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Nehring RB, Gu F, Lin HY, Gibson JL, Blythe MJ, Wilson R, Bravo Núñez MA, Hastings PJ, Louis EJ, Frisch RL, Hu JC, Rosenberg SM. An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. Nucleic Acids Res 2015; 44:e41. [PMID: 26578563 PMCID: PMC4797258 DOI: 10.1093/nar/gkv1131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/15/2015] [Indexed: 01/26/2023] Open
Abstract
With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter—ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing (‘forward genomics’) demonstrates a strategy that could similarly enable rapid screens in many other microbes.
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Affiliation(s)
- Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Franklin Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hsin-Yu Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Janet L Gibson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin J Blythe
- Deep Seq. Centre for Genetics and Genomics, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Ray Wilson
- Deep Seq. Centre for Genetics and Genomics, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - María Angélica Bravo Núñez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA Undergraduate Program in Genomic Sciences, National Autonomous University of Mexico, 62210 Cuernavaca, Mexico
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edward J Louis
- Deep Seq. Centre for Genetics and Genomics, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Ryan L Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James C Hu
- Department of Biochemistry and Biophysics, Texas A&M University and Texas Agrilife Research, College Station, TX 77843, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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Papatheodorou I, Oellrich A, Smedley D. Linking gene expression to phenotypes via pathway information. J Biomed Semantics 2015; 6:17. [PMID: 25901272 PMCID: PMC4404592 DOI: 10.1186/s13326-015-0013-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/19/2015] [Indexed: 11/10/2022] Open
Abstract
Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computational means to traverse from genes to gene expression, model pathways and classify phenotypes. Numerous ontologies and other controlled vocabularies have been developed, as well as computational methods to combine and mine these data sets and establish connections. Here we discuss these efforts and identify areas of future work that could lead to a better integration of genes, pathways and phenotypes to provide insights into the mechanisms under which gene mutations affect expression and pathways and how these effects are manifested onto the phenotype.
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Affiliation(s)
- Irene Papatheodorou
- Mouse Developmental Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB1 10SA, Hinxton, UK
| | - Anika Oellrich
- Mouse Developmental Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB1 10SA, Hinxton, UK
| | - Damian Smedley
- Mouse Developmental Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB1 10SA, Hinxton, UK
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