Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA+)

Abstract

There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. For laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. We determined the complete genome sequence of laboratory E. coli strain RR1 (HB101 RecA+), which has long been used as a general cloning host. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out. Finally, PCR and Sanger sequencing-based finishing were applied to resolve non-single nucleotide variant regions with aberrant read depths and breakpoints, most of them resulting from prophages and insertion sequence transpositions that are not present in the reference genome sequence. We found that 96.9% of the RR1 genome is derived from K-12, and identified exact crossover junctions between K-12 and B genomic fragments. However, because RR1 has experienced a series of genetic manipulations since branching from the common ancestor, it has a set of mutations different from those found in K-12 MG1655. As well as identifying all known genotypes of RR1 on the basis of genomic context, we found novel mutations. Our results extend current knowledge of the genotype of RR1 and its relatives, and provide insights into the pedigree, genomic background, and physiology of common laboratory strains.

Site-Specific Antimicrobial Activity of a Dual-Responsive Ciprofloxacin Prodrug

“…The antibiotic activity, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) of free ciprofloxacin and the prodrugs were assessed against laboratory strains of E. coli HB101 and S. aureus BB255 as well as the clinical isolate E.…”

“…55 Antimicrobial Activity of Prodrugs In Vitro. The antibiotic activity, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) of free ciprofloxacin and the prodrugs were assessed against laboratory strains of E. coli HB101 56 and S. aureus BB255 57 as well as the clinical isolate E. coli E38. 58 both the NTR-responsive single prodrug 2 and the H 2 Sresponsive single prodrug 4 showed ≥128-fold reduction in antibacterial activity, while the NTR + H 2 S-responsive dual prodrug 3 had a ≥8200-fold reduction in activity compared to free ciprofloxacin (1) (Table 1).…”

A smartphone-based genetically recombinant whole-cell biosensor for highly sensitive monitoring of polychlorinated biphenyls (PCBs)

“…Poor chassis, on the other hand, contain various genetic defects in energy or amino acid synthesis pathways. For example, DH5α strain lacks the GTP-pyrophosphate kinase synthesis gene relA , Top10 is a strain defective in the leucine synthesis gene, and DB3.1 lacks the γ-glutamyl phosphate reductase gene proA2 (Durfee et al, 2008; Jeong et al, 2017; Kwon et al, 2020). These defects may slow down the expression of sensing proteins and reporter genes, resulting in poorer WCB chassis.…”

Plasmids can transfer to Clostridium difficile CD37 and 630Δerm both by a DNase resistant conjugation-like mechanism and a DNase sensitive mechanism

“…Furthermore, the fact that the transfer frequency is much lower from HB101 than from CA434 indicates that transfer is via a different mechanism in the two strains. A search of the available HB101 genome https://www.ncbi.nlm.nih.gov/nuccore/CP011113 (Jeong et al, 2017) does show that this strain contains some tra genes although not all the genes required for conjugation are present, importantly no TraF-encoding gene or members of the trb operon could be found. These gene products are thought to be required for stable mating pair formation and encode proteins required for mating bridge formation (reviewed in Zatyka and Thomas 1998).…”