Stationary phase-specific expression of the fic gene in Escherichia coli K-12 is controlled by the rpoS gene product (σ38)

ABSTRACT The food-borne pathogen Escherichia coli O157:H7 is commonly exposed to organic acid in processed and preserved foods, allowing adaptation and the development of tolerance to pH levels otherwise lethal. Since little is known about the molecular basis of adaptation of E. coli to organic acids, we studied K-12 MG1655 and O157:H7 Sakai during exposure to acetic, lactic, and hydrochloric acid at pH 5.5. This is the first analysis of the pH-dependent transcriptomic response of stationary-phase E. coli. Thirty-four genes and three intergenic regions were upregulated by both strains during exposure to all acids. This universal acid response included genes involved in oxidative, envelope, and cold stress resistance and iron and manganese uptake, as well as 10 genes of unknown function. Acidulant- and strain-specific responses were also revealed. The acidulant-specific response reflects differences in the modes of microbial inactivation, even between weak organic acids. The two strains exhibited similar responses to lactic and hydrochloric acid, while the response to acetic acid was distinct. Acidulant-dependent differences between the strains involved induction of genes involved in the heat shock response, osmoregulation, inorganic ion and nucleotide transport and metabolism, translation, and energy production. E. coli O157:H7-specific acid-inducible genes were identified, suggesting that the enterohemorrhagic E. coli strain possesses additional molecular mechanisms contributing to acid resistance that are absent in K-12. While E. coli K-12 was most resistant to lactic and hydrochloric acid, O157:H7 may have a greater ability to survive in more complex acidic environments, such as those encountered in the host and during food processing.

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Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances inEscherichia coli pgiknockout evolutions

10.1101/342709 ◽

2018 ◽

Cited By ~ 1

Author(s):

Douglas McCloskey ◽

Sibei Xu ◽

Troy E. Sandberg ◽

Elizabeth Brunk ◽

Ying Hefner ◽

...

Keyword(s):

Escherichia Coli ◽

Gene Product ◽

Major Gene ◽

Regulatory Function ◽

Second Step ◽

Valuable Insight ◽

Adaptive Laboratory Evolution ◽

Laboratory Evolution ◽

K 12 ◽

Mg1655 Strain

AbstractA mechanistic understanding of how new phenotypes develop to overcome the loss of a gene product provides valuable insight on both the metabolic and regulatory function of the lost gene. Thepgigene, whose product catalyzes the second step in glycolysis, was deleted in a growth optimizedEscherichia coliK-12 MG1655 strain. The knock-out (KO) strain exhibited an 80% drop in growth rate, that was largely recovered in eight replicate, but phenotypically distinct, cultures after undergoing adaptive laboratory evolution (ALE). Multi omic data sets showed that the loss ofpgisubstantially shifted pathway usage leading to a redox and sugar phosphate stress response. These stress responses were overcome by unique combinations of innovative mutations selected for by ALE. Thus, we show the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after loss of a major gene product.ImportanceA mechanistic understanding of how new phenotypes develop to overcome the loss of a gene product provides valuable insight on both the metabolic and regulatory function of the lost gene. Thepgigene, whose product catalyzes the second step in glycolysis, was deleted in a growth optimizedEscherichia coliK-12 MG1655 strain. Eight replicate adaptive laboratory evolution (ALE) resulted in eight phenotypically distinct endpoints that were able to overcome the gene loss. Utilizing multi-omics analysis, we show the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after loss of a major gene product.

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Regulation of Tyrosine and Phenylalanine Biosynthesis in Escherichia coli K-12: Properties of the tyrR Gene Product

Journal of Bacteriology ◽

10.1128/jb.115.3.1135-1144.1973 ◽

1973 ◽

Vol 115 (3) ◽

pp. 1135-1144 ◽

Cited By ~ 15

Author(s):

H. Camakaris ◽

J. Pittard

Keyword(s):

Escherichia Coli ◽

Gene Product ◽

K 12

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Experimental Evolution ofEscherichia coliK-12 at High pH and with RpoS Induction

Applied and Environmental Microbiology ◽

10.1128/aem.00520-18 ◽

2018 ◽

Vol 84 (15) ◽

Cited By ~ 6

Author(s):

Issam Hamdallah ◽

Nadia Torok ◽

Katarina M. Bischof ◽

Nadim Majdalani ◽

Sriya Chadalavada ◽

...

Keyword(s):

Escherichia Coli ◽

Stationary Phase ◽

Experimental Evolution ◽

Sigma Factor ◽

Point Mutations ◽

Envelope Proteins ◽

Content Type ◽

High Ph ◽

K 12 ◽

Sigma Factor Rpos

ABSTRACTExperimental evolution ofEscherichia coliK-12 W3110 by serial dilutions for 2,200 generations at high pH extended the range of sustained growth from pH 9.0 to pH 9.3. pH 9.3-adapted isolates showed mutations in DNA-binding regulators and envelope proteins. One population showed an IS1knockout ofphoB(encoding the positive regulator of the phosphate regulon). AphoB::kanRknockout increased growth at high pH.phoBmutants are known to increase production of fermentation acids, which could enhance fitness at high pH. Mutations inpcnB[poly(A) polymerase] also increased growth at high pH. Three out of four populations showed deletions oftorI, an inhibitor of TorR, which activates expression oftorCAD(trimethylamineN-oxide respiration) at high pH. All populations showed point mutations affecting the stationary-phase sigma factor RpoS, either in the coding gene or in genes for regulators of RpoS expression. RpoS is required for survival at extremely high pH. In our microplate assay,rpoSdeletion slightly decreased growth at pH 9.1. RpoS protein accumulated faster at pH 9 than at pH 7. The RpoS accumulation at high pH required the presence of one or more antiadaptors that block degradation (IraM, IraD, and IraP). Other genes with mutations after high-pH evolution encode regulators, such as those encoded byyobG(mgrB) (PhoPQ regulator),rpoN(nitrogen starvation sigma factor),malI, andpurR, as well as envelope proteins, such as those encoded byompTandyahO. Overall,E. colievolution at high pH selects for mutations in key transcriptional regulators, includingphoBand the stationary-phase sigma factor RpoS.IMPORTANCEEscherichia coliin its native habitat encounters high-pH stress such as that of pancreatic secretions. Experimental evolution over 2,000 generations showed selection for mutations in regulatory factors, such as deletion of the phosphate regulator PhoB and mutations that alter the function of the global stress regulator RpoS. RpoS is induced at high pH via multiple mechanisms.

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