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Park SM, Yoon DK. Evaporation-induced self-assembly of liquid crystal biopolymers. MATERIALS HORIZONS 2024; 11:1843-1866. [PMID: 38375871 DOI: 10.1039/d3mh01585h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Evaporation-induced self-assembly (EISA) is a process that has gained significant attention in recent years due to its fundamental science and potential applications in materials science and nanotechnology. This technique involves controlled drying of a solution or dispersion of materials, forming structures with specific shapes and sizes. In particular, liquid crystal (LC) biopolymers have emerged as promising candidates for EISA due to their highly ordered structures and biocompatible properties after deposition. This review provides an overview of recent progress in the EISA of LC biopolymers, including DNA, nanocellulose, viruses, and other biopolymers. The underlying self-assembly mechanisms, the effects of different processing conditions, and the potential applications of the resulting structures are discussed.
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Affiliation(s)
- Soon Mo Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Department of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Dong Ki Yoon
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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2
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Kosmachevskaya OV, Novikova NN, Yakunin SN, Topunov AF. Formation of Supplementary Metal-Binding Centers in Proteins under Stress Conditions. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S180-S204. [PMID: 38621750 DOI: 10.1134/s0006297924140104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/21/2023] [Accepted: 10/29/2023] [Indexed: 04/17/2024]
Abstract
In many proteins, supplementary metal-binding centers appear under stress conditions. They are known as aberrant or atypical sites. Physico-chemical properties of proteins are significantly changed after such metal binding, and very stable protein aggregates are formed, in which metals act as "cross-linking" agents. Supplementary metal-binding centers in proteins often arise as a result of posttranslational modifications caused by reactive oxygen and nitrogen species and reactive carbonyl compounds. New chemical groups formed as a result of these modifications can act as ligands for binding metal ions. Special attention is paid to the role of cysteine SH-groups in the formation of supplementary metal-binding centers, since these groups are the main target for the action of reactive species. Supplementary metal binding centers may also appear due to unmasking of amino acid residues when protein conformation changing. Appearance of such centers is usually considered as a pathological process. Such unilateral approach does not allow to obtain an integral view of the phenomenon, ignoring cases when formation of metal complexes with altered proteins is a way to adjust protein properties, activity, and stability under the changed redox conditions. The role of metals in protein aggregation is being studied actively, since it leads to formation of non-membranous organelles, liquid condensates, and solid conglomerates. Some proteins found in such aggregates are typical for various diseases, such as Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and some types of cancer.
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Affiliation(s)
- Olga V Kosmachevskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | | | - Sergey N Yakunin
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Alexey F Topunov
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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3
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Romero-Romero ML, Garcia-Seisdedos H. Agglomeration: when folded proteins clump together. Biophys Rev 2023; 15:1987-2003. [PMID: 38192350 PMCID: PMC10771401 DOI: 10.1007/s12551-023-01172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 01/10/2024] Open
Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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4
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Krupyanskii YF. Determination of DNA architecture of bacteria under various types of stress, methodological approaches, problems, and solutions. Biophys Rev 2023; 15:1035-1051. [PMID: 37974993 PMCID: PMC10643406 DOI: 10.1007/s12551-023-01122-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023] Open
Abstract
Actively growing cells maintain a dynamic, far from equilibrium order through metabolism. Under starvation stress or under stress of exposure to the analog of the anabiosis autoinducer (4-hexylresorcinol), cells go into a dormant state (almost complete lack of metabolism) or even into a mummified state. In a dormant state, cells are forced to use the physical mechanisms of DNA protection. The architecture of DNA in the dormant and mummified state of cells was studied by x-ray diffraction of synchrotron radiation and transmission electron microscopy (TEM). Diffraction experiments indicate the appearance of an ordered organization of DNA. TEM made it possible to visualize the type of DNA ordering. Intracellular nanocrystalline, liquid-crystalline, and folded nucleosome-like structures of DNA have been found. The structure of DNA within a cell in an anabiotic dormant state and dormant state (starvation stress) coincides (forms nanocrystalline structures). Data suggest the universality of DNA condensation by a protein Dps for a dormant state, regardless of the type of stress. The mummified state is very different in structure from the dormant state (has no ordering within a cell). It turned out that it is possible to visualize DNA conformation in toroidal and liquid crystal structures in which there is either no or a very small amount of the Dps protein. Observation of the DNA conformation in nanocrystals and folded nucleosome-like structures so far has been inconclusive. The methodological advances described will facilitate high-resolution visualization of the DNA conformation in the near future.
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Affiliation(s)
- Yu. F. Krupyanskii
- N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Department of Structure of Matter, 119991, Kosygina 4, Moscow, Russia
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Loiko N, Tereshkina K, Kovalenko V, Moiseenko A, Tereshkin E, Sokolova OS, Krupyanskii Y. DNA-Binding Protein Dps Protects Escherichia coli Cells against Multiple Stresses during Desiccation. BIOLOGY 2023; 12:853. [PMID: 37372138 DOI: 10.3390/biology12060853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Gradual dehydration is one of the frequent lethal yet poorly understood stresses that bacterial cells constantly face in the environment when their micro ecotopes dry out, as well as in industrial processes. Bacteria successfully survive extreme desiccation through complex rearrangements at the structural, physiological, and molecular levels, in which proteins are involved. The DNA-binding protein Dps has previously been shown to protect bacterial cells from many adverse effects. In our work, using engineered genetic models of E. coli to produce bacterial cells with overproduction of Dps protein, the protective function of Dps protein under multiple desiccation stresses was demonstrated for the first time. It was shown that the titer of viable cells after rehydration in the experimental variants with Dps protein overexpression was 1.5-8.5 times higher. Scanning electron microscopy was used to show a change in cell morphology upon rehydration. It was also proved that immobilization in the extracellular matrix, which is greater when the Dps protein is overexpressed, helps the cells survive. Transmission electron microscopy revealed disruption of the crystal structure of DNA-Dps crystals in E. coli cells that underwent desiccation stress and subsequent watering. Coarse-grained molecular dynamics simulations showed the protective function of Dps in DNA-Dps co-crystals during desiccation. The data obtained are important for improving biotechnological processes in which bacterial cells undergo desiccation.
