1
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Pathni A, Wagh K, Rey-Suarez I, Upadhyaya A. Mechanical regulation of lymphocyte activation and function. J Cell Sci 2024; 137:jcs219030. [PMID: 38995113 PMCID: PMC11267459 DOI: 10.1242/jcs.219030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
Mechanosensing, or how cells sense and respond to the physical environment, is crucial for many aspects of biological function, ranging from cell movement during development to cancer metastasis, the immune response and gene expression driving cell fate determination. Relevant physical stimuli include the stiffness of the extracellular matrix, contractile forces, shear flows in blood vessels, complex topography of the cellular microenvironment and membrane protein mobility. Although mechanosensing has been more widely studied in non-immune cells, it has become increasingly clear that physical cues profoundly affect the signaling function of cells of the immune system. In this Review, we summarize recent studies on mechanical regulation of immune cells, specifically lymphocytes, and explore how the force-generating cytoskeletal machinery might mediate mechanosensing. We discuss general principles governing mechanical regulation of lymphocyte function, spanning from the molecular scale of receptor activation to cellular responses to mechanical stimuli.
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Affiliation(s)
- Aashli Pathni
- Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Kaustubh Wagh
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Rey-Suarez
- Insitute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
- Microcore, Universidad de Los Andes, Bogota, DC 111711, USA
| | - Arpita Upadhyaya
- Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Insitute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
- Biophysics Program, University of Maryland, College Park, MD 20742, USA
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2
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Lipps G. Definition of the binding specificity of the T7 bacteriophage primase by analysis of a protein binding microarray using a thermodynamic model. Nucleic Acids Res 2024; 52:4818-4829. [PMID: 38597656 PMCID: PMC11109968 DOI: 10.1093/nar/gkae215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/26/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
Protein binding microarrays (PBM), SELEX, RNAcompete and chromatin-immunoprecipitation have been intensively used to determine the specificity of nucleic acid binding proteins. While the specificity of proteins with pronounced sequence specificity is straightforward, the determination of the sequence specificity of proteins of modest sequence specificity is more difficult. In this work, an explorative data analysis workflow for nucleic acid binding data was developed that can be used by scientists that want to analyse their binding data. The workflow is based on a regressor realized in scikit-learn, the major machine learning module for the scripting language Python. The regressor is built on a thermodynamic model of nucleic acid binding and describes the sequence specificity with base- and position-specific energies. The regressor was used to determine the binding specificity of the T7 primase. For this, we reanalysed the binding data of the T7 primase obtained with a custom PBM. The binding specificity of the T7 primase agrees with the priming specificity (5'-GTC) and the template (5'-GGGTC) for the preferentially synthesized tetraribonucleotide primer (5'-pppACCC) but is more relaxed. The dominant contribution of two positions in the motif can be explained by the involvement of the initiating and elongating nucleotides for template binding.
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Affiliation(s)
- Georg Lipps
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
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3
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Lafargue-Hauret J, Lozac'h K, Kabore B, Bobé P. [CD45 pre-exclusion from the tips of microvilli : role in their activation]. Med Sci (Paris) 2024; 40:212-214. [PMID: 38411434 DOI: 10.1051/medsci/2023214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Affiliation(s)
| | | | | | - Pierre Bobé
- UMR 996 Inserm-université Paris-Saclay, France
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4
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Park JS, Chung IJ, Kim HR, Jun CD. The Immunosuppressive Potential of Cholesterol Sulfate Through T Cell Microvilli Disruption. Immune Netw 2023; 23:e29. [PMID: 37416932 PMCID: PMC10320417 DOI: 10.4110/in.2023.23.e29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/28/2023] [Accepted: 04/21/2023] [Indexed: 07/08/2023] Open
Abstract
Cholesterol (CL) is required for various biomolecular production processes, including those of cell membrane components. Therefore, to meet these needs, CL is converted into various derivatives. Among these derivatives is cholesterol sulfate (CS), a naturally produced CL derivative by the sulfotransferase family 2B1 (SULT2B1), which is widely present in human plasma. CS is involved in cell membrane stabilization, blood clotting, keratinocyte differentiation, and TCR nanocluster deformation. This study shows that treatment of T cells with CS resulted in the decreased surface expression of some surface T-cell proteins and reduced IL-2 release. Furthermore, T cells treated with CS significantly reduced lipid raft contents and membrane CLs. Surprisingly, using the electron microscope, we also observed that CS led to the disruption of T-cell microvilli, releasing small microvilli particles containing TCRs and other microvillar proteins. However, in vivo, T cells with CS showed aberrant migration to high endothelial venules and limited infiltrating splenic T-cell zones compared with the untreated T cells. Additionally, we observed significant alleviation of atopic dermatitis in mice injected with CS in the animal model. Based on these results, we conclude that CS is an immunosuppressive natural lipid that impairs TCR signaling by disrupting microvillar function in T cells, suggesting its usefulness as a therapeutic agent for alleviating T-cell-mediated hypersensitivity and a potential target for treating autoimmune diseases.
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Affiliation(s)
- Jeong-Su Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Ik-Joo Chung
- Department of Hematology-Oncology, Immunotherapy Innovation Center, Chonnam National University Medical School, Hwasun 58128, Korea
| | - Hye-Ran Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Division of Rare and Refractory Cancer, Tumor Immunology, Research Institute, National Cancer Center, Goyang 10408, Korea
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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5
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Park JS, Kim JH, Soh WC, Kim NY, Lee KS, Kim CH, Chung IJ, Lee S, Kim HR, Jun CD. Trogocytic molting of T cell microvilli upregulates T cell receptor surface expression and promotes clonal expansion. Nat Commun 2023; 14:2980. [PMID: 37221214 DOI: 10.1038/s41467-023-38707-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Although T cell activation is known to involve the internalization of the T cell antigen receptor (TCR), much less is known regarding the release of TCRs following T cell interaction with cognate antigen-presenting cells. In this study, we examine the physiological mechanisms underlying TCR release following T cell activation. We show that T cell activation results in the shedding of TCRs in T cell microvilli, which involves a combined process of trogocytosis and enzymatic vesiculation, leading to the loss of membrane TCRs and microvilli-associated proteins and lipids. Surprisingly, unlike TCR internalization, this event results in the rapid upregulation of surface TCR expression and metabolic reprogramming of cholesterol and fatty acid synthesis to support cell division and survival. These results demonstrate that TCRs are lost through trogocytic 'molting' following T cell activation and highlight this mechanism as an important regulator of clonal expansion.
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Affiliation(s)
- Jeong-Su Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Jun-Hyeong Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Won-Chang Soh
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Na-Young Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Kyung-Sik Lee
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Chang-Hyun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Ik-Joo Chung
- Department of Hematology-Oncology, Immunotherapy Innovation Center, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Sunjae Lee
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hye-Ran Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea.
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea.
- Division of Rare and Refractory Cancer, Tumor Immunology, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea.
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea.
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea.
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6
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Kim HR, Park JS, Soh WC, Kim NY, Moon HY, Lee JS, Jun CD. T Cell Microvilli: Finger-Shaped External Structures Linked to the Fate of T Cells. Immune Netw 2023; 23:e3. [PMID: 36911802 PMCID: PMC9995986 DOI: 10.4110/in.2023.23.e3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/11/2023] [Accepted: 02/11/2023] [Indexed: 03/07/2023] Open
Abstract
Microvilli are outer membrane organelles that contain cross-linked filamentous actin. Unlike well-characterized epithelial microvilli, T-cell microvilli are dynamic similar to those of filopodia, which grow and shrink intermittently via the alternate actin-assembly and -disassembly. T-cell microvilli are specialized for sensing Ags on the surface of Ag-presenting cells (APCs). Thus, these finger-shaped microprotrusions contain many signaling-related proteins and can serve as a signaling platforms that induce intracellular signals. However, they are not limited to sensing external information but can provide sites for parts of the cell-body to tear away from the cell. Cells are known to produce many types of extracellular vesicles (EVs), such as exosomes, microvesicles, and membrane particles. T cells also produce EVs, but little is known about under what conditions T cells generate EVs and which types of EVs are released. We discovered that T cells produce few exosomes but release large amounsts of microvilli-derived particles during physical interaction with APCs. Although much is unanswered as to why T cells use the same organelles to sense Ags or to produce EVs, these events can significantly affect T cell fate, including clonal expansion and death. Since TCRs are localized at microvilli tips, this membrane event also raises a new question regarding long-standing paradigm in T cell biology; i.e., surface TCR downmodulation following T cell activation. Since T-cell microvilli particles carry T-cell message to their cognate partner, these particles are termed T-cell immunological synaptosomes (TISs). We discuss the potential physiological role of TISs and their application to immunotherapies.
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Affiliation(s)
- Hye-Ran Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Division of Rare and Refractory Cancer, Tumor Immunology, Research Institute, National Cancer Center, Goyang 10408, Korea
| | - Jeong-Su Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Won-Chang Soh
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Na-Young Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Hyun-Yoong Moon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Ji-Su Lee
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Immune Synapse and Cell Therapy Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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7
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Alatoom A, ElGindi M, Sapudom J, Teo JCM. The T Cell Journey: A Tour de Force. Adv Biol (Weinh) 2023; 7:e2200173. [PMID: 36190140 DOI: 10.1002/adbi.202200173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/30/2022] [Indexed: 11/07/2022]
Abstract
T cells act as the puppeteers in the adaptive immune response, and their dysfunction leads to the initiation and progression of pathological conditions. During their lifetime, T cells experience myriad forces that modulate their effector functions. These forces are imposed by interacting cells, surrounding tissues, and shear forces from fluid movement. In this review, a journey with T cells is made, from their development to their unique characteristics, including the early studies that uncovered their mechanosensitivity. Then the studies pertaining to the responses of T cell activation to changes in antigen-presenting cells' physical properties, to their immediate surrounding extracellular matrix microenvironment, and flow conditions are highlighted. In addition, it is explored how pathological conditions like the tumor microenvironment can hinder T cells and allow cancer cells to escape elimination.
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Affiliation(s)
- Aseel Alatoom
- Laboratory for Immuno Bioengineering Research and Applications Division of Engineering, New York University Abu Dhabi, Saadiyat Campus, P.O. Box 127788, Abu Dhabi, UAE.,Department of Mechanical Engineering Tandon School of Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Mei ElGindi
- Laboratory for Immuno Bioengineering Research and Applications Division of Engineering, New York University Abu Dhabi, Saadiyat Campus, P.O. Box 127788, Abu Dhabi, UAE
| | - Jiranuwat Sapudom
- Laboratory for Immuno Bioengineering Research and Applications Division of Engineering, New York University Abu Dhabi, Saadiyat Campus, P.O. Box 127788, Abu Dhabi, UAE
| | - Jeremy C M Teo
- Laboratory for Immuno Bioengineering Research and Applications Division of Engineering, New York University Abu Dhabi, Saadiyat Campus, P.O. Box 127788, Abu Dhabi, UAE.,Department of Mechanical Engineering Tandon School of Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA.,Department of Biomedical Engineering Tandon School of Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
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8
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Lu CH, Pedram K, Tsai CT, Jones T, Li X, Nakamoto ML, Bertozzi CR, Cui B. Membrane curvature regulates the spatial distribution of bulky glycoproteins. Nat Commun 2022; 13:3093. [PMID: 35654773 PMCID: PMC9163104 DOI: 10.1038/s41467-022-30610-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 05/10/2022] [Indexed: 01/11/2023] Open
Abstract
The glycocalyx is a shell of heavily glycosylated proteins and lipids distributed on the cell surface of nearly all cell types. Recently, it has been found that bulky transmembrane glycoproteins such as MUC1 can modulate membrane shape by inducing membrane protrusions. In this work, we examine the reciprocal relationship of how membrane shape affects MUC1's spatial distribution on the cell membrane and its biological significance. By employing nanopatterned surfaces and membrane-sculpting proteins to manipulate membrane curvature, we show that MUC1 avoids positively-curved membranes (membrane invaginations) and accumulates on negatively-curved membranes (membrane protrusions). MUC1's curvature sensitivity is dependent on the length and the extent of glycosylation of its ectodomain, with large and highly glycosylated forms preferentially staying out of positive curvature. Interestingly, MUC1's avoidance of positive membrane curvature enables it to escape from endocytosis and being removed from the cell membrane. These findings also suggest that the truncation of MUC1's ectodomain, often observed in breast and ovarian cancers, may enhance its endocytosis and potentiate its intracellular accumulation and signaling.
