{"entity": "researcher", "timestamp": "2026-07-14T03:45:45.820Z", "family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8811-2629", "affiliations": ["Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden. m.johansson@icm.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/a7c7f4a540fa4bc2b5176c48bde2b0d7.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/a7c7f4a540fa4bc2b5176c48bde2b0d7"}}, "publications": [{"entity": "publication", "iuid": "d4b4f0a80cd14ee693ded92c677e97f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4b4f0a80cd14ee693ded92c677e97f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4b4f0a80cd14ee693ded92c677e97f8"}}, "title": "Dynamic binding of the bacterial chaperone Trigger factor to translating ribosomes in Escherichia coli.", "authors": [{"family": "H\u00e4vermark", "given": "Tora", "initials": "T", "orcid": "0000-0002-3794-3243", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8aca0712dea4996a8ba3f51b0a5d126.json"}}, {"family": "Metelev", "given": "Mikhail", "initials": "M", "orcid": "0000-0003-2829-6395", "researcher": {"href": "https://publications.scilifelab.se/researcher/39cdcb1c403140be9798d220fcf6e535.json"}}, {"family": "Lundin", "given": "Erik", "initials": "E", "orcid": "0000-0001-7490-1715", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c91e90244bd49d196b4ceee714d43dc.json"}}, {"family": "Volkov", "given": "Ivan L", "initials": "IL", "orcid": "0000-0001-7288-6363", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ee4772a638c4efb8c3a2cae1d6de400.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8811-2629", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7c7f4a540fa4bc2b5176c48bde2b0d7.json"}}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "1", "pages": "e2409536121", "issn-l": "0027-8424"}, "abstract": "The bacterial chaperone Trigger factor (TF) binds to ribosome-nascent chain complexes (RNCs) and cotranslationally aids the folding of proteins in bacteria. Decades of studies have given a broad, but often conflicting, description of the substrate specificity of TF, its RNC-binding dynamics, and competition with other RNC-binding factors, such as the Signal Recognition Particle (SRP). Previous RNC-binding kinetics experiments were commonly conducted on stalled RNCs in reconstituted systems, and consequently, may not be representative of the interaction of TF with ribosomes translating mRNA in the cytoplasm of the cell. Here, we used single-particle tracking (SPT) to measure TF binding to actively translating ribosomes inside living Escherichia coli. In cells, TF displays distinct binding modes-longer (ca 1 s) and shorter (ca 50 ms) RNC bindings. Consequently, we conclude that TF, on average, stays bound to the RNC for only a fraction of the translation cycle. Further, binding events are interrupted only by transient excursions to a freely diffusing state (ca 40 ms), suggesting a highly dynamic binding and unbinding cycle of TF in vivo. We also show that TF competes with SRP for RNC binding, and in doing so, tunes the binding selectivity of SRP.", "doi": "10.1073/pnas.2409536121", "pmid": "39739798", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11725819"}], "notes": [], "created": "2025-11-28T10:48:13.448Z", "modified": "2025-11-28T10:48:13.523Z"}, {"entity": "publication", "iuid": "549ae9e85a6d41c6be8acdeb3cfbf660", "links": {"self": {"href": "https://publications.scilifelab.se/publication/549ae9e85a6d41c6be8acdeb3cfbf660.json"}, "display": {"href": "https://publications.scilifelab.se/publication/549ae9e85a6d41c6be8acdeb3cfbf660"}}, "title": "Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization.", "authors": [{"family": "Amselem", "given": "Elias", "initials": "E", "orcid": "0000-0003-2846-9225", "researcher": {"href": "https://publications.scilifelab.se/researcher/b36dcc99173f461e84941241665eaedf.json"}}, {"family": "Broadwater", "given": "Bo", "initials": "B", "orcid": "0000-0002-5870-2457", "researcher": {"href": "https://publications.scilifelab.se/researcher/327b8749f1a4415781ab6bca7554a367.json"}}, {"family": "H\u00e4vermark", "given": "Tora", "initials": "T", "orcid": "0000-0002-3794-3243", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8aca0712dea4996a8ba3f51b0a5d126.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8811-2629", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7c7f4a540fa4bc2b5176c48bde2b0d7.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}], "type": "journal article", "published": "2023-03-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1336", "issn-l": "2041-1723"}, "abstract": "Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.", "doi": "10.1038/s41467-023-36879-1", "pmid": "36906676", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10008558"}, {"db": "pii", "key": "10.1038/s41467-023-36879-1"}], "notes": [], "created": "2023-11-27T21:47:54.647Z", "modified": "2024-01-16T13:48:33.841Z"}, {"entity": "publication", "iuid": "792a618f6c4e43b998c86cf7cb80f5be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/792a618f6c4e43b998c86cf7cb80f5be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/792a618f6c4e43b998c86cf7cb80f5be"}}, "title": "Direct measurements of mRNA translation kinetics in living cells.", "authors": [{"family": "Metelev", "given": "Mikhail", "initials": "M", "orcid": "0000-0003-2829-6395", "researcher": {"href": "https://publications.scilifelab.se/researcher/39cdcb1c403140be9798d220fcf6e535.json"}}, {"family": "Lundin", "given": "Erik", "initials": "E", "orcid": "0000-0001-7490-1715", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c91e90244bd49d196b4ceee714d43dc.json"}}, {"family": "Volkov", "given": "Ivan L", "initials": "IL", "orcid": "0000-0001-7288-6363", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ee4772a638c4efb8c3a2cae1d6de400.json"}}, {"family": "Gynn\u00e5", "given": "Arvid H", "initials": "AH", "orcid": "0000-0001-8087-7715", "researcher": {"href": "https://publications.scilifelab.se/researcher/818582a582334117bd83e47dbb555db3.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8811-2629", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7c7f4a540fa4bc2b5176c48bde2b0d7.json"}}], "type": "journal article", "published": "2022-04-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1852", "issn-l": "2041-1723"}, "abstract": "Ribosome mediated mRNA translation is central to life. The cycle of translation, however, has been characterized mostly using reconstituted systems, with only few techniques applicable for studies in the living cell. Here we describe a live-cell ribosome-labeling method, which allows us to characterize the whole processes of finding and translating an mRNA, using single-molecule tracking techniques. We find that more than 90% of both bacterial ribosomal subunits are engaged in translation at any particular time, and that the 30S and 50S ribosomal subunits spend the same average time bound to an mRNA, revealing that 30S re-initiation on poly-cistronic mRNAs is not prevalent in E. coli. Instead, our results are best explained by substantial 70S re-initiation of translation of poly-cistronic mRNAs, which is further corroborated by experiments with translation initiation inhibitors. Finally, we find that a variety of previously described orthogonal ribosomes, with altered anti-Shine-Dalgarno sequences, show significant binding to endogenous mRNAs.", "doi": "10.1038/s41467-022-29515-x", "pmid": "35388013", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-29515-x"}, {"db": "pmc", "key": "PMC8986856"}], "notes": [], "created": "2022-11-09T15:50:13.299Z", "modified": "2024-01-16T13:48:37.128Z"}]}