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Affiliation(s)
- Nataliya Loiko
- Winogradsky Institute of Microbiology, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ksenia Tereshkina
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Kovalenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrey Moiseenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Eduard Tereshkin
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yurii Krupyanskii
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
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6
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Tereshkin EV, Loiko NG, Tereshkina KB, Kovalenko VV, Krupyanskii YF. Possible Mechanisms of 4-Hexylresorcinol Influence on DNA and DNA–Dps Nanocrystals Affecting Stress Sustainability of Escherichia coli. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793122040285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Krupyanskii YF, Kovalenko VV, Loiko NG, Generalova AA, Moiseenko AV, Tereshkin EV, Sokolova OS, Tereshkina KB, El’-Registan GI, Popov AN. Architecture of Condensed DNA in the Nucleoid of Escherichia coli Bacterium. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922040133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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8
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Houston JE, Fruhner L, de la Cotte A, Rojo González J, Petrunin AV, Gasser U, Schweins R, Allgaier J, Richtering W, Fernandez-Nieves A, Scotti A. Resolving the different bulk moduli within individual soft nanogels using small-angle neutron scattering. SCIENCE ADVANCES 2022; 8:eabn6129. [PMID: 35776796 PMCID: PMC10883365 DOI: 10.1126/sciadv.abn6129] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The bulk modulus, K, quantifies the elastic response of an object to an isotropic compression. For soft compressible colloids, knowing K is essential to accurately predict the suspension response to crowding. Most colloids have complex architectures characterized by different softness, which additionally depends on compression. Here, we determine the different values of K for the various morphological parts of individual nanogels and probe the changes of K with compression. Our method uses a partially deuterated polymer, which exerts the required isotropic stress, and small-angle neutron scattering with contrast matching to determine the form factor of the particles without any scattering contribution from the polymer. We show a clear difference in softness, compressibility, and evolution of K between the shell of the nanogel and the rest of the particle, depending on the amount of cross-linker used in their synthesis.
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Affiliation(s)
| | - Lisa Fruhner
- Forschungszentrum Jülich GmbH Jülich Centre for Neutron Science (JCNS-1) and Institute for Biological Information Processing (IBI-8), 52425 Jülich, Germany
| | - Alexis de la Cotte
- Department of Condensed Matter Physics, University of Barcelona, 08028 Barcelona, Spain
| | - Javier Rojo González
- Department of Condensed Matter Physics, University of Barcelona, 08028 Barcelona, Spain
| | | | - Urs Gasser
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Ralf Schweins
- Institut Laue-Langevin ILL DS/LSS, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Jürgen Allgaier
- Forschungszentrum Jülich GmbH Jülich Centre for Neutron Science (JCNS-1) and Institute for Biological Information Processing (IBI-8), 52425 Jülich, Germany
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany
- JARA-SOFT, 52056 Aachen, Germany
| | - Alberto Fernandez-Nieves
- Department of Condensed Matter Physics, University of Barcelona, 08028 Barcelona, Spain
- ICREA-Institucio Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain
| | - Andrea Scotti
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany
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Abstract
The DNA-binding protein from starved cells, Dps, is a universally conserved prokaryotic ferritin that, in many species, also binds DNA. Dps homologs have been identified in the vast majority of bacterial species and several archaea. Dps also may play a role in the global regulation of gene expression, likely through chromatin reorganization. Dps has been shown to use both its ferritin and DNA-binding functions to respond to a variety of environmental pressures, including oxidative stress. One mechanism that allows Dps to achieve this is through a global nucleoid restructuring event during stationary phase, resulting in a compact, hexacrystalline nucleoprotein complex called the biocrystal that occludes damaging agents from DNA. Due to its small size, hollow spherical structure, and high stability, Dps is being developed for applications in biotechnology.
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Small Prokaryotic DNA-Binding Proteins Protect Genome Integrity throughout the Life Cycle. Int J Mol Sci 2022; 23:ijms23074008. [PMID: 35409369 PMCID: PMC8999374 DOI: 10.3390/ijms23074008] [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: 03/03/2022] [Revised: 03/27/2022] [Accepted: 04/01/2022] [Indexed: 12/17/2022] Open
Abstract
Genomes of all organisms are persistently threatened by endogenous and exogenous assaults. Bacterial mechanisms of genome maintenance must provide protection throughout the physiologically distinct phases of the life cycle. Spore-forming bacteria must also maintain genome integrity within the dormant endospore. The nucleoid-associated proteins (NAPs) influence nucleoid organization and may alter DNA topology to protect DNA or to alter gene expression patterns. NAPs are characteristically multifunctional; nevertheless, Dps, HU and CbpA are most strongly associated with DNA protection. Archaea display great variety in genome organization and many inhabit extreme environments. As of yet, only MC1, an archaeal NAP, has been shown to protect DNA against thermal denaturation and radiolysis. ssDNA are intermediates in vital cellular processes, such as DNA replication and recombination. Single-stranded binding proteins (SSBs) prevent the formation of secondary structures but also protect the hypersensitive ssDNA against chemical and nuclease degradation. Ionizing radiation upregulates SSBs in the extremophile Deinococcus radiodurans.
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11
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Taketomi Y, Yamaguchi Y, Sakurai S, Tanaka M. Evaluation of DNA-mediated electron transfer using a hole-trapping nucleobase under crowded conditions. Org Biomol Chem 2022; 20:2043-2047. [PMID: 35005766 DOI: 10.1039/d1ob01669e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of a crowded environment on DNA-mediated electron transfer were evaluated using a pyrene-modified oligonucleotide containing a hole-trapping nucleobase in poly(ethylene glycol) mixed solutions. Rapid decompositions of hole-trapping bases in condensed and noncondensed DNA showed that more efficient electron transfer occurred under crowded conditions than in dilute solutions.
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Affiliation(s)
- Yuuki Taketomi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Yuuki Yamaguchi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Shunsuke Sakurai
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Makiko Tanaka
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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12
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Suzina NE, Sorokin VV, Polivtseva VN, Klyueva VV, Emelyanova EV, Solyanikova IP. From Rest to Growth: Life Collisions of Gordonia polyisoprenivorans 135. Microorganisms 2022; 10:465. [PMID: 35208919 PMCID: PMC8879720 DOI: 10.3390/microorganisms10020465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
In the process of evolution, living organisms develop mechanisms for population preservation to survive in unfavorable conditions. Spores and cysts are the most obvious examples of dormant forms in microorganisms. Non-spore-forming bacteria are also capable of surviving in unfavorable conditions, but the patterns of their behavior and adaptive reactions have been studied in less detail compared to spore-forming organisms. The purpose of this work was to study the features of transition from dormancy to active vegetative growth in one of the non-spore-forming bacteria, Gordonia polisoprenivorans 135, which is known as a destructor of such aromatic compounds as benzoate, 3-chlorobenzoate, and phenol. It was shown that G. polyisoprenivorans 135 under unfavorable conditions forms cyst-like cells with increased thermal resistance. Storage for two years does not lead to complete cell death. When the cells were transferred to fresh nutrient medium, visible growth was observed after 3 h. Immobilized cells stored at 4 °C for at least 10 months regenerated their metabolic activity after only 30 min of aeration. A study of the ultrathin organization of resting cells by transmission electron microscopy combined with X-ray microanalysis revealed intracytoplasmic electron-dense spherical membrane ultrastructures with significant similarity to previously described acidocalcisomas. The ability of some resting G. polyisoprenivorans 135 cells in the population to secrete acidocalcisome-like ultrastructures into the extracellular space was also detected. These structures contain predominantly calcium (Ca) and, to a lesser extent, phosphorus (P), and are likely to serve as depots of vital macronutrients to maintain cell viability during resting and provide a quick transition to a metabolically active state under favorable conditions. The study revealed the features of transitions from active growth to dormant state and vice versa of non-spore-forming bacteria G. polyisoprenivorans 135 and the possibility to use them as the basis of biopreparations with a long shelf life.
