title: Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications.
abstract: BACKGROUND
  Evolvability is an intrinsic feature of all living cells. However, newly emerging, evolved features can be undesirable when genetic circuits, designed and fabricated by rational, synthetic biological approaches, are installed in the cell. Streamlined-genome E. coli MDS42 is free of mutation-generating IS elements, and can serve as a host with reduced evolutionary potential.
  
  
  RESULTS
  We analyze an extreme case of toxic plasmid clone instability, and show that random host IS element hopping, causing inactivation of the toxic cloned sequences, followed by automatic selection of the fast-growing mutants, can prevent the maintenance of a clone developed for vaccine production. Analyzing the molecular details, we identify a hydrophobic protein as the toxic byproduct of the clone, and show that IS elements spontaneously landing in the cloned fragment relieve the cell from the stress by blocking transcription of the toxic gene. Bioinformatics analysis of sequence reads from early shotgun genome sequencing projects, where clone libraries were constructed and maintained in E. coli, suggests that such IS-mediated inactivation of ectopic genes inhibiting the growth of the E. coli cloning host might happen more frequently than generally anticipated, leading to genomic instability and selection of altered clones.
  
  
  CONCLUSIONS
  Delayed genetic adaptation of clean-genome, IS-free MDS42 host improves maintenance of unstable genetic constructs, and is suggested to be beneficial in both laboratory and industrial settings.
authors.affiliation: Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, 62 Temesvari krt, H6726 Szeged, Hungary.
authors.forename: Kinga
authors.initials: K
authors.lastname: Umenhoffer
authors.forename: Tamás
authors.initials: T
authors.lastname: Fehér
authors.forename: Gabriella
authors.initials: G
authors.lastname: Balikó
authors.forename: Ferhan
authors.initials: F
authors.lastname: Ayaydin
authors.forename: János
authors.initials: J
authors.lastname: Pósfai
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Blattner
authors.forename: György
authors.initials: G
authors.lastname: Pósfai
mesh_terms: D019295:Computational Biology; D004251:DNA Transposable Elements; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D005798:Genes, Bacterial; D016366:Open Reading Frames; D010957:Plasmids / Q000235:genetics / Q000378:metabolism / Q000633:toxicity; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D011994:Recombinant Proteins