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Negroni YL, Doro I, Tamborrino A, Luzzi I, Fortunato S, Hensel G, Khosravi S, Maretto L, Stevanato P, Schiavo FL, Concettade Pinto M, Krupinska K, Zottini M. The Arabidopsis Mitochondrial Nucleoid-Associated Protein WHIRLY2 is Required for a Proper Response to Salt Stress. Plant Cell Physiol 2024:pcae025. [PMID: 38591870 DOI: 10.1093/pcp/pcae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024]
Abstract
In the last years, plant organelles have emerged as central coordinators of responses to internal and external stimuli which can induce stress. Mitochondria play a fundamental role as stress sensors being part of a complex communication network between the organelles and nucleus. Among the different environmental stresses, salt stress poses a significant challenge and requires efficient signaling and protective mechanisms. By using the why2 T-DNA insertion mutant and a novel knockout mutant prepared by CRISPR Cas9 mediated genome editing, this study revealed that WHIRLY2 is crucial in protecting mitochondrial DNA (mtDNA) integrity during salt stress. Loss-of-function mutants show an enhanced sensitivity to salt stress. The disruption of WHIRLY2 causes the impairement of mtDNA repair that results in the accumulation of aberrant recombination products, coinciding with severe alterations in nucleoid integrity and overall mitochondria morphology besides a compromised redox-dependent response and mis-regulation of antioxidant enzymes. The results of this study revealed that WHIRLY2 mediated structural features in mitochondria (nucleoid compactness, cristae) are important for an effective response to salt stress.
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Affiliation(s)
- Yuri L Negroni
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Irene Doro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Alberto Tamborrino
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Irene Luzzi
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Stefania Fortunato
- Department of Biosciences, Biotechnology and Environment, University of Bari, Campus Universitario, Via Orabona, 4, 70125 Bari, Italy
| | - Götz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, IPK, Corrensstraße 3,D-06466 Seeland, Gatersleben, Germany
| | - Solmaz Khosravi
- Plant Reproductive Biology, Department of Physiology and Cell Biology, IPK, Corrensstraße 3,D-06466 Seeland, Gatersleben, Germany
| | - Laura Maretto
- Department of Agronomy, Food, Natural Resources, Animal and Environment, University of Padova, Viale Università 16, 35020 Legnaro, Padova, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animal and Environment, University of Padova, Viale Università 16, 35020 Legnaro, Padova, Italy
| | - Fiorella Lo Schiavo
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Maria Concettade Pinto
- Department of Biosciences, Biotechnology and Environment, University of Bari, Campus Universitario, Via Orabona, 4, 70125 Bari, Italy
| | - Karin Krupinska
- Botanisches Institut, Christian-Albrechts-Universiat zu Kiel, 24098 Kiel, Germany
| | - Michela Zottini
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
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2
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Pla-Martín D, Babatz F, Schauss AC. Localization of Mitochondrial Nucleoids by Transmission Electron Microscopy Using the Transgenic Expression of the Mitochondrial Helicase Twinkle and APEX2. Methods Mol Biol 2023; 2615:173-188. [PMID: 36807792 DOI: 10.1007/978-1-0716-2922-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Reminiscent of their evolutionary origin, mitochondria contain their own genome (mtDNA) compacted into the mitochondrial chromosome or nucleoid (mt-nucleoid). Many mitochondrial disorders are characterized by disruption of mt-nucleoids, either by direct mutation of genes involved in mtDNA organization or by interfering with other vital proteins for mitochondrial function. Thus, changes in mt-nucleoid morphology, distribution, and structure are a common feature in many human diseases and can be exploited as an indicator of cellular fitness. Electron microscopy provides the highest possible resolution that can be achieved, delivering spatial and structural information about all cellular structures. Recently, the ascorbate peroxidase APEX2 has been used to increase transmission electron microscopy (TEM) contrast by inducing diaminobenzidine (DAB) precipitation. DAB has the ability to accumulate osmium during classical EM sample preparation and, due to its high electron density, provides strong contrast for TEM. Among the nucleoid proteins, the mitochondrial helicase Twinkle fused with APEX2 has been successfully used to target mt-nucleoids, providing a tool to visualize these subcellular structures with high contrast and with the resolution of an electron microscope. In the presence of H2O2, APEX2 catalyzes the polymerization of DAB, generating a brown precipitate that can be visualized in specific regions of the mitochondrial matrix. Here, we provide a detailed protocol to generate murine cell lines expressing a transgenic variant of Twinkle, suitable to target and visualize mt-nucleoids. We also describe all the necessary steps to validate the cell lines prior to electron microscopy imaging and offer examples of anticipated results.
