Abstract
Duplications are often attributed to "unequal recombination" between separated, directly repeated sequence elements (>.100 bp), events that leave a recombinant element at the duplication junction. However, in the bacterial chromosome, duplications form at high rates (10-3-10-5/cell/division) even without recombination (RecA). Here we describe 1800 spontaneous lac duplications trapped nonselectively on the low-copy F′128 plasmid, where lac is flanked by direct repeats of the transposable element IS3 (1258 bp) and by numerous quasipalindromic REP elements (30 bp). Duplications form at a high rate (10-4/cell/division) that is reduced only about 11-fold in the absence of RecA. With and without RecA, most duplications arise by recombination between IS3 elements (97%). Formation of these duplications is stimulated by IS3 transposase (Tnp) and plasmid transfer functions (TraI). Three duplication pathways are proposed. First, plasmid dimers form at a high rate stimulated by RecA and are then modified by deletions between IS3 elements (resolution) that leave a monomeric plasmid with an IS3-flanked lac duplication. Second, without RecA, duplications occur by singlestrand annealing of DNA ends generated in different sister chromosomes after transposase nicks DNA near participating IS3 elements. The absence of RecA may stimulate annealing by allowing chromosome breaks to persist. Third, a minority of lac duplications (3%) have short (0-36 bp) junction sequences (SJ), some of which are located within REP elements. These duplication types form without RecA, Tnp, or Tra by a pathway in which the palindromic junctions of a tandem inversion duplication (TID) may stimulate deletions that leave the final duplication.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 397-415 |
| Number of pages | 19 |
| Journal | Genetics |
| Volume | 192 |
| Issue number | 2 |
| DOIs | |
| State | Published - Oct 2012 |
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- Genetics
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Multiple pathways of duplication formation with and without recombination (RecA) in Salmonella enterica. / Reams, Andrew B.; Kofoid, Eric; Kugelberg, Elisabeth; Roth, John R.
In: Genetics, Vol. 192, No. 2, 10.2012, p. 397-415.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Multiple pathways of duplication formation with and without recombination (RecA) in Salmonella enterica
AU - Reams, Andrew B.
AU - Kofoid, Eric
AU - Kugelberg, Elisabeth
AU - Roth, John R.
PY - 2012/10
Y1 - 2012/10
N2 - Duplications are often attributed to "unequal recombination" between separated, directly repeated sequence elements (>.100 bp), events that leave a recombinant element at the duplication junction. However, in the bacterial chromosome, duplications form at high rates (10-3-10-5/cell/division) even without recombination (RecA). Here we describe 1800 spontaneous lac duplications trapped nonselectively on the low-copy F′128 plasmid, where lac is flanked by direct repeats of the transposable element IS3 (1258 bp) and by numerous quasipalindromic REP elements (30 bp). Duplications form at a high rate (10-4/cell/division) that is reduced only about 11-fold in the absence of RecA. With and without RecA, most duplications arise by recombination between IS3 elements (97%). Formation of these duplications is stimulated by IS3 transposase (Tnp) and plasmid transfer functions (TraI). Three duplication pathways are proposed. First, plasmid dimers form at a high rate stimulated by RecA and are then modified by deletions between IS3 elements (resolution) that leave a monomeric plasmid with an IS3-flanked lac duplication. Second, without RecA, duplications occur by singlestrand annealing of DNA ends generated in different sister chromosomes after transposase nicks DNA near participating IS3 elements. The absence of RecA may stimulate annealing by allowing chromosome breaks to persist. Third, a minority of lac duplications (3%) have short (0-36 bp) junction sequences (SJ), some of which are located within REP elements. These duplication types form without RecA, Tnp, or Tra by a pathway in which the palindromic junctions of a tandem inversion duplication (TID) may stimulate deletions that leave the final duplication.
AB - Duplications are often attributed to "unequal recombination" between separated, directly repeated sequence elements (>.100 bp), events that leave a recombinant element at the duplication junction. However, in the bacterial chromosome, duplications form at high rates (10-3-10-5/cell/division) even without recombination (RecA). Here we describe 1800 spontaneous lac duplications trapped nonselectively on the low-copy F′128 plasmid, where lac is flanked by direct repeats of the transposable element IS3 (1258 bp) and by numerous quasipalindromic REP elements (30 bp). Duplications form at a high rate (10-4/cell/division) that is reduced only about 11-fold in the absence of RecA. With and without RecA, most duplications arise by recombination between IS3 elements (97%). Formation of these duplications is stimulated by IS3 transposase (Tnp) and plasmid transfer functions (TraI). Three duplication pathways are proposed. First, plasmid dimers form at a high rate stimulated by RecA and are then modified by deletions between IS3 elements (resolution) that leave a monomeric plasmid with an IS3-flanked lac duplication. Second, without RecA, duplications occur by singlestrand annealing of DNA ends generated in different sister chromosomes after transposase nicks DNA near participating IS3 elements. The absence of RecA may stimulate annealing by allowing chromosome breaks to persist. Third, a minority of lac duplications (3%) have short (0-36 bp) junction sequences (SJ), some of which are located within REP elements. These duplication types form without RecA, Tnp, or Tra by a pathway in which the palindromic junctions of a tandem inversion duplication (TID) may stimulate deletions that leave the final duplication.
UR - http://www.scopus.com/inward/record.url?scp=84867183205&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84867183205&partnerID=8YFLogxK
U2 - 10.1534/genetics.112.142570
DO - 10.1534/genetics.112.142570
M3 - Article
C2 - 22865732
AN - SCOPUS:84867183205
VL - 192
SP - 397
EP - 415
JO - Genetics
JF - Genetics
SN - 0016-6731
IS - 2
ER -