{
  "abstract": "During plant genetic transformation, Agrobacterium transfers to its host cell a single-stranded segment of DNA (T-DNA), as a covalent complex with the virulence protein VirD2, which is ultimately integrated into the plant genome. The covalently bound VirD2 molecule is an obstacle to the ligation of the T-DNA 5’-end to host genomic DNA; therefore, VirD2 must be cleaved from the VirD2-T-DNA complex (T-complex) before the integration is completed. An interesting idea was raised that TDP2 (tyrosine phosphodiesterase 2), a protein known to resolve protein-DNA adducts, could represent a pathway for VirD2 removal from the T-complex; however, this function has not been proven directly. Here, we developed a simple technique to generate fluorescently labeled VirD2-ssDNA complexes in vitro and explored the DNA substrate requirements for the VirD2-mediated formation of these complexes, establishing a tractable experimental system for studying VirD2 removal from synthetic T-complexes. Using this system, we demonstrated that TDP2, from mammalian or plant origin, can specifically cleave VirD2 from these synthetic T-complexes; this activity was Mg2+-dependent and required a conserved C-terminal histidine residue of TDP2. Our results strongly support the hypothesis that plant TDP2 can remove VirD2 from the T-DNA before its integration into the plant genome. Author summary: Agrobacterium tumefaciens and related species are fascinating pathogenic bacteria that can genetically transform plants by transferring and integrating a segment of their own DNA into the genome of their host cells. This extraordinary ability has been harnessed as an essential tool for research and biotechnology. The transferred DNA (T-DNA) is exported from the bacterial cell to its host cell nucleus as a complex (named the T-complex) comprised of a single-stranded DNA segment covalently attached to the effector protein VirD2; it is thus necessary that VirD2 is cleaved from the T-DNA to allow its ligation to the genome DNA. Here, we generated fluorescently labeled artificial T-complexes and developed a system suitable for in vitro study of VirD2 removal from T-complex. Next, we demonstrated that purified TDP2 is indeed able to cleave precisely VirD2 from the imported T-DNA strand. Our findings provide new insights into the mechanism of Agrobacterium T-complex processing prior to T-DNA integration, and highlight how the activity of host plant factors can be recruited to facilitate Agrobacterium infection process.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Benoît Lacroix",
      "orcid": "0000-0002-3463-0452"
    },
    {
      "affs": [
        0
      ],
      "name": "Vitaly Citovsky"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5bchrcjccfyc8.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.ppat.1014750",
  "fulltext_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014750",
  "id": "5bchrcjccfyc8",
  "issns": [
    "1553-7374",
    "1553-7366"
  ],
  "landing_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014750",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Agrobacteria"
    ],
    [
      "heading",
      "Agrobacterium Tumefaciens"
    ],
    [
      "heading",
      "Animal Studies"
    ],
    [
      "heading",
      "Arabidopsis Thaliana"
    ],
    [
      "heading",
      "Bacteria"
    ],
    [
      "heading",
      "Biochemistry"
    ],
    [
      "heading",
      "Bioengineering"
    ],
    [
      "heading",
      "Biology and Life Sciences"
    ],
    [
      "heading",
      "Biology and life sciences"
    ],
    [
      "heading",
      "Biotechnology"
    ],
    [
      "heading",
      "Brassica"
    ],
    [
      "heading",
      "Chemical Compounds"
    ],
    [
      "heading",
      "Chemistry"
    ],
    [
      "heading",
      "Chlorides"
    ],
    [
      "heading",
      "DNA"
    ],
    [
      "heading",
      "DNA repair"
    ],
    [
      "heading",
      "Engineering and Technology"
    ],
    [
      "heading",
      "Eukaryota"
    ],
    [
      "heading",
      "Experimental Organism Systems"
    ],
    [
      "heading",
      "Fluorescence Imaging"
    ],
    [
      "heading",
      "Genetics"
    ],
    [
      "heading",
      "Genomics"
    ],
    [
      "heading",
      "Imaging Techniques"
    ],
    [
      "heading",
      "Magnesium Chloride"
    ],
    [
      "heading",
      "Materials"
    ],
    [
      "heading",
      "Materials Science"
    ],
    [
      "heading",
      "Microbiology"
    ],
    [
      "heading",