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Affiliation(s)
- David Pla-Martín
- Center for Physiology, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne, CMMC, University of Cologne, Cologne, Germany.
| | - Felix Babatz
- Cologne Cluster of Excellence on Cellular stress response in Aging-associated Disease, CECAD, University of Cologne, Cologne, Germany
| | - Astrid C Schauss
- Cologne Cluster of Excellence on Cellular stress response in Aging-associated Disease, CECAD, University of Cologne, Cologne, Germany
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3
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Aaltonen MJ, Antonicka H. Identification of Proximity Interactors of Mammalian Nucleoid Proteins by BioID. Methods Mol Biol 2023; 2615:153-72. [PMID: 36807791 DOI: 10.1007/978-1-0716-2922-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Mitochondrial nucleoids are compact nucleoprotein complexes, in which mtDNA is located, replicated, and transcribed. Several proteomic approaches have been previously employed to identify nucleoid proteins; however, a consensus list of nucleoid-associated proteins has not been generated. Here we describe a proximity-biotinylation assay, BioID, which allows identification of proximity interactors of mitochondrial nucleoid proteins. It uses a promiscuous biotin ligase fused to a protein of interest which covalently attaches biotin to lysine residues of its proximal neighbors. Biotinylated proteins can be further enriched by a biotin-affinity purification and identified by mass-spectrometry. BioID can identify transient and weak interactions and can be used to identify changes in the interactions upon different cellular treatments, for different protein isoforms or for pathogenic variants.
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4
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Motori E. Measurement of Nucleoid Size Using STED Microscopy. Methods Mol Biol 2023; 2615:107-117. [PMID: 36807788 DOI: 10.1007/978-1-0716-2922-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Mitochondria are equipped with their own DNA (mtDNA), which is packed into structures termed nucleoids . While nucleoids can be visualized in situ by fluorescence microscopy , the advent of super-resolution microscopy , and in particular of stimulated emission depletion (STED), has recently enabled the visualization of nucleoids at sub-diffraction resolution. Super-resolution microscopy has proved an invaluable tool for addressing fundamental questions in mitochondrial biology. In this chapter I describe how to achieve efficient labeling of mtDNA and how to quantify nucleoid diameter using an automated approach in fixed cultured cells by STED microscopy .
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Affiliation(s)
- Elisa Motori
- Institute for Biochemistry, University of Cologne, Cologne, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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5
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Bateman JM. Mitochondrial DNA Transport in Drosophila Neurons. Methods Mol Biol 2022; 2431:409-416. [PMID: 35412289 DOI: 10.1007/978-1-0716-1990-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondria are essential organelles that generate energy and play vital roles in cellular metabolism. The small circular mitochondrial genome encodes key components of the mitochondrial respiratory apparatus. Depletion of, or mutations in mitochondrial DNA (mtDNA) cause mitochondrial dysfunction and disease. mtDNA is packaged into nucleoids, which are transported throughout the cell within mitochondria. Efficient transport of nucleoids is essential in neurons, where mitochondrial function is required locally at synapses. Here I describe methods for visualization of nucleoids in Drosophila neurons using a GFP fusion of the mitochondrial transcription factor TFAM. TFAM-GFP, together with mCherry-labeled mitochondria, was used to visualize nucleoids in fixed larval segmental nerves. I also describe how these tools can be used for live imaging of nucleoid dynamics. Using Drosophila as a model system, these methods will enable further characterization and analysis of nucleoid dynamics in neurons.
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Affiliation(s)
- Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
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Cossa A, Wien F, Turbant F, Kaczorowski T, Węgrzyn G, Arluison V, Pérez-Berná AJ, Trépout S, Pereiro E. Evaluation of the Role of Bacterial Amyloid on Nucleoid Structure Using Cryo-Soft X-Ray Tomography. Methods Mol Biol 2022; 2538:319-333. [PMID: 35951309 DOI: 10.1007/978-1-0716-2529-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial chromosomal DNA is packed within a non-membranous structure, the nucleoid, thanks to nucleoid associated proteins (NAPs). The role of bacterial amyloid has recently emerged among these NAPs, particularly with the nucleoid-associated protein Hfq that plays a direct role in DNA compaction. In this chapter, we present a 3D imaging technique, cryo-soft X-ray tomography (cryo-SXT) to obtain a detailed 3D visualization of subcellular bacterial structures, especially the nucleoid. Cryo-SXT imaging of native unlabeled cells enables observation of the nucleoid in 3D with a high resolution, allowing to evidence in vivo the role of amyloids on DNA compaction. The precise experimental methods to obtain 3D tomograms will be presented.
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Affiliation(s)
- Antoine Cossa
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris-Saclay, CEA Saclay, Gif-sur-Yvette, France
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, Orsay, France
- National Center of Biotechnology, CSIC, Campus Univ. Autónoma de Madrid, Madrid, Spain
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris-Saclay, CEA Saclay, Gif-sur-Yvette, France
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris-Saclay, CEA Saclay, Gif-sur-Yvette, France
- Université de Paris Cité, Paris, France
| | | | - Sylvain Trépout
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, Orsay, France
| | - Eva Pereiro
- Mistral Beamline, Alba Light Source, Barcelona, Spain.
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Martins-Duarte ÉS, Sheiner L, Reiff SB, de Souza W, Striepen B. Replication and partitioning of the apicoplast genome of Toxoplasma gondii is linked to the cell cycle and requires DNA polymerase and gyrase. Int J Parasitol 2021; 51:493-504. [PMID: 33581138 PMCID: PMC8113025 DOI: 10.1016/j.ijpara.2020.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/30/2020] [Accepted: 11/08/2020] [Indexed: 10/26/2022]
Abstract
Apicomplexans are the causative agents of numerous important infectious diseases including malaria and toxoplasmosis. Most of them harbour a chloroplast-like organelle called the apicoplast that is essential for the parasites' metabolism and survival. While most apicoplast proteins are nuclear encoded, the organelle also maintains its own genome, a 35 kb circle. In this study we used Toxoplasma gondii to identify and characterise essential proteins involved in apicoplast genome replication and to understand how apicoplast genome segregation unfolds over time. We demonstrated that the DNA replication enzymes Prex, DNA gyrase and DNA single stranded binding protein localise to the apicoplast. We show in knockdown experiments that apicoplast DNA Gyrase A and B, and Prex are required for apicoplast genome replication and growth of the parasite. Analysis of apicoplast genome replication by structured illumination microscopy in T. gondii tachyzoites showed that apicoplast nucleoid division and segregation initiate at the beginning of S phase and conclude during mitosis. Thus, the replication and division of the apicoplast nucleoid is highly coordinated with nuclear genome replication and mitosis. Our observations highlight essential components of apicoplast genome maintenance and shed light on the timing of this process in the context of the overall parasite cell cycle.
