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High-throughput comparison of gene fitness among related bacteria
BACKGROUND: 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 Salmonella strains and thereby reveal diffe...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487940/ https://www.ncbi.nlm.nih.gov/pubmed/22646920 http://dx.doi.org/10.1186/1471-2164-13-212 |
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author | Canals, Rocio Xia, Xiao-Qin Fronick, Catrina Clifton, Sandra W Ahmer, Brian MM Andrews-Polymenis, Helene L Porwollik, Steffen McClelland, Michael |
author_facet | Canals, Rocio Xia, Xiao-Qin Fronick, Catrina Clifton, Sandra W Ahmer, Brian MM Andrews-Polymenis, Helene L Porwollik, Steffen McClelland, Michael |
author_sort | Canals, Rocio |
collection | PubMed |
description | BACKGROUND: 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 Salmonella strains and thereby reveal differences not apparent at the gene sequence level. RESULTS: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella 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 E. coli 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 (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498, STM14_2872, STM14_3360, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. CONCLUSIONS: 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. |
format | Online Article Text |
id | pubmed-3487940 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34879402012-11-03 High-throughput comparison of gene fitness among related bacteria Canals, Rocio Xia, Xiao-Qin Fronick, Catrina Clifton, Sandra W Ahmer, Brian MM Andrews-Polymenis, Helene L Porwollik, Steffen McClelland, Michael BMC Genomics Research Article BACKGROUND: 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 Salmonella strains and thereby reveal differences not apparent at the gene sequence level. RESULTS: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella 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 E. coli 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 (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498, STM14_2872, STM14_3360, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. CONCLUSIONS: 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. BioMed Central 2012-05-30 /pmc/articles/PMC3487940/ /pubmed/22646920 http://dx.doi.org/10.1186/1471-2164-13-212 Text en Copyright ©2012 Canals et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Canals, Rocio Xia, Xiao-Qin Fronick, Catrina Clifton, Sandra W Ahmer, Brian MM Andrews-Polymenis, Helene L Porwollik, Steffen McClelland, Michael High-throughput comparison of gene fitness among related bacteria |
title | High-throughput comparison of gene fitness among related bacteria |
title_full | High-throughput comparison of gene fitness among related bacteria |
title_fullStr | High-throughput comparison of gene fitness among related bacteria |
title_full_unstemmed | High-throughput comparison of gene fitness among related bacteria |
title_short | High-throughput comparison of gene fitness among related bacteria |
title_sort | high-throughput comparison of gene fitness among related bacteria |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487940/ https://www.ncbi.nlm.nih.gov/pubmed/22646920 http://dx.doi.org/10.1186/1471-2164-13-212 |
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