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Cordova A, Niese B, Sweet P, Kamat P, Phillip JM, Gordon V, Contreras LM. Quantitative morphological analysis of Deinococcus radiodurans elucidates complex dose-dependent nucleoid condensation during recovery from ionizing radiation. Appl Environ Microbiol 2024; 90:e0010824. [PMID: 38864629 DOI: 10.1128/aem.00108-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024] Open
Abstract
The extremophile Deinococcus radiodurans maintains a highly organized and condensed nucleoid as its default state, possibly contributing to its high tolerance to ionizing radiation (IR). Previous studies of the D. radiodurans nucleoid were limited by reliance on manual image annotation and qualitative metrics. Here, we introduce a high-throughput approach to quantify the geometric properties of cells and nucleoids using confocal microscopy, digital reconstructions of cells, and computational modeling. We utilize this novel approach to investigate the dynamic process of nucleoid condensation in response to IR stress. Our quantitative analysis reveals that at the population level, exposure to IR induced nucleoid compaction and decreased the size of D. radiodurans cells. Morphological analysis and clustering identified six distinct sub-populations across all tested experimental conditions. Results indicate that exposure to IR induced fractional redistributions of cells across sub-populations to exhibit morphologies associated with greater nucleoid condensation and decreased the abundance of sub-populations associated with cell division. Nucleoid-associated proteins (NAPs) may link nucleoid compaction and stress tolerance, but their roles in regulating compaction in D. radiodurans are unknown. Imaging of genomic mutants of known and suspected NAPs that contribute to nucleoid condensation found that deletion of nucleic acid-binding proteins, not previously described as NAPs, can remodel the nucleoid by driving condensation or decondensation in the absence of stress and that IR increased the abundance of these morphological states. Thus, our integrated analysis introduces a new methodology for studying environmental influences on bacterial nucleoids and provides an opportunity to further investigate potential regulators of nucleoid condensation.IMPORTANCEDeinococcus radiodurans, an extremophile known for its stress tolerance, constitutively maintains a highly condensed nucleoid. Qualitative studies have described nucleoid behavior under a variety of conditions. However, a lack of quantitative data regarding nucleoid organization and dynamics has limited our understanding of the regulatory mechanisms controlling nucleoid organization in D. radiodurans. Here, we introduce a quantitative approach that enables high-throughput quantitative measurements of subcellular spatial characteristics in bacterial cells. Applying this to wild-type or single-protein-deficient populations of D. radiodurans subjected to ionizing radiation, we identified significant stress-responsive changes in cell shape, nucleoid organization, and morphology. These findings highlight this methodology's adaptability and capacity for quantitatively analyzing the cellular response to stressors for screening cellular proteins involved in bacterial nucleoid organization.
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Affiliation(s)
- Antonio Cordova
- Interdisciplinary Life Sciences Graduate Program, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas, USA
| | - Brandon Niese
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, Texas, USA
| | - Philip Sweet
- Interdisciplinary Life Sciences Graduate Program, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Pratik Kamat
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jude M Phillip
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Institute for Nanobiotechnology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vernita Gordon
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas, USA
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, Texas, USA
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, USA
| | - Lydia M Contreras
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas, USA
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
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2
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Chen TT, Hua W, Zhang XZ, Wang BH, Yang ZS. The effects of pprI gene of Deinococcus radiodurans R1 on acute radiation injury of mice exposed to 60Co γ-ray radiation. Oncotarget 2018; 8:2008-2019. [PMID: 27974687 PMCID: PMC5356773 DOI: 10.18632/oncotarget.13893] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 11/15/2016] [Indexed: 11/25/2022] Open
Abstract
The role of the pprI gene from Deinococcus radiodurans R1 in therapy of acute radiation injury of a mammalian host was investigated. We injected a plasmid containing the pprI gene into the muscle of mice exposed to total 6Gy of 60Co γ-ray radiation. After injection, we used in vivo gene electroporation technology to transfer the pprI gene into the cell. We found the PprI protein was expressed significantly at 1 d after irradiation, but there was no expression of pprI gene 7 d post-irradiation. The expression of pprI gene evidently decreased the death rate of mice exposed to lethal dose radiation, significantly relieved effects on blood cells in the acute stage, shortened the persistence time of the decrease of lymphocytes, and decreased the apoptotic rates of spleen cells, thymocytes and bone marrow cells. The expression of Rad51 protein in the lungs, livers, and kidneys was significantly higher in the mice treated with the pprI plasmid after irradiation. However, there were no obvious differences for Rad52 protein expression. We conclude that the prokaryotic pprI gene of D. radiodurans R1 first was expressed in mammalian cells. The expressed prokaryotic PprI protein has distinct effects of the prevention and treatment on acute radiation injury of mammal. The effects of radio-resistance may relate to expression of Rad51 protein which is homologous with RecA from D. radiodurans.
