title: Reversible phase variation in the phnE gene, which is required for phosphonate metabolism in Escherichia coli K-12.
abstract: It is known that Escherichia coli K-12 is cryptic (Phn-) for utilization of methyl phosphonate (MePn) and that Phn+ variants can be selected for growth on MePn as the sole P source. Variants arise from deletion via a possible slip strand mechanism of one of three direct 8-bp repeat sequences in phnE, which restores function to a component of a putative ABC type transporter. Here we show that Phn+ variants are present at the surprisingly high frequency of >10(-2) in K-12 strains. Amplified-fragment length polymorphism analysis was used to monitor instability in phnE in various strains growing under different conditions. This revealed that, once selection for growth on MePn is removed, Phn+ revertants reappear and accumulate at high levels through reinsertion of the 8-bp repeat element sequence. It appears that, in K-12, phnE contains a high-frequency reversible gene switch, producing phase variation which either allows ("on" form) or blocks ("off" form) MePn utilization. The switch can also block usage of other metabolizable alkyl phosphonates, including the naturally occurring 2-aminoethylphosphonate. All K-12 strains, obtained from collections, appear in the "off" form even when bearing mutations in mutS, mutD, or dnaQ which are known to enhance slip strand events between repetitive sequences. The ability to inactivate the phnE gene appears to be unique to K-12 strains since the B strain is naturally Phn+ and lacks the inactivating 8-bp insertion in phnE, as do important pathogenic strains for which genome sequences are known and also strains isolated recently from environmental sources.
authors.affiliation: Microbiology Division, School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, United Kingdom.
authors.forename: Samina
authors.initials: S
authors.lastname: Iqbal
authors.forename: George
authors.initials: G
authors.lastname: Parker
authors.forename: Helen
authors.initials: H
authors.lastname: Davidson
authors.forename: Elham
authors.initials: E
authors.lastname: Moslehi-Rahmani
authors.forename: Robert L
authors.initials: RL
authors.lastname: Robson
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics* / Q000378:metabolism; D000251:Adenosine Triphosphatases / Q000235:genetics; D000615:Aminoethylphosphonic Acid / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D004258:DNA Polymerase III / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism*; D005798:Genes, Bacterial; D014644:Genetic Variation; D008969:Molecular Sequence Data; D051719:MutS DNA Mismatch-Binding Protein; D009154:Mutation; D009943:Organophosphorus Compounds / Q000378:metabolism*; D011995:Recombination, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D017384:Sequence Deletion
chemical_list: D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D009943:Organophosphorus Compounds; C032627:methylphosphonic acid; D000615:Aminoethylphosphonic Acid; D004258:DNA Polymerase III; C468316:dnaQ protein, E coli; D000251:Adenosine Triphosphatases; D051719:MutS DNA Mismatch-Binding Protein; C497175:MutS protein, E coli