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Affiliation(s)
- Chih-Hao Lu
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA
| | - Kayvon Pedram
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA ,grid.443970.dPresent Address: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 USA
| | - Ching-Ting Tsai
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA
| | - Taylor Jones
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA
| | - Xiao Li
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA ,grid.43169.390000 0001 0599 1243Present Address: School of Mechanical Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Melissa L. Nakamoto
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA
| | - Carolyn R. Bertozzi
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Stanford ChEM-H, Stanford University, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 USA
| | - Bianxiao Cui
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA 94305 USA
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9
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Residues located in the primase domain of the bacteriophage T7 primase-helicase are essential for loading the hexameric complex onto DNA. J Biol Chem 2022; 298:101996. [PMID: 35500649 PMCID: PMC9198812 DOI: 10.1016/j.jbc.2022.101996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
The T7 primase-helicase plays a pivotal role in the replication of T7 DNA. Using affinity isolation of peptide–nucleic acid crosslinks and mass spectrometry, we identify protein regions in the primase-helicase and T7 DNA polymerase that form contacts with the RNA primer and DNA template. The contacts between nucleic acids and the primase domain of the primase-helicase are centered in the RNA polymerase subdomain of the primase domain, in a cleft between the N-terminal subdomain and the topoisomerase-primase fold. We demonstrate that residues along a beta sheet in the N-terminal subdomain that contacts the RNA primer are essential for phage growth and primase activity in vitro. Surprisingly, we found mutations in the primase domain that had a dramatic effect on the helicase. Substitution of a residue conserved in other DnaG-like enzymes, R84A, abrogates both primase and helicase enzymatic activities of the T7 primase-helicase. Alterations in this residue also decrease binding of the primase-helicase to ssDNA. However, mass photometry measurements show that these mutations do not interfere with the ability of the protein to form the active hexamer.
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10
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Salay LE, Blee AM, Raza MK, Gallagher KS, Chen H, Dorfeuille AJ, Barton JK, Chazin WJ. Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase. Biochemistry 2022; 61:1113-1123. [PMID: 35617695 DOI: 10.1021/acs.biochem.2c00100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA synthesis during replication begins with the generation of an ∼10-nucleotide primer by DNA primase. Primase contains a redox-active 4Fe-4S cluster in the C-terminal domain of the p58 subunit (p58C). The redox state of this 4Fe-4S cluster can be modulated via the transport of charge through the protein and the DNA substrate (redox switching); changes in the redox state of the cluster alter the ability of p58C to associate with its substrate. The efficiency of redox switching in p58C can be altered by mutating tyrosine residues that bridge the 4Fe-4S cluster and the nucleic acid binding site. Here, we report the effects of mutating bridging tyrosines to phenylalanines in yeast p58C. High-resolution crystal structures show that these mutations, even with six tyrosines simultaneously mutated, do not perturb the three-dimensional structure of the protein. In contrast, measurements of the electrochemical properties on DNA-modified electrodes of p58C containing multiple tyrosine to phenylalanine mutations reveal deficiencies in their ability to engage in DNA charge transport. Significantly, this loss of electrochemical activity correlates with decreased primase activity. While single-site mutants showed modest decreases in activity compared to that of the wild-type primase, the protein containing six mutations exhibited a 10-fold or greater decrease. Thus, many possible tyrosine-mediated pathways for charge transport in yeast p58C exist, but inhibiting these pathways together diminishes the ability of yeast primase to generate primers. These results support a model in which redox switching is essential for primase activity.