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Affiliation(s)
- Érica S Martins-Duarte
- Laboratório de Quimioterapia de Protozoários Egler Chiari, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil.
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, 120 University Place Glasgow, United Kingdom
| | - Sarah B Reiff
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Wanderley de Souza
- Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil; Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA, USA; Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA. USA
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Zubov Aleksandr I, Semashko Tatiana A, Evsyutina Daria V, Ladygina Valentina G, Kovalchuk Sergey I, Ziganshin Rustam H, Galyamina Maria A, Fisunov Gleb Y, Pobeguts Olga V. Data on nucleoid-associated proteins isolated from Mycoplasma Gallisepticum in different growth phases. Data Brief 2020; 31:105853. [PMID: 32637477 PMCID: PMC7327420 DOI: 10.1016/j.dib.2020.105853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Mycoplasma gallisepticum (MG) is one of the smallest free-living and self-replicating organisms, it is characterized by lack of cell wall and reduced genome size. As a result of genome reduction, MG has a limited variety of DNA-binding proteins and transcription factors. To investigate the dynamic changes of the proteomic profile of MG nucleoid, that may assist in revealing its mechanisms of functioning, regulation of chromosome organization and stress adaptation, a quantitative proteomic study was performed on MG nucleoids obtained from the cell culture in logarithmic and stationary phases of synchronous growth. MG cells were grown on a liquid medium with a 9 h starvation period. Nucleoids were obtained from the cell culture at the 26th and the 50th hour (logarithmic and stationary growth phases respectively) by sucrose density gradient centrifugation. LC-MS analysis was carried out on an Ultimate 3000 RSLCnano HPLC system connected to a Fusion Lumos mass spectrometer, controlled by XCalibur software (Thermo Fisher Scientific) via a nanoelectrospray source (Thermo Fisher Scientific). For comprehensive peptide library generation one sample from each biological replicate was run in DDA mode. Then, all the samples were run in a single LC-MS DIA run. Identification of DDA files and DIA quantitation was performed with MaxQuant and Skyline software, correspondingly. All raw data generated from IDA and DDA acquisitions are presented in the PRIDE database with identifier PXD019077.
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Affiliation(s)
- I Zubov Aleksandr
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - A Semashko Tatiana
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - V Evsyutina Daria
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - G Ladygina Valentina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | | | - A Galyamina Maria
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Yu Fisunov Gleb
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - V Pobeguts Olga
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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9
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Ri JS, Choe SH, Schleusener J, Lademann J, Choe CS, Darvin ME. In vivo Tracking of DNA for Precise Determination of the Stratum Corneum Thickness and Superficial Microbiome Using Confocal Raman Microscopy. Skin Pharmacol Physiol 2019; 33:30-37. [PMID: 31614347 DOI: 10.1159/000503262] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/06/2019] [Indexed: 11/19/2022]
Abstract
The skin barrier function is mostly provided by the stratum corneum (SC), the uppermost layer of the epidermis. To noninvasively analyze the physiological properties of the skin barrier functionin vivo, it is important to determine the SC thickness. Confocal Raman microscopy (CRM) is widely used for this task. In the present in vivo study, a new method based on the determination of the DNA concentration profile using CRM is introduced for determining the SC thickness. The obtained SC thickness values are compared with those obtained using other CRM-based methods determining the water and lipid depth profiles. The obtained results show almost no significant differences in SC thickness for the utilized methods. Therefore, the results indicate that it is possible to calculate the SC thickness by using the DNA profile in the fingerprint region, which is comparable with the SC thickness calculated by the water depth profiles (ANOVA test p = 0.77) and the lipid depth profile (ANOVA test p = 0.74). This provides the possibility to measure the SC thickness by using the DNA profile, in case the water or lipid profile analyses are influenced by a topically applied formulation. The increase in DNA concentration in the superficial SC (0-2 µm) is related to the DNA presence in the microbiome of the skin, which was not present in the SC depth below 4 µm.
