Co-evolution of the tuf Genes Links Gene Conversion with the Generation of Chromosomal Inversions Diarmaid Hughes* Department of Cell and Molecular Biology, Uppsala University, Biomedical Center Box 596, SE-751 24 Uppsala Sweden The tufA and tufB genes in Salmonella typhimurium co-evolve by recombi- nation and exchange of genetic material. A model is presented which predicts that co-evolution is achieved by gene conversions and chromoso- mal inversions. Analysis of recombinants reveals that conversion and inversion each occur with similar rates and each depends on RecBCD activity. The model predicts sequence structures for different classes of post-recombination tuf genes. Sequence analysis reveals the presence of each of these structures and classes, with a predicted bias in the absence of mismatch repair. An implication of these data is that co-evolution of gene families can be linked with the generation of chromosomal rearrangements. # 2000 Academic Press Keywords: inversion; gene conversion; recombination; evolution; Salmonella typhimurium tufA, tufB Introduction Groups of genes within an organism having sig- ni®cant sequence similarity are called gene families. Over evolutionary time, genes within a family are expected to diverge in sequence. How- ever, some gene families avoid divergence and instead their members co-evolve. In cases where co-evolution involves non-tandem genes this may require the transfer of genetic information across considerable distances on a chromosome. This raises questions about how such exchanges occur, and whether these exchanges are associated with genome rearrangements. Co-evolution within gene families is often ascribed to gene conversion (Lindegren, 1953; Mitchell, 1955a,b; Olive, 1959; Holliday, 1964). Gene conversion implies homogenization of the sequences within a gene family, but not a speci®c mechanism. For example, mating-type switching in Saccharomyces cerevisiae is a programmed gene con- version involving double-strand break repair (Szostak et al., 1983), whereas intron loss in S. cere- visiae can occur via recombination with reverse- transcribed mRNA (Derr et al., 1991; Derr & Strathern, 1993). Other possible conversion mech- anisms include asymmetric repair of heteroduplex DNA in a recombination complex (the classical model described by Holliday, 1964), survival of asymmetric non-allelic heteroduplexes until repli- cation (discussed by Abdulkarim & Hughes, 1996), and non-allelic reciprocal exchanges between family sequences on sister chromosomes leading to apparent gene conversion when chromosomes seg- regate at cell division (discussed by Segall & Roth, 1994). Each mechanism of homogenization is associated in principle with speci®c consequences for genome evolution. Surprisingly, there is very little information on speci®c mechanisms of co- evolution of natural sequences by gene homogeniz- ation and how these impact on genome evolution. Here the question is addressed using the simple two-gene tuf family of Salmonella typhimurium. S. typhimurium has a circular 4.8 Mb chromosome and the tuf genes, separated by 700 kb, are situ- ated in inverse orientation on opposite sides of the origin of replication. The transfer of genetic infor- mation causing tuf sequence homogenisation has been experimentally demonstrated (Abdulkarim & Hughes, 1996). Homogenisation is strongly recA and recB-dependent (Abdulkarim & Hughes, 1996), arguing that it involves homologous recombination via a chromosomal double-strand break, substrate for the RecBCD enzyme complex (Myers & Stahl, 1994). Because the tuf genes are in inverse order on the chromosome, recombination between them can in principle also lead to inversion of the region bounded by the genes. E-mail address of the author: Hughes@alpha2.bmc.uu.se Abbreviations used: DSB, double-strand break; DSBR, DSB repair; DSGR, double-strand gap repair. doi:10.1006/jmbi.2000.3587 available online at http://www.idealibrary.com on J. Mol. Biol. (2000) 297, 355±364 0022-2836/00/020355±10 $35.00/0 # 2000 Academic Press