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Affiliation(s)
- Ting-Ting Chen
- Department of Oncology, The People`s Hospital of Subei, Yangzhou, China
| | - Wei Hua
- Department of Oncology, The People`s Hospital of Subei, Yangzhou, China
| | - Xi-Zhi Zhang
- Department of Oncology, The People`s Hospital of Subei, Yangzhou, China
| | - Bu-Hai Wang
- Department of Oncology, The People`s Hospital of Subei, Yangzhou, China
| | - Zhan-Shan Yang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
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3
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Bitran A, Chiang WY, Levine E, Prentiss M. Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA. PLoS Comput Biol 2017; 13:e1005421. [PMID: 28257444 PMCID: PMC5360337 DOI: 10.1371/journal.pcbi.1005421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/21/2017] [Accepted: 02/21/2017] [Indexed: 12/03/2022] Open
Abstract
Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with many nearly matched targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear. Here we consider a kinetic system, inspired by homology dependent pairing between double stranded DNA in bacteria. By considering a simplified tractable model, we identify different homology testing stages that naturally occur in the system. In particular, we first model dsDNA molecules as short rigid rods containing periodically spaced binding sites. The interaction begins when the centers of two rods collide at a random angle. For most collision angles, the interaction energy is weak because only a few binding sites near the collision point contribute significantly to the binding energy. We show that most incorrect pairings are rapidly rejected at this stage. In rare cases, the two rods enter a second stage by rotating into parallel alignment. While rotation increases the stability of matched and nearly matched pairings, subsequent rotational fluctuations reduce kinetic trapping. Finally, in vivo chromosome are much longer than the persistence length of dsDNA, so we extended the model to include multiple parallel collisions between long dsDNA molecules, and find that those additional interactions can greatly accelerate the searching. Protein folding and the binding of sequence dependent proteins to DNA are examples of self-assembling systems in which the binding energy varies continuously throughout the interaction. Previous theoretical work has highlighted the importance of dividing the interaction into separate stages characterized by interaction times and binding energies that vary by orders of magnitude. Insight into how such a division might naturally arise and promote accurate and efficient self-assembly is provided by our study of a simple tractable model inspired by the homology dependent pairing of double stranded DNA molecules in vivo. In the model, the binding energy is controlled by one single continuously tunable variable whose natural evolution creates stages that efficiently and accurately form stable products.
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Affiliation(s)
- Amir Bitran
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Wei-Yin Chiang
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Erel Levine
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
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4
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Milrot E, Mutsafi Y, Fridmann-Sirkis Y, Shimoni E, Rechav K, Gurnon JR, Van Etten JL, Minsky A. Virus-host interactions: insights from the replication cycle of the large Paramecium bursaria chlorella virus. Cell Microbiol 2015; 18:3-16. [PMID: 26248343 DOI: 10.1111/cmi.12486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/09/2015] [Accepted: 07/15/2015] [Indexed: 12/20/2022]
Abstract
The increasing interest in cytoplasmic factories generated by eukaryotic-infecting viruses stems from the realization that these highly ordered assemblies may contribute fundamental novel insights to the functional significance of order in cellular biology. Here, we report the formation process and structural features of the cytoplasmic factories of the large dsDNA virus Paramecium bursaria chlorella virus 1 (PBCV-1). By combining diverse imaging techniques, including scanning transmission electron microscopy tomography and focused ion beam technologies, we show that the architecture and mode of formation of PBCV-1 factories are significantly different from those generated by their evolutionary relatives Vaccinia and Mimivirus. Specifically, PBCV-1 factories consist of a network of single membrane bilayers acting as capsid templates in the central region, and viral genomes spread throughout the host cytoplasm but excluded from the membrane-containing sites. In sharp contrast, factories generated by Mimivirus have viral genomes in their core, with membrane biogenesis region located at their periphery. Yet, all viral factories appear to share structural features that are essential for their function. In addition, our studies support the notion that PBCV-1 infection, which was recently reported to result in significant pathological outcomes in humans and mice, proceeds through a bacteriophage-like infection pathway.
