{"entity": "researcher", "timestamp": "2026-08-20T20:37:06.693Z", "family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "affiliations": ["Department of Experimental Medical Science, Lund University, Lund, Sweden. gemma.atkinson@med.lu.se."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8"}}, "publications": [{"entity": "publication", "iuid": "3aece26036754a8f89bfecad5f024849", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3aece26036754a8f89bfecad5f024849.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3aece26036754a8f89bfecad5f024849"}}, "title": "Evidence for a functional interaction between yeast Pol \u03b5 and PCNA in vivo.", "authors": [{"family": "Singh", "given": "Noopur", "initials": "N"}, {"family": "Odai", "given": "Roni", "initials": "R", "orcid": "0009-0002-2280-3915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604a6d6e3cdb468d8c6acfb6a2e45ff9.json"}}, {"family": "Persson", "given": "Ulf", "initials": "U"}, {"family": "Bylund", "given": "G\u00f6ran O", "initials": "GO"}, {"family": "Obi", "given": "Ikenna", "initials": "I"}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bbda597fa314881a10de1f7a6ad09ee.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}, {"family": "Johansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8526-6224", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e8695cbe08e41e0a9ee097e2f38a37b.json"}}], "type": "journal article", "published": "2025-11-26", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "22", "issn-l": "0305-1048"}, "abstract": "DNA replication relies on precise coordination between proteins, including the sliding clamp proliferating cell nuclear antigen (PCNA), which encircles DNA to interact with key players in replication and repair. While biochemical studies have demonstrated interactions between PCNA and DNA polymerases \u03b4 and \u03b5 during DNA synthesis, the functional role of the Pol \u03b5-PCNA interaction in vivo, particularly during leading strand synthesis, remains to be elucidated. To address this question, we employed AlphaFold to model how PCNA interact with four-subunit yeast Pol \u03b5. Our models revealed two distinct points of interaction between Pol \u03b5 and PCNA: one at the P-domain and another at a PIP-box, a classical PCNA interaction motif. To validate these findings, we generated mutants that disrupted the Pol \u03b5-PCNA interaction interface. Biochemical assays demonstrated that the PIP-box is critical for this interaction, with the P-domain serving as a secondary contact point. Notably, introducing these mutants into yeast, caused no phenotype in a wild-type background. However, when fewer origins are firing, resulting in longer stretches of leading strand synthesis before forks converge, strains expressing a Pol \u03b5 mutant lacking interaction with PCNA showed slower growth. These findings suggest that PCNA enhances the processivity of Pol \u03b5 both in vitro and in vivo.", "doi": "10.1093/nar/gkaf1339", "pmid": "41404803", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12709181"}, {"db": "pii", "key": "8382373"}], "notes": [], "created": "2026-08-20T09:50:15.101Z", "modified": "2026-08-20T09:50:15.248Z"}, {"entity": "publication", "iuid": "d5dd1820f3d64bba98b64bc4c1396191", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d5dd1820f3d64bba98b64bc4c1396191.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d5dd1820f3d64bba98b64bc4c1396191"}}, "title": "The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes.", "authors": [{"family": "Odai", "given": "Roni", "initials": "R", "orcid": "0009-0002-2280-3915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604a6d6e3cdb468d8c6acfb6a2e45ff9.json"}}, {"family": "Leemann", "given": "Mich\u00e8le", "initials": "M", "orcid": "0009-0008-9641-8837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/124f42d408ce4e23aa91f3d82ab73f22.json"}}, {"family": "Al-Murad", "given": "Tamim", "initials": "T", "orcid": "0009-0009-9450-6734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09af3a6db1304f58ba96542af779c538.json"}}, {"family": "Abdullah", "given": "Minhal", "initials": "M", "orcid": "0000-0002-6018-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8fb279f2df41d2a5d86e7afbab9592.json"}}, {"family": "Shyrokova", "given": "Lena", "initials": "L", "orcid": "0000-0002-0361-6359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9e14037d4da48408ecfa16d12742d1f.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Pereira", "given": "Joana", "initials": "J", "orcid": "0000-0002-5588-6588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18123de080c84f7fba8ca71f1f294773.