Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria

Sekar, Karthik; Rusconi, Roberto; Sauls, John T.; Fuhrer, Tobias; Noor, Elad; Nguyen, Jen; Fernández, Vicente; Buffing, Marieke F.; Berney, Michael; Jun, Suckjoon; Stocker, Roman; Sauer, Uwe

doi:10.15252/msb.20188623

Cited by 60 publications

(86 citation statements)

References 66 publications

(82 reference statements)

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“…Many different mechanistic models have been found to be consistent with the 'adder' mode of size control, from titration mechanisms to various forms of control connected to chromosome replication 38,39 . Our additional observations may also be consistent with more than one model as well, but by demonstrating three distinctly different modes in three different situations, we believe that, combined with more systematic analyses of various mutants, this kind of experiments will help distinguish between possible mechanistic models 40,41 .…”

Section: Size Regulation During Entry and Exit From Stationary Phasesupporting

confidence: 74%

“…Specifically, many models of growth control invoke replication patterns, and as described above, those patterns are different in entry and exit from stationary phase 39,40 . However, dividing more times without additional protein production also causes changes in the levels of division proteins, which also have been invoked in explanations of growth control 41,48 . More detailed models of how these processes change during entry into and exit from stationary phase may thus help discriminate between various hypotheses, especially if also analyzing how various mutants control growth as they enter and exit stationary phase.…”

Section: Discussionmentioning

confidence: 99%

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Tracking bacterial lineages in complex and dynamic environments with applications to growth control and persistence

Bakshi

Leoncini

Baker

et al. 2020

Preprint

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As microbes deplete local resources and transition from exponential to stationary phase they can change greatly in size, morphology, growth and expression-profiles. These responses can also vary importantly between individual cells, as shown by population snapshots. However, it has been difficult to track individual cells along the growth curve to determine the progression of events or correlations between how cells enter and exit dormancy. We have developed a platform for tracking >10 5 parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track the batch population. This provides a microcosm of bulk growth with exceptional resolution and control, while enabling conventional bulk assays on the same culture. We used the platform to show that for both Escherichia coli and Bacillus subtilis, growth changes from an 'adder' mode in exponential phase to a mixed 'adder-timer' entering stationary phase, and then a near-perfect 'sizer' upon exit -creating broadly distributed cell sizes in stationary phase -and rapid return to narrowly distributed sizes upon exit. By high-throughput tracking of single cells as they enter and exit stationary phase, we further show that the heterogeneity in entry and exit behavior has little consequence in regular wake up from overnight stationary phase but can play important role in determining population fitness after long periods of dormancy or survival against antibiotics.

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Section: Size Regulation During Entry and Exit From Stationary Phasesupporting

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Tracking bacterial lineages in complex and dynamic environments with applications to growth control and persistence

Bakshi

Leoncini

Baker

et al. 2020

Preprint

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“…For nutrient shift experiments, two syringe pumps were used in conjunction with a manual Y-valve near the device inlet. Cells experienced the change in nutrients in a time interval shorter than the imaging interval 39 .…”

Section: Mother Machine Cell Preparation and Image Acquisitionmentioning

confidence: 99%

“…As a result, both initiation and division are delayed. For division, active degradation or antagonization of FtsZ could further hinder the triggering of constriction 39,40 .…”

Section: Initiation Size Is Invariant Even During Nutrient Shifts At mentioning

confidence: 99%

Gram-positive and Gram-negative Bacteria Share Common Principles to Coordinate Growth and the Cell Cycle at the Single-cell Level

Sauls

Cox

Doh

et al. 2019

Preprint

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Bacillus subtilis and Escherichia coli are evolutionarily divergent model organisms that have elucidated fundamental differences between Gram-positive and Gram-negative bacteria, respectively. Despite their differences in cell cycle control at the molecular level, both organisms follow the same phenomenological principle for cell size homeostasis known as the adder. We thus asked to what extent B. subtilis and E. coli share common physiological principles in coordinating growth and the cell cycle. To answer this question, we measured physiological parameters of B. subtilis under various steady-state growth conditions with and without translation inhibition at both population and single-cell level. These experiments revealed core shared physiological principles between B. subtilis and E. coli. Specifically, we show that both organisms maintain an invariant cell size per replication origin at initiation, with and without growth inhibition, and even during nutrient shifts at the single-cell level. Furthermore, both organisms also inherit the same "hierarchy" of physiological parameters ranked by their coefficient of variation. Based on these findings, we suggest that the basic coordination principles between growth and the cell cycle in bacteria may have been established in the very early stages of evolution.