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Affiliation(s)
- Elad Milrot
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yael Mutsafi
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yael Fridmann-Sirkis
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - James R Gurnon
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0900, USA
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0900, USA
| | - Abraham Minsky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
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5
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Infection cycles of large DNA viruses: Emerging themes and underlying questions. Virology 2014; 466-467:3-14. [DOI: 10.1016/j.virol.2014.05.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/20/2022]
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6
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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7
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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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8
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Ngo KV, Molzberger ET, Chitteni-Pattu S, Cox MM. Regulation of Deinococcus radiodurans RecA protein function via modulation of active and inactive nucleoprotein filament states. J Biol Chem 2013; 288:21351-21366. [PMID: 23729671 DOI: 10.1074/jbc.m113.459230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RecA protein of Deinococcus radiodurans (DrRecA) has a central role in genome reconstitution after exposure to extreme levels of ionizing radiation. When bound to DNA, filaments of DrRecA protein exhibit active and inactive states that are readily interconverted in response to several sets of stimuli and conditions. At 30 °C, the optimal growth temperature, and at physiological pH 7.5, DrRecA protein binds to double-stranded DNA (dsDNA) and forms extended helical filaments in the presence of ATP. However, the ATP is not hydrolyzed. ATP hydrolysis of the DrRecA-dsDNA filament is activated by addition of single-stranded DNA, with or without the single-stranded DNA-binding protein. The ATPase function of DrRecA nucleoprotein filaments thus exists in an inactive default state under some conditions. ATPase activity is thus not a reliable indicator of DNA binding for all bacterial RecA proteins. Activation is effected by situations in which the DNA substrates needed to initiate recombinational DNA repair are present. The inactive state can also be activated by decreasing the pH (protonation of multiple ionizable groups is required) or by addition of volume exclusion agents. Single-stranded DNA-binding protein plays a much more central role in DNA pairing and strand exchange catalyzed by DrRecA than is the case for the cognate proteins in Escherichia coli. The data suggest a mechanism to enhance the efficiency of recombinational DNA repair in the context of severe genomic degradation in D. radiodurans.
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Affiliation(s)
- Khanh V Ngo
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Eileen T Molzberger
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Sindhu Chitteni-Pattu
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael M Cox
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706.
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9
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Crystal structures of complexes of the branched-chain aminotransferase from Deinococcus radiodurans with α-ketoisocaproate and L-glutamate suggest the radiation resistance of this enzyme for catalysis. J Bacteriol 2012; 194:6206-16. [PMID: 22984263 DOI: 10.1128/jb.01659-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Branched-chain aminotransferases (BCAT), which utilize pyridoxal 5'-phosphate (PLP) as a cofactor, reversibly catalyze the transfer of the α-amino groups of three of the most hydrophobic branched-chain amino acids (BCAA), leucine, isoleucine, and valine, to α-ketoglutarate to form the respective branched-chain α-keto acids and glutamate. The BCAT from Deinococcus radiodurans (DrBCAT), an extremophile, was cloned and expressed in Escherichia coli for structure and functional studies. The crystal structures of the native DrBCAT with PLP and its complexes with L-glutamate and α-ketoisocaproate (KIC), respectively, have been determined. The DrBCAT monomer, comprising 358 amino acids, contains large and small domains connected with an interdomain loop. The cofactor PLP is located at the bottom of the active site pocket between two domains and near the dimer interface. The substrate (L-glutamate or KIC) is bound with key residues through interactions of the hydrogen bond and the salt bridge near PLP inside the active site pocket. Mutations of some interaction residues, such as Tyr71, Arg145, and Lys202, result in loss of the specific activity of the enzymes. In the interdomain loop, a dynamic loop (Gly173 to Gly179) clearly exhibits open and close conformations in structures of DrBCAT without and with substrates, respectively. DrBCAT shows the highest specific activity both in nature and under ionizing radiation, but with lower thermal stability above 60 °C, than either BCAT from Escherichia coli (eBCAT) or from Thermus thermophilus (HB8BCAT). The dimeric molecular packing and the distribution of cysteine residues at the active site and the molecular surface might explain the resistance to radiation but small thermal stability of DrBCAT.
