2
|
Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE. Mimivirus and the emerging concept of "giant" virus. Virus Res 2006; 117:133-44. [PMID: 16469402 DOI: 10.1016/j.virusres.2006.01.008] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 01/06/2006] [Accepted: 01/09/2006] [Indexed: 11/15/2022]
Abstract
The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (750 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries between viruses and parasitic cellular organisms. In addition, the analysis of its genome sequence identified many types of genes never before encountered in a virus, including aminoacyl-tRNA synthetases and other central components of the translation machinery previously thought to be the signature of cellular organisms. In this article, we examine how the finding of such a giant virus might durably influence the way we look at microbial biodiversity, and lead us to revise the classification of microbial domains and life forms. We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which makes them closer to small parasitic prokaryotes than to regular viruses.
Collapse
Affiliation(s)
- Jean-Michel Claverie
- Information Génomique et Structurale, CNRS UPR 2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France.
| | | | | | | | | | | |
Collapse
|
3
|
Zimmerman SB. Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase. J Struct Biol 2005; 153:160-75. [PMID: 16384714 DOI: 10.1016/j.jsb.2005.10.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/23/2005] [Accepted: 10/18/2005] [Indexed: 12/29/2022]
Abstract
The genomic DNA of Escherichia coli occurs in compact bodies known as nucleoids. Organization and structure of nucleoids are poorly understood. Compact, characteristically shaped, nucleoids isolated by the polylysine-spermidine procedure were visualized by DNA fluorescence microscopy. Treatment with urea or trypsin converted compact nucleoids to partially expanded forms. The transition in urea solutions was accompanied by release of most DNA-associated proteins; the transition point between compact and partially expanded forms was not changed by the loss of the proteins nor was it changed in nucleoids isolated from cells after exposure to chloramphenicol or from cells in which Dps, Fis, or H-NS and StpA had been deleted. Partially expanded forms became dispersed upon RNase exposure, indicating a role of RNA in maintaining the partial expansion. Partially expanded forms that had been stripped of most DNA-associated proteins were recompacted by polyethylene glycol 8,000, a macromolecular crowding agent, in a cooperative transition. DNA-associated proteins are suggested to have relatively little effect on the phase-like behavior of the cellular nucleoid. Changes in the urea transition indicate that a previously described procedure for compaction of polylysine-spermidine nucleoids may have an artifactual basis, and raise questions about reports of repetitive local structures involving the DNA of lysed cells.
Collapse
Affiliation(s)
- Steven B Zimmerman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0560, USA
| |
Collapse
|
4
|
Hodak JH, Downey CD, Fiore JL, Pardi A, Nesbitt DJ. Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET. Proc Natl Acad Sci U S A 2005; 102:10505-10. [PMID: 16024731 PMCID: PMC1180751 DOI: 10.1073/pnas.0408645102] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Docking kinetics and equilibrium of fluorescently labeled RNA molecules are studied with single-molecule FRET methods. Time-resolved FRET is used to monitor docking/undocking transitions for RNAs containing a single GAAA tetraloop-receptor tertiary interaction connected by a flexible single-stranded linker. The rate constants for docking and undocking are measured as a function of Mg2+, revealing a complex dependence on metal ion concentration. Despite the simplicity of this model system, conformational heterogeneity similar to that noted in more complex RNA systems is observed; relatively rapid docking/undocking transitions are detected for approximately two-thirds of the RNA molecules, with significant subpopulations exhibiting few or no transitions on the 10- to 30-s time scale for photobleaching. The rate constants are determined from analysis of probability densities, which allows a much wider range of time scales to be analyzed than standard histogram procedures. The data for the GAAA tetraloop receptor are compared with kinetic and equilibrium data for other RNA tertiary interactions.