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "40", "pages": "eadz8560", "issn-l": "2375-2548"}, "abstract": "Viruses are the most abundant and genetically diverse entities on Earth, yet the functions and evolution of most viral proteins remain poorly understood. Their rapid evolution often obscures evolutionary relationships, limiting the ability to assign functions using sequence-based methods. Although the conservation of protein fold can reveal deep homologies, viral proteins remain underrepresented in structural databases. We address this by clustering viral sequences from RefSeq and predicting the structures of ~27,000 representative proteins using AlphaFold2 to create the Viral AlphaFold Database (VAD). We uncover conserved folds in diverse viruses infecting bacteria, archaea, and eukaryotes. We predict homodimers and make comparisons to the Protein Data Bank, providing data on oligomerization potential. We reveal considerable functional darkness in the viral protein universe and report the discovery and validation of an uncharacterized toxin-antitoxin system. The VAD provides a foundation for exploring viral structure-function relationships, including ancient folds shaping viral interactions across all life.", "doi": "10.1126/sciadv.adz8560", "pmid": "41032608", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12487901"}], "notes": [], "created": "2026-08-20T11:59:12.908Z", "modified": "2026-08-20T11:59:13.115Z"}, {"entity": "publication", "iuid": "25cd7f5504364ef8a15a088efbc23866", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/25cd7f5504364ef8a15a088efbc23866.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/25cd7f5504364ef8a15a088efbc23866"}}, "title": "Mechanisms of neutralization of toxSAS from toxin-antitoxin modules.", "authors": [{"family": "Dominguez-Molina", "given": "Lucia", "initials": "L"}, {"family": "Kurata", "given": "Tatsuaki", "initials": "T"}, {"family": "Cepauskas", "given": "Albinas", "initials": "A"}, {"family": "Echemendia-Blanco", "given": "Dannele", "initials": "D"}, {"family": "Zedek", "given": "Safia", "initials": "S"}, {"family": "Talavera-Perez", "given": "Ariel", "initials": "A", "orcid": "0000-0002-1865-5959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b81a4477bdc945f782f9067806f4b0b3.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Garcia-Pino", "given": "Abel", "initials": "A", "orcid": "0000-0002-0634-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48acc9ebb8dd44668e3629de8dff9b93.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Nat. Chem. Biol.", "issn": "1552-4469", "volume": "21", "issue": "2", "pages": "182-192", "issn-l": "1552-4450"}, "abstract": "Toxic small alarmone synthetase (toxSAS) enzymes constitute a family of bacterial effectors present in toxin-antitoxin and secretion systems. toxSASs act through either translation inhibition mediated by pyrophosphorylation of transfer RNA (tRNA) CCA ends or synthesis of the toxic alarmone adenosine pentaphosphate ((pp)pApp) and adenosine triphosphate (ATP) depletion, exemplified by FaRel2 and FaRel, respectively. However, structural bases of toxSAS neutralization are missing. Here we show that the pseudo-Zn2+ finger domain (pZFD) of the ATfaRel2 antitoxin precludes access of ATP to the pyrophosphate donor site of the FaRel2 toxin, without affecting recruitment of the tRNA pyrophosphate acceptor. By contrast, (pp)pApp-producing toxSASs are inhibited by Tis1 antitoxin domains though occlusion of the pyrophosphate acceptor-binding site. Consequently, the auxiliary pZFD of AT2faRel is dispensable for FaRel neutralization. Collectively, our study establishes the general principles of toxSAS inhibition by structured antitoxin domains, with the control strategy directly coupled to toxSAS substrate specificity.", "doi": "10.1038/s41589-024-01630-4", "pmid": "38834893", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11782079"}, {"db": "pii", "key": "10.1038/s41589-024-01630-4"}], "notes": [], "created": "2026-08-20T09:01:35.683Z", "modified": "2026-08-20T09:01:35.803Z"}, {"entity": "publication", "iuid": "bcc70a507afc41a6878aab9d0b000d03", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc70a507afc41a6878aab9d0b000d03.