ArticleGenome biology2021
Compacting a synthetic yeast chromosome arm.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Synthetic Chromosomes in Yeast: A Platform for Understanding and Programming Eukaryotic Life.Microbial biotechnology · 2026Review
- Advances in large DNA fragment assembly for microbial cell factory engineering.Quantitative biology (Beijing, China) · 2026Review
- Synthetic rewriting technologies in mammalian cells.Nature communications · 2026Review
- Life beyond 6000 genes: from sequence to synthesis in a post-genomics era.FEMS yeast research · 2026Review
- Synthesis of Headful Packaging Phages Through Yeast Transformation-Associated Recombination.Viruses · 2024Article
- The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging.Nature communications · 2024Article
- Genome engineering on size reduction and complexity simplification: A review.Journal of advanced research · 2024Review
- An Optimized Genotyping Workflow for Identifying Highly SCRaMbLEd Synthetic Yeasts.ACS synthetic biology · 2024Article
- Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae.Nature communications · 2024Article
- Building synthetic chromosomes from natural DNA.Nature communications · 2023Article
- Building a eukaryotic chromosome arm by de novo design and synthesis.Nature communications · 2023Article
- Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics.Cell genomics · 2023Article
- Enabling technology and core theory of synthetic biology.Science China. Life sciences · 2023Review
- Building synthetic chromosomes from natural DNA.bioRxiv : the preprint server for biology · 2023Article
- Trimming the genomic fat: minimising and re-functionalising genomes using synthetic biology.Nature communications · 2023Review
- Investigation of Genome Biology by Synthetic Genome Engineering.Bioengineering (Basel, Switzerland) · 2023Review
- Genome-scale top-down strategy to generate viable genome-reduced phages.Nucleic acids research · 2022Article
- Article
- Systematic dissection of key factors governing recombination outcomes by GCE-SCRaMbLE.Nature communications · 2022Article
- Compacting a synthetic yeast chromosome arm.Genome biology · 2021Article
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Authors and funding
13 authors.
Funding
Abstract
backgroundRedundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which is proposed as an effective tool for genome minimization. As the Sc2.0 project is nearing its completion, we have begun to explore the application of the SCRaMbLE system in genome compaction.
resultsWe develop a method termed SCRaMbLE-based genome compaction (SGC) and demonstrate that a synthetic chromosome arm (synXIIL) can be efficiently reduced. The pre-introduced episomal essential gene array significantly enhances the compacting ability of SGC, not only by enabling the deletion of nonessential genes located in essential gene containing loxPsym units but also by allowing more chromosomal sequences to be removed in a single SGC process. Further compaction is achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30 °C in rich medium. Approximately 40% of the synthetic sequence, encoding 28 genes, is found to be dispensable for cell growth at 30 °C in rich medium and several genes whose functions are needed under specified conditions are identified.
conclusionsWe develop iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome.
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