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Affiliation(s)
- Lauren E Salay
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Alexandra M Blee
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Md Kausar Raza
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kaitlyn S Gallagher
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Huiqing Chen
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Andrew J Dorfeuille
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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11
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Brameshuber M, Klotzsch E, Ponjavic A, Sezgin E. Understanding immune signaling using advanced imaging techniques. Biochem Soc Trans 2022; 50:853-866. [PMID: 35343569 PMCID: PMC9162467 DOI: 10.1042/bst20210479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022]
Abstract
Advanced imaging is key for visualizing the spatiotemporal regulation of immune signaling which is a complex process involving multiple players tightly regulated in space and time. Imaging techniques vary in their spatial resolution, spanning from nanometers to micrometers, and in their temporal resolution, ranging from microseconds to hours. In this review, we summarize state-of-the-art imaging methodologies and provide recent examples on how they helped to unravel the mysteries of immune signaling. Finally, we discuss the limitations of current technologies and share our insights on how to overcome these limitations to visualize immune signaling with unprecedented fidelity.
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Affiliation(s)
- Mario Brameshuber
- Institute of Applied Physics – Biophysics, TU Wien, 1040 Vienna, Austria
| | - Enrico Klotzsch
- Humboldt-Universität zu Berlin, Institut für Biophysik, Experimentelle Biophysik Mechanobiologie, Sitz Invalidenstrasse 42, 10115 Berlin, Germany
| | - Aleks Ponjavic
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- School of Food Science and Nutrition, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
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12
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Measuring the Complex Effects of the Single-Stranded DNA-Binding Protein gp2.5 on Primer Synthesis and Extension by the Bacteriophage T7 Replisome. Methods Mol Biol 2021; 2281:323-332. [PMID: 33847969 DOI: 10.1007/978-1-0716-1290-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The single-stranded DNA-binding protein gp2.5 of bacteriophage T7 plays myriad functions in the replication of phage genomes. In addition to interacting with ssDNA, gp2.5 binds to the T7 DNA polymerase and primase/helicase proteins, regulating their enzymatic activities. Here we describe in vitro methods to examine the effects of gp2.5 on primer synthesis and extension by the T7 replisome.
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13
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The potential land requirements and related land use change emissions of solar energy. Sci Rep 2021; 11:2907. [PMID: 33536519 PMCID: PMC7859221 DOI: 10.1038/s41598-021-82042-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/14/2021] [Indexed: 01/30/2023] Open
Abstract
Although the transition to renewable energies will intensify the global competition for land, the potential impacts driven by solar energy remain unexplored. In this work, the potential solar land requirements and related land use change emissions are computed for the EU, India, Japan and South Korea. A novel method is developed within an integrated assessment model which links socioeconomic, energy, land and climate systems. At 25-80% penetration in the electricity mix of those regions by 2050, we find that solar energy may occupy 0.5-5% of total land. The resulting land cover changes, including indirect effects, will likely cause a net release of carbon ranging from 0 to 50 gCO2/kWh, depending on the region, scale of expansion, solar technology efficiency and land management practices in solar parks. Hence, a coordinated planning and regulation of new solar energy infrastructures should be enforced to avoid a significant increase in their life cycle emissions through terrestrial carbon losses.