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc70a507afc41a6878aab9d0b000d03"}}, "title": "A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis", "authors": [{"family": "Takada", "given": "Hiraku", "initials": "H", "orcid": "0000-0003-2034-5666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92f74a1a0bb543ed8504ed034144b2bc.json"}}, {"family": "Paternoga", "given": "Helge", "initials": "H", "orcid": "0000-0001-8335-3239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dead4106bf4c4cfbbd1243f24dac0f23.json"}}, {"family": "Fujiwara", "given": "Keigo", "initials": "K", "orcid": "0000-0002-5371-3552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e50ad1857fe4bbfa35f340df26f4819.json"}}, {"family": "Nakamoto", "given": "Jose A", "initials": "JA", "orcid": "0000-0001-8312-433X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590d08398d614e9ca3307803cd263b8d.json"}}, {"family": "Park", "given": "Esther N", "initials": "EN"}, {"family": "Dimitrova-Paternoga", "given": "Lyudmila", "initials": "L", "orcid": "0000-0001-5673-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e2c9d06032144eba8bd56299b1e1137.json"}}, {"family": "Beckert", "given": "Bertrand", "initials": "B", "orcid": "0000-0002-9507-3127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbb81c818c4d4aab85ef23963e50e30f.json"}}, {"family": "Saarma", "given": "Merilin", "initials": "M"}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Buskirk", "given": "Allen R", "initials": "AR"}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}, {"family": "Chiba", "given": "Shinobu", "initials": "S"}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c2d78750ccb42239a7363f99f58dcc5.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}], "type": "posted-content", "published": "2024-03-04", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.03.03.583159", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:52:33.672Z", "modified": "2026-08-20T10:52:33.843Z"}, {"entity": "publication", "iuid": "1102a74dd62944309e64d3922f7c28de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1102a74dd62944309e64d3922f7c28de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1102a74dd62944309e64d3922f7c28de"}}, "title": "Mechanism of phage sensing and abortion by toxin-antitoxin-chaperone systems", "authors": [{"family": "Mets", "given": "Toomas", "initials": "T", "orcid": "0000-0002-6796-7000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dbceebe30234575b3575ef4f44c0511.json"}}, {"family": "Kurata", "given": "Tatsuaki", "initials": "T", "orcid": "0000-0001-5986-7141", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3ed90eb741422db2af62827e8947e2.json"}}, {"family": "Ernits", "given": "Karin", "initials": "K", "orcid": "0000-0003-1072-4945", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f3dbd4a451c45878f71cb0b441c561d.json"}}, {"family": "Johansson", "given": "Marcus J O", "initials": "MJO", "orcid": "0000-0001-7117-7426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ee1c60ebb934dfd996e67a32790db16.json"}}, {"family": "Craig", "given": "Sophie Z", "initials": "SZ"}, {"family": "Evora", "given": "Gabriel Medina", "initials": "GM"}, {"family": "Buttress", "given": "Jessica A", "initials": "JA", "orcid": "0000-0001-8822-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f7cee57e9d94c53b46aed566af418e7.json"}}, {"family": "Odai", "given": "Roni", "initials": "R"}, {"family": "Coppieters\u2018t Wallant", "given": "Kyo", "initials": "K", "orcid": "0000-0003-2358-999X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6129bd7b08684155a424e8bec6b24e56.json"}}, {"family": "Nakamoto", "given": "Jose A", "initials": "JA", "orcid": "0000-0001-8312-433X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590d08398d614e9ca3307803cd263b8d.json"}}, {"family": "Shyrokova", "given": "Lena", "initials": "L"}, {"family": "Egorov", "given": "Artyom A", "initials": "AA", "orcid": "0000-0001-5578-5384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db620b86e13e45618e7cad6a06cd474e.json"}}, {"family": "Doering", "given": "Christopher Ross", "initials": "CR"}, {"family": "Brodiazhenko", "given": "Tetiana", "initials": "T", "orcid": "0000-0002-2591-9588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8747a493473b4ebcabf9b1847be69e29.json"}}, {"family": "Laub", "given": "Michael T", "initials": "MT"}, {"family": "Tenson", "given": "Tanel", "initials": "T"}, {"family": "Strahl", "given": "Henrik", "initials": "H"}, {"family": "Martens", "given": "Chloe", "initials": "C"}, {"family": "Harms", "given": "Alexander", "initials": "A", "orcid": "0000-0003-2106-1286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c54ff7663e84b4388af871371448d4a.json"}}, {"family": "Garcia-Pino", "given": "Abel", "initials": "A", "orcid": "0000-0002-0634-0300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48acc9ebb8dd44668e3629de8dff9b93.