Effects of growth rate and promoter activity on single-cell protein expression

Nordholt, Niclas; Heerden, Johan van; Kort, Remco; Bruggeman, Frank J.

doi:10.1038/s41598-017-05871-3

Cited by 38 publications

(34 citation statements)

References 48 publications

(92 reference statements)

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“…In combination with the NH 1 4 limitation experiment, the results demonstrate that phenotypic heterogeneity in a certain metabolic activity (i.e., N 2 fixation) can be driven by different modes of limitation (here limitation in NH 1 4 and H 2 S) in a single microbial population (i.e., C. phaeobacteroides). These results might be best understood in terms of a general feedback between growth state and gene expression (Klumpp et al, 2009;Scott et al, 2010;Kiviet et al, 2014;New et al, 2014;Solopova et al, 2014;Kotte et al, 2014;Guantes et al, 2016;Nordholt et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

Substrate and electron donor limitation induce phenotypic heterogeneity in different metabolic activities in a green sulphur bacterium

Zimmermann

Escrig

Lavik

et al. 2018

Environ Microbiol Rep

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Populations of genetically identical cells can display marked variation in phenotypic traits; such variation is termed phenotypic heterogeneity. Here, we investigate the effect of substrate and electron donor limitation on phenotypic heterogeneity in N and CO fixation in the green sulphur bacterium Chlorobium phaeobacteroides. We grew populations in chemostats and batch cultures and used stable isotope labelling combined with nanometer-scale secondary ion mass spectrometry (NanoSIMS) to quantify phenotypic heterogeneity. Experiments in H S (i.e. electron donor) limited chemostats show that varying levels of NH4+ limitation induce heterogeneity in N fixation. Comparison of phenotypic heterogeneity between chemostats and batch (unlimited for H S) populations indicates that electron donor limitation drives heterogeneity in N and CO fixation. Our results demonstrate that phenotypic heterogeneity in a certain metabolic activity can be driven by different modes of limitation and that heterogeneity can emerge in different metabolic processes upon the same mode of limitation. In conclusion, our data suggest that limitation is a general driver of phenotypic heterogeneity in microbial populations.

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Section: Resultsmentioning

confidence: 99%

Substrate and electron donor limitation induce phenotypic heterogeneity in different metabolic activities in a green sulphur bacterium

Zimmermann

Escrig

Lavik

et al. 2018

Environ Microbiol Rep

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“…The observed biphasic, non-exponential growth behaviour of a single cell along its cell-cycle raises the question of how its protein synthesis rate behaves. To address this, we exploited the fact that the B. subtilis strain used in this study expressed a constitutive fluorescent protein (GFP), from a genomic locus, that is controllable by an inducible promoter; we described this strain previously 8 . In this section we analyse the strain grown at full induction with 1 mM IPTG.…”

Section: Resultsmentioning

confidence: 99%

“…This growth mode is called balanced growth 1,2,3,4 . Yet, individual cells display molecular fluctuations that are the source for non-genetic heterogeneity within an isogenic population 5,6,7,8,9 and influence single cell growth behaviour 10 . How bacteria achieve the required homeostasis associated with balanced growth has been the subject of decades of microbial studies, both at the level of populations 11 and single-cells 12,13,14,15,16,17 .…”

Section: Introductionmentioning

confidence: 99%

Integrated biphasic growth rate, gene expression, and cell-size homeostasis behaviour of singleB. subtiliscells