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10
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Fudenberg G, Mirny LA. Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev 2012; 22:115-24. [PMID: 22360992 DOI: 10.1016/j.gde.2012.01.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 01/20/2012] [Accepted: 01/23/2012] [Indexed: 12/11/2022]
Abstract
Advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of higher-order interphase chromatin organization. By taking into account topological constraints acting on the chromatin fiber, recently developed polymer models of interphase chromatin can reproduce the observed scaling of distances between genomic loci, chromosomal territories, and probabilities of contacts between loci measured by chromosome conformation capture methods. Polymer models provide a framework for the interpretation of experimental data as ensembles of conformations rather than collections of loops, and will be crucial for untangling functional implications of chromosomal organization.
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Affiliation(s)
- Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, United States
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11
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Kalay Z. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry. Crit Rev Biochem Mol Biol 2011; 46:310-26. [DOI: 10.3109/10409238.2011.582081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ziya Kalay
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
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12
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Nevo U, Özarslan E, Komlosh ME, Koay CG, Sarlls JE, Basser PJ. A system and mathematical framework to model shear flow effects in biomedical DW-imaging and spectroscopy. NMR IN BIOMEDICINE 2010; 23:734-44. [PMID: 20886564 PMCID: PMC4164167 DOI: 10.1002/nbm.1591] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The pulsed-field gradient (PFG) MR experiment enables one to measure particle displacements, velocities, and even higher moments of complex fluid motions. In diffusion-weighted MRI (DWI) in living tissue, where the PFG MRI experiment is used to measure diffusion, Brownian motion is assumed to dominate the displacements causing the observed signal loss. However, motions of water molecules caused by various active biological processes occurring at different length and time scales may also cause additional dephasing of magnetization and signal loss. To help understand their relative effects on the DWI signal attenuation, we used an integrated experimental and theoretical framework: a Rheo-NMR, which served as an experimental model system to precisely prescribe a microscopic velocity distribution; and a mathematical model that relates the DW signal intensity in the Rheo-NMR to experimental parameters that characterize the impressed velocity field. A technical innovation reported here is our use of 'natural' (in this case, polar) coordinates both to simplify the description the fluid motion within the Couette cell of the Rheo-NMR, as well as to acquire and reconstruct magnitude and phase MR images obtained within it. We use this integrated model system to demonstrate how shear flows appears as pseudo-diffusion in magnitude DW MR signals obtained using PFG spin-echo (PGSE) NMR and MRI sequences. Our results lead us to reinterpret the possible causes of signal loss in DWI in vivo, in particular to revise and generalize the previous notion of intra-voxel incoherent motion (IVIM) in order to describe activity driven flows that appear as pseudo-diffusion over multiple length and time scales in living tissues.
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Affiliation(s)
- Uri Nevo
- Department of Biomedical Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
- Section on Tissue Biophysics and Biomimetics (STBB), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - Evren Özarslan
- Section on Tissue Biophysics and Biomimetics (STBB), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - Michal E. Komlosh
- Section on Tissue Biophysics and Biomimetics (STBB), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - Cheng Guan Koay
- Section on Tissue Biophysics and Biomimetics (STBB), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - Joelle E. Sarlls
- Section on Tissue Biophysics and Biomimetics (STBB), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - Peter J. Basser
- Section on Tissue Biophysics and Biomimetics (STBB), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
- Correspondence to: P. J. Basser, NIH, 13 South Drive, MSC 5772, Building 13, Room 3W16, Bethesda, MD 20892 USA.
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13
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Abstract
It is generally expected that the kinetics of reactions inside living cells differs from the situation in bulk solutions. Macromolecular crowding and specific binding interactions could change the diffusion properties and the availability of free molecules. Their impact on reaction kinetics in the relevant context of living cells is still elusive, mainly because the difficulty of capturing fast kinetics in vivo. This article shows spatially resolved measurements of DNA hybridization kinetics in single living cells. HeLa cells were transfected with a FRET-labeled dsDNA probe by lipofection. We characterized the hybridization reaction kinetics with a kinetic range of 10 micros to 1 s by a combination of laser-driven temperature oscillations and stroboscopic fluorescence imaging. The time constant of the hybridization depended on DNA concentration within individual cells and between cells. A quantitative analysis of the concentration dependence revealed several-fold accelerated kinetics as compared with free solution for a 16-bp probe and decelerated kinetics for a 12-bp probe. We did not find significant effects of crowding agents on the hybridization kinetics in vitro. Our results suggest that the reaction rates in vivo are specifically modulated by binding interactions for the two probes, possibly triggered by their different lengths. In general, the presented imaging modality of temperature oscillation optical lock-in microscopy allows to probe biomolecular interactions in different cell compartments in living cells for systems biology.
