title: The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types.
abstract: During growth under selection, mutant types appear that are rare in unselected populations. Stress-induced mechanisms may cause these structures or selection may favor a series of standard events that modify common preexisting structures. One such mutation is the short junction (SJ) duplication with long repeats separated by short sequence elements: AB*(CD)*(CD)*E (* = a few bases). Another mutation type, described here, is the tandem inversion duplication (TID), where two copies of a parent sequence flank an inverse-order segment: AB(CD)(E'D'C'B')(CD)E. Both duplication types can amplify by unequal exchanges between direct repeats (CD), and both are rare in unselected cultures but common after prolonged selection for amplification. The observed TID junctions are asymmetric (aTIDs) and may arise from a symmetrical precursor (sTID)-ABCDE(E'D'C'B'A')ABCDE-when sequential deletions remove each palindromic junction. Alternatively, one deletion can remove both sTID junctions to generate an SJ duplication. It is proposed that sTID structures form frequently under all growth conditions, but are usually lost due to their instability and fitness cost. Selection for increased copy number helps retain the sTID and favors deletions that remodel junctions, improve fitness, and allow higher amplification. Growth improves with each step in formation of an SJ or aTID amplification, allowing selection to favor completion of the mutation process.
authors.affiliation: Department of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616, USA. e.kugelberg@imperial.ac.uk
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Kugelberg
authors.forename: Eric
authors.initials: E
authors.lastname: Kofoid
authors.forename: Dan I
authors.initials: DI
authors.lastname: Andersson
authors.forename: Yong
authors.initials: Y
authors.lastname: Lu
authors.forename: Joseph
authors.initials: J
authors.lastname: Mellor
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.forename: John R
authors.initials: JR
authors.lastname: Roth
mesh_terms: D001483:Base Sequence; D007446:Chromosome Inversion / Q000235:genetics*; D020440:Gene Duplication; D015321:Gene Rearrangement / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D007763:Lac Operon / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000235:genetics; D009154:Mutation / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000235:genetics; D016133:Polymerase Chain Reaction; D019779:Salmonella enterica / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion / Q000235:genetics; D020080:Tandem Repeat Sequences / Q000235:genetics*