Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy

ABSTRACT In nature, bacteria must survive long periods of nutrient deprivation while maintaining the ability to recover and grow when conditions improve. This quiescent state is called stationary phase. The biochemistry of Escherichia coli in stationary phase is reasonably well understood. Much less...

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Autores principales:	Yanyu Zhu, Mainak Mustafi, James C. Weisshaar
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	E. coli stationary phase diffusive properties nucleoid morphology spatial distributions superresolution fluorescence microscopy Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/39c554eaac1b4ac2a03a17f0fad15a66
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spelling	oai:doaj.org-article:39c554eaac1b4ac2a03a17f0fad15a662021-11-15T15:56:46ZBiophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy10.1128/mBio.00143-202150-7511https://doaj.org/article/39c554eaac1b4ac2a03a17f0fad15a662020-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00143-20https://doaj.org/toc/2150-7511ABSTRACT In nature, bacteria must survive long periods of nutrient deprivation while maintaining the ability to recover and grow when conditions improve. This quiescent state is called stationary phase. The biochemistry of Escherichia coli in stationary phase is reasonably well understood. Much less is known about the biophysical state of the cytoplasm. Earlier studies of harvested nucleoids concluded that the stationary-phase nucleoid is “compacted” or “supercompacted,” and there are suggestions that the cytoplasm is “glass-like.” Nevertheless, stationary-phase bacteria support active transcription and translation. Here, we present results of a quantitative superresolution fluorescence study comparing the spatial distributions and diffusive properties of key components of the transcription-translation machinery in intact E. coli cells that were either maintained in 2-day stationary phase or undergoing moderately fast exponential growth. Stationary-phase cells are shorter and exhibit strong heterogeneity in cell length, nucleoid volume, and biopolymer diffusive properties. As in exponential growth, the nucleoid and ribosomes are strongly segregated. The chromosomal DNA is locally more rigid in stationary phase. The population-weighted average of diffusion coefficients estimated from mean-square displacement plots is 2-fold higher in stationary phase for both RNA polymerase (RNAP) and ribosomal species. The average DNA density is roughly twice as high as that in cells undergoing slow exponential growth. The data indicate that the stationary-phase nucleoid is permeable to RNAP and suggest that it is permeable to ribosomal subunits. There appears to be no need to postulate migration of actively transcribed genes to the nucleoid periphery. IMPORTANCE Bacteria in nature usually lack sufficient nutrients to enable growth and replication. Such starved bacteria adapt into a quiescent state known as the stationary phase. The chromosomal DNA is protected against oxidative damage, and ribosomes are stored in a dimeric structure impervious to digestion. Stationary-phase bacteria can recover and grow quickly when better nutrient conditions arise. The biochemistry of stationary-phase E. coli is reasonably well understood. Here, we present results from a study of the biophysical state of starved E. coli. Superresolution fluorescence microscopy enables high-resolution location and tracking of a DNA locus and of single copies of RNA polymerase (the transcription machine) and ribosomes (the translation machine) in intact E. coli cells maintained in stationary phase. Evidently, the chromosomal DNA remains sufficiently permeable to enable transcription and translation to occur. This description contrasts with the usual picture of a rigid stationary-phase cytoplasm with highly condensed DNA.Yanyu ZhuMainak MustafiJames C. WeisshaarAmerican Society for MicrobiologyarticleE. coli stationary phasediffusive propertiesnucleoid morphologyspatial distributionssuperresolution fluorescence microscopyMicrobiologyQR1-502ENmBio, Vol 11, Iss 3 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	E. coli stationary phase diffusive properties nucleoid morphology spatial distributions superresolution fluorescence microscopy Microbiology QR1-502
spellingShingle	E. coli stationary phase diffusive properties nucleoid morphology spatial distributions superresolution fluorescence microscopy Microbiology QR1-502 Yanyu Zhu Mainak Mustafi James C. Weisshaar Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy
description	ABSTRACT In nature, bacteria must survive long periods of nutrient deprivation while maintaining the ability to recover and grow when conditions improve. This quiescent state is called stationary phase. The biochemistry of Escherichia coli in stationary phase is reasonably well understood. Much less is known about the biophysical state of the cytoplasm. Earlier studies of harvested nucleoids concluded that the stationary-phase nucleoid is “compacted” or “supercompacted,” and there are suggestions that the cytoplasm is “glass-like.” Nevertheless, stationary-phase bacteria support active transcription and translation. Here, we present results of a quantitative superresolution fluorescence study comparing the spatial distributions and diffusive properties of key components of the transcription-translation machinery in intact E. coli cells that were either maintained in 2-day stationary phase or undergoing moderately fast exponential growth. Stationary-phase cells are shorter and exhibit strong heterogeneity in cell length, nucleoid volume, and biopolymer diffusive properties. As in exponential growth, the nucleoid and ribosomes are strongly segregated. The chromosomal DNA is locally more rigid in stationary phase. The population-weighted average of diffusion coefficients estimated from mean-square displacement plots is 2-fold higher in stationary phase for both RNA polymerase (RNAP) and ribosomal species. The average DNA density is roughly twice as high as that in cells undergoing slow exponential growth. The data indicate that the stationary-phase nucleoid is permeable to RNAP and suggest that it is permeable to ribosomal subunits. There appears to be no need to postulate migration of actively transcribed genes to the nucleoid periphery. IMPORTANCE Bacteria in nature usually lack sufficient nutrients to enable growth and replication. Such starved bacteria adapt into a quiescent state known as the stationary phase. The chromosomal DNA is protected against oxidative damage, and ribosomes are stored in a dimeric structure impervious to digestion. Stationary-phase bacteria can recover and grow quickly when better nutrient conditions arise. The biochemistry of stationary-phase E. coli is reasonably well understood. Here, we present results from a study of the biophysical state of starved E. coli. Superresolution fluorescence microscopy enables high-resolution location and tracking of a DNA locus and of single copies of RNA polymerase (the transcription machine) and ribosomes (the translation machine) in intact E. coli cells maintained in stationary phase. Evidently, the chromosomal DNA remains sufficiently permeable to enable transcription and translation to occur. This description contrasts with the usual picture of a rigid stationary-phase cytoplasm with highly condensed DNA.
format	article
author	Yanyu Zhu Mainak Mustafi James C. Weisshaar
author_facet	Yanyu Zhu Mainak Mustafi James C. Weisshaar
author_sort	Yanyu Zhu
title	Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy
title_short	Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy
title_full	Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy
title_fullStr	Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy
title_full_unstemmed	Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy
title_sort	biophysical properties of <named-content content-type="genus-species">escherichia coli</named-content> cytoplasm in stationary phase by superresolution fluorescence microscopy
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/39c554eaac1b4ac2a03a17f0fad15a66
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Biophysical Properties of <named-content content-type="genus-species">Escherichia coli</named-content> Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy

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