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14
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Weiner A, Zauberman N, Minsky A. Recombinational DNA repair in a cellular context: a search for the homology search. Nat Rev Microbiol 2009; 7:748-55. [PMID: 19756013 DOI: 10.1038/nrmicro2206] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Double-strand DNA breaks (DSBs) are the most detrimental lesion that can be sustained by the genetic complement, and their inaccurate mending can be just as damaging. According to the consensual view, precise DSB repair relies on homologous recombination. Here, we review studies on DNA repair, chromatin diffusion and chromosome confinement, which collectively imply that a genome-wide search for a homologous template, generally thought to be a pivotal stage in all homologous DSB repair pathways, is improbable. The implications of this assertion for the scope and constraints of DSB repair pathways and for the ability of diverse organisms to cope with DNA damage are discussed.
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Affiliation(s)
- Allon Weiner
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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15
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Abstract
We have generated extreme ionizing radiation resistance in a relatively sensitive bacterial species, Escherichia coli, by directed evolution. Four populations of Escherichia coli K-12 were derived independently from strain MG1655, with each specifically adapted to survive exposure to high doses of ionizing radiation. D(37) values for strains isolated from two of the populations approached that exhibited by Deinococcus radiodurans. Complete genomic sequencing was carried out on nine purified strains derived from these populations. Clear mutational patterns were observed that both pointed to key underlying mechanisms and guided further characterization of the strains. In these evolved populations, passive genomic protection is not in evidence. Instead, enhanced recombinational DNA repair makes a prominent but probably not exclusive contribution to genome reconstitution. Multiple genes, multiple alleles of some genes, multiple mechanisms, and multiple evolutionary pathways all play a role in the evolutionary acquisition of extreme radiation resistance. Several mutations in the recA gene and a deletion of the e14 prophage both demonstrably contribute to and partially explain the new phenotype. Mutations in additional components of the bacterial recombinational repair system and the replication restart primosome are also prominent, as are mutations in genes involved in cell division, protein turnover, and glutamate transport. At least some evolutionary pathways to extreme radiation resistance are constrained by the temporally ordered appearance of specific alleles.
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16
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Recovery of ionizing-radiation damage after high doses of gamma ray in the hyperthermophilic archaeon Thermococcus gammatolerans. Extremophiles 2009; 13:333-43. [DOI: 10.1007/s00792-008-0221-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
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17
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Chromatin organization and radio resistance in the bacterium Gemmata obscuriglobus. J Bacteriol 2008; 191:1439-45. [PMID: 19074379 DOI: 10.1128/jb.01513-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. Gemmata obscuriglobus, a member of the phylum Planctomycetes, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase G. obscuriglobus cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.
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18
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Blasius M, Sommer S, Hübscher U. Deinococcus radiodurans: what belongs to the survival kit? Crit Rev Biochem Mol Biol 2008; 43:221-38. [PMID: 18568848 DOI: 10.1080/10409230802122274] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Deinococcus radiodurans, one of the most radioresistant organisms known to date, is able to repair efficiently hundreds of DNA double- and single-strand breaks as well as other types of DNA damages promoted by ionizing or ultraviolet radiation. We review recent discoveries concerning several aspects of radioresistance and survival under high genotoxic stress. We discuss different hypotheses and possibilities that have been suggested to contribute to radioresistance and propose that D. radiodurans combines a variety of physiological tools that are tightly coordinated. A complex network of regulatory proteins may be discovered in the near future that might allow further understanding of radioresistance.
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Affiliation(s)
- Melanie Blasius
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich-Irchel, Zurich, Switzerland
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19
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Norris V, den Blaauwen T, Cabin-Flaman A, Doi RH, Harshey R, Janniere L, Jimenez-Sanchez A, Jin DJ, Levin PA, Mileykovskaya E, Minsky A, Saier M, Skarstad K. Functional taxonomy of bacterial hyperstructures. Microbiol Mol Biol Rev 2007; 71:230-53. [PMID: 17347523 PMCID: PMC1847379 DOI: 10.1128/mmbr.00035-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or "nucleolar" hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell.
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Affiliation(s)
- Vic Norris
- Department of Science, University of Rouen, 76821 Mont Saint Aignan Cedex, France.