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Affiliation(s)
- Jin Song Ri
- Kim Il Sung University, Pyongyang, Democratic People's Republic of Korea
| | - Se Hyok Choe
- Kim Il Sung University, Pyongyang, Democratic People's Republic of Korea
| | - Johannes Schleusener
- Center of Experimental and Applied Cutaneous Physiology, Department of Dermatology, Venerology and Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jürgen Lademann
- Center of Experimental and Applied Cutaneous Physiology, Department of Dermatology, Venerology and Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Chun Sik Choe
- Kim Il Sung University, Pyongyang, Democratic People's Republic of Korea
| | - Maxim E Darvin
- Center of Experimental and Applied Cutaneous Physiology, Department of Dermatology, Venerology and Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany,
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10
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Abstract
Decades of research have probed the interplay between chromatin (genomic DNA associated with proteins and RNAs) and transcription by RNA polymerase (RNAP) in all domains of life. In bacteria, chromatin is compacted into a membrane-free region known as the nucleoid that changes shape and composition depending on the bacterial state. Transcription plays a key role in both shaping the nucleoid and organizing it into domains. At the same time, chromatin impacts transcription by at least five distinct mechanisms: (i) occlusion of RNAP binding; (ii) roadblocking RNAP progression; (iii) constraining DNA topology; (iv) RNA-mediated interactions; and (v) macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and, in combination, mediate gene regulation. Here, we review the current understanding of these mechanisms with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. The myriad questions about transcription of bacterial chromatin are increasingly answerable due to methodological advances, enabling a needed paradigm shift in the field of bacterial transcription to focus on regulation of genes in their native state. We can anticipate answers that will define how bacterial chromatin helps coordinate and dynamically regulate gene expression in changing environments.
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Affiliation(s)
- Beth A Shen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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Lichocka M, Rymaszewski W, Morgiewicz K, Barymow-Filoniuk I, Chlebowski A, Sobczak M, Samuel MA, Schmelzer E, Krzymowska M, Hennig J. Nucleus- and plastid-targeted annexin 5 promotes reproductive development in Arabidopsis and is essential for pollen and embryo formation. BMC Plant Biol 2018; 18:183. [PMID: 30189843 PMCID: PMC6127919 DOI: 10.1186/s12870-018-1405-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/30/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Pollen development is a strictly controlled post-meiotic process during which microspores differentiate into microgametophytes and profound structural and functional changes occur in organelles. Annexin 5 is a calcium- and lipid-binding protein that is highly expressed in pollen grains and regulates pollen development and physiology. To gain further insights into the role of ANN5 in Arabidopsis development, we performed detailed phenotypic characterization of Arabidopsis plants with modified ANN5 levels. In addition, interaction partners and subcellular localization of ANN5 were analyzed to investigate potential functions of ANN5 at cellular level. RESULTS Here, we report that RNAi-mediated suppression of ANN5 results in formation of smaller pollen grains, enhanced pollen lethality, and delayed pollen tube growth. ANN5 RNAi knockdown plants also displayed aberrant development during the transition from the vegetative to generative phase and during embryogenesis, reflected by delayed bolting time and reduced embryo size, respectively. At the subcellular level, ANN5 was delivered to the nucleus, nucleolus, and cytoplasm, and was frequently localized in plastid nucleoids, suggesting a likely role in interorganellar communication. Furthermore, ANN5-YFP co-immunoprecipitated with RABE1b, a putative GTPase, and interaction in planta was confirmed in plastidial nucleoids using FLIM-FRET analysis. CONCLUSIONS Our findings let us to propose that ANN5 influences basal cell homeostasis via modulation of plastid activity during pollen maturation. We hypothesize that the role of ANN5 is to orchestrate the plastidial and nuclear genome activities via protein-protein interactions however not only in maturing pollen but also during the transition from the vegetative to the generative growth and seed development.
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Affiliation(s)
- Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Wojciech Rymaszewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Karolina Morgiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Izabela Barymow-Filoniuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Miroslaw Sobczak
- Department of Botany, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Marcus A. Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - Elmon Schmelzer
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Magdalena Krzymowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Jacek Hennig
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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12
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Abstract
The bacterial nucleoid is highly organized, yet it is dynamically remodeled by cellular processes such as transcription, replication, or segregation. Many principles of nucleoid organization have remained obscure due to the inability of conventional microscopy methods to retrieve structural information beyond the diffraction limit of light. Structured illumination microscopy has recently been shown to provide new levels of spatial details on bacterial chromosome organization by surpassing the diffraction limit. Its ease of use and fast 3D multicolor capabilities make it a method of choice for imaging fluorescently labeled specimens at the nanoscale. We describe a simple high-throughput method for imaging bacterial chromosomes using this technique.
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Affiliation(s)
- Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France.
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13
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Pagliuso A, Cossart P, Stavru F. The ever-growing complexity of the mitochondrial fission machinery. Cell Mol Life Sci 2018; 75:355-74. [PMID: 28779209 DOI: 10.1007/s00018-017-2603-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/24/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022]
Abstract
The mitochondrial network constantly changes and remodels its shape to face the cellular energy demand. In human cells, mitochondrial fusion is regulated by the large, evolutionarily conserved GTPases Mfn1 and Mfn2, which are embedded in the mitochondrial outer membrane, and by OPA1, embedded in the mitochondrial inner membrane. In contrast, the soluble dynamin-related GTPase Drp1 is recruited from the cytosol to mitochondria and is key to mitochondrial fission. A number of new players have been recently involved in Drp1-dependent mitochondrial fission, ranging from large cellular structures such as the ER and the cytoskeleton to the surprising involvement of the endocytic dynamin 2 in the terminal abscission step. Here we review the recent findings that have expanded the mechanistic model for the mitochondrial fission process in human cells and highlight open questions.