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Affiliation(s)
- Nataliya E. Suzina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (N.E.S.); (V.N.P.); (E.V.E.)
| | - Vladimir V. Sorokin
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 117312 Moscow, Russia;
| | - Valentina N. Polivtseva
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (N.E.S.); (V.N.P.); (E.V.E.)
| | - Violetta V. Klyueva
- Institute of Pharmacy, Chemistry and Biology, Regional Microbiological Center, Department of Biotechnology and Microbiology, Belgorod National Research University, 308015 Belgorod, Russia;
| | - Elena V. Emelyanova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (N.E.S.); (V.N.P.); (E.V.E.)
| | - Inna P. Solyanikova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia; (N.E.S.); (V.N.P.); (E.V.E.)
- Institute of Pharmacy, Chemistry and Biology, Regional Microbiological Center, Department of Biotechnology and Microbiology, Belgorod National Research University, 308015 Belgorod, Russia;
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13
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Tereshkin EV, Loiko NG, Tereshkina KB, Krupyanskii YF. Migration of 4-Hexylresorcinol Through Escherichia coli Cell Membranes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793121060099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Moiseenko A, Loiko N, Sokolova OS, Krupyanskii YF. Application of Special Electron Microscopy Techniques to the Study of DNA - Protein Complexes in E. coli Cells. Methods Mol Biol 2022; 2516:143-156. [PMID: 35922626 DOI: 10.1007/978-1-0716-2413-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Various electron microscopy techniques were applied recently to the study of DNA condensation in dormant bacterial cells. Here, we describe, in detail, the preparation of dormant Escherichia coli cells for electron microscopy studies and electron tomography and energy dispersive spectroscopy (EDS) approaches, which were used to reveal the structures of DNA-protein complexes in dormant Escherichia coli cells.
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Affiliation(s)
- Andrey Moiseenko
- Department of Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Structure of Matter, Semenov Federal Research Center of Chemical Physics, RAS, Moscow, Russia
| | - Nataliya Loiko
- Department of Microbiology, Federal Research Center 'Fundamentals of Biotechnology' RAS, Moscow, Russia
| | - Olga S Sokolova
- Department of Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Yurii F Krupyanskii
- Department of Structure of Matter, Semenov Federal Research Center of Chemical Physics, RAS, Moscow, Russia.
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15
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Nishikawa H, Araoka F. A New Class of Chiral Nematic Phase with Helical Polar Order. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101305. [PMID: 34278630 DOI: 10.1002/adma.202101305] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/25/2021] [Indexed: 06/13/2023]
Abstract
A novel chiral nematic phase with a polar helical order is realized via the introduction of helical twisting power into a polar nematogen. The properties of the induced polar nematic (polar cholesteric: Np*) phase differ from those of the conventional cholesteric (N*) phases existing thus far. Np*, which is a new class of N* structures, is characterized not only by its helically twisted nematic director, but also by a continuously twisted polarization. Transmission spectroscopy and helical pitch measurements in a wedge cell revealed that the half-helical pitch in the Np* phase vanished because of the polar response in the Np* helix. The inner polar director in the Np* phase is confirmed in dielectric and second-harmonic-generation studies. Furthermore, this unique Np*LC, which corresponds to a half-/full-pitch helix, enables ultrafast electro-optic switching (τ < 20 µs), and proposes new potential applications for electrically interchangeable photonic bandgaps.
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Affiliation(s)
- Hiroya Nishikawa
- RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Fumito Araoka
- RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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16
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Bergkessel M. Bacterial transcription during growth arrest. Transcription 2021; 12:232-249. [PMID: 34486930 PMCID: PMC8632087 DOI: 10.1080/21541264.2021.1968761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/12/2022] Open
Abstract
Bacteria in most natural environments spend substantial periods of time limited for essential nutrients and not actively dividing. While transcriptional activity under these conditions is substantially reduced compared to that occurring during active growth, observations from diverse organisms and experimental approaches have shown that new transcription still occurs and is important for survival. Much of our understanding of transcription regulation has come from measuring transcripts in exponentially growing cells, or from in vitro experiments focused on transcription from highly active promoters by the housekeeping RNA polymerase holoenzyme. The fact that transcription during growth arrest occurs at low levels and is highly heterogeneous has posed challenges for its study. However, new methods of measuring low levels of gene expression activity, even in single cells, offer exciting opportunities for directly investigating transcriptional activity and its regulation during growth arrest. Furthermore, much of the rich structural and biochemical data from decades of work on the bacterial transcriptional machinery is also relevant to growth arrest. In this review, the physiological changes likely affecting transcription during growth arrest are first considered. Next, possible adaptations to help facilitate ongoing transcription during growth arrest are discussed. Finally, new insights from several recently published datasets investigating mRNA transcripts in single bacterial cells at various growth phases will be explored. Keywords: Growth arrest, stationary phase, RNA polymerase, nucleoid condensation, population heterogeneity.
