ArticleMicrobial biotechnology2021
LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions.
Article in Microbial biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 15 citations in OpenAlex.
- Cas3-mediated genome reduction: demonstration in Cupriavidus necator H16 improves growth on heterotrophic and autotrophic carbon sources.Nucleic acids research · 2026Article
- Interactions between the genome and the nuclear lamina are multivalent and cooperative.Nature structural & molecular biology · 2025Article
- The promise of CRISPR-associated transposons for bacterial functional genomics.Current opinion in microbiology · 2025Review
- Review
- Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs.Nature communications · 2024Article
- Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts.Nature communications · 2024Article
- A review of synthetic biology tools in Yarrowia lipolytica.World journal of microbiology & biotechnology · 2023Review
- Gene editing tools for mycoplasmas: references and future directions for efficient genome manipulation.Frontiers in microbiology · 2023Review
- Gradients in gene essentiality reshape antibacterial research.FEMS microbiology reviews · 2022Review
- Bacterial genome reductions: Tools, applications, and challenges.Frontiers in genome editing · 2022Review
- Random genome reduction coupled with polyhydroxybutyrate biosynthesis to facilitate its accumulation inFrontiers in bioengineering and biotechnology · 2022Article
- LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions.Microbial biotechnology · 2021Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deepsequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via Cre recombinase, catalogued via deep sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from > 50 bp to 28 Kb, which represents 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions.
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