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Sellars LE, Bryant JA, Sánchez-Romero MA, Sánchez-Morán E, Busby SJW, Lee DJ. Development of a new fluorescent reporter:operator system: location of AraC regulated genes in Escherichia coli K-12. BMC Microbiol 2017; 17:170. [PMID: 28774286 PMCID: PMC5543585 DOI: 10.1186/s12866-017-1079-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In bacteria, many transcription activator and repressor proteins regulate multiple transcription units that are often distally distributed on the bacterial genome. To investigate the subcellular location of DNA bound proteins in the folded bacterial nucleoid, fluorescent reporters have been developed which can be targeted to specific DNA operator sites. Such Fluorescent Reporter-Operator System (FROS) probes consist of a fluorescent protein fused to a DNA binding protein, which binds to an array of DNA operator sites located within the genome. Here we have developed a new FROS probe using the Escherichia coli MalI transcription factor, fused to mCherry fluorescent protein. We have used this in combination with a LacI repressor::GFP protein based FROS probe to assess the cellular location of commonly regulated transcription units that are distal on the Escherichia coli genome. RESULTS We developed a new DNA binding fluorescent reporter, consisting of the Escherichia coli MalI protein fused to the mCherry fluorescent protein. This was used in combination with a Lac repressor:green fluorescent protein fusion to examine the spatial positioning and possible co-localisation of target genes, regulated by the Escherichia coli AraC protein. We report that induction of gene expression with arabinose does not result in co-localisation of AraC-regulated transcription units. However, measurable repositioning was observed when gene expression was induced at the AraC-regulated promoter controlling expression of the araFGH genes, located close to the DNA replication terminus on the chromosome. Moreover, in dividing cells, arabinose-induced expression at the araFGH locus enhanced chromosome segregation after replication. CONCLUSION Regions of the chromosome regulated by AraC do not colocalise, but transcription events can induce movement of chromosome loci in bacteria and our observations suggest a role for gene expression in chromosome segregation.
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Affiliation(s)
- Laura E. Sellars
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Jack A. Bryant
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | | | | | - Stephen J. W. Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - David J. Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- Department of Life Sciences, Birmingham City University, Edgbaston, Birmingham, B15 3TN UK
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15
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Feijoo-Siota L, Rama JLR, Sánchez-Pérez A, Villa TG. Considerations on bacterial nucleoids. Appl Microbiol Biotechnol 2017; 101:5591-5602. [PMID: 28664324 DOI: 10.1007/s00253-017-8381-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/21/2022]
Abstract
The classic genome organization of the bacterial chromosome is normally envisaged with all its genetic markers linked, thus forming a closed genetic circle of duplex stranded DNA (dsDNA) and several proteins in what it is called as "the bacterial nucleoid." This structure may be more or less corrugated depending on the physiological state of the bacterium (i.e., resting state or active growth) and is not surrounded by a double membrane as in eukayotic cells. The universality of the closed circle model in bacteria is however slowly changing, as new data emerge in different bacterial groups such as in Planctomycetes and related microorganisms, species of Borrelia, Streptomyces, Agrobacterium, or Phytoplasma. In these and possibly other microorganisms, the existence of complex formations of intracellular membranes or linear chromosomes is typical; all of these situations contributing to weakening the current cellular organization paradigm, i.e., prokaryotic vs eukaryotic cells.
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Affiliation(s)
- Lucía Feijoo-Siota
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - José Luis R Rama
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Angeles Sánchez-Pérez
- Discipline of Physiology and Bosch Institute, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tomás G Villa
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain.
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Abstract
This methods article described a protocol aiming at generating chromosome contact maps of bacterial species using a genome-wide derivative of the chromosome conformation capture (3C) technique. The approach is readily applicable on a broad variety of gram + and gram-bacterial species. It describes and addresses known caveats and technicalities associated with the technique, and should be of interest to any laboratory interested to perform a multiscale analysis of the genome structure of its species of interest.
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Affiliation(s)
- Martial Marbouty
- Groupe Régulation Spatiale des Génomes, Département Génomes et Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France. .,CNRS, UMR 3525, 75724, Paris Cedex 15, France. .,Centre de Bioinformatique, Biostatistique et Biologie Intégrative, USR 3756, Institut Pasteur, Paris Cedex 15, 75724, Paris Cedex 15, France.
| | - Romain Koszul
- Groupe Régulation Spatiale des Génomes, Département Génomes et Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France. .,CNRS, UMR 3525, 75724, Paris Cedex 15, France. .,Centre de Bioinformatique, Biostatistique et Biologie Intégrative, USR 3756, Institut Pasteur, Paris Cedex 15, 75724, Paris Cedex 15, France.
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17
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Sumitani M, Kondo M, Kasashima K, Endo H, Nakamura K, Misawa T, Tanaka H, Sezutsu H. Characterization of Bombyx mori mitochondrial transcription factor A, a conserved regulator of mitochondrial DNA. Gene 2016; 608:103-113. [PMID: 28027964 DOI: 10.1016/j.gene.2016.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/20/2016] [Indexed: 01/18/2023]
Abstract
In the present study, we initially cloned and characterized a mitochondrial transcription factor A (Tfam) homologue in the silkworm, Bombyx mori. Bombyx mori TFAM (BmTFAM) localized to mitochondria in cultured silkworm and human cells, and co-localized with mtDNA nucleoids in human HeLa cells. In an immunoprecipitation analysis, BmTFAM was found to associate with human mtDNA in mitochondria, indicating its feature as a non-specific DNA-binding protein. In spite of the low identity between BmTFAM and human TFAM (26.5%), the expression of BmTFAM rescued mtDNA copy number reductions and enlarged mtDNA nucleoids in HeLa cells, which were induced by human Tfam knockdown. Thus, BmTFAM compensates for the function of human TFAM in HeLa cells, demonstrating that the mitochondrial function of TFAM is highly conserved between silkworms and humans. BmTfam mRNA was strongly expressed in early embryos. Through double-stranded RNA (dsRNA)-based RNA interference (RNAi) in silkworm embryos, we found that the knockdown of BmTFAM reduced the amount of mtDNA and induced growth retardation at the larval stage. Collectively, these results demonstrate that BmTFAM is a highly conserved mtDNA regulator and may be a good candidate for investigating and modulating mtDNA metabolism in this model organism.
