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Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction.
Tripathi, Surya; Voogdt, Carlos Geert Pieter; Bassler, Stefan Oliver; Anderson, Mary; Huang, Po-Hsun; Sakenova, Nazgul; Capraz, Tümay; Jain, Sunit; Koumoutsi, Alexandra; Bravo, Afonso Martins; Trotter, Valentine; Zimmerman, Michael; Sonnenburg, Justin L; Buie, Cullen; Typas, Athanasios; Deutschbauer, Adam M; Shiver, Anthony L; Huang, Kerwyn Casey.
Afiliación
  • Tripathi S; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
  • Voogdt CGP; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Bassler SO; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany.
  • Anderson M; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  • Huang PH; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  • Sakenova N; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Capraz T; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  • Jain S; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
  • Koumoutsi A; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Bravo AM; Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
  • Trotter V; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Zimmerman M; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.
  • Sonnenburg JL; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Buie C; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  • Typas A; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany. Electronic address: typas@embl.de.
  • Deutschbauer AM; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: amdeutschbauer@lbl.gov.
  • Shiver AL; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: ashiver@stanford.edu.
  • Huang KC; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: kchuang@stanford.edu.
Cell Rep ; 43(1): 113517, 2024 01 23.
Article en En | MEDLINE | ID: mdl-38142397
ABSTRACT
Randomly barcoded transposon mutant libraries are powerful tools for studying gene function and organization, assessing gene essentiality and pathways, discovering potential therapeutic targets, and understanding the physiology of gut bacteria and their interactions with the host. However, construction of high-quality libraries with uniform representation can be challenging. In this review, we survey various strategies for barcoded library construction, including transposition systems, methods of transposon delivery, optimal library size, and transconjugant selection schemes. We discuss the advantages and limitations of each approach, as well as factors to consider when selecting a strategy. In addition, we highlight experimental and computational advances in arraying condensed libraries from mutant pools. We focus on examples of successful library construction in gut bacteria and their application to gene function studies and drug discovery. Given the need for understanding gene function and organization in gut bacteria, we provide a comprehensive guide for researchers to construct randomly barcoded transposon mutant libraries.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Elementos Transponibles de ADN / Secuenciación de Nucleótidos de Alto Rendimiento Idioma: En Revista: Cell Rep Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Elementos Transponibles de ADN / Secuenciación de Nucleótidos de Alto Rendimiento Idioma: En Revista: Cell Rep Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos