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Schneider AFL, Benz LS, Lehmann M, Hackenberger CPR. Zellpermeable Nanobodys ermöglichen Zwei‐Farben‐Superauflösungsmikroskopie in lebenden, nicht transfizierten Zellen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anselm F. L. Schneider
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Deutschland
- Institute of Chemistry and Biochemistry Freie Universität Berlin Takustraße 3 14189 Berlin Deutschland
| | - Laila S. Benz
- Institute of Chemistry and Biochemistry Freie Universität Berlin Takustraße 3 14189 Berlin Deutschland
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Deutschland
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Deutschland
- Department of Chemistry Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Deutschland
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Schneider AFL, Benz LS, Lehmann M, Hackenberger CPR. Cell-Permeable Nanobodies Allow Dual-Color Super-Resolution Microscopy in Untransfected Living Cells. Angew Chem Int Ed Engl 2021; 60:22075-22080. [PMID: 34288299 PMCID: PMC8518916 DOI: 10.1002/anie.202103068] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/28/2021] [Indexed: 11/06/2022]
Abstract
Super‐resolution microscopy in living cells can be restricted by the availability of small molecule probes, which only exist against few targets and genetically encoded tags. Here, we expand the applicability of live‐cell STED by engineering cell‐permeable and highly fluorescent nanobodies as intracellular targeting agents. To ensure bright fluorescent signals at low concentrations we used the concept of intramolecular photostabilization by ligating a fluorophore along with the photostabilizer trolox to the nanobody using expressed protein ligation (EPL). Furthermore, these semi‐synthetic nanobodies are equipped with a cleavable cell‐penetrating peptide for efficient cellular entry, which enables super‐resolution imaging of GFP and mCherry, as well as two endogenous targets, nuclear lamins and the DNA replication and repair protein PCNA. We monitored cell division and DNA replication via confocal and STED microscopy thus demonstrating the utility of these new intracellular tools for functional analysis.
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Affiliation(s)
- Anselm F L Schneider
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14189, Berlin, Germany
| | - Laila S Benz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14189, Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
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Li Y, Xue B, Zhang M, Zhang L, Hou Y, Qin Y, Long H, Su QP, Wang Y, Guan X, Jin Y, Cao Y, Li G, Sun Y. Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency. Genome Biol 2021; 22:206. [PMID: 34253239 PMCID: PMC8276456 DOI: 10.1186/s13059-021-02424-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/30/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. RESULTS We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired. CONCLUSION Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.
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Affiliation(s)
- Yongzheng Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yizhi Qin
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Haizhen Long
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Peter Su
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yao Wang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaodong Guan
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yanyan Jin
- Department of Neurobiology, Beijing Centre of Neural Regeneration and Repair, Capital Medical University, Beijing, 100101, China
| | - Yuan Cao
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
- College of Future Technology, Peking University, Beijing, 100871, China.
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Crocker K, London J, Medina A, Fishel R, Bundschuh R. Evolutionary advantage of a dissociative search mechanism in DNA mismatch repair. Phys Rev E 2021; 103:052404. [PMID: 34134264 DOI: 10.1103/physreve.103.052404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 04/08/2021] [Indexed: 01/10/2023]
Abstract
Protein complexes involved in DNA mismatch repair diffuse along dsDNA as sliding clamps in order to locate a hemimethylated incision site. They have been observed to use a dissociative mechanism, in which two proteins, while continuously remaining attached to the DNA, sometimes associate into a single complex sliding on the DNA and sometimes dissociate into two independently sliding proteins. Here, we study the probability that these complexes locate a given target site via a semi-analytic, Monte Carlo calculation that tracks the association and dissociation of the sliding complexes. We compare such probabilities to those obtained using a nondissociative diffusive scan in the space of physically realistic diffusion constants, hemimethylated site distances, and total search times to determine the regions in which dissociative searching is more or less efficient than nondissociative searching. We conclude that the dissociative search mechanism is advantageous in the majority of the physically realistic parameter space, suggesting that the dissociative search mechanism confers an evolutionary advantage.
