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High-throughput comparison of gene fitness among related bacteria
Canals, Rocio1; Xia, Xiao-Qin3; Fronick, Catrina5; Clifton, Sandra W.5; Ahmer, Brian M. M.4; Andrews-Polymenis, Helene L.6; Porwollik, Steffen2; McClelland, Michael1,2; McClelland, M (reprint author), Univ Calif Irvine, Irvine, CA 92717 USA.
2012-05-30
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume13
AbstractBackground: 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.; 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.
SubtypeArticle
KeywordEnterica Serovar Typhimurium Salmonella-enterica Escherichia-coli Response Regulator Iii Secretion Protein Typhi Specificity Expression Virulence
Department[Canals, Rocio; McClelland, Michael] Univ Calif Irvine, Irvine, CA 92717 USA; [Porwollik, Steffen; McClelland, Michael] Vaccine Res Inst San Diego, San Diego, CA USA; [Xia, Xiao-Qin] Chinese Acad Sci, Inst Hydrobiol, Wuhan, Peoples R China; [Ahmer, Brian M. M.] Ohio State Univ, Columbus, OH 43210 USA; [Fronick, Catrina; Clifton, Sandra W.] Washington Univ, St Louis, MO USA; [Andrews-Polymenis, Helene L.] Texas A&M Univ, Syst Hlth Sci Ctr, College Stn, TX USA
DOI10.1186/1471-2164-13-212
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationBeatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720] ; Beatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720] ; Beatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720] ; Beatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720]
Indexed BySCI
Language英语
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000310704900001
WOS KeywordENTERICA SEROVAR TYPHIMURIUM ; SALMONELLA-ENTERICA ; ESCHERICHIA-COLI ; RESPONSE REGULATOR ; III SECRETION ; PROTEIN ; TYPHI ; SPECIFICITY ; EXPRESSION ; VIRULENCE
Funding OrganizationBeatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720] ; Beatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720] ; Beatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720] ; Beatriu de Pinos fellowship; NIH [HHSN272200900040C]; PATRIC [AI039557 AI052237, AI073971, AI075093, AI077645 AI083646]; USDA [2009-03579-30127, 2011-67017-30127]; Binational Agricultural Research and Development Fund; CDMRP BCRP [W81XWH-08-1-0720]
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/17264
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorMcClelland, M (reprint author), Univ Calif Irvine, Irvine, CA 92717 USA.
Affiliation1.Univ Calif Irvine, Irvine, CA 92717 USA
2.Vaccine Res Inst San Diego, San Diego, CA USA
3.Chinese Acad Sci, Inst Hydrobiol, Wuhan, Peoples R China
4.Ohio State Univ, Columbus, OH 43210 USA
5.Washington Univ, St Louis, MO USA
6.Texas A&M Univ, Syst Hlth Sci Ctr, College Stn, TX USA
Recommended Citation
GB/T 7714
Canals, Rocio,Xia, Xiao-Qin,Fronick, Catrina,et al. High-throughput comparison of gene fitness among related bacteria[J]. BMC GENOMICS,2012,13.
APA Canals, Rocio.,Xia, Xiao-Qin.,Fronick, Catrina.,Clifton, Sandra W..,Ahmer, Brian M. M..,...&McClelland, M .(2012).High-throughput comparison of gene fitness among related bacteria.BMC GENOMICS,13.
MLA Canals, Rocio,et al."High-throughput comparison of gene fitness among related bacteria".BMC GENOMICS 13(2012).
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