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20
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Chen CD, Huang TF, Lin CH, Guan HH, Hsieh YC, Lin YH, Huang YC, Liu MY, Chang WC, Chen CJ. Purification, crystallization and preliminary X-ray crystallographic analysis of branched-chain aminotransferase from Deinococcus radiodurans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:492-4. [PMID: 17554170 PMCID: PMC2335077 DOI: 10.1107/s1744309107020842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Accepted: 04/26/2007] [Indexed: 11/10/2022]
Abstract
The branched-chain amino-acid aminotransferase (BCAT), which requires pyridoxal 5'-phosphate (PLP) as a cofactor, is a key enzyme in the biosynthetic pathway of the hydrophobic amino acids leucine, isoleucine and valine. DrBCAT from Deinococcus radiodurans, which has a molecular weight of 40.9 kDa, was crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction data to 2.50 A resolution from a DrBCAT crystal, the crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.37, b = 90.70, c = 155.47 A. Preliminary analysis indicates the presence of two DrBCAT molecules in the asymmetric unit, with a solvent content of 47.52%.
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Affiliation(s)
- Chung-Der Chen
- Department of Physics, National Tsing-Hua University, Hsinchu 30013, Taiwan
| | - Tien-Feng Huang
- Department of Physics, National Tsing-Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hao Lin
- Institute of Biological Chemistry, National Taiwan University, Taipei 110, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013, Taiwan
| | - Yin-Cheng Hsieh
- Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013, Taiwan
| | - Yi-Hung Lin
- Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yen-Chieh Huang
- Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Ming-Yih Liu
- Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Wen-Chang Chang
- Institute of Biological Chemistry, National Taiwan University, Taipei 110, Taiwan
- Correspondence e-mail: ,
| | - Chun-Jung Chen
- Department of Physics, National Tsing-Hua University, Hsinchu 30013, Taiwan
- Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Correspondence e-mail: ,
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21
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Eltsov M, Dubochet J. Study of the Deinococcus radiodurans nucleoid by cryoelectron microscopy of vitreous sections: Supplementary comments. J Bacteriol 2006; 188:6053-8; discussion 6059. [PMID: 16923871 PMCID: PMC1595392 DOI: 10.1128/jb.00230-06] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mikhail Eltsov
- Laboratoire d'Analyse Ultrastructurale, Biophore, Université de Lausanne, CH-1015 Lausanne, Switzerland.
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22
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Minsky A, Shimoni E, Englander J. Ring-like nucleoids and DNA repair through error-free nonhomologous end joining in Deinococcus radiodurans. J Bacteriol 2006; 188:6047-51; discussion 6052. [PMID: 16923869 PMCID: PMC1595378 DOI: 10.1128/jb.01951-05] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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23
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Flyvbjerg H, Keatch SA, Dryden DT. Strong physical constraints on sequence-specific target location by proteins on DNA molecules. Nucleic Acids Res 2006; 34:2550-7. [PMID: 16698961 PMCID: PMC3303175 DOI: 10.1093/nar/gkl271] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sequence-specific binding to DNA in the presence of competing non-sequence-specific ligands is a problem faced by proteins in all organisms. It is akin to the problem of parking a truck at a loading bay by the side of a road in the presence of cars parked at random along the road. Cars even partially covering the loading bay prevent correct parking of the truck. Similarly on DNA, non-specific ligands interfere with the binding and function of sequence-specific proteins. We derive a formula for the probability that the loading bay is free from parked cars. The probability depends on the size of the loading bay and allows an estimation of the size of the footprint on the DNA of the sequence-specific protein by assaying protein binding or function in the presence of increasing concentrations of non-specific ligand. Assaying for function gives an 'activity footprint'; the minimum length of DNA required for function rather than the more commonly measured physical footprint. Assaying the complex type I restriction enzyme, EcoKI, gives an activity footprint of approximately 66 bp for ATP hydrolysis and 300 bp for the DNA cleavage function which is intimately linked with translocation of DNA by EcoKI. Furthermore, considering the coverage of chromosomal DNA by proteins in vivo, our theory shows that the search for a specific DNA sequence is very difficult; most sites are obscured by parked cars. This effectively rules out any significant role in target location for mechanisms invoking one-dimensional, linear diffusion along DNA.
