{"entity": "researcher", "timestamp": "2026-08-20T20:49:47.208Z", "family": "Alvarez", "given": "Laura", "initials": "L", "orcid": "0000-0003-2429-7542", "affiliations": ["Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Ume\u00e5 Centre for Microbial Research, SciLifeLab, Ume\u00e5 University, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/329d8b1460fe44789dbef53ea0493294.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/329d8b1460fe44789dbef53ea0493294"}}, "publications": [{"entity": "publication", "iuid": "dda09c0a9a3140d7b58c2557a6137522", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dda09c0a9a3140d7b58c2557a6137522.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dda09c0a9a3140d7b58c2557a6137522"}}, "title": "LD-transpeptidation is crucial for fitness and polar growth in Agrobacterium tumefaciens.", "authors": [{"family": "Aliashkevich", "given": "Alena", "initials": "A"}, {"family": "Guest", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7868-0611", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0210aa68ff384d83947c28a5a65917e1.json"}}, {"family": "Alvarez", "given": "Laura", "initials": "L", "orcid": "0000-0003-2429-7542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/329d8b1460fe44789dbef53ea0493294.json"}}, {"family": "Gilmore", "given": "Michael C", "initials": "MC", "orcid": "0000-0002-6848-5134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afac90582c374ab9b15102bc27516d89.json"}}, {"family": "Rea", "given": "Daniel", "initials": "D", "orcid": "0009-0009-6904-1031", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f965bfb3ab44e82b84e6898fdf76ccf.json"}}, {"family": "Amstutz", "given": "Jennifer", "initials": "J"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf0d242aa894a66b60828456bbc22aa.json"}}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B", "orcid": "0000-0002-9771-467X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0d53293c611f44dda99e9249b1614132.json"}}, {"family": "Ruiz", "given": "I\u00f1igo", "initials": "I"}, {"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"}, {"family": "Brown", "given": "Pamela J B", "initials": "PJB", "orcid": "0000-0002-7558-7155", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724518d7b8f24b438cd852bea2119e61.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": "2024-10-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "20", "issue": "10", "pages": "e1011449", "issn-l": "1553-7390"}, "abstract": "Peptidoglycan (PG), a mesh-like structure which is the primary component of the bacterial cell wall, is crucial to maintain cell integrity and shape. While most bacteria rely on penicillin binding proteins (PBPs) for crosslinking, some species also employ LD-transpeptidases (LDTs). Unlike PBPs, the essentiality and biological functions of LDTs remain largely unclear. The Hyphomicrobiales order of the Alphaproteobacteria, known for their polar growth, have PG which is unusually rich in LD-crosslinks, suggesting that LDTs may play a more significant role in PG synthesis in these bacteria. Here, we investigated LDTs in the plant pathogen Agrobacterium tumefaciens and found that LD-transpeptidation, resulting from at least one of 14 putative LDTs present in this bacterium, is essential for its survival. Notably, a mutant lacking a distinctive group of 7 LDTs which are broadly conserved among the Hyphomicrobiales exhibited reduced LD-crosslinking and tethering of PG to outer membrane \u03b2-barrel proteins. Consequently, this mutant suffered severe fitness loss and cell shape rounding, underscoring the critical role played by these Hyphomicrobiales-specific LDTs in maintaining cell wall integrity and promoting elongation. Tn-sequencing screens further revealed non-redundant functions for A. tumefaciens LDTs. Specifically, Hyphomicrobiales-specific LDTs exhibited synthetic genetic interactions with division and cell cycle proteins, and a single LDT from another group. Additionally, our findings demonstrate that strains lacking all LDTs except one displayed distinctive phenotypic profiles and genetic interactions. Collectively, our work emphasizes the critical role of LD-crosslinking in A. tumefaciens cell wall integrity and growth and provides insights into the functional specialization of these crosslinking activities.", "doi": "10.1371/journal.pgen.1011449", "pmid": "39432536", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11527210"}, {"db": "pii", "key": "PGENETICS-D-24-00706"}], "notes": [], "created": "2026-08-20T12:43:54.428Z", "modified": "2026-08-20T12:43:54.645Z"}, {"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"}]}