Recombination Between Chromosomal IS 200 Elements Supports Frequent Duplication Formation in Salmonella typhimurium Kenneth

Spontaneous tandem chromosomal duplications are common in populations of Escherichia coli and Salmonella typhimun'um. They range in frequency for a given locus from lo-* to and probably form by Reddependent unequal sister strand exchanges between repetitive sequences in direct order. Certaiu duplications have been observed previously to confer a growth advantage under specific selective conditions. Tandem chromosomal duplications are unstable and are lost at high frequencies, representing a readily reversible source of genomic variation. Six copies of a small mobile genetic element IS200 are evenly distributed around the chromosome of S. typhimun'um strain LT2. A survey of 120 independent chromosomal duplications (20 for each of six loci) revealed that recombination between IS200elements accounted for the majority of the duplications isolated for three of the loci tested. Duplications of the his operon were almost exclusively due to recombination between repeated IS200 elements. These data add further support to the idea that mobile genetic elements provide sequence repeats that play an important role in recombinational chromosome rearrangements, which may contribute to adaptation of bacteria to stressful conditions. B ACTERIAL genomes are constantly in flux. Chromosomal duplications are common and are frequently selected in the laboratory and presumably in nature. Direct order repeated chromosomal sequences can serve as substrates for the recombinational machinery, and unequal exchanges between such repeats can result in formation of amplifications and deletions (DEONIER 1987; ROTH et al. 1996). RecA-dependent recombination between the repeated ribosomal RNA genes has been shown to result in formation of tandem duplications (HILL et al. 1977; ANDERSON and ROTH 1981), inversions (HILL and HARNISH 1981) and transpositions (HILL and HARNISH 1982). The repeated sequence, rhs, is found in multiple copies in Escherichia coli but is absent from Salmonella typhimurium; this sequence provides the homology required for the frequent tandem duplication of the glyS region (HILL and WAGE 1979; LIN et al. 1984). The S. typhimurium and E. coli genomes both contain REP sequences, small imperfect inverted repeats, scattered throughout the chromosome (HIGGINS et al. 1982). These REP sequences are generally found between genes, often within transcribed regions. Recombination between separated REP elements can result in rare tandem chromosomal duplications that fuse genes to foreign promoters at the duplication join point and thus provide novel regulaCorresponding author: John R. Roth, Department of Biology, Salt 'Present address: Department of Molecular and Cellular Biology, Lake City, UT 841 12. E-mail: [email protected] Harvard University, 7 Divinity Ave., Cambridge, MA 02138. Genetics 141: 1245-1252 (December, 1995) tory behavior (ANDERSON and ROTH 1978a; SHYAMALA et al. 1990). Such rearrangements generate diversity in bacterial populations. The ability to amplify chromosomal DNA sequences by tandem duplication has been shown to convey a selective advantage in chemostats. Growth of S. typhimurium on limiting malate or arabinose selects for duplication of a specific region of the chromosome (SONTI and ROTH 1989). This region encodes the crp locus and permease genes for several carbon sources. Duplication of this region confers improved growth on limiting levels of several carbon sources (R. SONTI and J. R. ROTH, unpublished results). These results suggest that the ability to amplify specific sets of genes can provide a reversible mechanism for bacterial adaptation. IS200 is a 708-bp (GIBERT et al. 1991) insertion sequence found predominately within species of Salmonella (LAM and ROTH 1983a) and sporadically in other enteric bacteria (GIBERT et al. 1990; BISERICIC and OCHMAN 1993b). Wild-type S. typhimurium LT2 has six chromosomal copies of IS200 (LAM and ROTH 1983a) evenly distributed around the chromosome (LAM and ROTH 1983b; SANDERSON et al. 1993). ANDERSON and ROTH described large spontaneous tandem chromosomal duplications in S. typhimurium LT2. Some of these duplications arose by unequal recombination between m loci, while others had endpoints that corresponded to the known map positions of IS200 elements (ANDERSON and ROTH 1978b, 1981). We have investigated the possibility that IS200 sequences could be used as sequence 1246 K. R. Haack and J. R. Roth