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Affiliation(s)
- Henrik Flyvbjerg
- Risø National Laboratory, Biosystems Department and Danish Polymer Centre Building BIO-776, PO Box 49, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
- Isaac Newton Institute for Mathematical Sciences 20 Clarkson Road, Cambridge, CB3 0EH, UK
| | - Steven A. Keatch
- School of Chemistry, The King's Buildings, The University of Edinburgh Edinburgh, EH9 3JJ, UK
| | - David T.F. Dryden
- School of Chemistry, The King's Buildings, The University of Edinburgh Edinburgh, EH9 3JJ, UK
- Isaac Newton Institute for Mathematical Sciences 20 Clarkson Road, Cambridge, CB3 0EH, UK
- To whom correspondence should be adressed. Tel: +0131 650 4735; Fax: +0131 650 6453;
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24
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Keatch SA, Leonard PG, Ladbury JE, Dryden DTF. StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI. Nucleic Acids Res 2005; 33:6540-6. [PMID: 16299353 PMCID: PMC1289078 DOI: 10.1093/nar/gki951] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The nucleoid-associated protein, StpA, of Escherichia coli binds non-specifically to double-stranded DNA (dsDNA) and apparently forms bridges between adjacent segments of the DNA. Such a coating of protein on the DNA would be expected to hinder the action of nucleases. We demonstrate that StpA binding hinders dsDNA cleavage by both the non-specific endonuclease, DNase I, and by the site-specific type I restriction endonuclease, EcoKI. It requires approximately one StpA molecule per 250–300 bp of supercoiled DNA and approximately one StpA molecule per 60–100 bp on linear DNA for strong inhibition of the nucleases. These results support the role of StpA as a nucleoid-structuring protein which binds DNA segments together. The inhibition of EcoKI, which cleaves DNA at a site remote from its initial target sequence after extensive DNA translocation driven by ATP hydrolysis, suggests that these enzymes would be unable to function on chromosomal DNA even during times of DNA damage when potentially lethal, unmodified target sites occur on the chromosome. This supports a role for nucleoid-associated proteins in restriction alleviation during times of cell stress.
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Affiliation(s)
| | - P. G. Leonard
- Department of Biochemistry and Molecular Biology, University College LondonGower Street, London WC1E 6BT, UK
| | - J. E. Ladbury
- Department of Biochemistry and Molecular Biology, University College LondonGower Street, London WC1E 6BT, UK
| | - D. T. F. Dryden
- To whom correspondence should be addressed. Tel: +44 131 650 4735; Fax: +44 131 650 6453;
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25
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Ohba H, Satoh K, Yanagisawa T, Narumi I. The radiation responsive promoter of the Deinococcus radiodurans pprA gene. Gene 2005; 363:133-41. [PMID: 16203111 DOI: 10.1016/j.gene.2005.07.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 07/05/2005] [Accepted: 07/13/2005] [Indexed: 11/27/2022]
Abstract
In a previous study, we identified a novel radiation-inducible protein PprA that plays a critical role in the radiation resistance of Deinococcus radiodurans [Narumi, I., Satoh, K., Cui, S., Funayama, T., Kitayama, S., Watanabe, H., 2004. PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation. Mol. Microbiol. 54, 278-285.]. Despite the interest in mechanisms underlying radiation responses in D. radiodurans, little is known about the radiation responsive promoter for radiation-inducible proteins. In this study, three transcriptional start points for pprA mRNA were identified by primer extension analysis, located at positions -156, -154 and -22 upstream from the pprA translation initiation site. The amount of the three extended products increased in cells exposed to 2 kGy followed by a 0.5-h post-incubation. This suggested the existence of at least two radiation responsive promoters for pprA expression. Functional characterization of the upstream region of the pprA gene using a luciferase reporter assay revealed that the distal promoter is located between positions -208 and -156 from the translation initiation site, while the proximal promoter is located between positions -57 and -22. The region located between positions -57 and -38 was indispensable for proximal promoter activity. Site-directed mutagenesis of a thymine positioned at -33 resulted in severe impairment of promoter activity, and suggested that the thymine functions as a master base for the proximal radiation responsive promoter. The product of the D. radiodurans pprI gene is thought to be a general switch in the radiation response [Hua, Y., Narumi, I., Gao, G., Tian, B., Satoh, K., Kitayama, S., Shen, B., 2003. PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans. Biochem. Biophys. Res. Commun. 306, 354-360.]. We examined the effect of pprI disruption on pprA promoter activity. The results suggested that up-regulation of pprA expression by the pprI gene product is triggered at the promoter level.