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}], "type": "posted-content", "published": "2024-02-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.02.24.581848", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:52:22.356Z", "modified": "2026-08-20T10:52:22.534Z"}, {"entity": "publication", "iuid": "6efe7d5b58f0438b98b30c5d36a8f8a3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6efe7d5b58f0438b98b30c5d36a8f8a3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6efe7d5b58f0438b98b30c5d36a8f8a3"}}, "title": "Resolution of ribosomal stalling by ABCF ATPases YfmR and YkpA/YbiT", "authors": [{"family": "Takada", "given": "Hiraku", "initials": "H", "orcid": "0000-0003-2034-5666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92f74a1a0bb543ed8504ed034144b2bc.json"}}, {"family": "Fujiwara", "given": "Keigo", "initials": "K", "orcid": "0000-0002-5371-3552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e50ad1857fe4bbfa35f340df26f4819.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}, {"family": "Shinobu", "given": "Chiba", "initials": "C"}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}], "type": "posted-content", "published": "2024-01-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.01.25.577322", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:51:55.654Z", "modified": "2026-08-20T10:51:55.756Z"}, {"entity": "publication", "iuid": "1a559ed2dafd466d8e52c3a17f62d0f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a559ed2dafd466d8e52c3a17f62d0f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a559ed2dafd466d8e52c3a17f62d0f5"}}, "title": "The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems.", "authors": [{"family": "Ernits", "given": "Karin", "initials": "K"}, {"family": "Saha", "given": "Chayan Kumar", "initials": "CK", "orcid": "0000-0002-5357-517X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3d0b705fbd94f5a82d2825b0f7d40cb.json"}}, {"family": "Brodiazhenko", "given": "Tetiana", "initials": "T"}, {"family": "Chouhan", "given": "Bhanu", "initials": "B"}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Buttress", "given": "Jessica A", "initials": "JA", "orcid": "0000-0001-8822-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f7cee57e9d94c53b46aed566af418e7.json"}}, {"family": "Duque-Pedraza", "given": "Juli\u00e1n J", "initials": "JJ"}, {"family": "Bojar", "given": "Veda", "initials": "V"}, {"family": "Nakamoto", "given": "Jose A", "initials": "JA", "orcid": "0000-0001-8312-433X", "researcher": {"href": 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"orcid": "0000-0003-2885-6241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ff5ff6b4a5a4b3ba1f08f4d34440d4c.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Garcia-Pino", "given": "Abel", "initials": "A"}, {"family": "Strahl", "given": "Henrik", "initials": "H", "orcid": "0000-0003-4416-2178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/17b2bf7837f7474dac625be9421a223e.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": 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Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "120", "issue": "33", "pages": "e2305393120", "issn-l": "0027-8424"}, "abstract": "Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and a neutralizing antitoxin. Using our tool NetFlax (standing for Network-FlaGs for toxins and antitoxins), we have performed a large-scale bioinformatic analysis of proteinaceous TAs, revealing interconnected clusters constituting a core network of TA-like gene pairs. To understand the structural basis of toxin neutralization by antitoxins, we have predicted the structures of 3,419 complexes with AlphaFold2. Together with mutagenesis and functional assays, our structural predictions provide insights into the neutralizing mechanism of the hyperpromiscuous Panacea antitoxin domain. In antitoxins composed of standalone Panacea, the domain mediates direct toxin neutralization, while in multidomain antitoxins the neutralization is mediated by other domains, such as PAD1, Phd-C, and ZFD. We hypothesize that Panacea acts as a sensor that regulates TA activation. We have experimentally validated 16 NetFlax TA systems and used domain annotations and metabolic labeling assays to predict their potential mechanisms of toxicity (such as membrane disruption, and inhibition of cell division or protein synthesis) as well as biological functions (such as antiphage defense). We have validated the antiphage activity of a RosmerTA system encoded by Gordonia phage Kita, and used fluorescence microscopy to confirm its predicted membrane-depolarizing activity. The interactive version of the NetFlax TA network that includes structural predictions can be accessed at http://netflax.webflags.se/.", "doi": "10.1073/pnas.2305393120", "pmid": "37556498", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10440598"}], "notes": [], "created": "2026-08-20T09:31:27.979Z", "modified": "2026-08-20T09:31:28.324Z"}, {"entity": "publication", "iuid": "528de81a6f214d86a9366806efd87b77", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/528de81a6f214d86a9366806efd87b77.