratt, 2003, Fisher et al, 2013) and many other bacterial species (Gray et al, 2019). In contrast, when DNA is released from the cell, it expands to a volume that exceeds the cell volume by about 1000-fold (Cunha et al, 2001, Romantsov et al, 2007, Wegner et al, 2012.…”

Section: Introductionmentioning

confidence: 99%

The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid

Yang

Männik

Retterer

et al. 2019

Preprint

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DNA binding proteins, supercoiling, macromolecular crowders, and transient DNA attachments to the cell membrane have all been implicated in the organization of the bacterial chromosome. However, it is unclear what role these factors play in compacting the bacterial DNA into a distinct organelle-like entity, the nucleoid. By analyzing the effects of osmotic shock and mechanical squeezing on Escherichia coli, we show that macromolecular crowders play a dominant role in the compaction of the DNA into the nucleoid. We find that a 30% increase in the crowder concentration from physiological levels leads to a 3-fold decrease in the nucleoid's volume. The compaction is anisotropic, being higher along the long axes of the cell at low crowding levels. At higher crowding levels the compression becomes isotropic, implying that E. coli nucleoids lack a well-defined backbone. We furthermore show that the compressibility of the nucleoid is not significantly affected by cell growth rates and by prior treatment with rifampicin. The latter results point out that in addition to poly-ribosomes, soluble cytoplasmic proteins have a significant contribution in determining the size of the nucleoid.

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Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

Cited by 117 publications

References 125 publications

Direct observation of independently moving replisomes in Escherichia coli

Direct observation of independently moving replisomes in Escherichia coli

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

The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid

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