{
  "abstract": "Synthetic auxotrophs are a useful means for developing genetically encoded biocontainment systems. Current methods for developing synthetic auxotrophs are complicated or expensive, limiting access and adoption of biocontainment technologies. To address this gap, we developed a simple and modular platform for creating synthetic auxotrophs based on ligand-dependent translational gating of essential genes. By inserting a theophylline-responsive riboswitch upstream of essential genes in Escherichia coli, we created strains whose viability depends on the presence of theophylline. We systematically applied this approach to 29 essential genes, obtained ligand-dependent growth phenotypes for 19 targets, and found that 18 of these essential genes yielded stringent live-die synthetic auxotrophs. These strains exhibited robust theophylline dependence with escape frequencies ranging from 1 × 10−5 to 1 × 10−6 (most below limit of detection). Our modular design allows for the rapid (<1 week), low-cost, and reliable generation of synthetic auxotrophs. This work introduces ligand-dependent translational control as a new mechanism for engineering synthetic auxotrophy and provides an accessible platform that expands the biocontainment toolkit.",
  "abstract_shown": true,
  "affiliations": [
    "Synvivia, Inc., Emeryville, California, United States of America"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Carlos Gonzalez-Lopez"
    },
    {
      "name": "Adrian Overly"
    },
    {
      "name": "Saahil Singh"
    },
    {
      "name": "Charlie Huang"
    },
    {
      "name": "Gabriel Lopez"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/by5m44wamj16e.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0360098",
  "fulltext_url": null,
  "id": "by5m44wamj16e",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0360098",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "1312|RNA and protein synthesis mechanisms"
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      "plos",
      "/Biology and life sciences/Biochemistry/Biosynthesis"
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      "plos",
      "/Biology and life sciences/Biochemistry/Enzymology/Enzymes/Ribozymes/Riboswitches"
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    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA recombination/Homologous recombination"
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    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/Ribozymes/Riboswitches"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Proteins/Enzymes/Ribozymes/Riboswitches"
    ],
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      "/Biology and life sciences/Bioengineering"
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      "/Biology and life sciences/Bioengineering/Biotechnology/Genetic engineering"
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      "/Biology and life sciences/Genetics/DNA/DNA recombination/Homologous recombination"
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      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Escherichia coli"
    ],
    [
      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ],
    [
      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial genetic recombination/Gene targeting"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Enterobacteriaceae/Escherichia/Escherichia coli"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Gut bacteria/Escherichia/Escherichia coli"
    ],
    [
      "plos",
      "/Engineering and technology/Bioengineering"
    ],
    [
      "plos",
      "/Engineering and technology/Bioengineering/Biotechnology/Genetic engineering"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Escherichia coli"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Model organisms/Escherichia coli"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Prokaryotic models/Escherichia coli"
    ],
    [
      "plos",
      "/Research and analysis methods/Model organisms/Escherichia coli"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Artificial genetic recombination/Gene targeting"
    ]
  ],
  "openalex": "W7221014962",
  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0360098&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-08",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/by5m44wamj16e.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:30Z",
      "native_id": "10.1371/journal.pone.0360098",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0360098"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "plos:molecular biology",
      "subfield": "molecular-biology"
    },
    {
      "field": "biology",
      "origin": "plos:bioengineering",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "A modular toolkit for theophylline-dependent synthetic auxotrophs via riboswitch-gated essential genes",
  "title_text": "A modular toolkit for theophylline-dependent synthetic auxotrophs via riboswitch-gated essential genes",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:30Z",
  "url": "https://research.draconitic.com/paper/by5m44wamj16e",
  "venue": "PLOS One",
  "versions": []
}