{"entity": "researcher", "timestamp": "2026-08-20T20:49:48.610Z", "family": "Ter Beek", "given": "Josy", "initials": "J", "orcid": "0000-0003-4165-9277", "affiliations": ["Department of Medical Biochemistry and Biophysics, Ume\u00e5 University, Ume\u00e5, Sweden.", "Wallenberg Centre for Molecular Medicine, Ume\u00e5 University, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3d76493e80b4b57a951a0f94e6123ca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3d76493e80b4b57a951a0f94e6123ca"}}, "publications": [{"entity": "publication", "iuid": "bfcbb43625f64058942fd2f5b18f87d4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bfcbb43625f64058942fd2f5b18f87d4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bfcbb43625f64058942fd2f5b18f87d4"}}, "title": "Breaking Barriers: pCF10 Type 4 Secretion System relies on a self-regulating muramidase to modulate the cell wall", "authors": [{"family": "Sun", "given": "Wei Sheng", "initials": "WS", "orcid": "0000-0001-9738-8862", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d00b7dff289b4b988e3c21f921f8dc11.json"}}, {"family": "Torrens", "given": "Gabriel", "initials": "G", "orcid": "0000-0002-0450-1430", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a84794f089441ea8700f06f5a59fc2f.json"}}, {"family": "Beek", "given": "Josy ter", "initials": "Jt", "orcid": "0000-0003-4165-9277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3d76493e80b4b57a951a0f94e6123ca.json"}}, {"family": "Cava", "given": "Felipe", "initials": "F", "orcid": "0000-0001-5995-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbcff12a06814d54afea533e125a1213.json"}}, {"family": "Berntsson", "given": "Ronnie P A", "initials": "RPA", "orcid": "0000-0001-6848-322X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb9399248b784100a8020261949fb910.json"}}], "type": "posted-content", "published": "2024-02-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.02.15.580431", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:52:16.449Z", "modified": "2026-08-20T10:52:16.557Z"}, {"entity": "publication", "iuid": "33463bd996d148f7abd7b70bcdca36c1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/33463bd996d148f7abd7b70bcdca36c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/33463bd996d148f7abd7b70bcdca36c1"}}, "title": "A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria.", "authors": [{"family": "Espaillat", "given": "Akbar", "initials": "A"}, {"family": "Alvarez", "given": "Laura", "initials": "L", "orcid": "0000-0003-2429-7542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/329d8b1460fe44789dbef53ea0493294.json"}}, {"family": "Torrens", "given": "Gabriel", "initials": "G", "orcid": "0000-0002-0450-1430", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a84794f089441ea8700f06f5a59fc2f.json"}}, {"family": "Ter Beek", "given": "Josy", "initials": "J", "orcid": "0000-0003-4165-9277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3d76493e80b4b57a951a0f94e6123ca.json"}}, {"family": "Miguel-Ruano", "given": "Vega", "initials": "V", "orcid": "0000-0002-2492-7164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ee0be393f7b44f3aeb6c926d39dfac9.json"}}, {"family": "Irazoki", "given": "Oihane", "initials": "O"}, {"family": "Gago", "given": "Federico", "initials": "F", "orcid": "0000-0002-3071-4878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f4b917616c44f69acace2feeb97763d.json"}}, {"family": "Hermoso", "given": "Juan A", "initials": "JA"}, {"family": "Berntsson", "given": "Ronnie P-A", "initials": "RP", "orcid": "0000-0001-6848-322X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb9399248b784100a8020261949fb910.json"}}, {"family": "Cava", "given": "Felipe", "initials": "F", "orcid": "0000-0001-5995-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbcff12a06814d54afea533e125a1213.json"}}], "type": "journal article", "published": "2024-02-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1343", "issn-l": "2041-1723"}, "abstract": "The bacterial cell-wall peptidoglycan is made of glycan strands crosslinked by short peptide stems. Crosslinks are catalyzed by DD-transpeptidases (4,3-crosslinks) and LD-transpeptidases (3,3-crosslinks). However, recent research on non-model species has revealed novel crosslink types, suggesting the existence of uncharacterized enzymes. Here, we identify an LD-transpeptidase, LDTGo, that generates 1,3-crosslinks in the acetic-acid bacterium Gluconobacter oxydans. LDTGo-like proteins are found in Alpha- and Betaproteobacteria lacking LD3,3-transpeptidases. In contrast with the strict specificity of typical LD- and DD-transpeptidases, LDTGo can use non-terminal amino acid moieties for crosslinking. A high-resolution crystal structure of LDTGo reveals unique features when compared to LD3,3-transpeptidases, including a proline-rich region that appears to limit substrate access, and a cavity accommodating both glycan chain and peptide stem from donor muropeptides. Finally, we show that DD-crosslink turnover is involved in supplying the necessary substrate for LD1,3-transpeptidation. This phenomenon underscores the interplay between distinct crosslinking mechanisms in maintaining cell wall integrity in G. oxydans.", "doi": "10.1038/s41467-024-45620-5", "pmid": "38351082", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10864386"}, {"db": "pii", "key": "10.1038/s41467-024-45620-5"}], "notes": [], "created": "2026-08-20T08:53:08.705Z", "modified": "2026-08-20T08:53:08.995Z"}, {"entity": "publication", "iuid": "427fd23a473f4521932a6b59e2d344af", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/427fd23a473f4521932a6b59e2d344af.