{"entity": "researcher", "timestamp": "2026-07-19T09:15:54.997Z", "family": "Alarc\u00f3n", "given": "Leonarda Ach\u00e1", "initials": "LA", "orcid": "0000-0002-9453-7479", "affiliations": ["Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481"}}, "publications": [{"entity": "publication", "iuid": "1ff43766eb154a0eaf667914e8c3c386", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ff43766eb154a0eaf667914e8c3c386.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ff43766eb154a0eaf667914e8c3c386"}}, "title": "Marine-Inspired Antimicrobial Peptides Disrupt Gene Expression at the DNA Level.", "authors": [{"family": "Beyer", "given": "Luisa I", "initials": "LI"}, {"family": "Thoma", "given": "Johannes", "initials": "J", "orcid": "0000-0003-3584-8274", "researcher": {"href": "https://publications.scilifelab.se/researcher/98d27ad4d2224fbaa840469f85a596e4.json"}}, {"family": "Acha Alarcon", "given": "Leonarda", "initials": "L", "orcid": "0000-0002-9453-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}}, {"family": "Unksov", "given": "Ivan N", "initials": "IN"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Inda-D\u00edaz", "given": "Juan S", "initials": "JS"}, {"family": "Tietze", "given": "Alesia A", "initials": "AA", "orcid": "0000-0002-9281-548X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c9c55ec11d84630a4b4472cd21ef96b.json"}}], "type": "journal article", "published": "2026-01-09", "journal": {"title": "ACS Infect Dis", "issn": "2373-8227", "volume": "12", "issue": "1", "pages": "447-459", "issn-l": null}, "abstract": "Genome mining of Streptomyces sp. H-KF8 combined with sequence engineering yielded two serum-stable, noncytotoxic, nonlytic antimicrobial peptides, L3 and L3-K. Initial studies in uropathogenic Escherichia coli suggested membrane effects and nucleoid relaxation, prompting a comprehensive investigation of their mode of action. In this study tandem mass tag (TMT)-based quantitative proteomics revealed extensive proteome remodeling, with 175 and 120 differentially expressed proteins (DEPs) after treatment with L3 and L3-K, respectively. L3 induced predominantly upregulated responses linked to metabolism, RNA processing, transport, and homeostasis, whereas L3-K mainly caused the downregulation of proteins involved in metabolism, transport, and cell structure. Both peptides disrupted ABC transporter-mediated nutrient uptake and elicited stress responses, while L3 specifically perturbed the mal regulon, indicative of broader transcriptional dysregulation. Complementary fluorescent dye displacement and in vitro transcription/translation assays demonstrated nonspecific DNA binding, stronger for L3 than L3-K, and potent inhibition of transcriptional and translational processes. Strikingly, inhibitory concentrations paralleled their minimum inhibitory concentrations, directly linking DNA binding and interference with central information processing to antimicrobial activity. These findings reveal that L3 and L3-K primarily act by targeting DNA and interfering with the transcription-translation machinery. Beyond offering mechanistic insights, this study underscores peptides' potential to act as scaffolds for next-generation antimicrobial peptides with DNA-binding and nonmembrane-lytic activity.", "doi": "10.1021/acsinfecdis.5c01000", "pmid": "41363146", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12797237"}], "notes": [], "created": "2026-01-27T13:32:34.240Z", "modified": "2026-01-27T13:32:34.344Z"}, {"entity": "publication", "iuid": "837fd5a3e240418a922a7efe0a36c863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/837fd5a3e240418a922a7efe0a36c863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/837fd5a3e240418a922a7efe0a36c863"}}, "title": "Identification of Streptococcus pneumoniae-Specific Proteins by Surface-Shaving Proteomics.", "authors": [{"family": "Acha Alarcon", "given": "Leonarda", "initials": "L", "orcid": "0000-0002-9453-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}}, {"family": "Segu\u00ed", "given": "Guillem", "initials": "G"}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B"}, {"family": "Svetlicic", "given": "Ema", "initials": "E"}, {"family": "Kondori", "given": "Nahid", "initials": "N"}, {"family": "Gomila", "given": "Margarita", "initials": "M"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2025-12-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "12", "pages": "6154-6173", "issn-l": "1535-3893"}, "abstract": "Streptococcus pneumoniae (pneumococcus) is a prominent cause of bacterial pneumonia, meningitis, and septicemia, causing high morbidity and high mortality, particularly