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17
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Zaveri A, Bose A, Sharma S, Rajendran A, Biswas P, Shenoy AR, Visweswariah SS. Mycobacterial STAND adenylyl cyclases: The HTH domain binds DNA to form biocrystallized nucleoids. Biophys J 2021; 120:1231-1246. [PMID: 33217386 PMCID: PMC8059089 DOI: 10.1016/j.bpj.2020.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023] Open
Abstract
Mycobacteria harbor a unique class of adenylyl cyclases with a complex domain organization consisting of an N-terminal putative adenylyl cyclase domain fused to a nucleotide-binding adaptor shared by apoptotic protease-activating factor-1, plant resistance proteins, and CED-4 (NB-ARC) domain, a tetratricopeptide repeat (TPR) domain, and a C-terminal helix-turn-helix (HTH) domain. The products of the rv0891c-rv0890c genes represent a split gene pair, where Rv0891c has sequence similarity to adenylyl cyclases, and Rv0890c harbors the NB-ARC-TPR-HTH domains. Rv0891c had very low adenylyl cyclase activity so it could represent a pseudoenzyme. By analyzing the genomic locus, we could express and purify Rv0890c and find that the NB-ARC domain binds ATP and ADP, but does not hydrolyze these nucleotides. Using systematic evolution of ligands by exponential enrichment (SELEX), we identified DNA sequences that bound to the HTH domain of Rv0890c. Uniquely, the HTH domain could also bind RNA. Atomic force microscopy revealed that binding of Rv0890c to DNA was sequence independent, and binding of adenine nucleotides to the protein induced the formation of higher order structures that may represent biocrystalline nucleoids. This represents the first characterization of this group of proteins and their unusual biochemical properties warrant further studies into their physiological roles in future.
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Affiliation(s)
- Anisha Zaveri
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Avipsa Bose
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Suruchi Sharma
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Abinaya Rajendran
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Priyanka Biswas
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Avinash R Shenoy
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India.
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18
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Dubrovin EV, Dadinova LA, Petoukhov MV, Soshinskaya EY, Mozhaev AA, Klinov DV, Schäffer TE, Shtykova EV, Batishchev OV. Spatial organization of Dps and DNA-Dps complexes. J Mol Biol 2021; 433:166930. [PMID: 33713674 DOI: 10.1016/j.jmb.2021.166930] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 02/04/2023]
Abstract
DNA co-crystallization with Dps family proteins is a fundamental mechanism, which preserves DNA in bacteria from harsh conditions. Though many aspects of this phenomenon are well characterized, the spatial organization of DNA in DNA-Dps co-crystals is not completely understood, and existing models need further clarification. To advance in this problem we have utilized atomic force microscopy (AFM) as the main structural tool, and small-angle X-scattering (SAXS) to characterize Dps as a key component of the DNA-protein complex. SAXS analysis in the presence of EDTA indicates a significantly larger radius of gyration for Dps than would be expected for the core of the dodecamer, consistent with the N-terminal regions extending out into solution and being accessible for interaction with DNA. In AFM experiments, both Dps protein molecules and DNA-Dps complexes adsorbed on mica or highly oriented pyrolytic graphite (HOPG) surfaces form densely packed hexagonal structures with a characteristic size of about 9 nm. To shed light on the peculiarities of DNA interaction with Dps molecules, we have characterized individual DNA-Dps complexes. Contour length evaluation has confirmed the non-specific character of Dps binding with DNA and revealed that DNA does not wrap Dps molecules in DNA-Dps complexes. Angle analysis has demonstrated that in DNA-Dps complexes a Dps molecule contacts with a DNA segment of ~6 nm in length. Consideration of DNA condensation upon complex formation with small Dps quasi-crystals indicates that DNA may be arranged along the rows of ordered protein molecules on a Dps sheet.
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Affiliation(s)
- Evgeniy V Dubrovin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia; Lomonosov Moscow State University, Faculty of Physics, Leninskie Gory 1 bld 2, 119991 Moscow, Russia.
| | - Liubov A Dadinova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Ekaterina Yu Soshinskaya
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
| | - Tilman E Schäffer
- University of Tübingen, Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Oleg V Batishchev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia
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19
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Krupyanskii YF. Architecture of Nucleoid in the Dormant Cells of Escherichia coli. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2021. [DOI: 10.1134/s199079312102007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Pathological ATX3 Expression Induces Cell Perturbations in E. coli as Revealed by Biochemical and Biophysical Investigations. Int J Mol Sci 2021; 22:ijms22020943. [PMID: 33477953 PMCID: PMC7835732 DOI: 10.3390/ijms22020943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 02/06/2023] Open
Abstract
Amyloid aggregation of human ataxin-3 (ATX3) is responsible for spinocerebellar ataxia type 3, which belongs to the class of polyglutamine neurodegenerative disorders. It is widely accepted that the formation of toxic oligomeric species is primarily involved in the onset of the disease. For this reason, to understand the mechanisms underlying toxicity, we expressed both a physiological (ATX3-Q24) and a pathological ATX3 variant (ATX3-Q55) in a simplified cellular model, Escherichia coli. It has been observed that ATX3-Q55 expression induces a higher reduction of the cell growth compared to ATX3-Q24, due to the bacteriostatic effect of the toxic oligomeric species. Furthermore, the Fourier transform infrared microspectroscopy investigation, supported by multivariate analysis, made it possible to monitor protein aggregation and the induced cell perturbations in intact cells. In particular, it has been found that the toxic oligomeric species associated with the expression of ATX3-Q55 are responsible for the main spectral changes, ascribable mainly to the cell envelope modifications. A structural alteration of the membrane detected through electron microscopy analysis in the strain expressing the pathological form supports the spectroscopic results.
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Garcia-Seisdedos H, Heidenreich M, Levy ED. Not Going with the Flow: How Cells Adapt Internal Physics. Cell 2020; 183:1462-1463. [PMID: 33306951 DOI: 10.1016/j.cell.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Defining the principles underlying the organization of biomolecules within cells is a key challenge of current cell biology research. Persson et al. now identify a powerful layer of regulation that allows cells to decouple diffusion from temperature by modulating their intracellular viscosity. This so-called viscoadaptation is mediated through trehalose and glycogen activities, which alter diffusion dynamics and self-assembly propensity inside the cell globally.
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Affiliation(s)
| | - Meta Heidenreich
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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22
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Maturation of Pseudo-Nucleus Compartment in P. aeruginosa, Infected with Giant phiKZ Phage. Viruses 2020; 12:v12101197. [PMID: 33096802 PMCID: PMC7589130 DOI: 10.3390/v12101197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022] Open
Abstract
The giant phiKZ phage infection induces the appearance of a pseudo-nucleus inside the bacterial cytoplasm. Here, we used RT-PCR, fluorescent in situ hybridization (FISH), electron tomography, and analytical electron microscopy to study the morphology of this unique nucleus-like shell and to demonstrate the distribution of phiKZ and bacterial DNA in infected Pseudomonas aeruginosa cells. The maturation of the pseudo-nucleus was traced in short intervals for 40 min after infection and revealed the continuous spatial separation of the phage and host DNA. Immediately after ejection, phage DNA was located inside the newly-identified round compartments; at a later infection stage, it was replicated inside the pseudo-nucleus; in the mature pseudo-nucleus, a saturated internal network of filaments was observed. This network consisted of DNA bundles in complex with DNA-binding proteins. On the other hand, the bacterial nucleoid underwent significant rearrangements during phage infection, yet the host DNA did not completely degrade until at least 40 min after phage application. Energy dispersive x-ray spectroscopy (EDX) analysis revealed that, during the infection, the sulfur content in the bacterial cytoplasm increased, which suggests an increase of methionine-rich DNA-binding protein synthesis, whose role is to protect the bacterial DNA from stress caused by infection.