Collapse
Affiliation(s)
- Jose H Hodak
- JILA, National Institute of Standards and Technology, University of Colorado, Boulder, CO 80309, USA
| | | | | | | | | |
Collapse
|
5
|
Cowman MK, Spagnoli C, Kudasheva D, Li M, Dyal A, Kanai S, Balazs EA. Extended, relaxed, and condensed conformations of hyaluronan observed by atomic force microscopy. Biophys J 2004; 88:590-602. [PMID: 15489305 PMCID: PMC1305036 DOI: 10.1529/biophysj.104.049361] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The conformation of the polysaccharide hyaluronan (HA) has been investigated by tapping mode atomic force microscopy in air. HA deposited on a prehydrated mica surface favored an extended conformation, attributed to molecular combing and inhibition of subsequent chain recoil by adhesion to the structured water layer covering the surface. HA deposited on freshly cleaved mica served as a defect in a partially structured water layer, and favored relaxed, weakly helical, coiled conformations. Intramolecularly condensed forms of HA were also observed, ranging from pearl necklace forms to thick rods. The condensation is attributed to weak adhesion to the mica surface, counterion-mediated attractive electrostatic interactions between polyelectrolytes, and hydration effects. Intermolecular association of both extended and condensed forms of HA was observed to result in the formation of networks and twisted fibers, in which the chain direction is not necessarily parallel to the fiber direction. Whereas the relaxed coil and partially condensed conformations of HA are relevant to the native structure of liquid connective tissues, fully condensed rods may be more relevant for HA tethered to a cell surface or intracellular HA, and fibrous forms may be relevant for HA subjected to shear flow in tight intercellular spaces or in protein-HA complexes.
Collapse
Affiliation(s)
- Mary K Cowman
- Othmer Department of Chemical and Biological Sciences and Engineering, Polytechnic University, Brooklyn, New York 11201, USA.
| | | | | | | | | | | | | |
Collapse
|
6
|
Di Cola E, Plucktaveesak N, Waigh TA, Colby RH, Tan JS, Pyckhout-Hintzen W, Heenan RK. Structure and Dynamics in Aqueous Solutions of Amphiphilic Sodium Maleate-Containing Alternating Copolymers. Macromolecules 2004. [DOI: 10.1021/ma049260h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Di Cola
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK; Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802; Imaging Materials and Media, Research and Development, Eastman Kodak Company, Rochester, New York 14650-2116; Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK
| | - N. Plucktaveesak
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK; Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802; Imaging Materials and Media, Research and Development, Eastman Kodak Company, Rochester, New York 14650-2116; Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK
| | - T. A. Waigh
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK; Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802; Imaging Materials and Media, Research and Development, Eastman Kodak Company, Rochester, New York 14650-2116; Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK
| | - R. H. Colby
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK; Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802; Imaging Materials and Media, Research and Development, Eastman Kodak Company, Rochester, New York 14650-2116; Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK
| | - J. S. Tan
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK; Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802; Imaging Materials and Media, Research and Development, Eastman Kodak Company, Rochester, New York 14650-2116; Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK
| | - W. Pyckhout-Hintzen
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK; Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802; Imaging Materials and Media, Research and Development, Eastman Kodak Company, Rochester, New York 14650-2116; Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK
| | - R. K. Heenan
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK; Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802; Imaging Materials and Media, Research and Development, Eastman Kodak Company, Rochester, New York 14650-2116; Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, UK
| |
Collapse
|
8
|
Wang H, Grimes S, Anderson DL, Serwer P. Terminal protein-induced stretching of bacteriophage phi29 DNA. J Microsc 2004; 213:172-9. [PMID: 14731300 DOI: 10.1111/j.1365-2818.2004.01283.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stretching of DNA molecules helps to resolve detail during the fluorescence microscopy of both single DNA molecules and single DNA-protein complexes. To make stretching occur, intricate procedures of specimen preparation and manipulation have been developed in previous studies. By contrast, the present study demonstrates that conventional procedures of specimen preparation cause DNA stretching to occur, if the specimen is the double-stranded DNA genome of bacteriophage phi29. Necessary for this stretching is a protein covalently bound at both 5' termini of phi29 DNA molecules. Some DNA molecules are attached to a cover glass only at the two ends. Others are attached at one end only with the other end free in solution. The extent of stretching varies from approximately 50% overstretched to approximately 50% understretched. The understretched DNA molecules are internally mobile to a variable extent. In addition to stretching, some phi29 DNA molecules also undergo assembly to form both linear and branched concatemers observed by single-molecule fluorescence microscopy. The assembly also requires the terminal protein. The stretched DNA molecules are potentially useful for observing DNA biochemistry at the single molecule level.
Collapse
Affiliation(s)
- H Wang
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | | | | | | |
Collapse
|