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Affiliation(s)
- Megumi Sumitani
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Owashi, Tsukuba 305-8634, Japan.
| | - Mari Kondo
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Chiba, Japan
| | - Katsumi Kasashima
- Division of Functional Biochemistry, Department of Biochemistry, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Hitoshi Endo
- Division of Functional Biochemistry, Department of Biochemistry, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Kaoru Nakamura
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Owashi, Tsukuba 305-8634, Japan
| | - Toshihiko Misawa
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Owashi, Tsukuba 305-8634, Japan
| | - Hiromitsu Tanaka
- Insect-Microbe Research Unit, Division of Insect Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Owashi, Tsukuba 305-8634, Japan
| | - Hideki Sezutsu
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Owashi, Tsukuba 305-8634, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Chiba, Japan.
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18
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Wang M, Jiang L, Da Q, Liu J, Feng D, Wang J, Wang HB, Jin HL. DELAYED GREENING 238, a Nuclear-Encoded Chloroplast Nucleoid Protein, Is Involved in the Regulation of Early Chloroplast Development and Plastid Gene Expression in Arabidopsis thaliana. Plant Cell Physiol 2016; 57:2586-2599. [PMID: 27818379 DOI: 10.1093/pcp/pcw172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
Chloroplast development is an essential process for plant growth that is regulated by numerous proteins. Plastid-encoded plastid RNA polymerase (PEP) is a large complex that regulates plastid gene transcription and chloroplast development. However, many proteins in this complex remain to be identified. Here, through large-scale screening of Arabidopsis mutants by Chl fluorescence imaging, we identified a novel protein, DELAYED GREENING 238 (DG238), which is involved in regulating chloroplast development and plastid gene expression. Loss of DG238 retards plant growth, delays young leaf greening, affects chloroplast development and lowers photosynthetic efficiency. Moreover, blue-native PAGE (BN-PAGE) and Western blot analysis indicated that PSII and PSI protein levels are reduced in dg238 mutants. DG238 is mainly expressed in young tissues and is regulated by light signals. Subcellular localization analysis showed that DG238 is a nuclear-encoded chloroplast nucleoid protein. More interestingly, DG238 was co-expressed with FLN1, which encodes an essential subunit of the PEP complex. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP) assays showed that DG238 can also interact with FLN1. Taken together, these results suggest that DG238 may function as a component of the PEP complex that is important for the early stage of chloroplast development and helps regulate PEP-dependent plastid gene expression.
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Affiliation(s)
- Menglong Wang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Lan Jiang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Qingen Da
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Jun Liu
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Dongru Feng
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Jinfa Wang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Hong-Bin Wang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Hong-Lei Jin
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
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19
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Liyanage SU, Coyaud E, Laurent EMN, Hurren R, Maclean N, Wood SR, Kazak L, Shamas-Din A, Holt I, Raught B, Schimmer A. Characterizing the mitochondrial DNA polymerase gamma interactome by BioID identifies Ruvbl2 localizes to the mitochondria. Mitochondrion 2016; 32:31-35. [PMID: 27845271 DOI: 10.1016/j.mito.2016.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/13/2016] [Accepted: 11/02/2016] [Indexed: 10/20/2022]
Abstract
Human mitochondrial DNA (mtDNA) is replicated by the mitochondrial DNA polymerase gamma (POLG). Using proximity dependent biotin labelling (BioID), we characterized the POLG interactome and identified new interaction partners involved in mtDNA maintenance, transcription, translation and protein quality control. We also identified interaction with the nuclear AAA+ ATPase Ruvbl2, suggesting mitochondrial localization for this protein. Ruvbl2 was detected in mitochondria-enriched fractions in leukemic cells. Additionally, transgenic overexpression of Ruvbl2 from an alternative translation initiation site resulted in mitochondrial co-localization. Overall, POLG interactome mapping identifies novel proteins which support mitochondrial biogenesis and a potential novel mitochondrial isoform of Ruvbl2.
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Affiliation(s)
- Sanduni U Liyanage
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, ON, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neil Maclean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Stuart R Wood
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Lawrence Kazak
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Aisha Shamas-Din
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ian Holt
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aaron Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, ON, Canada.
