{"entity": "researcher", "timestamp": "2026-08-20T20:51:47.102Z", "family": "Savitski", "given": "Mikhail M", "initials": "MM", "orcid": "0000-0003-2011-9247", "affiliations": ["Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/374222bd4bce42f282690629b9679628.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/374222bd4bce42f282690629b9679628"}}, "publications": [{"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"}, {"entity": "publication", "iuid": "292b6c1981dd454a9db47e7dd46315f2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/292b6c1981dd454a9db47e7dd46315f2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/292b6c1981dd454a9db47e7dd46315f2"}}, "title": "Deep thermal profiling for detection of functional proteoform groups.", "authors": [{"family": "Kurzawa", "given": "Nils", "initials": "N", "orcid": "0000-0002-7846-2817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/082e8989ae6e4d61bea479a19a0f0de3.json"}}, {"family": "Leo", "given": "Isabelle Rose", "initials": "IR"}, {"family": "Stahl", "given": "Matthias", "initials": "M"}, {"family": "Kunold", "given": "Elena", "initials": "E"}, {"family": "Becher", "given": "Isabelle", "initials": "I"}, {"family": "Audrey", "given": "Anastasia", "initials": "A", "orcid": "0000-0002-8172-8575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/436d3f91960447c384d04bf8535b35a9.json"}}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Huber", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-0474-2218", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/138102f5e406446a8b5f9c421ea1e595.json"}}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf0d242aa894a66b60828456bbc22aa.json"}}, {"family": "Savitski", "given": "Mikhail M", "initials": "MM", "orcid": "0000-0003-2011-9247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/374222bd4bce42f282690629b9679628.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Chem. Biol.", "issn": "1552-4469", "volume": "19", "issue": "8", "pages": "962-971", "issn-l": "1552-4450"}, "abstract": "The complexity of the functional proteome extends considerably beyond the coding genome, resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases but challenging to perform systematically. Here we applied thermal proteome profiling with deep peptide coverage to detect functional proteoform groups in acute lymphoblastic leukemia cell lines with different cytogenetic aberrations. We detected 15,846 proteoforms, capturing differently spliced, cleaved and post-translationally modified proteins expressed from 9,290 genes. We identified differential co-aggregation of proteoform pairs and established links to disease biology. Moreover, we systematically made use of measured biophysical proteoform states to find specific biomarkers of drug sensitivity. Our approach, thus, provides a powerful and unique tool for systematic detection and functional annotation of proteoform groups.", "doi": "10.1038/s41589-023-01284-8", "pmid": "36941476", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10374440"}, {"db": "pii", "key": "10.1038/s41589-023-01284-8"}], "notes": [], "created": "2026-08-20T09:01:33.664Z", "modified": "2026-08-20T09:01:33.770Z"}]}