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23
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Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells. PLoS One 2020; 15:e0231562. [PMID: 33006967 PMCID: PMC7531825 DOI: 10.1371/journal.pone.0231562] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/15/2020] [Indexed: 11/28/2022] Open
Abstract
One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline, liquid crystalline, and the folded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of the Dps protein is tightly bound to nucleoid DNA. The dps-null cells contained only one type of condensed DNA structure, liquid crystalline, thus, differing from those with Dps. The results obtained here shed some light on the phenomenon of DNA condensation in dormant prokaryotic cells and on the general problem of developing a response to stress. We demonstrated that the population of dormant cells is structurally heterogeneous, allowing them to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.
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24
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Sakurai S, Jo K, Kinoshita H, Esumi M, Tanaka M. Guanine damage by singlet oxygen from SYBR Green I in liquid crystalline DNA. Org Biomol Chem 2020; 18:7183-7187. [PMID: 32897281 DOI: 10.1039/d0ob01723j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
It is known that double-stranded DNA (dsDNA) turns into a liquid crystalline phase by the addition of a high concentration of polymer with salt. SYBR Green I (SG) is a well-known sensitive fluorescent stain for dsDNA, and is intercalated in liquid crystalline DNA. Formation of the liquid crystalline dsDNA-SG complex has been confirmed by CD spectral measurements, fluorescence spectral measurements and confocal fluorescence microscopy. SG in dsDNA was also used as a singlet oxygen generator. We conducted photoirradiation experiments using three kinds of 42-mer oligonucleotides with SG. The amount of guanine decomposition by selective irradiation of SG was analyzed using HPLC after digestion of dsDNA in each sample solution. We found that singlet oxygen produced in liquid crystalline DNA promoted guanine damage much more efficiently than in homogeneous solution.
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Affiliation(s)
- Shunsuke Sakurai
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Kento Jo
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Hikari Kinoshita
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Mayu Esumi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Makiko Tanaka
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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Chuev MA, Prutskov GV, Novikova NN, Pashaev EM, Konovalov OV, Stepina ND, Rogachev AV, Yakunin SN. Theoretical Approach to Analysis of X-Ray Grazing-Incidence Diffraction from 2D Crystals. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520050041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Liang Q, Jiang Y, Chen JZY. Orientationally ordered states of a wormlike chain in spherical confinement. Phys Rev E 2019; 100:032502. [PMID: 31640076 DOI: 10.1103/physreve.100.032502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Indexed: 06/10/2023]
Abstract
One of the basic characteristics of a linear dsDNA molecule is its persistence length, typically of order 50 nm. The DNA chain inflicts a large energy penalty if it is bent sharply at that length scale. Viruses of bacteria, known as bacteriophages, typically have a dimension of a few tens of nanometers. Yet, it is known that a bacteriophage actively packages viral DNA inside the capsid and ejects it afterwards. Here, adopting a commonly used polymer model known as the wormlike chain, we answer an idealized question: Placing a linear DNA molecule inside a spherical cavity, what ordered states can we derive from known tools in statistical physics? Solving the model in a rigorous field-theory framework, we report a universal phase diagram for four orientationally ordered and disordered states, in terms of two relevant physical parameters.
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Affiliation(s)
- Qin Liang
- Faculty of Mathematics and Computational Science, Xiangtan University, Xiangtan, Hunan 411105, China
- School of Chemistry, Beihang University, Beijing 100191, China
| | - Ying Jiang
- School of Chemistry, Beihang University, Beijing 100191, China
| | - Jeff Z Y Chen
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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27
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Tereshkin EV, Tereshkina KB, Kovalenko VV, Loiko NG, Krupyanskii YF. Structure of DPS Protein Complexes with DNA. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2019. [DOI: 10.1134/s199079311905021x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Projection structures reveal the position of the DNA within DNA-Dps Co-crystals. Biochem Biophys Res Commun 2019; 517:463-469. [DOI: 10.1016/j.bbrc.2019.07.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 07/26/2019] [Indexed: 01/30/2023]
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29
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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30
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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31
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Tereshkin E, Tereshkina K, Loiko N, Chulichkov A, Kovalenko V, Krupyanskii Y. Interaction of deoxyribonucleic acid with deoxyribonucleic acid-binding protein from starved cells: cluster formation and crystal growing as a model of initial stages of nucleoid biocrystallization. J Biomol Struct Dyn 2018; 37:2600-2607. [PMID: 30033848 DOI: 10.1080/07391102.2018.1492458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The paper represents the study of interaction between deoxyribonucleic acid (DNA) and deoxyribonucleic acid-binding protein from starved cells (DPS) cluster formation and crystal growing within a cell. This study is a part of the project that includes European Synchrotron Radiation Facility (ESRF) investigations of in vivo and in vitro nanocrystallization processes of Escherichia coli (E. coli) nucleoid under stress condition combined with theoretical molecular dynamics approaches. Nucleoid biocrystallization is an adaptive mechanism of bacterial cells under stress. It is poorly understood at the present time. Understanding crystal formation process is a very important for molecular biology, pharmacology and other areas. In the simulation part the coarse-grained modeling of various combinations of the following molecules was used: DPS proteins (from 1 to 108 DPS dodecamers in simulation box), short DNA fragments with a length of 24 base pairs (b.p., from 1 to 100 DNA fragments in simulation box) and a part of pBluescript SK(+) plasmide with a length of 161 b.p., in the presence of ions. We defined structural, energetic and dynamic properties of DPS-DPS and DPS-DNA complexes in clusters and crystals that allow us to predict crystal formation and the structure of these crystals in experimental systems. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Eduard Tereshkin
- a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia
| | - Ksenia Tereshkina
- a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia
| | - Natalia Loiko
- a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia.,b Laboratory of Viability of Microorganisms, Research Center of Biotechnology , Russian Academy of Sciences , Moscow , Russia
| | - Alexei Chulichkov
- a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia
| | - Vladislav Kovalenko
- a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia
| | - Yurii Krupyanskii
- a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia
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32
