ArticleScientific reports2018
Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia pastoris.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 39 citations in OpenAlex.
- Progresses of transposon research inSynthetic and systems biotechnology · 2026Review
- High-throughput editing boosts the construction of next-generation microbial cell factories.Synthetic and systems biotechnology · 2026Review
- The power of many: when genetics met yeasts and high-throughput.Biological reviews of the Cambridge Philosophical Society · 2026Review
- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 2026Article
- Deletion of low-essentiality, secretion-associated genes enhances recombinant protein production in Komagataella phaffii.Microbial cell factories · 2026Article
- Genome-Wide Landscape of Position Effect Variegation inJournal of fungi (Basel, Switzerland) · 2026Article
- Mechanistic insights into sodium citrate-induced metabolic rewiring for enhanced S-adenosylmethionine synthesis via transcriptomics and constraint-based modeling.Bioprocess and biosystems engineering · 2026Article
- Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map.Molecular systems biology · 2025Article
- Essential Genes Discovery in Microorganisms by Transposon-Directed Sequencing (Tn-Seq): Experimental Approaches, Major Goals, and Future Perspectives.International journal of molecular sciences · 2024Review
- Genome engineering on size reduction and complexity simplification: A review.Journal of advanced research · 2024Review
- Genome-wide quantification of contributions to sexual fitness identifies genes required for spore viability and health in fission yeast.PLoS genetics · 2022Article
- Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 inJournal of fungi (Basel, Switzerland) · 2022Article
- Applying the auxin-based degron system for the inducible, reversible and complete protein degradation iniScience · 2022Article
- SAturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- What makes Komagataella phaffii non-conventional?FEMS yeast research · 2021Review
- Article
- DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools.Nucleic acids research · 2021Article
- Hijacking Transposable Elements for Saturation Mutagenesis in Fungi.Frontiers in fungal biology · 2021Review
- CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms.Database : the journal of biological databases and curation · 2020Article
- Transposon Insertion Sequencing, a Global Measure of Gene Function.Annual review of genetics · 2020Review
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
In many prokaryotes but limited eukaryotic species, the combination of transposon mutagenesis and high-throughput sequencing has greatly accelerated the identification of essential genes. Here we successfully applied this technique to the methylotrophic yeast Pichia pastoris and classified its conditionally essential/non-essential gene sets. Firstly, we showed that two DNA transposons, TcBuster and Sleeping beauty, had high transposition activities in P. pastoris. By merging their insertion libraries and performing Tn-seq, we identified a total of 202,858 unique insertions under glucose supported growth condition. We then developed a machine learning method to classify the 5,040 annotated genes into putatively essential, putatively non-essential, ambig1 and ambig2 groups, and validated the accuracy of this classification model. Besides, Tn-seq was also performed under methanol supported growth condition and methanol specific essential genes were identified. The comparison of conditionally essential genes between glucose and methanol supported growth conditions helped to reveal potential novel targets involved in methanol metabolism and signaling. Our findings suggest that transposon mutagenesis and Tn-seq could be applied in the methylotrophic yeast Pichia pastoris to classify conditionally essential/non-essential gene sets. Our work also shows that determining gene essentiality under different culture conditions could help to screen for novel functional components specifically involved in methanol metabolism.
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