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14
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Hernandez AJ, Lee SJ, Chang S, Lee JA, Loparo JJ, Richardson CC. Catalytically inactive T7 DNA polymerase imposes a lethal replication roadblock. J Biol Chem 2020; 295:9542-9550. [PMID: 32430399 DOI: 10.1074/jbc.ra120.013738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/18/2020] [Indexed: 11/06/2022] Open
Abstract
Bacteriophage T7 encodes its own DNA polymerase, the product of gene 5 (gp5). In isolation, gp5 is a DNA polymerase of low processivity. However, gp5 becomes highly processive upon formation of a complex with Escherichia coli thioredoxin, the product of the trxA gene. Expression of a gp5 variant in which aspartate residues in the metal-binding site of the polymerase domain were replaced by alanine is highly toxic to E. coli cells. This toxicity depends on the presence of a functional E. coli trxA allele and T7 RNA polymerase-driven expression but is independent of the exonuclease activity of gp5. In vitro, the purified gp5 variant is devoid of any detectable polymerase activity and inhibited DNA synthesis by the replisomes of E. coli and T7 in the presence of thioredoxin by forming a stable complex with DNA that prevents replication. On the other hand, the highly homologous Klenow fragment of DNA polymerase I containing an engineered gp5 thioredoxin-binding domain did not exhibit toxicity. We conclude that gp5 alleles encoding inactive polymerases, in combination with thioredoxin, could be useful as a shutoff mechanism in the design of a bacterial cell-growth system.
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Affiliation(s)
- Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seung-Joo Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaehun A Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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15
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Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR. Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome. Biochemistry 2019; 58:4466-4479. [PMID: 31659895 DOI: 10.1021/acs.biochem.9b00525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent structural studies of the bacteriophage T7 DNA replication system have shed light on how multiple proteins assemble to copy two antiparallel DNA strands. In T7, acidic C-terminal tails of both the primase-helicase and single-stranded DNA binding protein bind to two basic patches on the DNA polymerase to aid in replisome assembly, processivity, and coordinated DNA synthesis. Although these electrostatic interactions are essential for DNA replication, the molecular details for how these tails bind the polymerase are unknown. We have determined an X-ray crystal structure of the T7 DNA polymerase bound to both a primer/template DNA and a peptide that mimics the C-terminal tail of the primase-helicase. The structure reveals that the essential C-terminal phenylalanine of the tail binds to a hydrophobic pocket that is surrounded by positive charge on the surface of the polymerase. We show that alterations of polymerase residues that engage the tail lead to defects in viral replication. In the structure, we also observe dTTP bound in the exonuclease active site and stacked against tryptophan 160. Using both primer/extension assays and high-throughput sequencing, we show how mutations in the exonuclease active site lead to defects in mismatch repair and an increase in the level of mutagenesis of the T7 genome. Finally, using small-angle X-ray scattering, we provide the first solution structures of a complex between the single-stranded DNA binding protein and the DNA polymerase and show how a single-stranded DNA binding protein dimer engages both one and two copies of DNA polymerase.
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Affiliation(s)
- Brittni M Foster
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Daniel Rosenberg
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Graduate Group in Biophysics , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Henry Salvo
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Kasie L Stephens
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Brittania J Bintz
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , Missouri 63110 , United States
| | - Maria D Gainey
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Jamie R Wallen
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
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16
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Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 540] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
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Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
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17
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Rossboth B, Arnold AM, Ta H, Platzer R, Kellner F, Huppa JB, Brameshuber M, Baumgart F, Schütz GJ. TCRs are randomly distributed on the plasma membrane of resting antigen-experienced T cells. Nat Immunol 2018; 19:821-827. [PMID: 30013143 PMCID: PMC6071872 DOI: 10.1038/s41590-018-0162-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/14/2018] [Indexed: 12/29/2022]
Abstract
The main function of T cells is to identify harmful antigens as quickly and precisely as possible. Super-resolution microscopy data have indicated that global clustering of T cell antigen receptors (TCRs) occurs before T cell activation. Such pre-activation clustering has been interpreted as representing a potential regulatory mechanism that fine tunes the T cell response. We found here that apparent TCR nanoclustering could be attributed to overcounting artifacts inherent to single-molecule-localization microscopy. Using complementary super-resolution approaches and statistical image analysis, we found no indication of global nanoclustering of TCRs on antigen-experienced CD4+ T cells under non-activating conditions. We also used extensive simulations of super-resolution images to provide quantitative limits for the degree of randomness of the TCR distribution. Together our results suggest that the distribution of TCRs on the plasma membrane is optimized for fast recognition of antigen in the first phase of T cell activation.
