1
|
A Pathfinder in High-Pressure Bioscience: In Memoriam of Gaston Hui Bon Hoa. BIOLOGY 2021; 10:biology10080778. [PMID: 34440010 PMCID: PMC8389544 DOI: 10.3390/biology10080778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/23/2022]
|
2
|
Kaddour H, Lucchi H, Hervé G, Vergne J, Maurel MC. Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth. BIOLOGY 2021; 10:720. [PMID: 34439952 PMCID: PMC8389264 DOI: 10.3390/biology10080720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/17/2022]
Abstract
A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1-3000 bar). It appears that the initial rate of this reaction decreases when pressure increases, revealing a positive ΔV≠ of activation, which correlates with the domain closure accompanying the reaction and the decrease of the surface of the viroid exposed to the solvent. Although, as expected, temperature increases the rate of the reaction whose energy of activation was determined, it appeared that it does not significantly influence the ΔV≠ of activation and that pressure does not influence the energy of activation. These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid. The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world.
Collapse
Affiliation(s)
- Hussein Kaddour
- Department of pharmacology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Honorine Lucchi
- Société PYMABS, 5 rue Henri Auguste Desbyeres, 91000 Évry-Courcouronnes, France;
| | - Guy Hervé
- Laboratoire BIOSIPE, Institut de biologie Paris-Seine, Sorbonne Université, 7 quai Saint-Bernard, 75005 Paris, France;
| | - Jacques Vergne
- Institut de Systématique, Evolution, Biodiversité, (ISYEB), Sorbonne Université, Museum National d’Histoire Naturelle, CNRS, EPHE, F 75005 Paris, France;
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, (ISYEB), Sorbonne Université, Museum National d’Histoire Naturelle, CNRS, EPHE, F 75005 Paris, France;
| |
Collapse
|
3
|
Moreno M, Vázquez L, López-Carrasco A, Martín-Gago J, Flores R, Briones C. Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy. RNA Biol 2019; 16:295-308. [PMID: 30734641 PMCID: PMC6380281 DOI: 10.1080/15476286.2019.1572436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 11/01/2022] Open
Abstract
Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.
Collapse
Affiliation(s)
- M. Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - L. Vázquez
- Departamento de Superficies y Recubrimientos, Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid, Spain
| | - A. López-Carrasco
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - J.A. Martín-Gago
- Departamento de Superficies y Recubrimientos, Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid, Spain
| | - R. Flores
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - C. Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
| |
Collapse
|
4
|
Kruglik SG, Royo F, Guigner JM, Palomo L, Seksek O, Turpin PY, Tatischeff I, Falcón-Pérez JM. Raman tweezers microspectroscopy of circa 100 nm extracellular vesicles. NANOSCALE 2019; 11:1661-1679. [PMID: 30620023 DOI: 10.1039/c8nr04677h] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The technique of Raman tweezers microspectroscopy (RTM) for the global biomolecular content characterization of a single extracellular vesicle (EV) or a small number of EVs or other nanoscale bioparticles in an aqueous dispersion in the difficult-to-access size range of near 100 nm is described in detail. The particularities and potential of RTM are demonstrated using the examples of DOPC liposomes, exosomes from human urine and rat hepatocytes, and a mixed sample of the transfection reagent FuGENE in diluted DNA solution. The approach of biomolecular component analysis for the estimation of the main biomolecular contributions (proteins, lipids, nucleic acids, carotenoids, etc.) is proposed and discussed. Direct Raman evidence for strong intra-sample biomolecular heterogeneity of individual optically trapped EVs, due to variable contributions from nucleic acids and carotenoids in some preparations, is reported. On the basis of the results obtained, we are making an attempt to convince the scientific community that RTM is a promising method of single-EV research; to our knowledge, it is the only technique available at the moment that provides unique information about the global biomolecular composition of a single vesicle or a small number of vesicles, thus being capable of unravelling the high diversity of EV subpopulations, which is one of the most significant urgent challenges to overcome. Possible RTM applications include, among others, searching for DNA biomarkers, cancer diagnosis, and discrimination between different subpopulations of EVs, lipid bodies, protein aggregates and viruses.
Collapse
Affiliation(s)
- Sergei G Kruglik
- Laboratoire Jean Perrin, Sorbonne Université, CNRS UMR 8237, 4 place Jussieu, Paris, 75005, France.
