The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli.

Frontiers in Microbiology
Ashley SmithStefano Pagliara

Abstract

Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings con...Continue Reading

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Citations

Oct 8, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Urszula ŁapińskaStefano Pagliara
Jul 31, 2020·Scientific Reports·Yi-Kai LiuChi-Chung Chou
Nov 5, 2020·Genes·Rubén Sánchez-ClementeRafael Blasco
Apr 13, 2021·Frontiers in Cell and Developmental Biology·Rikke MorrishNicholas Stone
Aug 3, 2021·Frontiers in Microbiology·Hyun Ju KimSang Jun Lee
Oct 20, 2018·Journal of Proteome Research·Jordy Evan SulaimanHenry Lam
Aug 7, 2021·FEMS Microbiology Reviews·J UrbaniecJ McFadden
Oct 13, 2021·PLoS Biology·Erin L AttrillStefano Pagliara

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Methods Mentioned

BETA
PCA
RNA-seq
phosphotransferase
GTPase

Software Mentioned

DESeq2
goseq
bowtie
mcf
tophat2
fastq

Related Concepts

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