      "Model Organisms"
    ],
    [
      "heading",
      "Nucleic acids"
    ],
    [
      "heading",
      "Oligomers"
    ],
    [
      "heading",
      "Organisms"
    ],
    [
      "heading",
      "Physical Sciences"
    ],
    [
      "heading",
      "Plant Biotechnology"
    ],
    [
      "heading",
      "Plant Genetics"
    ],
    [
      "heading",
      "Plant Genomics"
    ],
    [
      "heading",
      "Plant Microbiology"
    ],
    [
      "heading",
      "Plant Science"
    ],
    [
      "heading",
      "Plant and Algal Models"
    ],
    [
      "heading",
      "Plants"
    ],
    [
      "heading",
      "Research Article"
    ],
    [
      "heading",
      "Research and Analysis Methods"
    ],
    [
      "openalex",
      "1311|Bacterial Genetics and Biotechnology"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA repair"
    ],
    [
      "plos",
      "/Biology and life sciences/Bioengineering/Biotechnology/Plant biotechnology/Plant genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/DNA/DNA repair"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Plant genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Plant genetics/Plant genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Plant microbiology/Agrobacteria"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Plant microbiology/Agrobacteria/Agrobacterium tumefaciens"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Agrobacteria"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Agrobacteria/Agrobacterium tumefaciens"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Eukaryota/Plants/Brassica/Arabidopsis thaliana"
    ],
    [
      "plos",
      "/Biology and life sciences/Plant science/Plant biotechnology/Plant genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Plant science/Plant genetics/Plant genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Plant science/Plant microbiology/Agrobacteria"
    ],
    [
      "plos",
      "/Biology and life sciences/Plant science/Plant microbiology/Agrobacteria/Agrobacterium tumefaciens"
    ],
    [
      "plos",
      "/Engineering and technology/Bioengineering/Biotechnology/Plant biotechnology/Plant genomics"
    ],
    [
      "plos",
      "/Physical sciences/Chemistry/Chemical compounds/Chlorides/Magnesium chloride"
    ],
    [
      "plos",
      "/Physical sciences/Materials science/Materials/Oligomers"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Model organisms/Arabidopsis thaliana"
    ],
    [
      "plos",
      "/Research and analysis methods/Animal studies/Experimental organism systems/Plant and algal models/Arabidopsis thaliana"
    ],
    [
      "plos",
      "/Research and analysis methods/Imaging techniques/Fluorescence imaging"
    ],
    [
      "plos",
      "/Research and analysis methods/Model organisms/Arabidopsis thaliana"
    ]
  ],
  "openalex": "W7223707163",
  "pdf_url": "https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1014750&type=printable",
  "pmcid": "PMC13727043",
  "pmid": "42932378",
  "published": "2026-10-26",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/5bchrcjccfyc8.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:17Z",
      "native_id": "10.1371/journal.ppat.1014750",
      "source": "plos",
      "url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014750"
    },
    {
      "first_seen": "2026-11-05T12:23:15Z",
      "native_id": "PMC13727043",
      "source": "pmc",
      "url": "https://doi.org/10.1371/journal.ppat.1014750"
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  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "heading:Biochemistry",
      "subfield": "general"
    },
    {
      "field": "biology",
      "origin": "plos:genetics",
      "subfield": "genetics-genomics"
    },
    {
      "field": "biology",
      "origin": "plos:plant science",
      "subfield": "plant-biology"
    },
    {
      "field": "biology",
      "origin": "plos:biotechnology",
      "subfield": "systems-synthetic"
    },
    {
      "field": "chemistry",
      "origin": "heading:Materials Science",
      "subfield": "materials-polymers"
    }
  ],
  "title": "Removal of VirD2 from a synthetic T-DNA complex of Agrobacterium by the host DNA repair protein TDP2",
  "title_text": "Removal of VirD2 from a synthetic T-DNA complex of Agrobacterium by the host DNA repair protein TDP2",
  "type": "peer-reviewed",
  "updated_at": "2026-11-05T12:23:15Z",
  "url": "https://research.draconitic.com/paper/5bchrcjccfyc8",
  "venue": "PLOS Pathogens",
  "versions": []
}