{"entity": "researcher", "timestamp": "2026-08-20T20:48:39.334Z", "family": "Johansson", "given": "Marcus J O", "initials": "MJO", "orcid": "0000-0001-7117-7426", "affiliations": ["Department of Experimental Medicine, Lund University, Lund 221 84, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ee1c60ebb934dfd996e67a32790db16.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ee1c60ebb934dfd996e67a32790db16"}}, "publications": [{"entity": "publication", "iuid": "d87946bf3ec84fec90305daa1c867032", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d87946bf3ec84fec90305daa1c867032.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d87946bf3ec84fec90305daa1c867032"}}, "title": "Characterization of five environmental phages infecting Escherichia coli K-12 isolated during a phage biology training course.", "authors": [{"family": "Shyrokova", "given": "Lena", "initials": "L"}, {"family": "Egorov", "given": "Artyom A", "initials": "AA"}, {"family": "Cole", "given": "Astrid", "initials": "A"}, {"family": "Duque-Pedraza", "given": "Julian J", "initials": "JJ"}, {"family": "Tyagi", "given": "Anu", "initials": "A"}, {"family": "Ernits", "given": "Karin", "initials": "K"}, {"family": "Mets", "given": "Toomas", "initials": "T"}, {"family": "Kurata", "given": "Tatsuaki", "initials": "T"}, {"family": "Juozapaitis", "given": "Jonas", "initials": "J"}, {"family": "Yang", "given": "Alessio Ling Jie", "initials": "ALJ"}, {"family": "Ibarra Chavez", "given": "Rodrigo", "initials": "R"}, {"family": "Graversgaard Henriksen", "given": "Frederik Oskar", "initials": "FO"}, {"family": "Lassen", "given": "Swenja", "initials": "S"}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC"}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Johansson", "given": "Marcus J O", "initials": "MJO", "orcid": "0000-0001-7117-7426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ee1c60ebb934dfd996e67a32790db16.json"}}], "type": "journal article", "published": "2025-12-02", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "volume": "13", "issue": "12", "pages": "e0227425", "issn-l": null}, "abstract": "Phage collections are essential tools for discovering and dissecting bacterial anti-phage defense systems. Here, we report the isolation, characterization, and annotated genome sequences of five environmental Escherichia coli-infecting phages, obtained during the 2023 Fundamentals of Basic and Applied Phage Biology course at Lund University. The phages were isolated using a motile E. coli K-12 BW25113 strain, whose motility is conferred by an IS5 insertion upstream of the flhDC operon, the master regulator of flagellar synthesis. The isolated Escherichia phages include Lubas (LuPh1) and Lucat (LuPh2) of the genus Tequatrovirus; Lupin (LuPh3) and Lucris (LuPh4) of the genus Tequintavirus; and Kompetensportalen (LuPh5) of the genus Chivirus. Transmission electron microscopy confirmed myovirus and siphovirus morphologies typical of these genera. Consistent with its classification in the flagellotropic Chivirus genus, LuPh5 did not infect a poorly motile BW25113 strain lacking the IS5 element upstream of flhDC, but did infect the motile laboratory Salmonella enterica subsp. enterica serovar Typhimurium strain 12023s. By testing a panel of eight previously described anti-phage defense systems, we found that LuPh1 and LuPh2 are inhibited by the toxin-antitoxin-chaperone CmdTAC system; LuPh5 is inhibited by both the restriction-modification system EcoRI and the abortive infection reverse transcriptase AbiK; and all five phages are sensitive to the hybrid artificial CmdTA-HigC system. Collectively, our findings expand the toolkit for probing phage-host interactions and underscore the pedagogical value of incorporating phage isolation into practical training for emerging researchers.IMPORTANCEBacterial anti-phage defense systems are central to microbiology and have applications in biotechnology and medicine. Phage collections are key tools for uncovering and studying these systems. By isolating and characterizing five E. coli K12-infecting phages, including three newly identified species, this work expands resources for probing phage-host interactions. It also shows that hands-on phage isolation in educational settings can contribute meaningfully to both training and research.", "doi": "10.1128/spectrum.02274-25", "pmid": "41196041", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12671086"}, {"db": "GENBANK", "key": "PV806335"}, {"db": "GENBANK", "key": "PV806337"}, {"db": "GENBANK", "key": "PV806336"}, {"db": "GENBANK", "key": "PV806339"}, {"db": "GENBANK", "key": "CP195189"}, {"db": "GENBANK", "key": "CP195190"}, {"db": "GENBANK", "key": "PV806338"}], "notes": [], "created": "2026-08-20T12:01:20.928Z", "modified": "2026-08-20T12:01:21.006Z"}, {"entity": "publication", "iuid": "e684a9aac9ab4fb6ae43f6f5249eaec7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e684a9aac9ab4fb6ae43f6f5249eaec7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e684a9aac9ab4fb6ae43f6f5249eaec7"}}, "title": "The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.", "authors": [{"family": "Turnbull", "given": "Kathryn", "initials": "K", "orcid": "0000-0002-0899-974X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02a543194bb94a0e89f62e7288cc2036.json"}}, {"family": "Paternoga", "given": "Helge", "initials": "H"}, {"family": "von der Weth", "given": "Esther", "initials": "E"}, {"family": "Egorov", "given": "Artyom A", "initials": "AA", "orcid": "0000-0001-5578-5384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db620b86e13e45618e7cad6a06cd474e.json"}}, {"family": "Pochopien", "given": "Agnieszka A", "initials": "AA"}, {"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Nersisyan", "given": "Lilit", "initials": "L"}, {"family": "Margus", "given": "T\u00f5nu", "initials": "T", "orcid": "0000-0003-4966-1291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/24ca36e3fdea4ecaaf8418d10e94bdc4.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": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.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": "journal article", "published": "2024-05-29", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.", "doi": "10.1101/2024.05.29.596377", "pmid": "38854126", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11160720"}, {"db": "pii", "key": "2024.05.29.596377"}], "notes": [], "created": "2026-08-20T10:54:59.624Z", "modified": "2026-08-20T10:54:59.751Z"}, {"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": "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": "https://publications-affiliated.scilifelab.se/researcher/590d08398d614e9ca3307803cd263b8d.json"}}, {"family": "Kurata", "given": "Tatsuaki", "initials": "T"}, {"family": "Egorov", "given": "Artyom A", "initials": "AA"}, {"family": "Shyrokova", "given": "Lena", "initials": "L", "orcid": "0000-0002-0361-6359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9e14037d4da48408ecfa16d12742d1f.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": "Mets", "given": "Toomas", "initials": "T", "orcid": "0000-0002-6796-7000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dbceebe30234575b3575ef4f44c0511.json"}}, {"family": "Rustamova", "given": "Aytan", "initials": "A"}, {"family": "D\u017eigurski", "given": "Jelisaveta", "initials": "J", "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": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.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": "2023-08-15", "journal": {"title": "Proc. 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": 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