Abstract
Tandem genetic duplications arise frequently between the seven directly repeated 5.5-kb
rrn
loci that encode ribosomal RNAs in
Salmonella enterica
. The closest
rrn
genes,
rrnB
and
rrnE
, flank a 40-kb region that includes the
purHD
operon. Duplications of
purHD
arise by exchanges between
rrn
loci and form at a high rate (10
−3
/cell/division) that remains high in strains blocked for early steps in recombination (
recA
,
recB
, and/or
recF
), but drops 30-fold in mutants blocked for later Holliday junction resolution (
ruvC recG
). The duplication defect of a
ruvC recG
mutant was fully corrected by an added mutation in any one of the
recA
,
recB
, or
recF
genes. To explain these results, we propose that early recombination defects activate an alternative single-strand annealing pathway for duplication formation. In wild-type cells,
rrn
duplications form primarily by the action of RecFORA on single-strand gaps. Double-strand breaks cannot initiate
rrn
duplications because
rrn
loci lack Chi sites, which are essential for recombination between two separated
rrn
sequences. A
recA
or
recF
mutation allows unrepaired gaps to accumulate such that different
rrn
loci can provide single-strand
rrn
sequences that lack the RecA coating that normally inhibits annealing. A
recB
mutation activates annealing by allowing double-strand ends within
rrn
to avoid digestion by RecBCD and provide a new source of
rrn
ends for use in annealing. The equivalent high rates of
rrn
duplication by recombination and annealing pathways may reflect a limiting economy of gaps and breaks arising in heavily transcribed, palindrome-rich
rrn
sequences.