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/427fd23a473f4521932a6b59e2d344af"}}, "title": "A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha and Betaproteobacteria", "authors": [{"family": "Espaillat", "given": "Akbar", "initials": "A", "orcid": "0000-0003-0835-368X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70b05075063e4b0ebca0375644b5a4b6.json"}}, {"family": "Alvarez", "given": "Laura", "initials": "L", "orcid": "0000-0003-2429-7542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/329d8b1460fe44789dbef53ea0493294.json"}}, {"family": "Torrens", "given": "Gabriel", "initials": "G", "orcid": "0000-0002-0450-1430", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a84794f089441ea8700f06f5a59fc2f.json"}}, {"family": "Beek", "given": "Josy ter", "initials": "Jt", "orcid": "0000-0003-4165-9277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3d76493e80b4b57a951a0f94e6123ca.json"}}, {"family": "Miguel-Ruano", "given": "Vega", "initials": "V", "orcid": "0000-0002-2492-7164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ee0be393f7b44f3aeb6c926d39dfac9.json"}}, {"family": "Irazoki", "given": "Oihane", "initials": "O", "orcid": "0000-0002-8896-7480", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92d1aa46064a4ca1824bc91ffd7141c9.json"}}, {"family": "Gago", "given": "Federico", "initials": "F", "orcid": "0000-0002-3071-4878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f4b917616c44f69acace2feeb97763d.json"}}, {"family": "Hermoso", "given": "Juan A", "initials": "JA", "orcid": "0000-0002-1862-8950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb3d6a3d6ce34ce5a011f6036876cf69.json"}}, {"family": "Berntsson", "given": "Ronnie Per Arne", "initials": "RPA", "orcid": "0000-0001-6848-322X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb9399248b784100a8020261949fb910.json"}}, {"family": "Cava", "given": "Felipe", "initials": "F", "orcid": "0000-0001-5995-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbcff12a06814d54afea533e125a1213.json"}}], "type": "posted-content", "published": "2023-11-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.10.31.564931", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:48:43.639Z", "modified": "2026-08-20T10:49:16.855Z"}, {"entity": "publication", "iuid": "0a8add1340db46c8acdea6e91aa01ab1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0a8add1340db46c8acdea6e91aa01ab1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0a8add1340db46c8acdea6e91aa01ab1"}}, "title": "D-amino acids signal a stress-dependent run-away response in Vibrio cholerae.", "authors": [{"family": "Irazoki", "given": "Oihane", "initials": "O", "orcid": "0000-0002-8896-7480", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92d1aa46064a4ca1824bc91ffd7141c9.json"}}, {"family": "Ter Beek", "given": "Josy", "initials": "J", "orcid": "0000-0003-4165-9277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3d76493e80b4b57a951a0f94e6123ca.json"}}, {"family": "Alvarez", "given": "Laura", "initials": "L", "orcid": "0000-0003-2429-7542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/329d8b1460fe44789dbef53ea0493294.json"}}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf0d242aa894a66b60828456bbc22aa.json"}}, {"family": "Colin", "given": "Remy", "initials": "R", "orcid": "0000-0001-9051-8003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48fcedae27254c06880cc48ad7276d9f.json"}}, {"family": "Typas", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-0797-9018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d38ea7a531ad47cfa26df998f0e54dbe.json"}}, {"family": "Savitski", "given": "Mikhail M", "initials": "MM", "orcid": "0000-0003-2011-9247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/374222bd4bce42f282690629b9679628.json"}}, {"family": "Sourjik", "given": "Victor", "initials": "V", "orcid": "0000-0003-1053-9192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6aef6aa6af54827905ff16a446d27d0.json"}}, {"family": "Berntsson", "given": "Ronnie P-A", "initials": "RP", "orcid": "0000-0001-6848-322X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb9399248b784100a8020261949fb910.json"}}, {"family": "Cava", "given": "Felipe", "initials": "F", "orcid": "0000-0001-5995-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbcff12a06814d54afea533e125a1213.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "volume": "8", "issue": "8", "pages": "1549-1560", "issn-l": "2058-5276"}, "abstract": "To explore favourable niches while avoiding threats, many bacteria use a chemotaxis navigation system. Despite decades of studies on chemotaxis, most signals and sensory proteins are still unknown. Many bacterial species release D-amino acids to the environment; however, their function remains largely unrecognized. Here we reveal that D-arginine and D-lysine are chemotactic repellent signals for the cholera pathogen Vibrio cholerae. These D-amino acids are sensed by a single chemoreceptor MCPDRK co-transcribed with the racemase enzyme that synthesizes them under the control of the stress-response sigma factor RpoS. Structural characterization of this chemoreceptor bound to either D-arginine or D-lysine allowed us to pinpoint the residues defining its specificity. Interestingly, the specificity for these D-amino acids appears to be restricted to those MCPDRK orthologues transcriptionally linked to the racemase. Our results suggest that D-amino acids can shape the biodiversity and structure of complex microbial communities under adverse conditions.", "doi": "10.1038/s41564-023-01419-6", "pmid": "37365341", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10390336"}, {"db": "pii", "key": "10.1038/s41564-023-01419-6"}], "notes": [], "created": "2026-08-20T08:55:21.117Z", "modified": "2026-08-20T08:55:21.397Z"}]}