The metal-uptake-deficient Escherichia coli strain GR536 contains the ϕ80 prophage

Abstract

Abstract We report the genome sequence of Escherichia coli GR536, a previously constructed metal-uptake-deficient strain derived from E. coli W3110. Growth of GR536 in an iron-restricted liquid medium resulted in apparent lysis during the early exponential growth phase. This effect was exacerbated in cells transformed with pBAD30, a commonly used arabinose-inducible expression vector. Whole-genome sequencing confirmed the expected gene disruptions (entC, feoABC, mntH, zupT::cat and fecABCDE::kan). However, comparison to E. coli W3110 identified the presence of the ϕ80 prophage (46.16 kbp) and cryptic prophage CPZ-55 (6.763 kbp), as well as the absence of cryptic prophage e14 (15.193 kbp). We also identified 9 IS-element deletions, 3 IS-element insertions, 7 other deletions or insertions and 74 candidate individual nucleotide changes. The growth defect in GR536 correlated with lysis due to the production of ϕ80 virions as determined by the inability of isolated phage to infect an E. coli strain lacking the phage receptor (∆fhuA) and the BamHI digestion pattern of the purified phage DNA. We further determined that the ϕ80-dependent lysis in GR536 is exacerbated by the presence of the chloramphenicol- and kanamycin-resistance markers introduced during construction of GR536 and the pBAD30 plasmid multiple cloning site. Removal of the markers (E. coli GR536*) and disruption of the pBAD30 multiple cloning site generated a strain that showed a 104-fold reduction in ϕ80 production. Furthermore, construction of a W3110 lysogen containing the ϕ80 prophage and comparison with GR536* grown under the same conditions showed a ~104-fold higher level of phage production by the parent strain, indicating that phage-dependent lysis was not increased by the deletion of the metal-uptake genes and thus independent of iron availability. These observations clarify growth conditions that limit the effects of ϕ80-dependent lysis when using GR536 to identify metal-uptake genes by complementation, specifically, removal of the antibiotic resistance markers and the avoidance of using intact pBAD30 as a negative control.