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Affiliation(s)
- Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - James London
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Andrés Medina
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ralf Bundschuh
- Department of Physics, Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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Hedglin M, Aitha M, Pedley A, Benkovic SJ. Replication protein A dynamically regulates monoubiquitination of proliferating cell nuclear antigen. J Biol Chem 2019; 294:5157-5168. [PMID: 30700555 DOI: 10.1074/jbc.ra118.005297] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/17/2019] [Indexed: 11/06/2022] Open
Abstract
DNA damage tolerance permits bypass of DNA lesions encountered during S-phase and may be carried out by translesion DNA synthesis (TLS). Human TLS requires selective monoubiquitination of proliferating cell nuclear antigen (PCNA) sliding clamps encircling damaged DNA. This posttranslational modification (PTM) is catalyzed by Rad6/Rad18. Recent studies revealed that replication protein A (RPA), the major ssDNA-binding protein, is involved in the regulation of PCNA monoubiquitination and interacts directly with Rad18 on chromatin and in the nucleoplasm. However, it is unclear how RPA regulates this critical PTM and what functional role(s) these interactions serve. Here, we developed an in vitro assay to quantitatively monitor PCNA monoubiquitination under in vivo scenarios. Results from extensive experiments revealed that RPA regulates Rad6/Rad18 activity in an ssDNA-dependent manner. We found that "DNA-free" RPA inhibits monoubiquitination of free PCNA by directly interacting with Rad18. This interaction is promoted under native conditions when there is an overabundance of free RPA in the nucleoplasm where Rad6/Rad18 and a significant fraction of PCNA reside. During DNA replication stress, RPA binds the ssDNA exposed downstream of stalled primer/template (P/T) junctions, releasing Rad6/Rad18. RPA restricted the resident PCNAs to the upstream duplex regions by physically blocking diffusion of PCNA along ssDNA, and this activity was required for efficient monoubiquitination of PCNA on DNA. Furthermore, upon binding ssDNA, RPA underwent a conformational change that increased its affinity for Rad18. Rad6/Rad18 complexed with ssDNA-bound RPA was active, and this interaction may selectively promote monoubiquitination of PCNA on long RPA-coated ssDNA.
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Affiliation(s)
- Mark Hedglin
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Mahesh Aitha
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Anthony Pedley
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Stephen J Benkovic
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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Dennis CV, Suh LS, Rodriguez ML, Kril JJ, Sutherland GT. Human adult neurogenesis across the ages: An immunohistochemical study. Neuropathol Appl Neurobiol 2016; 42:621-638. [PMID: 27424496 PMCID: PMC5125837 DOI: 10.1111/nan.12337] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022]
Abstract
AIMS Neurogenesis in the postnatal human brain occurs in two neurogenic niches; the subventricular zone (SVZ) in the wall of the lateral ventricles and the subgranular zone (SGZ) of the hippocampus. The extent to which this physiological process continues into adulthood is an area of ongoing research. This study aimed to characterize markers of cell proliferation and assess the efficacy of antibodies used to identify neurogenesis in both neurogenic niches of the human brain. METHODS Cell proliferation and neurogenesis were simultaneously examined in the SVZ and SGZ of 23 individuals aged 0.2-59 years, using immunohistochemistry and immunofluorescence in combination with unbiased stereology. RESULTS There was a marked decline in proliferating cells in both neurogenic niches in early infancy with levels reaching those seen in the adjacent parenchyma by 4 and 1 year of age, in the SVZ and SGZ, respectively. Furthermore, the phenotype of these proliferating cells in both niches changed with age. In infants, proliferating cells co-expressed neural progenitor (epidermal growth factor receptor), immature neuronal (doublecortin and beta III tubulin) and oligodendrocytic (Olig2) markers. However, after 3 years of age, microglia were the only proliferating cells found in either niche or in the adjacent parenchyma. CONCLUSIONS This study demonstrates a marked decline in neurogenesis in both neurogenic niches in early childhood, and that the sparse proliferating cells in the adult brain are largely microglia.