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Krupyanskii YF, Loiko NG, Sinitsyn DO, Tereshkina KB, Tereshkin EV, Frolov IA, Chulichkov AL, Bokareva DA, Mysyakina IS, Nikolaev YA, El’-Registan GI, Popov VO, Sokolova OS, Shaitan KV, Popov AN. Biocrystallization in Bacterial and Fungal Cells and Spores. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518040144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Meder F, Thomas SS, Bollhorst T, Dawson KA. Ordered Surface Structuring of Spherical Colloids with Binary Nanoparticle Superlattices. NANO LETTERS 2018; 18:2511-2518. [PMID: 29579388 DOI: 10.1021/acs.nanolett.8b00173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface-patterning colloidal matter in the sub-10 nm regime generates exceptional functionality in biology and photonic and electronic materials. Techniques of artificially generating functional patterns in the small nanoscale advanced in a fascinating manner in the last several years. However, they remain often restricted to planar and noncolloidal substrates. Patterning colloidal matter in solution via bottom-up assembly of smaller subunits on larger core particles is highly challenging because it is necessary to force the subunits onto randomly moving objects. Consequently, the non-equilibrium conditions present during nanoparticle self-assembly are difficult to control to eventually achieve the desired material structures. Here, we describe the formation of surface patterns with intrinsic periodic repeats of 8.9 ± 0.9 nm and less on hard, amorphous colloidal core particles by assembling binary nanoparticle superlattices on the curved particle surface. The colloidal environment is preserved during the entire bottom-up crystallization of variable building blocks (here, monodispersed 5 nm Au and 2.4 nm Pd nanoparticles (NPs) and 230 nm SiO2 core particles) into AB13-like, binary, and isotropic superlattice domains on the amorphous cores. The three-dimensional, bottom-up assembly technique is a new tool for patterning colloidal matter in the sub-10 nm surface regime for gaining access to multicomponent metamaterials for bionanoscience, photonics, and electronics.
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Affiliation(s)
- Fabian Meder
- Centre for BioNano Interactions , University College Dublin, School of Chemistry and Chemical Biology , Belfield, Dublin 4, Ireland
| | - Steffi S Thomas
- Centre for BioNano Interactions , University College Dublin, School of Chemistry and Chemical Biology , Belfield, Dublin 4, Ireland
| | - Tobias Bollhorst
- Department of Production Engineering , Advanced Ceramics, University of Bremen , Bremen 28359 , Germany
| | - Kenneth A Dawson
- Centre for BioNano Interactions , University College Dublin, School of Chemistry and Chemical Biology , Belfield, Dublin 4, Ireland
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Shurshina AS, Galina AR, Chernova VV, Kuzina LG, Kulish EI. Supramolecular Conformational Effect in Complexations of Pectin and Chitosan Polysaccharides with Some Cephalosporin and Aminoglycoside Antibiotics. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2018. [DOI: 10.1134/s1990793118010256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome. mSystems 2018; 3:mSystems00070-17. [PMID: 29404422 PMCID: PMC5781258 DOI: 10.1128/msystems.00070-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/20/2017] [Indexed: 12/24/2022] Open
Abstract
The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth. Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress. IMPORTANCE The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.
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Loiko NG, Suzina NE, Soina VS, Smirnova TA, Zubasheva MV, Azizbekyan RR, Sinitsyn DO, Tereshkina KB, Nikolaev YA, Krupyanskii YF, El’-Registan GI. Biocrystalline structures in the nucleoids of the stationary and dormant prokaryotic cells. Microbiology (Reading) 2017. [DOI: 10.1134/s002626171706011x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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37
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Sinitsyn DO, Loiko NG, Gularyan SK, Stepanov AS, Tereshkina KB, Chulichkov AL, Nikolaev AA, El-Registan GI, Popov VO, Sokolova OS, Shaitan KV, Popov AN, Krupyanskii YF. Biocrystallization of bacterial nucleoid under stress. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2017. [DOI: 10.1134/s1990793117050128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Abstract
Liquid crystals play an important role in biology because the combination of order and mobility is a basic requirement for self-organisation and structure formation in living systems. Cholesteric liquid crystals are omnipresent in living matter under both in vivo and in vitro conditions and address the major types of molecules essential to life. In the animal and plant kingdoms, the cholesteric structure is a recurring design, suggesting a convergent evolution to an optimised left-handed helix. Herein, we review the recent advances in the cholesteric organisation of DNA, chromatin, chitin, cellulose, collagen, viruses, silk and cholesterol ester deposition in atherosclerosis. Cholesteric structures can be found in bacteriophages, archaea, eukaryotes, bacterial nucleoids, chromosomes of unicellular algae, sperm nuclei of many vertebrates, cuticles of crustaceans and insects, bone, tendon, cornea, fish scales and scutes, cuttlebone and squid pens, plant cell walls, virus suspensions, silk produced by spiders and silkworms, and arterial wall lesions. This article specifically aims at describing the consequences of the cholesteric geometry in living matter, which are far from being fully defined and understood, and discusses various perspectives. The roles and functions of biological cholesteric liquid crystals include maximisation of packing efficiency, morphogenesis, mechanical stability, optical information, radiation protection and evolution pressure.
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Affiliation(s)
- Michel Mitov
- Centre d'Elaboration de Matériaux et d'Etudes Structurales (CEMES), CNRS, BP 94347, 29 rue Jeanne-Marvig, F-31055 Toulouse Cedex 4, France.
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Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2017; 114:E2440-E2449. [PMID: 28265086 DOI: 10.1073/pnas.1615575114] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyphosphate (polyP) granule biogenesis is an ancient and ubiquitous starvation response in bacteria. Although the ability to make polyP is important for survival during quiescence and resistance to diverse environmental stresses, granule genesis is poorly understood. Using quantitative microscopy at high spatial and temporal resolution, we show that granule genesis in Pseudomonas aeruginosa is tightly organized under nitrogen starvation. Following nucleation as many microgranules throughout the nucleoid, polyP granules consolidate and become transiently spatially organized during cell cycle exit. Between 1 and 3 h after nitrogen starvation, a minority of cells have divided, yet the total granule number per cell decreases, total granule volume per cell dramatically increases, and individual granules grow to occupy diameters as large as ∼200 nm. At their peak, mature granules constitute ∼2% of the total cell volume and are evenly spaced along the long cell axis. Following cell cycle exit, granules initially retain a tight spatial organization, yet their size distribution and spacing relax deeper into starvation. Mutant cells lacking polyP elongate during starvation and contain more than one origin. PolyP promotes cell cycle exit by functioning at a step after DNA replication initiation. Together with the universal starvation alarmone (p)ppGpp, polyP has an additive effect on nucleoid dynamics and organization during starvation. Notably, cell cycle exit is temporally coupled to a net increase in polyP granule biomass, suggesting that net synthesis, rather than consumption of the polymer, is important for the mechanism by which polyP promotes completion of cell cycle exit during starvation.