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Affiliation(s)
- Hirofumi Ohba
- Research Group for Biotechnology Development, Department of Ion-beam-applied Biology, Japan Atomic Energy Research Institute, 1233 Watanuki-machi, Takasaki, Gunma 370-1292, Japan
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26
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Keatch SA, Su TJ, Dryden DTF. Alleviation of restriction by DNA condensation and non-specific DNA binding ligands. Nucleic Acids Res 2004; 32:5841-50. [PMID: 15520467 PMCID: PMC528803 DOI: 10.1093/nar/gkh918] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During conditions of cell stress, the type I restriction and modification enzymes of bacteria show reduced, but not zero, levels of restriction of unmethylated foreign DNA. In such conditions, chemically identical unmethylated recognition sequences also occur on the chromosome of the host but restriction alleviation prevents the enzymes from destroying the host DNA. How is this distinction between chemically identical DNA molecules achieved? For some, but not all, type I restriction enzymes, alleviation is partially due to proteolytic degradation of a subunit of the enzyme. We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands. The type I restriction enzyme is able to destroy the 'naked' DNA using a complex reaction linked to DNA translocation, but this essential translocation process is inhibited by DNA condensation and the presence of non-specific ligands bound along the DNA.
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Affiliation(s)
- Steven A Keatch
- School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JJ, UK
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27
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Englander J, Klein E, Brumfeld V, Sharma AK, Doherty AJ, Minsky A. DNA toroids: framework for DNA repair in Deinococcus radiodurans and in germinating bacterial spores. J Bacteriol 2004; 186:5973-7. [PMID: 15342565 PMCID: PMC515169 DOI: 10.1128/jb.186.18.5973-5977.2004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Joseph Englander
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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28
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Frenkiel-Krispin D, Sack R, Englander J, Shimoni E, Eisenstein M, Bullitt E, Horowitz-Scherer R, Hayes CS, Setlow P, Minsky A, Wolf SG. Structure of the DNA-SspC complex: implications for DNA packaging, protection, and repair in bacterial spores. J Bacteriol 2004; 186:3525-30. [PMID: 15150240 PMCID: PMC415783 DOI: 10.1128/jb.186.11.3525-3530.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial spores have long been recognized as the sturdiest known life forms on earth, revealing extraordinary resistance to a broad range of environmental assaults. A family of highly conserved spore-specific DNA-binding proteins, termed alpha/beta-type small, acid-soluble spore proteins (SASP), plays a major role in mediating spore resistance. The mechanism by which these proteins exert their protective activity remains poorly understood, in part due to the lack of structural data on the DNA-SASP complex. By using cryoelectron microscopy, we have determined the structure of the helical complex formed between DNA and SspC, a characteristic member of the alpha/beta-type SASP family. The protein is found to fully coat the DNA, forming distinct protruding domains, and to modify DNA structure such that it adopts a 3.2-nm pitch. The protruding SspC motifs allow for interdigitation of adjacent DNA-SspC filaments into a tightly packed assembly of nucleoprotein helices. By effectively sequestering DNA molecules, this dense assembly of filaments is proposed to enhance and complement DNA protection obtained by DNA saturation with the alpha/beta-type SASP.
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29
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Matic I, Taddei F, Radman M. Survival versus maintenance of genetic stability: a conflict of priorities during stress. Res Microbiol 2004; 155:337-41. [PMID: 15207865 DOI: 10.1016/j.resmic.2004.01.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Accepted: 01/20/2004] [Indexed: 11/24/2022]
Abstract
Bacteria are constantly facing many different environmental assaults, which may be of such severity that numerous survivors have important alterations in their genetic material. Some genetic systems induced in response to such stresses, for example the SOS system and the sigmaS regulon, actively participate in the generation of genetic alterations. The key priority of those genetic systems during stress is to ensure survival. Therefore, the repair of lethal DNA lesions is an absolute necessity, while perfect restoration of original genetic information is not. Furthermore, the nature of DNA lesions might render error-free repair too costly, or even impossible for stressed bacterial cells. Although the majority of these genetic alterations are deleterious, the rare advantageous alterations may have long-term evolutionary consequences independently of whether the selection of molecular mechanisms involved in their generation is linked to survival strategies or not.
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Affiliation(s)
- Ivan Matic
- INSERM U571, Faculté de Médecine Necker-Enfants Malades, Université Paris V, 156 rue de Vaugirard, 75730 Paris Cedex 15, France.
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