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Affiliation(s)
| | | | - Haisen Ta
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - René Platzer
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Florian Kellner
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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18
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Hernandez AJ, Richardson CC. Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein. Semin Cell Dev Biol 2018; 86:92-101. [PMID: 29588157 DOI: 10.1016/j.semcdb.2018.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/29/2018] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
The essential bacteriophage T7-encoded single-stranded DNA binding protein is the nexus of T7 DNA metabolism. Multiple layers of macromolecular interactions mediate its function in replication, recombination, repair, and the maturation of viral genomes. In addition to binding ssDNA, the protein binds to DNA polymerase and DNA helicase, regulating their activities. The protein displays potent homologous DNA annealing activity, underscoring its role in recombination.
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Affiliation(s)
- Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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19
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Seco EM, Ayora S. Bacillus subtilis DNA polymerases, PolC and DnaE, are required for both leading and lagging strand synthesis in SPP1 origin-dependent DNA replication. Nucleic Acids Res 2017; 45:8302-8313. [PMID: 28575448 PMCID: PMC5737612 DOI: 10.1093/nar/gkx493] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/23/2017] [Indexed: 01/08/2023] Open
Abstract
Firmicutes have two distinct replicative DNA polymerases, the PolC leading strand polymerase, and PolC and DnaE synthesizing the lagging strand. We have reconstituted in vitro Bacillus subtilis bacteriophage SPP1 θ-type DNA replication, which initiates unidirectionally at oriL. With this system we show that DnaE is not only restricted to lagging strand synthesis as previously suggested. DnaG primase and DnaE polymerase are required for initiation of DNA replication on both strands. DnaE and DnaG synthesize in concert a hybrid RNA/DNA ‘initiation primer’ on both leading and lagging strands at the SPP1 oriL region, as it does the eukaryotic Pol α complex. DnaE, as a RNA-primed DNA polymerase, extends this initial primer in a reaction modulated by DnaG and one single-strand binding protein (SSB, SsbA or G36P), and hands off the initiation primer to PolC, a DNA-primed DNA polymerase. Then, PolC, stimulated by DnaG and the SSBs, performs the bulk of DNA chain elongation at both leading and lagging strands. Overall, these modulations by the SSBs and DnaG may contribute to the mechanism of polymerase switch at Firmicutes replisomes.
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Affiliation(s)
- Elena M Seco
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Silvia Ayora
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
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20
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Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase. Sci Rep 2017; 7:5797. [PMID: 28724886 PMCID: PMC5517523 DOI: 10.1038/s41598-017-05534-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/19/2017] [Indexed: 12/22/2022] Open
Abstract
Lagging strand DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase. The N-terminal primase domain of the gene 4 protein of phage T7 comprises a zinc-binding domain that recognizes a specific DNA sequence and an RNA polymerase domain that catalyzes RNA polymerization. Based on its crystal structure, the RNA polymerase domain contains two Mg(II) ions. Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase. NMR analysis revealed that upon binding Mn(II), T7 DNA primase undergoes conformational changes near the metal cofactor binding site that are not observed when the enzyme binds Mg(II). A machine-learning algorithm called linear discriminant analysis (LDA) was trained by using the large collection of Mn(II) and Mg(II) binding sites available in the protein data bank (PDB). Application of the model to DNA primase revealed a preference in the enzyme's second metal binding site for Mn(II) over Mg(II), suggesting that T7 DNA primase activity modulation when bound to Mn(II) is based on structural changes in the enzyme.