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Abstract
In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA-binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps-DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states.
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Dittmann C, Han HM, Grabenbauer M, Laue M. Dormant Bacillus spores protect their DNA in crystalline nucleoids against environmental stress. J Struct Biol 2015; 191:156-64. [DOI: 10.1016/j.jsb.2015.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 06/10/2015] [Accepted: 06/18/2015] [Indexed: 12/23/2022]
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Charuvi D, Nevo R, Shimoni E, Naveh L, Zia A, Adam Z, Farrant JM, Kirchhoff H, Reich Z. Photoprotection conferred by changes in photosynthetic protein levels and organization during dehydration of a homoiochlorophyllous resurrection plant. PLANT PHYSIOLOGY 2015; 167:1554-65. [PMID: 25713340 PMCID: PMC4378169 DOI: 10.1104/pp.114.255794] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/20/2015] [Indexed: 05/18/2023]
Abstract
During desiccation, homoiochlorophyllous resurrection plants retain most of their photosynthetic apparatus, allowing them to resume photosynthetic activity quickly upon water availability. These plants rely on various mechanisms to prevent the formation of reactive oxygen species and/or protect their tissues from the damage they inflict. In this work, we addressed the issue of how homoiochlorophyllous resurrection plants deal with the problem of excessive excitation/electron pressures during dehydration using Craterostigma pumilum as a model plant. To investigate the alterations in the supramolecular organization of photosynthetic protein complexes, we examined cryoimmobilized, freeze-fractured leaf tissues using (cryo)scanning electron microscopy. These examinations revealed rearrangements of photosystem II (PSII) complexes, including a lowered density during moderate dehydration, consistent with a lower level of PSII proteins, as shown by biochemical analyses. The latter also showed a considerable decrease in the level of cytochrome f early during dehydration, suggesting that initial regulation of the inhibition of electron transport is achieved via the cytochrome b6f complex. Upon further dehydration, PSII complexes are observed to arrange into rows and semicrystalline arrays, which correlates with the significant accumulation of sucrose and the appearance of inverted hexagonal lipid phases within the membranes. As opposed to PSII and cytochrome f, the light-harvesting antenna complexes of PSII remain stable throughout the course of dehydration. Altogether, these results, along with photosynthetic activity measurements, suggest that the protection of retained photosynthetic components is achieved, at least in part, via the structural rearrangements of PSII and (likely) light-harvesting antenna complexes into a photochemically quenched state.
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Affiliation(s)
- Dana Charuvi
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Reinat Nevo
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Eyal Shimoni
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Leah Naveh
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Ahmad Zia
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Zach Adam
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Jill M Farrant
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Helmut Kirchhoff
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
| | - Ziv Reich
- Department of Biological Chemistry (D.C., R.N., Z.R.) and Electron Microscopy Unit (E.S.), Weizmann Institute of Science, Rehovot 76100, Israel;Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (L.N., Z.A.);Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 (A.Z., H.K.); andDepartment of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa (J.M.F.)
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Sun S, Liu M, Dong F, Fan S, Yao Y. A histone-like protein induces plasmid DNA to form liquid crystals in vitro and gene compaction in vivo. Int J Mol Sci 2013; 14:23842-57. [PMID: 24322443 PMCID: PMC3876081 DOI: 10.3390/ijms141223842] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/17/2013] [Accepted: 11/21/2013] [Indexed: 12/15/2022] Open
Abstract
The liquid crystalline state is a universal phenomenon involving the formation of an ordered structure via a self-assembly process that has attracted attention from numerous scientists. In this study, the dinoflagellate histone-like protein HCcp3 is shown to induce super-coiled pUC18 plasmid DNA to enter a liquid crystalline state in vitro, and the role of HCcp3 in gene condensation in vivo is also presented. The plasmid DNA (pDNA)-HCcp3 complex formed birefringent spherical particles with a semi-crystalline selected area electronic diffraction (SAED) pattern. Circular dichroism (CD) titrations of pDNA and HCcp3 were performed. Without HCcp3, pUC18 showed the characteristic B conformation. As the HCcp3 concentration increased, the 273 nm band sharply shifted to 282 nm. When the HCcp3 concentration became high, the base pair (bp)/dimer ratio fell below 42/1, and the CD spectra of the pDNA-HCcp3 complexes became similar to that of dehydrated A-form DNA. Microscopy results showed that HCcp3 compacted the super-coiled gene into a condensed state and that inclusion bodies were formed. Our results indicated that HCcp3 has significant roles in gene condensation both in vitro and in histone-less eukaryotes in vivo. The present study indicates that HCcp3 has great potential for applications in non-viral gene delivery systems, where HCcp3 may compact genetic material to form liquid crystals.
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Affiliation(s)
- Shiyong Sun
- Key Laboratory of Solid Waste Treatment and Resource Recycle & Fundamental Science on Nuclear Waste and Environmental Security Laboratory, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mail:
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mails: (S.F.); (Y.Y.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (F.D.); Tel./Fax: +86-816-2419569 (S.S.)
| | - Mingxue Liu
- Key Laboratory of Solid Waste Treatment and Resource Recycle & Fundamental Science on Nuclear Waste and Environmental Security Laboratory, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mail:
| | - Faqin Dong
- Key Laboratory of Solid Waste Treatment and Resource Recycle & Fundamental Science on Nuclear Waste and Environmental Security Laboratory, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (F.D.); Tel./Fax: +86-816-2419569 (S.S.)
| | - Shenglan Fan
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mails: (S.F.); (Y.Y.)
| | - Yanchen Yao
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mails: (S.F.); (Y.Y.)