Nordholt

Heerden²,

Bruggeman³

2019

Preprint

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Integrated biphasic growth rate, gene expression, 1 and cell-size homeostasis behaviour of single B. 2 subtilis cells 3 Niclas Nordholt 1,2+ 7 2 Current affiliation: Bundesanstalt für Materialforschung und 8 -prüfung, Running title: Biphasic growth behaviour of single B. subtilis cells 12 1 Biphasic growth behaviour of single B. subtilis cells ABSTRACT 13The growth rate of single bacterial cells is continuously disturbed by random fluctu-14 ations in biosynthesis rates and by deterministic cell-cycle events, such as division, 15 genome duplication, and septum formation. It is not understood whether, and 16 how, bacteria reject these disturbances. Here we quantified growth and consti-17 tutive protein expression dynamics of single Bacillus subtilis cells, as a function 18 of cell-cycle-progression. Variation in birth size and growth rate, resulting from 19 unequal cell division, is largely compensated for when cells divide again. We anal-20 ysed the cell-cycle-dynamics of these compensations and found that both growth 21 and protein expression exhibited biphasic behaviour. During a first phase of vari-22 able duration, the absolute rates were approximately constant and cells behaved 23 as sizers. In the second phase, rates increased and growth behaviour exhibited 24 characteristics of a timer-strategy. This work shows how cell-cycle-dependent rate 25 adjustments of biosynthesis and growth are integrated to compensate for physio-26 logical disturbances caused by cell division. 27 28 IMPORTANCE 29 Under constant conditions, bacterial populations can maintain a fixed average 30 cell size and constant exponential growth rate. At the single cell-level, however, 31 cell-division can cause significant physiological perturbations, requiring compen-32 satory mechanisms to restore the growth-related characteristics of individual cells 33 toward that of the average cell. Currently, there is still a major gap in our under-34 standing of the dynamics of these mechanisms, i.e. how adjustments in growth, 35 metabolism and biosynthesis are integrated during the bacterial cell-cycle to com-36 pensate the disturbances caused by cell division. Here we quantify growth and 37 constitutive protein expression in individual bacterial cells at sub-cell-cycle reso-38 lution. Significantly, both growth and protein production rates display structured 39 and coordinated cell-cycle-dependent dynamics. These patterns reveal the dy-40 namics of growth rate and size compensations during cell-cycle progression. Our 41 findings provide a dynamic cell-cycle perspective that offers novel avenues for the 42 interpretation of physiological processes that underlie cellular homeostasis in bac-43 teria. 44 Under constant conditions, isogenic populations of bacteria maintain time-invariant 46 distributions of cell size, generation time and macromolecular composition. This 47growth mode is called balanced growth 1,2,3,4 . Yet, individual cells display molec-48 ular fluctuations that are the source for non-genetic heterogeneity within an iso-49 geni...

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“…A large effort has been spent to investigate such phenotypic heterogeneity since it is supposed to be involved in cellular growth control and cancer initiation (see [12] and references therein). Within this framework, metabolism has recently gained interest since the intrinsic noise in gene expression and enzymes accumulation has been shown to propagate to growth rate fluctuations through metabolic fluxes, according to singlecell experiments [9], [13], [22].…”

Section: Introductionmentioning

confidence: 99%

Noise propagation in metabolic pathways: the role of growth-mediated feedback

Borri

Palumbo

Singh

2020

Preprint

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Metabolic networks are known to deal with the chemical reactions responsible to fuel cellular activities with energy and carbon source and, as a matter of fact, to set the growth rate of the cell. To this end, feedback and regulatory networks play a crucial role to handle adaptation to external perturbations and internal noise. In this work, a cellular resource is assumed to be activated at the end of a metabolic pathway, by means of a cascade of transformations. Such a cascade is triggered by the catalytic action of an enzyme that promotes the first transformation. The final product is responsible for the cellular growth rate modulation. This mechanism acts in feedback at the enzymatic level, since the enzyme (as well as all species) is subject to dilution, with the dilution rate set by growth. Enzymatic production is modeled by the occurrence of noisy bursts: a Stochastic Hybrid System is exploited to model the network and to investigate how such noise propagates on growth fluctuations. A major biological finding is that, differently from other models of metabolic pathways disregarding growth-mediated feedback, fluctuations in enzyme levels do not produce only local effects, but propagate up to the final product (hence to the growth rate). Furthermore, the delay provided by the cascade length helps in reducing the impact of enzymatic noise on to growth fluctuations. Analytical results are supported by Monte Carlo simulations.

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Effects of growth rate and promoter activity on single-cell protein expression

Cited by 38 publications

References 48 publications

Substrate and electron donor limitation induce phenotypic heterogeneity in different metabolic activities in a green sulphur bacterium

Substrate and electron donor limitation induce phenotypic heterogeneity in different metabolic activities in a green sulphur bacterium

Integrated biphasic growth rate, gene expression, and cell-size homeostasis behaviour of singleB. subtiliscells

Noise propagation in metabolic pathways: the role of growth-mediated feedback

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