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Gontran E, Juchaux M, Deroulers C, Kruglik S, Huang N, Badoual M, Seksek O. Assessment of the ability of poly(l-lysine)-poly(ethylene glycol) (PLL-PEG) hydrogels to support the growth of U87-MG and F98 glioma tumor cells. J Appl Polym Sci 2018. [DOI: 10.1002/app.46287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Emilie Gontran
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS UMR 8165, Univ Paris-Sud; Univ Paris Diderot; Orsay 91405 France
| | - Marjorie Juchaux
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS UMR 8165, Univ Paris-Sud; Univ Paris Diderot; Orsay 91405 France
| | - Christophe Deroulers
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS UMR 8165, Univ Paris-Sud; Univ Paris Diderot; Orsay 91405 France
| | - Sergei Kruglik
- Laboratoire Jean Perrin, Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 8237; Paris 75005 France
| | - Nicolas Huang
- Institut Galien Paris-Sud, CNRS UMR 8612, Univ Paris-Sud; Université Paris-Saclay, Faculté de Pharmacie, 5 rue J.B. Clément; Châtenay-Malabry 92296 France
| | - Mathilde Badoual
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS UMR 8165, Univ Paris-Sud; Univ Paris Diderot; Orsay 91405 France
| | - Olivier Seksek
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS UMR 8165, Univ Paris-Sud; Univ Paris Diderot; Orsay 91405 France
| |
Collapse
|
6
|
López-Carrasco A, Flores R. The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins. J Gen Virol 2017; 98:1913-1922. [PMID: 28699864 DOI: 10.1099/jgv.0.000846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.
Collapse
Affiliation(s)
- Amparo López-Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| |
Collapse
|
7
|
Kruglik SG, Yoo BK, Lambry JC, Martin JL, Negrerie M. Structural changes and picosecond to second dynamics of cytochrome c in interaction with nitric oxide in ferrous and ferric redox states. Phys Chem Chem Phys 2017; 19:21317-21334. [DOI: 10.1039/c7cp02634j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
After dissociation NO rebinds to Cyt c in 10 ps whereas Met80 rebinds in 5 μs after NO release from Cyt c. A complete view of heme – NO dynamics within 12 orders of magnitude of time in Cyt c is presented.
Collapse
Affiliation(s)
- Sergei G. Kruglik
- Laboratoire Jean Perrin
- Sorbonne Universités
- UPMC Univ. Paris 06
- CNRS
- 75005 Paris
| | - Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | | | - Jean-Louis Martin
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| |
Collapse
|
8
|
Leclerc F, Zaccai G, Vergne J, Řìhovà M, Martel A, Maurel MC. Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study. Sci Rep 2016; 6:30287. [PMID: 27456224 PMCID: PMC4960562 DOI: 10.1038/srep30287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 01/16/2023] Open
Abstract
In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.
Collapse
Affiliation(s)
- Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), Dept. of Genome Biology, CEA, CNRS, Université Paris Sud, Gif-sur-Yvette, F-91198, France
| | - Giuseppe Zaccai
- Institut Laue Langevin, Grenoble, F-38042, France.,Institut de Biologie Structurale (IBS), CNRS, Grenoble, F-38044, France.,IBS, CEA, Grenoble, F-38044, France.,IBS, Univ Grenoble Alpes, Grenoble, F-38044, France
| | - Jacques Vergne
- Institut de Systématique, Evolution, Biodiversité ISyEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50 Paris, F-75005, France
| | - Martina Řìhovà
- Institut de Systématique, Evolution, Biodiversité ISyEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50 Paris, F-75005, France.,Institute of Physics, Charles University, Faculty of Mathematics and Physics, Prague 2, CZ-121 16, Czech Republic
| | - Anne Martel
- Institut Laue Langevin, Grenoble, F-38042, France
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité ISyEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50 Paris, F-75005, France
| |
Collapse
|
9
|
Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Res 2015; 209:136-45. [PMID: 25738582 DOI: 10.1016/j.virusres.2015.02.027] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 12/31/2022]
Abstract
The discovery of viroids about 45 years ago heralded a revolution in Biology: small RNAs comprising around 350 nt were found to be able to replicate autonomously-and to incite diseases in certain plants-without encoding proteins, fundamental properties discriminating these infectious agents from viruses. The initial focus on the pathological effects usually accompanying infection by viroids soon shifted to their molecular features-they are circular molecules that fold upon themselves adopting compact secondary conformations-and then to how they manipulate their hosts to be propagated. Replication of viroids-in the nucleus or chloroplasts through a rolling-circle mechanism involving polymerization, cleavage and circularization of RNA strands-dealt three surprises: (i) certain RNA polymerases are redirected to accept RNA instead of their DNA templates, (ii) cleavage in chloroplastic viroids is not mediated by host enzymes but by hammerhead ribozymes, and (iii) circularization in nuclear viroids is catalyzed by a DNA ligase redirected to act upon RNA substrates. These enzymes (and ribozymes) are most probably assisted by host proteins, including transcription factors and RNA chaperones. Movement of viroids, first intracellularly and then to adjacent cells and distal plant parts, has turned out to be a tightly regulated process in which specific RNA structural motifs play a crucial role. More recently, the advent of RNA silencing has brought new views on how viroids may cause disease and on how their hosts react to contain the infection; additionally, viroid infection may be restricted by other mechanisms. Representing the lowest step on the biological size scale, viroids have also attracted considerable interest to get a tentative picture of the essential characteristics of the primitive replicons that populated the postulated RNA world.
Collapse
|