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Jin DJ, Cagliero C, Zhou YN. Role of RNA polymerase and transcription in the organization of the bacterial nucleoid. Chem Rev 2013; 113:8662-82. [PMID: 23941620 PMCID: PMC3830623 DOI: 10.1021/cr4001429] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ding Jun Jin
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
| | - Cedric Cagliero
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
| | - Yan Ning Zhou
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
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Shechter N, Zaltzman L, Weiner A, Brumfeld V, Shimoni E, Fridmann-Sirkis Y, Minsky A. Stress-induced condensation of bacterial genomes results in re-pairing of sister chromosomes: implications for double strand DNA break repair. J Biol Chem 2013; 288:25659-25667. [PMID: 23884460 DOI: 10.1074/jbc.m113.473025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genome condensation is increasingly recognized as a generic stress response in bacteria. To better understand the physiological implications of this response, we used fluorescent markers to locate specific sites on Escherichia coli chromosomes following exposure to cytotoxic stress. We find that stress-induced condensation proceeds through a nonrandom, zipper-like convergence of sister chromosomes, which is proposed to rely on the recently demonstrated intrinsic ability of identical double-stranded DNA molecules to specifically identify each other. We further show that this convergence culminates in spatial proximity of homologous sites throughout chromosome arms. We suggest that the resulting apposition of homologous sites can explain how repair of double strand DNA breaks might occur in a mechanism that is independent of the widely accepted yet physiologically improbable genome-wide search for homologous templates. We claim that by inducing genome condensation and orderly convergence of sister chromosomes, diverse stress conditions prime bacteria to effectively cope with severe DNA lesions such as double strand DNA breaks.
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Affiliation(s)
| | | | | | - Vlad Brumfeld
- Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
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46
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Norris V, Nana GG, Audinot JN. New approaches to the problem of generating coherent, reproducible phenotypes. Theory Biosci 2013; 133:47-61. [PMID: 23794321 DOI: 10.1007/s12064-013-0185-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/03/2013] [Indexed: 12/01/2022]
Abstract
Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. Both competitive coherence and life on the scales deal with the problem of reconciling conflicting constraints. Here, we bring together these concepts in the common framework of hyperstructures and make predictions that may be tested using a learning program, Coco, and secondary ion mass spectrometry.
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Affiliation(s)
- Vic Norris
- Theoretical Biology Unit, University of Rouen, 76821, Mont Saint Aignan, France,
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47
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Randomness and multilevel interactions in biology. Theory Biosci 2013; 132:139-58. [PMID: 23637008 DOI: 10.1007/s12064-013-0179-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 02/11/2013] [Indexed: 10/26/2022]
Abstract
The dynamic instability of living systems and the "superposition" of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems' dynamics. Biological randomness is then presented not only as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting of, and interaction between many levels of organization, but also as a key component of its structural stability. We will note as well that increasing organization, while increasing "order", induces growing disorder, not only by energy dispersal effects, but also by increasing variability and differentiation. Finally, we discuss the cooperation between diverse components in biological networks; this cooperation implies the presence of constraints due to the particular nature of bio-entanglement and bio-resonance, two notions to be reviewed and defined in the paper.
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48
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Cagliero C, Jin DJ. Dissociation and re-association of RNA polymerase with DNA during osmotic stress response in Escherichia coli. Nucleic Acids Res 2013; 41:315-26. [PMID: 23093594 PMCID: PMC3592413 DOI: 10.1093/nar/gks988] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 11/12/2022] Open
Abstract
The thermodynamic association of RNA polymerase (RNAP) with DNA is sensitive to salt concentration in vitro. Paradoxically, previous studies of changes in osmolarity during steady-state cell growth found no dependence between the association of RNAP to DNA and K(+) concentration in Escherichia coli. We reevaluated this issue by following the interaction of RNAP and genomic DNA in time-course experiments during the hyper-osmotic response. Our results show that the interaction is temporally controlled by the same physical chemistry principle in the cell as in vitro. RNAP rapidly dissociates from the genome during the initial response when the cytoplasmic K(+) accumulates transiently, and concurrently the nucleoid becomes hyper-condensed. The freed RNAP re-associates with the genome during a subsequent osmoadaptation phase when organic osmoprotectants accumulate as K(+) levels decrease. RNAP first surrounds the hyper-condensed nucleoid forming a sphere of RNAP before it progressively moves in to the center of the nucleoid. Our findings reinterpret the dynamic protein-DNA interactions during osmotic stress response. We discuss the implications of the dissociation/association of RNAP for osmotic protection and nucleoid structure.
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Affiliation(s)
| | - Ding Jun Jin
- Transcription control section, Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
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Kumari S, Swaminathan A, Chatterjee S, Senapati P, Boopathi R, Kundu TK. Chromatin organization, epigenetics and differentiation: an evolutionary perspective. Subcell Biochem 2013; 61:3-35. [PMID: 23150244 DOI: 10.1007/978-94-007-4525-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genome packaging is a universal phenomenon from prokaryotes to higher mammals. Genomic constituents and forces have however, travelled a long evolutionary route. Both DNA and protein elements constitute the genome and also aid in its dynamicity. With the evolution of organisms, these have experienced several structural and functional changes. These evolutionary changes were made to meet the challenging scenario of evolving organisms. This review discusses in detail the evolutionary perspective and functionality gain in the phenomena of genome organization and epigenetics.
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Affiliation(s)
- Sujata Kumari
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Post, Bangalore, 560064, India
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50
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Norris V, Amar P. Chromosome Replication in Escherichia coli: Life on the Scales. Life (Basel) 2012; 2:286-312. [PMID: 25371267 PMCID: PMC4187155 DOI: 10.3390/life2040286] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 10/01/2012] [Accepted: 10/15/2012] [Indexed: 12/22/2022] Open
Abstract
At all levels of Life, systems evolve on the 'scales of equilibria'. At the level of bacteria, the individual cell must favor one of two opposing strategies and either take risks to grow or avoid risks to survive. It has been proposed in the Dualism hypothesis that the growth and survival strategies depend on non-equilibrium and equilibrium hyperstructures, respectively. It has been further proposed that the cell cycle itself is the way cells manage to balance the ratios of these types of hyperstructure so as to achieve the compromise solution of living on the two scales. Here, we attempt to re-interpret a major event, the initiation of chromosome replication in Escherichia coli, in the light of scales of equilibria. This entails thinking in terms of hyperstructures as responsible for intensity sensing and quantity sensing and how this sensing might help explain the role of the DnaA protein in initiation of replication. We outline experiments and an automaton approach to the cell cycle that should test and refine the scales concept.
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Affiliation(s)
- Vic Norris
- Theoretical Biology Unit, EA 3829, Department of Biology, University of Rouen, 76821, Mont Saint Aignan, France.
| | - Patrick Amar
- Laboratoire de Recherche en Informatique, Université Paris-Sud, and INRIA Saclay - Ile de France, AMIB Project, Orsay, France.
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