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“…Link et al recently achieved high temporal resolution on many metabolites by developing an automated real-time metabolomics platform that samples liquid cultures of single cells and directly injects them onto a time-of-flight mass spectrometer every 15-30s 11 . The group have more recently probed the interactions between biomass synthesis and cell division in E. coli using this method 12…”

mentioning

confidence: 99%

Continuous in vivo metabolism by NMR

Judge¹,

Wu²,

Tayyari³

et al. 2018

Preprint

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Dense time-series metabolomics data are essential for unraveling the underlying dynamic properties of metabolism. Here we extend high-resolution-magic angle spinning (HR-MAS) to enable continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) and provide analysis tools for these data. First, we reproduced a result in human chronic lymphoid leukemia cells by using isotope-edited CIVM-NMR to rapidly and unambiguously demonstrate unidirectional flux in branched-chain amino acid metabolism. We then collected untargeted CIVM-NMR datasets for Neurospora crassa, a classic multicellular model organism, and uncovered dynamics between central carbon metabolism, amino acid metabolism, energy storage molecules, and lipid and cell wall precursors. Virtually no sample preparation was required to yield a dynamic metabolic fingerprint over hours to days at ~4-min temporal resolution with little noise. CIVM-NMR is simple and readily adapted to different types of cells and microorganisms, offering an experimental complement to kinetic models of metabolism for diverse biological systems. composition with 4-8 min resolution for chronic lymphoid leukemia. Sedimentation and line broadening are major factors that limit standard NMR measurements of complex samples like cells. Koczula et al. were able to mitigate sedimentation by immobilizing the single cells in agarose 13 .Alternatively, HR-MAS enables high-resolution NMR measurements on mixed-phase samples such as tissues 14 , or more recently, living organisms 10,15-18 with minimal line broadening. In this study, we extended HR-MAS to real-time continuous in vivo measurements of metabolism in cells. Using isotope editing, CIVM-NMR was able to reproduce and more directly observe a surprising branched-chain amino acid (BCAA) flux result reported last year in human myeloid leukemia cells 19 . We found that CIVM-NMR was not only easier but faster and more conclusive than traditional approaches for flux measurements in human cell cultures. We then applied CIVM-NMR to the multicellular filamentous fungus, N. crassa, in both aerobic and anaerobic environments. We observed highly reproducible dynamics in central carbon and amino acid metabolism with ~4 min resolution over 11 hours. The continuous nature of these measurements facilitated metabolite annotation, and semi-automated peak tracing provided relative quantification of known and unknown compounds. We developed several new MATLAB functions and workflows, freely available through GitHub, for the analysis and visualization of these novel data. As CIVM-NMR can be applied widely to cells, tissues, and small multicellular organisms, it enables new opportunities in fields such as developmental and chronobiology for monitoring high-resolution metabolic time-series data. Importantly, it will enable more robust and experimentally-based kinetic metabolic models for diverse biological systems.We thank the A. Simpson lab for discussions and advice on drilling holes in rotor caps, M. Case, Clifford Slayman, and Z. Lewis for discussions on Neuros...

show abstract

Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria

Cited by 60 publications

References 66 publications

Tracking bacterial lineages in complex and dynamic environments with applications to growth control and persistence

Tracking bacterial lineages in complex and dynamic environments with applications to growth control and persistence

Gram-positive and Gram-negative Bacteria Share Common Principles to Coordinate Growth and the Cell Cycle at the Single-cell Level

Continuous in vivo metabolism by NMR

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