Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction.

CP: Microbiology RB-Tn-seq arrayed libraries functional genomics gut microbiota in vitro screening magic pools protein function transposon mutagenesis

Journal

Cell reports
ISSN: 2211-1247
Titre abrégé: Cell Rep
Pays: United States
ID NLM: 101573691

Informations de publication

Date de publication:
22 Dec 2023
Historique:
received: 27 07 2023
revised: 22 10 2023
accepted: 14 11 2023
medline: 24 12 2023
pubmed: 24 12 2023
entrez: 24 12 2023
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1016/j.celrep.2023.113517 PMID: 38142397
pubmed: 38142397
pii: S2211-1247(23)01529-2
doi: 10.1016/j.celrep.2023.113517
pii:
doi:

Types de publication

Journal Article Review

Langues

eng

Sous-ensembles de citation

IM

Pagination

113517

Informations de copyright

Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests The authors declare no competing interests.

Auteurs

Surya Tripathi (S)

Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

Carlos Geert Pieter Voogdt (CGP)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.

Stefan Oliver Bassler (SO)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany.

Mary Anderson (M)

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Po-Hsun Huang (PH)

Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Nazgul Sakenova (N)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.

Tümay Capraz (T)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Sunit Jain (S)

Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.

Alexandra Koumoutsi (A)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.

Afonso Martins Bravo (AM)

Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.

Valentine Trotter (V)

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Michael Zimmerman (M)

Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.

Justin L Sonnenburg (JL)

Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Cullen Buie (C)

Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Athanasios 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.

Adam M 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.

Anthony L Shiver (AL)

Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: ashiver@stanford.edu.

Kerwyn Casey 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.

Classifications MeSH