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20
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Melonek J, Oetke S, Krupinska K. Multifunctionality of plastid nucleoids as revealed by proteome analyses. Biochim Biophys Acta 2016; 1864:1016-38. [PMID: 26987276 DOI: 10.1016/j.bbapap.2016.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/25/2016] [Accepted: 03/09/2016] [Indexed: 01/08/2023]
Abstract
Protocols aimed at the isolation of nucleoids and transcriptionally active chromosomes (TACs) from plastids of higher plants have been established already decades ago, but only recent improvements in the mass spectrometry methods enabled detailed proteomic characterization of their components. Here we present a comprehensive analysis of the protein compositions obtained from two proteomic studies of TAC fractions isolated from Arabidopsis/mustard and spinach chloroplasts, respectively, as well as nucleoid fractions from Arabidopsis, maize and pea. Interestingly, different approaches as well as the use of diverse starting materials resulted in the detection of varying protein catalogues with a number of shared proteins. Possible reasons for the discrepancies between the protein repertoires and for missing out some of the nucleoid proteins that have been identified previously by other means than mass spectrometry as well as the repeated identification of "unexpected" proteins indicating potential links between DNA/RNA-associated nucleoid core functions and energy metabolism as well as biosynthetic activities of plastids will be discussed. In accordance with the nucleoid association of proteins involved in key functions of plastids including photosynthesis, the phenotypes of mutants lacking one or the other plastid nucleoid-associated protein (ptNAP) show the importance of nucleoid proteins for overall plant development and growth. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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21
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Wegner AS, Wintraecken K, Spurio R, Woldringh CL, de Vries R, Odijk T. Compaction of isolated Escherichia coli nucleoids: Polymer and H-NS protein synergetics. J Struct Biol 2016; 194:129-37. [PMID: 26868106 DOI: 10.1016/j.jsb.2016.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 10/22/2022]
Abstract
Escherichia coli nucleoids were compacted by the inert polymer polyethylene glycol (PEG) in the presence of the H-NS protein. The protein by itself appears to have little impact on the size of the nucleoids as determined by fluorescent microscopy. However, it has a significant impact on the nucleoidal collapse by PEG. This is quantitatively explained by assuming the H-NS protein enhances the effective diameter of the DNA helix leading to an increase in the depletion forces induced by the PEG. Ultimately, however, the free energy of the nucleoid itself turns out to be independent of the H-NS concentration. This is because the enhancement of the supercoil excluded volume is negligible. The experiments on the nucleoids are corroborated by dynamic light scattering and EMSA analyses performed on DNA plasmids in the presence of PEG and H-NS.
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Affiliation(s)
- Anna S Wegner
- Complex Fluids Theory, Kluyver Institute for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, Kruislaan 316, 1098 SM Amsterdam, The Netherlands
| | - Kathelijne Wintraecken
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703HB Wageningen, The Netherlands
| | - Roberto Spurio
- University of Camerino, School of Biosciences and Veterinary Medicine, 62032 Camerino, MC, Italy
| | - Conrad L Woldringh
- Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, Kruislaan 316, 1098 SM Amsterdam, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703HB Wageningen, The Netherlands
| | - Theo Odijk
- Complex Fluids Theory, Kluyver Institute for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Lorentz Institute for Theoretical Physics, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.
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22
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Redrejo-Rodríguez M, Salas M. Multiple roles of genome-attached bacteriophage terminal proteins. Virology 2014; 468-470:322-329. [PMID: 25232661 DOI: 10.1016/j.virol.2014.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 07/31/2014] [Accepted: 08/04/2014] [Indexed: 11/29/2022]
Abstract
Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in linear genomes, including viruses, gram-positive bacteria, linear plasmids and mobile elements. By this mechanism a specific amino acid primes replication and becomes covalently linked to the genome ends. Despite the fact that TPs lack sequence homology, they share a similar structural arrangement, with the priming residue in the C-terminal half of the protein and an accumulation of positively charged residues at the N-terminal end. In addition, various bacteriophage TPs have been shown to have DNA-binding capacity that targets TPs and their attached genomes to the host nucleoid. Furthermore, a number of bacteriophage TPs from different viral families and with diverse hosts also contain putative nuclear localization signals and localize in the eukaryotic nucleus, which could lead to the transport of the attached DNA. This suggests a possible role of bacteriophage TPs in prokaryote-to-eukaryote horizontal gene transfer.
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Affiliation(s)
- Modesto Redrejo-Rodríguez
- Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad de Madrid), Universidad Autónoma, Nicolás Cabrera, 1, Cantoblanco, 28049 Madrid, Spain
| | - Margarita Salas
- Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad de Madrid), Universidad Autónoma, Nicolás Cabrera, 1, Cantoblanco, 28049 Madrid, Spain.
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Cech GM, Pakuła B, Kamrowska D, Węgrzyn G, Arluison V, Szalewska-Pałasz A. Hfq protein deficiency in Escherichia coli affects ColE1-like but not λ plasmid DNA replication. Plasmid 2014; 73:10-5. [PMID: 24811974 DOI: 10.1016/j.plasmid.2014.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 04/21/2014] [Accepted: 04/23/2014] [Indexed: 12/19/2022]
Abstract
Hfq is a nucleic acid-binding protein involved in controlling several aspects of RNA metabolism. It achieves this regulatory function by modulating the translational activity and stability of different mRNAs, generally via interactions with stress-related small regulatory sRNAs. However, besides its role in the coordination of translation of bacterial mRNA, Hfq is also a nucleoid-associated DNA-binding protein. Motivated by the above property of Hfq, we investigated if hfq gene mutation has implications for the regulation of DNA replication. Efficiency of ColE1-like (pMB1- and p15A replicons) and bacteriophage λ-derived plasmids' replication has been investigated in wild-type strain and otherwise isogenic hfq mutant of Escherichia coli. Significant differences in plasmid amount and kinetics of plasmid DNA synthesis were observed between the two tested bacterial hosts for ColE1-like replicons, but not for λ plasmid. Furthermore, ColE1-like plasmids replicated more efficiently in wild-type cells than in the hfq mutant in the early exponential phase of growth, but less efficiently in late exponential and early stationary phases. Hfq levels in the wild-type host, estimated by Western-blotting, were increased at the latter phases relative to the former one. Moreover, effects of the hfq mutation on ColE1-like plasmid replication were impaired in the absence of the rom gene, coding for a protein enhancing RNA I-RNA II interactions during the control of the replication initiation. These results are discussed in the light of a potential mechanism by which Hfq protein may influence replication of some, but not all, replicons in E. coli.