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21
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RNA primer-primase complexes serve as the signal for polymerase recycling and Okazaki fragment initiation in T4 phage DNA replication. Proc Natl Acad Sci U S A 2017; 114:5635-5640. [PMID: 28507156 DOI: 10.1073/pnas.1620459114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The opposite strand polarity of duplex DNA necessitates that the leading strand is replicated continuously whereas the lagging strand is replicated in discrete segments known as Okazaki fragments. The lagging-strand polymerase sometimes recycles to begin the synthesis of a new Okazaki fragment before finishing the previous fragment, creating a gap between the Okazaki fragments. The mechanism and signal that initiate this behavior-that is, the signaling mechanism-have not been definitively identified. We examined the role of RNA primer-primase complexes left on the lagging ssDNA from primer synthesis in initiating early lagging-strand polymerase recycling. We show for the T4 bacteriophage DNA replication system that primer-primase complexes have a residence time similar to the timescale of Okazaki fragment synthesis and the ability to block a holoenzyme synthesizing DNA and stimulate the dissociation of the holoenzyme to trigger polymerase recycling. The collision with primer-primase complexes triggering the early termination of Okazaki fragment synthesis has distinct advantages over those previously proposed because this signal requires no transmission to the lagging-strand polymerase through protein or DNA interactions, the mechanism for rapid dissociation of the holoenzyme is always collision, and no unique characteristics need to be assigned to either identical polymerase in the replisome. We have modeled repeated cycles of Okazaki fragment initiation using a collision with a completed Okazaki fragment or primer-primase complexes as the recycling mechanism. The results reproduce experimental data, providing insights into events related to Okazaki fragment initiation and the overall functioning of DNA replisomes.
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22
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Hernandez AJ, Richardson CC. Kinetics of Lagging-strand DNA Synthesis In Vitro by the Bacteriophage T7 Replication Proteins. J Vis Exp 2017. [PMID: 28287575 DOI: 10.3791/55312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Here we provide protocols for the kinetic examination of lagging-strand DNA synthesis in vitro by the replication proteins of bacteriophage T7. The T7 replisome is one of the simplest replication systems known, composed of only four proteins, which is an attractive feature for biochemical experiments. Special emphasis is placed on the synthesis of ribonucleotide primers by the T7 primase-helicase, which are used by DNA polymerase to initiate DNA synthesis. Because the mechanisms of DNA replication are conserved across evolution, these protocols should be applicable, or useful as a conceptual springboard, to investigators using other model systems. The protocols described here are highly sensitive and an experienced investigator can perform these experiments and obtain data for analysis in about a day. The only specialized piece of equipment required is a rapid-quench flow instrument, but this piece of equipment is relatively common and available from various commercial sources. The major drawbacks of these assays, however, include the use of radioactivity and the relative low throughput.
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Affiliation(s)
- Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School;
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School
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23
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Cryo-EM structure of the replisome reveals multiple interactions coordinating DNA synthesis. Proc Natl Acad Sci U S A 2017; 114:E1848-E1856. [PMID: 28223502 DOI: 10.1073/pnas.1701252114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present a structure of the ∼650-kDa functional replisome of bacteriophage T7 assembled on DNA resembling a replication fork. A structure of the complex consisting of six domains of DNA helicase, five domains of RNA primase, two DNA polymerases, and two thioredoxin (processivity factor) molecules was determined by single-particle cryo-electron microscopy. The two molecules of DNA polymerase adopt a different spatial arrangement at the replication fork, reflecting their roles in leading- and lagging-strand synthesis. The structure, in combination with biochemical data, reveals molecular mechanisms for coordination of leading- and lagging-strand synthesis. Because mechanisms of DNA replication are highly conserved, the observations are relevant to other replication systems.
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