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Affiliation(s)
- C V Dennis
- Discipline of Pathology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - L S Suh
- Discipline of Pathology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Dementia Research Unit, School of Medical Sciences, University of New South Wales, Kensington, NSW, Australia
| | - M L Rodriguez
- Discipline of Pathology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - J J Kril
- Discipline of Pathology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - G T Sutherland
- Discipline of Pathology, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
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Widera D, Klenke C, Nair D, Heidbreder M, Malkusch S, Sibarita JB, Choquet D, Kaltschmidt B, Heilemann M, Kaltschmidt C. Single-particle tracking uncovers dynamics of glutamate-induced retrograde transport of NF-κB p65 in living neurons. NEUROPHOTONICS 2016; 3:041804. [PMID: 27226975 PMCID: PMC4870386 DOI: 10.1117/1.nph.3.4.041804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
Retrograde transport of NF-κB from the synapse to the nucleus in neurons is mediated by the dynein/dynactin motor complex and can be triggered by synaptic activation. The caliber of axons is highly variable ranging down to 100 nm, aggravating the investigation of transport processes in neurites of living neurons using conventional light microscopy. We quantified for the first time the transport of the NF-κB subunit p65 using high-density single-particle tracking in combination with photoactivatable fluorescent proteins in living mouse hippocampal neurons. We detected an increase of the mean diffusion coefficient ([Formula: see text]) in neurites from [Formula: see text] to [Formula: see text] after stimulation with glutamate. We further observed that the relative amount of retrogradely transported p65 molecules is increased after stimulation. Glutamate treatment resulted in an increase of the mean retrograde velocity from [Formula: see text] to [Formula: see text], whereas a velocity increase from [Formula: see text] to [Formula: see text] was observed for anterogradely transported p65. This study demonstrates for the first time that glutamate stimulation leads to an increased mobility of single NF-κB p65 molecules in neurites of living hippocampal neurons.
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Affiliation(s)
- Darius Widera
- University of Bielefeld, Cell Biology, Universitätsstr. 25, 33501 Bielefeld, Germany
- University of Reading, School of Pharmacy, Stem Cell Biology and Regenerative Medicine, Whiteknights, Reading RG6 6UB, United Kingdom
| | - Christin Klenke
- University of Bielefeld, Cell Biology, Universitätsstr. 25, 33501 Bielefeld, Germany
| | - Deepak Nair
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 146 rue Léo-Saignat, Bordeaux 33077, France
- CNRS UMR 5297, 146 rue Léo-Saignat, Bordeaux 33077, France
| | - Meike Heidbreder
- Julius-Maximilians-Universität, Department of Biotechnology and Biophysics, Am Hubland, Würzburg 97074, Germany
| | - Sebastian Malkusch
- Johann Wolfgang Goethe-University, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Street 7, Frankfurt 60438, Germany
| | - Jean-Baptiste Sibarita
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 146 rue Léo-Saignat, Bordeaux 33077, France
- CNRS UMR 5297, 146 rue Léo-Saignat, Bordeaux 33077, France
- Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM, France
| | - Daniel Choquet
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 146 rue Léo-Saignat, Bordeaux 33077, France
- CNRS UMR 5297, 146 rue Léo-Saignat, Bordeaux 33077, France
| | - Barbara Kaltschmidt
- University of Bielefeld, Cell Biology, Universitätsstr. 25, 33501 Bielefeld, Germany
- University of Bielefeld, Molecular Neurobiology, Universitätsstr. 25, Bielefeld 33501, Germany
| | - Mike Heilemann
- Johann Wolfgang Goethe-University, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Street 7, Frankfurt 60438, Germany
| | - Christian Kaltschmidt
- University of Bielefeld, Cell Biology, Universitätsstr. 25, 33501 Bielefeld, Germany
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