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Chai Q, Singh B, Peisker K, Metzendorf N, Ge X, Dasgupta S, Sanyal S. Organization of ribosomes and nucleoids in Escherichia coli cells during growth and in quiescence. J Biol Chem 2014; 289:11342-11352. [PMID: 24599955 DOI: 10.1074/jbc.m114.557348] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have examined the distribution of ribosomes and nucleoids in live Escherichia coli cells under conditions of growth, division, and in quiescence. In exponentially growing cells translating ribosomes are interspersed among and around the nucleoid lobes, appearing as alternative bands under a fluorescence microscope. In contrast, inactive ribosomes either in stationary phase or after treatment with translation inhibitors such as chloramphenicol, tetracycline, and streptomycin gather predominantly at the cell poles and boundaries with concomitant compaction of the nucleoid. However, under all conditions, spatial segregation of the ribosomes and the nucleoids is well maintained. In dividing cells, ribosomes accumulate on both sides of the FtsZ ring at the mid cell. However, the distribution of the ribosomes among the new daughter cells is often unequal. Both the shape of the nucleoid and the pattern of ribosome distribution are also modified when the cells are exposed to rifampicin (transcription inhibitor), nalidixic acid (gyrase inhibitor), or A22 (MreB-cytoskeleton disruptor). Thus we conclude that the intracellular organization of the ribosomes and the nucleoids in bacteria are dynamic and critically dependent on cellular growth processes (replication, transcription, and translation) as well as on the integrity of the MreB cytoskeleton.
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Affiliation(s)
- Qian Chai
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Bhupender Singh
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Kristin Peisker
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Nicole Metzendorf
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden.
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Afanasieva K, Chopei M, Zazhytska M, Vikhreva M, Sivolob A. DNA loop domain organization as revealed by single-cell gel electrophoresis. Biochim Biophys Acta 2013; 1833:3237-3244. [PMID: 24100159 DOI: 10.1016/j.bbamcr.2013.09.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 09/23/2013] [Accepted: 09/26/2013] [Indexed: 01/04/2023]
Abstract
At higher order levels chromatin is organized into loops. This looping, which plays an important role in transcription regulation and other processes, remains poorly understood. We investigated the kinetics of DNA loop migration during single cell gel electrophoresis (the comet assay). The migration of a part of the loops was shown to be reversible after switching off electrophoresis and to be sensitive to intercalation-induced changes in supercoiling. Another group of the loops migrates rapidly, the rate being insensitive to the supercoiling level. The largest part of the loops cannot migrate at all, presumably because of their large size. The loop ends can be detached in the presence of high concentrations of intercalators or protein denaturants, thus increasing the fraction of DNA that cannot migrate in the gel. The distribution of the loop length up to 100kilobases appears to be consistent with the fractal globule organization.
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Affiliation(s)
- Katerina Afanasieva
- Department of General and Molecular Genetics, Taras Shevchenko National University, 64/13, Volodymyrska Street, 01601 Kiev, Ukraine
| | - Marianna Chopei
- Department of General and Molecular Genetics, Taras Shevchenko National University, 64/13, Volodymyrska Street, 01601 Kiev, Ukraine
| | - Marianna Zazhytska
- Department of General and Molecular Genetics, Taras Shevchenko National University, 64/13, Volodymyrska Street, 01601 Kiev, Ukraine
| | - Maria Vikhreva
- Department of General and Molecular Genetics, Taras Shevchenko National University, 64/13, Volodymyrska Street, 01601 Kiev, Ukraine
| | - Andrei Sivolob
- Department of General and Molecular Genetics, Taras Shevchenko National University, 64/13, Volodymyrska Street, 01601 Kiev, Ukraine.
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Abstract
Mitochondria play a crucial role in the development and function of germ cells. Mitochondria contain a maternally inherited genome that should be transmitted to offspring without reactive oxygen species‐induced damage during germ line development. Germ cells are also involved in the mitochondrial DNA (mtDNA) bottleneck; thus, the appropriate regulation of mtDNA in these cells is very important for this characteristic transmission. In this review, we focused on unique regulation of the mitochondrial genome in animal germ cells; paternal elimination and the mtDNA bottleneck in females. We also summarized the mitochondrial nucleoid factors involved in various mtDNA regulation pathways. Among them, mitochondrial transcription factor A (TFAM), which has pleiotropic and essential roles in mtDNA maintenance, appears to have putative roles in germ cell regulation.
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Affiliation(s)
- Katsumi Kasashima
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Yasumitsu Nagao
- Center for Experimental Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498 Japan
| | - Hitoshi Endo
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
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