UC San Diego

Broad host range serovars of Salmonella enterica have a conserved chromosomal gene order, or arrangement type, similar to that of the close relative E.coli. In contrast, host-specific serovars nearly always have large-scale rearrangements with endpoints in rRNA, or rrn operons. As these rearrangements are an important but poorly understood evolutionary process, two hypotheses for what causes these rearrangements were tested. One hypothesis proposes that horizontal gene transfer of phages and pathogenicity islands imbalances DNA replication, and rearrangements then occur to restore balance. Another hypothesis suggests that aspects of the host-specific lifestyle, such as the ability to establish a chronic carrier state in the host, either reduces selective pressure to maintain gene order or increases the rearrangement frequency. The arrangement types that occur naturally were compared to the theoretical possibility, and the amount of imbalance of each arrangement type was estimated using a PERL script. Out of 1,440 theoretical arrangement types, only 5̃0 were found to occur naturally. While most natural arrangement types were well-balanced, the majority of theoretical arrangement types were very imbalanced. Furthermore, the most common types of rearrangements that were identified did not affect balance. The relative fitness of Salmonella strains having transposon-held duplications of varying size that introduced up to 23⁰ of imbalance was determined. The sizes of the duplications were similar to many of the horizontally transferred genetic elements in Salmonella. While no correlation was found between the amount of introduced imbalance and fitness, the duplication of some chromosomal regions was detrimental to fitness. The arrangement types of serovar Typhi strains isolated from human carriers over time were also analyzed. Strains isolated from the same carrier almost always had different arrangement types. Furthermore, various arrangement types were identified in colonies isolated from archived slants of these strains; however, rearrangements were not detected in colonies derived from standard culturing conditions. Finally rearrangements occurring over time did not improve balance. Taken together these results refute the hypothesis that imbalanced replication causes the rearrangements, while supporting the hypothesis that aspects of lifestyle are responsible for the rearrangements found in host-specific serovars of Salmonella enterica