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/528de81a6f214d86a9366806efd87b77"}}, "title": "The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems", "authors": [{"family": "Ernits", "given": "Karin", "initials": "K", "orcid": "0000-0003-1072-4945", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f3dbd4a451c45878f71cb0b441c561d.json"}}, {"family": "Saha", "given": "Chayan Kumar", "initials": "CK", "orcid": "0000-0002-5357-517X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3d0b705fbd94f5a82d2825b0f7d40cb.json"}}, {"family": "Brodiazhenko", "given": "Tetiana", "initials": "T", "orcid": "0000-0002-2591-9588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8747a493473b4ebcabf9b1847be69e29.json"}}, {"family": "Chouhan", "given": "Bhanu", "initials": "B", "orcid": "0000-0002-3918-5925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68a24320b5684139a54e7700443360ac.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Duque-Pedraza", "given": "Julian J", "initials": "JJ", "orcid": "0009-0008-6943-2967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/726403acf6a14088b5a3f48ecda03004.json"}}, {"family": "Bojar", "given": "Veda", "initials": "V", "orcid": "0009-0009-0321-143X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f7668b4f044fe689251d5bab9edf60.json"}}, {"family": "Nakamoto", "given": "Jose A", "initials": "JA", "orcid": "0000-0001-8312-433X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590d08398d614e9ca3307803cd263b8d.json"}}, {"family": "Kurata", "given": "Tatsuaki", "initials": "T", "orcid": "0000-0001-5986-7141", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3ed90eb741422db2af62827e8947e2.json"}}, {"family": "Egorov", "given": "Artyom", "initials": "A", "orcid": "0000-0001-5578-5384", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Atkinson", "given": "Gemma Catherine", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}], "type": "posted-content", "published": "2023-03-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.03.22.533649", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:44:41.759Z", "modified": "2026-08-20T10:44:42.195Z"}, {"entity": "publication", "iuid": "929a8fbe91f349eab9bb2497b8742c98", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/929a8fbe91f349eab9bb2497b8742c98.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/929a8fbe91f349eab9bb2497b8742c98"}}, "title": "Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR", "authors": [{"family": "Obana", "given": "Nozomu", "initials": "N", "orcid": "0000-0002-0637-7904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2290976e0452407dbd17f050cd24c483.json"}}, {"family": "Takada", "given": "Hiraku", "initials": "H", "orcid": "0000-0003-2034-5666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92f74a1a0bb543ed8504ed034144b2bc.json"}}, {"family": "Crowe-McAuliffe", "given": "Caillan", "initials": "C", "orcid": "0000-0003-2157-4639", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa481aef6bef42f49b6e9032313ee880.json"}}, {"family": "Iwamoto", "given": "Mizuki", "initials": "M"}, {"family": "Egorov", "given": "Artyom A", "initials": "AA", "orcid": "0000-0001-5578-5384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db620b86e13e45618e7cad6a06cd474e.json"}}, {"family": "Wu", "given": "Kelvin J Y", "initials": "KJY", "orcid": "0000-0002-5561-6369", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75c30b5728a9477782e7a6be6936582c.json"}}, {"family": "Murina", "given": "Victoriia", "initials": "V", "orcid": "0000-0003-1523-1816", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9740d251142342abb619fdbd58743f3a.json"}}, {"family": "Paternoga", "given": "Helge", "initials": "H", "orcid": "0000-0001-8335-3239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dead4106bf4c4cfbbd1243f24dac0f23.json"}}, {"family": "Tresco", "given": "Ben I C", "initials": "BIC"}, {"family": "Nomura", "given": "Nobuhiko", "initials": "N", "orcid": "0000-0003-1103-9157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb1421ef3ed349d5a30fbf08084fb75d.json"}}, {"family": "Myers", "given": "Andrew G", "initials": "AG", "orcid": "0000-0001-9602-6915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/771a0e9f40674c18ade2da6f399eb487.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c2d78750ccb42239a7363f99f58dcc5.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}], "type": "posted-content", "published": "2022-12-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.12.05.519065", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:42:40.968Z", "modified": "2026-08-20T10:42:41.285Z"}]}