in children and the elderly. In this study, proteomics- and genomics-based approaches were used for the identification of pneumococcal protein and peptide biomarkers of S. pneumoniae for diagnostics and prospective targets for treatment. Through a pan-genome analysis, 11 S. pneumoniae strains, demonstrating genetic variation within the species, were selected for proteomic characterization. Mass spectrometry-based proteomics, in combination with bacterial surface-shaving, were used to study the cell-surface proteome of S. pneumoniae. The data obtained from three biological replicates per strain were analyzed to identify and rank the proteins and peptides according to their presence in the strains, as well as their presence in all available S. pneumoniae proteomes (8,892) archived in public databases. Several highly ranked proteins have been described as \"species-specific\" for S. pneumoniae and as surface-associated virulence factors or demonstrate highly antigenic properties. Proteins (34) previously not recognized as S. pneumoniae-specific were proposed to be novel biomarkers, demonstrating high degrees of prevalence in all analyzed proteomes, with little or no sequence similarities to closely related species but common among the genetically diverse strains included in this study.", "doi": "10.1021/acs.jproteome.5c00716", "pmid": "41212599", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12687362"}], "notes": [], "created": "2025-11-20T18:17:19.599Z", "modified": "2026-01-26T15:08:00.860Z"}, {"entity": "publication", "iuid": "55595ac6dbaf426ebbbaa4d12d7c4901", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55595ac6dbaf426ebbbaa4d12d7c4901.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55595ac6dbaf426ebbbaa4d12d7c4901"}}, "title": "Surface-Shaving of Staphylococcus aureus Strains and Quantitative Proteomic Analysis Reveal Differences in Protein Abundance of the Surfaceome.", "authors": [{"family": "Karlsson", "given": "Anders", "initials": "A"}, {"family": "Alarc\u00f3n", "given": "Leonarda Ach\u00e1", "initials": "LA", "orcid": "0000-0002-9453-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B"}, {"family": "Jacobsson", "given": "Gunnar", "initials": "G"}, {"family": "Skovbjerg", "given": "Susann", "initials": "S"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Kopparapu", "given": "Pradeep Kumar", "initials": "PK", "orcid": "0000-0003-3941-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d0d9c2301c8413899a867ace6877cb2.json"}}, {"family": "Jin", "given": "Tao", "initials": "T", "orcid": "0000-0001-9039-0628", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ca682de4fe4a7eb667dc63cae88335.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2024-08-21", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "12", "issue": "8", "issn-l": "2076-2607"}, "abstract": "Staphylococcus aureus is a pathogen known to cause a wide range of infections. To find new targets for identification and to understand host-pathogen interactions, many studies have focused on surface proteins. We performed bacterial-cell surface-shaving, followed by tandem mass tag for quantitative mass spectrometry proteomics, to examine the surfaceome of S. aureus. Two steps were performed, the first step including surface protein-deficient mutants of S. aureus Newman strain lacking important virulence genes (clfA and spa, important for adhesion and immune evasion and srtAsrtB, linking surface-associated virulence factors to the surface) and the second step including isolates of different clinical origin. All strains were compared to the Newman strain. In Step 1, altogether, 7880 peptides were identified, corresponding to 1290 proteins. In Step 2, 4949 peptides were identified, corresponding to 919 proteins and for each strain, approximately 20 proteins showed differential expression compared to the Newman strain. The identified surface proteins were related to host-cell-adherence and immune-system-evasion, biofilm formation, and survival under harsh conditions. The results indicate that surface-shaving of intact S. aureus bacterial strains in combination with quantitative proteomics is a useful tool to distinguish differences in protein abundance of the surfaceome, including the expression of virulence factors.", "doi": "10.3390/microorganisms12081725", "pmid": "39203567", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Clinical Genomics Gothenburg": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11357550"}, {"db": "pii", "key": "microorganisms12081725"}], "notes": [], "created": "2024-09-15T11:45:41.565Z", "modified": "2024-11-27T16:31:45.417Z"}]}