Escherichia coli adaptation and response to exposure to heavy atmospheric pollution

Abstract

90% of the world population is exposed to heavy atmospheric pollution. This is a major public health issue causing 7 million death each year. Air pollution comprises an array of pollutants such as particulate matters, ozone and carbon monoxide imposing a multifactorial stress on living cells. Here, Escherichia coli was used as model cell and adapted for 390 generations to atmospheric pollution to assess its long-term effects at the genetic, transcriptomic and physiological levels. Over this period, E. coli evolved to grow faster and acquired an adaptive mutation in rpoB, which encodes the RNA polymerase β subunit. Transcriptomic and biochemical characterization showed alteration of the cell membrane composition resulting in lesser permeability after the adaptation process. A second significant change in the cell wall structure of the adapted strain was the greater accumulation of the exopolysaccharides colanic acid and cellulose in the extracellular fraction. Results also indicated that amino acids homeostasis was involved in E. coli response to atmospheric pollutants. This study demonstrates that adaptive mutation with transformative physiological impact can be fixed in genome after exposure to atmospheric pollution and also provides a comprehensive portrait of the cellular response mechanisms involved.

Figure 1

Growth and adaptation of E. coli BW25113 under heavy atmospheric pollution. (A) Wild type grew under SLA, UPA230 and DEA613. SEM images of wild type grew under (B) SLA or (C) DEA613. (D) Growth rates of different transfers under DEA613. Growth of DEA613-adapted T56 culture and purified clones under (E) DEA or (F) SLA. Each growth curves are the mean of three replicates.

Figure 2

Differentially-expressed genes coding for proteins involved in the cell wall structure. Log₂ fold change (Log₂FC) values represent adapted T56-1 versus wt both grown under DEA613 (blue), UPA230-grown wt versus SLA-grown wt (purple), and DEA613-grown wt versus SLA-grown wt (pink), respectively. OM: outer membrane, Per.: periplasm, CM: cytoplasmic membrane.

Figure 3

Cell membrane changes in the DEA613-adapted strain T56-1. (A) Differential expression of genes involved in the glycerol-3-phosphate (glycerol-3P) metabolism, (B) in glycerophospholipid degradation, and (C) in fatty acid β-oxidation. Log₂FC values represent adapted T56-1 versus wt both grown under DEA613 (blue), and UPA230-grown wt versus SLA-grown wt (purple), respectively. (D) Outer membrane permeability. Higher fluorescence caused by NPN insertion in the membrane corresponds to higher OM permeability. Fluorescence values were normalized with OD 600 nm and results are the mean and standard deviation of three replicates. Cyt.: cytoplasm.

Figure 4

Exopolysaccharides accumulation in the DEA613-adapted strain T56-1. (A) Differential expression of genes involved in colanic acid and cellulose biosynthesis. Log₂FC values represent adapted T56-1 versus wt both grown under DEA613 (blue), and UPA230-grown wt versus SLA-grown wt (purple), respectively. (B) Colanic acid accumulation in both adapted strain T56-1 and wt grown under SLA or DEA613. To measure colanic acid, concentration of fucose, which is specific to the colanic acid monomer, was evaluated in the exopolysaccharide fraction. (C) Cellulose accumulation in both adapted strain T56-1 and wt grown under SLA or DEA613. Cellulose in the exopolysaccharide fraction was digested with cellulase and the resulting glucose was measured. Colanic acid and cellulose results were normalized with OD 600 nm and are the mean and standard deviation of three replicates. Fuc: fucose, Glu: glucose, Gal: galactose, Glc: glucuronic acid.

Figure 5

Amino acids metabolism in the DEA613-adapted strain T56-1. (A) Differential expression of genes involved in amino acids metabolism. (B) The tryptophan biosynthesis pathway. Log₂FC values in blue, purple and pink represent adapted T56-1 versus wt both grown under DEA613, UPA230-grown wt versus SLA-grown wt, and DEA613-grown wt versus SLA-grown wt, respectively. (C) Tryptophan concentration fold change in both adapted strain T56-1 and wt grown under SLA or DEA613. Tryptophan concentration results were normalized with OD 600 nm and are the mean and standard deviation of three replicates.

Figure 6

Differential expression of genes involved in the detoxification of RES in E. coli. (A) (Methyl) glyoxals and (B) quinones detoxification. Log₂FC values in blue and pink represent adapted T56-1 versus wt both grown under DEA613, and DEA613-grown wt versus SLA-grown wt, respectively.