High-throughput comparison of gene fitness among related bacteria

• Main Authors: Canals Rocio, Xia Xiao-Qin, Fronick Catrina, Clifton Sandra W, Ahmer Brian MM, Andrews-Polymenis Helene L, Porwollik Steffen, McClelland Michael
• Format: Article
• Language: English
• Published: BMC 2012-05-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/13/212

<p>Abstract</p> <p>Background</p> <p>The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related <it>Salmonella</it> strains and thereby reveal differences not apparent at the gene sequence level.</p> <p>Results</p> <p>A transposon Tn5 derivative was used to construct mutants in <it>Salmonella</it> Typhimurium ATCC14028 (STM1) and <it>Salmonella</it> Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 isolate (STY2) and essential genes identified in <it>E. coli</it> K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of transposon insertions or had very few. For three of these nine genes, part of the annotated gene lacked transposon integrations (<it>yejM</it>, <it>ftsN</it> and <it>murB)</it>. At least one of the other six genes, <it>trpS</it>, had a potentially functionally redundant gene encoded elsewhere in <it>Salmonella</it> but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three <it>Salmonella</it> strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (<it>STM14_1498</it>, <it>STM14_2872</it>, <it>STM14_3360</it>, and <it>STM14_5442</it>) are not found in <it>E. coli</it>. Notable differences in the extent of gene selection were also observed among the three different <it>Salmonella</it> isolates. Mutations in <it>hns</it>, for example, were selected against in STM1 but not in the two STY strains, which have a defect in <it>rpoS</it> rendering <it>hns</it> nonessential.</p> <p>Conclusions</p> <p>Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene contributions to fitness among syntenic homologs. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology.</p>